G2Cdb::Gene report

Gene id
Gene symbol
Homo sapiens
coatomer protein complex, subunit alpha
G00000695 (Mus musculus)

Databases (8)

Curated Gene
OTTHUMG00000033111 (Vega human gene)
ENSG00000122218 (Ensembl human gene)
1314 (Entrez Gene)
1094 (G2Cdb plasticity & disease)
COPA (GeneCards)
601924 (OMIM)
Marker Symbol
HGNC:2230 (HGNC)
Protein Sequence
P53621 (UniProt)

Synonyms (1)


Literature (34)

Pubmed - other

  • Defining the human deubiquitinating enzyme interaction landscape.

    Sowa ME, Bennett EJ, Gygi SP and Harper JW

    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA.

    Deubiquitinating enzymes (Dubs) function to remove covalently attached ubiquitin from proteins, thereby controlling substrate activity and/or abundance. For most Dubs, their functions, targets, and regulation are poorly understood. To systematically investigate Dub function, we initiated a global proteomic analysis of Dubs and their associated protein complexes. This was accomplished through the development of a software platform called CompPASS, which uses unbiased metrics to assign confidence measurements to interactions from parallel nonreciprocal proteomic data sets. We identified 774 candidate interacting proteins associated with 75 Dubs. Using Gene Ontology, interactome topology classification, subcellular localization, and functional studies, we link Dubs to diverse processes, including protein turnover, transcription, RNA processing, DNA damage, and endoplasmic reticulum-associated degradation. This work provides the first glimpse into the Dub interaction landscape, places previously unstudied Dubs within putative biological pathways, and identifies previously unknown interactions and protein complexes involved in this increasingly important arm of the ubiquitin-proteasome pathway.

    Funded by: NIA NIH HHS: AG085011, R01 AG011085, R01 AG011085-16; NIGMS NIH HHS: GM054137, GM67945, R01 GM054137, R01 GM054137-14, R01 GM067945

    Cell 2009;138;2;389-403

  • Yip1A regulates the COPI-independent retrograde transport from the Golgi complex to the ER.

    Kano F, Yamauchi S, Yoshida Y, Watanabe-Takahashi M, Nishikawa K, Nakamura N and Murata M

    Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan.

    Yip1A, a mammalian homologue of yeast Yip1p, is a multi-spanning membrane protein that is considered to be involved in transport between the endoplasmic reticulum (ER) and the Golgi. However, the precise role of Yip1A in mammalian cells remains unclear. We show here that endogenous Yip1A is localized to the ER-Golgi intermediate compartment (ERGIC). Knockdown of Yip1A by RNAi did not induce morphological changes in the Golgi, ER, or ERGIC. By analyzing a number of intracellular transport pathways, we found that Yip1A knockdown delayed the transport of Shiga toxin from the Golgi to the ER, but did not affect the anterograde transport of VSVGts045. We also found that a recombinant protein that corresponded to the N-terminal domain of Yip1A inhibited the COPI-independent retrograde transport of GFP-tagged galactosyltransferase, GT-GFP, but not the COPI-dependent retrograde transport of p58/ERGIC53. Furthermore, we found that Yip1A knockdown resulted in the dissociation of Rab6 from the membranes. These results suggested that Yip1A has a role in COPI-independent retrograde transport from the Golgi to the ER and regulates the membrane recruitment of Rab6.

    Journal of cell science 2009;122;Pt 13;2218-27

  • Purification and identification of G protein-coupled receptor protein complexes under native conditions.

    Daulat AM, Maurice P, Froment C, Guillaume JL, Broussard C, Monsarrat B, Delagrange P and Jockers R

    Department of Cell Biology, Institut Cochin, INSERM U567, CNRS UMR 8104, Université Paris Descartes, France.

    G protein-coupled receptors (GPCRs) constitute the largest family of membrane receptors and are of major therapeutic importance. The identification of GPCR-associated proteins is an important step toward a better understanding of these receptors. However, current methods are not satisfying as only isolated receptor domains (intracellular loops or carboxyl-terminal tails) can be used as "bait." We report here a method based on tandem affinity purification coupled to mass spectrometry that overcomes these limitations as the entire receptor is used to identify protein complexes formed in living mammalian cells. The human MT(1) and MT(2) melatonin receptors were chosen as model GPCRs. Both receptors were tagged with the tandem affinity purification tag at their carboxyl-terminal tails and expressed in human embryonic kidney 293 cells. Receptor solubilization and purification conditions were optimized. The method was validated by the co-purification of G(i) proteins, which are well known GPCR interaction partners but which are difficult to identify with current protein-protein interaction assays. Several new and functionally relevant MT(1)- and MT(2)-associated proteins were identified; some of them were common to both receptors, and others were specific for each subtype. Taken together, our protocol allowed for the first time the purification of GPCR-associated proteins under native conditions in quantities suitable for mass spectrometry analysis.

    Molecular & cellular proteomics : MCP 2007;6;5;835-44

  • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.

    Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P and Mann M

    Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark.

    Cell signaling mechanisms often transmit information via posttranslational protein modifications, most importantly reversible protein phosphorylation. Here we develop and apply a general mass spectrometric technology for identification and quantitation of phosphorylation sites as a function of stimulus, time, and subcellular location. We have detected 6,600 phosphorylation sites on 2,244 proteins and have determined their temporal dynamics after stimulating HeLa cells with epidermal growth factor (EGF) and recorded them in the Phosida database. Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF, and these were classified by their temporal profiles. Surprisingly, a majority of proteins contain multiple phosphorylation sites showing different kinetics, suggesting that they serve as platforms for integrating signals. In addition to protein kinase cascades, the targets of reversible phosphorylation include ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different transcriptional regulators. The dynamic phosphoproteome provides a missing link in a global, integrative view of cellular regulation.

    Cell 2006;127;3;635-48

  • A probability-based approach for high-throughput protein phosphorylation analysis and site localization.

    Beausoleil SA, Villén J, Gerber SA, Rush J and Gygi SP

    Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, USA.

    Data analysis and interpretation remain major logistical challenges when attempting to identify large numbers of protein phosphorylation sites by nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS) (Supplementary Figure 1 online). In this report we address challenges that are often only addressable by laborious manual validation, including data set error, data set sensitivity and phosphorylation site localization. We provide a large-scale phosphorylation data set with a measured error rate as determined by the target-decoy approach, we demonstrate an approach to maximize data set sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs), and we present a probability-based score, the Ascore, that measures the probability of correct phosphorylation site localization based on the presence and intensity of site-determining ions in MS/MS spectra. We applied our methods in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we identified 1,761 nonredundant phosphorylation sites from 491 proteins with a peptide false-positive rate of 1.3%.

    Funded by: NHGRI NIH HHS: HG03456; NIGMS NIH HHS: GM67945

    Nature biotechnology 2006;24;10;1285-92

  • Insights into COPI coat assembly and function in living cells.

    Lippincott-Schwartz J and Liu W

    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Building 18T Room 101, 18 Library Drive, Bethesda, MD 20892-5430, USA. jlippin@helix.nih.gov

    Eukaryotic cells use an elaborate machinery involving the COPI coat complex to control protein trafficking in the secretory pathway. Although individual components of this complex are well known and their roles in deforming lipid membranes into coated carriers are well described, the precise sequence of molecular events by which these components assemble into and release from the COPI coat lattice remains unclear. Here, we present images and movies characterizing the dynamics of protein components of the COPI coat in living cells. We discuss the self-assembly of these coat components into a molecular machine for sorting and trafficking membranes.

    Trends in cell biology 2006;16;10;e1-4

  • A human protein-protein interaction network: a resource for annotating the proteome.

    Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksöz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H and Wanker EE

    Max Delbrueck Center for Molecular Medicine, 13092 Berlin-Buch, Germany.

    Protein-protein interaction maps provide a valuable framework for a better understanding of the functional organization of the proteome. To detect interacting pairs of human proteins systematically, a protein matrix of 4456 baits and 5632 preys was screened by automated yeast two-hybrid (Y2H) interaction mating. We identified 3186 mostly novel interactions among 1705 proteins, resulting in a large, highly connected network. Independent pull-down and co-immunoprecipitation assays validated the overall quality of the Y2H interactions. Using topological and GO criteria, a scoring system was developed to define 911 high-confidence interactions among 401 proteins. Furthermore, the network was searched for interactions linking uncharacterized gene products and human disease proteins to regulatory cellular pathways. Two novel Axin-1 interactions were validated experimentally, characterizing ANP32A and CRMP1 as modulators of Wnt signaling. Systematic human protein interaction screens can lead to a more comprehensive understanding of protein function and cellular processes.

    Cell 2005;122;6;957-68

  • Immunoaffinity profiling of tyrosine phosphorylation in cancer cells.

    Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, Zhang H, Zha XM, Polakiewicz RD and Comb MJ

    Cell Signaling Technology Inc., 166B Cummings Center, Beverly, Massachusetts 01915, USA.

    Tyrosine kinases play a prominent role in human cancer, yet the oncogenic signaling pathways driving cell proliferation and survival have been difficult to identify, in part because of the complexity of the pathways and in part because of low cellular levels of tyrosine phosphorylation. In general, global phosphoproteomic approaches reveal small numbers of peptides containing phosphotyrosine. We have developed a strategy that emphasizes the phosphotyrosine component of the phosphoproteome and identifies large numbers of tyrosine phosphorylation sites. Peptides containing phosphotyrosine are isolated directly from protease-digested cellular protein extracts with a phosphotyrosine-specific antibody and are identified by tandem mass spectrometry. Applying this approach to several cell systems, including cancer cell lines, shows it can be used to identify activated protein kinases and their phosphorylated substrates without prior knowledge of the signaling networks that are activated, a first step in profiling normal and oncogenic signaling networks.

    Funded by: NCI NIH HHS: 1R43CA101106

    Nature biotechnology 2005;23;1;94-101

  • Large-scale characterization of HeLa cell nuclear phosphoproteins.

    Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villén J, Li J, Cohn MA, Cantley LC and Gygi SP

    Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.

    Determining the site of a regulatory phosphorylation event is often essential for elucidating specific kinase-substrate relationships, providing a handle for understanding essential signaling pathways and ultimately allowing insights into numerous disease pathologies. Despite intense research efforts to elucidate mechanisms of protein phosphorylation regulation, efficient, large-scale identification and characterization of phosphorylation sites remains an unsolved problem. In this report we describe an application of existing technology for the isolation and identification of phosphorylation sites. By using a strategy based on strong cation exchange chromatography, phosphopeptides were enriched from the nuclear fraction of HeLa cell lysate. From 967 proteins, 2,002 phosphorylation sites were determined by tandem MS. This unprecedented large collection of sites permitted a detailed accounting of known and unknown kinase motifs and substrates.

    Funded by: NHGRI NIH HHS: HG00041, K22 HG000041, T32 HG000041; NIGMS NIH HHS: GM67945, GMS6203, R01 GM056203, R01 GM067945

    Proceedings of the National Academy of Sciences of the United States of America 2004;101;33;12130-5

  • Novel isotypic gamma/zeta subunits reveal three coatomer complexes in mammals.

    Wegmann D, Hess P, Baier C, Wieland FT and Reinhard C

    Biochemie-Zentrum Heidelberg, 69120 Heidelberg, Germany.

    In early secretory transport, coat recruitment for the formation of coat protein I (COPI) vesicles involves binding to donor Golgi membranes of the small GTPase ADP-ribosylation factor 1 and subsequent attachment of the cytoplasmic heptameric complex coatomer. Various hypotheses exist as to the precise role of and possible routes taken by COPI vesicles in the mammalian cell. Here we report the ubiquitous expression of two novel isotypes of coatomer subunits gamma- and zeta-COP that are incorporated into coatomer, and show that three isotypes exist of the complex defined by the subunit combinations gamma 1/zeta 1, gamma 1/zeta 2, and gamma 2/zeta 1. In a liver cytosol, these forms make up the total coatomer in a ratio of about 2:1:2, respectively. The coatomer isotypes are located differentially within the early secretory pathway, and the gamma 2/zeta 1 isotype is preferentially incorporated into COPI vesicles. A population of COPI vesicles was characterized that almost exclusively contains gamma 2/zeta 1 coatomer. This existence of three structurally different forms of coatomer will need to be considered in future models of COPI-mediated transport.

    Molecular and cellular biology 2004;24;3;1070-80

  • The human phosphatidylinositol phosphatase SAC1 interacts with the coatomer I complex.

    Rohde HM, Cheong FY, Konrad G, Paiha K, Mayinger P and Boehmelt G

    Boehringer Ingelheim Austria GmbH, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria.

    The Saccharomyces cerevisiae SAC1 gene encodes an integral membrane protein of the endoplasmic reticulum (ER) and the Golgi apparatus. Yeast SAC1 mutants display a wide array of phenotypes including inositol auxotrophy, cold sensitivity, secretory defects, disturbed ATP transport into the ER, or suppression of actin gene mutations. At present, it is not clear how these phenotypes relate to the finding that SAC1 displays polyphosphoinositide phosphatase activity. Moreover, it is still an open question whether SAC1 functions similarly in mammalian cells, since some phenotypes are yeast-specific. Potential protein interaction partners and, connected to that, possible regulatory circuits have not been described. Therefore, we have cloned human SAC1 (hSAC1), show that it behaves similar to ySac1p in terms of substrate specificity, demonstrate that the endogenous protein localizes to the ER and Golgi, and identify for the first time members of the coatomer I (COPI) complex as interaction partners of hSAC1. Mutation of a putative COPI interaction motif (KXKXX) at its C terminus abolishes interaction with COPI and causes accumulation of hSAC1 in the Golgi. In addition, we generated a catalytically inactive mutant, demonstrate that its lipid binding capacity is unaltered, and show that it accumulates in the Golgi, incapable of interacting with the COPI complex despite the presence of the KXKXX motif. These results open the possibility that the enzymatic function of hSAC1 provides a switch for accessibility of the COPI interaction motif.

    The Journal of biological chemistry 2003;278;52;52689-99

  • Positional mapping for amplified DNA sequences on 1q21-q22 in hepatocellular carcinoma indicates candidate genes over-expression.

    Wong N, Chan A, Lee SW, Lam E, To KF, Lai PB, Li XN, Liew CT and Johnson PJ

    Department of Clinical Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, N.T., SAR Hong Kong, People's Republic of China. natwong@cuhk.edu.hk

    Comparative genomic hybridization analysis on hepatocellular carcinoma (HCC) indicated frequent gains of 1q and an amplicon at 1q21-q22. Current cytogenetic evidences confer much importance on 1q21-q22, where a role in drug resistance, tumor metastasis and shorter patient survival had been implicated.

    Methods: Using positional mapping by interphase cytogenetics, we investigated the amplicon 1q21-q22 in five HCC cases. Three amplification maxima represented by yeast artificial chromosomes (YACs) 955E11, 876B11 and 945D5 that mapped to regions 1q21.1, 1q21.2 and 1q22, respectively, were indicated. We further investigated candidate genes expression in the mapped YACs by quantitative reverse-transcription-polymerase chain reaction. A panel of genes encoding protein transcripts involved in apoptosis, cell cycle progression, calcium binding and jumping translocation was studied.

    Results: Among ten HCC cases with the amplicon 1q21-q22 examined, we found a significant gene expression level of JTB, SHC1, CCT3 and COPA in the tumors than the paired adjacent non-malignant liver tissues (P< or =0.04).

    Conclusions: Our interphase findings on 1q21-q22 pinpointed three affected loci between D1S305 and D1S2369. Up-regulation of candidate genes identified within these over-represented regions may represent targets in the progression of HCC and may carry prognostic significance.

    Journal of hepatology 2003;38;3;298-306

  • ARFGAP1 promotes the formation of COPI vesicles, suggesting function as a component of the coat.

    Yang JS, Lee SY, Gao M, Bourgoin S, Randazzo PA, Premont RT and Hsu VW

    Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.

    The role of GTPase-activating protein (GAP) that deactivates ADP-ribosylation factor 1 (ARF1) during the formation of coat protein I (COPI) vesicles has been unclear. GAP is originally thought to antagonize vesicle formation by triggering uncoating, but later studies suggest that GAP promotes cargo sorting, a process that occurs during vesicle formation. Recent models have attempted to reconcile these seemingly contradictory roles by suggesting that cargo proteins suppress GAP activity during vesicle formation, but whether GAP truly antagonizes coat recruitment in this process has not been assessed directly. We have reconstituted the formation of COPI vesicles by incubating Golgi membrane with purified soluble components, and find that ARFGAP1 in the presence of GTP promotes vesicle formation and cargo sorting. Moreover, the presence of GTPgammaS not only blocks vesicle uncoating but also vesicle formation by preventing the proper recruitment of GAP to nascent vesicles. Elucidating how GAP functions in vesicle formation, we find that the level of GAP on the reconstituted vesicles is at least as abundant as COPI and that GAP binds directly to the dilysine motif of cargo proteins. Collectively, these findings suggest that ARFGAP1 promotes vesicle formation by functioning as a component of the COPI coat.

    The Journal of cell biology 2002;159;1;69-78

  • GS15 forms a SNARE complex with syntaxin 5, GS28, and Ykt6 and is implicated in traffic in the early cisternae of the Golgi apparatus.

    Xu Y, Martin S, James DE and Hong W

    Membrane Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 117609, Singapore.

    The subcellular localization, interacting partners, and function of GS15, a Golgi SNARE, remain to be established. In our present study, it is revealed that unlike proteins (Bet1 and the KDEL receptor) cycling between the Golgi and the intermediate compartment (IC, inclusive of the ER exit sites), GS15 is not redistributed into the IC upon incubation at 15 degrees C or when cells are treated with brefeldin A. Immuno-electron microscopy (immuno-EM) reveals that GS15 is mainly found in the medial-cisternae of the Golgi apparatus and adjacent tubulo-vesicular elements. Coimmunoprecipitation experiments suggest that GS15 exists in a distinct SNARE complex that contains SNAREs (syntaxin5, GS28, and Ykt6) that are implicated in both ER-to-Golgi and intra-Golgi transport but not with SNAREs involved exclusively in ER-to-Golgi traffic. Furthermore, components of COPI coat can be selectively coimmunoprecipitated with GS15 from Golgi extracts. Overexpression of mutant forms of GS15 affects the normal distribution of cis- and medial-Golgi proteins (GS28, syntaxin 5, and Golgi mannosidase II), whereas proteins of the trans-Golgi and TGN (Vti1-rp2/Vti1a and syntaxin 6) and Golgi matrix/scaffold (GM130 and p115) are less affected. When the level of GS15 is reduced by duplex 21-nt small interfering RNA (siRNA)-mediated knockdown approach, diverse markers of the Golgi apparatus are redistributed into small dotty and diffuse labeling, suggesting an essential role of GS15 in the Golgi apparatus.

    Molecular biology of the cell 2002;13;10;3493-507

  • Ykt6 forms a SNARE complex with syntaxin 5, GS28, and Bet1 and participates in a late stage in endoplasmic reticulum-Golgi transport.

    Zhang T and Hong W

    Membrane Biology Laboratory, Institute of Molecular and Cell Biology, Singapore 117609, Singapore.

    The yeast SNARE Ykt6p has been implicated in several trafficking steps, including vesicular transport from the endoplasmic reticulum (ER) to the Golgi, intra-Golgi transport, and homotypic vacuole fusion. The functional role of its mammalian homologue (Ykt6) has not been established. Using antibodies specific for mammalian Ykt6, it is revealed that it is found mainly in Golgi-enriched membranes. Three SNAREs, syntaxin 5, GS28, and Bet1, are specifically associated with Ykt6 as revealed by co-immunoprecipitation, suggesting that these four SNAREs form a SNARE complex. Double labeling of Ykt6 and the Golgi marker mannosidase II or the ER-Golgi recycling marker KDEL receptor suggests that Ykt6 is primarily associated with the Golgi apparatus. Unlike the KDEL receptor, Ykt6 does not cycle back to the peripheral ER exit sites. Antibodies against Ykt6 inhibit in vitro ER-Golgi transport of vesicular stomatitis virus envelope glycoprotein (VSVG) only when they are added before the EGTA-sensitive stage. ER-Golgi transport of VSVG in vitro is also inhibited by recombinant Ykt6. In the presence of antibodies against Ykt6, VSVG accumulates in peri-Golgi vesicular structures and is prevented from entering the mannosidase II compartment, suggesting that Ykt6 functions at a late stage in ER-Golgi transport. Golgi apparatus marked by mannosidase II is fragmented into vesicular structures in cells microinjected with Ykt6 antibodies. It is concluded that Ykt6 functions in a late step of ER-Golgi transport, and this role may be important for the integrity of the Golgi complex.

    The Journal of biological chemistry 2001;276;29;27480-7

  • COP I domains required for coatomer integrity, and novel interactions with ARF and ARF-GAP.

    Eugster A, Frigerio G, Dale M and Duden R

    Department of Clinical Biochemistry, University of Cambridge, Hills Road, Cambridge CB2 2XY, UK

    We performed a systematic mapping of interaction domains on COP I subunits to gain novel insights into the architecture of coatomer. Using the two-hybrid system, we characterize the domain structure of the alpha-, beta'-, epsilon-COP and beta-, gamma-, delta-, zeta-COP coatomer subcomplexes and identify links between them that contribute to coatomer integrity. Our results demonstrate that the domain organization of the beta-, gamma-, delta-, zeta-COP subcomplex and AP adaptor complexes is related. Through in vivo analysis of alpha-COP truncation mutants, we characterize distinct functional domains on alpha-COP. Its N-terminal WD40 domain is dispensable for yeast cell viability and overall coatomer function, but is required for KKXX-dependent trafficking. The last approximately 170 amino acids of alpha-COP are also non-essential for cell viability, but required for epsilon-COP incorporation into coatomer and maintainance of normal epsilon-COP levels. Further, we demonstrate novel direct interactions of coatomer subunits with regulatory proteins: beta'- and gamma-COP interact with the ARF-GTP-activating protein (GAP) Glo3p, but not Gcs1p, and beta- and epsilon-COP interact with ARF-GTP. Glo3p also interacts with intact coatomer in vitro.

    The EMBO journal 2000;19;15;3905-17

  • Secretory protein trafficking and organelle dynamics in living cells.

    Lippincott-Schwartz J, Roberts TH and Hirschberg K

    Cell Biology and Metabolism Branch, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA. jlippin@helix.nih.gov

    Green fluorescent protein chimerae acting as reporters for protein localization and trafficking within the secretory membrane system of living cells have been used in a wide variety of applications, including time-lapse imaging, double-labeling, energy transfer, quantitation, and photobleaching experiments. Results from this work are clarifying the steps involved in the formation, translocation, and fusion of transport intermediates; the organization and biogenesis of organelles; and the mechanisms of protein retention, sorting, and recycling in the secretory pathway. In so doing, they are broadening our thinking about the temporal and spatial relationships among secretory organelles and the membrane trafficking pathways that operate between them.

    Annual review of cell and developmental biology 2000;16;557-89

  • A single binding site for dilysine retrieval motifs and p23 within the gamma subunit of coatomer.

    Harter C and Wieland FT

    Biochemie-Zentrum Heidelberg, Ruprecht-Karls-Universität, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.

    Coatomer, the major component of the coat of COPI transport vesicles, binds both to the dilysine motif of resident membrane proteins of the endoplasmic reticulum and to the cytoplasmic domain of p23, a major type I membrane protein of COPI vesicles. Using a photocrosslinking approach, we find that under native conditions a peptide analogous to the cytoplasmic domain of p23 interacts with coatomer exclusively through its gamma subunit and shares its binding site with a KKXX retrieval motif. However, upon dissociation of coatomer, interaction with various subunits, including an alpha-, beta'-, epsilon-COP subcomplex, of the photoreactive peptide is observed. We suggest that, under physiological conditions, interaction of coatomer with both endoplasmic reticulum retrieval motifs and the cytoplasmic domain of p23 is mediated by gamma-COP.

    Proceedings of the National Academy of Sciences of the United States of America 1998;95;20;11649-54

  • Reversible dissociation of coatomer: functional characterization of a beta/delta-coat protein subcomplex.

    Pavel J, Harter C and Wieland FT

    Biochemie-Zentrum Heidelberg Ruprecht-Karls-Universität, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.

    COPI-coated vesicles mediate protein transport within the early secretory pathway. Their coat consists of ADP ribosylation factor (ARF1, a small guanosine nucleotide binding protein), and coatomer, a cytosolic complex composed of seven subunits, alpha- to zeta-coat proteins (COPs). For coat formation that initiates budding of a vesicle, ARF1 is recruited to the Golgi membrane from the cytosol in its GTP-bound form, and subsequently, coatomer can bind to the membrane. To identify a minimal structure of coatomer capable to bind to Golgi membranes in an ARF1-dependent manner, we have established a procedure to dissociate coatomer under conditions that allow reassociation of the subunits to a complete and functional complex. After dissociation, subunits or subcomplexes can be isolated and may be expected to be functional. Herein we describe isolation of a subcomplex of coatomer consisting of beta- and delta-COPs that is able to bind to Golgi membranes in an ARF1- and GTP-dependent manner.

    Proceedings of the National Academy of Sciences of the United States of America 1998;95;5;2140-5

  • Xenin--a review.

    Feurle GE

    DRK-Krankenhaus Neuwied, Germany.

    Xenin, a 25 amino acid peptide, has been identified in human gastric mucosa in the search for a counterpart to the amphibian octapeptide xenopsin. Xenin is structurally related also to the hypothalamic and ileal peptide neurotensin and is, therefore, a member of the xenopsin/neurotensin/xenin peptide family. The biological activities of these peptides are similar: Xenin has been shown to inhibit pentagastrin-stimulated secretion of acid, to induce exocrine pancreatic secretion and to affect small and large intestinal motility. In the gut, xenin interacts with the neurotensin receptor. Radioimmunoassay and chromatography of postprandial plasma in humans indicate the release of xenin into the circulation. The identification of a 35-amino acid precursor peptide of xenin - proxenin, and a review of the Gen-bank revealed that xenin represents the N terminus of a cytosolic coat protein (alpha-COP) from which xenin can be cleaved by aspartic proteinases such as pepsin and cathepsin E. The physiological role of the peptide xenin is not known.

    Peptides 1998;19;3;609-15

  • Alpha coat protein COPA (HEP-COP): presence of an Alu repeat in cDNA and identity of the amino terminus to xenin.

    Chow VT and Quek HH

    Department of Microbiology, Faculty of Medicine, National University of Singapore, Singapore.

    We previously sequenced the 4333-nucleotide cDNA of the COPA (HEP-COP) gene which encodes the human homologue of the alpha-subunit of the coatomer protein complex, involved in intracellular protein transport. Within the 3' untranslated region at nucleotides 4049-4333 was observed an Alu repeat containing conserved A and B block elements, and showing high homology to the human Alu-Sx subfamily consensus sequence. Upstream of the Alu repeat were noted a TATA box, a CAAT motif and two activating transcription factor (ATF)-like binding sites, which represent putative regulatory elements directing Alu transcription. In addition, the 25 and 35 N-terminal amino acid residues of COPA and its bovine homologue were identical to xenin-25 and proxenin, respectively. Xenin-25 is a gastrointestinal hormone that stimulates exocrine pancreatic secretion. This peptide is related to xenopsin, neurotensin and neuromedin N which are bioactive peptides derived from larger precursors via proteolytic cleavage by cathepsin E at processing sites determined by conserved C-terminal sequences, i.e. proline/valine-X-X-hydrophobic amino acid. Given the conformity of the C-terminal residues of xenin-25 (PWIL) and of its progenitor molecule, proxenin (VIQL), it is proposed that these peptides are generated by a similar mechanism of post-translational modification involving a parent precursor represented by the alpha-subunit of coatomer.

    Annals of human genetics 1997;61;Pt 4;369-73

  • Association of coatomer proteins with the beta-receptor for platelet-derived growth factor.

    Hansen K, Rönnstrand L, Rorsman C, Hellman U and Heldin CH

    Ludwig Institute for Cancer Research, Biomedical Center, Uppsala, Sweden.

    The nonreceptor tyrosine kinase Src binds to and is activated by the beta-receptor for platelet-derived growth factor (PDGF). The interaction leads to Src phosphorylation of Tyr934 in the kinase domain of the receptor. In the course of the functional characterization of this phosphorylation, we noticed that components of 136 and 97 kDa bound to a peptide from this region of the receptor in a phosphorylation-independent manner. These components have now been purified and identified as alpha- and beta'-coatomer proteins (COPs), respectively. COPs are a family of proteins involved in the regulation of intracellular vesicle transport. In order to explore the functional significance of the interaction between alpha- and beta'-COP and the PDGF receptor, a receptor mutant was made in which the conserved histidine residue 928 was mutated to an alanine residue. The mutant receptor, which was unable to bind alpha- or beta'-COP, showed a normal ligand-induced autophosphorylation. The mutant receptor also behaved like the wildtype receptor with regard to biosynthesis and maturation, and mediated a mitogenic signal. The possible functional importance of the interaction between the PDGF beta-receptor and alpha- and beta'-COP, is discussed.

    Biochemical and biophysical research communications 1997;235;3;455-60

  • Molecular and cellular studies of the human homolog of the 160-kD alpha-subunit of the coatomer protein complex.

    Quek HH and Chow VT

    Department of Microbiology, Faculty of Medcine, National University of Singapore, Republic of Singapore.

    The traffic of proteins through the eukaryotic secretory pathway is achieved in part by nonclathrin-coated vesicles mediating transport between the Golgi network and the endoplasmic reticulum. These transit vesicles are coated with coat proteins (COP), which assemble to form a complex of seven polypeptides known as coatomer. From the Hep3B human hepatocellular carcinoma cell line, we have previously isolated and sequenced the cDNA of a novel gene, HEP-COP, whose predicted amino acid sequence, calculated relative molecular mass, and hydrophilicity are strikingly similar to the 160-kD alpha-subunit of the coatomer complex in yeast. Four synthetic peptides were designed for immunizing pairs of rabbits to generate polyclonal antisera. In Western blot experiments, these antibodies could specifically recognize protein bands of 160 kD, which were absent when control preimmune sera were used. Immunoblotting of subcellular components of Hep3B cells probed with one of the antisera revealed 160-kD protein bands predominantly in the microsomal and cytosolic fractions, but virtually none in the nuclear compartment. Indirect immunofluorescence of Hep3B cells using the same antibody exhibited fluorescent staining chiefly in the cytoplasm. Taken together with the cDNA data, the results of this immunological analysis of the putative HEP-COP protein support the suggestion that the latter is the human homolog of alpha-COP.

    DNA and cell biology 1997;16;3;275-80

  • Genomic organization and mapping of the human HEP-COP gene (COPA) to 1q.

    Quek HH and Chow VT

    Department of Microbiology, Faculty of Medicine, National University of Singapore, Kent Ridge, Republic of Singapore.

    In eukaryotic cells, protein transport between the endoplasmic reticulum and Golgi compartments is mediated in part by non-clathrin-coated vesicular coat proteins (COP). Seven COP subunits have been recognized, and represent components of a complex known as coatomer. We have previously isolated the cDNA of the human homolog of alpha-COP, designated HEP-COP and given the official gene symbol COPA. Here we report the genomic organization of COPA, which contains 33 exons ranging in size from 67 to 611 bp. Mapped by PCR and cycle sequencing, all the exon-intron junctions conformed with the GT-AG rule, the 32 introns ranging from about 80 bp to 4 kbp, with the genomic DNA of COPA estimated to span approximately 37 kb. Southern blot analysis of genomic DNAs of nine eukaryotic species, from human to yeast, revealed identical signals totaling 36 kb each for man and monkey only. Using 5' RACE and primer extension analysis, the putative transcriptional start site was localized to 466 nucleotides upstream of the translation initiation codon. Comprising a 126-nucleotide 5' untranscribed genomic sequence and a 466-nucleotide 5' noncoding cDNA sequence, the 592-nucleotide 5' CpG island lacked TATA and CAAT boxes but displayed a high G+C content, was enriched for CpG dinucleotides, and contained a potential Sp1-binding site, i.e., features compatible with a housekeeping gene. COPA was mapped by fluorescence in situ hybridization to chromosome region 1q23-->q25.

    Cytogenetics and cell genetics 1997;76;3-4;139-43

  • In vivo assembly of coatomer, the COP-I coat precursor.

    Lowe M and Kreis TE

    Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211 Geneva, Switzerland. kreis@sc2a.unige.ch

    Coatomer, a seven-subunit hetero-oligomeric complex, is the major component of the COP-I membrane coat of transport vesicles of the early secretory pathway. We have followed the assembly of this complex in vivo by pulse-chase experiments and immunoprecipitation of native coatomer subunits and found that it is an ordered process that takes 1-2 h to complete. During assembly, direct interactions between alpha-, beta'- and delta-COP, beta- and delta-COP, and gamma-, zeta-, and delta-COP occur. Coatomer, once it has assembled, is stable with a half-life of approximately 28 h. No significant amounts of partial coatomer complexes have been detected. The only subunit to exist at steady state out of the complex is zeta-COP, which has a similar half-life to coatomer subunits within the complex. Assembly is inhibited by brefeldin A, suggesting that it may be a regulated process. These results describe for the first time in vivo assembly of a coat protein complex involved in membrane traffic and extend our knowledge of how coatomer is structured.

    The Journal of biological chemistry 1996;271;48;30725-30

  • Architecture of coatomer: molecular characterization of delta-COP and protein interactions within the complex.

    Faulstich D, Auerbach S, Orci L, Ravazzola M, Wegchingel S, Lottspeich F, Stenbeck G, Harter C, Wieland FT and Tschochner H

    Institut für Biochemie I, Heidelberg, Germany.

    Coatomer is a cytosolic protein complex that forms the coat of COP I-coated transport vesicles. In our attempt to analyze the physical and functional interactions between its seven subunits (coat proteins, [COPs] alpha-zeta), we engaged in a program to clone and characterize the individual coatomer subunits. We have now cloned, sequenced, and overexpressed bovine alpha-COP, the 135-kD subunit of coatomer as well as delta-COP, the 57-kD subunit and have identified a yeast homolog of delta-COP by cDNA sequence comparison and by NH2-terminal peptide sequencing. delta-COP shows homologies to subunits of the clathrin adaptor complexes AP1 and AP2. We show that in Golgi-enriched membrane fractions, the protein is predominantly found in COP I-coated transport vesicles and in the budding regions of the Golgi membranes. A knock-out of the delta-COP gene in yeast is lethal. Immunoprecipitation, as well as analysis exploiting the two-hybrid system in a complete COP screen, showed physical interactions between alpha- and epsilon-COPs and between beta- and delta-COPs. Moreover, the two-hybrid system indicates interactions between gamma- and zeta-COPs as well as between alpha- and beta' COPs. We propose that these interactions reflect in vivo associations of those subunits and thus play a functional role in the assembly of coatomer and/or serve to maintain the molecular architecture of the complex.

    The Journal of cell biology 1996;135;1;53-61

  • Bimodal interaction of coatomer with the p24 family of putative cargo receptors.

    Fiedler K, Veit M, Stamnes MA and Rothman JE

    Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.

    Cytoplasmic domains of members of the p24 family of putative cargo receptors were shown to bind to coatomer, the coat protein of COPI-coated transport vesicles. Domains that contained dilysine endoplasmic reticulum retrieval signals bound the alpha-, beta'-, and epsilon-COP subunits of coatomer, whereas other p24 domains bound the beta-, gamma-, and zeta-COP subunits and required a phenylalanine-containing motif. Transit of a CD8-p24 chimera from the endoplasmic reticulum through the Golgi complex was slowed when the phenylalanine motif was mutated, suggesting that this motif may function as an anterograde transport signal. The either-or bimodal binding of coatomer to p24 tails suggests models for how coatomer can potentially package retrograde-directed and anterograde-directed cargo into distinct COPI-coated vesicles.

    Science (New York, N.Y.) 1996;273;5280;1396-9

  • Coat proteins and vesicle budding.

    Schekman R and Orci L

    Department of Molecular and Cell Biology, University of California, Berkeley, 94720-3202, USA.

    The trafficking of proteins within eukaryotic cells is achieved by the capture of cargo and targeting molecules into vesicles that bud from a donor membrane and deliver their contents to a receiving department. This process is bidirectional and may involve multiple organelles within a cell. Distinct coat proteins mediate each budding event, serving both to shape the transport vesicle and to select by direct or indirect interaction the desired set of cargo molecules. Secretion, which has been viewed as a default pathway, may require sorting and packaging signals on transported molecules to ensure their rapid delivery to the cell surface.

    Science (New York, N.Y.) 1996;271;5255;1526-33

  • HEP-COP, a novel human gene whose product is highly homologous to the alpha-subunit of the yeast coatomer protein complex.

    Chow VT and Quek HH

    Department of Microbiology, Faculty of Medicine, National University of Singapore.

    A 4333-bp novel human cDNA sequence designated HEP-COP was isolated from the Hep3B hepatocellular carcinoma cell line by the RACE technique. Within HEP-COP was identified an ORF of 3672 bp encoding a deduced 1224-amino-acid (aa) sequence which exhibited striking homology with the 1201-aa sequence of RET1P, the alpha-subunit of the coatomer complex (alpha-COP) in Saccharomyces cerevisiae which participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The aa homology was highest in their N-terminal regions which each contained six WD-40 repeat motifs [Van der Voorn and Ploegh, FEBS Lett. 307 (1992) 131-134], and both proteins were predicted to be hydrophilic with similar estimated molecular masses of 138 324 and 135 599 Da, respectively. Northern blot hybridization demonstrated that HEP-COP was expressed in a wide range of human adult and fetal tissues. RT-PCR analysis revealed no differential expression of HEP-COP in 14 human cancer cell lines, as compared with normal control cells. Considering the close similarities between HEP-COP and yeast alpha-COP, and the ubiquitous expression of HEP-COP implying an essential cellular role, it is likely that HEP-COP is the human homologue of alpha-COP.

    Gene 1996;169;2;223-7

  • In vitro assembly and disassembly of coatomer.

    Lowe M and Kreis TE

    Département de Biologie Cellulaire, Université de Genève, Sciences III, Geneva, Switzerland.

    Coatomer, a complex of seven proteins, is the major component of the non-clathrin (COP I) membrane coat. We report here the first system to reversibly disassemble and reassemble this complex in vitro. Coatomer disassembles at high salt concentrations and reassembles when returned to a more physiological buffer. Using this system, we show that alpha-, beta'-, and epsilon-COP interact directly and that gamma-COP interacts with zeta-COP. A partial complex comprising alpha-, beta'-, and epsilon-COP, obtained after coatomer disassembly, can bind to membranes in vitro. This binding is, at least in part, mediated by interactions with cytoplasmic KKXX motifs of proteins normally retained in or retrieved to the endoplasmic reticulum. Using coatomer disassembly and epitope-specific antibodies, we also demonstrate that the N- and C-terminal domains of beta-COP are buried within the native coatomer complex. These results provide the first insights into how the coatomer is structured.

    The Journal of biological chemistry 1995;270;52;31364-71

  • The ARF1 GTPase-activating protein: zinc finger motif and Golgi complex localization.

    Cukierman E, Huber I, Rotman M and Cassel D

    Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel.

    Hydrolysis of guanosine triphosphate (GTP) by the small guanosine triphosphatase (GTPase) adenosine diphosphate ribosylation factor-1 (ARF1) depends on a GTPase-activating protein (GAP). A complementary DNA encoding the ARF1 GAP was cloned from rat liver and predicts a protein with a zinc finger motif near the amino terminus. The GAP function required an intact zinc finger and additional amino-terminal residues. The ARF1 GAP was localized to the Golgi complex and was redistributed into a cytosolic pattern when cells were treated with brefeldin A, a drug that prevents ARF1-dependent association of coat proteins with the Golgi. Thus, the GAP is likely to be recruited to the Golgi by an ARF1-dependent mechanism.

    Science (New York, N.Y.) 1995;270;5244;1999-2002

  • Coated vesicle assembly in the Golgi requires only coatomer and ARF proteins from the cytosol.

    Orcl L, Palmer DJ, Amherdt M and Rothman JE

    Department of Morphology, University of Geneva Medical Center, Switzerland.

    Transport vesicles derived from the Golgi apparatus are thought to mediate biosynthetic transport across the Golgi stack. These vesicles are surrounded by a protein coat whose principal constituents are coatomer (a complex of seven distinct subunits or COPs) and ADP-ribosylation factor (ARF, an N-myristylated small GTP-binding protein). The coat proteins of the COP-coated vesicles were originally defined by ultrastructural criteria, however, and it is possible that important but minor coat proteins or cytoplasmic proteins needed for coat assembly may have been overlooked. Here we show that coatomer and ARF are the only cytoplasmic proteins needed for the assembly and budding of COP-coated vesicles. COP-coated buds may therefore form essentially by self-assembly from Golgi cisternae after an initial step in which GTP is used to allow ARF binding.

    Nature 1993;364;6439;732-4

  • Identification of xenin, a xenopsin-related peptide, in the human gastric mucosa and its effect on exocrine pancreatic secretion.

    Feurle GE, Hamscher G, Kusiek R, Meyer HE and Metzger JW

    Stadtkrankenhaus Neuwied, Federal Republic of Germany.

    One of the peptides previously discovered in amphibians is the octapeptide xenopsin. As immunohistochemistry has also indicated the presence of xenopsin immunoreactivity in man, we extracted in the present investigation xenopsin-immunoreactive material from human gastric mucosa and purified it to homogeneity with several high performance liquid chromatography (HPLC) reverse phase and ion exchange chromatographic steps. The eluates were monitored with a radioimmunoassay for amphibian xenopsin. Determination of the amino acid sequence revealed a 25-amino acid peptide having 6 C-terminal amino acids in common with amphibian xenopsin. The sequence of this peptide, termed xenin 25, is M-L-T-K-F-E-T-K-S-A-R-V-K-G-L-S-F-H-P-K-R-P-W-I-L. The peptide was custom-synthesized. Mass spectrometry of the synthetic and the extracted peptide revealed identical molecular mass. Purification of 250 ml of human postprandial plasma with Sep-Pak C18 cartridges, reverse phase HPLC, and ion exchange chromatography demonstrated circulating xenin immunoreactivity at a retention time identical to xenin 25. The amount of xenin immunoreactivity at the position of xenin 25 on C18-HPLC increased significantly after a meal. A radioimmunoassay utilizing antibodies to xenin 25 and a 125I-labeled analogue of xenin 25 was used to measure immunoreactive xenin in the plasma of 10 volunteers. There was a significant rise of xenin immunoreactivity in the plasma after a meal. Intravenous infusion of the synthetic peptide in dogs stimulated exocrine pancreatic secretion beginning at a dose of 4 pmol/kg/min. The maximal effect was seen with 64 pmol/kg/min. We have detected, therefore, a new peptide, xenin 25, in human gastric mucosa; we have provided evidence for the presence of this peptide in the human circulation, and have shown a rise of plasma xenin concentrations after a meal. This peptide stimulates exocrine pancreatic secretion. Its physiologic role deserves further investigation.

    The Journal of biological chemistry 1992;267;31;22305-9

Gene lists (4)

Gene List Source Species Name Description Gene count
L00000009 G2C Homo sapiens Human PSD Human orthologues of mouse PSD adapted from Collins et al (2006) 1080
L00000016 G2C Homo sapiens Human PSP Human orthologues of mouse PSP adapted from Collins et al (2006) 1121
L00000069 G2C Homo sapiens BAYES-COLLINS-HUMAN-PSD-FULL Human cortex biopsy PSD full list 1461
L00000071 G2C Homo sapiens BAYES-COLLINS-MOUSE-PSD-FULL Mouse cortex PSD full list (ortho) 1556
© G2C 2014. The Genes to Cognition Programme received funding from The Wellcome Trust and the EU FP7 Framework Programmes:
EUROSPIN (FP7-HEALTH-241498), SynSys (FP7-HEALTH-242167) and GENCODYS (FP7-HEALTH-241995).

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