The Kinesin Superfamily Protein KIF17: One Protein with Many Functions
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Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
XP725 Antibody List Lot 129K4830
Panorama® Antibody Microarray-XPRESS Profiler725, XP725 List of Antibodies Lot: 129K4830 Reactivity Number Antibody Sigma No. Gene Ids Gene Symbols P/M Accessions Human Mouse Rat 3 Actin A5060 58 ACTA1 P NP_001091.1 n/d n/d n/d 5 Actin, αβ-Smooth Muscle A5228 59 ACTA2 M NP_001135417.1, NP_001604.1, yyy 6 β-Actin A1978 60 ACTB M NP_001092.1 yyy 7 β-Actin A2228 60 ACTB M NP_001092.1 yyy 8 a-Actinin A5044 87 ACTN1 M NP_001093.1 y y n/d 555 PARP P7605 142 PARP1 P NP_001609.2 y n/d n/d 11 β1 and β2-Adaptins A4450 162 AP1B1 M NP_001118.3 y n/d y 167 Chondroitin Sulfate C8035 176 ACAN M NP_001126.3, NP_037359.3 yyy 574 Protein Kinase Ba /Akt1 P2482 207 AKT1 M NP_001014431.1,NP_001014432.1 , NP_005154.2, yyy 575 Protein Kinase Ba /Akt1 P1601 207 AKT1 P NP_001014431.1,NP_001014432.1 , NP_005154.2, yyy 577 phospho-PKB (pSer473) P4112 207 AKT1 P NP_001014431.1,NP_001014432.1 , NP_005154.2, n/d y y 578 phospho-PKB (pThr308) P3862 207 AKT1 P NP_001014431.1,NP_001014432.1 , NP_005154.2, n/d y y 22 Annexin V A8604 308 ANXA5 M NP_001145.1 y n/d n/d 23 Annexin VII A4475 310 ANXA7 M NP_001147.1 yyy 29 Apaf1, N-Terminal A8469 317 APAF1 P NP_001151.1 y y n/d 457 Mint2 M3319 321 APBA2 P NP_001123886.1 n/d n/d y 28 AP Endonuclease A2105 328 APEX1 M NP_001632.2,NP_542379.1,NP_542380.1 yyy 692 Survivin S8191 332 BIRC5 P NP_001012270.1 yyy 17 β-Amyloid A8354 351 APP M NP_000475.1,NP_001129488.1 ,NP_001129601.1 ,NP_001129602.1 ,NP_001129603.1 ,NP_001191230.1 ,NP_001191231.1 ,NP_001191232.1,NP_958816.1,NP_9 y n/d n/d 18 Amyloid Precursor Protein, C-Terminal A8717 -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Investigations Into Neuronal Cilia Utilizing Mouse Models
INVESTIGATIONS INTO NEURONAL CILIA UTILIZING MOUSE MODELS OF BARDET-BIEDL SYNDROME Dissertation Presented In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of the Ohio State University By Nicolas F. Berbari, BS ***** The Ohio State University 2008 Dissertation Committee: Approved by: Kirk Mykytyn, PhD, Adviser Virginia Sanders, PhD __________________________________________ Georgia Bishop, PhD Adviser Michael Robinson, PhD Integrated Biomedical Sciences Graduate Program ABSTRACT Cilia are hair-like microtubule based cellular appendages that extend 5-30 microns from the surface of most vertebrate cells. Since their initial discovery over a hundred years ago, cilia have been of interest to microbiologists and others studying the dynamics and physiological relevance of their motility. The more recent realization that immotile or primary cilia dysfunction is the basis of several human genetic disorders and diseases has brought the efforts of the biomedical research establishment to bear on this long overlooked and underappreciated organelle. Several human genetic disorders caused by cilia defects have been identified, and include Bardet-Biedl syndrome, Joubert syndrome, Meckel-Gruber syndrome, Alstrom syndrome and orofaciodigital syndrome. One theme of these disorders is their multitude of clinical features such as blindness, cystic kidneys, cognitive deficits and obesity. The fact that many of these cilia disorders present with several features may be due to the ubiquitous nature of the primary cilium and their unrecognized roles in most tissues and cell types. The lack of known function for most primary cilia is no more apparent than in the central nervous system. While it has been known for some time that neurons throughout the brain have primary cilia, their functions remain unknown. -
Supplemental Information For
Supplemental Information for: Gene Expression Profiling of Pediatric Acute Myelogenous Leukemia Mary E. Ross, Rami Mahfouz, Mihaela Onciu, Hsi-Che Liu, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Stanley Pounds, Cheng Cheng, Jing Ma, Raul C. Ribeiro, Jeffrey E. Rubnitz, Kevin Girtman, W. Kent Williams, Susana C. Raimondi, Der-Cherng Liang, Lee-Yung Shih, Ching-Hon Pui & James R. Downing Table of Contents Section I. Patient Datasets Table S1. Diagnostic AML characteristics Table S2. Cytogenetics Summary Table S3. Adult diagnostic AML characteristics Table S4. Additional T-ALL characteristics Section II. Methods Table S5. Summary of filtered probe sets Table S6. MLL-PTD primers Additional Statistical Methods Section III. Genetic Subtype Discriminating Genes Figure S1. Unsupervised Heirarchical clustering Figure S2. Heirarchical clustering with class discriminating genes Table S7. Top 100 probe sets selected by SAM for t(8;21)[AML1-ETO] Table S8. Top 100 probe sets selected by SAM for t(15;17) [PML-RARα] Table S9. Top 63 probe sets selected by SAM for inv(16) [CBFβ-MYH11] Table S10. Top 100 probe sets selected by SAM for MLL chimeric fusion genes Table S11. Top 100 probe sets selected by SAM for FAB-M7 Table S12. Top 100 probe sets selected by SAM for CBF leukemias (whole dataset) Section IV. MLL in combined ALL and AML dataset Table S13. Top 100 probe sets selected by SAM for MLL chimeric fusions irrespective of blast lineage (whole dataset) Table S14. Class discriminating genes for cases with an MLL chimeric fusion gene that show uniform high expression, irrespective of blast lineage Section V. -
Cilium Structure, Assembly, and Disassembly Regulated by the Cytoskeleton
Biochemical Journal (2018) 475 2329–2353 https://doi.org/10.1042/BCJ20170453 Review Article Cilium structure, assembly, and disassembly regulated by the cytoskeleton Mary Mirvis1,*, Tim Stearns2,3 and W. James Nelson1,2 1Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, U.S.A.; 2Department of Biology, Stanford University, Stanford, CA 94305, U.S.A.; 3Department of Genetics, Stanford University, Stanford, CA 94305, U.S.A. Correspondence: W. James Nelson ([email protected]) The cilium, once considered a vestigial structure, is a conserved, microtubule-based organelle critical for transducing extracellular chemical and mechanical signals that control cell polarity, differentiation, and proliferation. The cilium undergoes cycles of assembly and disassembly that are controlled by complex inter-relationships with the cytoskeleton. Microtubules form the core of the cilium, the axoneme, and are regulated by post-translational modifications, associated proteins, and microtubule dynamics. Although actin and septin cytoskeletons are not major components of the axoneme, they also regulate cilium organization and assembly state. Here, we discuss recent advances on how these different cytoskeletal systems affect cilium function, structure, and organization. Introduction Cilia are specialized, conserved organelles that are evolutionarily optimized for interaction with the world outside of the cell. They protrude into the extracellular space, are structurally resilient but also flexible and dynamic, and have unique mechanisms to tightly control their internal and membrane composition. These features ensure that the cilium is primed to perform highly regulated signaling, mechanosensory, and motile functions. In this review, we consider cilia mostly from the perspective of vertebrate animal cells, with additional information from the wide range of ciliated eukaryotes where appropriate. -
Overexpression of Motor Protein KIF17 Enhances Spatial and Working Memory in Transgenic Mice
Overexpression of motor protein KIF17 enhances spatial and working memory in transgenic mice Richard Wing-Chuen Wong, Mitsutoshi Setou, Junlin Teng, Yosuke Takei, and Nobutaka Hirokawa* Department of Cell Biology and Anatomy, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan Edited by Tomas Hokfelt, Karolinska Institute, Stockholm, Sweden, and approved September 11, 2002 (received for review June 28, 2002) The kinesin superfamily proteins (KIFs) play essential roles in where noted. Control WT mice were chosen from the same receptor transportation along the microtubules. KIF17 transports littermates. For the behavioral experiments, the same groups of the N-methyl-D-aspartate receptor NR2B subunit in vitro, but its male mice were used (10–12 wk). role in vivo is unknown. To clarify this role, we generated trans- genic mice overexpressing KIF17 tagged with GFP. The KIF17 Histological Analysis and Electron Microscopy. Mice (10–12 wk) were transgenic mice exhibited enhanced learning and memory in a anesthetized and fixed in FEA solution (5% formalin͞70% etha- series of behavioral tasks, up-regulated NR2B expression with the nol͞5% acetic acid). The brain tissues were then removed, washed, potential involvement of a transcriptional factor, the cAMP-depen- dehydrated in a graded series of ethanol, and embedded in Para- dent response element-binding protein, and increased phosphor- plast (Oxford Labware, St. Louis). The blocks were cut by using a ylation of the cAMP-dependent response element-binding protein. rotatory microtome (HM355; Rotary Microtome Zeiss) and sec- Our results suggest that the motor protein KIF17 contributes to tioned serially at 12-m thickness by using the same microtome. -
Extending Our Understanding of Cardiovascular Risk From
EDITORIALS www.jasn.org multiprotein cilia-destined cargo within the cell. Then through 13. Tyler KM, Fridberg A, Toriello KM, Olson CL, Cieslak JA, Hazlett TL, association of an adaptor molecule containing a cilia-targeting Engman DM: Flagellar membrane localization via association with lipid rafts. J Cell Sci 122: 859–866, 2009 motif, perhaps such as cystin, multiple proteins deliver to the 14. Rohatgi R, Milenkovic L, Scott MP: Patched1 regulates hedgehog cilium. Further complexity in this model arises from the fact signaling at the primary cilium. Science 317: 372–376, 2007 that not all proteins constitutively localize to cilia but require an external stimulus that promotes cilia entry. A good example of this is Hedgehog signaling. It was recently shown upon bind- See related article, “Cystin Localizes to Primary Cilia via Membrane Microdo- ing of Hedgehog to its receptor Patched, the protein Smooth- mains and a Targeting Motif,” on pages 2570–2580. ened is targeted to the cilium14; therefore, multiple targeting motifs and adaptors likely regulate ciliary entry of proteins either in a constitutive manner or in response to a specific cue. Understanding these targeting signals will be key as we con- It’s about Time: Extending our tinue to unravel the mysteries of the cilia. Understanding of Cardiovascular Risk from DISCLOSURES Chronic Kidney Disease This work was supported in part by National Institutes of Health (NIH DK069605) and Polycystic Kidney Disease Foundation (162G08a) grants. Ann Young and Amit X. Garg Division of Nephrology and Department of Epidemiology and Bio- statistics, University of Western Ontario, London, Ontario, Canada REFERENCES J Am Soc Nephrol 20: 2486–2487, 2009. -
Polycystin-2 Takes Different Routes to the Somatic and Ciliary Plasma Membrane
JCB: Article Polycystin-2 takes different routes to the somatic and ciliary plasma membrane Helen Hoffmeister,1 Karin Babinger,1 Sonja Gürster,1 Anna Cedzich,1,2 Christine Meese,1 Karin Schadendorf,3 Larissa Osten,1 Uwe de Vries,1 Anne Rascle,1 and Ralph Witzgall1 1Institute for Molecular and Cellular Anatomy, University of Regensburg, 93053 Regensburg, Germany 2Medical Research Center, Klinikum Mannheim, University of Heidelberg, 68167 Mannheim, Germany 3Center for Electron Microscopy, University of Regensburg, 93053 Regensburg, Germany olycystin-2 (also called TRPP2), an integral mem- a COPII-dependent fashion at the endoplasmic reticulum, brane protein mutated in patients with cystic kidney that polycystin-2 reaches the cis side of the Golgi appara- P disease, is located in the primary cilium where it is tus in either case, but that the trafficking to the somatic thought to transmit mechanical stimuli into the cell interior. plasma membrane goes through the Golgi apparatus After studying a series of polycystin-2 deletion mutants we whereas transport vesicles to the cilium leave the Golgi identified two amino acids in loop 4 that were essential for apparatus at the cis compartment. Such an interpretation the trafficking of polycystin-2 to the somatic (nonciliary) is supported by the finding that mycophenolic acid treat- plasma membrane. However, polycystin-2 mutant proteins ment resulted in the colocalization of polycystin-2 with in which these two residues were replaced by alanine GM130, a marker of the cis-Golgi apparatus. Remark- were still sorted into the cilium, thus indicating that the ably, we also observed that wild-type Smoothened, an trafficking routes to the somatic and ciliary plasma mem- integral membrane protein involved in hedgehog signaling brane compartments are distinct. -
The Transition Zone: an Essential Functional Compartment of Cilia Szymanska and Johnson
The transition zone: an essential functional compartment of cilia Szymanska and Johnson Szymanska and Johnson Cilia 2012, 1:10 http://www.ciliajournal.com/content/1/1/10 Szymanska and Johnson Cilia 2012, 1:10 http://www.ciliajournal.com/content/1/1/10 REVIEW Open Access The transition zone: an essential functional compartment of cilia Katarzyna Szymanska and Colin A Johnson* Abstract Recent studies of the primary cilium have begun to provide further insights into ciliary ultrastructure, with an emerging picture of complex compartmentalization and molecular components that combine in functional modules. Many proteins that are mutated in ciliopathies are localized to the transition zone, a compartment of the proximal region of the cilium. The loss of these components can disrupt ciliary functions such as the control of protein entry and exit from the cilium, the possible trafficking of essential ciliary components, and the regulation of signaling cascades and control of the cell cycle. The discovery of functional modules within the primary cilium may help in understanding the variable phenotypes and pleiotropy in ciliopathies. Keywords: Cilia, Transition zone, IFT, Ciliopathies Review crucial role in left-right patterning. They are located at Cilia are microtubule-based, hair-like organelles that the embryonic node, and although they have a “9+0” occur on the apical surface of most mammalian cells in microtubule pattern they mediate a leftward flow at the G0/G1 of the cell cycle [1], with the exception of bone node in a “whirlpool”-likemannerduetotheretention marrow-derived cells [2]. Defects in cilia structure or of dynein arms between microtubules. The leftward function are the cause of a suite of congenital conditions flow is thought to transport morphogens that are essen- known as ciliopathies, which now include polycystic kid- tial for the first step of symmetry breaking in the devel- ney disease, nephronophthisis, Senior-Løken syndrome, opmental of the mammalian body plan [2]. -
The Ciliopathy Gene Nphp-2 Functions in Multiple Gene Networks and Regulates
THE CILIOPATHY GENE NPHP-2 FUNCTIONS IN MULTIPLE GENE NETWORKS AND REGULATES CILIOGENESIS IN C. ELEGANS By SIMON ROBERT FREDERICK WARBURTON-PITT A dissertation submitted to the Graduate School – New Brunswick and The Graduate School of Biomedical Sciences Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Molecular Genetics and Microbiology Written under the direction of Maureen M. Barr, PhD And approved by New Brunswick, New Jersey January, 2015 © 2015 Simon Warburton-Pitt ALL RIGHTS RESERVED ABSTRACT OF THE DISSERTATION The ciliopathy gene nphp-2 functions in multiple gene networks and regulates ciliogenesis in C. elegans By SIMON ROBERT FREDERICK WARBURTON-PITT Dissertation Director: Maureen Barr Cilia are hair-like organelles that function as cellular antennae. Cilia are conserved across eukaryotes, and play a vital role in many biological processes including signal transduction, signal cascades, cell-cell signaling, cell orientation, cell-cell adhesion, motility, interorganismal communication, building extracellular matrix, and inducing fluid flow. In humans, cilia are present in a majority of tissue types, and cilia dysfunction can lead to a range of syndromic ciliopathies, including nephronopthisis (NPHP) and Meckel Syndrome (MKS). Cilia have a microtubule backbone, the axoneme, and are composed of multiple subcompartments, each with a specific function and composition: the transition zone (TZ) anchoring to the axoneme to the membrane, the doublet region extending from the TZ, and in some cilia types, the singlet region extending from the doublet region. The nematode C. elegans is a well-established model of cilia biology, and possesses cilia at the distal end of sensory dendrites. -
Cystin, Cilia, and Cysts: Unraveling Trafficking Determinants
EDITORIALS www.jasn.org UP FRONT MATTERS Cystin, Cilia, and Cysts: cilia, and photoreceptor outer segments, respectively.5–7 In photoreceptors, this motif binds the small G-protein, Arf4, Unraveling Trafficking and in conjunction with Rab11, FIP3, and ASAP1 promotes budding of ciliary-destined cargo from the transgolgi net- Determinants work.7 8 † In this issue of JASN, Tao et al. identify a novel ciliary Toby W. Hurd* and Ben Margolis trafficking determinant in the cystoprotein cystin that fur- Departments of *Pediatrics and †Internal Medicine, University of Michigan, Ann Arbor, Michigan thers our understanding of how proteins are selectively tar- geted to the cilium. This group previously identified cystin as J Am Soc Nephrol ●●: –, 2009. the gene disrupted in the cpk (congenital polycystic kidney) doi: 10.1681/ASN.2009090996 mouse model of autosomal recessive PKD.9 Of particular in- terest is the previous observation that the cystin protein lo- The past 10 yr has seen an exponential increase in research calizes to renal cilia3; however, little was known about the into a previously often ignored organelle, the primary cilium. function of this protein or the mechanism by which it traffics This is largely as a result of the discovery that ciliary dysfunc- to the cilium. tion underlies many human inheritable disorders, termed cil- Sequence and domain analyses of cystin yield no sequence iopathies.1 These include polycystic kidney disease (PKD), homology to other proteins, although it is predicted to be nephronophthisis, and retinal degeneration. Cilia are micro- myristoylated at the amino-terminus. Tao et al.8 test this hy- tubule-based organelles whose core components, the in- pothesis by in vivo labeling and indeed prove this is the case.