Molecular Mechanisms Controlling Centriole Duplication

Item Type text; Electronic Dissertation

Authors Boese, Cody

Citation Boese, Cody. (2020). Molecular Mechanisms Controlling Centriole Duplication (Doctoral dissertation, University of Arizona, Tucson, USA).

Publisher The University of Arizona.

Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author.

Download date 05/10/2021 17:34:06

Link to Item http://hdl.handle.net/10150/648667 MOLECULAR MECHANISMS CONTROLLING CENTRIOLE DUPLICATION

Cody Boese

______

A Dissertation Submitted to the Faculty of the

GRADUATE INTERDISCIPLINARY PROGRAM IN CANCER BIOLOGY

In Partial Fulfillment of the Requirements

For the Degree of

DOCTOR OF PHILOSOPHY

In the Graduate College

THE UNIVERSITY OF ARIZONA

2020

THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE

As members of the Dissertation Committee, we certify that we have read the dissertation prepared by: Cody Boese titled: Molecular mechanisms controlling centriole assembly

and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of

Doctor of Philosophy.

Gregory C Rogers Date: Jul 21, 2020 Gregory C Rogers

Date: Jul 21, 2020

Anne E Cress

Date: Oct 22, 2020 Keith Maggert

Date: Jul 21, 2020 Ghassan Mouneimne

Date: Aug 3, 2020 Nathan Ellis

Final approval and acceptance of this dissertation is contingent upon the candidate’s submission

of the final copies of the dissertation to the Graduate College.

I hereby certify that I have read this dissertation prepared under my direction and recommend that it be accepted as fulfilling the dissertation requirement.

Gregory C Rogers Date: Jul 21, 2020

Gregory C Rogers Cellular and Molecular Medicine

ACKNOWLEDGEMENTS

I would like to thank my P.I., Greg Rogers for mentoring me and teaching me, but mostly

for being so supportive of all my ideas. I would like to thank my committee, Nathan Ellis, Keith

Maggert, Gus Mouneimne, and Anne Cress for always being willing to meet with me and for

helping me think critically about my research.

I would like to thank all members of the Rogers lab for their ideas and help with technical aspects of my project, but mostly for being an all-around good group to be around.

Lastly, a special thanks to my family and friends, especially my fiancé, Irene Moreno for her never ending, all-around support throughout these years.

TABLE OF CONTENTS

LIST OF FIGURES………...……………………………………………………………………7

LIST OF TABLES………………………...…………………………………………….……….9

ABSTRACT…………………………………………………………………………….……….10

CHAPTER ONE: CENTROSOMES – AN OVERVIEW

1.1 Introduction…………………………………………………………………………………12

1.2 Centrosome Dysregulation and Cancer………………………….………………………..12

1.3 The Centriole – The Key to Centrosome Duplication……………………………………17

1.4 Molecular Regulation of Centrosome Duplication……………………………………….17

A. Forming the Spot of Centriole Assembly……………………………………………...17

B. From Procentriole Spot to Cartwheel Formation…………………………………….20

C. Centriole Growth………………………………………………………..……………...22

D. Centriole Disengagement and Licensing for Reduplication………..………………...23

1.5 Molecular Regulation of Centrosome Function…………………………………………..25

A. Pericentriolar Material Assembly……………………………………………………..25

B. Centrosome Separation………………………………………………………………...27

1.6 Figures……………………………………………………………………………………….29

1.7 Tables………………………………………………………………………………………..33

CHAPTER TWO: ASTERLESS IS A POLO-LIKE KINASE 4 SUBSTRATE THAT

BOTH ACTIVATES AND INHIBITS KINASE ACTIVITY DEPENDING ON ITS

PHOSPHORYLATION STATE

2.1 Abstract…………………………………………………………………………………...…35

2.2 Introduction…………………………………………………………………………………36

2.3 Results……………………………………………………………………………………….38

2.4 Discussion…………………………………………………………………………………...50

2.5 Materials and Methods……………………………………………………………………..54

2.6 Figures……………………………………………………………………………………….62

2.7 Tables………………………………………………………………………………………..83

CHAPTER THREE: ASTERLESS PHOSPHORYLATION PROMOTES SINGLE SITE

OF CENTRIOLE ASSEMBLY

3.1 Abstract………………………………………………………………………….………..…85

3.2 Introduction……………………………………………………………………….……..….85

3.3 Results and Discussion…………………………………………………………………...…88

3.4 Materials and Methods…………………………………………………………………..…98

3.5 Figures……………………………………………………………………………………...103

CHAPTER 4: FUTURE DIRECTIONS AND CONCLUSIONS

4.1 Identification of a Cellular Plk4 Inhibitor………...………………………………..……119

4.2 Formation of the Procentriole Spot by Wdb……………………………...………..……121

4.3 Further Molecular Characterizations of the Asl-Plk4 Interaction …………….……...123

4.4 Figures…………………………………………………………………………………...…125

APPENDIX A: PUBLICATIONS …….……………….………………………………….…131

COMPLETE LIST OF REFERENCES…………………………..…………………….…...132

LIST OF FIGURES

1.1 The Centrosome: A Mother-Daughter Centriole Pair Surrounded my Pericentriolar

Material…………………………………………..………………………………………….29

1.2 Two Centrosomes Facilitate Bipolar Mitotic Spindle Formation……………………….30

1.3 Centriole Duplication Cycle – An Overview……………………………………………...31

1.4 Centrioles Exhibit a Nine-Fold Radial Symmetry………………………………………..32

2.1 Plk4 Phosphorylates the N-terminal Domain of Asl….……………………………..……62

2.2 Asl-A Phosphomutants are Largely α-helical and Self-Oligomerize……………..……..64

2.3 The Phosphorylation State of Asl-A Controls Plk4 Activity……………………………..67

2.4 Nonphosphorylatable Asl-A (13A) Stimulates Plk4 Activity In Vitro……………….….69

2.5 Asl-A Phosphomutants Control Kinase Activity by Modulating Plk4 Inhibition……...71

2.6 Plk4 Phosphorylates Its Kinase domain and Asl-A, Generating a State that Inhibits

Kinase Activity…..……………………………………………………………………………...73

S2.1 Full-length Asl Phosphomutants Induce Centriole Amplification……….…………….75

S2.2 The Phosphorylation State of Asl-A Does Not Influence Cellular Aggregate Formation

and has Little Effect on Binding to Plk4 PB1-PB2………………….………………………..77

S2.3 Plk4 S228 Phosphomutants are Catalytically Active but do not Bind Asl-A When

Lacking PB1-PB2…………………………………….………………………………………....80

3.1 Phosphorylation of T3 and S7 in Asterless-A is Necessary and Sufficient to Block

Centriole Duplication………………………..……………………………………………...…103

3.2 Asl-A-Plk4 Interaction is Required for Asl-A-2PM to Block Centriole Duplication…106

3.3 Phospho-Asl Forms a Ring of Puncta at the Mother Centriole that may Prohibit

Daughter Centriole Assembly.………………………………………………………………..108

3.4 Wdb Interacts with Asl and Promotes Active Site of Centriole Assembly…………….110

S3.1 Development of Plk4 and Asl Phospho-Specific Antibodies…..………………………113

S3.2 Wdb and Wrd Localize to Centrioles and Cause Centriole Amplification When

Overexpressed…………………………...…………………………………………………….115

S3.3 Wdb Interacts with Ana2 and Forms a Complex with Plk4 and Asl-A.……………..117

4.1 Screen to Determine Co-Inhibitor of Plk4……………..………………………………...125

4.2 Utilization of a Proximity-Dependent Biotinylation Assay……………………………..126

4.3 Centriolar Localization of Wdb and Ana2………………………………………………128

4.4 Asl-A dimerization is Required for its Interaction with Plk4…………………………..129

LIST OF TABLES

1.1 A List of Centrosome Associated Proteins and Their Functions……….….…………….33

2.1 Phosphorylation Sites of Asl-A……………...………………………………………….….83

ABSTRACT

Centrioles are barrel shaped, non-membrane bound organelles that typically exist in pairs

where the younger ‘daughter’ centriole emanates orthogonally off of the proximal end of the

older ‘mother’ centriole. The mother-daughter centriole pair and their surrounding proteins

constitute the centrosome, which is the primary regulator of chromosome separation and cell

division in animal cells. The centrosome controls these processes by acting as the microtubule

organizing center (MTOC) of the cell – it nucleates microtubules during mitosis to form the

mitotic spindle required to promote chromosome segregation. In order for proper chromosome

segregation to occur, each cell needs to contain only two centrosomes entering mitosis – one at

each pole to achieve spindle bipolarity. To achieve this, each centrosome must duplicate itself

throughout the cell cycle. This duplication event is orchestrated by the centrioles – a single

daughter centriole is built off of each mother centriole as the cell cycle progresses. The formation

of excess daughter centrioles around a mother is a mechanism of centriole amplification, which

is a driver of aneuploidy and tumor formation. Because of this, the process of centriole

duplication is tightly controlled on a molecular level.

The process of centriole duplication is coordinated in part by two conserved proteins: the

Ser/Thr kinase Plk4 and its multifunctional regulator, Asterless. Previous work has shown that an

excess of Asl protein levels, Plk4 protein levels and Plk4 catalytic activity can contribute to

centriole amplification. Thus, it is crucial to obtain a complete understanding of how Plk4 and

Asl coordinate their functions to ensure centrioles duplicate properly. It is known that Asl can regulate Plk4 by targeting it to the centriole as well as control its stability in a cell-cycle

dependent manner. However, we still have an incomplete understanding of exactly how these two proteins promote the formation of a single daughter centriole during each cell cycle. Here we

identify multiple new regulatory mechanisms that Plk4 and Asl utilize in order to control

centriole assembly. First, we identify Asl as a multifunctional phosphorylation-dependent regulator of Plk4 catalytic activity. When dephosphorylated, Asl can bind Plk4 and stimulate its activity. Asl itself then becomes phosphorylated, and functions as a Plk4 inhibitor, invoking a negative feedback mechanism to thought prevent Plk4 from inducing centriole amplification through its catalytic activity. In the following chapter, we identify the two phospho-residues in

Asl necessary for Plk4 inhibition, while also determining that this inhibition is dependent on the

interaction between Plk4 and Asl. Importantly, we describe a role for this negative feedback

mechanism in limiting centriole assembly: Phospho-Asl localizes to puncta around the mother

centriole where they keep Plk4 inhibited. The phosphatase PP2A is then recruited to the centriole

to dephosphorylate Asl at only one of the puncta, where Plk4 can then be activated to promote

centriole assembly. Lastly, we reveal data that will be important for future studies on this topic,

such as the mechanism of PP2A recruitment to the centriole, dynamics of Plk4 activation and

inhibition, and the possible existence of an unidentified cellular Plk4 inhibitor.

CHAPTER ONE: CENTROSOMES – AN OVERVIEW This chapter was written entirely by me. It is being prepared as a chapter submission to the Encyclopedia of Biological Chemistry. The figures, graph and table were generated by me, with technical help and guidance from Greg Rogers. 1.1 Introduction The centrosome is a non-membrane bound organelle that functions as the primary

regulator of chromosome separation and cell division in animal cells. It is comprised of two

microtubule-based barrel shaped structures called centrioles, as well as an amorphous cloud of

proteins termed the pericentriolar material (PCM) (Figure 1.1)1. Together, these components

function as the microtubule organizing center of the cell (MTOC). During mitosis, the

centrosome concentrates and nucleates microtubules to form a spindle which promotes

chromosome segregation. The mitotic spindle acts to ensure the proper segregation of

chromosomes into each new daughter cell after cytokinesis. When this process goes awry, it can

cause a missegregation of chromosomes and result in daughter cells that are aneuploid – a

common driver of tumorigenesis2,3. In order to ensure the daughter cells each have normal ploidy after cytokinesis, a bipolar spindle must be formed, that is, one centrosome nucleating microtubules at each end of the cell (Figure 1.2)4. The bipolar spindle can only be achieved when

there are exactly two centrosomes in the cell entering mitosis. After cytokinesis, one centrosome

is retained in each new daughter cell, respectively. This means that before the next division, cells

must duplicate their centrosome. Here, we discuss the dire consequences that arise when the

centrosome duplication pathway is dysregulated, and the intricate molecular mechanisms

required for the proper maintenance of centrosome number in a cell.

1.2 Centrosome Dysregulation in Cancer Aberrations in centrosome number have long been observed in cancer tissue. Increases in

centrosome number (centrosome amplification) have been reported in numerous cancer types,

and recently it was shown that centrosome loss occurs in prostate cancer5,6. It was hypothesized

that a dysregulation of centrosome function would compromise spindle integrity and lead to

errors in chromosome segregation, generating aneuploidy and genomic instability – a hallmark

of cancer7. Until recently however, it was not known whether centrosome abnormalities could

drive genomic instability and tumor formation, or if these abnormalities were just “passengers”

or side effects of the tumor.

A pair of landmark studies in 2009 played a pivotal role in showing that alterations in

centrosome number, specifically centrosome amplification, can in fact drive genomic instability

and aneuploidy8,9. First, Ganem et al. and Silkworth et al. showed that although a number of

cancer cell lines exhibited centrosome amplification, these cell lines rarely underwent multipolar

divisions. Instead, the cells with supernumerary centrosomes were found to cluster their

centrosomes to form a “pseudo-bipolar” spindle, thereby circumventing multipolar spindle

formation, which typically results in apoptosis. Interestingly, during this centrosome clustering process, merotelic kinetochore attachments were created at the chromosomes. This resulted in the formation of lagging chromosomes during segregation; and generated aneuploid daughter cells after cytokinesis.

Another landmark study highlighting the connection between centrosomes and cancer investigated the surprising role centrosome amplification plays in the process of tumor progression and metastasis10. To do this, Godinho and colleagues induced centrosome

amplification in non-transformed human mammary epithelial cells. Interestingly, they found that

centrosome amplification in these cells induced the formation of actin-based cytoplasmic extensions that invaded the surrounding extracellular matrix. These protrusions were able to provide tracks for collective migration of clusters of cells, not unlike the collective migration

13 model of metastasis in in vivo tumor models. Mechanistically, they found that the increased microtubule nucleation from excess centrosomes hyperactivated the GTPase Rac1, responsible for Arp2/3 mediated actin assembly of these invasive structures. It remains to be seen how exactly microtubule nucleation hyperactivates Rac1, or whether the observed invasive structures are able to promote metastasis in in vivo models. Even so, an intriguing connection is being developed between centrosome abnormalities and multiple steps throughout the process of tumor initiation and cancer progression.

Importantly, more recent work has shown that centrosome amplification was able to drive tumor formation in in vivo mouse models. In one particular study, Sercin and colleagues found that if they induced transient centrosome amplification in epidermal cells lacking the tumor suppressor gene TRP53 (TP53 in humans; encoding the protein p53), mice formed more tumors, and at a significantly increased rate, compared to TRP53 mutant mice with no centrosome amplification11. This suggests that the genomic instability generated by centrosome amplification can form tumors at a rapid rate when cells are lacking genomic gatekeeping proteins such as p53, which is the most commonly mutated gene in cancer12.

Although the previously mentioned study might indicate that an upstream driver mutation, such as in TP53, might be required in order for centrosome amplification to have a tumorigenic effect, a different study showed centrosomes alone can drive cancer formation, even in wild-type cells13. This study was performed by inducing chronic centrosome amplification in a variety of different tissues that were TP53 proficient in a mouse model. Intriguingly, this led to highly aneuploid cells, as the cells presumably underwent centrosome clustering in order to prevent cell death. These aneuploid cells then went on to form several different types tumors.

Based on the results of the two aforementioned studies, centrosome amplification may cause

14 tumorigenesis by (at least) two mechanisms: 1. Transient amplification causes highly aneuploid cells that are able to thrive in the absence of p53 protein, and 2. Chronic, longer term amplification generates populations of aneuploid cells that are able to evade the p53 inhibitory response.

In addition to centrosome amplification, centrosome loss has also been shown to have problematic effects on dividing cells. When centrosomes were experimentally depleted from vertebrate somatic cells, they are still able to form an acentrosomal bipolar spindle in mitosis14.

The formation of these spindles is thought to be attributed to a chromatin mediated microtubule assembly pathway that becomes more active in the absence of proper centrosomes15. However, these cells fail to complete cytokinesis a significant portion of the time16. Additionally, when only centrioles (but not pericentriolar material) were depleted from a centrosome, cells were able to form acentriolar microtubule organizing centers composed primarily of the remaining pericentriolar material. Although these microtubule organizing centers could facilitate the formation of a bipolar spindle, they eventually accumulated high levels of chromosomal instability – possibility indicating that fully intact centrosomes are necessary to form proper microtubule attachments at the chromosomes17. Pericentriolar material plays an important role in the formation of the mitotic spindle since it recruits proteins that facilitate microtubule nucleation, such as gamma-tubulin. However, pericentriolar material also plays an intriguing role in centriole duplication. Upon mitotic exit, the pericentriolar material disassembles – a dephosphorylation cascade initiated by the phosphatase PP2A causes the dissolution of protein- protein interactions that keep the pericentriolar material localized around the centrioles18. If pericentriolar material disassembly is blocked at the end of mitosis, the cell fails to duplicate its centrioles during the next cell cycle19. More work is needed to determine the molecular

mechanism that blocks centriole duplication in the presence of pericentriolar material.

Pericentriolar material assembly involves several of the same proteins involved in centriole

duplication (discussed in further detail in section 1.5A). Possibly, these proteins can switch

functions, cycling between centriole duplication and pericentriolar material function. In this case

then, the presence of pericentriolar material may be the dominant factor in deciding the function

of these proteins - their role in microtubule nucleation means they cannot simultaneously function as centriole duplicating factors. It will be interesting to determine the roles of individual proteins in pericentriolar function versus centriole duplication, and how their roles may switch on a cell cycle dependent basis.

When centriole duplication is transiently blocked in cancer cells by inhibiting the

essential centriolar kinase Plk4, cells are able to continually divide and proliferate, all while

accumulating increasing amounts of genomic instability. Intriguingly, when the same molecular

inhibition is applied to normal human cells (RPE-1), cells cease proliferation, instead undergoing

a cell cycle arrest in G1 phase20. Subsequent studies showed that the G1 arrest was dependent on

a USP28-53BP1-p53-p21 signaling cascade, and when any of these factors were removed,

proliferation could occur in the absence of centrioles21–23. Thus, these data suggest inhibition of

centriole duplication may be a useful treatment strategy in rapidly proliferating tumor cells with a wild-type TP53 gene but may prove ineffective in the many cancer types where p53 protein function is compromised. Since cancers that have no alteration in the p53 pathway are rarely observed, it might be useful to consider blockage to centriole duplication in combination with other agents such as microtubule-based inhibitors as a form of cancer treatment.

1.3 The Centriole – The Key to Centrosome Duplication

The core duplicating element of the centrosome is the centriole. Each centrosome

contains a pair of centrioles – an older, ‘mother’ centriole and a younger ‘daughter’ centriole that

emanates orthogonally from the base of the mother2. During late mitosis, the mother and the

daughter centriole disengage from each other, allowing for new centrioles to grow from each of

them during the next cell cycle24. Beginning in the following G1/S phase, a new centriole

(termed ‘procentriole’) begins to form at the base of each existing centriole from a pre-selected molecular spot (termed pre-procentriole)25. The procentrioles continue to grow and mature

throughout S and G2 phase until they become fully formed daughter centrioles at the onset of

mitosis. At this point, the cell has two pairs of centrioles that recruit factors that form the

pericentriolar material, giving the centrosome its microtubule nucleating ability26,27. The two

now fully mature centrosomes separate and migrate to opposite sides of the cell to nucleate

microtubules and form the bipolar spindle24. After chromosome segregation, the centriole pairs

once again disengage, and the process is repeated (Figure 1.3)1.

1.4 Molecular Regulation of Centrosome Duplication

A. Forming the Spot of Centriole Assembly

The complexity of the centrosome duplication process, coupled with the notion that

proper centrosome duplication can decrease chances of aneuploidy, means that it needs to be

tightly controlled on a molecular level28. The conserved protein Polo-like kinase 4 (Plk4) is a

Ser/Thr kinase that is essential for centriole assembly29,30. When depleted from cells or its

enzymatic activity is compromised, no new centrioles can form in the cell. Conversely, when

overexpressed, Plk4 promotes rampant centriole amplification31–33. Because of this, its cellular

localization, protein levels, and enzymatic activity are carefully regulated34. In human cells, Plk4

is localized to the centriole by a pair of scaffolding proteins, Cep152 and Cep192 (Asterless and

Spd-2 in Drosophila, respectively)35–39. During interphase, Plk4 adopts a ring-like conformation

around the wall of the mother centriole while scaffolded to Cep15240. As the cell progresses

through the cell cycle, the Plk4 ring remodels into one spot while Cep152 maintains its ring

conformation41–43. This spot becomes then becomes the site of future centriole assembly: In

human cells, it has been shown that the conserved protein STIL localizes directly to this spot,

where it is able to bind Plk4 and stimulate its kinase activity41–44. This results in STIL

phosphorylation which promotes the recruitment of Sas-6, which is a key structural component

of the new growing centriole41,44,45.

How is a single site of centriole assembly generated? This is currently a key question in

the field. The answer likely lies in the intricate regulation of Plk4 and its interaction partners. It

is known that an abundance of Plk4 at the centriole can cause the formation of multiple daughter

centrioles around one mother – a primary mechanism of centriole amplification46. Thus, it is

likely that both Plk4 levels and enzymatic activity are being held in check at the centriole to

prevent amplification. Plk4 self-regulates its stability and activity via an elegant mechanism: it

can exist in an autoinhibited conformation where its linker domain blocks access to the activation

loop of its kinase domain47. In human cells, when activation is necessary, STIL is able to bind

Plk4 in its ordered Polo Box 3 domain and enable relief of autoinhibition, presumably by

preventing the interaction between the kinase domain and the inhibitory linker44. In turn, Plk4

autophosphorylates the linker to keep it inactive, as well as the activation loop of its kinase

domain to further promote its activity47. While active, Plk4 is known to phosphorylate

STIL/Ana2 in human cells and Drosophila cells in an ordered manner to promote centriole

assembly41,44,45,48–50. Conversely, it can phosphorylate its scaffold protein, Asterless (Asl;

Cep152 in humans) which promotes its own inhibition, a form of negative feedback that is

thought to prevent the formation of too many daughter centrioles around one mother51. Notably,

while Cep152 phosphorylation by Plk4 has been reported in human cells, it remains to be seen

whether the same inhibitory mechanism occurs resulting from the phosphorylation event37. Plk4

can also control its own protein turnover through autophosphorylation. While in an active dimer,

it can autophosphorylate its Downstream Regulatory Element (DRE), leading to the recruitment

of the E3 ubiquitin ligase SCF/βTrCP (SCF/Slimb in Drosophila), which ubiquitinates and

targets Plk4 degradation46,52–57. Due to this mechanism, cellular Plk4 levels are typically very

low during interphase, which is thought to provide another failsafe to prevent centriole

amplification in cells46,58. Importantly, Plk4 is stabilized in mitosis by the activity of the

phosphatase PP2A, which dephosphorylates its DRE to prevent its degradation so Plk4 can act to

promote centriole assembly59.

Seemingly, all of these regulatory processes work together coherently to form a single spot for daughter centriole at the site of a mother centriole, but the mechanism of how exactly one spot is selected (rather than 2 or 3 or 0, etc.) remains elusive. Perhaps, the selection process for the single site of centriole assembly occurs in a hierarchical fashion that is timed by the cell- cycle regulated proteins in conjunction with the self-regulating properties of Plk4. As previously mentioned, Plk4 forms a ring around mother centrioles during interphase. As the cell cycle progresses into mitosis, the Plk4 ring mysteriously coalesces into a single spot that becomes the site of new centriole assembly. Recent work has shown that Plk4 rings maintain an asymmetric conformation with a bias toward a spot contained within the ring42,60. This biased distribution

exists prior to STIL localization, however STIL recruitment and Plk4 kinase activity are required

for coalescence of the Plk4 ring into one spot. Additionally, recent high-resolution stimulated emission depletion (STED) microscopy has indicated that the Plk4 ring around the mother centriole consists of multiple puncta as opposed to a continuous ring61. Notably, in human cells,

Plk4’s scaffold Cep152 also formed puncta around the mother, albeit at an average of twice as

many puncta as Plk4. In essence, since Cep152 acts as a scaffold for Plk4 at the centriole, Plk4

has twice as many spots available to occupy than it actually occupies. It has been suggested that

a mechanism of ‘lateral inhibition’ exists at the Plk4 puncta whereby Plk4 can phosphorylate

neighboring Plk4 molecules to promote their degradation or dissociation off of the centriole,

potentially explaining why Plk4 occupies six spots around the mother centriole instead of the

twelve spots provided by Cep15260. Perhaps the Plk4 molecules are grouped together by

phosphorylation state, forming separate condensates, and therefore distinct spots, as has been

suggested62. Recent mathematical modeling studies have taken these data into account to create

models whereby Plk4 auto-activity, with the help of STIL binding and stimulation, acts to

coalesce Plk4 into a single spot around the mother centriole where the daughter centriole will

eventually form61,63. In the future, it will be interesting so see how other centriolar Plk4

regulators, such as Cep192/Spd-2 (humans/Drosophila) and Cep152/Asl (humans/Drosophila)

fit into this model.

B. From Procentriole Spot to Cartwheel Formation

Once the spot of daughter centriole assembly is selected, an array of proteins is recruited in an ordered fashion to ensure proper structure and function of the new centriole. It has been shown in both humans and Drosophila that in late mitosis, Plk4 coalesces into one spot with

STIL/Ana2, where it can be hyperactivated. It then performs multiple phosphorylation events on different STIL/Ana2 domains in an ordered fashion. Namely, the phosphorylation of the N-

terminus triggers a conformational change in STIL/Ana2 that allows the C-terminal STAN

(STil/ANa2) domain to become phosphorylated49,50. Once hyperphosphorylated, STIL/Ana2

forms a tight interaction with the structural centriole component CPAP (Sas-4 in Drosophila),

which is able to bind microtubules at the wall of the mother centriole64,65. The high affinity

interaction between phospho-STIL/Ana2 and CPAP/Sas-4 allows for the accumulation of

increasing amounts of STIL/Ana2 at the procentriole spot. This accumulation is thought to

eventually reach a threshold that triggers recruitment of the core structural component Sas-664.

Once Sas-6 is recruited, a proper daughter centriole can begin being built. One of the

defining features of a mature centriole is its radial symmetry, which exists because of the nine-

fold radial organization of its microtubule bundles66. Intriguingly, the nine-fold radial symmetry

of the centriole is extremely well conserved throughout evolution, suggesting a highly conserved mechanism is in place to assemble this structure67. Accordingly, the centriole achieves such

symmetry through an elaborate molecular structure known as the cartwheel. The cartwheel itself

adopts a nine-fold symmetry, localizing to the procentriole spot and forming the structural base

of the new daughter centriole66. Furthermore, the cartwheels have been shown to stack on top of

one another, lending structural stability to the base of the centriole68,69. This cartwheel is

comprised primarily of the highly conserved centriole protein Sas-6. Two groundbreaking

studies have revealed intricate details about the molecular structure of Sas-6 within the

cartwheel70,71. Sas-6 contains an N-terminal globular head domain and a long rod-like coiled-coil domain - it can dimerize through its rod-like domain and oligomerize by head-to-head interactions in their in globular domains. Strikingly, Sas-6 was found to self-assemble into a nine-fold radial symmetry, whereby nine Sas-6 dimers assemble into a ring through interactions between their globular head domains. Thus, the nine-fold symmetry of centrioles appears to be

dependent on Sas-6 self-organization (Figure 1.4). Another conserved centriole protein, Cep135,

is then thought to link Sas-6 molecules to the inner centriole wall through its two interaction

domains – an N-terminal microtubule binding domain and a C-terminal domain that interacts

with the C-terminal rod-like domain in Sas-672,73.

C. Centriole Growth

Once the cartwheel is fully formed, tubulin accumulates and organizes itself into bundles of microtubules, giving the centriole its distinct structure74. New tubulin is recruited to the

growing centriole by the tubulin-nucleator, ℽ-tubulin, which acts as a part of the ℽ-tubulin ring complex (ℽ-Turc) and is essential for centriole growth and proper mitotic spindle formation75.

New research has indicated that Sas-6 forms interactions with components of the ℽ-Turc, providing a direct link between the cartwheel and the microtubules that form the centriole76.

Interestingly, the microtubule bundles that make up the centriole wall can differ in architecture based on which organism that they originate from. In humans, the centriole is composed of microtubule triplet bundles, with a fully formed ‘A’ tubule and partially formed ‘B’ and ‘C’ tubules growing off of the A tubule. In Drosophila and C. elegans, however, the microtubule bundles are made of doublets and singlets, respectively67. The primary reason behind the

evolutionary differences in centriole wall architecture is unclear and merits further investigation.

While the centriole can grow outward from its distal end by the addition of tubulin

subunits to the microtubule bundles at the centriole wall, a recent study has identified another

mechanism of centriole growth77. Using the Drosophila melanogaster syncytial embryo as a

model, authors found that cartwheel structures are added to the proximal end of the growing

daughter centriole in order to help achieve its final length. Surprisingly, this mechanism has a

distinct periodicity that is cell cycle and Plk4 activity-dependent, highlighting yet another role

for Plk4 in the control of centriole formation.

As the centriole grows throughout S phase, it is important to consider the mechanisms in

place to carefully achieve a set length. Mature centriole length can vary greatly between

organisms and cell types, but the lengths of each centriole in any given cell typically remain

consistent. Furthermore, aberrant regulation of centriole length has been commonly observed in

cancer cells, where one study found that multiple cancer cell lines contained overly long

centrioles, and that their centrioles were prone to over-elongation in prolonged mitosis78. This

prolific centriole growth appeared to be dependent on the essential mitotic kinase Polo-like

kinase 1 (Plk1), indicating there are molecular mechanisms in place that promote further centriole growth into mitosis. Interestingly, when cells were arrested in S-phase, the primary growth phase of the centriole, the centriole did not become overly long. This indicates that S- phase growth is either strictly dependent on cell-cycle periodicity, as referenced earlier, or there are distinct molecular mechanisms in place specifically in S-phase to prevent over-elongation of the centriole. Proteins like Cep97, CP110 and CPAP/Sas-4, which have been shown to localize to the centriole and control their growth, are attractive candidates to be the primary regulators of centriole length control in S-phase79–83. Additionally, Asterless is known to localize along the length of the centriole and help control length in flies through its interaction with Cep9784–86. In

the future it will be pivotal to identify additional factors that control centriole length, as well as

determine mechanisms of how exactly the length of each centriole is set.

D. Centriole Disengagement and Licensing for Reduplication

As the daughter centriole grows orthogonally from the mother centriole, it remains tightly

connected, or ‘engaged’ to the mother at its base24. This connection is facilitated by a network of

proteins functioning to hold the daughter centriole in place while its growth and development

occurs. At the core of this network are the proteins Cep57, Cep68, Cep215 (Centrosomin in

Drosophila) and Pericentrin (Pcnt; Plp in Drosophila)24. These ‘centriole engagement’ proteins

are likely tethered to the bases of the mother and daughter centrioles by the Cep57-Cep63-

Cep152 complex that has been shown to localize to the proximal end of centrioles87–89. The mother-daughter centriole pair remains engaged until late mitosis when a series of molecular events occur that cause them to disengage from each other. The primary drivers of this disengagement event are the kinase Plk1 and the protease Separase, both of which are known key promoters of mitotic progression90–92. Recent studies have shown that Plk1 has multiple

mechanistic roles regulating disengagement: 1. Plk1 activity promotes increased spacing

between the mother and daughter centriole towards the beginning of mitosis93, 2. It

phosphorylates PCNT which leads to its cleavage by Separase, which is required to break the

physical bond between mother and daughter centriole94, and 3. It phosphorylates Cep68, which is

required for its proteosomal degradation by the E3 ubiquitin ligase βTrCP95. The latter two steps

promote the release of Cep215 from the PCM, which is also required for disengagement to

occur94,95.

Under normal cellular conditions, mother-daughter centriole disengagement is a key event in the licensing mechanism to allow each centriole to re-duplicate. When the disengagement event is blocked, the centriole pair fails to build more centrioles during the next cell cycle. Why does an engaged mother-daughter centriole pair fail to duplicate? It was originally thought that the presence of a daughter centriole at the base of a mother spatially precludes a new centriole from forming96–98. However, more recent experimental evidence has

indicated that this must not be the case, because when Plk4 is overexpressed, mother centrioles

have been observed assembling multiple daughters46. As discussed in the previous section, Plk4

localization and activity at the centriole are required for new centriole formation, and

consequently, when Plk4 is depleted or its activity is blocked, a new daughter centriole fails to

form. Thus, it can be proposed that the licensing for centriole reduplication is a two-step event:

1. Centriole disengagement between the mother and the daughter and 2. Plk4 localization and activity at the spot of new centriole formation.

Centriole disengagement occurs in late mitosis, and it is essential that this event is properly timed99. When mitotic entry is delayed, centrioles may disengage before microtubule

nucleation and spindle formation. As a result, each disengaged centriole acquires the microtubule

nucleating abilities and a multipolar spindle can form100,101. This results in cell death, or in the

case where centrosome clustering occurs, chromosomal instability. Intriguingly, a recent study

observed that this premature disengagement can be induced by mild DNA replication stress by a

mechanism involving Plk1, cell cycle regulator Cdk1, and the DNA damage signaling factor

ATR102. This study also identified premature centriole disengagement as a mechanism occurring

in multiple cancer cell lines that contain chromosomal instability: Premature disengagement

results in the formation of multiple microtubule organizing centers that lead to multipolar mitotic

spindles. This suggests a new mechanism for generating genomic instability that involves a

dysregulation of centrosome function.

1.5 Molecular Regulation of Centrosome Function

A. Pericentriolar Material Assembly

In order to become a fully functional centrosome, the mother-daughter centriole pair

undergoes a maturation process in G2 phase where they accumulate PCM, thereby enabling them

to nucleate microtubules to form the mitotic spindle – a process that has been termed the

‘centriole-to-centrosome conversion26,27,103. Perhaps not surprisingly, PCM assembly requires

many of the same factors involved in centriole duplication as well as

engagement/disengagement, as PCM integrity is important for centriole engagement during early

M phase95,104–106. As such, in some cases it is difficult to separate centriole proteins and PCM

proteins into distinct groups, but rather, it might be more helpful to consider the centriole and its

PCM as a connected network of proteins. The procentriole assembly factors Cep135 and Cep295

(Ana1 in Drosophila), co-dependently localize to the daughter centriole during G2 phase, and

both of which are required to recruit Cep152/Asl103. Together, these proteins span from the inner

centriole to the outer centriole wall, where they are properly positioned to bind other key PCM

factors. In Drosophila, Asl has been shown to interact with known PCM components such as

Plp, Cnn, Spd-2 and TACC, although more work is needed to determine the functional

significance of each interaction as it relates to PCM assembly107. Multiple kinases have also been

shown to influence PCM assembly and function. In humans, Plk1 phosphorylation of Pcnt/Plp is

required for the recruitment of Cep192/Spd-2108. And work in Drosophila and C. elegans shows

a phosphorylated form of Spd-2 recruits Plk1 (Polo in Drosophila), which in turn phosphorylates

Cnn (Spd-5 in C. elegans) in order to promote PCM expansion109–114. In addition, the mitotic

kinase Aurora A has been shown to play multiple roles in PCM assembly whereby it

phosphorylates CPAP to maintain PCM integrity, and it phosphorylates TACC3 to stabilize ℽ-

Turc assembly, allowing for the formation of astral microtubules at the centrosome115,116.

Importantly, Aurora A is responsible for phosphorylating and activating Plk1 in humans, which

likely promotes PCM assembly through Cep192 and ℽ-Turc117–119.

B. Centrosome Separation

Once it acquires its full capacity to nucleate microtubules, each centrosome needs to migrate to opposite ends of the cell in order form the bipolar spindle. Shortly after centriole disengagement in G1 phase, a proteinaceous linker develops between each mother centriole24.

The centrioles are thought to remain connected through this linker until the onset of mitosis.

Three primary components of the linker are C-Nap-1, Cep68, and Rootletin - C-Nap-1 localizes to the base of each mother centriole while Cep68 and Rootletin form long fibers to connect the two pools of C-Nap-1120–124. Recent high-resolution imaging has revealed that the

Cep68/Rootletin fibers form a web-like network, allowing for flexibility of the linker125. In late

G2 phase, just before the onset of mitosis the centrosome linker is disrupted in a process termed

‘centrosome disjunction,’ making the centrosomes available for migration to opposite ends of the cell. Centrosome disjunction is primarily controlled by NIMA-related kinase 2 (NEK2)126. The catalytic activity of NEK2 is cell-cycle regulated, and peaks towards the end of G2 phase where it phosphorylates C-Nap-1 and Rootletin to promote their dissolution from centrosomes, thereby destroying the linker123,127,128.

Notably, the centrosomal linker is thought to be absent in Drosophila cell culture, mostly because mature centrioles to not appear to be attached to each other using conventional microscopy, and there has not been evidence showing expression of centrosomal linker proteins in there cells24. This leaves to question why the linker is necessary in human cells but not in

Drosophila cells. Since there are many more centrosome associated proteins in humans than there are in Drosophila, one possibility is that some of the proteins unique to humans require large local concentrations in order to properly function at the centrosome, and keeping both

mother centriole close together throughout the cell cycle helps to achieve higher local

concentrations of protein, however this has yet to be shown directly.

The physical separation of centrosomes at the onset of mitosis then is driven by Eg5,

which belongs to the kinesin-5 family of motor proteins24. These are homotetrameric proteins

that are able to move along microtubules using plus-end directed motors. Eg5 localizes to

centrosomes in early mitosis to drive separation along microtubules, towards opposite ends of the

cell. Intriguingly, when NEK2 is depleted from cells, and thus the centrosomal linker cannot be

molecularly dissolved, Eg5 motor activity is sufficient to break the linker by force and enable

centrosome separation129,130. This indicates there are ‘check’ mechanisms in place to ensure the

critical event of separation before mitotic spindle formation.

In the preceding sections, the myriad of proteins involved in the basic molecular

mechanisms of centriole assembly, duplication, growth and centrosome-based microtubule

organization have been described (Table 1.1). In this field of research, there remains several

intriguing questions. Importantly, why does the selection process of centriole assembly occur in

a 6/12-fold radius while the architecture of microtubule bundles occur in a 9-fold radius?

Intriguingly, under experimental conditions that drive centriole amplification (such as Plk4 overexpression), the most centrioles observed being built off of a mother centriole is six46.

Perhaps there are special limitations to the growth of daughter centrioles and the molecular

mechanisms governing this growth have evolved to support this. Furthermore, what are the

molecular events that occur in order to select a site of new daughter centriole formation at the

mother centriole? The following sections will seek to help answer this question by examining the

role of Asterless in the regulation of Plk4 activity to control the site of centriole assembly.

1.6 Figures Figure 1.1 – The Centrosome: A Mother-Daughter Centriole Pair Surrounded by

Pericentriolar Material

The centrosome exists as a mother-daughter centriole pair. The daughter centriole (D) grows at

the proximal end of the mother (M), emanating orthogonally off of it. At the base of the pair is

the cloud of proteins termed the pericentriolar material (PCM) that enable microtubule

nucleation (MTs).

Figure 1.2 – Two Centrosomes Facilitate Bipolar Mitotic Spindle Formation

During mitosis, two centrosomes, each containing a mother-daughter centriole pair surrounded by PCM, migrate to the poles of the cell and nucleate microtubules (green) to form the mitotic spindle. These microtubules facilitate the proper segregation of chromosomes (blue).

Figure 1.3 – Centriole Duplication Cycle – An Overview

An overview of the cell-cycle dependent centriole duplication process. Upon mitotic exit (M), the

pair of centrioles disengage from each other. During G1/S phase, a procentriole begins to form from a preselected molecular spot (pre-procentriole). Throughout S-phase the new daughter

centriole (procentriole) can be seen growing off of the base of the mother centriole. During G2

phase, the centriole pair matures by acquiring pericentriolar material (PCM) necessary for

nucleating microtubules for the mitotic spindle (top).

Figure 1.4 Centrioles Exhibit a Nine-Fold Radial Symmetry

Top-down view of the centriole core. In humans, the centriole wall is composed of a nine-fold array of microtubule triplet bundles. The nine-fold symmetry is organized by Sas-6, which self- oligomerizes to form the central hub and the spokes (center). The spokes are then attached to a pinhead that links them to the microtubule bundles

1.7 Tables

Table 1.1 – A List of Centrosome-Associated Proteins and their Functions*

Human Protein Name (Drosophila Function name if applicable) Tubulin Centriole assembly, mitotic spindle assembly Actin Cell migration Rac1 Cell migration Arp2/3** Cell migration p53 Genome maintenance, cell cycle control USP28 Genome maintenance, cell cycle control 53BP1 Genome maintenance, cell cycle control p21 Genome maintenance, cell cycle control Plk4 Procentriole assembly Cep152 (Asl) Procentriole assembly, PCM assembly, centriole length control Cep192 (Spd-2) Procentriole assembly, PCM assembly STIL (Ana2) Procentriole assembly, cartwheel assembly Sas-6 Procentriole assembly, cartwheel assembly SCF-βTrCP (SCF-Slimb) Plk4 regulation PP2A** Plk4 regulation CPAP/CENPJ (Sas-4) Procentriole assembly, cartwheel assembly, centriole length control Cep135 Procentriole assembly, cartwheel assembly ℽ-Turc** Centriole assembly, mitotic spindle assembly Plk1 (Polo) PCM assembly, centriole length control, centriole disengagement Cep97 Centriole length control CP110 Centriole length control Cep57 Centriole engagement, PCM assembly Cep68 Centriole engagement, PCM assembly, centrosome linker Cep215 (Cnn) Centriole engagement, PCM assembly Cep63 Centriole engagement, procentriole assembly Separase Centriole disengagement Pcnt (Plp) Centriole engagement, PCM assembly ATR Centriole disengagement Cdk1 Centriole disengagement Cep295 (Ana1) Procentriole assembly

TACC3 (TACC) PCM assembly Aurora A PCM assembly, centriole disengagement C-Nap1 Centrosome linker Rootletin Centrosome linker NEK2 Centrosome disjunction, centrosome separation Eg5 (Klp61F) Centrosome separation

* This list of proteins is not comprehensive, but rather meant to organize the proteins that have been discussed in this chapter. Similarly, the functions listed for each protein are as they relate to their function in the centrosome pathways as discussed. Each listed protein may have one or several cellular functions that have not been discussed here.

**Complex of proteins listed by their complex name for simplicity’s sake.

CHAPTER TWO: ASTERLESS IS A POLO-LIKE KINASE 4 SUBSTRATE

THAT BOTH ACTIVATES AND INHIBITS KINASE ACTIVITY

DEPENDING ON ITS PHOSPHORYLATION STATE

This chapter was written entirely by me, with oversight and editing by Greg Rogers, Dan Buster and Nasser Rusan. I performed all western blot experiments, with the exception of panels 2.2B,

2.3D and S2.1E, which were performed in collaboration with Jon Nye and Greg Rogers. I performed all centriole count experiments, with the exception of panel S2.1B which was performed by Jon Nye and panel 2.5A, which was performed in collaboration between myself and Jon Nye. Dan Buster performed the in vitro kinase assays in panel 2.1C and Figure 2.4 and prepared Table 2.1, with oversight from Greg Rogers and me. Dan Buster also performed the in vitro binding assay in panel S2.2B. Tiffany McLamarrah performed the circular dichroism experiments in Figure 2.2C in collaboration with Kevin Slep and Amber Byrnes. Kevin Slep performed the size exclusion chromatography experiments in Figure 2.2D. I performed all microscopy imaging in this chapter. Greg Rogers and I collaborated on the drawing in Figure

2.4C. This chapter has been published as an article in the Molecular Biology of the Cell, Vol. 29,

No. 23.

2.1 Abstract

Centriole assembly initiates when Polo-like kinase 4 (Plk4) interacts with a centriole

“targeting-factor.” In Drosophila, Asterless/Asl (Cep152 in humans) fulfills the targeting role.

Interestingly, Asl also regulates Plk4 levels. The N-terminus of Asl (Asl-A; amino acids 1-374) binds Plk4 and promotes Plk4 self-destruction, although it is unclear how this is achieved.

Moreover, Plk4 phosphorylates the Cep152 N-terminus, but the functional consequence is unknown.

Here, we show that Plk4 phosphorylates Asl and mapped 13 phospho-residues in Asl-A.

Nonphosphorylatable alanine (13A) and phosphomimetic (13PM) mutants did not alter Asl function, presumably because of the dominant role of the Asl C-terminus in Plk4 stabilization and centriolar targeting. To address how Asl-A phosphorylation specifically affects Plk4 regulation, we generated

Asl-A fragment phospho-mutants and expressed them in cultured Drosophila cells. Asl-A-13A stimulated kinase activity by relieving Plk4 autoinhibition. In contrast, Asl-A-13PM inhibited Plk4 activity by a novel mechanism involving auto-phosphorylation of Plk4’s kinase domain. Thus, Asl-

A’s phosphorylation state determines which of Asl-A’s two opposing effects are exerted on Plk4.

Initially, nonphosphorylated Asl binds Plk4 and stimulates its kinase activity, but after Asl is phosphorylated, a negative-feedback mechanism suppresses Plk4 activity. This dual regulatory effect by Asl-A may limit Plk4 to bursts of activity that modulate centriole duplication.

2.2 Introduction

Centrioles give rise to several physiologically important organelles including cilia, flagella, and centrosomes, and so centriole copy number must be strictly controlled in cells103,131.

In the case of dividing cells, centriole overduplication (or “amplification”) interferes with proper

spindle morphology (or orientation) and chromosome attachment, which can compromise mitotic

fidelity and lead to oncogenic transformation8,9,11,13,132. Centriole assembly is controlled by the conserved Ser/Thr kinase Polo-like kinase 4 whose activity is tightly regulated, like other Polo family members, because an increase in Plk4 protein level (and thus activity) causes rampant centriole amplification31–34,133.

Currently, Plk4 regulation is believed to occur primarily through two mechanisms: autoinhibition and self-destruction. Newly translated Plk4 is autoinhibited by its Linker 1 domain

(L1), which is thought to inhibit trans-autophosphorylation of the activation loop within the

nearby kinase domain, thereby suppressing kinase activity47,56. Relief of autoinhibition occurs

through interactions between Plk4’s Polo box 3 domain (PB3) and SCL/TAL1 Interrupting

Locus (STIL), the human homologue of the conserved SAS-5/Ana2/ STIL family of centriole proteins43,44 Plk4 autoinhibition can also be relieved by autophosphorylation of L147. During

most of the cell cycle, Plk4 acts as a suicide kinase, homodimerizing (perhaps in a concentration- dependent process) through its tandem PB1-PB2 domains and then trans-autophosphorylating its downstream regulatory element (DRE), inducing the recruitment of SCFSlimb ubiquitin ligase

(Figure 2.1A)46,47,52,53,55–57,134. Polyubiquitination of PB1 mediates Plk4 proteolysis, which is

critical in suppressing centriole amplification47.

In addition to STIL, the conserved coiled-coil protein Asterless (Asl) acts as a Plk4

“regulator” and, notably, first interacts with Plk4 before STIL/Ana2 is recruited to the nascent

procentriole132. Intriguingly, both overexpression and depletion of Asl stabilize cellular Plk4

levels135. This is likely because Asl contains two spatially distinct Plk4-binding domains within its Asl-A and Asl-C regions (Figure 2.1B), and, curiously, these regions display opposing effects on Plk4 levels during the cell cycle37–39,135. Asl stabilizes Plk4 during mitosis when levels of the

kinase peak; this activity is primarily attributed to the C-terminal Asl-C region, which is sufficient to suppress Plk4 turnover and to target the kinase to centrioles135. In contrast, the N-

terminal Asl-A region induces Plk4 homodimerization and auto-phosphorylation in interphase cells135. Because Asl-A stimulates kinase activity (and thus Plk4 self-destruction), Asl-A

functions as a Plk4 activator, though the mechanism of activation is unknown. Furthermore,

previous studies have identified the N-terminus of Cep152 (the human homologue of Asl) as a

Plk4 substrate37. However, the phosphoresidues in Cep152 have not been mapped, and the

functional significance of Cep152 phosphorylation is unknown.

In this study, we show that phosphorylation of Asl by Plk4 is conserved in Drosophila

and map 13 phosphosites in the N-terminal Asl-A region. We examine the functional significance of these phosphorylation events by replacing endogenous Asl with phospho-mutant

Asl-A variants in cells, and testing their impact on Plk4 binding, turnover, and activity, and ultimately, centriole duplication. Additionally, we use biochemical approaches to test whether phosphorylation of Asl-A can impact Plk4 kinase activity directly. Overall, our study reveals important insights into the complex mechanisms of Plk4 regulation, and how these mechanisms directly affect centriole assembly.

2.3 Results

The Asterless N-terminus (Asl-A) is phosphorylated by Plk4 in vitro and in cells

To determine whether phosphorylation of Asl by Plk4 occurs in flies, we performed in vitro kinase assays by incubating a minimal Drosophila Plk4 construct containing the kinase domain and DRE (amino acids 1–317) with purified GST-tagged Asl regions (Asl-A, B, and C) and ℽ-32P-ATP. In addition to labeling itself, Plk4 phosphorylated Asl-A but not Asl-B, Asl-C, or

control GST (Figure 2.1C), consistent with a previous in vitro study48. To identify the

phosphorylated residues, we performed tandem mass spectrometry (MS/MS) on Asl-A mixed

with Plk4 and ATP, as well as a control sample containing Asl-A and ATP. We identified seven

phosphorylated residues in Asl-A incubated with Plk4, none of which was phosphorylated in

control Asl-A (Table 2.1). In parallel, we used MS/MS analysis of full-length (FL) Asl-GFP

immunoprecipitated (IPed) from lysates of fly S2 cells coexpressing catalytically active Plk4 (or

kinase-dead [KD]-Plk4 as a control) to identify Asl-A residues phosphorylated in cells. Within

the Asl-A region, we identified 10 phosphorylated residues when purified from cells coexpressing active Plk4 (Table 2.1); total coverage of the Asl-A region was 83%. No phosphorylated peptides from the Asl-A region were recovered from cells coexpressing control

KD-Plk4; although the coverage for this control was low (53%), coverage included all of the residues identified from the in vivo active-Plk4 sample. In total, we identified 13 phosphorylated residues that primarily cluster at the N- and C-termini of the Asl-A region (Figure 2.1D).

Asl phosphorylation in Drosophila cells was also examined with two-dimensional (2D)

immunoblot analysis of lysates from S2 cells coexpressing Asl-A-V5 with either negative-

control green fluorescent protein (GFP), inactive Plk4-KD-GFP, or an active nondegradable

(ND) Plk4-GFP mutant. Asl-A appeared as multiple discrete spots when coexpressed with GFP

or with Plk4-KD (Figure 1E, arrowheads), suggesting that it is phosphorylated to different

extents when expressed in cells. Strikingly, Asl-A shifted to a more negatively charged (i.e., more acidic) species when coexpressed with active ND-Plk4, suggesting that Asl-A phosphorylation increases in the presence of active Plk4 in cells (Figure 2.1E). These data further support the conclusion that Plk4 phosphorylates the N-terminus of Asl, and that phosphorylation of the Asl/Cep152 N-termini by Plk4 is a conserved event in Drosophila and humans.

Within the FL Asl protein, the presence of Asl-C masks potential phenotypes arising from

Asl-A phosphorylation

Some Asl-A phosphopeptides recovered from the MS/MS analyses contained multiple, closely spaced Ser/Thr residues. For example, the recovered phosphopeptides included some derived from the C-terminus of Asl-A, which contains a tight cluster of three Thr residues: T337,

T338, and T339. Even though two or more of these residues were identified as phosphosites in both the in vitro and in vivo samples, the contiguity of the residues usually prevented the

phosphosites from being identified with high confidence (i.e., with phosphate localization

probability ≥95%; Table 2.1). Given the proximity of these residues and their potential to be

phosphorylated, we combined the phosphosites found in the in vitro and in vivo MS/MS data and

included them in the pool of potential Plk4-targeted phosphosites in Asl-A. This approach was used to avoid overlooking functionally important sites. Thus, we made nonphosphorylatable and phosphomimetic (PM) Asl-GFP constructs by mutating all 13 identified residues to alanines

(13A) or aspartates/glutamates (13PM) within the FL protein (Figure 2.2A).

Next, we examined the subcellular localizations of the wild-type(WT) and mutant Asl constructs and their effects on centriole duplication by counting centrioles in transiently transfected S2 cells immunostained for pericentrin-like protein (PLP), a centriole marker136.

Because Asl oligomerizes, we first eliminated the possible influence of endogenous Asl on the

localization of transgenic Asl by targeting the Asl untranslated region with RNAi107,135. After depletion of endogenous Asl, all of the GFP-Asl variants still localized to centrioles (Figure

S2.1A). Next, measurement of the centriole numbers revealed that RNAi-induced Asl depletion caused centriole loss in control cells, but expression of GFP-Asl proteins not only rescued centriole duplication but induced centriole amplification regardless of its pseudophosphorylation state (Figure S2.1B). Moreover, Plk4 co-IPed with both FL Asl mutants (Figure S2.1C). These results seemingly suggest that the phosphorylation state of the N-terminal Asl region does not regulate centriole assembly or Plk4 binding. However, the use of FL Asl in these assays may fail to reveal Asl-A activities because these Asl constructs contain the centriole-targeting Asl-C region that, by itself, contains a Plk4-binding domain (as does the Asl-A region) and is sufficient to induce centriole amplification when overexpressed135. Therefore, the use of FL Asl in these

assays risks masking phosphorylation-dependent changes of Asl-A function because the

potentially dominant Asl-C region is always present.

Replacement of endogenous Asl with Asl-A phosphorylation mutants modulates Plk4

protein levels in a manner that requires kinase activity

To analyze the biological functions of Asl-A phosphorylation apart from the potentially dominant effects of Asl-C, we generated truncation constructs that express only Asl-A and

transfected these into cells depleted of endogenous Asl. Notably, Asl depletion blocks centriole

duplication and was not rescued by overexpression of WT or phosphomutant Asl-A proteins

(unpublished data), likely because they lack the Asl-C region38,135. Although most of these cells

contained no centrioles, we could identify cells in transfected proliferating cultures that

contained remnant centrioles with which to assess Asl-A localization. Unlike the FL Asl mutants

that localized to centrioles, phospho-Asl-A mutant proteins were cytoplasmic and weakly

localized to centrioles (Figure S2.1D), as we previously reported for the Asl-A-WT fragment135.

Because Asl-A uniquely facilitates Plk4 homodimerization and trans-

autophosphorylation in S2 cells, we next examined the effects of 13A and 13PM Asl-A mutants

on coexpressed Plk4-GFP protein levels (Figure 2.2B)135. As previously reported, Asl depletion

without replacement significantly increased Plk4 levels (Figure 2.2B; compare lanes 1 and 2);

without Asl, Plk4 accumulates because proteolysis is diminished135. Notably, we observed a

sevenfold increase in Plk4 levels compared with a twofold increase in the previous study,

possibly due to a more efficient Asl knockdown in these experiments135. Curiously, replacement

with Asl-A-WT only partially reduced the Plk4 level (lane 3), whereas replacement with Asl-A-

13A completely restored Plk4 to its low level (lane 4). Strikingly, the Plk4 level after

replacement with Asl-A-13PM was not significantly different than the level in the endogenous

Asl-depleted control (lane 5 vs. lane 2). When this experiment was repeated in S2 cells

expressing KD Plk4, levels were not significantly altered by any Asl-A variant (Figure S2.1E),

indicating that Asl-A modulation of Plk4 levels is dependent on Plk4 kinase activity. Thus, the

phosphorylation state of Asl-A regulates Plk4 levels and, because Asl-mediated regulation

requires Plk4 catalytic activity, our findings suggest that nonphosphorylated Asl-A promotes

Plk4 self-destruction. In contrast, Plk4 is stable in the presence of phosphorylated Asl-A.

Because the cells used in these experiments were depleted of endogenous Asl and mostly lacked centrioles, it is likely that Asl-A modulation of Plk4 levels occurs in the cytoplasm and not on centrioles. Moreover, coexpression of Plk4 and Asl-A (WT or phosphomutants) did not induce the formation of cytoplasmic aggregates (Figure S2.2A), a potential Plk4-stabilizing effect that we previously observed when Plk4 was coexpressed with either FL Asl or the Asl-C fragment135.

The Asl-A phosphorylation state does not influence its structure, oligomerization, or ability

to bind Plk4

The Asl-A phosphorylation state could regulate Plk4 self-destruction in different ways.

We first explored the possibility that the introduction of 13A and 13PM mutations into Asl could

disrupt the structure of the proteins and thus compromise their ability to regulate Plk4 levels.

Circular dichroism (CD) analysis of purified Asl-A mutant proteins revealed that the largely

alpha-helical structure of Asl-A was unaffected by the changing phosphostate of the mutants

(Figure 2.2C). These results suggest that the 13 phosphomutations do not alter Asl-A structure.

Asl-A is known to form a homodimer that binds to two Plk4 molecules and likely

facilitates Plk4 homodimerization and autophosphorylation135. Possibly, Asl-A phosphorylation

disrupts its ability to dimerize and, consequently, Plk4 homodimers fail to form. To test this, we

used size exclusion chromatography with multiangle light scattering (SEC-MALS) to examine

the oligomeric state of purified Asl-A phosphomutants. Our analysis revealed that Asl-A-WT,

13A, and 13PM oligomerize, based on measurements of their molecular mass (Figure 2.2D). In addition, we used IP from S2 cell lysates depleted of endogenous Asl to examine whether self- association of Asl-A is influenced by phosphorylation. Both Asl-A-13A and 13PM were able to co-IP themselves (Figure 2.2E), suggesting that Asl-A phosphorylation state does not affect its oligomerization.

Another possibility is that Asl-A phosphorylation blocks Plk4 binding, potentially explaining why Plk4 fails to self-destruct when coexpressed with Asl-A-13PM (Figure 2.2B). To test this, we performed GST-pulldown assays using purified Asl-A-His6 proteins and GST-PB1-

PB2 (the Asl-binding domain in Plk4)37–39. No differences in Plk4 binding by the Asl-A

phosphomutants in vitro were observed (Figure S2.2B). We also examined PB1-PB2-GFP

binding to Asl-A proteins in S2 cells by using anti-GFP–coated resin to purify transgenic PB1-

PB2-GFP from endogenous Asl-depleted S2 cell lysates. Again, the expressed Asl-A constructs

did not differ in their association with PB1-PB2 (Figure S2.2C). (The Asl-A mutants did not bind a Plk4 truncation mutant lacking PB1-PB2 [Plk4-1-381; Figure S2.2D]). Finally, quantitative co-

IP experiments using FL Plk4, instead of the PB1-PB2 fragment, also showed no differences in the binding of Asl-A-WT or phosphomutants (Figure 2.3, A and B). Thus, the phosphorylation state of Asl-A does not affect Plk4 binding.

Phospho-null Asl-A (13A) stimulates Plk4 kinase activity, whereas phosphomimetic Asl-A

(13PM) inhibits Plk4 catalytic activity

Because phosphorylation of Asl-A does not control its oligomerization or Plk4 binding, we next asked whether Asl-A’s phosphorylation state directly regulates Plk4 kinase activity. If this regulation exists, then our previous results predict that Asl-A-13A should activate Plk4 and

Asl-A-13PM should inhibit. To test this, we first examined Plk4 mobility on SDS–PAGE as a

readout of Plk4 autophosphorylation activity. Catalytically active Plk4 extensively auto-

phosphorylates and normally migrates as a multiband smear; in contrast, Plk4 collapses to a

single fast-migrating band if mutated to KD or when expressed in Asl-depleted cells52,135. (These

electrophoretic shifts in mobility were most obvious when Plk4 was immunoprecipitated from

cell lysates). In cells depleted of endogenous Asl, coexpression of Plk4 with Asl-A-WT partially restored Plk4 activity, producing multiple bands that included a species with intermediate mobility (lane 2). However, when coexpressed with Asl-A-13A, Plk4 shifted to a low-mobility, hyperphosphorylated form (lane 3). In contrast, coexpression with Asl-A-13PM had little to no effect on Plk4 mobility, appearing most similar to Plk4 from cells with no Asl-A replacement

(lane 4). As an additional readout of kinase activity, we quantified the amount of Slimb that co-

IPed with Plk4 in Asl-depleted cells because Slimb binds only autophosphorylated Plk452,54,55,57.

Compared to cells coexpressing Asl-A- WT, Plk4 bound significantly more Slimb (threefold)

when expressed with Asl-A-13A but bound less Slimb when expressed with Asl-A-13PM

(Figure 2.3, A and C). Results from both experimental approaches support the conclusion that

Plk4 activity is highest in cells expressing the phospho-null Asl-A-13A mutant and least with

phosphomimetic Asl-A-13PM.

In addition to Plk4 itself, we examined phosphorylation of another Plk4 substrate. To do

this, we used a phosphospecific antibody generated against phosphorylated S318 (pS318) in

Ana2 (Figure S2.2E; McLamarrah et al., 2018), a conserved residue phosphorylated by Plk4

41,44,45,48. Western blots of GFP-Ana2 purified by IP from cell lysates were probed with the anti-

pS318 antibody. This antibody recognized GFP-Ana2 when coexpressed with ND Plk4 (Figure

2.3E, lane 2). Surprisingly, coexpression of Asl-A-WT with ND- Plk4 decreased Ana2

phosphorylation, as indicated by the relatively diminished pS318 band observed by Western blot

(lane 3). Possibly, Asl-A-WT is a preferred Plk4 substrate in cells, resulting in decreased Ana2

phosphorylation. In comparison, Asl-A-13A coexpression increased the detected pS318 (lane 4),

whereas the pS318 level in cells coexpressing Asl-A-13PM was nearly undetectable, similar to the level in control cells lacking active ND-Plk4 (lanes 1 and 5).

We next performed in vitro kinase assays to address whether the phosphostate of Asl-A can modulate Plk4 catalytic activity directly. Purified FL Plk4 was mixed with each Asl-A phosphomutant and ℽ-32P-ATP, and Plk4 kinase activity was evaluated by measuring its

autophosphorylation over time (Figure 2.4A). For each condition, the extent of Plk4

autophosphorylation was compared with the autophosphorylation of control (Plk4 alone) at the

first time point (5 min). We found that Plk4 alone is relatively inactive, presumably because it is

autoinhibited (Figure 2.4A, lanes 1–3)47. In contrast, the phospho-null mutant Asl-A-13A significantly stimulated Plk4 activity (Figure 2.4, A, lanes 7–9, B, and C). Unlike the 13A mutant, Asl-A-13PM did not activate Plk4 (Figure 2.4, A, lanes 10–12, B, and C), perhaps because the phosphomimetic mutant cannot relieve Plk4 autoinhibition. However, we were surprised to observe that Asl-A-13PM failed to completely inhibit Plk4 kinase activity because our previous experiments (above) support the conclusion that Plk4 activity is suppressed by the

13PM mutant in cells. Likewise, the addition of Asl-A-WT had no significant effect on Plk4 autophosphorylation compared with the control (Figure 2.4, A, lanes 4–6, B, and C), possibly because Asl-A-WT relieves Plk4 autoinhibition only until Asl-A is phosphorylated and then resembles Asl-A-13PM. If Asl-A-WT phosphorylation is rapid in vitro, Plk4 autoinhibition could quickly resume and prevent substantial autophosphorylation. These in vitro results support

our observations that Asl-A-13A directly activates Plk4 in cells. The lack of inhibition by Asl-A-

13PM in vitro was unexpected.

Phosphomimetic Asl-A (13PM) inhibits centriole duplication

If Asl-A-13PM inhibits Plk4 activity in cells, it follows that its expression should block

centriole duplication. Therefore, we over-expressed Asl-A-GFP proteins in S2 cells (containing

endogenous Asl) for 3 d, immunolabeled centrioles with anti-PLP antibody, and then measured

centriole numbers (Figure 2.5A). Expression of Asl-A-WT or 13A did not significantly alter

centriole numbers compared with GFP-expressing control cells. However, Asl-A-13PM expression significantly increased the number of cells with less than two centrioles. Although

Asl-A-13A stimulates Plk4 kinase activity, over-expression of Asl-A-13A by itself was not sufficient to cause significant centriole amplification (Figure 2.5A). Thus, Asl-A-13PM acts as a dominant negative and inhibits centriole duplication in cells. In contrast, overexpression of Asl-C has the opposite effect and induced centriole amplification (Figure 2.5A), as we previously reported135. Therefore, we asked whether co-overexpression of Asl-C could mask the dominant- negative effect of Asl- A-13PM. We found that overexpression of Asl-C with Asl-A-13PM also showed centriole amplification, demonstrating that the presence of Asl-C, either in cis (Figure

S2.1B) or trans (Figure 2.5A), masks the effects of an Asl-A variant.

To test whether the effect of Asl-A-13PM on centrioles is likely due to Plk4 inhibition, we generated “dual-gene” vectors that express inducible Asl-A and Plk4 from the same plasmid, thereby ensuring that transfected cells contain both proteins (Figure 2.5B). In this approach, Asl-

A mutants were expressed at higher than endogenous Asl levels but similar to one another

(Figure S2.3A). Plk4 overexpression by itself caused significant centriole amplification compared with control. However, coexpression of Plk4 with Asl-A-13PM, but not WT or 13A,

not only blocked amplification but caused significant centriole loss (Figure 2.5B). Thus,

expression of Asl-A-13PM inhibits both centriole duplication and Plk4-induced centriole

amplification.

Asl-A stimulates Plk4 kinase activity by relieving L1-mediated autoinhibition

To understand how the phosphorylation state of Asl-A regulates Plk4 kinase activity, we next examined whether Asl-A influences Plk4 autoinhibition. Plk4 initially exists in an autoinhibited conformation mediated by Linker 1 (L1)47. Current models suggest that L1 interacts with the activation loop of the kinase domain and blocks its trans- autophosphorylation43,44,47. Relief of autoinhibition occurs when PB3 binds the conserved

centriole protein STIL, which repositions L1 so that it no longer obstructs activation loop

phosphorylation43,44. To test whether Asl-A requires Ana2 (the fly homologue of STIL) to regulate Plk4 activity, we replaced endogenous Asl with Asl-A proteins and examined the

electrophoretic mobility of Plk4 IPed from lysates of Ana2-depleted cells (Figure 2.5C).

Notably, Ana2 depletion had no observable effect on the ability of Asl-A-WT or the phosphomutants to modulate Plk4 autophosphorylation. Thus, if Asl-A controls Plk4 autoinhibition, then it does so in an Ana2-independent manner.

Previously, we showed that Plk4 lacking PB3 (∆PB3) is catalytically inactive because it cannot relieve autoinhibition, and its expression in cultured cells causes centriole loss47. Unlike

STIL/Ana2, Asl binds PB1-PB2, but not PB337–39. Therefore, we reasoned that expression of

Asl-A might relieve autoinhibition in the Plk4-∆PB3 mutant. To test this, we redesigned our dual-gene plasmid to coexpress Plk4-∆PB3 and Asl-A proteins, and measured centriole numbers in transfected cells (Figure 2.5D). As expected, cells expressing only Plk4-∆PB3 displayed increased centriole loss (less than two centrioles). Remarkably, coexpression of Plk4-∆PB3 with

Asl-A-WT or Asl-A-13A induced centriole amplification, whereas centrioles were lost after

coexpression with Asl-A-13PM. The simplest interpretation of these results is that Asl-A can

directly relieve Plk4 autoinhibition and activate the kinase, bypassing the need for PB3 to do so.

However, this is not the case when Asl-A is phosphorylated.

Plk4 autophosphorylation of its kinase domain promotes Asl-A-13PM–mediated inhibition

The ability of Asl-A-13A to activate Plk4-∆PB3 could be explained if the 13A mutant

repositions the inhibitory L1 domain so that it no longer interferes with kinase activity, whereas

13PM cannot. Therefore, we generated a dual-gene plasmid to express Plk4 lacking L1 (∆L1, which cannot autoinhibit) alone or with the Asl-A mutants, and then measured centriole numbers in cells, with the expectation that all Asl-A proteins would induce centriole amplification (Figure

2.5E). We found that expression of Plk4-∆L1 alone or with Asl-A-WT or Asl-A-13A resulted in a significant increase in cells with more than two centrioles. Surprisingly, coexpression with Asl-

A-13PM still produced significant centriole loss. These results suggest that Asl-A-13PM suppresses catalytic activity in an L1-independent manner.

How does phosphomimetic Asl-A-13PM inhibit Plk4 kinase activity if not through L1- mediated autoinhibition? Similarities with Plk1 regulation might hold a clue. Like Plk4, Plk1 is autoinhibited by its L1, but Plk1 has an additional mechanism of autoinhibition: L1-independent autoinhibition occurs when its two Polo boxes bind the kinase domain, which rigidifies the hinge region of the kinase domain and inhibits catalytic activity134. This autoinhibition is relieved by

phosphorylation of a hinge residue in Plk1 that disrupts the interaction137–139. Similarly, Asl-A-

13PM may bind Plk4’s kinase domain in a unique conformation that could, for example, block

the active site.

We previously identified a residue in the fly Plk4 kinase domain (S228) that is

autophosphorylated both in vitro and in vivo, but the functional consequence of this modification

is unknown47. The crystal structure of the human Plk4 kinase domain places this residue within an exposed loop near the kinase domain’s C-terminus (which we refer to as the “C-loop”; Figure

2.6A)20. Although the corresponding residue is not conserved in humans (A226 in human Plk4),

in vitro autophosphorylation of a nearby C-loop residue (S232) in human Plk4 has been reported

(Figure 2.6A)140. Thus, we explored the possibility that autophosphorylation of S228 contributes

to Asl-A-13PM’s inhibitory mechanism.

First, we generated nonphosphorylatable S228A and phospho-mimetic S228D Plk4 and

determined that these S228 substitutions do not compromise kinase activity because, unlike KD-

Plk4, their expression promotes centriole amplification and maintains low Plk4 protein levels in

cells, similar to WT-Plk4 (Figure S2.3, B and C). If phosphorylation of S228 does contribute to

the inhibitory activity of Asl-A-13PM, then coexpression of Plk4-S228A should prevent this.

Therefore, we altered our dual-gene plasmid to coexpress Asl-A with Plk4-S228A and measured

centriole numbers in transfected cells (Figure 2.6B). As before, coexpression of Asl-A-13PM prevented WT-Plk4 from amplifying centrioles and caused significant centriole loss. Strikingly, however, when coexpressed with Plk4-S228A, Asl-A-13PM no longer suppressed centriole assembly and amplification ensued. Thus, our findings suggest that, in order to generate an inhibitory conformation with Asl-A, Plk4 phosphorylates not only Asl-A but its kinase domain as well.

One possible model for this inhibition is that Asl-A-13PM directly binds the kinase domain of Plk4 (containing phospho-S228) and inhibits its enzymatic activity (e.g., competitively or allosterically). Possible interactions between Asl-A mutants and mutant Plk4

fragments containing only the kinase domain and DRE (amino acids 1–317) were tested using

co-IPs from lysates of cells expressing the constructs, but no such interactions were detected

(Figure S2.3D), demonstrating the requirement of PB1-PB2 for stable Asl-A/Plk4 binding.

Additionally, we performed co-IPs to see whether the S228D mutation in FL Plk4 would result in a significant increase in Asl-A-13PM binding. Perhaps not surprisingly, we did not observe an

increase in binding (Figure S2.3E), presumably due to the stable interaction between Asl-A-

13PM and Plk4 PB1-PB2 (Figure S2.2, B and C). Taken together, our findings suggest that in order for Asl-A-13PM to inhibit Plk4 kinase activity, it requires the presence of an unidentified factor.

2.4 Discussion

Plk4 kinase activity is required for centriole duplication, and a number of Plk4-mediated phosphorylation events that promote centriole assembly have been described37,41,45,48,50,107,140–144.

Of these, the most conserved targets include autophosphorylation of its activation loop (required

for full kinase activation) and the STAN domain in STIL/Ana2, which promotes binding of the

cartwheel protein, Sas641,44,45,47,48,56. Plk4 activity also suppresses centriole duplication by down-

regulating itself via autophosphorylation of its DRE, which induces ubiquitin-mediated

proteolysis52,54,55,57.

In this study, we have identified another conserved Plk4 target, namely, the Asl N- terminus; using mass spectrometry, 13 phospho-residues of Asl-A were identified that primarily cluster at both ends of the Asl-A region. Overexpression of mutants containing phospho-null or phosphomimetic substitutions in all of these sites within the FL Asl protein had no effect on

centriole duplication, Plk4 binding, or centriole localization in cultured cells. We attribute this to

the presence of the Asl-C region because Asl-C contains a second Plk4-binding site as well as the centriole-targeting domain, and, most importantly, overexpression of Asl-C alone is sufficient to induce centriole amplification135. The conclusion that the presence of the Asl-C

region can obscure the biological effects of Asl-A phosphorylation is further supported by our

finding that coexpression of Asl-A-13PM does not significantly alter centriole amplification

induced by Asl-C overexpression (Figure 2.5A). Thus, Asl is a multifunction protein whose

activities are parsed between its domains and, interestingly, the effects of the Asl-C region on

centriole assembly are apparently dominant over the Asl-A region. Understanding how these two

domains coordinate their functions to regulate centriole duplication is an important goal.

To determine how Asl-A modification may affect Plk4 regulation, we employed an

approach that involved depleting endogenous Asl (via RNAi) and replacing it with an

overexpressed Asl-A fragment. Though CRISPR/Cas9 genome editing could be used to express

a mutated Asl gene at endogenous levels and has been used in Drosophila S2 cells, the technique

is not without its challenges because S2 cells possess a stable aneuploid genome with

approximately two X chromosomes and two major autosomes, where each autosome is present in

four copies142–144. Although we note that our results must be appraised carefully because of

potential difficulties arising from overexpression, our replacement experimental strategy allowed

us to coexpress a variety of Asl and Plk4 mutant constructs and use techniques (such as

immunoprecipitation) to rapidly probe a new complex mechanism of Plk4 regulation. We also

performed in vitro kinase assays and discovered that nonphospho Asl-A activates Plk4, whereas

WT and phosphomimetic Asl-A do not, suggesting that the observed in vivo phenotypes are not

simply artifacts of protein over-expression. Under these conditions, Asl-A-WT functions like

Asl-A-13PM presumably because it is rapidly phosphorylated in vitro and then (like 13PM) can

no longer relieve Plk4 autoinhibition, restoring Plk4 to its low basal rate of autophosphorylation.

Surprisingly, in contrast to our in vivo observations, Asl-A-13PM did not inhibit Plk4 activity compared with Plk4 alone. Thus, we propose that phospho Asl-A requires an additional, unidentified factor to inhibit Plk4, and that the factor is probably not Ana2 (Figure 2.5C).

This study revealed a functional significance of Asl phosphorylation by Plk4, and we summarize our major findings in the following model that diagrams a new mechanism regulating

Plk4 kinase activity (Figure 2.6C). We propose that Asl-A binds PB1-PB2 in Plk4 and initially

relieves autoinhibition of inactive Plk4 (stage 1) by repositioning L1 in a PB3-independent

manner (stage 2). In turn, Plk4 trans-autophosphorylates its activation loop and residue S228 of

its C-loop, in addition to extensively phosphorylating the N- and C-termini of Asl-A (stage 3).

Phosphorylation of Asl-A and Plk4’s C-loop result in Plk4 inactivation, perhaps after the recruitment of an unidentified protein to form an inhibitory complex (stage 4). Our model of this novel inhibitory mechanism resembles the “product inhibition” commonly observed in metabolic pathways, because Plk4 phosphorylates Asl-A to generate a modified product that then

suppresses kinase activity145. Kinase inhibition could occur in a variety of ways; stage 4 of our

model depicts only one possibility, where the active site is obstructed and competitively

inhibited. Future studies of the molecular structures of the activating and inhibitory complexes

would be very informative.

Asl-mediated activation of Plk4 followed immediately by negative feedback to inhibit the

kinase could function to ensure that Plk4 kinase activity is limited to brief bursts when

encountering Asl. How then could Asl-A–mediated activation/inactivation of Plk4 participate in

the centriole duplication cycle? We propose that the Asl-A mechanism described here likely

occurs in the cytoplasm, facilitating Plk4 destruction to suppress rampant centriole amplification

in interphase cells. Specifically, Plk4 activity would be confined to just the Asl-Plk4 complex, ensuring that 1) autophosphorylation of the DRE triggers Plk4 ubiquitination and 2) phosphorylated Asl-A, perhaps with an unidentified binding partner, holds the kinase in an inactivate state to prevent unwanted centriole assembly while Plk4 awaits degradation. If true, then

Asl is the primary facilitator of interphase Plk4 degradation in Drosophila cells. Supporting this idea is the finding that Asl RNAi increases Plk4 protein levels in interphase cells135. Moreover,

the stabilized Plk4 in Asl-depleted cells migrates as a fast-migrating single polypeptide on SDS–

PAGE (similar to KD Plk4; Klebba et al., 2015a), suggesting that, without Asl, Plk4 accumulates

in an autoinhibited, nonphosphorylated state47. Interestingly, a similar phenotype is observed in

human cells depleted of STIL, suggesting that STIL replaced Asl/Cep152 as the predominant

interphase Plk4 activator during human evolution44.

Although Asl-C overexpression by itself induces centriole amplification, we predict that

under physiologic conditions the Asl-A and Asl-C domains coordinate their respective Plk4

regulatory functions to ensure centriole duplication occurs only once per cell cycle. During

mitotic exit when procentriole assembly is initiated, the Asl-C domain likely stabilizes Plk4 at

the centriole48,135. Plk4 activation/deactivation mediated by Asl-A then could ensure that Plk4

activity is restricted both spatially and temporally at the parent centriole surface. Like the Asl-A region, STIL stimulates Plk4 kinase activity, probably by also relieving auto-inhibition42,43.

Thus, Asl is the second Plk4 activator identified to date. Notably, Plk4 is predicted to be

regulated by Asl before Ana2/STIL based on the hierarchal recruitment of the two regulators to

procentrioles103. In this regard, Asl-A–mediated activation of Plk4 may play a role in STIL

recruitment, as Plk4 kinase activity is required to maintain STIL on centrioles44. In this scenario,

Asl could direct Plk4 activity to an initial set of essential centriole substrates before handing off

Plk4 to STIL/Ana2, which, after binding and stimulating Plk4, facilitates Sas6

recruitment41,44,45,48. Additionally, a recent study has shown that Plk4 controls the rate of

centriole growth during early fly embryogenesis, and that oscillations in Plk4 activity during

different cell cycle phases are likely required to establish proper centriole length77. Our finding

that Asl-A can both stimulate and inhibit Plk4 activity suggests that Asl may be a primary

regulator of these oscillations in Plk4 activity, thus ensuring that centrioles reach their proper

size during each cell cycle. Future studies are necessary to determine when this new mechanism

of Plk4 regulation occurs during the centrosome cycle and whether additional Plk4 “activators”

exist, as they may be necessary to stimulate additional centriole assembly steps.

2.5 Materials and Methods

Drosophila cell culture

Drosophila S2 cell culture was performed as previously described146. S2 cells (Life

Technologies; catalogue no. R69007) were cultured at room temperature (20–25°C) in Sf900II

SFM medium (Life Technologies; catalogue no. 10902104).

Double-stranded RNA (dsRNA) interference

dsRNA interference (RNAi) was performed as previously described146. Briefly, cells were cultured in six-well plates at 50–90% confluency in 1 ml of medium. Cells were treated with 5–10 μg dsRNA every day for 5–7 d. Control dsRNA was synthesized from noncoding

DNA in a pET28a vector template (Clontech) using the primers 5’-ATCAG GCGCTCTTCCGC and 5’-GTTCGTGCACACAGCCC. (All primers used for dsRNA synthesis begin with the T7 promoter sequence 5’-TAATACGACTCACTATAGGG, followed by template-specific

sequence.) DNA template for Asl dsRNA (which targeted coding sequence not present in the

Asl-A coding sequence) was generated using the primers 5’-CGTCTGATCCATCGCCC-3’ and

5’-CATCGCCTCTTCGTGGG-3’. The DNA template for Ana2 dsRNA was generated using the primers 5’-TAATACGACTCACGCTCTGGTATCCC-3’ and 5’-TAATAC

GACTCACGTTGCTCCTCGGG-3’ to amplify a region of coding sequence from Ana2 cDNA.

Immunoblots confirmed the depletion of endogenous Asl or Ana2 (Figures 2.2B and 2.5C, respectively).

Immunofluorescence microscopy

S2 cells were fixed and processed as previously described (Rogers and Rogers, 2008) by spreading cells on concanavalin A–coated glass bottom dishes and fixing with 10% formaldehyde for 10 min. Primary antibodies were diluted to concentrations ranging from 1 to 20

μg/ml and included rabbit anti-PLP (our laboratory) and guinea pig anti-Asl (our laboratory).

Secondary antibodies (conjugated with Cy5 or Rhodamine red-X [Jackson ImmunoResearch

Laboratories]) were used at a dilution of 1:1500. To stain DNA, Hoechst 33342 (Life

Technologies; catalogue no. H3570) was used at a final concentration of 3.2 μM. Cells were mounted in phosphate-buffered saline (PBS) containing 0.1 M n-propyl galate, 90% (by volume) glycerol. Specimens were imaged using a DeltaVision Core system (Applied Precision) equipped with an Olympus IX71 microscope, a 100X objective (NA 1.4) and a cooled charge-coupled device camera (Cool- SNAP HQ2; Photometrics). Images were acquired with softWoRx v1.2 software (Applied Science).

Immunoblotting

S2 cell extracts were produced by lysing cells in cold PBS containing 0.1% Triton X-100.

Laemmli sample buffer was then added and the samples were boiled for 5 min. Samples of equal

total protein were resolved by SDS–PAGE, blotted, probed with primary and secondary

antibodies, and scanned on an Odyssey imager (Li-Cor Biosciences). Care was taken to avoid

saturating the scans of blots. Antibodies used for Western blotting include guinea pig anti-Asl

(our laboratory), rat anti-Asl (our laboratory), rabbit anti-Ana2 (our laboratory), mouse anti-GFP

monoclonal JL-8 (Clontech; catalogue no. 632380), mouse anti-V5 monoclonal (Life

Technologies; catalogue no. R960-25), mouse anti-myc (Cell Signaling Technology; catalogue no. 2276S), and mouse anti-α tubulin (Sigma-Aldrich; catalogue no. T9026) at dilutions ranging from 1:1000 to 1:3000. IRDye 800CW secondary antibodies (Li-Cor Biosciences) were prepared according to manufacturer’s instructions and used at 1:3000 dilution.

To generate anti-phosphospecific S318 Ana2 antibody, rat polyclonal antibodies were raised against the phosphopeptide: AKPNTEK{pSer}MVMNELAC. A nonphosphopeptide with the sequence AKPNTEKSMVMNELAC was also generated (Pocono Rabbit Farm, PA).

Antibodies were affinity purified from antisera using phosphopeptide coupled to Affi-Gel. The anti-phosphopeptide solution was concentrated using 10k Ultrafree concentrators (Millipore).

Antibodies were used at a 1:500 dilution.

For 2D gel electrophoresis, S2 cell extracts were produced by lysing cells in sample rehydration buffer (8 M urea, 33 mM CHAPS, 0.5% Zoom carrier ampholytes [Novex; catalogue no. ZM0022], 20 mM dithiothreitol [DTT], 0.002% bromophenol blue) and clarified by centrifugation at 16,100 x g for 10 min. Protein (200 μg) was loaded onto a polyacrylamide gel strip (Novex) by soaking the sample with the strip for 2 h at room temperature. Isoelectric focusing was performed at 175 V for 15 min followed by 175–200 V ramp for 45 min and 2000

V for 105 min. The strips were then soaked in 1X lithium dodecyl sulfate (LDS) sample buffer

with 50 mM DTT for 15 min and resolved by SDS–PAGE. Western blots were performed as

described above.

Constructs and transfection

FL cDNAs of Drosophila Asl, Plk4, and Ana2 were subcloned into a pMT vector

containing in-frame coding sequences for EGFP, V5, or myc under control of the inducible

metallothionein promoter. Mutants of Plk4 and Asl were generated by PCR-based site directed

mutagenesis with Phusion polymerase (ThermoFisher; catalogue no. F530S). For transient

transfections, (2–5) x 106 S2 cells were pelleted by centrifugation and resuspended in 100 μl of

transfection solution (5 mM KCl, 15 mM MgCl2, 120 mM sodium phosphate, 50 mM d-

mannitol, pH 7.2) containing 0.2–2 μg of purified plasmid. The resuspension was then

transferred to a 2-mm gap cuvette and electroporated using a Nucleofector 2b (Lonza), program

G-030. Transfected cells were immediately diluted in 1 ml of SF-900 II medium and placed in a six-well tissue culture plate. Cells were typically allowed to recover for ~24 h before inducing by the addition of 0.5–2 mM CuSO4 to the culture medium.

Immunoprecipitation assays

GFP-binding protein (GBP) was fused to the Fc domain of human IgG (pIg-Tail; R&D

Systems), tagged with His6 in pET28a (EMD Biosciences), expressed in Escherichia coli, and

purified on HisPur resin (ThermoFisher; catalogue no. 88221) as described previously147,148.

Purified GBP was bound to magnetic Dyna Beads (ThermoFisher; catalogue no. 10001D), and then cross-linked to the resin by incubating with 20 mM dimethyl pimelimidate dihydrochloride in PBS, pH 8.3, 2 h at 22°C, then quenched by incubation with 0.2 M ethanolamine, pH 8.3, 1 h

at 22°C. Antibody-coated beads were washed three times with PBS-Tween20 (0.02%), then

equilibrated in 1.0 ml of cell lysis buffer (CLB; 50 mM Tris, pH 7.2, 125 mM NaCl, 2 mM DTT,

0.1% Triton X-100, and 0.1 mM phenylmethylsulfonyl fluoride [PMSF]). Transfected cells

expressing recombinant proteins were lysed in CLB, and the lysates clarified by centrifugation at

16,100 x g for 5 min at 4°C. Inputs (0.5–1%) were used for immunoblots. GBP-coated beads were rocked with lysate for 30 min at 4°C, washed three times with 1 ml CLB, and then boiled in

Laemmli sample buffer.

Circular dichroism

Asl-A WT, 13A, and 13PM CD spectra were collected at 20 and 94°C using a Chirascan- plus CD spectrometer (Applied Photophysics). Samples were diluted to 0.1 mg/ml in CD buffer

(10 mM sodium phosphate, pH 7.4, 50 mM sodium fluoride) and injected into a 1-mm–path

length cuvette. CD spectra were acquired from 260 to 185 nm with a step size of 0.5 nm every

1.25 s. A buffer CD spectrum was subtracted from each Asl-A spectrum and the data were

smoothed using Chirascan-plus software.

Size exclusion chromatography-multiangle light scattering

Size exclusion chromatography–multiangle light scattering (SEC-MALS) was performed

as previously described135. Briefly, Asl mutants (50 μM, 100 μl) were injected onto a Superdex

200 10/30 GL size exclusion column (GE Healthcare Life Sciences) at 0.5 ml/min in buffer (25

mM HEPES, pH 7.5, 300 mM NaCl, 0.1% β-mercaptoethanol, and 0.2 g/l sodium azide). Eluent

was analyzed by a tandem RI detector/Dawn Heleos II multiangle static light scattering (MALS)

detector (Wyatt Technology). Light scattering and refractive index data were used to calculate

the weight-averaged molar mass using Wyatt Astra V software (Wyatt Technology).

In vitro binding assay

Plk4 PB1-PB2 (amino acids 382–602) was subcloned into pGEX-6p2 plasmid (GE

Healthcare Life Sciences) to generate a GST-PB1-PB2 construct. Asl-A (WT, 13A, or 13PM;

amino acids 1–374) was subcloned into pET28a (Life Technologies) to generate Asl-A-His6.

Proteins were bacterially expressed and purified from lysates using either glutathione or HisPur resins according to manufacturer’s instructions. For each construct, optimal elution fractions

(determined after SDS–PAGE analysis) were pooled, concentrated using centrifugal filters

(Ultracel, Amicon), and exchanged into binding buffer (40 mM HEPES, pH 7.3, 150 mM NaCl,

5 mM MgCl2, 0.5 mM MnCl2, 1 mM DTT). Purified GST-PB1-PB2 was rebound to glutathione resin, washed, and the quantity of protein bound to the resin was determined from the difference in the quantities of soluble GST-PB1-PB2 present before and after rebinding. To assess Asl-A binding to PB1-PB2, different quantities of the GST-PB1-PB2 beads were mixed with a constant quantity of purified, soluble Asl-A-His6 (WT, 13A, or 13PM) in order to test a range of molar ratios of Asl-A to PB1-PB2 (on beads). Each assay also contained an appropriate quantity of purified GST bound to glutathione beads to keep the total molar quantity of GST and volume of beads the same in each assay. Mixtures were gently agitated for 30 min at 23°C, after which samples of the supernatant (S) and twice-washed resin (P) were resolved by SDS–PAGE.

Integrated intensities of the Coomassie-stained Asl-A bands in the gels were measured using

ImageJ (National Institutes of Health [NIH]) software.

In vitro kinase assays

Bacterially expressed constructs of Drosophila Plk4 (amino acids 1–317 and FL) C- terminally tagged with FLAG-His6 and Drosophila Asl fragments A (amino acids 1–374), B

(amino acids 375–630), and C (amino acids 631–994) N-terminally tagged with GST (in the

59 pGEX-6p2 vector; GE Healthcare) were prepared as described above for in vitro binding assays.

For in vitro phosphorylation assays, purified proteins (Plk4 and Asl; both were 0.25 μM in

Figure 2.4, but were 10 μM when preparing samples for tandem mass spectrometry analysis) were incubated with 100 μM ATP for 1 h at 25°C in reaction buffer (40 mM Na HEPES, pH 7.3,

150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 10% [by volume] glycerol). Samples were resolved by SDS–PAGE, and proteins visualized by Coomassie staining. Phosphorylation of protein substrates was evaluated by including ℽ-32P-ATP in assays and, subsequently, the presence of radiolabeled substrates detected by autoradiography or phosphorimaging of dried gels.

Phosphorylated residues within proteins were identified by tandem mass spectrometry (Table

2.1) of purified bacterially expressed proteins phosphorylated in vitro (described above) in the presence of nonradioactive ATP.

Mass spectrometry

Samples of Asl were resolved by SDS–PAGE and Coomassie-stained. Appropriate bands were cut from gels, destained (50% acetonitrile, 25 mM ammonium bicarbonate), reduced (10

μM DTT, 55°C, 1 h), alkylated (55 mM iodoacetamide, 23°C, 45 min), dehydrated (100% acetonitrile), and then digested in-gel for 12 h with ~1.5 ng/μl of either trypsin (37°C) or chymotrypsin (23°C). Peptides were extracted with 50% acetonitrile, 1% formic acid, dried by speed-vac (with lowest heat setting), and stored at 4°C. Mass spectrometry was performed at the

NHLBI Proteomics Core Facility (NIH). Desalted peptide samples were separated on a 10-cm

Picofrit Biobasic C18 analytical column (New Objective, Woburn, MA) using a 90-min linear gradient of 5–35% acetonitrile/water containing 0.1% formic acid at a flow rate of 250 nl/min, ionized by electrospray ionization (ESI) in positive mode, and analyzed on a LTQ Orbitrap

Velos mass spectrometer. All LC-MS analyses were carried out in “data-dependent” mode in

which the top six most intense precursor ions detected in the MS1 precursor scan (m/z 300–

2000) were selected for fragmentation via collision-induced dissociation (CID). Precursor ions were measured in the Orbitrap at a resolution of 60,000 (m/z 400) and all fragment ions were measured in the ion trap. Protein sequences were matched to spectra using Mascot software

(Matrix Science), and the corresponding Mascot values for peptide identification are shown

(Table 2.1). Ascores, phosphate localization probabilities, and spectral counts were obtained from ScaffoldPTM 3.1 (Proteome Software).

Statistics

Means of measurements were analyzed for significant differences by one-way analysis of variance followed by Tukey’s posttest (to evaluate differences between treatment pairs) using

Prism 6 (GraphPad) software. Means are taken to be significantly different if P <0.05. P values shown for pairwise comparisons of Tukey’s posttest are adjusted for multiplicity. In figures, * indicates 0.05 > P ≥ 0.01; ** indicates 0.01 > P ≥ 0.001; *** indicates 0.001 > P; and ns indicates P ≥ 0.05 for the indicated pairwise comparison. Error bars in all figures indicate SEM.

2.6 Figures

Figure 2.1 - Plk4 Phosphorylates the N-terminal Domain of Asl

(A, B) Linear maps of Drosophila Plk4 and Asterless (Asl) showing functional and structural

domains. CC, coiled-coil; DRE, downstream regulatory element (contains the SCFSlimb-binding

motif); PB, Polo boxes; L1 and L2, linkers. The three regions of Asl are indicated with circled

letters. Both Asl-A and Asl-C bind Plk4.

GST-tagged Asl regions, and ℽ-32P-ATP. Plk4 phosphorylates itself and Asl-A but not Asl-B, Asl-

C, or the GST control. Coomassie-stained SDS–PAGE gels and corresponding autoradiographs

(or phosphorimage) are shown.

(D) Linear map of Asl-A showing phosphorylated residues identified by MS/MS from samples of

purified Asl-A incubated with Plk4 in vitro (top) or immunoprecipitated Asl from lysates of S2

cells coexpressing Plk4 (bottom).

(E) Lysates of S2 cells coexpressing Asl-A-V5 and either GFP, kinase-dead (KD) Plk4-GFP, or active nondegradable (ND) Plk4-GFP were resolved by 2D electrophoresis and the Western blot probed with anti-V5 antibody. Resolution in the horizontal axis is by isoelectric point. Note that expressed Asl-A exists as multiple differently charged species and that coexpression of active

Plk4 causes an acidic shift for the majority of Asl-A.

Figure 2.2 – Asl-A Phosphomutants are Largely α-helical and Self-Oligomerize

(A) Abbreviated primary sequence of Asl-A indicating the 13 hydroxyl residues phosphorylated

by Plk4 (bold) and mutated to nonphosphorylatable alanine (13A) or phosphomimetic

aspartate/glutamate (13PM). Gray highlight indicates regions of predicted coiled-coil.

(B) In the absence of endogenous Asl, expressed Asl-A-13A restores Plk4 self-destruction, whereas Asl-A-13PM has no effect on Plk4 protein levels. S2 cells were treated with Asl-C

dsRNA for 6 d to deplete endogenous Asl without affecting transgenic Asl-A. On day 4, cells

were transfected with inducible Plk4-GFP alone or with the indicated Asl-A-V5 construct and then induced to express the next day for 24 h. Immunoblots of lysates were probed with anti-

GFP, V5, Asl, and α-tubulin (loading control). The graph shows the relative amounts of Plk4-

GFP as determined by densitometry of the anti-GFP immunoblots, normalized to α-tubulin, and plotted relative to control (Cntrl). Error bars, SEM. n = 4 experiments. In all figures, asterisks indicate significance and error bars show SEM.

(C) Asl-A mutants exhibit no significant differences of secondary structure. Circular dichroism analysis of Asl-A mutants suggests that Asl-A retains its α-helical structure even after phosphomimetic and nonphospho mutations are introduced.

(D) Asl-A-WT, 13A, and 13PM constructs analyzed using SEC-MALS. Elution time from the

Superdex 200 column is indicated on the x-axis in minutes. Normalized refractive index is indicated on the left y-axis (gray trace) and molecular mass is indicated on the right y-axis

(black trace, kDa). Asl-A-WT elutes just after 20 min with an experimentally determined average molecular mass of 85.2 kDa, indicative of a stable dimeric state (calculated formula weights for

Asl-A oligomeric states are monomer: 41.5 kDa; dimer: 83.0 kDa; trimer: 123.5 kDa; tetramer:

166.0 kDa; theoretical oligomeric masses are indicated by horizontal dashed lines). Control runs using bovine serum albumin (BSA; unpublished data) revealed that the globular BSA dimer

(132 kDa) eluted at 25 min, suggesting that the Asl-A dimer, which has a slightly smaller molecular mass but elutes earlier, likely adopts an extended conformation. Asl-A-13A and 13PM constructs elute earlier than the Asl-A-WT protein and show higher experimentally determined molecular masses (110.9 and 100.6 kDa, respectively), suggesting that these mutant dimers may transiently self-associate into higher molecular weight complexes during the course of the gel

filtration run. The vertical dashed line indicates the position of the elution peak for Asl-A-WT.

(E) Asl-A phosphomutants retain the ability to homodimerize. S2 cells were RNAi-treated for 6 d to deplete Asl. On day 4, cells were cotransfected with the indicated GFP-tagged and V5-tagged

Asl-A constructs and then induced to express the next day for 24 h. Samples were prepared by anti-GFP immunoprecipitation from cell lysates. Immunoblots were probed for GFP, V5, and α- tubulin.

Figure 2.3 – The Phosphorylation State of Asl-A Controls Plk4 activity

(A) Asl-A-13A enhances Slimb binding to Plk4, whereas Asl-A-13PM diminishes this interaction.

Samples of anti-GFP immunoprecipitates were prepared from lysates of S2 cells treated as described in Figure 2.2B. Immunoblots were probed for GFP, V5, Slimb, and α-tubulin.

(B, C) Graphs show relative amounts of Asl-A-V5 (B) or Slimb (C) bound to Plk4-GFP. Values were measured by densitometry of anti-V5 or anti-Slimb immunoblots of IP samples, normalized to the respective Plk4-GFP band intensity, and plotted relative to WT control. n = 3 experiments. ns, not significantly different.

(D) Asl-A mutants modulate Plk4 autophosphorylation state. Samples of anti-GFP immunoprecipitates were prepared from lysates of S2 cells treated as described in Figure 2.2B except, in this experiment, cells were cotransfected with inducible Plk4-myc. Immunoblots were probed for GFP, myc, V5, and α-tubulin. Dashed lines mark Plk4-myc with different electrophoretic mobilities, indicating changes in phosphorylation state.

(E) Asl-A-13PM suppresses Plk4-dependent Ana2 phosphorylation. Anti-GFP immunoprecipitates were prepared from lysates of S2 cells expressing GFP-Ana2, nondegradable Plk4-ND-myc, and the indicated Asl-V5 construct. Samples of anti-GFP immunoprecipitates were prepared from lysates of S2 cells treated as described in Figure 2.2B.

Immunoblots were probed with anti-GFP to detect total GFP-Ana2 levels and with anti-pS318 to detect phospho-Ana2.

Figure 2.4 – Nonphosphorylatable Asl-A (13A) Stimulates Plk4 Activity In Vitro

(A) Purified Plk4-Flag-His6 was mixed with equimolar amounts of Asl-A and incubated with ℽ-

32P-ATP. Reactions were sampled at 5, 30, and 60 min, and the samples resolved by SDS–PAGE.

Top, Coomassie-stained gel; bottom, corresponding autoradiogram. Arrows indicate Plk4 bands presumably differing by phosphorylation state; the asterisk marks a contaminating band from an added reagent (a protease inhibitor) that migrates between the Plk4 bands.

(B) Graphical representation of Plk4 autophosphorylation over time. y-Axis values are measurements of radioactivity in the Plk4 bands for each sample, expressed as the fold increase of a sample measurement over the Plk4 radioactivity present in the control (Plk4-only) at the

initial (5 min) time point. n = 3 except Asl-A-13PM where n = 2. SEMs smaller than the radii of the graphing points are not plotted.

(C) Asl-A-13A significantly increases Plk4 activity. The average values for Plk4 phosphorylation at the last time point (60 min) from the in vitro kinase assays shown in B are graphed. ns, not significant.

Figure 2.5 – Asl-A Phosphomutants Control Kinase Activity by Modulating Plk4 Inhibition

(A) Asl-A-13PM expression causes centriole loss. The indicated Asl-GFP constructs were transfected into S2 cells and then induced the next day to express for 72 h. Cells were

immunostained for PLP to mark centrioles. Significant centriole loss (less than two centrioles)

occurs in cells expressing Asl-A-13PM. In contrast, centrioles are amplified (more than two

centrioles) in cells expressing Asl-C, and centrioles are similarly amplified in cells coexpressing

Asl-C and Asl-A-13PM. n = 3 experiments per construct (total 300 cells/construct).

(B) Coexpressed Asl-A-13PM not only blocks the centriole amplification induced by Plk4

expression but causes significant centriole loss. Plk4-GFP/Asl-A-V5 dual-gene expression

plasmids were transfected into S2 cells, and then were induced the next day to express for 72 h.

Cells were immunostained for PLP to mark centrioles, and centriole numbers measured. n = 3

experiments per construct (total 300 cells/construct).

of endogenous Asl and Ana2 for 7 d. On day 5, Plk4-GFP and the indicated Asl-A-V5 constructs

were cotransfected into cells and expression was induced the next day. Immunoblots of cell

lysates were probed for Ana2, GFP, V5, and α-tubulin.

(D) Asl-A-WT and Asl-A-13A can activate an autoinhibited Plk4-∆PB3 mutant. S2 cells were

transfected with Plk4-∆PB3-GFP/Asl-A-V5 dual-gene expression plasmids, and samples were

prepared as in B. n = 3 experiments per construct (total 300 cells/construct).

(E) A Plk4 mutant incapable of autoinhibition is inhibited by Asl-A-13PM. S2 cells were transfected with Plk4-∆L1-GFP/Asl-A-V5 dual-gene expression plasmids, and samples were prepared as in B. n = 3 experiments per construct (total 300 cells/construct).

Figure 2.6 – Plk4 Phosphorylates its Kinase Domain and Asl-A, Generating a State that

Inhibits Kinase Activity

(A) Atomic structure of the human Plk4 kinase domain (Wong et al., 2015). The residue, A226, is

the human equivalent of Drosophila S228 within the C-loop. Human Plk4 autophosphorylates C-

loop residue S232 in vitro (Sillibourne et al., 2010).

(B) Asl-A-13PM does not inhibit Plk4-S228A from amplifying centrioles. Plk4-GFP/Asl-A-V5 dual-gene expression plasmids were transfected into cells and the next day were induced to express for 72 h. Centrioles were visualized with PLP immunostaining, and the number of centrioles per cell was counted. n = 3 experiments per construct (total 300 cells/construct).

process of stimulation followed by negative feedback. 1. Initially, Plk4 is autoinhibited by its L1

domain, which masks its activation loop. 2. Nonphosphorylated Asl-A binds Plk4 and relieves

autoinhibition to activate the kinase. 3. Homodimerized Plk4 phosphorylates itself (including its

activation and C-loops) and, importantly, Asl-A. 4. Together, phospho-Asl-A and the phospho-C-

loop recruit an unknown factor(s) to inactivate Plk4, perhaps by generating a complex that

obstructs or distorts the active site.

Figure S2.1 – Full-Length Asl Phosphomutants Induce Centriole Amplification

(A) Full-length (FL) Asl phosphomutants localize to centrioles. S2 cells were depleted of endogenous Asl for 7 days. On day 4, cells were transfected with wild-type or phosphomutant

Asl-FL-GFP. The next day, expression was induced for 72 hours. Cells were immunostained for

PLP to mark centrioles. Each Asl construct co-localizes with PLP. Scale, 5 µm.

(B) Expression of FL Asl phosphomutants induces centriole amplification independent of their phosphorylation state. S2 cells were treated as described in A, and the number of centrioles per cell were measured. Nlp-GFP was used as a control. n = 3 experiments per construct (total 300 cells/construct). In all figures, asterisks indicate significant differences and error bars show

SEM. ns, not statistically significant.

(C) Plk4 binds FL Asl independently of Asl’s phosphorylation state. A non-degradable (Slimb- binding mutant – SBM) Plk4-myc was co-transfected with the indicated Asl-FL-GFP construct into S2 cells, and the next day expression was induced for 24 hours. Samples were prepared by anti-GFP immunoprecipitation from lysates, and immunoblots were probed for GFP, myc and α- tubulin (loading control).

(D) Asl-A phosphomutants weakly localize to centrioles. S2 cells were depleted of endogenous

Asl for 7 days. On day 4, cells were transfected with wild-type or phosphomutant Asl-A-GFP and the following day were induced to express for 72 hours. Cells were immunostained for PLP to mark centrioles. Expression of each Asl-A-GFP construct was diffuse throughout the cytoplasm and only weakly localized to centrioles. Scale, 5 µm.

(E) Expression of Asl-A phosphomutants has no effect on the protein levels of kinase-dead (KD)

Plk4. S2 cells were treated with control or Asl RNAi for 6 days. On day 4, cells were transfected with inducible Plk4-KD-GFP either alone or with the indicated Asl-A-V5 construct, and then induced to express the next day for 24 hours. Immunoblots of lysates were probed with anti-

GFP, V5, and Asl. Co-transfected Nlp-GFP was used as a loading control.

Figure S2.2 – The Phosphorylation State of Asl-A Does Not Influence Cellular Aggregate

Formation and Has Little Effect on Binding to Plk4 PB1-PB2

(A) Co-expression of Plk4 and Asl-A does not induce the formation of intracellular aggregates.

S2 cells were co-transfected with Plk4-GFP and the indicated Asl-A-V5 construct and induced to

express the next day for 24 hours. Since aggregates were rarely observed, images shown are

representative images. Scale, 5 µm.

(B) A constant amount of purified Asl-A-His6 (WT, 13A, or 13PM) was incubated with a varying amount of GST-PB1-PB2 bound to glutathione resin. Each assay included an appropriate amount of purified GST on glutathione resin to ensure that the total molar quantity of GST and resin volume were similar in each binding assay. The post-incubation supernatant (S) and twice- washed resin (P) were analyzed by SDS-PAGE, and the Coomassie-stained gels are shown (left).

The molar ratios of Asl-A to GST-PB1-PB2are indicated (top) as well as the positions of the Asl-

A-His6 and GST-PB1-PB2 proteins (left and right-side arrowheads, respectively). (Below) The average percent of resin-bound Asl-A is graphed for the four different molar ratios of Asl-

A:GST-PB1-PB2. n = 3 experiments. Error bars, SEM. Generally, the pseudo-phosphorylation state of Asl-A does not have much impact on the binding of Asl-A to the tandem PB1-PB2 domains of Plk4.

(C) The phospho-Asl-A mutants associate with Plk4 PB1-PB2 by immunoprecipitation. S2 cells were depleted of endogenous Asl for 6 days. On day 4, cells were co-transfected with inducible

PB1-PB2-GFPand the indicated Asl-A-V5 construct, and then induced to express the next day

for 24 hours. Samples were prepared by anti-GFP immunoprecipitation from cell lysates.

Immunoblots were probed for GFP, V5 and α-tubulin (loading control).

(D) Neither Asl-A-13A nor 13PM mutant associates with Plk4 1-381 (which lacks PB1-PB2; see

Figure 2.1A) by immunoprecipitation. Plk4 1-381-GFP and the indicated Asl-A-V5 constructs

were co-transfected into S2 cells. Samples were prepared by anti-GFP immunoprecipitation of

cell lysates. Immunoblots were probed for GFP, V5 and α-tubulin.

(E) Validation of the anti-Ana2 phospho-specific antibody. Bacterially expressed and purified

MBP-Ana2was incubated with ATP and +/- purified active Plk4. The anti-pS318 antibodies detect only Ana2incubated with Plk4. Immunoblots probed with 2 different affinity-purified anti-

pS318 polyclonal antibodies are shown.

Figure S2.3 – Plk4 S228 Phosphomutants are Catalytically Active But Do Not Bind Asl-A

When Lacking PB1-PB2

(A) Comparison of expressed Asl-A-V5 and endogenous Asl levels. Plk4-GFP/Asl-A-V5 dual expression plasmids were transfected into S2 cells. The next day, expression was induced for 72 hrs with the same concentration of CuSO4 (2mM) used in all centriole counting experiments.

Blots were probed using Asl-A antibody to compare expressed Asl-A-V5 and endogenous Asl levels.

(B) Plk4 S228 phospho-mutants do not inhibit Plk4 self-destruction. S2 cells were transfected with indicated Plk4-GFP constructs and the next day were induced to express for 24 hours.

Lysates were immunoblotted for GFP. Kinase-dead (KD) Plk4 was used as negative control.

Nlp-GFP was used as loading control. Note that the levels of WT, S228A, and S228D Plk4 constructs are similar and clearly less than KD Plk4, indicating the S228A and S228D mutants retain the ability to autophosphorylate and thereby stimulate Slimb-mediated proteolysis.

(C) Plk4 S228 phospho-mutants promote centriole amplification (>2 centrioles) in S2 cells when overexpressed. The indicated Plk4-GFP constructs were transfected into S2 cells and induced to express the next day for 72 hours. Centrioles were counted after immunostaining fixed cells to visualize PLP, a centriolar marker. This result further confirms that the S228 mutants are active kinases.

(D) S228 phospho-mutants of a Plk4 construct (amino acids 1-381) truncated to remove PB1-

PB2 do not stably associate with Asl-A WT or phospho-mutants. Plk4-GFP and Asl-A constructs were co-transfected into S2 cells and the next day were induced to express for 24 hours. Samples were prepared by anti-GFP immunoprecipitation of cell lysates. Immunoblots were probed for

GFP, V5 and α-tubulin.

(E) Asl-A-13PM does not exhibit increased binding to full length Plk4 S228D mutant. Plk4-GFP

and Asl-A constructs were co-transfected into S2 cells and the next day were induced to express

for 24 hours. Samples were prepared by anti-GFP immunoprecipitation of cell lysates.

Immunoblots were probed for GFP, V5 and α-tubulin. Graph shows the average Asl-A-13D-V5

(normalized to the quantity of Plk4-GFP in the IP) that immunoprecipitates with Plk4-S228D-

GFP relative to control (Plk4-WT-GFP). n = 2 experiments. Error bar, SEM.

2.7 Tables

Table 2.1 – Phosphorylation Sites of Asl-A

To identify in vitro phosphorylated residues of Asl-A, bacterially-expressed and purified Asl-A was incubated with purified Plk4 kinase domain and MgATP, resolved by SDS-PAGE, prepared for mass spectrometry (MS) (i.e., reduced, alkylated, and proteolyzed), and then analyzed by LC-

MS/MS (see Materials and Methods 2.5). Phosphorylated Ser or Thr residues of recovered peptides are underlined and bold font. To identify in vivo phosphorylated residues, transgenic

GFP-tagged full-length Asl was co-transfected with either mutant kinase-dead mutant Plk4

(control) or active Plk4 (experimental). Asl was immunoprecipitated from lysates of transfected

S2 cells (see Materials and Methods 2.5), prepared for MS as mentioned above, and then

analyzed by LC-MS/MS. No phosphorylated peptides were recovered for the Asl-A regions of the

in vitro and in vivo control samples. Coverages of the Asl-A regions of samples were: in vitro control, 94%; in vitro experimental, 98%; in vivo control, 53%; in vivo experimental, 84%. All of the residues listed in the table for ‘in vitro experimental’ were present in the recovered peptides of ‘in vitro control’, with the exception of S7. All of the listed residues for ‘in vivo experimental’ were present in the recovered peptides of ‘in vivo control’.

CHAPTER THREE: ASTERLESS PHOSPHORYLATION PROMOTES A

SINGLE SITE OF CENTRIOLE ASSEMBLY

This chapter was written entirely by me. All experiments were performed by me, with technical assistance from John Ryniawec on the super-resolution microscopy. Experiments were designed and analyzed by myself, Greg Rogers and Dan Buster. This chapter is being prepared as a manuscript but has yet to be submitted to any journal.

3.1 Abstract

Phosphorylation of the conserved centriolar scaffolding protein Asterless has been shown to prevent centriole duplication by inhibiting the enzymatic activity of Plk4, the master regulator of centriole assembly. In this study, we identify T3 and S7 as phospho-residues in Asl sufficient for inhibiting Plk4 and blocking centriole assembly, and that the Plk4-Asl interaction is required for Plk4 inhibition. We show that phospho-Asl localizes to distinct puncta around the mother centriole to block Plk4 activity at inappropriate locations. Recruitment of the phosphatase PP2A-

Wdb to the centriole then promotes the formation of the procentriole by dephosphorylating Asl at only one of these sites. Manipulation of Wdb levels by overexpression or RNAi can alter the number of procentrioles assembled around the mother centriole, thus controlling the sites of daughter centriole assembly.

3.2 Introduction

Centrioles are the core duplicating components of the centrosome - the primary microtubule organizing center of the cell. The process of centriole duplication in cells is highly conserved and tightly controlled. This process involves semi-conservative replication of a

‘daughter’ centriole that grows off of the older ‘mother’ centriole which serves as a template2,149.

During each cell cycle, only one new daughter centriole is formed on each mother centriole, and

at the start of the next cell cycle the process repeats itself. The formation of too many daughter

centrioles around one mother centriole is one mechanism of a phenomenon termed centriole

amplification, which has been shown to contribute to chromosome missegregation, aneuploidy

and tumor formation8,9,11,13,132. Likewise, the loss of centrioles through the failure of a mother

centriole to form a new daughter during a cell cycle can also lead to chromosome segregation

errors and tumorigenesis6,20,150. Because of this, the formation of exactly one daughter centriole from each mother during each cell cycle is crucial, and this process is tightly regulated on a molecular level.

The primary driver the centriole duplication cycle is the conserved Ser/Thr kinase Polo- like kinase 4 (Plk4)2,34. It is targeted to centrioles during mitosis where its catalytic activity can

promote the recruitment of core structural components of a new daughter centriole34. When Plk4

protein levels or catalytic activity are too high, it can cause centriole amplification, likely by the

formation of multiple daughter centrioles around a single mother centriole31–33,46. Because of

this, Plk4 is regulated in several different ways. Intriguingly, Plk4 activity can control its own

stability, as Plk4 autophosphorylation in its Downstream Regulatory Element (DRE) has been

shown to promote its ubiquitin-mediated degradation46,52–55,57. At the centriole, Plk4 is activated

by Ana2 (STIL in humans) thereby promoting Ana2 phosphorylation, which acts to recruit Sas-

6, a core structural component of the centriole41,43–45,48–50. Additionally, the Drosophila coiled- coil centriole protein Asterless (Asl; Cep152 in humans) is a multifunctional regulator of Plk4.

Asl is responsible for localizing Plk4 to centriole, as well as regulating its stability throughout the cell-cycle37–39,135. Our previous work in Drosophila S2 cells has shown that Asl is also a Plk4

86 substrate that can regulate Plk4 activity in a phosphorylation dependent manner51. Non- phosphorylated Asl can bind and hyperactivate Plk4, allowing it to phosphorylate other substrates to promote centriole assembly. While activated, Plk4 can also phosphorylate Asl on 13

Ser/Thr residues in its N-terminus, which stabilizes Plk4 protein levels while also inhibiting further enzymatic activity. This negative feedback mechanism is thought to prevent the formation of too many centrioles while keeping Plk4 available to be reactivated when necessary.

Additionally, other recent studies have shown that the physical distribution of Plk4 around the mother centriole contributes to its activation and ultimately, the spot at which the new centriole is formed42,60,61. It remains unclear how the negative feedback mechanism provided by Asl coordinates with the physical spacing of Plk4 to form a single site of centriole assembly.

Here, we show that the phosphorylation of Asl by Plk4 on two key residues, T3 and S7, is necessary and sufficient for Plk4 inhibition. Phospho-Asl forms a partial ring of five puncta around the outer wall of the mother centriole, and these puncta are thought to inhibit Plk4 and thus, inappropriate locations of centriole assembly. We observe that there is an empty “sixth spot” where phospho-Asl does not localize and thus Plk4 can remain active, promoting new centriole formation. Lastly, we show that the phosphatase PP2A-Wdb can interact with Asl and control the number of phospho-Asl puncta at the mother centriole, thereby controlling the number of daughter centrioles formed. Thus, we have uncovered a detailed novel mechanism of how centriole number is controlled in cells involving the master regulator kinase, Plk4, its inhibitor, Asl, and the conserved phosphatase PP2A.

3.3 Results and Discussion

Phosphorylation of Asl N-terminus (Asl-A) on two key residues is necessary and sufficient

for Plk4 inhibition.

Asl is a conserved scaffolding protein that is required for centriole duplication84,85.

Functionally, it is broken down into three domains, Asl-A (1-374), Asl-B (375-630), and Asl-C

(631-994)135. Structurally, it contains multiple coiled-coil interacting domains throughout (Figure

3.1A). Previous work from our lab had shown that the kinase Plk4 - the master regulator of

centriole duplication – phosphorylates Asl-A on 13 Ser/Thr residues in vitro and in S2 cells

(Figure 3.1A, lower)51. When all 13 Ser/Thr residues were mutated to phospho-mimetic (PM)

Asp/Glu residues and Asl-A was expressed in cells, the 13PM mutant acted as a dominant

negative, suppressing centriole duplication by inhibiting Plk4 activity. For this study, we first

wanted to see which of these 13 residues were required to achieve this phenotype. We

hypothesized that the required phospho-residues would be on the far N-terminus of Asl,

potentially enabling steric inhibition of the Plk4 kinase domain by phospho-Asl. We generated

various N-terminal Asl-A phospho-mutants by site directed mutagenesis and expressed them in

Drosophila S2 cells to assay their effects on centriole duplication (Figure 3.1B). As previously

reported, expression of the “wild-type” Asl-A fragment has no effect on centriole duplication, as

there was no significant change in the number of cells with less than 2 centrioles compared to the

GFP only control, and the expression of the 13PM mutant caused a significant increase in the

number of cells with less than 2 centrioles51,135. Intriguingly, expression of the 11PM mutant, which had all of the same mutations as 13PM except for T3 and S7, had no effect on centriole number, while the T3E/S7D mutant, like the 13PM mutant, had a significant increase in the number of cells with less than 2 centrioles, suggesting that phosphorylation of these two residues

may be sufficient to block centriole duplication. When the other two far-N-terminal Plk4 substrate residues, S19/T20, were mutated, they had no effect on centriole number compared to control. Interestingly, when T3 and S7 were individually mutated, they also had no effect on centriole number, suggesting they both must be phosphorylated in order to inhibit centriole duplication.

Asl, specifically its N-terminal Asl-A domain, is known to control Plk4 stability by promoting its dimerization and activation which triggers its autophosphorylation and ubiquitin- mediated destruction135. Accordingly, depletion of endogenous Asl from cells results in an

increase in Plk4 protein levels. Our last study showed that replacement of endogenous Asl with

Asl-A-13PM could not rescue Plk4 levels, likely because catalytic inhibition of Plk4 by this

mutant prevented Plk4 from autophosphorylating and thus triggering its own degradation51. We

explored whether replacement with the Asl-A-T3E/S7D mutant (henceforth referred to as Asl-A-

2PM) would cause an equivalent phenotype. Endogenous Asl was depleted from cells for 5 d using dsRNA targeted toward a region of the gene that would not affect expression of the transgenic Asl-A-V5 construct. Co-transfection of Asl-A with Plk4-GFP, using Nlp-GFP as a transfection control, then allowed us to assay for Plk4 protein levels (Figure 3.1C). As expected, depletion of Asl stabilized Plk4 protein levels while replacement with Asl-A-WT returned Plk4 levels to control conditions (lanes 1-3). Expression of Asl-A-13PM or Asl-A-2PM each significantly stabilized Plk4 to similar levels compared to the control (lanes 4 and 5). This indicates that expression of Asl-A-2PM may stabilize Plk4 levels by blocking its autophosphorylation and degradation just as efficiently as Asl-A-13PM.

To directly test whether expression of Asl-A-2PM can directly affect Plk4 autophosphorylation, we generated a phospho-specific antibody directed at T172 in the

activation loop of Plk4. This residue is known to be phosphorylated by Plk4 and its

phosphorylation is required to maintain Plk4 activity47,56. We first tested the specificity of the

antibody on bacterially expressed and purified fragment of Plk4 containing its kinase domain

(Figure S3.1A). As expected, the pT172 antibody recognized the “wild-type” (WT) kinase

domain that had been mixed with ATP but not the kinase-dead (KD) mutant. Additionally, the antibody did not recognize WT or KD kinase domain that had been phosphatase treated. This indicates the pT172 antibody is indeed phospho-specific in vitro. Next, we tested the

effectiveness of the antibody on transgenic Plk4 constructs expressed in and immunoprecipitated

from cells (Figure S3.1B). We observed that the pT172 could recognize a nondegradable Plk4

mutant (S293A/T297A, “ND”; used because it expresses at higher levels than wild-type Plk4)

but not a KD mutant46. Ultimately, we co-expressed and immunoprecipitated Asl-A-2PM with

Plk4-ND and used the pT172 antibody to test whether the 2PM mutant could directly affect Plk4 autophosphorylation (Figure 3.1D). Not surprisingly, Asl-A-2PM caused a significant reduction in Plk4 pT172 levels, presumably by inhibiting the ability of Plk4 to autophosphorylate.

The Asl-Plk4 interaction is required for Plk4 inhibition

In order to ensure that the effect of the Asl-A-2PM mutant on blocking centriole duplication is through its interaction with Plk4, we generated an Asl-A mutant that was unable to bind Plk4. Based on previous studies in Drosophila, C. elegans and Humans, there is a conserved acidic patch in the N-terminus of Asl/Cep152 that is responsible for interacting with a surface basic patch on Plk4 (Figure 3.2A)36,151. The interaction was disrupted by mutating a

series of four consecutive negatively charged glutamic acid residues to positively charged lysine

residues (this Asl-A E25K, E26K, E27K, E28K mutant is henceforth referred to as Plk4-binding-

mutant or PBM; Figure 3.2B). As expected, Asl-A-WT and Asl-A-2PM interacted with Plk4 by

immunoprecipitation, however the Asl-A-PBM and Asl-A-2PM-PBM mutants did not, indicating that these E to K mutations do in fact disrupt binding and that the 2PM mutations do not affect the interaction. Additionally, Asl-A has been shown to self-oligomerize and is thought to primarily act as a dimer in cells51,135. We used immunoprecipitations to see if the ability of

Asl-A to oligomerize was retained in Asl-A-PBM and found that it can in fact still interact with

itself and that once again, the 2PM mutations were not affecting these interactions (Figure 3.2C).

Lastly, we expressed the Asl-A-PBM and Asl-A-2PM-PBM mutants in cells to test their effect on the centriole duplication process (Figure 2D). Interestingly, unlike expression of the Asl-A-

2PM mutant where we once again observed a significance increase in the number of cells with

less than two centrioles, we found that expression of the Asl-A-PBM or the Asl-A-2PM-PBM mutants had no effect on centriole number. While it is possible that Asl-A-2PM may be blocking centriole duplication by unforeseen mechanisms, this data taken in conjunction with the conclusions from Figure 3.1 suggest that Asl-A-2PM must interact with Plk4 to inhibit it and have a downstream effect on blockage to centriole duplication.

Phospho-Asl forms an incomplete ring of puncta around the mother centriole that may inhibit daughter centriole assembly

Multiple studies have shown that Asl/Cep152 localizes to a ring around the mother centriole and can play a role in tethering Plk4 at the centriole to promote assembly35,36,40,107,152–

155. However, we have an incomplete mechanistic understanding of the Plk4/Asl relationship at

the centriole, particularly in regard to Asl phosphorylation and Plk4 inhibition. To address this

question, we first generated a phospho-specific antibody targeting the pT3 and pS7 residues in

Asl that are responsible for Plk4 inhibition. We confirmed that the antibody was phospho- specific by western blot, where we observed the antibody recognizes Asl-A-WT expressed in

cells but not a non-phosphorylatable T3A/S7A (2A) Asl mutant (Figure 3.3A). Additionally, we

observed that the overexpression of Plk4 drove higher levels of phospho-Asl (pAsl) (Figure

3.3B). Since Plk4 is not known to control the activity of any other kinases, and Asl is not known

to be phosphorylated by any other kinases, this strongly suggests this antibody is specific to

phosphorylation modifications created by Plk4. Since we know that Asl can by phosphorylated

by Plk4 on more residues than just T3 and S7 (Figure 3.1A, lower), we wanted to ensure that

Plk4 overexpression does not affect the specificity of the antibody51. Accordingly, we observed

that the pAsl antibody cannot recognize the Asl-A-2A mutant even under Plk4 overexpression conditions (Figure S3.1C).

We next wanted to use this tool to investigate patterns of pAsl localization at the centriole in fixed cells. Using super resolution structured illumination microscopy (SIM), we observed pAsl localizing to distinct puncta around the wall of the mother centriole, which was marked using an antibody directed at the N-terminus of endogenous Asl (Figure 3.3C). A recent study in

human cells has shown that when imaged by stimulated emission depletion microscopy (STED),

Cep152 can adopt a 12-fold symmetry around the mother centriole, while Plk4 is able to adopt a

6-fold symmetry61. Intriguingly, when quantifying the puncta, we observed pAsl typically forms

5 spots around the mother centriole – it has the spacing for a 6-fold symmetry but is usually

missing one spot (Figure 3.3D). Additionally, like Plk4 from the recent study, pAsl may be

dynamic. Conformations with 3, 4 and 6 spots were commonly observed, but centrioles with

more than 6 spots were very rarely seen. Coupled with our observation that expression of Asl-A-

2PM can block centriole duplication and inhibit Plk4 activity, this led us to investigate the role pAsl may have in controlling new procentriole formation at the mother centriole.

Proteins such as Sas-4 and Cep135 have been shown to localize to a spot where the new

daughter centriole forms, and removal of either of these proteins induces a blockage to centriole

duplication for a variety of mechanistic reasons103,152–156. We were interested in examining the

co-localization of pAsl with these procentriole markers using SIM (Figure 3.3E). Examining these images from a top-down view where you can observe a mother centriole barrel with a daughter centriole growing from a spot off of the side of it, as expected, Sas-4 formed a spot

marking the older mother centriole, as well as another spot adjacent to it, while pAsl formed 5

spots in a partial ring formation. Intriguingly, the merged image indicates that pAsl and Sas-4 do

not co-localize, but rather, the pAsl spots form a partial ring around the mother spot, with an

opening left where the Sas-4 daughter spot has formed. Furthermore, we observed a similar

phenotype with Cep135 – which by G2 phase is known to form a spot on the mother centriole

and an additional spot on the new daughter centriole103,152,153. Phospho-Asl once again formed a

partial ring around the mother centriole (marked with Plp) with no localization at the Cep135

daughter spot. In summary, pAsl primarily forms 5 spots in a partial ring around the mother

centriole, while Plk4 is known to form up 6 spots that get reduced into a single spot to promote

procentriole assembly. On top of that, the daughter centriole spot is formed where pAsl does not

localize. Coupled with our previous mechanistic data showing pAsl can inhibit Plk4, this

suggests pAsl is keeping Plk4 turned off at 5 of its 6 spots around the mother, while allowing for

Plk4 to induce procentriole assembly to at the spot where Asl is not phosphorylated.

Wrd and Wdb localize to centrioles and cause amplification when overexpressed

If the formation of 5 pAsl spots at the mother centriole controls the formation of only one

daughter centriole, it was necessary to obtain a better understanding of how exactly 5 spots are

93 formed. If Plk4 can be active at 6 spots around the mother, and Asl is present in the entire ring, then it would be presumed that Asl is available for phosphorylation at each of the six spots61.

This brings into question how Plk4 can be active in its 6th spot without phosphorylating Asl and becoming inactivated. Perhaps, a phosphatase could be counteracting Plk4-induced Asl phosphorylation to form the site of centriole assembly. The conserved phosphatase PP2A plays a myriad of roles throughout the cell cycle and is known to dephosphorylate a large variety of substrates157. Furthermore, a previous study from our lab identified Plk4 as a substrate for PP2A and its regulatory subunit Twins (PP2A-Tws), and that PP2A-Tws dephosphorylates Plk4 to stabilize it and promote centriole duplication59. Interestingly, another study identified two other

PP2A regulatory subunits - Well-rounded (Wrd) and Widerborst (Wdb) - that may play a role in centriole assembly, as their co-depletion from S2 cells by RNAi resulted in a loss of centrioles158.

The mechanism by how Wrd or Wdb might be promoting centriole assembly remains unknown. Accordingly, we expressed GFP-tagged Wrd or Wdb in cells and examined their localization by conventional immunofluorescence microscopy (Figure S3.2A). We found that although expression of Wrd and Wdb was diffuse throughout the cytoplasm, they each formed distinct puncta while co-localizing with the centriolar marker Plp (Figure S3.2A, insets). We then assayed for changes in centriole number in these cells compared to the expression of GFP alone.

Perhaps not surprisingly, we found that the overexpression of either Wrd or Wdb caused a significant increase in the number of cells with more than two centrioles (Figure S3.2B). In summary, Wrd and Wdb cause centriole loss when co-depleted, they each cause centriole amplification when overexpressed individually, and they each localize distinctly to centrioles.

This led us to hypothesize that Wrd and/or Wdb might be counteracting Asl phosphorylation at

the centriole to promote centriole assembly.

Wdb interacts with Asl and can promote the site of new centriole assembly

To test our hypothesis, we first examined whether Wrd or Wdb could interact with Asl in

cells. GFP-tagged Wdb and Wrd were expressed in cells and immunoprecipitated, then lysates

were examined by western blot to investigate binding partners (Figure 3.4A). Interestingly, we

found that endogenous Asl formed a strong interaction with Wdb, but no such interaction could

be detected between Asl and Wrd. Since the N-terminus of Asl is the region that gets

phosphorylated and is responsible for Plk4 inhibition, we repeated the binding experiments using

expression of the Asl-A domain (Figure S3.2C). We found that the Asl-A region does in fact

bind to Wdb, but not Wrd. To keep within the scope of our study, we continued by investigating

the mechanism by which Asl and Wdb control centriole assembly. The role of Wrd in the

process of centriole duplication merits further future studies.

Since overexpressed Wdb was observed localizing to the centriole by conventional

microscopy, we wanted to investigate the localization of endogenous Wdb at the centriole using

SIM. Like transgenic Wdb, endogenous localizes diffusely throughout the cytoplasm.

Interestingly, however, like many centriolar proteins it forms multiple puncta in the regions in

and surrounding the mother centriole. In fact, in some images it was seen co-localized with

Cep135 at the interface of its mother and daughter centriole spots (Figure 3.4B, top). In other instances, it could be seen partially localized with Cep135 while also forming other spots in and around the mother centriole ring (Figure 3.4B, bottom). This indicates that Wdb can localize to the site of centriole assembly, but also, its localization is dynamic around the mother centriole.

We next wanted to examine the mechanism by which Wdb overexpression causes

centriole amplification. We expressed V5-Wdb in cells and examined its co-localization with

pAsl using SIM (Figure 3.4C, top panels). Interestingly, we found that while V5-Wdb is also

able to localize to puncta around the mother centriole, we rarely observed co-localization with

pAsl. Unlike pAsl, there was no set pattern of spots that V5-Wdb localized to, however it

appeared as though the number of pAsl dots was usually decreased on V5-Wdb positive

centrioles. Upon quantification, we confirmed that Wdb overexpression does in fact reduce the

number of pAsl spots at the centriole (Figure 3.4E left; Figure S3.3D). Furthermore, when Wdb

overexpressing cells were stained for daughter centriole marker Cep97, we observed the

formation of multiple daughter centriole spots (Figure 3.4C, bottom panels). This indicates that

Wdb overexpression induces centriole amplification by promoting the formation of multiple

daughter centrioles around a single mother centriole.

Conversely, co-depletion of Wrd and Wdb was previously shown to block centriole

duplication158. Since we observed that the overexpression of Wdb can alter the number of pAsl

dots at the centriole, we examined how co-depletion of Wrd and Wdb by RNAi affected this phenotype (Figure S3.2D). Interestingly, when Wrd and Wdb were depleted for 7 d in cells and then imaged using SIM, we observed a large increase in the number of centrioles with 6 pAsl spots (Figure 3.4D; Figure 3.4E right; Figure S3.3D).

In all, our data suggest that modulating Wdb levels can control centriole assembly by altering the number of pAsl puncta at the centriole (Model – Figure 3.4F). In wild-type cells,

Wdb localizes to a spot to dephosphorylate Asl, thus allowing Plk4 to be active at that site only,

where its activity will promote centriole assembly. When Wdb is overexpressed, it can

dephosphorylate more than one spot, suggesting Wdb levels at the centriole are a limiting factor

in its ability to dephosphorylate one or more pAsl spots. At the centrioles where Wdb

dephosphorylated more than one pAsl spot, multiple daughter centrioles can be formed.

Conversely, when Wdb is depleted, 6 pAsl spots are commonly seen and centriole duplication is

blocked. These data suggest that Wdb is likely carefully regulated to control the number of pAsl

spots at the centriole and in turn, select the site of daughter centriole assembly. Furthermore,

pAsl is a primary player in the increasingly complicated mechanism cells use to generate a single daughter centriole off of each mother.

There are important questions that remain unanswered. In the future, it will be crucial to

determine the mechanism of Wdb recruitment to a single spot at the centriole. Preliminary

experiments indicate that overexpressed transgenic Ana2 is able to interact with Wdb

immunoprecipitated from cells (Figure S3.4A). Interestingly, endogenous Ana2 was not found to

interact (Figure 3.4A). Perhaps these results hold a clue to the workings of Wdb at the centriole.

When Ana2 levels are high, i.e. when they are concentrated to a spot at the procentriole, the

protein concentration is sufficient to bind Wdb and localize it into one spot. The accumulation of

Wdb at that spot then allows for localized dephosphorylation of Asl, promoting centriole

assembly. In the future, it will be important to investigate the mechanism of Asl

dephosphorylation at the centriole. Our data strongly suggest pAsl keeps Plk4 inhibited at the

centriole and that dephosphorylation by Wdb allows for Plk4 activity to resume. Intriguingly, we

observed that like Asl, Plk4 can also interact with Wdb by immunoprecipitation and furthermore

Asl, Plk4 and Wdb can bind in a complex with each other (Figure S3.4 B-C). The creation of an

Asl mutant that cannot bind Wdb and therefore be dephosphorylated, will be important to determine the direct effect of the Asl/Wdb interaction on the centriole duplication cycle.

Furthermore, it will be crucial to determine whether there is a potential handoff mechanism

between Ana2, Wdb, Plk4, Asl and any other unidentified components of this pathway.

3.4 Materials and Methods

Drosophila cell culture

Drosophila S2 cells (Drosophila Genomics Resource Center, S2-DRSC) were cultured at room temperature (20-25℃) in SF900II serum free medium (Thermo Fisher Scientific 10902-

088).

Double-stranded RNA interference

Double-stranded RNA interference (RNAi) was performed as previously described

(Rogers and Rogers, 2008). Briefly, cells were cultured in a 6-well plate at 50-90% confluency.

To deplete the gene of interest, 5-10µg of double-stranded RNA (dsRNA) was added to each well daily for 4-7d. All primers used for dsRNA synthesis begin with the T7 RNA polymerase promoter sequence 5’-TAATACGACTCACTATAGGG-3’ followed by the gene-target specific sequence. Control dsRNA was synthesized from a noncoding region of the pET28a vector

(Novagen, 69864-3) using the primers 5’-ATCAGGCGCTCTTCCGC-3’ and 5’-

GTTCGTGCACACAGCCC-3’. The DNA template for Asl dsRNA (which targeted a sequence in Asl not affecting transgenic Asl-A expression) was generated using the primers 5’-

CGTCTGATCCATCGCCC-3’ and 5’-CATCGCCTCTTCGTGGG-3’. The DNA template for

Widerborst dsRNA was generated using the primers 5’-CTTGCCCCTGAAGGCCG-3’ and 5’-

TGGAGGTAAGCTCGTCG. The DNA template for Well-Rounded dsRNA was generated using the primers 5’-CGGAGGAGGATGAGCCC-3’ and 5’-GCTAGGATCCTTCTCCAGG-3’.

Constructs

Full length cDNAs of Asl and Plk4 were subcloned into a pMT/V5-His vector containing

the in-frame coding sequence for GFP, V5, or myc and under control of the inducible

metallothionein promoter. Mutants of Asl and Plk4 were generated using PCR-based site

directed mutagenesis using Phusion polymerase (ThermoFisher, F530S).

Transfection and expression

Confluent S2 cells were pelleted by centrifugation and resuspended in 150µl of

transfection reagent (5 mM KCl, 15 mM MgCl2, 120 mM sodium phosphate, 50 mM D- mannitol, pH 7.2) containing 0.2-2µg of plasmid DNA, which was transferred to a 2-mm gap cuvette (Fisher Scientific, FB102) and electroporated using a Nucleofector 2b (Lonza), program

G-030. Transfected cells were immediately diluted in SF900II serum free media and transferred to a 6-well culture plate. 24h later, cell culture media was treated with 0.1-2µM CuSO4 for 18-

72h to induce expression.

Immunofluorescence microscopy

S2 cells were processed for immunofluorescence microscopy by spreading them on concavalin A coated glass-bottom plates. For centriole counting and general observations, cells were fixed in 10% formaldehyde at room temperature for 10 min, washed three times in PBS containing 0.1% Triton-X-100 and blocked in 5% Normal Goat Serum for 15 min. Plates were incubated with the rabbit anti-PLP (our laboratory) primary antibody diluted 1:5,000 in blocking buffer for 1 hr at room temperature. Secondary antibodies conjugated with either Cy2, Cy5 or

Rhodamine red-x (Jackson Immunoresearch Laboratories) were used at a 1:1,500 dilution and incubated for 30 min in the dark at room temperature. To stain DNA, Hoechst 33342 was used at a final concentration of 3.2µM and included in the secondary antibody incubation. Cells were

mounted in PBS containing 0.1% n-propyl gallate and 90% (by volume) glycerol. Samples were

imaged using a Deltavision Core system (Applied Precision) equipped with an Olympus IX71

microscope, a 63X (NA 1.42) or 100X (NA 1.4) objective and a cooled charge-coupled device

camera (Cool-SNAP HQ2; Photometrics). Images were acquired using softWoRx software,

version 7.0 (Applied Science).

For super-resolution imaging, cells were fixed in ice-cold methanol for 7 min at -20℃.

Samples were washed in PBS three times and blocked in PBS containing 1% BSA and 0.05%

Triton-X-100 for 30 min. Samples were then incubated overnight at 4℃ with primary antibodies

including rabbit anti-Plp, rat anti-Asl-A, rat anti-Cep135, rat anti-Sas-4, chicken anti-Cep97,

guinea pig anti-phospho-Asl (all from our laboratory), guinea pig anti-Widerborst (Sehgal

laboratory), mouse anti-V5 monoclonal (Life Technologies, R96025), mouse anti-phospho-

Histone H3 monoclonal (Cell Signaling Technology, 9706S) used at dilutions ranging from

1:250-1:5,000 in blocking buffer. Following three washes with PBS, samples were next

incubated with secondary antibodies conjugated with Rhodamine red-X, Cy5 (Jackson

Immunoresearch Laboratories), Alexa Fluor 488, or Alexa Fluor 405 (Life Technologies) at

1:1,500 dilution along with Hoechst 3342 in the dark for 1 h at room temperature. Samples were

washed three more times and mounted in Vectashield (Vector Laboratories, H1000) or Prolong

Glass Antifade Mountant (Life Technologies, P36984). Super-resolution structured illumination

microscopy was performed using a Zeiss Elyra S1 system equipped with an Axio Observer Z1

inverted microscope with transmitted tungsten-halogen, UV mercury short arc lamp, and solid-

state (405/488/561/642 nm) laser illumination sources, three rotations and an EM-charge- coupled device camera (Andor iXon). The objectives used were an Alpha Pan-APO 100x (NA

100

1.46) and a Plan-Apochromat 63x (NA 1.40). Images were acquired and processed with ZEN

2011 software.

Immunoblotting

Whole-cell extracts were prepared by lysing S2 cells in cold PBS containing 0.1% Triton

X-100. Laemmli sample buffer was then added before boiling the samples for 5 min. Samples were resolved by SDS-PAGE gel, transferred to nitrocellulose, probed with primary and secondary antibodies, and scanned using an Odyssey CLx imaging system (Li-Cor Biosciences).

Primary antibodies used for immunoblots included mouse anti-GFP monoclonal JL-8 (Clontech,

632380), mouse anti-V5 monoclonal (Life Technologies, R96025), mouse anti-myc (Cell

Signaling Technology, 2276S), mouse anti-α tubulin (Sigma-Aldrich, T9026), rat anti-Asl (our laboratory), and guinea pig anti-Wdb (Sehgal laboratory) and were used dilutions ranging from

1:1,000 to 1,3000 in 5% milk.

To generate the anti-phospho-specific T3/S7 Asl antibody, guinea pig polyclonal antibodies were raised against the phosphopeptide: MN(pThr)PG(pSer)LFQGADAC. A nonphosphopeptide sequence of MNTPGSLFQGADAC was also generated (Pocono Rabbit Farm and Laboratory). Antibodies were affinity purified from antisera by using phosphopeptide coupled to Affi-gel resin, and specificity was improved by purifying antibody over nonphosphopeptide coupled resin. The anti-phosphopeptide solution was concentrated using 10k

Ultrafree concentrators (Millipore, UFC501024). Phospho-antibodies were used at a 1:250 dilution.

101

Immunoprecipitation assays

For GFP immunoprecipitation assays, GFP-binding protein (GBP) was fused to the Fc

domain of human IgG (pIg-Tail; R&D Systems), tagged with His6 in a pET28a vector (EMD

Biosciences) and expressed in E. coli. His-GBP was then purified on HisPur resin

(ThermoFisher, 88221) as described previously (Buster et al. 2013), bound to magnetic Dyna

Beads (ThermoFisher, 10001D) and cross-linked to the resin by incubating with 20 mM dimethyl pimelimidate dihydrochloride in PBS, pH 8.3 for 2 h at 22℃ then quenched by incubation with

0.2 M ethanolamine, pH 8.3 for 1 h at 22℃. Antibody-coated beads were then washed three

times with PBS-Tween 20 (0.02%) and equilibrated in 1.0 ml of immunoprecipitation buffer (IP

buffer; 50 mM Tris, pH 7.2, 125 mM NaCl, 1 mM EGTA, 2 mM DTT, 0.1 mM

phenylmethylsulfonyl fluoride [PMSF], 0.05 mM Soybean Trypsin Inhibitor [SBTI] and 0.5%

Triton X-100. Transfected S2 cells expressing recombinant proteins were lysed in IP buffer and

clarified by centrifugation at 10,000 x g for 5 min at 4℃. At this point, 10% of the clarified

lysate was removed to be used as input controls for immunoblots. The rest of the lysate was

incubated with 50 µl of GBP-Dyna Beads for 30 min at 4℃, washed four times in 1 ml IP buffer,

and boiled in sample buffer for 5 min.

102

3.5 Figures

3.1 Phosphorylation of T3 and S7 in Asterless-A is Necessary and Sufficient to Block

Centriole Duplication

103

(A) Asterless is a conserved coiled-coil protein comprised of three functional domains (Asl-A,

Asl-B, Asl-C) - including Plk4 binding regions in Asl-A and Asl-C; CC, coiled coil.

(B) Asl-A (Asterless 1-374) contains several coiled-coil domains and is phosphorylated by Plk4 on the indicated Ser/Thr residues.

(C) Like Asl-A-13PM, expression of Asl-A-2PM causes centriole loss. The indicated Asl-A-GFP constructs were transfected into S2 cells and induced to express for 72 hr. Cells were fixed and stained for Plp to mark centrioles. Expression of Asl-A-2PM and Asl-A-13PM caused significant centriole loss (less than 2 centrioles) compared to GFP control. N = 3 experiments per construct

(100 cells per experiment). In all figures, asterisks indicate significance and error bars indicate

SEM.

(D) Expression of Asl-A-2PM or Asl-A-13PM cannot rescue effect of Asl on Plk4 protein levels.

S2 cells were treated with Asl-C dsRNA for 7 d to deplete endogenous Asl without affecting Asl-A expression. Plk4-GFP, Nlp-GFP (transfection control) and the indicated Asl-A-V5 construct were transfected on day 5 and induced to express the next day for 24hr. Immunoblots of lysates were probed using anti-GFP, V5 and Asl. The graph shows relative amounts of Plk4-GFP as determined by densitometry from anti-GFP immunoblots, normalized to Nlp-GFP and plotted relative to control (lane 1). N = 3 experiments.

(E) Plk4 activation is inhibited by expression of Asl-A-2PM. Plk4-GFP and Asl-A-2PM-V5 or an empty vector control construct were transfected in S2 cells and induced to express the next day for 24 hr. Anti-GFP immunoprecipitates were prepared from lysates of these cells. Samples were immunoblotted for GFP, V5, Plk4-pT172 to assay Plk4 activation, and Tubulin as a loading

104 control. Graph indicates levels of Plk4-pT172 relative to total Plk4-GFP levels. N = 5 experiments.

105

Figure 3.2 – The Asl-A-Plk4 Interaction is Required for Asl-A-2PM to Block Centriole

Duplication

106

(A) Asl-A contains a conserved acidic region that is required for Plk4 binding in C. elegans and

H. sapiens. Adapted from Shimanovskaya et al. The four negatively charged glutamic acid

residues at the N-terminal end of the pocket (gray box) were mutated to positively charged lysine

residues to generate the Asl-A-Plk4 binding mutant (Asl-A-PBM).

(B) Asl-A-PBM and Asl-A-2PM-PBM fail to interact with Plk4 in S2 cells. The indicated Asl-A-

GFP constructs were transfected into S2 cells along with Plk4-myc and the next day induced to express for 24 hr. Anti-GFP immunoprecipitates were prepared from the lysates of these cells and samples were immunoblotted for GFP, myc and tubulin as a loading control.

Asl-A-V5 constructs were transfected into S2 cells and the next day induced to express for 24hr.

Anti-GFP immunoprecipitates were prepared from the lysates of these cells and samples were immunoblotted for GFP, V5 and tubulin as a loading control.

(D) Expression of Asl-A-2PM-PBM fails to block centriole duplication. The indicated Asl-A-GFP constructs were transfected into S2 cells and induced to express for 72 hr. Cells were fixed and stained for Plp to mark centrioles. Expression of Asl-A-2PM, but not Asl-A-2PM-PBM caused significant centriole loss compared to control. N=3 experiments construct, 100 cells per experiment.

107

Figure 3.3 - Phospho-Asl Forms a Ring of Puncta at the Mother Centriole that May

Prohibit Daughter Centriole Assembly

108

(A) Asl residues T3 and S7 are phosphorylated in S2 cells and are recognized by phospho-

specific Asl antibody. Wild-type Asl-A-GFP or Asl-A-GFP with T3A/S7A non-phosphorylatable

mutations (Asl-A-2A) constructs were transfected into S2 cells, induced to express and

immunoprecipitated as described above. Immunoprecipitates were blotted for GFP and

phospho-Asl (pAsl), which recognizes the wild-type Asl-A fragment but not Asl-A-2A.

(B) Plk4 overexpression increases Asl T3 and S7 phosphorylation in S2 cells. S2 cells were transfected with the indicated construct, induced to express and immunoprecipitated as described above. Immunoprecipitates were blotted for GFP, myc and pAsl. More pAsl is recognized by western blot in cells where Plk4 is overexpressed.

(C) pAsl forms multiple puncta in a ring around the mother centriole in interphase. S2 cells were immunostained for Asl-A (red) to mark the surface of mature centrioles and pAsl (green) to visualize where pAsl localized around the centriole surface. Cells were then imaged using super- resolution microscopy. The image is representative of the most commonly observed pAsl conformation (5 spots).

(D) Quantification of number of pAsl puncta per centriole in interphase cells. N=152 centrioles counted.

(E) pAsl localization with procentriolar markers. S2 cells were immunostained for pAsl, Plp to mark the surface of the mature centriole, and Cep135, or Sas-4 to mark the mother centriole and procentriole. Cells were then imaged using super-resolution microscopy. The images are representative of the most commonly observed localization of pAsl and procentriole markers.

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Figure 3.4 - Wdb Interacts with Asl and Promotes Active Site of Centriole Assembly

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(A) Asl interacts with Wdb-GFP but not Wrd-GFP. Cells were transfected with constructs containing GFP alone, Wdb-GFP or Wrd-GFP. Constructs were induced to express the next day for 24 hr. Samples were prepared by GFP-immunoprecipitation from cell lysates. Immunoblots were probed for GFP, Asl, Ana2 and Tubulin.

(B) Wdb localizes to the centriole and can be observed at the site of daughter centriole assembly.

Wild-type S2 cells were plated, fixed and then immunostained overnight for Plp (red) to mark the surface of mature centrioles, as well as Cep135 (green) to mark the mother centriole and procentriole and Wdb (blue).

centriole markers. An expression vector containing V5-Wdb was transfected into cells and induced to express for 72 hr. Cells were then plated, fixed and immunostained overnight for V5-

Wdb and pAsl to quantify pAsl spots and examine co-localization. In parallel, cells were immunostained for V5-Wdb and the distal centriole marker Cep97 to observe spots of daughter centriole assembly. Anti-Plp was included to mark the surface of mature centrioles in the latter experiment. Cells were imaged using super-resolution microscopy.

(D) Co-depletion of Wrd and Wdb increases the number of pAsl spots per centriole. Cells were treated with Wrd and Wdb dsRNA daily for 7 d. On the seventh day, cells were fixed and immunostained overnight for pAsl and Plp. Cells were imaged using super-resolution microscopy.

(E) Quantification of number of pAsl puncta per centriole in WT, V5-Wdb expressing, or

Wrd/Wdb depleted cells. Left graph: Number of centrioles with <5 spots, includes total number of centrioles counted with 0, 1, 2, 3, and 4 spots. Right graph: Number of centrioles with 6 spots.

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The WT data set is the same data set represented in Figure 3.3D. WT: n=152 centrioles counted.

Wdb OE: n=66 centrioles counted. Wrd/Wdb RNAi: n=73 centrioles counted. A full graphical representation of the data can be found in Figure S3.4D.

(F) Model. Left: pAsl forms five spots in a ring around the centriole surface functioning to block inappropriate centriole assembly, while the phosphatase PP2A-Wdb actively dephosphorylates

Asl at a sixth site to promote centriole assembly. Middle: Overexpression of Wdb results in the dephosphorylation of Asl at more than one site, leading to multiple spots of daughter centriole assembly around the mother centriole. Right: Depletion of Wrd and Wdb results in the accumulation of pAsl in a sixth spot around the mother centriole, thereby blocking daughter centriole assembly.

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Figure S3.1 – Development of Plk4 and Asl Phospho-Specific Antibodies

(A) Development of a phospho-specific antibody that recognizes phospho-T172 (pT172) in the activation loop of Plk4. Bacterially expressed and purified Plk4 1-317-His6 or kinase dead (KD)

Plk4 1-317-His6 was incubated with ATP and either treated with λ-phosphatase or mock treated as a control. The anti-pT172 antibody specifically recognizes mock treated Plk4 but not λ- phosphatase treated or KD (bottom). The Coomassie stained gel (top) is shown as a loading control.

(B) The anti-pT172 antibody recognizes phosphorylated Plk4 that has been immunoprecipitated from S2 cells. GFP-tagged non-degradable (ND) Plk4 or kinase dead (KD) Plk4 were transfected into cells and the next day were induced to express for 24hr. Anti-GFP

immunoprecipitates were then made from the lysates of these cells, and samples were

immunoblotted for GFP and pT172.

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transfected into cells with either Asl-A-WT-GFP or Asl-A-2A-GFP. The next day, cells were induced to express for 24 hr. Samples were prepared by GFP immunoprecipitation from cell lysates. Immunoblots were probed for GFP, myc and pAsl.

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Figure S3.2 - Wdb and Wrd Localize to Centrioles and Cause Centriole Amplification

When Overexpressed

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(A) Wdb and Wrd localize to centrioles. GFP-tagged Wdb or Wrd were transfected into S2 cells and induced to express for 24 hr before being fixed and stained for Plp to mark centrioles. Wdb-

GFP and Wrd-GFP can be visualized diffusely throughout the cytoplasm, but also co-localize

with Plp and form distinct puncta at the centriole (inset).

(B) Overexpression of Wrd or Wdb result in centriole amplification. GFP alone or GFP-tagged

Wdb or Wrd were transfected into S2 cells and induced to express for 72 hr before being fixed

and stained for Plp to mark centrioles. Wdb-GFP and Wrd-GFP expression each result in a

significant increase in the number of cells with greater than 2 centrioles. N = 3 experiments, 100

cells per experiment.

indicated GFP-tagged and V5-tagged constructs and induced to express the next day for 24 hr.

Samples were prepared by GFP-immunoprecipitation from cell lysates. Immunoblots were

probed for GFP, V5 and Tubulin.

(D) 7 d RNAi depletes cellular Wdb levels by 70%. S2 cells were treated with 10ug Wdb dsRNA

each day for 7 d. Lysates of cellular extracts were then made to assess the efficiency of Wdb

knockdown. Lysates were blotted for Wdb and Tubulin as a loading control. Wdb was depleted

by 70%, normalized to Tubulin, as determined by densitometry using ImageJ.

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Figure S3.3 – Wdb Interacts with Ana2 and Forms a Complex with Plk4 and Asl-A

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(A) Wdb interacts with transgenic Ana-2. Cells were co-transfected with expression vectors

containing Wdb-GFP or GFP alone and V5-Ana2 and the next day induced to express for 24 h.

Lysates were then made and a GFP immunoprecipitation was performed, and samples were

blotted for GFP, V5 and Tubulin as a loading control.

(B) Plk4 interacts with Wdb. Cells were co-transfected with expression vectors containing Wdb-

GFP or GFP alone and Plk4-ND-myc and the next day induced to express for 24 h. Anti-GFP immunoprecipitates were made from the lysates of these cells and samples were blotted for GFP, myc and Tubulin as a loading control.

(C) The Asl-A-Wdb interaction is stabilized by the presence of Plk4. Wdb-GFP or GFP alone and Asl-A-V5 were co-transfected into S2 cells with or without Plk4-ND-myc and the next day induced to express for 24 hr. Anti-GFP immunoprecipitates were prepared as described above and samples were immunoblotted for GFP, V5, myc and Tubulin.

(D) Quantitation of phospho-Asl spots in wild type cells, cells depleted or Wrd and Wdb, and cells overexpressing V5-Wdb. This is a graphical representation of the complete data obtained in

Figure 3.4E. WT: n=152 centrioles counted. Wdb OE: n=66 centrioles counted. Wrd/Wdb RNAi: n=73 centrioles counted.

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CHAPTER 4: FUTURE DIRECTIONS AND CONCLUSIONS

This chapter was written entirely by me. All experiments were performed by me, with the

exception of the RNAi screen which was performed by Greg Rogers and Nasser Rusan. All

experiments were designed and analyzed by Greg Rogers and myself.

4.1 Identification of a Cellular Plk4 Inhibitor

In chapters 2 and 3 we describe a mechanism whereby Plk4 binds and phosphorylates

Asl, which in turn results in the catalytic inhibition of Plk451. This negative feedback mechanism is likely responsible for limiting the assembly of only one new centriole per mother centriole during the next cell cycle159. Notably, all forms of evidence that we present for Plk4 inhibition

has been in an in vivo cell culture environment, where expression of phospho-Asl blocks Plk4 autophosphorylation and centriole assembly. When we attempted to visualize inhibition of Plk4 activity by phospho-Asl using an in vitro assay, we found that addition of purified phospho-Asl-

A cannot affect Plk4 activity compared to the Plk4-alone control (Figure 2.4). Since phospho-

Asl-A can clearly influence Plk4 activity in cells but not in vitro, this either suggests technical limitations of our in vitro model, such as an ineffective phospho-mimetic protein, or it suggests the existence of an unidentified co-factor that coordinates with phospho-Asl in order to inhibit

Plk4 in cells. We also found that Asl-A cannot interact with transgenic constructs containing only the Plk4 kinase domain, as Plk4’s tandem Polo-Boxes are required for the Asl-A-Plk4 interaction (Figure S2.2, S2.3)134. Furthermore, the Asl-A-Plk4 interaction seems to be required for Plk4 inhibition in cells (Figure 3.2). This means that this prospective unknown co-inhibitor

could function by bridging between phospho-Asl and the Plk4 kinase domain to allow for direct

inhibition.

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There will be a bi-directional approach to identifying the cellular inhibitor. It is

hypothesized that 1. It normally functions during the centriole duplication cycle to block

centriole assembly, and 2. It binds to phospho-Asl-A and Plk4 in a complex. Therefore, centriole

amplification should be induced when the inhibitor gene is depleted by RNAi, and it should also

be identifiable by mass spectrometry (Figure 4.1). Our lab has performed a genome-wide RNAi

screen and identified over 400 genes that may function to block centriole duplication (centriole

amplification is induced when they are depleted). Additionally, we have performed an

experiment where GFP-tagged phosphomimetic Asl-A was co-expressed with Plk4 and

immunoprecipitated, then the immunoprecipitate was sent for protein identification by mass

spectrometry. Using non-phosphorylatable Asl-A as a negative control, we were able to identify proteins that could bind in a specific stable complex with phospho-Asl and Plk4. When this list was cross referenced to the RNAi screen, there were only 5 proteins that fulfilled both criteria of a Plk4 inhibitor. Unfortunately, none of these proteins could be validated as a Plk4 inhibitor in cells.

It is possible that the inhibitory complex formed by Asl-A, Plk4 and the unknown factor

is transient and unstable, whereby Asl-A recruits it to Plk4 where it is briefly inhibited or modified in a way that would allow for inhibition (i.e. dephosphorylation of an activation residue). This protein then may not bind to Plk4 and Asl-A in a standard immunoprecipitation experiment. To address this, we will utilize a proximity-dependent biotinylation assay, where a promiscuous biotin ligase (miniTurbo) is fused to a gene of interest (in our case Asl-A)160. The miniTurbo-Asl-A construct can then be expressed in cells and, upon the addition of exogenous biotin, can biotinylate any protein that comes within close proximity, including transient interactors (Figure 4.2). Biotinylated proteins can then be isolated using streptavidin-coated

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beads and sent for identification by mass spectrometry. Future experiments with potential hits

will involve in vivo testing of the activity-specific Plk4 antibody and in vitro kinase assays to test

how Plk4 activity is affected.

4.2 Formation of the Procentriole Spot by Wdb

The Drosophila protein Widerborst (Wdb) functions as a regulatory subunit of the

Protein Phosphatase 2A (PP2A) complex. Like the PP2A complex as a whole, Wdb has been

implicated in cell cycle regulatory mechanisms and microtubule organization158,161. Notably, it

was previously suggested that Wdb and another PP2A regulatory subunit, Well-rounded (Wrd)

may coordinate with each other to promote centriole assembly, as their co-depletion by RNAi

caused a loss of centrioles in cells158. In chapter 3, we show that Wdb and Wrd can each localize to the centriole and that their overexpression can cause amplification (Figure S3.2). We then describe a potential mechanism of how Wdb is promoting centriole duplication – by binding Asl and controlling its phosphorylation patterns at the centriole (Figure 3.4). In turn, we see that manipulation of phospho-Asl patterns control the number of new daughter centrioles around the mother. Intriguingly, we observed that under physiological conditions, Wdb usually only dephosphorylates Asl at one spot around the mother centriole, allowing for the formation of only one daughter centriole. On many occasions, Wdb was observed localizing to more than one spot on the mother centriole, but only one daughter centriole was assembled. This suggests that the initial localization of Wdb around the mother centriole is not the key step in site selection for centriole assembly and brings into question how exactly this site is selected. Perhaps, other centriole proteins are involved in the recruitment of Wdb to a single spot during late mitosis when Plk4 activation is required.

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In the concluding paragraphs of chapter 3, we identify the centriole protein Ana2 as

another interacting partner of Wdb (Figure S3.3). Interestingly, Ana2 could only interact with

Wdb when it was overexpressed, as endogenous Ana2 was not observed binding in a Wdb-GFP

immunoprecipitation (Figure 3.4). Notably, Ana2 is also known to interact with Asl, and is an

interacting partner and substrate of Plk434,107. Most importantly, Ana2 localizes to the spot of

future centriole assembly34. Because of this, we examined the co-localization of Ana2 and Wdb

at the centriole using high-resolution microscopy (Figure 4.3A). As expected, Ana2 localized to spots on the mother and newly forming daughter centriole. As previously observed, Wdb localized to the centriole, forming spots at multiple locations, but interestingly it formed prominent puncta at spots where it co-localized with Ana2. When Ana2 was depleted from cells by RNAi, mother centrioles with 6 phospho-Asl spots were commonly observed, which is thought to be a localization pattern that blocks centriole duplication (Figure 4.3B). Furthermore, when the Ana2 knockdown cells were stained Wdb, we found multiple instances where it failed to localize to the centriole (which almost never occurred in the control cells). This observation, taken together with the finding that high levels of Ana2 are needed to bind Wdb, suggest that

Ana2 could be directly involved with the recruitment of Wdb to the spot of centriole assembly.

Perhaps Wdb initially localizes to areas all-around the mother centriole, then the recruitment of

Ana2 concentrates Wdb into a single spot at the site of centriole assembly, with the concentration of Wdb eventually reaching the threshold required for PP2A-Wdb to dephosphorylate Asl.

In the future, it will be necessary to perform additional microscopy experiments in order to quantify the aforementioned observations. Namely, does Ana2 depletion cause an increase in phospho-Asl spots at the centriole and decrease in Wdb localization at the centriole?

Furthermore, more work is needed to determine the significance of the Wdb-Asl and the Wdb-

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Ana2 interactions at the centriole. The development of Asl and Ana2 mutants that fail to bind

Wdb will be a necessary step, as well as in vitro competitive binding assays that could help

determine how Ana2 accumulation recruits Wdb to the procentriole spot. Lastly, since Wdb is a

part of the PP2A complex, it will be important to examine whether Asl and Ana2 are PP2A-Wdb

substrates, and if so, which residues get dephosphorylated in order to promote centriole assembly

and the kinetics of the dephosphorylation reaction.

Notably, we found that Wrd failed to interact with Asl, and did not pursue further

mechanisms in relation to its ability to control centriole duplication. As previously mentioned,

Wrd and Wdb play other roles in regulating the cell cycle, and it is possible that modulating

levels of either of these proteins may have an indirect effect on the centriole duplication cycle in

cells. In the future it will be interesting to use high-resolution microscopy to examine the localization of Wdb within the centriole, as well as search for any additional centriolar binding partners and substrates to identify how it is able to cause centriole amplification when overexpressed.

4.3 Further Molecular Characterizations of the Asl-Plk4 Interaction

Previous studies have shown that Asl can interact with Plk4 through two regions: its N-

terminal Asl-A domain and its C-terminal Asl-C domain37–39,135. It was found that the Asl-C-Plk4 interaction is sufficient for centriole localization and new centriole assembly135. However, the

Asl-A-Plk4 interaction can contribute to Plk4 dimerization, autophosphorylation, degradation,

activation and inhibition51,135. Our work in chapter 2, 3 and 4.1 has detailed several of these

mechanisms, but clearly there is much more work necessary in order to determine when and how

each of these processes occur. To do this, we need to acquire as much information as we can

about the Asl-A-Plk4 interaction.

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Asl is a long coiled-coil scaffolding protein, and Asl-A itself contains multiple coiled-coil

domains of various sizes (Figure 4.4A). Asl-A is also known to homo-dimerize, but the regions

of self-interaction have never been mapped51,135. We hypothesized that Asl-A would

homodimerize through one of its coiled-coil regions, which typically provide excellent structure

for protein interactions162. To do this, we generated mutants of Asl-A that lack each of its three coiled-coil regions and co-immunoprecipitated them with wild-type Asl-A to see which mutants would fail to interact. We observed that fragments lacking Coiled Coil 3 (CC3) completely failed to interact with Asl-A, suggesting this domain is responsible for Asl-A self-interaction (Figure

4.4B). Next, we wanted to investigate whether Asl-A dimerization was required for its interaction with Plk4. Since we found that Asl-A dimerizes through its CC3 and Asl-A was shown to interact with Plk4 through residues outside of that region (Figure 3.2B), we predicted that deletion of CC3 would not affect its interaction with Plk4. Surprisingly, we found that Asl-A constructs lacking CC3 were not able to interact with Plk4, suggesting Asl-A dimerization is a prerequisite to its interaction with Plk4 (Figure 4.4C). In the future more structural analysis is necessary in order to determine molecular specifics of Asl-A’s regulation of Plk4. Ideally, we would be able to obtain a crystal structure of Asl-A in a complex with Plk4. Coupled with other in vitro assays such as SEC-MALS to determine molecular binding ratios and FRET to determine dynamics of Plk4 activation, we could gain a much better understanding of the relationship between Asl and Plk4, which is clearly becoming one of the most important relationships in the regulation of centriole assembly.

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4.4 Figures

4.1 Screen to Determine Co-Inhibitor of Plk4

The unidentified Plk4 inhibitor likely will meet two criteria: it binds phospho-Asl-A but not nonphospho-Asl-A, and depletion of the gene will induce centriole amplification.

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Figure 4.2 – Utilization of a Proximity-Dependent Biotinylation Assay

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Cells were transfected with expression constructs containing V5-miniTurbo-Asl-A-2A or V5- miniTurbo-Asl-A-2PM and the following day were induced to express for 16 hr. Simultaneously,

50uM of exogenous biotin was added to the cell culture media for 16 hr. As a negative control, expression of each construct was induced without the addition of 50uM biotin (left two lanes).

Lysates were made from these cells and immunoblotted for Strep-HRP, which binds to biotin, and Tubulin as a loading control. Addition of biotin to the media resulted in a significant increase in the amount of biotinylated proteins in the sample, indicating the miniTurbo enzyme was catalytically active. MT = miniTurbo, HRP = Horseradish Peroxidase.

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Figure 4.3 Centriolar Localization of Wdb and Ana2

(A) Cells were transfected with Sas6-promoter driven mNeon-Ana2 (the Sas-6 promoter allows for lower level, near endogenous expression levels) and allowed to express for 48 hr. After which, cells were plated, fixed and stained for Wdb and Plp to mark the surface of mature centrioles.

(B) Ana2 was depleted from cells by treatment with dsRNA for 7 d then plated, fixed and stained for Wdb, Cep135 to mark mother and daughter centrioles, and Plp to mark the surface of mature centrioles.

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Figure 4.4 – Asl-A Dimerization is Required for its Interaction with Plk4

(A) The structure of Asl-A contains 3 predicted coiled-coil domains of various sizes.

(B) Cells were co-transfected with GFP-tagged Asl-A and the indicated Asl-A-V5 mutant construct. The next day, cells were induced to express these constructs. Lysates were made from

129 these cells and immunoprecipitated. Immunoprecipitates were blotted for GFP, V5 and Tubulin as a loading control.

(C) Cells were co-transfected with the indicated constructs and lysates and immunoprecipitates were prepared as described above. Samples were blotted for GFP, V5, and Tubulin as a loading control.

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APPENDIX A: PUBLICATIONS

1. Boese, C.J. and Rogers, G.C. 2020. Centrosomes – An overview. Manuscript in preparation for

submission to Encyclopedia of Biological Chemistry.

2. Boese, C.J., Buster, D.W., Ryniawec, J.M., Rogers, G.C., 2020. Asterless phosphorylation

promotes a single site of centriole assembly. Manuscript in preparation.

3. Ryniawec, J.M., Buster, D.W., Boese, C.J., Slep, K.C., Rogers, G.C. 2020. Concentration

dependent dimerization and activation of Plk4. Manuscript in preparation.

4. Boese, C.J., Nye, J., Buster, D.W., McLamarrah, T.A., Byrnes, A.E., Slep, K.C., Rusan, N.M.,

Rogers, G.C., 2018. Asterless is a Polo-like kinase 4 substrate that both activates and inhibits

kinase activity depending on its phosphorylation state. Mol. Biol. Cell 29, 2874–2886.

5. McLamarrah, T.A., Buster, D.W., Galletta, B.J., Boese, C.J., Ryniawec, J.M., Hollingsworth,

N.A., Byrnes, A.E., Brownlee, C.W., Slep, K.C., Rusan, N.M., Rogers, G.C., 2018. An ordered

pattern of Ana2 phosphorylation by Plk4 is required for centriole assembly. J. Cell Biol. 217,

1217–1231.

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