MIAMI UNIVERSITY
The Graduate School
Certificate for Approving the Dissertation
We hereby approve the Dissertation
of
Matthew F. Rouhier
Candidate for the Degree:
Doctor of Philosophy
______Director (Dr. Ann Hagerman)
______Reader (Dr.Chris Makaroff)
______Reader (Dr.Gary Lorigan)
______Reader (Dr. Richard Taylor)
______Graduate School Representative (Dr. Paul James)
! ABSTRACT
CHARACTERIZATION OF YDR036C FROM Saccharomyces cerevisiae
by Matthew F. Rouhier
Beta-hydroxyisobutyryl-CoA (HIBYL-CoA) hydrolases are found ubiquitously in eukaryotes where they function in the catabolism of valine. A homologous enzyme (YDR036C) is also present in yeast where valine catabolism is distinctly different and does not require a HIBYL-CoA hydrolase. Like the other eukaryotic hydrolases, the yeast hydrolase is a member of the crotonase super-family which catalyzes various reactions using CoA thioester substrates. Crotonases typically function in fatty acid degradation which is peroxisomal in yeast while YDR036C is found strictly in mitochondria. Like other HIBYL-CoA hydrolases the yeast enzyme demonstrated activity toward beta-hydroxyacyl-CoAs, but unlike the other HIBYL-CoA hydrolases the yeast activity is greatest with beta-hydroxypropionyl-CoA (3-HP-CoA). Further characterization of the active site has determined that the preference of the hydrolases for 3-HP- CoA or HIBYL-CoA is dependent upon the residue at position 177. The glutamate at position 121 is responsible for the coordination with the beta-hydroxyl group and replacement with valine renders the enzyme non-specific for a hydroxyl group. Another unique feature to yeast hydrolases is the presence of a C-terminal tail of 80 amino acids, which when removed renders the enzyme inactive, suggesting that it may play a role in substrate binding. Serial truncation of the enzyme demonstrated that the tail residues between 472 and 500 are critical for the proper hydrolase activity. Similarly the enzyme can be inactivated by placing a phosphate ester-mimic in place of serine 428. Although the active site seems optimized for 3-HP-CoA this compound is not a known metabolite of yeast. This suggests that YDR036C may be serving a unique function in yeast. High-throughput studies have identified a mild phenotype in fluid-phase endoyctosis in ydr036c mutants. The same phenotype is observed in knockouts of ergosterol synthesis enzymes. Ergosterol quantification in the ydr036c knockout showed reduced total cellular ergosterol when compared to wild-type. Ergosterol was subsequently docked to a model of the enzyme and shown to bind at the active site pocket. Since the storage mechanism for yeast sterols is sterol esters, this study proposes that YDR036C is not a HIBYL-CoA hydrolase, but instead may function as a mitochondrial sterol esterase.
!
CHARACTERIZATION OF YDR036C FROM Saccharomyces cerevisiae
A DISSERTATION
Submitted to the Faculty of
Miami University in partial
Fulfillment of the requirements
for a degree of
Doctor of Philosophy
Department of Chemistry and Biochemistry
by
Matthew F. Rouhier
Miami University
Oxford, Ohio
2011
! Table of Contents
Chapter 1: Introduction ...... 1
1.1 Crotonase ...... 1
1.1.1 Crotonase ...... 1
1.2 !-hydroxyisobutyryl-CoA hydrolase ...... 1
1.2.1 HIBYL-CoA hydrolase homology ...... 1
1.2.2 HIBYL-CoA hydrolase and valine metabolism ...... 2
1.2.3 HIBYL-CoA hydrolase structure ...... 2
1.2.4 HIBYL-CoA hydrolase mechanism ...... 2
1.2.5 HIBYL-CoA hydrolase specificity ...... 2
1.3 References ...... 4
Chapter 2: Characterization of YDR036C ...... 10
2.1 Introduction ...... 10
2.1.1 YDR036C and HIBYL-CoA hydrolase ...... 10
2.2 Materials and Methods ...... 11
2.2.1 Materials and cell lines ...... 11
2.2.2 Cloning and mutagenesis ...... 11
2.2.3 Protein over-expression and purification ...... 12
2.2.4 Assay of hydrolase activity ...... 13
2.2.5 pH profile of YDR036C and variants ...... 13
2.2.6 Modeling of YDR036C ...... 13
2.2.7 Docking of substrates ...... 13
2.3 Results ...... 14
2.3.1 Sequence alignment & homology ...... 14
2.3.2 Hydrolase activities ...... 14
""!! 2.3.3 Modeling and docking ...... 15
2.3.4 Residues controlling methyl group preference ...... 15
2.3.5 Residues controlling hydroxyl group and carbon chain requirement ...... 16
2.4 Discussion ...... 17
2.5 References ...... 19
Chapter 3: Phosphorylation of HIBYL-CoA hydrolase ...... 29
3.1 Introduction ...... 29
3.1.1 HIBYL-CoA hydrolase regulation ...... 29
3.1.2 Mitochondrial regulation by phosphorylation ...... 29
3.1.3 Determination of phosphorylation state ...... 29
3.2 Materials and Methods ...... 29
3.2.1 Cloning and mutagenesis ...... 29
3.2.2 Assay of hydrolase activity ...... 30
3.3 Results and Discussion ...... 30
3.3.1 Sequence alignment of HIBYL-CoA hydrolases ...... 30
3.3.2 Phosphorylation mimics ...... 30
3.3.3 Future work ...... 31
3.4 References ...... 32
Chapter 4: Potential role of YDR036C in regulating ergosterol metabolism ...... 38
4.1 Introduction ...... 38
4.1.1 YDR036C homology to valine hydrolase ...... 38
4.1.2 Hydrolase activity ...... 38
4.1.3 Homology modeling ...... 38
4.1.4 Ergosterol ...... 39
4.1.5 Synthesis of ergosterol in the ER ...... 39
"""!! 4.1.6 Shuttling of ergosterol to the LP ...... 40
4.1.7 Shuttling of ergosterol to the PM ...... 40
4.1.8 Detoxification by Atf2 and Say1 ...... 40
4.1.9 Hydrolysis of sterol esters ...... 40
4.2 Methods and Materials ...... 41
4.2.1 Materials and cell lines ...... 41
4.2.2 Modelling of YDR036C ...... 41
4.2.3 Docking of substrates ...... 42
4.2.4 Extraction and quantification of ergosterol ...... 42
4.3 Results and Discussion ...... 42
4.3.1 Saccharomyces cerevisiae ydr036c! ...... 43
4.3.2 Ergosterol content of ydr036c knockout S. cerevisiae ...... 43
4.3.3 Other evidence for a role for YDR036C in mitochondrial ergosterol regulation .. 44
4.4 Conclusions ...... 44
4.4.1 Ergosterol conclusions ...... 44
4.4.2 Implication for higher eukaryotes ...... 45
4.4.3 Future work ...... 45
4.5 References ...... 47
Chapter 5: Conclusions ...... 56
5.1 YDR036C and other yeast hydrolases ...... 56
"#!! !
List of Tables
Table 2.1 The kinetic parameters of the site-directed mutants of human and S. cerevisiae HIBYL-CoA hydrolases.…..………………………………………………….…21
Table 2.2 The kcat and turnover ratio of human, A. thaliana, S. cerevisiae, S. pombe, C. albicans, and D. hansenii HIBYL-CoA hydrolases.………………...…………...22
Table 2.3 The kcat of S. cerevisiae wild-type and truncated HIBYL-CoA hydrolases...... 23
Table 2.4 The kcat of S. cerevisiae wild-type and glutamate 121 mutants of HIBYL-CoA hydrolase. …………………………………………………………………….….24
Table 3.1 The kcat of human and S. cerevisiae wild-type and mutant hydrolases….….……37
#!! List of Figures
Figure 1.1 Secondary structure of the crotonase super-family core…………………………..5
Figure 1.2 Crystal structure of crotonase (2DUB) and HIBYL-CoA hydrolase (3BPT)...... 6
Figure 1.3 A clustalw [15] alignment of several members of the crotonase super-family…...7
Figure 1.4 Mechanism of HIBYL-CoA hydrolase. ………………………………………….8
Figure 1.5 Catabolic pathway for the branched chain amino acids………..………………....9
Figure 2.1 The proposed mechanism of 3-HP-CoA hydrolysis based on the mechanism demonstrated for Pseudomonas HIBYL-CoA hydrolase………………………...25
Figure 2.2 The clustalw alignment of HIBYL-CoA hydrolases from A. thaliana. H. sapiens. S. pombe. C. albicans. D. hansenii. S. cerevisiae. C. glabrata. and K. lactis……26
Figure 2.3 The modeled structure of the S. cerevisiae hydrolase, YDR036C….……………27
Figure 2.4 The Michaelis-Menten kinetic graphs of human and S. cerevisae HIBYL-CoA hydrolases………………………………………………………………………...28
Figure 3.1 Catabolic pathway of the branched chain amino acids…………………………..33
Figure 3.2 The clustalw alignment of HIBYL-CoA hydrolases from A. thaliana. H. sapiens. S. pombe. C. albicans. D. hansenii. S. cerevisiae. C. glabrata. and K. lactis……34
Figure 3.3 Structure of HIBYL-CoA hydrolase……………………………………………..35
Figure 4.1 Structures of quercetin and (3'(N-carboxymethyl)carbomyl-3,4',5,7- tetrahydroxyflavone) (QC12)……………………………………………...... 50
Figure 4.2 Overlay of ergosterol and quercetin in the YDR036C active site………………..51
Figure 4.3 Structures of sterols (ergosterol, cholesterol, and lanosterol), and the steroid pregnenolone……………………………………………………………………..52
Figure 4.4 The structures of coenzyme A and the truncated 3-HP-CoA used for docking with AutoDock4……………………………………………………………………….53
Figure 4.5 The ergosterol content of wild-type and ydr036c! strains of S. cerevisiae in YPD and the growth of wild-type and ydr036c! strains on YPD agar containing the antifungal compound clorimazole……………………………………………...... 54
#"!! Figure 4.6 Proposed sterol trafficking in S. cerevisiae………………………………………55
#""! ! Dedication
First and foremost, I would like to dedicate this work to my wife, my love. If not for her continual support I may have lost my way. Second I would like to honor John Hawes for his guidance and friendship during my graduate career and beyond. He will be sorely missed. Lastly, I would like to thank the members of my committee, especially Dr. Ann Hagerman and Dr. Chris Makaroff, who have guided me in John’s absence.
#"""! ! Acknowledgments
I would like to acknowledge the Chemistry Department at Miami University for providing an excellent training in biochemistry, and how to succeed after graduate school. I would also like to acknowledge Dr. Richard Taylor, Dr. Gary Lorigan, and Dr. Paul James for serving on my committee.
"$!! Chapter 1: Introduction
1.1 Crotonase
1.1.1 Crotonase
The crotonase super-family is one of the largest and arguably most catalytically diverse groups of enzymes [1-3]. The first enzyme of its type to be characterized was enoyl-CoA hydratase, also known as crotonase, which lends its name to the super-family [4, 5]. Since the initial characterization of crotonase many other members of the super-family have been added based on their sequence homology. The structure of crotonase was experimentally determined in 1996 [6] and revealed the structures of the canonical fold and oxyanion hole which are common to all super-family members.
The canonical fold is generated by repeating !!" units as seen in Figure 1.1 and 1.2 [2]. The units form two beta sheets that are approximately perpendicular to one another (colored blue in Figure 1.2) generating the scaffolding of the active site and CoA recognition site [7, 8]. The oxyanion hole is a hallmark of enzyme chemistry that accelerates carbonyl chemistry by the stabilization of enolate or other unstable anionic intermediates. Stabilization of the oxyanion, a negatively charged oxygen alpha to a double bond, is typically achieved by hydrogen bonding. The dipole-dipole interaction of the oxyanion hole is sufficient to stabilize intermediates that otherwise would be highly unfavorable. An example of this stabilization is the oxyanion hole in crotonase (colored yellow in Figure 1.2A and B) [6], where amide hydrogens of the peptide backbone stabilize the oxyanion.
The crotonase super-family enzymes generally utilize similar chemistries to perform their reactions owing their catalytic efficacy to both the oxyanion hole and the energy provided by the CoA substrates. Most crotonase family enzymes utilize acyl-CoAs as substrates. Not surprisingly, the areas of greatest conservation among the super-family are within the CoA binding regions, oxyanion hole, and to a lesser extent the residues that participate in the catalysis, while the overall sequence similarity is low, often less than 20% [1] (Figure 1.3).
1.2 !-hydroxyisobutyryl-CoA hydrolase
1.2.1 HIBYL-CoA hydrolase homology
Hydroxyisobutyryl-CoA hydrolase (HIBYL-CoA hydrolase) is a crotonase super-family enzyme that catalyzes the hydrolysis of hydroxyisobutyryl-CoA to hydroxybutyrate and free CoA (Figure 1.4). HIBYL-CoA hydrolase is ubiquitous throughout prokaryotes and eukaryotes, where it is believed to aid in the removal of a toxic intermediate of valine metabolism, methacrylyl-CoA [9]. Similar to the rest of the crotonase super-family, HIBYL-CoA hydrolase homologues do not
1! ! ! exhibit high similarity over the entire sequence, but the residues in key structural features required for catalysis are conserved.
1.2.2 HIBYL-CoA hydrolase and valine metabolism
A subset of amino acids is known as the branched chain amino acids, which include valine, leucine and isoleucine. All three branched chain amino acids have similar hydrophobic properties that are critical for the proper formation of most globular proteins. The similar structures allow the amino acids to share the initial steps of their degradation before diverging to accommodate each individual amino acid (Figure 1.5) [10]. The common pathway consists of deamination followed by the removal of a carboxylate, and then dehydrogenation to yield a beta unsaturated acyl-CoA. The pathways all maintain a CoA ester throughout degradation except for valine. The valine pathway breaks the CoA ester bond (step 8, Figure 1.5) only to regenerate a new CoA ester bond in a subsequent step. The seemingly wasted energy of breaking and reforming the CoA ester is believed to function as a protective mechanism to prevent the buildup of methacrylyl-CoA [11]. Methacrylyl-CoA is a good Michael addition acceptor that is capable of modifying thiol groups such as those found in glutathione, free CoA, and cysteines in the active sites of the cysteine proteases. Methacrylyl-CoA represents a significant danger to the cell if allowed to accumulate because of its reactivity. The reaction catalyzed by HIBYL-CoA hydrolase (step 8, Figure 1.5), unlike most of the enzymes in valine degradation, is not reversible and therefore can behave as a one-way valve to ensure the continued progression of intermediates in the valine degradation pathway and prevent methacrylyl-CoA accumulation.
1.2.3 HIBYL-CoA hydrolase structure
HIBYL-CoA hydrolase bears only minor differences from other members of the crotonase super- family, with the most significant difference being the addition of a C-terminus whose secondary structure forms a cap over the crotonase active site groove (C-terminal is orange in Figure 1.2). The capping of the active site groove effectively prevents the catalysis of long chain acyl-CoAs generating the selectivity of HIBYL-CoA hydrolase for smaller acyl- chains. The active site is comprised of two amide hydrogens forming the oxyanion hole and an acidic residue to perform catalysis [3].
1.2.4 HIBYL-CoA hydrolase mechanism
HIBYL-CoA hydrolase has a different mechanism than many other enzymes of the crotonase super-family [3]. While many crotonases have an enolate intermediate that is stabilized by the oxyanion hole, HIBYL-CoA hydrolase forms an enzyme-bound anhydride that is stabilized by the oxyanion hole (Figure 1.4). Hydrolysis is initiated by attack of a glutamate residue on the carbonyl oxygen of the CoA thioester, with formation of a tetrahedral intermediate. The intermediate collapses to the glutamyl anhydride upon release of free Coenzyme A. Subsequent 2! ! ! attack by water on either the substrate carboyl (shown in Figure 1.4) or the glutamyl carbonyl (not shown) releases the free HIBA and restores the active site glutamate.
1.2.5 HIBYL-CoA hydrolase specificity
The activity of the hydrolase is specific for HIBYL-CoA and 3-hydroxypropionyl-CoA, but not equally toward both, as the enzyme has 3-fold lower activity towards 3-hydroxypropional-CoA. Both of these substrates share the common features of a three-carbon backbone and a hydroxyl group at the beta position [12, 13]. A variety of other CoAs have been assayed with HIBYL- CoA hydrolases, including substrates that contain hydroxyl groups at positions other than the beta position as well as carbon backbones other than 3 carbons, but the enzyme does not demonstrate significant activity towards other compounds.
Our interest in yeast HIBYL-CoA hydrolases was generated by the paradox that yeast retains a HIBYL-CoA hydrolase-like enzyme, YDR036C, despite not containing any pathways or proteins involved in conventional HIBYL-CoA metabolism. We hypothesized that characterization of the yeast enzyme may provide insight into the purpose of this enzyme as well as shed light on the known phenotypes of knockout strains. The chapters of this dissertation will describe in detail the structure/function and substrate specificity relationships in Chapter 2, the possible regulation by phosphorylation in Chapter 3, and experiments on the phenotypes and possible metabolic roles of YDR036C in Chapter 4.
3! ! ! 1.3 References
[1] R.B. Hamed, E.T. Batchelar, I.J. Clifton, C.J. Schofield, Cell Mol. Life Sci. 65 (2008) 2507- 2527.
[2] H.M. Holden, M.M. Benning, T. Haller, J.A. Gerlt, Acc. Chem. Res. 34 (2001) 145-157.
[3] B.J. Wong and J.A. Gerlt, J. Am. Chem. Soc. 125 (2003) 12076-12077.
[4] J.C. Fong and H. Schulz, J. Biol. Chem. 252 (1977) 542-547.
[5] J.C. Fong, H. Schulz, Meth. Enzymol. 71 (1981) 390-398.
[6] C.K. Engel, M. Mathieu, J.P. Zeelen, J.K. Hiltunen, R.K. Wierenga, EMBO J. 15 (1996) 5135-5145.
[7] J.T. Rasmussen,!T. Börchers, J. Knudsen, Biochem. J. 265 (1990) 849-855.
[8] B.J. Wong and J.A. Gerlt, Biochemistry 43 (2004) 4646-4654.
[9] Y. Shimomura, T. Murakami, N. Nakai, B. Huang, J. Hawes, R. Harris, Meth. Enzymol. 324 (2000) 229-240.
[10] L.K. Massey, J. Sokatch, R. Conrad, Bacteriol. Rev. 40 (1976) 42-54.
[11] Y. Shimomura, T. Murakami, N. Fujitsuka, N. Nakai, Y. Sato, S. Sugiyama, N. Shimomura, J. Irwin, J.W. Hawes, R.A. Harris, J. Biol. Chem. 269 (1994) 14248-14253.
[12] J.W. Hawes, J. Jaskiewicz, Y. Shimomura, B. Huang, J. Bunting, E.T. Harper, R.A. Harris, J. Biol. Chem. 271 (1996) 26430-26434.
[13] B.K. Zolman, M. Monroe-Augustus, B. Thompson, J.W. Hawes, K.A. Krukenberg, S.P.T. Matsuda, B. Bartel, J. Biol. Chem. 276 (2001) 31037-31046.
[14] C.K. Engel, T.R. Kiema, J.K. Hiltunen, R.K. Wierenga, J. Mol. Bio. 275 (1998) 847-859.
[15] J.D. Thompson, D.G. Higgins, T.J. Gisbon, Nucleic Acid Res. 22 (1994) 4673-4680.
4! ! ! Figure 1.1 Secondary structure of the crotonase superfamily core.
The crotonase superfamily core is composed of repeating subunits. Arrows and cylinders represent beta sheets and alpha helixes respectively. The figure is a graphical representation of NCBI CCD “CD06558: crotonase-like”.
C
N
5! ! ! Figure 1.2 Crystal Structure of crotonase (2DUB) [14] and HIBYL-CoA hydrolase (3BPT).
The structures of Rattus norvegicus crotonase (A,B) and H. sapiens HIBYL-CoA hydrolase (C,D) are presented in ribbon fashion where the crotonase superfamily core is colored by secondary structure, blue representing beta sheets and red representing alpha helixes. The orange ribbon represents the C-terminal of the crotonase core in HIBYL-CoA hydrolase. The catalytic residues are represented in yellow. Figures B,D are rotated 90 degrees about the z-axis.
6! ! ! Figure 1.3 A clustalw [15] alignment of several members of the crotonase super-family. Residues that are identical or similar are highlighted in black and the residues involved in the formation!"#$%&'()* of the! oxyanion hole are denoted by asterisks. ! !"#!$%&#!'()*+,"-# $.!!./012!3455667..6228&387$3.9/:2;.95.3.90$/<$=:<#>?## /@#&)*A*@,"-# # 9;<=$$3622BBBBBBBBB8291178.$<.9/:25.95.&98.$66.9<5#CD## 5"#4-E,+*F-@,"-# # BB0=65$5=/BBBBBBBBBB7.68756$3$9.:/=/95.17<50261.45#GH## 1,#4!95#1'@AE,"-## ./6=46$2=6BBBBBBBBBB;=68$5273$9/:67/95;3:237560$45#CH## :I#&0:#1'@AE,"-# # B07;669146BBBBBBBBBBBBBB7/7$3.4!:92!9:;1/3.6317245#GJ## 1A#4!:5#KL'F-@,"-# 6..:6;7/386760657!.6//4875/.30&/44/.95648<<7440635#DMM# .N#00#4-I,)O*L'+,"-# 77<.36.898BBBBBBBBBBBBBB77<$3P24611/98;1:1$768./!&#GH## /@#-@*'+B&*5#$"*N-),"-# 7485//;192/7.762BBB68658$5702;29::B791.1.6;.36;7$1#QH## 5"#%4!#!'()*+,"-## ;32=69.!;!/BBBBBBBBB4698$.67/0!39811.7;3823!/6;:45#JR## 5-#%&#.',"-# # :12=/!S1.53486$53.3.9$46488$/:8=2.2.91=4.874$6.!45#QH## #################################################################################### ###########################################################T# !"#!$%&#!'()*+,"-## .22S6<4:B63;.$$$28588BBBBBBBB25;&5884$/7$1656252BB#??M# /@#&)*A*@,"-# # .63;664:B5785$7.3886BBBBBBBBB25;55854$260<9/3;<4BB#HM## 5"#4-E,+*F-@,"-# # .9/56441B878570$3856BBBBBBBBB45;&58;=./6$:.498$68$#>H## 1,#4!95#1'@AE,"-## ;1/5/44
HIBYL-CoA is attacked at the carbonyl carbon generating a covalently linked tetrahedral intermediate. The loss of free Coenzyme A produces the anhydride. Water attacks the substrate carbonyl (shown here) or the glutamyl carbonyl to release product and the active site glutamate.
HIBYL-CoA HIBA
8! ! ! Figure 1.5 Catabolic pathways for the branched chain amino acids.
1 2
3
1: Branched Chain Amino Acid Aminotransferase 2: Branched Chain Amino Dehydrogenase 3: Acyl-CoA Dehydrogenase 4: Enoyl-CoA Hydratase 5: Beta-hydroxyacyl-CoA Dehydrogenase 6: Acyl-CoA Acetyltransferase 7: Enoyl-CoA Hydratase 4 7 11 8: Beta-hydroxyisobutyryl-CoA Hydrolase 9: Beta-hydroxyisobuterate Dehydrogenase 10: Methylmalonate Semialdehyde Dehydrogenase 11: Beta-methylcrotonyl-CoA Carboxylase 12: Beta-methylglutaconyl-CoA Hydratase 13: HMG-CoA Lyase 5 8 12
6 9 13
10
9! ! ! Chapter 2: Characterization of YDR036C
2.1 Introduction
2.1.1 YDR036C and HIBYL-CoA hydrolase
!-Hydroxyisobutyryl-CoA hydrolase (HIBYL-CoA hydrolase, E.C. 3.1.2.4) is a member of the incredibly diverse crotonase superfamily [1]. The diversity of the superfamily revolves around changes within a common structural framework. The members of the superfamily generally have low levels of amino acid sequence similarity but share a common fold created from repeated !!" units [2]. Changes in the overall crotonase superfamily folds result in the wide variety of functions; however, almost all of the family members have a conserved oxyanion hole. Two amide hydrogens form an oxyanion hole that stabilizes anionic reaction intermediates, lowering the activation energy for the reaction [3].
In higher eukaryotes HIBYL-CoA hydrolase hydrolyzes HIBYL-CoA producing free CoA and !-hydroxyisobutyric acid during valine catabolism. Valine degradation using HIBYL-CoA hydrolase has been demonstrated in both prokaryotes and eukaryotes [4-6]; however, yeasts metabolize valine through the fusel alcohol pathway, apparently eliminating the need for a HIBYL-CoA hydrolase [7, 8]. Yet, a search through the Saccharomyces cerevisiae and other genome databases revealed that many yeast genomes do contain a HIBYL-CoA hydrolase homologue, YDR036C.
HIBYL-CoA hydrolases contain several conserved residues that are responsible for catalysis within the crotonase superfamily. Site directed mutagenesis of two acidic residues in human and Arabidopsis thaliana HIBYL-CoA hydrolase demonstrated that a conserved glutamate is responsible for the formation of an enzyme anhydride (Figure 2.1). The second acidic residue, aspartate, is not believed to participate directly in catalysis due to the ability to retain significant activity when mutated to asparagine [1]. Nonetheless, it may have a secondary role or structural importance since mutation to alanine results in an inactive protein [4].
Experimentation with HIBYL-CoA hydrolases shows that they are specific for acyl-CoAs that contain a three carbon chain and a hydroxyl-group in the beta position. There are two substrates that fit this criteria, HIBYL-CoA and 3-hydroxypropionyl-CoA (3-HP-CoA). Human and A. thaliana enzymes show activity toward 3-HP-CoA that is about one third of the activity toward HIBYL-CoA. The enzyme was not active against Acyl-CoAs without a hydroxyl group or against acyl-CoAs with hydroxyl groups in a position other than at the beta carbon [4, 9]. The features controlling the high degree of substrate specificity are not known.
The present study was undertaken to examine the enzymatic properties of YDR036C and similar enzymes [10] from S. cerevisiae and other yeasts. These enzymes were found to be !-
10! ! ! hydroxyacyl-CoA hydrolase homologues, but with a substrate specificity different from other eukaryotic hydrolases. Structural modeling and site-directed mutagenesis revealed that several subtle differences can contribute to this unusual substrate specificity.
2.2 Materials and methods
2.2.1 Materials and cell lines
All chemicals were purchased from Sigma-Aldrich (St. Louis, MO) unless otherwise noted.
3-Hydroxypropionate was synthesized according to Herter et al. [11]. 3-Hydroxyisobutyrate was synthesized according to Rougraff et al. [12]. Hydroxypropionyl-, hydroxybutyryl-, and hydroxyisobutyryl-CoAs were synthesized from mixed anhydrides using ethyl-chloroformate as described by Fong et al. [13] and Hawes et al. [14]. Acetyl-, propionyl-, butyryl-, and valyryl- CoAs were all synthesized from the corresponding anhydrides. Isobutyryl-CoA was purchased from Sigma- Aldrich. Saccharomyces cerevisiase (BY4743) was obtained from Open Biosystems (Huntsville, AL). The type strains of Candida albicans (NRRL Y-12983) and Debaryomyces hansenii (NRRLY-7426) were obtained from the USDA Agricultural Research Services (ARS) Culture Collection. The type strain of Schizosaccharomyces pombe (NRRL Y- 12796) was a generous gift from Dr. Jian- Qiu Wu, Department of Molecular Genetics, The Ohio State University, Columbus, Ohio. Full length cDNAs of the A. thaliana genes At5g65940, At2g30660, and At2g30650 were obtained from the Arabidopsis Biological Resource Center DNA Stock Center, The Ohio State University, Columbus, Ohio.
2.2.2 Cloning and mutagenesis
Cloning of the human hydrolase was performed previously by Hawes et al. [9]. The A. thaliana gene At5g65940 (CHY1) was amplified from the full length cDNA and ligated into pTrcHisTOPO (Invitrogen, Carlsbad, CA). The remaining hydrolase cDNAs were amplified from genomic DNA. DNA was prepared using the “Bust n’ Grab” method of Harju et al. [15]. The amplified genes were ligated into pGEM-T easy vector (Promega, Madison, WI), and the resulting plasmids were digested using the primer-added restriction sites and ligated into pET28a (Novagen, Gibbstown, NJ) for expression. The following primers were used for the amplifications (with restriction sites bolded):
• A. thaliana: aaaacatatggcagtcgagatggc and tttaagcttcagctttgcgatcccta • C. albicans:aaaacatatgggtgaagagccagttg and ttttaagcttttattttgtaggctctt • D. hansenii: aaaacatatgtatgcggaggatgatg and ttttggatccttattctatccaagag • S. cerevisiae: aaaacatatgactactcaaccccagc and ttttggatccttatttccatcttaagccatcg • S. pombe: aaaaggatcctcaaatgatacagttttatacg and ttttgcggccgcttataaataaggataagtcttataatt
11! ! ! Overlapping PCR was utilized for the construction of the site directed mutants. In brief, the cDNAs were amplified twice, once with mutagenic primers and a second time with full length primers. The first reactions created a fragment from the 5’ end to the mutation and from the mutation to the 3’ end. The gel-purified fragments were used in a second PCR reaction at a ratio of 4:1 with the native primers to generate the full mutated gene. The following primers were used in the mutagenic amplifications (with mutated sites bolded and in capital letters):
• E124A: ttttttactgatgCatattctttgaa and ttcaaagaatatGcatcagtaaaaaa • E124V: ttttttactgatgTatattctttgaa and ttcaaagaatatGcatcagtaaaaaa • F177L: gacattggtttAtttccagatg and cacatctggaaaTaaaccaatgtccat • L174F: actgcaataggaTtTttccctgatgtg and cagggaaAaAtcctatt • S. cerevisiae tail addition: TTGAATTTcattctaaataccaattgcct and TTTAGAATGAAAtttcaaatcactgcttcc • S. cerevisiae truncation: ttttggatccTtAtcttagtaatgaca
The addition of the S. cerevisiae tail to the human cDNA was performed using the overlapping method with the following primers for human and S. cerevisiae respectively:
• tttagaatgaaatttcaaatcactgcttcc • ggaagcagtgatttgaaatttcattctaaa
Inverse PCR was utilized for the construction of truncations of the S. cerevisiae cDNA by the addition of a BamHI site to the 3’ site for truncation followed by digestion and ligation to the BamHI site present in pET28a. The following primers were used for the 432, 452, 472, and 492 amino acid truncation sites:
• ttttggatccttAgtatttagaatg • ttttggatccTcAagtgtcatcatt • ttttggatcctcAtctagaaggaat • ttttggatccTTAttcttcacattt • agatggaaaTAAggatccgaattcg
2.2.3 Protein over-expression and purification
Protein over-expression was carried out using the Escherichia coli strain BL21(DE3) (Stratagene, La Jolla, CA) in auto-induction medium [17]. Cultures of 100 mL were grown in 250 mL baffle flasks at 190 rpm. The temperature for induction with 1 mM IPTG varied between 37 ºC and 24 ºC as stated. Proteins were purified on 1 mL of Sigma Ni-chelate affinity matrix (Ni-CAM), and glycerol was added to 10%. Proteins were stored at -80 ºC until assayed. Ni- CAM was washed with a minimum of 5 column volumes of 6 M guanidine HCl, pH 7.5, after
12! ! ! each use, before storage in 20% ethanol.
2.2.4 Assay of hydrolase activity
Assays were performed at 37 ºC in a total volume of 1 mL containing 0.1 M Tris-HCl, pH 8.0, and 1 mM 5,5’-dithio-bis(2-nitrobenezoic acid) (DTNB). The reaction was initiated by the addition of the enzyme to the buffer which contained the substrate. The reaction was monitored by measuring the DTNB-adduct of the liberated CoA at 412 nm with a Varian-Cary E1 UV- visible spectrophotometer with a temperature controlled water jacket [6, 9, 16]. Km and kcat were determined using Graphpad Prism program version 5 (La Jolla, CA).
2.2.5 pH profile of YDR036C and variants
Assays were performed at 37 ºC in a total volume of 1 mL containing 30 mM CAPS, 30 mM Hepes, 30 mM Mes, 30 mM TAPS and 1 mM dithiodipyridine (DTDP) adjusted to pH 5.3, 6.0, 7.0, 8.0, 9.0, and 10.5 by the addition of NaOH [17]. The reaction was initiated by the addition of enzyme to the buffer containing substrate. The liberation of free CoA was monitored by the increase in absorbance at 324 nm using a Varian-Cary E1 UV-visible spectrophotometer. The extinction coefficient of 21400 M-1 cm-1 was corrected for different pH values using a standard curve of free CoA [18].
2.2.6 Modeling of YDR036C
A model of the first 423 residues of the S. cerevisiae hydrolase was developed using the sequence (accession number NP_010321.1). BLASTP analysis indicated a 34% sequence identity and 53% sequence similarity for the entire alignment of S. cerevisiae and H. sapiens (PDB ID:3BPT). The residues within 20 Å of the active site are 43% identical and 61% similar and within 15Å of the active site are 52% identical and 64% similar. The PDB ID: 3BPT was used as a template for building a homology model with the SWISS-MODEL server. Anolea [19], Gromos [20], and Verify3D [21, 22] were used to verify the validity of the model. The alignment adjustments were undertaken with Deep View/Swiss-PdbViewer version 3.7 [23] and the figures were generated using UCSF Chimera [24]. The secondary structure was predicted using several different servers (Porter SS prediction [31], Jpred3 [32], and PFRMAT SS [33]).
2.2.7 Docking of substrates
Docking of hydroxyisobutyryl-CoA and 3-hydroxypropionyl-CoA was carried out using AutoDock 4. The substrate molecules were generated using ghemical (http://www.bioinformatics.org/ghemical) and saved in pdb format before they were assessed in Chimera. The CoA esters were truncated by the removal of the adenosine to reduce the flexibility of the substrate molecules when docking. Both the human crystal structure (3BPT) and the S.
13! ! ! cerevisiae model were prepared for docking using UCSF Chimera [24]. The default AutoDock4 [24] settings were used except the gridbox was set as 60X60X60 and was centered on the opening of the active site pocket. For each structure and substrate 100 docking runs were evaluated and the largest clustered result was considered representative and was used to assign the binding free energy.
2.3 Results
2.3.1 Sequence alignment & homology
The S. cevervisiae enzyme, YDR036C, has 34% identity and 52% similarity to the human hydrolase characterized by Hawes et al. [9] as well as 34% identity and 53% similarity to A. thaliana CHY1 [4]. As is typical of the crotonase superfamily, identity and similarity between enzymes are low, but alignment of the sequences revealed that the crotonase core, including the catalytic residues and proposed substrate binding residues, are well-conserved [2]. Homologues from all yeast species have a strong predicted mitochondrial leader sequence denoted by the presence of repeated basic residues in an extended N-terminal peptide, shown in gray in Figure 2.2 [25]. Confirming the predicted localization, YDR036C was shown to be mitochondrial by multiple high throughput studies [26, 27]. The A. thaliana active site residues, as determined by Zolman et al. [4], are glutamate 142 and aspartate 150, indicated by the arrows in Figure 2.2, and these are conserved throughout the yeast enzymes. The residues with amide hydrogens that participate in forming the oxyanion hole (indicated by the daggers in Figure 2.2 and fuchsia in Figure 2.3) are also conserved. The most similar regions of the protein are colored in orange in Figure 2.3A,B and surround the active site pocket. The less similar regions comprise the remainder of the protein. The yeast enzymes contain distinct differences from the human and A. thaliana enzymes, including a C-terminal 80-90 amino acid tail and a phenylalanine at position 177 in the active site indicated by the double dagger in Figure 2.2 and in blue in Figure 2.3. The D. hansenii and S. pombe enzymes are unique among the yeast hydrolases as the D. hansenii enzyme contains a leucine at position 177, similar to the human and A. thaliana hydrolases, and the S. pombe enzyme does not have a C-terminal tail. The tail region is absent in all the other HIBYL-CoA hydrolases but highly conserved among yeast.
2.3.2 Hydrolase activities
All enzymes were over-expressed, purified and assayed under the same conditions. The kcat values for the human hydrolase are in agreement with previously published data [4, 9, 17] and the specificity ratios (kcat/Km) clearly indicate the strong preference of the enzyme for HIBYL- CoA over 3-HP-CoA (Table 2.1). In contrast, the S. cerevisiae enzyme, YRD036C, has a much smaller kcat with HIBYL-CoA compared to the human enzyme, and the specificity ratio indicates a preference for 3-HP-CoA (Table 2.1).
14! ! ! Enzymes from other species were not purified in sufficient quantities to determine all kinetic constants, but kcat values were obtained for the hydrolase from A. thaliana and for the YDR036C homologue from S. pombe, C. albicans, and D. hansenii (Table 2.2). In order to assess substrate preferences, we calculated turnover ratios by taking the kcat for HP-CoA as a percent of the kcat for HIBYL-CoA (Table 2.2). Consistent with the specificity ratios, the turnover ratio indicated that the human enzyme had a strong preference for HIBYL-CoA and the S. cerevisiae enzyme a preference for 3-HP-CoA. The A. thaliana enzyme, which functions as a HIBYL-CoA hydrolase, has a turnover ratio similar to the human enzyme. The enzymes from S. pombe and from C. albicans are to be similar to the enzyme from S. cerevisiae, with preference for 3-HP- CoA. The enzyme from D. hansenii has a turnover ratio more similar to the human and Arabidopsis enzymes, consistent with its sequence homology. As described above, the human and Arabidopsis HIBYL-CoA hydrolases and the enzyme from D. hansenii have a leucine at position 177, while the yeast enzymes, which prefer 3-HP-CoA, have a phenylalanine at that site.
2.3.3 Modeling and docking
In an effort to understand the structural differences that lead to the strong preference for 3-HP- CoA, S. cerevisiae YDR036C, was modeled against the human structure 3BPT. The model was generated using the alignment in Figure 2.2 by the Swiss Model Server [28-30]. Since no suitable structure was available, the tail region was not included. The S. cerevisiae model confirms that the conserved residues, glutamate 172 and aspartate 180, as well as the amides for the oxyanion hole, are all within close proximity to one another (Figure 2.3C). The active site of the S. cerevisiae enzyme is almost identical to that of the human hydrolase except for a single residue; leucine at 174 in the human hydrolase is a phenylalanine in the S. cerevisiae enzyme (Figure 2.3C, leucine depicted in cyan, phenylalanine in blue).
Docking was also used to evaluate the differences in substrate preferences for YDR036C. Docking of HIBYL-CoA and 3-HP-CoA analogs predicted similar changes in free energy upon binding. The most common conformation for 3-HP-CoA with the S. cerevisiae model is depicted in Figure 2.3D.
2.3.4 Residues controlling methyl group preference
To assess possible features that may be specific for HIBYL-CoA or 3-HP-CoA, site-directed mutagenesis was performed. Based on the modeling there is a clear difference in the residues at position 177 (Figure 2.3C). Possible steric hindrance from the phenylalanine in the yeast enzymes may account for the substrate preference of 3-HP-CoA. Based on this observation phenylalanine 177 in the S. cerevisiae enzyme was mutated to a leucine and leucine 174 in the human enzyme was mutated to phenylalanine. Both kcat and Km changed as a result of the mutation, Figure 2.4. For the yeast enzyme the mutant demonstrated an increase of kcat for HIBYL-CoA and a decrease of kcat for 3-HP-CoA compared to wild-type. As a result the 15! ! ! turnover ratio of the mutant was only about 114 compared to about 284 for the wild-type. This suggested a smaller preference for 3-HP-CoA in the F177L mutant and indeed the specificity ratio of the mutant was greater for HIBYL-CoA.
For the human L174F mutant, the kcat for 3-HP-CoA and HIBYL-CoA decreased compared to wild-type, but to a greater extent for HIBYL-CoA. As a result, the turnover ratio for the mutant human enzyme, 92, was similar to the turnover ratio for the yeast enzyme mutation. The human mutant also demonstrated slight increase in Km for each substrate, but also greater for HIBYL-
CoA. The changes in kcat and Km were sufficiently large to alter the specificity ratio of the mutant human enzyme to be greater with 3-HP-CoA than HIBYL-CoA (Table 2.1). The wild- type human enzyme had a specificity ratio that suggested a preference for HIBYL-CoA, while the L174F specificity ratio indicated a preference for 3-HP-CoA.
A second series of mutations was produced to investigate the functionality of the tail region. The tail region of the S. cerevisiae enzyme was truncated, and S. cerevisiae tail was added to the human enzyme. The truncated S. cerevisiae enzyme was purified and soluble but was found to be inactive with both substrates. The human enzyme with the addition of the S. cerevisiae tail was active and demonstrated a similar kcat for both substrates (Table 2.1). Additionally, the enzyme was mutated a second time to include the L174F point mutation. The double mutant did not display a turnover ratio greater than L174F alone (Table 2.1).
The S. cerevisiae tail was not modeled because sufficiently homologous crystal structures were not available to serve as templates. Instead, the secondary structure was predicted using several different servers (Porter SS prediction [31], Jpred3 [32], and PFRMAT SS [33]) and all the predictions agreed that the tail might contain 3 helices and 2 beta-strands. Since the truncation of the full S. cerevisiae tail resulted in a soluble, but inactive enzyme, the tail region was then truncated in succession beginning at the C-terminus until the full tail was removed. The removal of only eight amino acids 492-500 resulted in a greater than 4-fold decrease in kcat for 3-HP-CoA (Table 2.3). Truncation of amino acids 472-500 produced an enzyme with a further twelve-fold decrease in kcat while the truncation of amino acids 452-500 and 432-500 yielded an enzyme that had no detectable activity despite being both stable and soluble.
2.3.5 Residues controlling hydroxyl group and carbon chain requirement
The common characteristics of HIBYL-CoA hydrolase substrates are an acyl-chain of three carbons in length and the presence of a hydroxyl group at the beta position. Based upon the docking experiments it appeared that both of these requirements could be the result of the residues at the bottom of the active site pocket. Docking results suggested that the hydroxyl group could be interacting with glutamate 124 (S. cerevisiae). Two mutants of the S. cerevisiae enzyme were generated to assess the functionality of glutamate 124. The first mutant was E124A that resulted in an enzyme that could not be purified. Repeated attempts to express this 16! ! ! enzyme resulted in cell death upon the addition of IPTG. It is possible that the enzyme was toxic to the host E. coli during induction. The second mutation, E124V, was purified. The E124V mutant had hydrolytic activity with substrates ranging in length from two to five carbons but was most active toward butyryl-CoA (Table 2.4). The kcat for acetyl-CoA was 100 fold smaller than for butyryl-CoA (Table 2.4). The kcat for the branched isobutyryl-CoA was lower than that of the straight chain, butyryl-CoA. This mutation also altered the preference for hydroxyl groups, resulting in smaller kcat values for each of the !-hydroxyl substrates compared to the non- hydroxyl substrates (Table 2.4). The E124V mutant was also evaluated for activity over a range of pH values from 5.3 to 10.5. It was determined that the pH profile of E124V was the same as that of the wild-type and F177L enzymes, with optimum activity at pH 9.0.
2.4 Discussion
The alignments of the hydrolase sequences and the overlay of the S. cerevisiae, YDR036C, model with the human crystal structure showed that position 177 is filled by a phenylalanine in S. cerevisiae, but by leucine in enzymes from other sources such as human, A. thaliana, or D. hansenii. This difference could account for the substrate specificity of the yeast enzyme. In support of this hypothesis, we found that the S. cerevisiae F177L mutant had similar kcat values for HIBYL-CoA and 3-HP-CoA as does the hydrolase from D. hansenii. In contrast, the wild type enzyme from S. cerevisiae has a much larger kcat with HP-CoA than with HIBYL-CoA. The structural model also suggests that phenylalanine may partially confine the active site for HIBYL-CoA. The human L174F mutant decreased in specific activity toward HIBYL-CoA and the yeast F177L mutant increased in specific activity toward HIBYL-CoA.
The activity of the human L174F enzyme also supports the hypothesis that phenylalanine substitution yields an enzyme with greater 3-HP-CoA activity while the native leucine enzyme is more active with HIBYL-CoA. However, the kcat /Km ratios suggest that another feature of the protein, possibly outside of the active site, could be responsible for substrate specificity. To further investigate, the yeast tail was added to the human enzyme. The resulting protein had a similar kcat for both substrates supporting the possibility that it may affect substrate specificity. Unfortunately, due to a lack of structural knowledge of the tail at this time, this specificity cannot be attributed to any specific structural changes. However it is clear from the truncation experiments that the yeast enzyme’s tail is important. These residues could interact with the CoA to stabilize the substrate for hydrolysis. Alternatively, the tail itself may not be involved in the structure of the active site pocket, but could be an important component of the tertiary structure such that its removal results in a subtle change to active site. Either role could affect the rate at which HIBYL-CoA or 3-HP-CoA is hydrolyzed.
The yeast enzymes are highly similar to the higher eukaryotic enzymes in the functional regions of the protein, so substrates were docked to both the human crystal structure and the S. cerevisiae
17! ! ! model to compare the binding of both 3-HP-CoA and HIBYL-CoA. The docking revealed several pieces of information about the potential interaction between the CoA substrates and the enzymes. The length of the acyl chain is constrained by the depth of the active site pocket and the beta-hydroxyl group can interact with the non-catalytic glutamate in the active site. Docking demonstrated that the methyl group of the HIBYL-CoA may prevent optimal binding to S. cerevisiae YDR036C, whereas the phenylalanine may select for 3-HP-CoA. Docking also clearly demonstrated that the catalytic glutamate residues are aligned with the ester bonds of the acyl-CoA substrates. This supports the suggestion that the conserved glutamate at position 121 is responsible for binding of the beta-hydroxyl group.
The docking also helped establish the specificity for three carbon substrates. Figure 2.3B depicts the active site of the S. cerevisiae model, which is not an active site groove like other members of the crotonase superfamily, but rather is a pocket. The substrate docked into the active site pocket (Figure 2.3D) reveals that the addition of carbons to the acyl-CoA carbon backbone would not allow the catalytic residues to have access to the anhydride bond for hydrolysis. Although the depth of the active site pocket prevents the hydrolysis of longer chains it does not account for the inability to hydrolyze smaller acyl-CoAs, such as propionyl-CoA or acetyl-CoA.
Both YDR036C and all other HIBYL-CoA hydrolases have an absolute requirement for the presence of a hydroxyl group at the beta carbon. The docked substrates show that the conserved glutamate at position 121 could hydrogen bond with the hydroxyl group. The point mutation of glutamate 121 to a valine resulted in an enzyme that maintains the ability to hydrolyze beta- hydroxy substrates and gained the ability to hydrolyze a broad range of acyl-CoAs. In fact, the specific activities for the hydroxylated substrates are lower than the non-hydroxyl substrates, which would be expected if the binding was less favorable. This is the first determination of the residue controlling the requirement for a beta- hydroxyl group.
In this study we have shown that the S. cerevisiae HIBYL-CoA hydrolase homolog as well as there from other yeasts have a preference toward 3-HP-CoA and that the highly conserved glutamate 124 and phenylalanine 177 play key roles in substrate specificity. Despite the knowledge gained from this study, it is still unclear what the main function of this enzyme is in yeast, but it does not seem likely to involve HIBYL-CoA. We also demonstrated that through the substitution of key residues this enzyme can be tuned to hydrolyze different substrates, which could be useful in the production of various 3-hydroxyacids, which are currently under investigation for biotechnological production as precursor chemicals.
18! ! ! 2.5 References
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20! ! ! !
Table 2.1. The kinetic parameters of the site-directed mutants of human and S. cerevisiae HIBYL-CoA hydrolases.
-1 The kcat measured in s , error is equal to the standard deviation. Km is expressed in micromolar. Uncertainty is equal to the standard deviation. ND = Not determined. (N = 3-6)
HIBYL-CoA 3-HP-CoA
-1 kcat/Km -1 kcat/Km kcat 3-HP-CoA kcat (s ) Km (µM) -1 -1 kcat (s ) Km (µM) -1 -1 (µM s ) (µM s ) % kcat HIBYL-CoA -3 -3 9.10 x 102 ± 5.54 x 10 ± 1.62 x 105 ± 2.59 x 103 ± 9.51 x 10 ± 2.72 x 105 ± S. cerevisiae 2 -3 5 3 -3 5 284 0.31 x 10 1.88 x 10 0.16 x 10 0.04 x 10 0.79 x 10 0.56 x 10 -2 -2 1.33 x 103 ± 1.46 x 10 ± 9.12 x 104 ± 1.52 x 103 ± 5.00 x 10 ± 3.04 x 104 ± S. cerevisiae F177L 114 0.04 x 103 -2 1.83 x 104 0.06 x 103 -2 0.84 x 104 21 0.24 x 10 0.76 x 10
S. cerevisiae w/o No Activity - - No Activity - - - tail -2 -2 4.75 x 105 ± 1.50 x 10 ± 3.18 x 107 ± 3.41 x 105 ± 4.13 x 10 ± 8.25 x 106 ± Human 5 -2 7 5 -2 6 72 0.26 x 10 0.47 x 10 0.56 x 10 0.10 x 10 0.50 x 10 1.92 x 10 -1 -2 4.96 x 104 ± 1.86 x 10 ± 2.67 x 105 ± 4.58 x 104 ± 4.91 x 10 ± 9.32 x 105 ± Human L174F 4 -1 5 4 -2 5 92 0.36 x 10 0.30 x 10 1.20 x 10 0.28 x 10 0.86 x 10 3.25 x 10 1.65 x 104 ± 1.63 x 104 ± Human w/ tail ND - ND - 99 0.22 x 104 0.05 x 104 Human L174F w/ 6.43 x 104 ± 6.01 x 104 ± ND - ND - 93 tail 0.17 x 104 0.47 x 104
! ! !
Table 2.2. The kcat and turnover ratio of human, A. thaliana, S. cerevisiae, S. pombe, C. albicans, and D. hansenii HIBYL-CoA hydrolases.
Error is equal to the standard deviation, N=5-6.
kcat kcat kcat 3-HP-CoA -1 -1 HIBYL-CoA (s ) 3-HP-CoA (s ) % kcat HIBYL-CoA Human 4.75 x 105 ± 0.26 x 105 3.41 x 105 ± 0.10 x 105 72
A. thaliana 5.09 x 105 ± 0.44 x 105 2.26 x 105 ± 0.11 x 105 44
S. cerevisiae 9.10 x 102 ± 0.31 x 102 2.59 x 103 ± 0.04 x 103 284
S. pombe 6.48 x 103 ± 0.30 x 103 2.77 x 104 ± 0.15 x 104 427
C. albicans 3.62 x 104 ± 0.38 x 104 1.18 x 105 ± 0.94 x 105 326
D. hansenii 2.71 x 104 ± 0.33 x 104 2.32 x 104 ± 0.25 x 104 86
! 22 ! !
Table 2.3: The kcat of S. cerevisiae wild-type and truncated HIBYL-CoA hydrolases.
Error is equal to the standard deviation. (N ! 5).
-1 -1 S. cerevisiae kcat HIBYL-CoA (s ) kcat 3-HP-CoA (s )
Truncation 416 No Activity No Activity
Truncation 432 No Activity No Activity
Truncation 452 No Activity No Activity
Truncation 472 1.16 x 101 ± 0.13 x 101 4.84 x 101 ± 0.07 x 101
Truncation 492 2.03 x 102 ± 0.49 x 102 6.03 x 102 ± 0.18 x 102
Full Length 9.10 x 102 ± 0.31 x 102 2.59 x 103 ± 0.04 x 103
! 23 !
2 3 2 4 3 4 2 3
) x 10 x 10 1 x 10 x 10 x 10 x 10 x 10 x 10
-
8 42 ± 0.64 ± 0.10 ± ± 0.67 ± 0.0 ± 0.18 ± 0.28 ± 0. ± 0.71 ±
2 4 3 4 2 3 2 3 E124V (s
x 10 x 10 x 10 x 10 x 10 x 10 cat cat x 10 x 10
k 9 5
9 .71 . 2.73 1 1.74 3.6 5.63 1.27 5.60 5.
3 2
) 1 - CoA hydrolase - x 10 x 10
type (s type - ± 0.04 ± 0.31 ±
3 2 of HIBYL
wild
No Activity No Activity No Activity No Activity No Activity No Activity
x 10 x 10
cat k ! 2.59 9.10 mutant
24
5)
! N type and the glutamate 124 glutamate the and type ( - wild
CoA CoA
-
-
CoA
S. cerevisiae S. cerevisiae - of CoA CoA
- - CoA CoA CoA - - cat - Acetyl . The k . The Valeryl Butyryl Propionyl Isobutyryl Hydroxybutryl - Hydroxypropionyl 3 Hydroxyisobutyryl - - 3 3 Table 2.4 Table deviation. standard the to is equal Error ! !
!
! 24 !
Figure 2.1 The proposed mechanism of 3-HP-CoA hydrolysis based on the mechanism demonstrated for Pseudomonas HIBYL-CoA hydrolase [1].
HIBYL-CoA HIBA
25! ! ! !
Figure 2.2 The clustal alignment of HIBYL-CoA hydrolases from A. thaliana (At) and H. sapiens (Hs) with YDR036C from S. pombe (Sp), C. albicans (Ca), D. hansenii (Dh), S. cerevisiae (Sc), C. glabrata (Cg), and K. lactis (Kl).
At MAVEMASQSQVLVEEKSSVRILTLNRPKQLNALSFHMI 38 Hs MGQREMWRLMSRFNAFKRTNTILHHLRMSKHTDAAEEVLLEKKGCTGVITLNRPKFLNALTLNMI 65 Sp MGLKLNISNDLKKSGFMLRQSLLKTSVSNFLSLNASSTMSRAFIRNPKFYSTSSNDTVLYESKNGARIFTLNRPKVLNAINVDMI 85 Ca MLRLNNSISLLKQVRKIATTSINMSSKLSTNHTSGGEEPVVLSSVKNHARLITLNRVKKLNSLNTEMI 68 Dh MLKANLKKVISNNKFNTQLTKMTSNYSTGSNIIGYAEDDVLFSNKNMARLVTLNRPKKLNSLNTSMV 67 Sc MLRNTLKCAQLSSKYGFKTTTRTFMTTQPQLNVTDAPPVLFTVQDTARVITLNRPKKLNALNAEMS 66 Cg MLRAPAAGFPRLIQKTSYRAFSSTLAKMSESETPVLFSVQETARIVTLNRPKKLNALNEEMC 62 Kl MLRHSYCRAQQQSLRHVLKTRLAVNQLRFMSEVKFRVDSTARVVTLDRPKKLNALDVEMC 60
† * † At SRLLQLFLAFEEDPSVKLVILKGHG--RAFCAGGDVAAVVRDINQGNWRLGANYFSSEYMLNYVMATYSKAQVSILNGIVMGGGA 121 Hs RQIYPQLKKWEQDPETFLIIIKGAGG-KAFCAGGDIR-VISEAEKAKQKIAPVFFREEYMLNNAVGSCQKPYVALIHGITMGGGV 148 Sp DSILPKLVSLEESNLAKVIILKGNG--RSFSSGGDIKAAALSIQDGKLPEVRHAFAQEYRLSHTLATYQKPVVALMNGITMGGGS 168 Ca ELMTPPILEYAKSKENNVIILTSN-SPKALCAGGDVAECAVQIRKGNPGYGADFFDKEYNLNYIISTLPKPYISLMDGITFGGGV 152 Dh SKIMPRLLEYSKSSVNNVIILNST-LAKGLCAGGDVTECAKQIKAGNAAYASDFFQREYNLNYLISTYPKPYVALMDGITMGGGV 151 Sc ESMFKTLNEYAKSDTTNLVILKSSNRPRSFCAGGDVATVAIFNFNKEFAKSIKFFTDEYSLNFQIATYLKPIVTFMDGITMGGGV 151 Cg SSIFNTLTEYSKSDAANLILIKSNNSPRSLCAGGDVASVAQSNLDKNFESSINCFKSEYSLNFQLATYQKPVVVFMDGITMGGGV 147 Kl SAILPTLQEYAKSTVNNVVILNSSASPRAFCSGGDVAQVAKLVKEGNFDYAREFFTKEYSLNLALATLNKPVISIMDGITMGGGV 145
! ‡ ! At GVSVHGRFRIATENTVFAMPETALGLFPDVGASYFLSRLP------GFFGEYVGLTGARLDGAEMLACGLATHFVPSTRLTALEA 200 Hs GLSVHGQFRVATEKCLFAMPETAIGLFPDVGGGYFLPRLQ------GKLGYFLALTGFRLKGRDVYRAGIATHFVDSEKLAMLEE 227 Sp GLAMHVPFRIACEDTMFAMPETGIGYFTDVAASFFFSRLP------GYFGTYLGLTSQIVKGYDCLRTGIATHFVPKHMFPHLED 247 Ca GLSVHAPFRVATEKTKLAMPEMDIGFFPDVGTTFFLPRLN------DKLGYYVALTGSVLPGLDAYFAGFATHYIKSEKIPQLIN 231 Dh GLSVHAPFRVSTERTKLAMPETDIGLFPDVGTTFFLPRLD------DKIGYYLALTGQVLSGLDCYMLGFATHYVPSDRIDSLVN 230 Sc GLSIHTPFRIATENTKWAMPEMDIGFFPDVGSTFALPRIVTLANSNSQMALYLCLTGEVVTGADAYMLGLASHYVSSENLDALQK 236 Cg GLSIHTPFRIATENTKWAMPETDIGFFPDVGTTFALPRLITLANKNAQMALYLCLTGDVISGEDAYLLGLASHYIPHSNLEKLQT 232 Kl GLSTHIPFRIATENTRWAMPEMDIGFFPDVGATFSIPKLTTVGGSNGQLAQYLCMTGDILNGADAYVAGVASHYVPHDQISNLQA 230
At DLCRINSND------PTFASTILDAYTQHPRLKQQSAYR---RLDVIDRCFSRRT---VEEIISALEREAT 259 Hs DLLALKSPS------KENIASVLENYHTESKIDRDKSFILEEHMDKINSCFSANT---VEEIIENLQ---- 285 Sp RLAELNTSD------ISKINNTILEFAEFASSSPPTFTP--DVMDVINKCFCKND---TVDIIRALKEYAS 307 Ca RLADLQPPAIEDD------ITVLSGNNQYFNQVNDILNDFSEKKLPEDYKFFLSTEDIATINKAFSQDT---IDDVLKYLE---- 303 Dh RLSNLQPPSVNDNKPEDNHASILNNNKEYYAQVNQAIEEFTENKLPEDYKYPFTTEQLKLIKNAFSQPS---IEEVLSYLE---- 308 Sc RLGEISPPFNNDPQS------AYFFGMVNESIDEFVSP-LPKDYVFKYSNEKLNVIEACFNLSKNGTIEDIMNNLRQYEG 309 Cg RLGELRPALDIKFFS------DEFFDSVNLAIEEFTTP-LPTNHKFKFSKDQLEVIEKCFDISSGESINAIFSKLEAFEG 305 Kl RLAELHLTEATSQSTN------RDDEIFDVVNHAIEEFNAP-LPRDYKFKYTADELNVIEQCFDIGN—-SLKQIYSKLDEVIA 304
At -----QEADGWISATIQALKKGSPASLKISLRSIREGRLQGVGQCLIREYRMVCHVMKGEI-SKDFVEGCRAILVDKDKN---PK 335 Hs -----QDGSSFALEQLKVINKMSPTSLKITLRQLMEGSSKTLQEVLTMEYRLSQACMRG----HDFHEGVRAVLIDKDQS---PK 358 Sp N---TSALAEFAKSTVKTLYSKSPTSIAVTNRLIKSAAKWSISEAFYYDHIVSYYMLKQ----PDFVEGVNAQLITKTKN---PK 382 Ca -----NDGSPFARKTLETLLKKPKSSLAVGFELMNHGAKNSIKKQFELEMVSATNIMSIPAEKNDFAKGVIHKLVDKIKDPFFPK 383 Dh -----KDGSEFAQKTYKTLLLKSPTSLKVAFELLNRGAENSIRQQFELEMITATNLVNIKPEENDFVKGVSHKLIDKIKEPAYPE 388 Sc ----SAEGKAFAQEIKTKLLTKSPSSLQIALRLVQENSRDHIESAIKRDLYTAANMCMNQDSLVEFSEATKHKLIDKQRV---PY 387 Cg ----TPEMMQFARDTKKKLESKSMTSMQVGIRLMQENSRDDIESALKRDLTTAVNMCVNDSGIAEFSAATKHKLLDKQKV---PY 383 Kl GKTVSQTAQEFAAKTKQMLASKSPVSLEIAKELFQRNSFTDIQTALTQDLITATKMSESPD-LCEFAEATSHKLLEKNKT---PY 385
At -WEPRRLEDMKDSMVEQYFERVEREDDLKLPPRNNLPALGIAKL 378 Hs -WKPADLKEVTEEDLNNHFKSLG-SSDLKF 386 Sp -WS--KSHEYHFKDLENYFKLPSEYNNGISFAAKGRRKTPLWNYKTYPYL 429 Ca -WS---DPSTVTQQFLSNILSTSKNTDKYLKTPFIKKWFG-VDFEDYPHQM--GLPTNKQVADYISGSDGSNRTYLPTPAEVFKH 460 Dh -WNSNKQPSGISSEFVQKALSKSIHSTK-LNEPLIEKLFG-INYKSYPYNM--GLPNGNQVKSYITGNDGSGRSYLPTPTEVTKY 468 Sc PWT------KKEQLFVSQLTSITSPKPSLPMSLLRNTSNVTWTQYPYHSKYQLPTEQEIAAYIEKRTNDDTGAKVTEREVLNH 464 Cg PWK------QRTELTPQQVTSLIAPKPSLPVSLIRNNSNVTWSQYPHSLKYQLPRDYEIEQQVEKLIKRGP---IKKNDVVKY 457 Kl QWK------IKDLKLAQISVLISQNSSNPVSLIRPSNLVTFSEYPHHSKYQLPNETLVEKYITGADNHGRQTAVTKKEAVKF 461
At Hs Sp Ca FKQKTNN---KLGVDEKIKQILDLHGETAKYDHKYVTWKEEPTK 502 Dh FKQSTSN---KLGVELKVQSILDHHGEASKYDNKYVSWIE 505 Sc FANVIPSRRGKLGIQSLCKIVCERK--CEEVNDG-LRWK 500 Cg FTDFNPQTKAKLGVEQYCDLLFDWKLSFDHA-SG-LRWKK 495 Kl FQQLNPATKSKTGVDYLVGFIIDRK--CVPNPDGFLRWKTSSAKL 504
Basic residues indicating mitochondrial sequence and peroxisomal (AKL) targeting sequences are highlighted in gray. Conserved residues and highly similar residues are highlighted in black or orange. The catalytic residues are colored blue. The residues involved in the oxyanion hole are denoted by a dagger (†), the residues known to catalyze hydrolysis are denoted by an arrow (!), the glutamate that were mutated is denoted by a star (*) and the phenylalanine/leucine that was mutates is denoted by a double dagger (‡). 26! ! ! !
Figure 2.3 The modeled structure of S. cerevisiae hydrolase YDR036C.
A: The surface rendering of S. cerevisiae model YDR036C with the conserved regions of the protein designated in orange and the N-terminus in red. The residues that participate in the oxyanion hole are fuchsia and the active site residue phenylalanine is colored in blue. B: The S. cerevisiae model is rotated 90 degrees clockwise and is slabbed to show the active site pocket. C: The active site of the model is shown with the 3 acidic active site residues shown in stick representation and blue, glutamate 172, aspartate 180, and glutamate 124 from left to right. Phenylalanine 177 and the human equivalent leucine 174 are displayed in blue and cyan respectively. D: The docking of HIBYL-CoA into the model by AutoDock4. HIBYL-CoA is colored by element and predicted hydrogen bonds are colored in yellow.
27! ! ! !
Figure 2.4 The Michaelis-Menten kinetic graphs of human and S. cerevisae HIBYL-CoA hydrolases.
Human (WT) Human (L174F)
250 400 d d
n 200 umoles CoA/sec HIBYL (WT) n o o
c c 300
e umoles CoA/sec HP (WT) e umoles CoA/sec HIBYL (L174F) s s / 150 /
A A umoles CoA/sec HP (L174F)
o o 200 C C
s 100 s e e l l
o o 100
m 50 m u u
0 0 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.1 0.2 0.3 0.4 0.5 umoles Substrate umoles Substrate
S. cerevisiae (WT) S. cerevisiae (F177L)
100 40 d d n n 80 o o c c 30 e e umoles CoA/sec HP (WT) umoles CoA/sec HP (F177L) s s / / 60 umoles CoA/sec HIBYL (WT) A A umoles CoA/sec HIBYL (F177L) o o 20 C C
s s 40 e e l l o o 10 m m 20 u u
0 0 0.0 0.1 0.2 0.3 0.0 0.1 0.2 0.3 umoles Substrate umoles Substrate
28! ! ! !
Chapter 3: Phosphorylation of HIBYL-CoA Hydrolase
3.1 Introduction
3.1.1 HIBYL-CoA hydrolase regulation
Genetic defects in the HIBYL-CoA hydrolase gene of higher eukaryotes may result in low abundance or the generation of a dysfunctional protein, both of which represent a hazard to cellular health. To date, no specific mechanisms are known for the regulation of the valine catabolism, although regulatory mechanisms for metabolism of the group of branched chain amino acids are known [1]. The best characterized event in the regulation is the phosphorylation of branched chain amino acid dehydrogenase (BCKDH). BCKDH performs the second step in the degradation of the branched chain amino acids (Figure 3.1). Upon phosphorylation BCKDH is rendered catalytically inactivate, effectively preventing entrance of the branched chain amino acids to the degradation pathway [1].
3.1.2 Mitochondrial regulation by phosphorylation
Recent discoveries of kinases, phosphatases, and phospho-proteins in the mitochondria suggest that mitochondrial processes might be regulated by phosphorylation similar to processes within other areas of the cell [2, 3]. The growing interest in the phosphorylation of mitochondrial proteins can be seen by the increasing numbers of research groups generating phospho- proteomes of S. cerevisiae. High throughput studies have identified several proteins that are phosphorylated in mitochondria, including YDR036C [4].
3.1.3 Determination of phosphorylation state
The following work was performed to assess the possibility that the activity of HIBYL-CoA hydrolase or the yeast analog YDR036C can be affected by the phosphorylation state of the enzyme. The human and S. cerevisiae enzymes were mutated to mimic phosphorylation. Activation and deactivation were assessed in relationship to the phosphorylation mimics.
3.2 Materials and methods
3.2.1 Cloning and mutagenesis
Overlapping PCR was utilized for the construction of the site directed mutants. In brief, the gene cDNAs were amplified twice, once with mutagenic primers and second time with full length primers. The first reactions created a fragment from the 5’ end to the mutation and from the mutation to the 3’ end. The gel-purified fragments were used in a second PCR reaction at a ratio of 4:1 with the native primers to generate the fully mutated gene. The following primers were used in the mutagenic amplifications (with mutated sites in capital letters.) 29! ! ! !
• S. cerevisiae S328A: ttaaccaagGcaccatcctc and gaggatggtgCcttggttaa • S. cerevisiae S324E: ttaaccaagGAaccatcctc and gaggatggtTCcttggttaa • H. sapiens S303A: 5phos- attaataaaatgGctccaacatctcta and atgttggagCcatttta • H. sapiens S303E: 5phos- attaataaaatgGAAccaacatctcta and atgttggTTCcatttta
3.2.2 Assay of Hydrolase Activity
Assays were performed at 37 ºC in a total volume of 1 mL containing 0.1 M Tris-HCl, pH 8.0, and 1 mM 5,5’-dithio-bis(2-nitrobenezoic acid) (DTNB). The reaction was initiated by the addition of the enzyme to the buffer-containing substrate. The reaction was monitored by following the reaction of DTNB with the liberated thiol at 412 nm [6, 9, 16] with a Varian-Cary
E1 UV-visible spectrophotometer equipped with a temperature controlled water jacket. Km and kcat were determined using Graphpad Prism program version 5 (La Jolla, CA).
3.3 Results and Discussion
3.3.1 Sequence alignment of HIBYL-CoA hydrolases
High throughput studies revealed that YDR036C is phosphorylated in S. cerevisiae mitochondria [4]. The method for detecting phosphorylated proteins also gives additional information including the fragment of the protein that was modified. The MS-MS technique showed the phosphate was present on either the serine at position 328 or the threonine at position 331. Manual inspection of the MS fragmentation pattern did not clearly indicate which of these residues was phophorylated. Knowing that either of these residues could be phosphorylated the sequence was aligned to HIBYL-CoA hydrolases from several other eukaryotes (Figure 3.2). The alignment showed that the area around these residues was highly conserved. The serine residue of interest was present in all species examined except C. albicans, while the threonine was present in only one of the eight hydrolases. Two pieces of software were used to identify probable phosphorylation sites and both agreed that the S328 was the stronger candidate with probability scores of 0.865 and 0.943, whereas T326 received scores of 0.746 and 0.565 with NetPhos [9] and NetPhosYeast, [10] respectively. For these reasons serine 328 was chosen for mutagenesis.
3.3.2 Phosphorylation mimics
The serine to alanine (S328A) substiutuion in YDR036C did not result in a change in activity (Table 3.1), suggesting that the enzyme is active in the absence of phosphorylation at S328. To mimic phosphorylation the serine was then mutated to glutamate. The enzyme was inactive; repeated purifications yielded soluble protein that was inactive. Taken together, these results suggest that phosphorylation of HIBYL-CoA hydrolase at S328 results in a catalytically inactivated enzyme while the non-phosphorylated enzyme is the active form. Because of the high 30! ! ! ! degree of similarity between S. cerevisiae and human this process was repeated with the human HIBYL-CoA hydrolase. The human S303 mutants exhibited similar activity patterns (Table 3.1).
The serine appears to be accessible and at the exterior of the protein, as shown in yellow ribbon (Figure 3.3A,B). It is positioned adjacent to the conserved active site. Distance measurements in the structures show the hydroxyl group of serine is less than 5Å from the peptide backbone of two amino acids and within the alpha helix of the catalytic glutamate. Therefore, it is possible that the addition of phosphate to serine 328 may shift the positioning of the glutamate sufficiently to prevent catalysis.
3.3.3 Future work
The presented results in this chapter suggest that HIBYL-CoA hydrolases and the homologous enzymes in yeasts are activated and deactivated by phosphorylation. Additional indirect support for a role for phosphorylation in the regulation of HIBYL-CoA hydrolase in humans is provided by the observation that in liver disease, HIBYL-CoA hydrolase activity is down regulated to only 46% that of normal livers, but expression of the hydrolase did not decrease [11]. An important question raised by these preliminary findings is under what condition(s) is this enzyme phosphorylated. Since methacyryl-CoA represents a toxic substance to the cell, under what condition(s) would inactivation of HIBYL-CoA hydrolase and accumulation of methacyryl-CoA be acceptable?
The kinase(s) and phosphatase(s) that would be required to phosphorylate/dephosphorylate HIBYL-CoA hydrolase are unknown. The discovery of the kinase(s) could give some insight into the conditions in which the enzyme is deactivated or indicate if HIBYL-CoA hydrolase is a member of a signaling cascade.
A few key experiments have provided support for the hypothesis that the S. cerevisiae HIBYL- CoA hydrolase is phosphorylated, and that the likely phosphorylation residue is the serine present at position 328. Homology comparisons show that this residue is highly conserved and inspection of the crystal structure demonstrates that changes at this serine could influence the catalytic glutamate. Furthermore, mutations at position 328 demonstrate that a phosphorylation mimic has no activity with either HIBYL-CoA or 3-HP-CoA. This was also demonstrated to be the case with serine 303 in the human homologue. These data suggest that HIBYL-CoA hydrolases can be deactivated by phosphorylation. In humans and other higher eukaryotes, phosphorylation/dephosphorylation may provide specific regulation of valine catabolism. Since the role of this hydrolase in yeast is unknown, the significance of this putative regulation is unclear.
31! ! ! !
3.4 References
[1] Y. Shimomura, T. Murakami, N. Nakai, M. Nagasaki, R.A. Harris, J. Nutr. 134 (2004) 1583S-1587.
[2] D.J. Pagliarini, S.E. Wiley, M.E. Kimple, J.R. Dixon, P. Kelly, C.A. Worby, P.J. Casey, J.E. Dixon, Mol. Cell 19 (2005) 197-207.
[3] D.J. Pagliarini and J.E. Dixon, Trends Biochem. Sci. 31 (2006) 26-34.
[4] J. Reinders, K. Wagner, R.P. Zahedi, D. Stojanovski, B. Eyrich, M. van der Laan, P. Rehling, A. Sickmann, N. Pfanner, C. Meisinger, Mol. Cell. Prot. 6 (2007) 1896-1906.
[5] G.K. Brown, S.M. Hunt, R. Scholem, K. Fowler, A. Grimes, J.F. Mercer, R.M. Truscott, R.G. Cotton, J.G. Rogers, D.M. Danks, Pediatrics 70 (1982) 532-538.
[6] J.W. Hawes, J. Jaskiewicz, Y. Shimomura, B. Huang, J. Bunting, E.T. Harper, R.A. Harris, J. Biol. Chem. 271 (1996) 26430-26434.
[7] Y. Shimomura, T. Murakami, N. Fujitsuka, N. Nakai, Y. Sato, S. Sugiyama, N. Shimomura, J. Irwin, J.W. Hawes, R.A. Harris, J. Biol. Chem. 269 (1994) 14248-14253.
[8] J. Reinders, K. Wagner, R.P. Zahedi, D. Stojanovski, B. Eyrich, M. van der Laan, P. Rehling, A. Sickmann, N. Pfanner, C. Meisinger, Mol. Cell. Prot. 6 (2007) 1896-1906.
[9] N. Blom, S. Gammeltoft, S. Brunak, J. Mol. Biol. 294 (1999) 1351-1362.
[10] C.R. Ingrell, M.L. Miller, O.N. Jensen, N. Blom, Bioinformatics 23 (2007) 895-897.
[11] K. Ishigure, Y. Shimomura, T. Murakami, T. Kaneko, S. Takeda, S. Inoue, S. Nomoto, K. Koshikawa, T. Nonami, A. Nakao, Clin. Chim. Acta 312 (2001) 115-121.
32! ! ! !
Figure 3.1 Catabolic pathways of the branched chain amino acids.
1 2
3
1: Branched Chain Amino Acid Aminotransferase 2: Branched Chain Amino Dehydrogenase 3: Acyl-CoA Dehydrogenase 4: Enoyl-CoA Hydratase 5: Beta-hydroxyacyl-CoA Dehydrogenase 6: Acyl-CoA Acetyltransferase 7: Enoyl-CoA Hydratase 4 7 11 8: Beta-hydroxyisobutyryl-CoA Hydrolase 9: Beta-hydroxyisobuterate Dehydrogenase 10: Methylmalonate Semialdehyde Dehydrogenase 11: Beta-methylcrotonyl-CoA Carboxylase 12: Beta-methylglutaconyl-CoA Hydratase 13: HMG-CoA Lyase 5 8 12
6 9 13
10
!
33! ! ! !
Figure 3.2 The clustalw alignment of HIBYL-CoA hydrolases from A. thaliana (At) and H. sapiens (Hs) with YDR036C from S. pombe (Sp), C. albicans (Ca), D. hansenii (Dh), S. cerevisiae (Sc), C. glabrata (Cg), and K. lactis (Kl).
At MAVEMASQSQVLVEEKSSVRILTLNRPKQLNALSFHMI 38 Hs MGQREMWRLMSRFNAFKRTNTILHHLRMSKHTDAAEEVLLEKKGCTGVITLNRPKFLNALTLNMI 65 Sp MGLKLNISNDLKKSGFMLRQSLLKTSVSNFLSLNASSTMSRAFIRNPKFYSTSSNDTVLYESKNGARIFTLNRPKVLNAINVDMI 85 Ca MLRLNNSISLLKQVRKIATTSINMSSKLSTNHTSGGEEPVVLSSVKNHARLITLNRVKKLNSLNTEMI 68 Dh MLKANLKKVISNNKFNTQLTKMTSNYSTGSNIIGYAEDDVLFSNKNMARLVTLNRPKKLNSLNTSMV 67 Sc MLRNTLKCAQLSSKYGFKTTTRTFMTTQPQLNVTDAPPVLFTVQDTARVITLNRPKKLNALNAEMS 66 Cg MLRAPAAGFPRLIQKTSYRAFSSTLAKMSESETPVLFSVQETARIVTLNRPKKLNALNEEMC 62 Kl MLRHSYCRAQQQSLRHVLKTRLAVNQLRFMSEVKFRVDSTARVVTLDRPKKLNALDVEMC 60
! At SRLLQLFLAFEEDPSVKLVILKGHG--RAFCAGGDVAAVVRDINQGNWRLGANYFSSEYMLNYVMATYSKAQVSILNGIVMGGGA 121 Hs RQIYPQLKKWEQDPETFLIIIKGAGG-KAFCAGGDIR-VISEAEKAKQKIAPVFFREEYMLNNAVGSCQKPYVALIHGITMGGGV 148 Sp DSILPKLVSLEESNLAKVIILKGNG--RSFSSGGDIKAAALSIQDGKLPEVRHAFAQEYRLSHTLATYQKPVVALMNGITMGGGS 168 Ca ELMTPPILEYAKSKENNVIILTSN-SPKALCAGGDVAECAVQIRKGNPGYGADFFDKEYNLNYIISTLPKPYISLMDGITFGGGV 152 Dh SKIMPRLLEYSKSSVNNVIILNST-LAKGLCAGGDVTECAKQIKAGNAAYASDFFQREYNLNYLISTYPKPYVALMDGITMGGGV 151 Sc ESMFKTLNEYAKSDTTNLVILKSSNRPRSFCAGGDVATVAIFNFNKEFAKSIKFFTDEYSLNFQIATYLKPIVTFMDGITMGGGV 151 Cg SSIFNTLTEYSKSDAANLILIKSNNSPRSLCAGGDVASVAQSNLDKNFESSINCFKSEYSLNFQLATYQKPVVVFMDGITMGGGV 147 Kl SAILPTLQEYAKSTVNNVVILNSSASPRAFCSGGDVAQVAKLVKEGNFDYAREFFTKEYSLNLALATLNKPVISIMDGITMGGGV 145
! ! At GVSVHGRFRIATENTVFAMPETALGLFPDVGASYFLSRLP------GFFGEYVGLTGARLDGAEMLACGLATHFVPSTRLTALEA 200 Hs GLSVHGQFRVATEKCLFAMPETAIGLFPDVGGGYFLPRLQ------GKLGYFLALTGFRLKGRDVYRAGIATHFVDSEKLAMLEE 227 Sp GLAMHVPFRIACEDTMFAMPETGIGYFTDVAASFFFSRLP------GYFGTYLGLTSQIVKGYDCLRTGIATHFVPKHMFPHLED 247 Ca GLSVHAPFRVATEKTKLAMPEMDIGFFPDVGTTFFLPRLN------DKLGYYVALTGSVLPGLDAYFAGFATHYIKSEKIPQLIN 231 Dh GLSVHAPFRVSTERTKLAMPETDIGLFPDVGTTFFLPRLD------DKIGYYLALTGQVLSGLDCYMLGFATHYVPSDRIDSLVN 230 Sc GLSIHTPFRIATENTKWAMPEMDIGFFPDVGSTFALPRIVTLANSNSQMALYLCLTGEVVTGADAYMLGLASHYVSSENLDALQK 236 Cg GLSIHTPFRIATENTKWAMPETDIGFFPDVGTTFALPRLITLANKNAQMALYLCLTGDVISGEDAYLLGLASHYIPHSNLEKLQT 232 Kl GLSTHIPFRIATENTRWAMPEMDIGFFPDVGATFSIPKLTTVGGSNGQLAQYLCMTGDILNGADAYVAGVASHYVPHDQISNLQA 230
At DLCRINSND------PTFASTILDAYTQHPRLKQQSAYR---RLDVIDRCFSRRT---VEEIISALEREAT 259 Hs DLLALKSPS------KENIASVLENYHTESKIDRDKSFILEEHMDKINSCFSANT---VEEIIENLQ---- 285 Sp RLAELNTSD------ISKINNTILEFAEFASSSPPTFTP--DVMDVINKCFCKND---TVDIIRALKEYAS 307 Ca RLADLQPPAIEDD------ITVLSGNNQYFNQVNDILNDFSEKKLPEDYKFFLSTEDIATINKAFSQDT---IDDVLKYLE---- 303 Dh RLSNLQPPSVNDNKPEDNHASILNNNKEYYAQVNQAIEEFTENKLPEDYKYPFTTEQLKLIKNAFSQPS---IEEVLSYLE---- 308 Sc RLGEISPPFNNDPQS------AYFFGMVNESIDEFVSP-LPKDYVFKYSNEKLNVIEACFNLSKNGTIEDIMNNLRQYEG 309 Cg RLGELRPALDIKFFS------DEFFDSVNLAIEEFTTP-LPTNHKFKFSKDQLEVIEKCFDISSGESINAIFSKLEAFEG 305 Kl RLAELHLTEATSQSTN------RDDEIFDVVNHAIEEFNAP-LPRDYKFKYTADELNVIEQCFDIGN—-SLKQIYSKLDEVIA 304
* At -----QEADGWISATIQALKKGSPASLKISLRSIREGRLQGVGQCLIREYRMVCHVMKGEI-SKDFVEGCRAILVDKDKN---PK 335 Hs -----QDGSSFALEQLKVINKMSPTSLKITLRQLMEGSSKTLQEVLTMEYRLSQACMRG----HDFHEGVRAVLIDKDQS---PK 358 Sp N---TSALAEFAKSTVKTLYSKSPTSIAVTNRLIKSAAKWSISEAFYYDHIVSYYMLKQ----PDFVEGVNAQLITKTKN---PK 382 Ca -----NDGSPFARKTLETLLKKPKSSLAVGFELMNHGAKNSIKKQFELEMVSATNIMSIPAEKNDFAKGVIHKLVDKIKDPFFPK 383 Dh -----KDGSEFAQKTYKTLLLKSPTSLKVAFELLNRGAENSIRQQFELEMITATNLVNIKPEENDFVKGVSHKLIDKIKEPAYPE 388 Sc ----SAEGKAFAQEIKTKLLTKSPSSLQIALRLVQENSRDHIESAIKRDLYTAANMCMNQDSLVEFSEATKHKLIDKQRV---PY 387 Cg ----TPEMMQFARDTKKKLESKSMTSMQVGIRLMQENSRDDIESALKRDLTTAVNMCVNDSGIAEFSAATKHKLLDKQKV---PY 383 Kl GKTVSQTAQEFAAKTKQMLASKSPVSLEIAKELFQRNSFTDIQTALTQDLITATKMSESPD-LCEFAEATSHKLLEKNKT---PY 385
At -WEPRRLEDMKDSMVEQYFERVEREDDLKLPPRNNLPALGIAKL 378 Hs -WKPADLKEVTEEDLNNHFKSLG-SSDLKF 386 Sp -WS--KSHEYHFKDLENYFKLPSEYNNGISFAAKGRRKTPLWNYKTYPYL 429 Ca -WS---DPSTVTQQFLSNILSTSKNTDKYLKTPFIKKWFG-VDFEDYPHQM--GLPTNKQVADYISGSDGSNRTYLPTPAEVFKH 460 Dh -WNSNKQPSGISSEFVQKALSKSIHSTK-LNEPLIEKLFG-INYKSYPYNM--GLPNGNQVKSYITGNDGSGRSYLPTPTEVTKY 468 Sc PWT------KKEQLFVSQLTSITSPKPSLPMSLLRNTSNVTWTQYPYHSKYQLPTEQEIAAYIEKRTNDDTGAKVTEREVLNH 464 Cg PWK------QRTELTPQQVTSLIAPKPSLPVSLIRNNSNVTWSQYPHSLKYQLPRDYEIEQQVEKLIKRGP---IKKNDVVKY 457 Kl QWK------IKDLKLAQISVLISQNSSNPVSLIRPSNLVTFSEYPHHSKYQLPNETLVEKYITGADNHGRQTAVTKKEAVKF 461
At Hs Sp Ca FKQKTNN---KLGVDEKIKQILDLHGETAKYDHKYVTWKEEPTK 502 Dh FKQSTSN---KLGVELKVQSILDHHGEASKYDNKYVSWIE 505 Sc FANVIPSRRGKLGIQSLCKIVCERK--CEEVNDG-LRWK 500 Cg FTDFNPQTKAKLGVEQYCDLLFDWKLSFDHA-SG-LRWKK 495 Kl FQQLNPATKSKTGVDYLVGFIIDRK--CVPNPDGFLRWKTSSAKL 504
Basic residues indicating a mitochondrial leader sequence and peroxisomal (AKL) targeting sequences are highlighted in gray. Conserved residues and highly similar residues are highlighted in black. The residues involved in the catalysis are denoted by an arrow (!) and the residue that was mutated are denoted by a star (*).
34! ! ! !
Figure 3.3 Structure of HIBYL-CoA hydrolase.
A. The model of YDR036C is represented in ribbon structure and colored by secondary structure. Blue color represents beta sheets and red represents alpha helixes. The active site residues are represented in green and the phosphorylation site is shown in yellow ribbon with the serine and threonine R-groups depicted in gray stick form.
35! ! ! !
B. The model of YDR036C detailing the phosphorylation site and the proximity to the alpha helix of the active site. The pink dotted line represents the distance from the hydroxyl group of the serine to the amide of the peptide backbone.
36! ! ! !
Table 3.1 The kcat of the human and S. cerevisiae wild-type and mutant hydrolases.
-1 The kcat of the human and S. cerevisiae wild-type and mutant hydrolases. kcat measure in s . Error is equal to the standard deviation (N=5-6).
kcat HIBYL-CoA kcat 3-HP-CoA
Human 2.56 x 103 ± 0.16 1.85 x 103 ± 0.05
Human S303A 2.28 x 103 ± 0.16 1.96 x 103 ± 0.16
Human S303E No Activity No Activity
S. cerevisiae 2.46 x 102 ± 0.06 7.56 x 102 ± 0.30
S. cerevisiae S328A 2.20 x 102 ± 0.15 6.82 x 102 ± 0.42
S. cerevisiae S328E No Activity No Activity
37! ! ! !
Chapter 4: Potential role of YDR036C in regulating ergosterol metabolism
4.1 Introduction
4.1.1 YDR036C homology to valine hydrolase
Our initial investigation of S. cerevisiae YDR036C was stimulated by its homology to HIBYL- CoA hydrolases found in higher eukaryotes. HIBYL-CoA hydrolase catalyzes an important step in the degradation of valine. After deamination, branched chain amino acids form CoA esters. In the leucine and isoleucine branches of the pathway, all the intermediates are CoA esters. However, the CoA ester bond of valine is hydrolyzed and reformed by HIBYL-CoA hydrolase before the completion of degradation. While this process appears to be energy expensive and wasteful, it actually uses the irreversible hydrolysis as a one-way valve to prevent the buildup of a toxic intermediate, methacrylyl-CoA [1]. While the purpose of the hydrolase is clear in higher eukaryotes, yeast do not perform this type of valine degradation and lack several of the enzymes required to produce this CoA intermediate [2]. Yeast branched chain amino acid degradation uses the Ehrlich pathway to generate fusel alcohol end products. Yeast do not produce HIBYL-CoA during valine metabolism, but they do possess a protein homologous to HIBYL-CoA hydrolase. The biological function of this enzyme is unknown.
4.1.2 Hydrolase activity
The yeast hydrolase does not participate in valine degradation, but can hydrolyze HIBYL-CoA and 3-HP-CoA, although with lower catalytic efficiency than its homologs from higher eukaryotes (Chapter 2, this dissertation). An alternative pathway that could use the hydrolase is beta- oxidation of fatty acids. The HIBYL-CoA hydrolases belong to the crotonase super-family, which includes several enzymes utilized for fatty acid degradation. Hitlunin et al. [3] initially investigated the yeast enzyme for its role in beta-oxidation, and determined that it could not function in that capacity for two reasons. First, it was not active with the substrates of beta- oxidation and second, it was located within mitochondria like its mammalian counterparts, but beta- oxidation is strictly peroxisomal in yeast [4-6]. The conservation of this enzyme throughout yeast genomes suggests its importance, but its hydrolytic activity does not point to a clear metabolic role. We hypothesized that investigating the structure of the enzyme might reveal other possible functions for the protein in yeast.
4.1.3 Homology modeling
No structural information is available for the S. cerevisiae hydrolase, but the human homolog has been crystallized (3BPT). The yeast enzyme and the human enzyme are 34% identical, with the greatest similarity occuring within the active site and CoA binding regions. Of particular interest was the co- crystallization of the human hydrolase with the pro-drug of quercetin, (3'(N-
38! ! ! ! carboxymethyl)carbomyl-3,4',5,7-tetrahydroxyflavone) (QC12). This compound was developed as a bioavailable form of the flavon-3-ol quercetin [7] (Figure 4.1). QC12 co-crystallized near the active site of the human HIBYL-CoA hydrolase, aligning with the residues associated with CoA binding. The highly hydrophobic nature of quercetin and its multi-ringed structure are similar to that of ergosterol, the main sterol of yeast. Therefore we speculated that ergosterol might bind to the yeast hydrolase. We attempted to dock ergosterol into a structural model of the S. cerevisiae protein using UCSF Autodock (Figure 4.2). The ester-forming hydroxyl groups of both quercetin and ergosterol align with the residues known to be responsible for hydrolysis of CoA esters. This provided preliminary support for our hypothesis that ergosterol could be a substrate of YDR036C.
4.1.4 Ergosterol
Sterols are a vital component of the eukaryotic membrane. The type and amount of sterol has an overwhelming influence on the properties of the membrane. The primary sterol of yeast is ergosterol, which differs from cholesterol by the addition of a methyl group at C24 and the presence of double bonds at C22-23 and C7-8 (Figure 4.3). These structural differences are the basis of the majority of antifungal medications. For example, terbinafine, the active compound in Lamisil, inhibits an enzyme specific to ergosterol synthesis, so cholesterol synthesis is unaffected and the drug affects yeasts but not mammals.
There are two main functions of ergosterol within the membrane; the first is to control fluidity and the second is to provide impermeability. Impermeability and fluidity of the membrane play a role in structure and function of membrane-bound proteins [11], and both of these functions are based on the hydrophobic interactions of ergosterol with the tail groups of fatty acids [8-10]. The attributes that ergosterol provides to the membrane can be detrimental if the level of the sterol exceeds the usual amounts. Increased levels of ergosterol reduce the cells ability to perform endocytosis [12]. Improper regulation of ergosterol can lead to toxicity for the same reasons. One method to prevent the toxicity of ergosterol overabundance is to slow down or halt its production.
4.1.5 Synthesis of ergosterol in the ER
Ergosterol synthesis has been studied extensively and it is well established that ergosterol is generated in an oxygen-dependent manner in the endoplasmic reticulum (ER) [13]. The synthesis is the culmination of two pathways. The first is the production of farnesyl pyrophosphate, a precursor for several biological molecules, and second is the dedicated ergosterol pathway. The latter half of the pathway is performed by 14 proteins, 11 of which are localized to the ER [14]. The synthetic pathway is tightly regulated and yeast do not typically take up exogenous sterols, despite the fact that synthesis is an energetically expensive process. To buffer against the need for exogenous sterols, ergosterol is produced beyond the immediate needs of the membranes and is 39! ! ! ! stored as sterol esters (SE) in lipid particles (LP).
4.1.6 Shuttling of ergosterol to the LP
Since ergosterol is synthesized in the ER, there needs to be an active mechanism to control its trafficking to other membranes of the cell or it will buildup, and alter the stability of the ER membrane. To circumvent potential accumulation, ergosterol and its precursors are esterified by acyl-CoA transferases, chiefly, Are1 and Are2 [15, 16]. Are1 has a preference for the intermediates of ergosterol synthesis, mainly lanosterol, (Figure 4.3) [17], and forms sterol esters of fatty acids with a higher ratio of C16/C18 fatty acid than Are2 [18]. Once the ester is formed, the amphiphilic sterol is very hydrophobic and aggregates with similar SE and triacylglycerides (TAG). The aggregation forms a hydrophobic bubble of SE and TAG within the ER membrane, which, when sufficiently large, will bud off from the ER membrane forming a LP. The LP is composed of an extremely hydrophobic SE and TAG core surrounded by a phospholipid monolayer [19]. The LP contains a mixture of the precursor sterols as well as mature ergosterol. It is believed that the bias toward the precursor sterols by Are1 is a detoxification mechanism to prevent the effects of improper sterol levels within the membrane [18].
4.1.7 Shuttling of ergosterol to the PM
Are2 is believed to have a broader role. It participates in the generation of ergosterol esters destined for storage, and in the generation of ergosterol esters that are to be hydrolyzed for integration into the plasma membrane. Are2 is highly preferential for ergosterol [17], which agrees with the tendency of ergosterol to be incorporated into the plasma membrane. Are2 preferentially uses C18 fatty acids as the source of the acyl-chain. The bias for C18 fatty acids could represent a mechanism for the cell to differentiate which sterols should be incorporated into the plasma membrane and which should not.
4.1.8 Detoxification by Atf2 and Say1
There is a third, less common, ergosterol ester, acetyl ester, is generated in the ER, which is not generally considered in the export of sterol esters from the ER [20]. The formation of an ester with acetate by the enzyme Atf2 was discovered as a detoxification pathway for exogenous sterols. The acetylated sterols are exported to the media or hydrolyzed by the esterase Say1. For example the exogenous sterol, pregnenolone (Figure 4.3), is esterified with C2 or C3 acids by Atf2 and exported [21]. Another acyl-transferase esterifies pregnenolone with C18 acids in the Atf2 knockout [20]. The exogenous C18 SE is not exported, suggesting that retention / storage or export is not dependent on the sterol itself but on the length of the acyl-chain. Low levels of acetate esterification of ergosterol by Atf2 have been noted [20].
4.1.9 Hydrolysis of sterol esters
40! ! ! !
Sterol esters cannot associate with the membrane due to their hydrophobicity. In order for sterols to be recovered from their storage form for use, the SE must be hydrolyzed. A specialized group of hydrolases is present in different membranes to accomplish this task. Yeh1 is present within the LP, where it preferentially hydrolyzes precursor sterols, which are then returned to the ER for the remaining steps of ergosterol synthesis [21-22]. Yeh2 is located within the plasma membrane, where it has preferential activity toward ergosterol esters. This activity releases ergosterol for direct use within the membrane [23, 25]. The localization and preference of the Yeh enzymes should not be overlooked. Yeh1, found in LP, acts preferentially toward precursor sterols and shorter acyl-chains, which are required to pass through the ER for the final steps of ergosterol synthesis. In contrast, Yeh2 is located within the PM and prefers ergosterol and longer acyl- chains, thereby limiting the amount of precursor sterol that can be incorporated. The other hydrolase Say1 is localized within the ER membrane. Say 1 hydrolyzes precursor sterols for the completion of ergosterol synthesis.
Processes and genes pertaining to sterol metabolism in human or yeast are often shared. While this is true for almost every aspect involving sterols, higher eukaryotes produce steroids from sterols, a process that is not present in yeasts. The conversion of a sterol into a steroid involves the removal of the side chain, which is dependent upon P450scc enzyme, found within mitochondria [26]. Ergosterol is present in the mitochondrial membrane [27, 28], and mitochondria are required for ergosterol synthesis [29]. Despite this connection between sterols and the mitochondria in eukaryotes there is still no clear link between ergosterol trafficking and yeast mitochondria. We propose here the possibility that YDR036C could link this function to the organelle by serving as a sterol ester hydrolase.
4.2 Methods and materials
4.2.1 Materials and cell lines
All chemicals were purchased from Sigma-Aldrich (St. Louis, MO) unless otherwise noted. Wild-type Saccharomyces cerevisiae (BY4743) and a homozygous diploid knockout of ydr036c! (Clone ID 33975) were obtained from Open Biosystems (Huntsville, AL).
4.2.2 Modelling of YDR036C
A model of the first 423 residues of the S. cerevisiae hydrolase was obtained using its sequence (accession number NP_010321.1). BLASTP analysis indicates 34% sequence identity and 53% similarity for the entire alignment of S. cerevisiae and Homo sapiens (PDB ID: 3BPT). The residues within 20Å of the active site have 43% sequence identity and 61% similarity and within 15Å have 52% sequence identity and 64% similarity. The PDB structure for the human hydrolase, ID: 3BPT, was used as a template for building a homology model with the SWISS- MODEL server [30, 31]. Anolea [32], gromos [33], and Verify3D were used to verify the 41! ! ! ! validity of the model. The alignment adjustments were undertaken with Deep View/Swiss- PdbViewer version 3.7 [34] and the figures were generated using UCSF Chimera
4.2.3 Docking of substrates
Docking of 3-hydroxypropionyl-CoA and ergosterol was carried out using AutoDock 4 [36]. The substrate molecules were generated using ghemical (http://www.bioinformatics.org/ghemical) and saved in pdb format before they were assessed in Chimera. The 3-hydroxypropionyl-CoA was truncated by the removal of the adenosine to reduce the flexibility of the substrate molecules when docking (Figure 4.4). Both the human crystal structure (3BPT) and the S. cerevisiae model where prepared for docking using UCSF Chimera. The default AutoDock4 settings were used except the gridbox was set as 60X60X60 and was centered on the opening of the active site pocket. For each structure and substrate 100 docking runs were evaluated and the largest clustered result was considered representative and was used to assign the binding free energy.
4.2.4 Extraction and quantification of ergosterol
YPD in 1 L culture flasks was inoculated and grown at 30˚C and 200 rpm [35]. Aliquots were collected every 6 h (400 mL, 150 mL, 75 mL, 50 mL, 50 mL, 50 mL, and 50 mL) and pelleted. The cells were washed twice with 50 mL of phosphate buffered saline (137 mM NaCl, 2.7 mM
KCl, 10 mM Na2HPO4, and 1.76 mM KH2PO4, pH 7.4) and lyophilized. Two hundred milligrams of dried yeast was weighed into 15 mL screw top test tubes. Alcoholic KOH (5g of KOH in 7.0 mL of water and 20 mL of 100% ethanol) was added (3 mL to each tube) and the samples were vortexed for 1 min. The tubes were maintained at 80˚C for 1 h and then cooled to room temperature before adding 1 mL of sterile water and 3 mL of hexanes. The mixture was vortexed for 3 min and layers were allowed to separate. The hexanes layer was transferred to a new glass vial and stored at -20˚C until it could be quantified by UV measurement.
UV measurements were carried out using a Cary 100 UV-Vis spectrophotometer and matched quartz cuvettes. Samples were prepared by 5-fold dilution in ethanol (350 "L of ergosterol extract was added to 1400 "L of ethanol). Samples were scanned from 225 nm to 300 nm. The maximum absorbencies at 281.5 nm and 230.0 nm were recorded and ergosterol was quantified using the following formulas.
1. [(Abs281.5/290) x Dilution Factor] / Pellet Weight
2. [(Abs280/518) x Dilution Factor] / Pellet Weight
% Ergosterol = 1 – 2
4.3 Results and discussion
42! ! ! !
4.3.1 Saccharomyces cerevisiae ydr036c!
We explored several roles for the YDR036C using a ydr036c knockout strain for phenotype analyses. When growth rates were assessed, the knockout strain is not more sensitive than wild- type to any of the branched chain amino acids (valine, leucine, isoleucine) or to methionine, or to their degradation intermediates (methacyrylate, acrylate, or propionate). This is consistent with the absence of hydroxylacyl-CoA substrates in the branched chain amino acid pathways in yeast.
Other investigators have obtained DNA array data that shows an increase in ydr036c gene expression during treatment of yeast with menadione as well as with hydrogen peroxide [37]. It is possible that hydroxyacyl-CoA could be generated from peroxidized lipids, but we found that ydr036c and wild-type strain cells were equally sensitive to hydrogen peroxide, tertiary butyl- peroxide or menadione treatment. This suggests that this enzyme is not vital for normal growth under laboratory conditions.
The only obvious phenotype observed with yeast HIBYL-CoA hydrolase knockouts is a mild phenotype associated with fluid-phase endocytosis, where the uptake of luciferase yellow was inhibited compared to wild-type [35]. The importance of sterols in endocyotsis [12], and the ability of HIBYL-CoA hydrolase to bind the sterol analog QC12 [7] as well as to dock ergosterol in our modeling studies, suggested that we should explore sterol accumulation in the knockouts.
4.3.2 Ergosterol content of S. cerevisiae ydr036c knockouts
To investigate the possible role of YDR036C as a sterol ester hydrolase, ergosterol was quantified in both wild-type and ydr036c! (Figure 4.5A). In each case cells were grown in YPD until the designated time point and then an aliquot was removed, washed with phosphate buffered saline and lyophilized [38]. There was a significantly lower ergosterol content in ydr036c! cells than wild-type (Figure 4.5A). This result is in agreement with S. cerevisiae knockouts of yeh1 and yeh2, where the deletions resulted in lower total amounts of ergosterol within the cell [23]. The decrease could be a consequence of feedback inhibition of ergosterol synthesis. We speculate that the accumulation of large amounts of sterol ester, the storage form of ergosterol, signals that the levels of ergosterol are sufficient within the cell so that production is decreased, leading to lower overall amounts of ergosterol in sterol ester hydrolase knockouts.
The wild-type and ydr036c! cells were also grown in the presence of antifungal compounds that affect ergosterol synthesis and stability. In the presence of two separate antifungal compounds the knockouts showed a growth defect. Treatment with clotrimazole, which acts on the synthesis of ergosterol, yielded slightly reduced growth in the ydr036c! cells. Treatment with amphotericin- B, which binds to ergosterol in the membrane, also showed a growth phenotype (Figure 4.5B). Both phenotypes are consistent with the lower ergosterol content in ydr036c! cells.
43! ! ! !
4.3.3 Other evidence for a role for YDR036C in mitochondrial ergosterol regulation
High- throughput studies have identified ydr036c! as having a mild phenotype in endocytosis [39]. Wiederkehr et al. demonstrated that the fluid phase endocytosis was reduced in ydr036c!, because the intensity of the luciferase yellow within vacuoles was less than in the wild-type, but all other aspects of endocytosis appeared normal [39]. This effect is also seen in the knockout of ergosterol synthesis enzymes, erg4!erg5!, as demonstrated by Hesse-Peck [40].
Another high-throughput study that yielded information about YDR036C was an investigation of mitochondrial enzymes that increase the number of petite mutants [41]. Petite mutants are a particular subset of S. cerevisiae strains that grow similarly under aerobic or anaerobic conditions, as they have few mitochondria. The ydr036c! line shows a very mild increase in the number of petite colonies, so it was chosen to cross with other very mild petite phenotypes. Two previous uncharacterized genes, fmp10 and yir026c, were identified. In a double knockout with ydr036c!, either of these genes increases petite colony formation [41]. The functions of these enzymes are not clear, but Fmp10 has low level homology to known esterases.
Finally, an investigation of meiotic cell cycle gene expression in S. pombe also yielded information about YDR036C [42]. Expression of the hydrolase is up regulated between meiosis I and meiosis II, during the time in the cell cycle when new membrane is formed.
4.4 Conclusions
4.4.1 Ergosterol conclusions
The data presented above suggests that YDR036C may be involved in the metabolism of ergosterol in S. cerevisiae, possibly functioning as an ergosterol esterase. Taketani et al. suggested in 1978 that there is a mitochondrial sterol esterase [43], but identification of the enzyme responsible has remained elusive.
Here we propose the following with regards to YDR036C and ergosterol esters. Sterol ester trafficking of S. cerevisiae is reliant upon two principles. First, the sterol moiety designates what general type of acyl-chain is used to generate a SE and that acyl-chain designates where the SE will localize. Second, the acyl-chain recognition by the hydrolase determines where the sterol will be reintegrated into membrane (Figure 4.6). Based on that model, YDR036C could act as a mitochondrial SE hydrolase for the short chain acyl-group (C2-C3) esters that localize to mitochondria.
44! ! ! !
4.4.2 Implication for higher eukaryotes
The crotonase super-family is composed of many hydrolases but there are no examples of these enzymes catalyzing sterol ester hydrolysis. Evidence of such activity could add a new member to the crotonase super-family of enzymes. The inclusion of the crotonase super-family could aid in the discovery of new sterol esters, and sterol esterases, that have not been identified.
An example of potential sterol esterases may be seen in higher eukaryotes such as A. thaliana where there are 8 homologs of HIBYL-CoA hydrolase. Several of these HIBYL-CoA hydrolases have been shown by complementation studies to have non-overlapping functions [44]. There is a clear pathway for the degradation of valine in peroxisomes, but there are two additional isoforms that are also believed to be located in peroxisomes. There are three isoforms that are believed to be mitochondrial, one that localizes to the chloroplast, and one isoform that may be cytosolic. Wide spread localization, and duplicate isoforms within organelles point to multiple functions in addition to the degradation of valine. The same pattern can be seen in many plants and mammals where sterols are much more prevalent than in yeast.
Several disease states are associated with a change in the sterol regulation of the cells. The maintenance of sterol esters affects not only the specific membranes within cells but also the levels of cholesterol and LDLs within the blood. Excess SE in the form of LP has been noted as a risk factor for atherosclerosis, obesity, and type II diabetes [18, 45, 46]. It is possible that hydroxyacyl-CoA hydrolase has evolved in higher eukaryotes to function not only in valine metabolism, but also to function in the hydrolysis of sterol esters, as reflected by the many isoforms of the enzyme within the same organelle.
4.4.3 Future work
On the basis of the preceding work the following experiments would demonstrate whether YDR036C is functioning as an ergosterol ester hydrolase: Quantification of sterols from yeast mitochondria and assay of YDR036C for hydrolytic activity with radiolabeled ergosterol.
The preparation of yeast mitochondria is traditionally a lengthy and difficult process, requiring many steps of differential centrifugation, but recently a shortened procedure has been adapted for use with S. cerevisiae, greatly reducing the centrifugation steps and time required. The method utilizes lyticase from Arthrobacter luteus to lyse the cell wall, cell membrane rupture using a Dounce homogenizer, and a two-step centrifugation. All reagents are available in kit form from Sigma (St. Louis, MO) (product number: MITOISO3). Our hypothesis suggests that isolated mitochondria from wild-type strains will have more ergosterol while mitochondria from ydr036c# strains will contain more ergosterol ester, and testing that hypothesis might be simplified with this new method for mitochondrial isolation.
45! ! ! !
To assay YDR036C for hydrolytic activity with ergosterol esters it is necessary to use radiolabeled ergosterol. The purified enzyme would be incubated with radiolabeled ergosterol esters, with the label in the sterol or the acyl chain. Following an incubation the reaction products would be separated by thin layer chromatography and individual bands quantified by scintillation counting. A range of different acyl groups should be assayed to determine the correct substrate. The above experiments could more fully test the hypothesis that YDR036C is a mitochondrial ergosterol esterase.
46! ! ! !
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Figure 4.1 Structures of quercetin and (3'(N-carboxymethyl)carbomyl-3,4',5,7- tetrahydroxyflavone) (QC12).
Quercetin
QC12
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Figure 4.2 Overlay of ergosterol and quercetin in the YDR036C active site.
Ergosterol (green) and quercetin (blue) were docked into the active site of the homology model of YDR036C using UCSF AutoDock6. The model is shown with surface rendering and is slabbed to reveal the active site pocket. The hydrolytic glutamate of YDR036C and the ester forming hydroxyl groups of ergosterol and quercetin are colored in red.
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Figure 4.3 Structures of sterols (ergosterol, cholesterol, and lanosterol), and the steroid pregnenolone.
Ergosterol Cholesterol
Lanosterol Prognenolone
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Figure 4.4 The structures of Coenzyme A and the truncated 3-HP-CoA used for docking with AutoDock4.
Coenzyme A
3-HP-CoA
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Figure 4.5 The ergosterol content of wild-type and ydr036c! strains of S. cerevisiae in YPD and the growth of wild-type and ydr036c! strains on YPD agar containing the antifungal compound clorimazole.
Ergosterol content of wild-type (BY4743) and ydr036c! strains from 12 to 96 hours (A). p <0.05 (*), p <0.01 (**). Wild-type and ydr036c! strains (top three and bottom three respectively) plated on YPD agar contain 0, 5, and 10 µM clotrimazole after 24 hours of growth (B).
A.
Ergosterol Content
3
WT $ 2.5 KO $$! $ 2 $$! 1.5
1 % Ergosterol (dry wt)
0.5
0 12H 24H 48H 72H 96H
B.
Control 10 "# Clotrimazole 5 "# Clotrimazole
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Figure 4.6 Proposed sterol trafficking in S. cerevisiae.
The proposed mechanisms for transporting ergosterol and sterol esters between the membranes of S. cerevisiae. In the ER membrane Are1 synthesizes ergosterol and ergosterol precursors into sterol esters primarily with an acyl chain 16 carbons in length (LanC16), which is deposited in LP. The predominant activity of Are2 is synthesis of C18 ergosterol esters (ErgC18), which are deposited in the PM. Atf2 acetylates ergosterol (ErgC2) for recycling. Transport to the mitochondria maybe controlled by a similar mechanism in which YDR036C hydrolyzes an ergosterol esterified by a three-carbon acid (ErgC3).
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Chapter 5: Conclusions
5.1 YDR036C and other yeast hydrolases
Based on the sequence homology between YDR036C and known HIBYL-CoA hydrolases, it seems plausible that the two enzymes would have similar functions. There are three common metabolic pathways that generate substrates similar to HIBYL-CoA, beta-oxidation of fatty acids, peroxidative lipid degradation and valine degradation. Each of these metabolic systems was explored by the Hawes lab and others without identifying a definitive role for YDR036C. While clearly not involved in the valine catabolism of yeast, the enzyme does retain the ability to hydrolyze HIBYL-CoA.
However, YDR036C is not most active with HIBYL-CoA, but instead has a higher specificity toward 3-HP-CoA. Interestingly, 3-HP-CoA has yet to be identified as a metabolite generated by yeast, but further searching of yeast genome databases revealed that many yeast also contain an analog of HIBYL-CoA hydrolase. Cloning and assay showed that in 2 out of 3 yeast species, YDR036C-type enzymes have greater activities toward 3-HP-CoA than towards HIBYL-CoA. The notable exception was the enzyme from D. hasenii. The sequence alignments as well as the crystal structures were analyzed to determine the basis for the substrate preferences.
Sequence and structural alignments identified a clear difference divide between the hydrolases that correlated with substrate specificity. The hydrolases of the higher eukaryotes (human and A. thaliana) and D. hansenii all prefer to hydrolyze HIBYL-CoA, and have a leucine occupying the position 174. The typical yeast hydrolases prefer to hydrolyze 3-HP-CoA and contain an aromatic amino acid, phenylalanine or tyrosine in the corresponding position. Mutagenesis experiments demonstrated kinetic consequences of replacing this critical residue in either direction (human, L174F or S. cerevisiae, F177L). The kcat for each substrate shifted, but neither enzyme was fully converted to the alternative specificity.
A second residue that was identified during the comparison of the structures and sequence alignments was the fully conserved glutamate at position 121/124. Mutagenesis of this glutamate to a valine generated a hydrolase that was no longer specific for substrates that contained a beta hydroxyl group. The E124V mutant was able to hydrolyze acyl-CoAs that varied in length from two carbons to five carbon backbones, while the wild-type enzyme was only capable of hydrolyzing substrates that contained a three-carbon backbone. This mutant demonstrated the glutamate at position 121/124 controls both the requirement for a three-carbon backbone, and the hydroxyl group.
Phospho-proteomics identified a serine of YDR036C that was a potential site of phosphorylation and was subsequently shown to be conserved between the yeast, human and A. thaliana enzymes. The generation and assay of phospho-mimics suggests that phosphorylation 56! ! ! ! of serine 303/328 results in a catalytically inactivated enzyme while the non-phosphorylated enzyme is the active form. In humans and other higher eukaryotes, phosphorylation/dephosphorylation may provide specific regulation of valine catabolism. Since the role of this hydrolase in yeast is unknown, the significance of this putative regulation is unclear.
The question that remains unanswered about YDR036C is the metabolic or physiological role of the enzyme. There is preliminary evidence suggesting that YDR036C might be related to three seemingly unconnected processes: endocytosis, petite colony formation, and meiosis. A common theme to all these processes is their reliance on the integrity of membranes. A key component of the membrane stability is sterols and sterol esters. Sterol esters are multi-ringed structures esterified to acyl chains and there is a set of specific hydrolases for these compounds. The sterol ester hydrolases are localized to the membranes in which they generate free sterols, but to date no hydrolase has been identified for the yeast mitochondrial membrane. A mitochondrial sterol ester hydrolase that is knocked out could account for the phenotypes associated with ydr036c!.
We predicted that ydr036c! would have low overall sterol levels due to feedback inhibition of sterol synthesis. We established that the amount of ergosterol in a ydr036c! strain is lower than that of the wild-type consistent with our prediction. Growth of the ydr036c! strain is also more inhibited by clotrimazole, an inhibitor of ergosterol synthesis, than is growth of the wild type. Therefore, YDR036C may affect ergosterol regulation and may act as the mitochondrial hydrolase of ergosterol esters.
The work presented in this dissertation has demonstrated that the conserved HIBYL-CoA hydrolase present in yeast is likely not involved in the metabolism of beta-hydroxyisobutyryl- CoA generated from valine, peroxidated lipids, or beta-oxidation. The enzyme prefers 3-HP-CoA but there is no clear pathway, or a phenotype associated with propionyl-CoA, making unlikely that the primary function of this enzyme is to serve as a 3-HP-CoA hydrolase. On the other hand the hydrolase does appears to have putative regulation through the phosphorylation of a single serine residue suggesting that the role of YDR036C is responsive. An alternate possibility is that YDR036C could be involved in the regulation of ergosterol transfer in the mitochondrial membrane, and some evidence presented here supports that claim. This work demonstrates that there are several metabolic and physiological functions in common yeast that may require YDR036C, but currently the function of this enzyme is not known.
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