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Andreev I, Laidlaw KME, Giovanetti SM, Urtecho G, Shriner D, Bloom JS, MacDonald C, Sadhu MJ. Discovery of a rapidly evolving yeast defense factor, KTD1, against the secreted killer toxin K28. Proc Natl Acad Sci U S A 2023; 120:e2217194120. [PMID: 36800387 PMCID: PMC9974470 DOI: 10.1073/pnas.2217194120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/09/2022] [Indexed: 02/18/2023] Open
Abstract
Secreted protein toxins are widely used weapons in conflicts between organisms. Elucidating how organisms genetically adapt to defend themselves against these toxins is fundamental to understanding the coevolutionary dynamics of competing organisms. Within yeast communities, "killer" toxins are secreted to kill nearby sensitive yeast, providing a fitness advantage in competitive growth environments. Natural yeast isolates vary in their sensitivity to these toxins, but to date, no polymorphic genetic factors contributing to defense have been identified. We investigated the variation in resistance to the killer toxin K28 across diverse natural isolates of the Saccharomyces cerevisiae population. Using large-scale linkage mapping, we discovered a novel defense factor, which we named KTD1. We identified many KTD1 alleles, which provided different levels of K28 resistance. KTD1 is a member of the DUP240 gene family of unknown function, which is rapidly evolving in a region spanning its two encoded transmembrane helices. We found that this domain is critical to KTD1's protective ability. Our findings implicate KTD1 as a key polymorphic factor in the defense against K28 toxin.
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Affiliation(s)
- Ilya Andreev
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Kamilla M. E. Laidlaw
- Biology Department, University of York, YorkYO10 5DD, UK
- York Biomedical Research Institute, University of York, YorkYO10 5NG, UK
| | - Simone M. Giovanetti
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Guillaume Urtecho
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, CA90095
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Joshua S. Bloom
- Department of Human Genetics, University of California, Los Angeles, CA90095
- Department of Biological Chemistry, University of California, Los Angeles, CA90095
- HHMI, University of California, Los Angeles, CA90095
- Institute for Quantitative and Computational Biology, University of California, Los Angeles, CA90095
- Department of Computational Medicine, University of California, Los Angeles, CA90095
| | - Chris MacDonald
- Biology Department, University of York, YorkYO10 5DD, UK
- York Biomedical Research Institute, University of York, YorkYO10 5NG, UK
| | - Meru J. Sadhu
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
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2
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Solinger JA, Spang A. Sorting of cargo in the tubular endosomal network. Bioessays 2022; 44:e2200158. [DOI: 10.1002/bies.202200158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Affiliation(s)
| | - Anne Spang
- Biozentrum University of Basel Basel Switzerland
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3
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Godara A, Kao KC. Adaptive laboratory evolution of β-caryophyllene producing Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:106. [PMID: 34044821 PMCID: PMC8157465 DOI: 10.1186/s12934-021-01598-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/20/2021] [Indexed: 11/10/2022] Open
Abstract
Background β-Caryophyllene is a plant terpenoid with therapeutic and biofuel properties. Production of terpenoids through microbial cells is a potentially sustainable alternative for production. Adaptive laboratory evolution is a complementary technique to metabolic engineering for strain improvement, if the product-of-interest is coupled with growth. Here we use a combination of pathway engineering and adaptive laboratory evolution to improve the production of β-caryophyllene, an extracellular product, by leveraging the antioxidant potential of the compound. Results Using oxidative stress as selective pressure, we developed an adaptive laboratory evolution that worked to evolve an engineered β-caryophyllene producing yeast strain for improved production within a few generations. This strategy resulted in fourfold increase in production in isolated mutants. Further increasing the flux to β-caryophyllene in the best evolved mutant achieved a titer of 104.7 ± 6.2 mg/L product. Genomic analysis revealed a gain-of-function mutation in the a-factor exporter STE6 was identified to be involved in significantly increased production, likely as a result of increased product export. Conclusion An optimized selection strategy based on oxidative stress was developed to improve the production of the extracellular product β-caryophyllene in an engineered yeast strain. Application of the selection strategy in adaptive laboratory evolution resulted in mutants with significantly increased production and identification of novel responsible mutations. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01598-z.
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Affiliation(s)
- Avinash Godara
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Katy C Kao
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA. .,Department of Chemical and Materials Engineering, San Jose State University, One Washington Sq, San Jose, CA, 95192, USA.
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4
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Ma W, Goldberg E, Goldberg J. ER retention is imposed by COPII protein sorting and attenuated by 4-phenylbutyrate. eLife 2017; 6. [PMID: 28594326 PMCID: PMC5464768 DOI: 10.7554/elife.26624] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/18/2017] [Indexed: 01/07/2023] Open
Abstract
Native cargo proteins exit the endoplasmic reticulum (ER) in COPII-coated vesicles, whereas resident and misfolded proteins are substantially excluded from vesicles by a retention mechanism that remains unresolved. We probed the ER retention process using the proteostasis regulator 4-phenylbutyrate (4-PBA), which we show targets COPII protein to reduce the stringency of retention. 4-PBA competes with p24 proteins to bind COPII. When p24 protein uptake is blocked, COPII vesicles package resident proteins and an ER-trapped mutant LDL receptor. We further show that 4-PBA triggers the secretion of a KDEL-tagged luminal resident, implying that a compromised retention mechanism causes saturation of the KDEL retrieval system. The results indicate that stringent ER retention requires the COPII coat machinery to actively sort biosynthetic cargo from diffusible misfolded and resident ER proteins. DOI:http://dx.doi.org/10.7554/eLife.26624.001
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Affiliation(s)
- Wenfu Ma
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Elena Goldberg
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Jonathan Goldberg
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, New York, United States
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5
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Gomez-Navarro N, Miller E. Protein sorting at the ER-Golgi interface. J Cell Biol 2016; 215:769-778. [PMID: 27903609 PMCID: PMC5166505 DOI: 10.1083/jcb.201610031] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/02/2016] [Accepted: 11/17/2016] [Indexed: 01/01/2023] Open
Abstract
In this review, Gomez-Navarro and Miller summarize the principles of cargo sorting by the vesicle traffic machinery and consider the diverse mechanisms by which cargo proteins are selected and captured into different transport vesicles. Protein traffic is of critical importance for normal cellular physiology. In eukaryotes, spherical transport vesicles move proteins and lipids from one internal membrane-bound compartment to another within the secretory pathway. The process of directing each individual protein to a specific destination (known as protein sorting) is a crucial event that is intrinsically linked to vesicle biogenesis. In this review, we summarize the principles of cargo sorting by the vesicle traffic machinery and consider the diverse mechanisms by which cargo proteins are selected and captured into different transport vesicles. We focus on the first two compartments of the secretory pathway: the endoplasmic reticulum and Golgi. We provide an overview of the complexity and diversity of cargo adaptor function and regulation, focusing on recent mechanistic discoveries that have revealed insight into protein sorting in cells.
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Affiliation(s)
- Natalia Gomez-Navarro
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, England, UK
| | - Elizabeth Miller
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, England, UK
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6
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Kilisch M, Lytovchenko O, Arakel EC, Bertinetti D, Schwappach B. A dual phosphorylation switch controls 14-3-3-dependent cell surface expression of TASK-1. J Cell Sci 2016; 129:831-42. [PMID: 26743085 PMCID: PMC4760375 DOI: 10.1242/jcs.180182] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/29/2015] [Indexed: 11/20/2022] Open
Abstract
The transport of the K+ channels TASK-1 and TASK-3 (also known as KCNK3 and KCNK9, respectively) to the cell surface is controlled by the binding of 14-3-3 proteins to a trafficking control region at the extreme C-terminus of the channels. The current model proposes that phosphorylation-dependent binding of 14-3-3 sterically masks a COPI-binding motif. However, the direct effects of phosphorylation on COPI binding and on the binding parameters of 14-3-3 isoforms are still unknown. We find that phosphorylation of the trafficking control region prevents COPI binding even in the absence of 14-3-3, and we present a quantitative analysis of the binding of all human 14-3-3 isoforms to the trafficking control regions of TASK-1 and TASK-3. Surprisingly, the affinities of 14-3-3 proteins for TASK-1 are two orders of magnitude lower than for TASK-3. Furthermore, we find that phosphorylation of a second serine residue in the C-terminus of TASK-1 inhibits 14-3-3 binding. Thus, phosphorylation of the trafficking control region can stimulate or inhibit transport of TASK-1 to the cell surface depending on the target serine residue. Our findings indicate that control of TASK-1 trafficking by COPI, kinases, phosphatases and 14-3-3 proteins is highly dynamic. Summary: Phosphorylation of a previously neglected serine residue in the trafficking control region of TASK-1 interferes with the binding of trafficking machinery and enables complex regulation by physiological stimuli.
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Affiliation(s)
- Markus Kilisch
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen 37073, Germany
| | - Olga Lytovchenko
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen 37073, Germany
| | - Eric C Arakel
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen 37073, Germany
| | | | - Blanche Schwappach
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen 37073, Germany Max-Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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7
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Springer S, Malkus P, Borchert B, Wellbrock U, Duden R, Schekman R. Regulated Oligomerization Induces Uptake of a Membrane Protein into COPII Vesicles Independent of Its Cytosolic Tail. Traffic 2014; 15:531-45. [DOI: 10.1111/tra.12157] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 01/07/2014] [Accepted: 01/30/2014] [Indexed: 12/22/2022]
Affiliation(s)
| | - Per Malkus
- Department of Systems Biology; Harvard Medical School; Boston MA 02115 USA
| | - Britta Borchert
- Biochemistry and Cell Biology; Jacobs University Bremen; Bremen Germany
| | - Ursula Wellbrock
- Biochemistry and Cell Biology; Jacobs University Bremen; Bremen Germany
| | - Rainer Duden
- Centre for Structural and Cell Biology in Medicine, Institute of Biology; University of Lübeck; Lübeck Germany
| | - Randy Schekman
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology; University of California, Berkeley; Berkeley CA 94720 USA
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8
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Abstract
The secretory pathway is responsible for the synthesis, folding, and delivery of a diverse array of cellular proteins. Secretory protein synthesis begins in the endoplasmic reticulum (ER), which is charged with the tasks of correctly integrating nascent proteins and ensuring correct post-translational modification and folding. Once ready for forward traffic, proteins are captured into ER-derived transport vesicles that form through the action of the COPII coat. COPII-coated vesicles are delivered to the early Golgi via distinct tethering and fusion machineries. Escaped ER residents and other cycling transport machinery components are returned to the ER via COPI-coated vesicles, which undergo similar tethering and fusion reactions. Ultimately, organelle structure, function, and cell homeostasis are maintained by modulating protein and lipid flux through the early secretory pathway. In the last decade, structural and mechanistic studies have added greatly to the strong foundation of yeast genetics on which this field was built. Here we discuss the key players that mediate secretory protein biogenesis and trafficking, highlighting recent advances that have deepened our understanding of the complexity of this conserved and essential process.
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9
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David C, Koch J, Oeljeklaus S, Laernsack A, Melchior S, Wiese S, Schummer A, Erdmann R, Warscheid B, Brocard C. A combined approach of quantitative interaction proteomics and live-cell imaging reveals a regulatory role for endoplasmic reticulum (ER) reticulon homology proteins in peroxisome biogenesis. Mol Cell Proteomics 2013; 12:2408-25. [PMID: 23689284 DOI: 10.1074/mcp.m112.017830] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Peroxisome biogenesis initiates at the endoplasmic reticulum (ER) and maturation allows for the formation of metabolically active organelles. Yet, peroxisomes can also multiply by growth and division. Several proteins, called peroxins, are known to participate in these processes but little is known about their organization to orchestrate peroxisome proliferation. Here, we demonstrate that regulation of peroxisome proliferation relies on the integrity of the tubular ER network. Using a dual track SILAC-based quantitative interaction proteomics approach, we established a comprehensive network of stable as well as transient interactions of the peroxin Pex30p, an integral membrane protein. Through association with merely ER resident proteins, in particular with proteins containing a reticulon homology domain, and with other peroxins, Pex30p designates peroxisome contact sites at ER subdomains. We show that Pex30p traffics through the ER and segregates in punctae to which peroxisomes specifically append, and we ascertain its transient interaction with all subunits of the COPI coatomer complex suggesting the involvement of a vesicle-mediated transport. We establish that the membrane protein Pex30p facilitates the connection of peroxisomes to the ER. Taken together, our data indicate that Pex30p-containing protein complexes act as focal points from which peroxisomes can form and that the tubular ER architecture organized by the reticulon homology proteins Rtn1p, Rtn2p and Yop1p controls this process.
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Affiliation(s)
- Christine David
- University of Vienna, Max F. Perutz Laboratories, Center of Molecular Biology, Department of Biochemistry and Cell Biology, Dr. Bohr-Gasse 9, A-1030, Vienna, Austria
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10
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Delic M, Valli M, Graf AB, Pfeffer M, Mattanovich D, Gasser B. The secretory pathway: exploring yeast diversity. FEMS Microbiol Rev 2013; 37:872-914. [PMID: 23480475 DOI: 10.1111/1574-6976.12020] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 02/14/2013] [Accepted: 02/17/2013] [Indexed: 12/11/2022] Open
Abstract
Protein secretion is an essential process for living organisms. In eukaryotes, this encompasses numerous steps mediated by several hundred cellular proteins. The core functions of translocation through the endoplasmic reticulum membrane, primary glycosylation, folding and quality control, and vesicle-mediated secretion are similar from yeasts to higher eukaryotes. However, recent research has revealed significant functional differences between yeasts and mammalian cells, and even among diverse yeast species. This review provides a current overview of the canonical protein secretion pathway in the model yeast Saccharomyces cerevisiae, highlighting differences to mammalian cells as well as currently unresolved questions, and provides a genomic comparison of the S. cerevisiae pathway to seven other yeast species where secretion has been investigated due to their attraction as protein production platforms, or for their relevance as pathogens. The analysis of Candida albicans, Candida glabrata, Kluyveromyces lactis, Pichia pastoris, Hansenula polymorpha, Yarrowia lipolytica, and Schizosaccharomyces pombe reveals that many - but not all - secretion steps are more redundant in S. cerevisiae due to duplicated genes, while some processes are even absent in this model yeast. Recent research obviates that even where homologous genes are present, small differences in protein sequence and/or differences in the regulation of gene expression may lead to quite different protein secretion phenotypes.
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Affiliation(s)
- Marizela Delic
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria; Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
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11
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Wang L, Zheng W, Zhao H, Deng M. Statistical analysis reveals co-expression patterns of many pairs of genes in yeast are jointly regulated by interacting loci. PLoS Genet 2013; 9:e1003414. [PMID: 23555313 PMCID: PMC3610942 DOI: 10.1371/journal.pgen.1003414] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 02/11/2013] [Indexed: 11/30/2022] Open
Abstract
Expression quantitative trait loci (eQTL) studies have generated large amounts of data in different organisms. The analyses of these data have led to many novel findings and biological insights on expression regulations. However, the role of epistasis in the joint regulation of multiple genes has not been explored. This is largely due to the computational complexity involved when multiple traits are simultaneously considered against multiple markers if an exhaustive search strategy is adopted. In this article, we propose a computationally feasible approach to identify pairs of chromosomal regions that interact to regulate co-expression patterns of pairs of genes. Our approach is built on a bivariate model whose covariance matrix depends on the joint genotypes at the candidate loci. We also propose a filtering process to reduce the computational burden. When we applied our method to a yeast eQTL dataset profiled under both the glucose and ethanol conditions, we identified a total of 225 and 224 modules, with each module consisting of two genes and two eQTLs where the two eQTLs epistatically regulate the co-expression patterns of the two genes. We found that many of these modules have biological interpretations. Under the glucose condition, ribosome biogenesis was co-regulated with the signaling and carbohydrate catabolic processes, whereas silencing and aging related genes were co-regulated under the ethanol condition with the eQTLs containing genes involved in oxidative stress response process. eQTL studies collect both gene expression and genotype data, and they are highly informative as to how genes regulate expressions. Although much progress has been made in the analysis of such data, most studies have considered one marker at a time. As a result, those markers with weak marginal yet strong interactive effects may not be inferred from these single-marker-based analyses. In this article, using joint expression patterns between two genes (versus one gene) as the primary phenotype, we propose a novel statistical method to conduct an exhaustive search for joint marker analysis. When our method is applied to a well-studied dataset, we were able to identify many novel features that were overlooked by existing methods. Our general strategy has general applicability to other scientific problems.
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Affiliation(s)
- Lin Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Wei Zheng
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- * E-mail: (HZ); (MD)
| | - Minghua Deng
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- LMAM, School of Mathematical Sciences, Peking University, Beijing, China
- Center for Statistical Science, Peking University, Beijing, China
- * E-mail: (HZ); (MD)
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Abstract
Two recent structural studies reveal how cargo proteins interact with vesicle coats, which may also explain vesicle formation of retrograde transport vesicles. (2013) 32:11, 926–937 doi:10.1038/emboj.2013.41; published online 03122013 (2012) 23: 1255–62 doi:10.1016/j.devcel.2012.10.017; published online 12112012 How specific cargo recognition by coat proteins is achieved and how this recognition event may regulate vesicle formation are still under investigation. In two recent papers by the Owen and Goldberg labs, the binding mode of dilysine motifs to the coatomer of the COPI coat has been analysed. Collectively, their findings suggest that the dilysine motif containing cargo proteins may stabilize coat complexes on membranes and enhance the chance for coat polymerization and vesicle budding.
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13
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Ma W, Goldberg J. Rules for the recognition of dilysine retrieval motifs by coatomer. EMBO J 2013; 32:926-37. [PMID: 23481256 PMCID: PMC3616288 DOI: 10.1038/emboj.2013.41] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 02/07/2013] [Indexed: 12/29/2022] Open
Abstract
Cytoplasmic dilysine motifs on transmembrane proteins are captured by coatomer α-COP and β′-COP subunits and packaged into COPI-coated vesicles for Golgi-to-ER retrieval. Numerous ER/Golgi proteins contain K(x)Kxx motifs, but the rules for their recognition are unclear. We present crystal structures of α-COP and β′-COP bound to a series of naturally occurring retrieval motifs—encompassing KKxx, KxKxx and non-canonical RKxx and viral KxHxx sequences. Binding experiments show that α-COP and β′-COP have generally the same specificity for KKxx and KxKxx, but only β′-COP recognizes the RKxx signal. Dilysine motif recognition involves lysine side-chain interactions with two acidic patches. Surprisingly, however, KKxx and KxKxx motifs bind differently, with their lysine residues transposed at the binding patches. We derive rules for retrieval motif recognition from key structural features: the reversed binding modes, the recognition of the C-terminal carboxylate group which enforces lysine positional context, and the tolerance of the acidic patches for non-lysine residues. Transmembrane proteins interact with COPI coatomers for their vesicular Golgi-ER transport. Crystal structures of the coatomers α-COP and β′-COP bound to a series of cargo retrieval motifs uncover the molecular basis of distinct recognition mechanisms.
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Affiliation(s)
- Wenfu Ma
- Memorial Sloan-Kettering Cancer Center, Howard Hughes Medical Institute and the Structural Biology Program, New York, NY, USA
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14
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Logsdon BA, Mezey J. Gene expression network reconstruction by convex feature selection when incorporating genetic perturbations. PLoS Comput Biol 2010; 6:e1001014. [PMID: 21152011 PMCID: PMC2996324 DOI: 10.1371/journal.pcbi.1001014] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2010] [Accepted: 10/27/2010] [Indexed: 01/18/2023] Open
Abstract
Cellular gene expression measurements contain regulatory information that can be used to discover novel network relationships. Here, we present a new algorithm for network reconstruction powered by the adaptive lasso, a theoretically and empirically well-behaved method for selecting the regulatory features of a network. Any algorithms designed for network discovery that make use of directed probabilistic graphs require perturbations, produced by either experiments or naturally occurring genetic variation, to successfully infer unique regulatory relationships from gene expression data. Our approach makes use of appropriately selected cis-expression Quantitative Trait Loci (cis-eQTL), which provide a sufficient set of independent perturbations for maximum network resolution. We compare the performance of our network reconstruction algorithm to four other approaches: the PC-algorithm, QTLnet, the QDG algorithm, and the NEO algorithm, all of which have been used to reconstruct directed networks among phenotypes leveraging QTL. We show that the adaptive lasso can outperform these algorithms for networks of ten genes and ten cis-eQTL, and is competitive with the QDG algorithm for networks with thirty genes and thirty cis-eQTL, with rich topologies and hundreds of samples. Using this novel approach, we identify unique sets of directed relationships in Saccharomyces cerevisiae when analyzing genome-wide gene expression data for an intercross between a wild strain and a lab strain. We recover novel putative network relationships between a tyrosine biosynthesis gene (TYR1), and genes involved in endocytosis (RCY1), the spindle checkpoint (BUB2), sulfonate catabolism (JLP1), and cell-cell communication (PRM7). Our algorithm provides a synthesis of feature selection methods and graphical model theory that has the potential to reveal new directed regulatory relationships from the analysis of population level genetic and gene expression data. Determining a unique set of regulatory relationships underlying the observed expression of genes is a challenging problem, not only because of the many possible regulatory relationships, but also because highly distinct regulatory relationships can fit data equally well. In addition, most expression data-sets have relatively small sample sizes compared to the number of genes measured, causing high sampling variability that leads to a significant reduction in power and inflation of the false positive rate for any network reconstruction method. We propose a novel algorithm for network reconstruction that uses a theoretically and empirically well-behaved method for selecting regulatory features, while leveraging genetic perturbations arising from cis-expression Quantitative Trait Loci (cis-eQTL) to maximally resolve a network. Our algorithm has good performance for realistic samples sizes and can be used to identify a unique set of acyclic or cyclic regulatory relationships that explain observed gene expression.
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Affiliation(s)
- Benjamin A. Logsdon
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Jason Mezey
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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15
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Spang A, Shiba Y, Randazzo PA. Arf GAPs: gatekeepers of vesicle generation. FEBS Lett 2010; 584:2646-51. [PMID: 20394747 DOI: 10.1016/j.febslet.2010.04.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 03/26/2010] [Accepted: 04/03/2010] [Indexed: 11/17/2022]
Abstract
Arf GAP proteins are a versatile and diverse group of proteins. They control the activity of the GTP-binding proteins of the ARF family by inducing the hydrolysis of GTP that is bound to Arf proteins. The best-studied role of Arf GAPs is in intracellular traffic. In this review, we will focus mainly on the Arf GAPs that play a role in vesicle formation, Arf GAP1, Arf GAP2 and Arf GAP3 and their yeast homologues, Gcs1p and Glo3p. We discuss the roles of Arf GAPs as regulators and effectors for Arf GTP-binding proteins.
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Affiliation(s)
- Anne Spang
- University of Basel, Growth and Development, Biozentrum, Switzerland.
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16
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On vesicle formation and tethering in the ER–Golgi shuttle. Curr Opin Cell Biol 2009; 21:531-6. [DOI: 10.1016/j.ceb.2009.03.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2009] [Revised: 03/24/2009] [Accepted: 03/24/2009] [Indexed: 01/13/2023]
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17
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Banks E, Nabieva E, Chazelle B, Singh M. Organization of physical interactomes as uncovered by network schemas. PLoS Comput Biol 2008; 4:e1000203. [PMID: 18949022 PMCID: PMC2561054 DOI: 10.1371/journal.pcbi.1000203] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 09/09/2008] [Indexed: 11/18/2022] Open
Abstract
Large-scale protein-protein interaction networks provide new opportunities for understanding cellular organization and functioning. We introduce network schemas to elucidate shared mechanisms within interactomes. Network schemas specify descriptions of proteins and the topology of interactions among them. We develop algorithms for systematically uncovering recurring, over-represented schemas in physical interaction networks. We apply our methods to the S. cerevisiae interactome, focusing on schemas consisting of proteins described via sequence motifs and molecular function annotations and interacting with one another in one of four basic network topologies. We identify hundreds of recurring and over-represented network schemas of various complexity, and demonstrate via graph-theoretic representations how more complex schemas are organized in terms of their lower-order constituents. The uncovered schemas span a wide range of cellular activities, with many signaling and transport related higher-order schemas. We establish the functional importance of the schemas by showing that they correspond to functionally cohesive sets of proteins, are enriched in the frequency with which they have instances in the H. sapiens interactome, and are useful for predicting protein function. Our findings suggest that network schemas are a powerful paradigm for organizing, interrogating, and annotating cellular networks.
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Affiliation(s)
- Eric Banks
- Department of Computer Science & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Elena Nabieva
- Department of Computer Science & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Bernard Chazelle
- Department of Computer Science & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mona Singh
- Department of Computer Science & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
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18
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Kamena F, Diefenbacher M, Kilchert C, Schwarz H, Spang A. Ypt1p is essential for retrograde Golgi-ER transport and for Golgi maintenance in S. cerevisiae. J Cell Sci 2008; 121:1293-302. [PMID: 18388317 DOI: 10.1242/jcs.016998] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The small GTPase Ypt1p of the Rab family is required for docking of ER-derived transport vesicles with the Golgi prior to fusion. However, the identity of the Rab protein that mediates docking of Golgi-derived COPI vesicles with the ER in retrograde transport remains elusive. Here, we show that in yeast Ypt1p is essential for retrograde transport from the Golgi to the ER. Retrieval of gpalphaF-HDEL (glycolylated pro-alpha-factor with an HDEL tag at the C-terminus) was blocked in Deltaypt1/SLY1-20 membranes at the restrictive temperature in vitro. Moreover, Ypt1p and the ER-resident t-SNARE Ufe1p interact genetically and biochemically, indicating a role for Ypt1p in consumption of COPI vesicles at the ER. Ypt1p is also essential for the maintenance of the morphology and the protein composition of the Golgi. Interestingly, the concentrations of the Golgi enzymes Anp1p and Mnn1p, the cargo protein Emp47p and the v-SNARE Sec22p were all substantially reduced in Golgi from a Deltaypt1/SLY1-20 strain as compared with wild-type Golgi, while the concentration of Arf1p and of coatomer were mildly affected. Finally, COPI vesicles generated from Deltaypt1/SLY1-20 Golgi membranes in vitro were depleted of Emp47p and Sec22p. These data demonstrate that Ypt1p plays an essential role in retrograde transport from the Golgi to the ER.
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Affiliation(s)
- Faustin Kamena
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
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19
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Pitre S, North C, Alamgir M, Jessulat M, Chan A, Luo X, Green JR, Dumontier M, Dehne F, Golshani A. Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences. Nucleic Acids Res 2008; 36:4286-94. [PMID: 18586826 PMCID: PMC2490765 DOI: 10.1093/nar/gkn390] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Protein–protein interaction (PPI) maps provide insight into cellular biology and have received considerable attention in the post-genomic era. While large-scale experimental approaches have generated large collections of experimentally determined PPIs, technical limitations preclude certain PPIs from detection. Recently, we demonstrated that yeast PPIs can be computationally predicted using re-occurring short polypeptide sequences between known interacting protein pairs. However, the computational requirements and low specificity made this method unsuitable for large-scale investigations. Here, we report an improved approach, which exhibits a specificity of ∼99.95% and executes 16 000 times faster. Importantly, we report the first all-to-all sequence-based computational screen of PPIs in yeast, Saccharomyces cerevisiae in which we identify 29 589 high confidence interactions of ∼2 × 107 possible pairs. Of these, 14 438 PPIs have not been previously reported and may represent novel interactions. In particular, these results reveal a richer set of membrane protein interactions, not readily amenable to experimental investigations. From the novel PPIs, a novel putative protein complex comprised largely of membrane proteins was revealed. In addition, two novel gene functions were predicted and experimentally confirmed to affect the efficiency of non-homologous end-joining, providing further support for the usefulness of the identified PPIs in biological investigations.
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Affiliation(s)
- S Pitre
- School of Computer Science, Carleton University, Ottawa, Canada
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20
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Aguilera-Romero A, Kaminska J, Spang A, Riezman H, Muñiz M. The yeast p24 complex is required for the formation of COPI retrograde transport vesicles from the Golgi apparatus. ACTA ACUST UNITED AC 2008; 180:713-20. [PMID: 18283113 PMCID: PMC2265561 DOI: 10.1083/jcb.200710025] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The p24 family members are transmembrane proteins assembled into heteromeric complexes that continuously cycle between the ER and the Golgi apparatus. These cargo proteins were assumed to play a structural role in COPI budding because of their major presence in mammalian COPI vesicles. However, this putative function has not been proved conclusively so far. Furthermore, deletion of all eight yeast p24 family members does not produce severe transport phenotypes, suggesting that the p24 complex is not essential for COPI function. In this paper we provide direct evidence that the yeast p24 complex plays an active role in retrograde transport from Golgi to ER by facilitating the formation of COPI-coated vesicles. Therefore, our results demonstrate that p24 proteins are important for vesicle formation instead of simply being a passive traveler, supporting the model in which cargo together with a small GTPase of the ARF superfamily and coat subunits act as primer for vesicle formation.
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21
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Michelsen K, Schmid V, Metz J, Heusser K, Liebel U, Schwede T, Spang A, Schwappach B. Novel cargo-binding site in the beta and delta subunits of coatomer. ACTA ACUST UNITED AC 2007; 179:209-17. [PMID: 17954604 PMCID: PMC2064757 DOI: 10.1083/jcb.200704142] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Arginine (R)-based ER localization signals are sorting motifs that confer transient ER localization to unassembled subunits of multimeric membrane proteins. The COPI vesicle coat binds R-based signals but the molecular details remain unknown. Here, we use reporter membrane proteins based on the proteolipid Pmp2 fused to GFP and allele swapping of COPI subunits to map the recognition site for R-based signals. We show that two highly conserved stretches—in the β- and δ-COPI subunits—are required to maintain Pmp2GFP reporters exposing R-based signals in the ER. Combining a deletion of 21 residues in δ-COP together with the mutation of three residues in β-COP gave rise to a COPI coat that had lost its ability to recognize R-based signals, whilst the recognition of C-terminal di-lysine signals remained unimpaired. A homology model of the COPI trunk domain illustrates the recognition of R-based signals by COPI.
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Affiliation(s)
- Kai Michelsen
- Zentrum für Molekulare Biologie der Universität Heidelberg, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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22
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Edwards-Ingram L, Gitsham P, Burton N, Warhurst G, Clarke I, Hoyle D, Oliver SG, Stateva L. Genotypic and physiological characterization of Saccharomyces boulardii, the probiotic strain of Saccharomyces cerevisiae. Appl Environ Microbiol 2007; 73:2458-67. [PMID: 17293506 PMCID: PMC1855594 DOI: 10.1128/aem.02201-06] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Saccharomyces boulardii, a yeast that was isolated from fruit in Indochina, has been used as a remedy for diarrhea since 1950 and is now a commercially available treatment throughout Europe, Africa, and South America. Though initially classified as a separate species of Saccharomyces, recent publications have shown that the genome of S. boulardii is so similar to Saccharomyces cerevisiae that the two should be classified as conspecific. This raises the question of the distinguishing molecular and phenotypic characteristics present in S. boulardii that make it perform more effectively as a probiotic organism compared to other strains of S. cerevisiae. This investigation reports some of these distinguishing characteristics including enhanced ability for pseudohyphal switching upon nitrogen limitation and increased resistance to acidic pH. However, these differences did not correlate with increased adherence to epithelial cells or transit through mouse gut. Pertinent characteristics of the S. boulardii genome such as trisomy of chromosome IX, altered copy number of a number of individual genes, and sporulation deficiency have been revealed by comparative genome hybridization using oligonucleotide-based microarrays coupled with a rigorous statistical analysis. The contributions of the different genomic and phenotypic features of S. boulardii to its probiotic nature are discussed.
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Affiliation(s)
- Laura Edwards-Ingram
- Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
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23
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Béthune J, Kol M, Hoffmann J, Reckmann I, Brügger B, Wieland F. Coatomer, the coat protein of COPI transport vesicles, discriminates endoplasmic reticulum residents from p24 proteins. Mol Cell Biol 2006; 26:8011-21. [PMID: 16940185 PMCID: PMC1636745 DOI: 10.1128/mcb.01055-06] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In the formation of COPI vesicles, interactions take place between the coat protein coatomer and membrane proteins: either cargo proteins for retrieval to the endoplasmic reticulum (ER) or proteins that cycle between the ER and the Golgi. While the binding sites on coatomer for ER residents have been characterized, how cycling proteins bind to the COPI coat is still not clear. In order to understand at a molecular level the mechanism of uptake of such proteins, we have investigated the binding to coatomer of p24 proteins as examples of cycling proteins as well as that of ER-resident cargos. The p24 proteins required dimerization to interact with coatomer at two independent binding sites in gamma-COP. In contrast, ER-resident cargos bind to coatomer as monomers and to sites other than gamma-COP. The COPI coat therefore discriminates between p24 proteins and ER-resident proteins by differential binding involving distinct subunits.
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Affiliation(s)
- Julien Béthune
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.
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24
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Despons L, Wirth B, Louis VL, Potier S, Souciet JL. An evolutionary scenario for one of the largest yeast gene families. Trends Genet 2005; 22:10-5. [PMID: 16269202 DOI: 10.1016/j.tig.2005.10.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Revised: 08/11/2005] [Accepted: 10/07/2005] [Indexed: 11/29/2022]
Abstract
The DUP gene family of Saccharomyces cerevisiae comprises 23 members that can be divided into two subfamilies--DUP240 and DUP380. The location of the DUP loci suggests that at least three mechanisms were responsible for their genomic dispersion: nonreciprocal translocation at chromosomal ends, tandem duplication and Ty-associated duplication. The data we present here suggest that these nonessential genes encode proteins that facilitate membrane trafficking processes. Dup240 proteins have three conserved domains (C1, C2 and C3) and two predicted transmembrane segments (H1 and H2). A direct repetition of the C1-H1-H2-C2 module is observed in Dup380p sequences. In this article, we propose an evolutionary model to account for the emergence of the two gene subfamilies.
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Affiliation(s)
- Laurence Despons
- UMR 7156 University Louis Pasteur-CNRS, Department of Microorganisms, Genomes and the Environment, 28 rue Goethe, 67083 Strasbourg Cedex, France
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25
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Luedeke C, Frei SB, Sbalzarini I, Schwarz H, Spang A, Barral Y. Septin-dependent compartmentalization of the endoplasmic reticulum during yeast polarized growth. ACTA ACUST UNITED AC 2005; 169:897-908. [PMID: 15967812 PMCID: PMC2171641 DOI: 10.1083/jcb.200412143] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Polarized cells frequently use diffusion barriers to separate plasma membrane domains. It is unknown whether diffusion barriers also compartmentalize intracellular organelles. We used photobleaching techniques to characterize protein diffusion in the yeast endoplasmic reticulum (ER). Although a soluble protein diffused rapidly throughout the ER lumen, diffusion of ER membrane proteins was restricted at the bud neck. Ultrastructural studies and fluorescence microscopy revealed the presence of a ring of smooth ER at the bud neck. This ER domain and the restriction of diffusion for ER membrane proteins through the bud neck depended on septin function. The membrane-associated protein Bud6 localized to the bud neck in a septin-dependent manner and was required to restrict the diffusion of ER membrane proteins. Our results indicate that Bud6 acts downstream of septins to assemble a fence in the ER membrane at the bud neck. Thus, in polarized yeast cells, diffusion barriers compartmentalize the ER and the plasma membrane along parallel lines.
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Affiliation(s)
- Cosima Luedeke
- Biology Department, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), ETH-Hönggerberg, 8093 Zürich, Switzerland
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26
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Lee MCS, Miller EA, Goldberg J, Orci L, Schekman R. Bi-directional protein transport between the ER and Golgi. Annu Rev Cell Dev Biol 2005; 20:87-123. [PMID: 15473836 DOI: 10.1146/annurev.cellbio.20.010403.105307] [Citation(s) in RCA: 686] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The endoplasmic reticulum (ER) and the Golgi comprise the first two steps in protein secretion. Vesicular carriers mediate a continuous flux of proteins and lipids between these compartments, reflecting the transport of newly synthesized proteins out of the ER and the retrieval of escaped ER residents and vesicle machinery. Anterograde and retrograde transport is mediated by distinct sets of cytosolic coat proteins, the COPII and COPI coats, respectively, which act on the membrane to capture cargo proteins into nascent vesicles. We review the mechanisms that govern coat recruitment to the membrane, cargo capture into a transport vesicle, and accurate delivery to the target organelle.
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Affiliation(s)
- Marcus C S Lee
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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27
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Trautwein M, Dengjel J, Schirle M, Spang A. Arf1p provides an unexpected link between COPI vesicles and mRNA in Saccharomyces cerevisiae. Mol Biol Cell 2004; 15:5021-37. [PMID: 15356266 PMCID: PMC524765 DOI: 10.1091/mbc.e04-05-0411] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The small GTPase Arf1p is involved in different cellular processes that require its accumulation at specific cellular locations. The recruitment of Arf1p to distinct points of action might be achieved by association of Arf1p with different proteins. To identify new interactors of Arf1p, we performed an affinity chromatography with GTP- or GDP-bound Arf1p proteins. A new interactor of Arf1p-GTP was identified as Pab1p, which binds to the polyA-tail of mRNAs. Pab1p was found to associate with purified COPI-coated vesicles generated from Golgi membranes in vitro. The stability of the Pab1p-Arf1p complex depends on the presence of mRNA. Both symmetrically distributed mRNAs as well as the asymmetrically localized ASH1 mRNA are found in association with Arf1p. Remarkably, Arf1p and Pab1p are both required to restrict ASH1 mRNA to the bud tip. Arf1p and coatomer play an unexpected role in localizing mRNA independent and downstream of the SHE machinery. Hereby acts the SHE machinery in long-range mRNA transport, whereas COPI vesicles could act as short-range and localization vehicles. The endoplasmic reticulum (ER)-Golgi shuttle might be involved in concentrating mRNA at the ER.
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Affiliation(s)
- Mark Trautwein
- Friedrich Miescher Laboratorium, Max Planck Gesellschaft, D-72076 Tübingen, Germany
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28
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Lewis SM, Poon PP, Singer RA, Johnston GC, Spang A. The ArfGAP Glo3 is required for the generation of COPI vesicles. Mol Biol Cell 2004; 15:4064-72. [PMID: 15254269 PMCID: PMC515341 DOI: 10.1091/mbc.e04-04-0316] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Revised: 06/25/2004] [Accepted: 07/01/2004] [Indexed: 11/11/2022] Open
Abstract
The small GTPase Arf and coatomer (COPI) are required for the generation of retrograde transport vesicles. Arf activity is regulated by guanine exchange factors (ArfGEF) and GTPase-activating proteins (ArfGAPs). The ArfGAPs Gcs1 and Glo3 provide essential overlapping function for retrograde vesicular transport from the Golgi to the endoplasmic reticulum. We have identified Glo3 as a component of COPI vesicles. Furthermore, we find that a mutant version of the Glo3 protein exerts a negative effect on retrograde transport, even in the presence of the ArfGAP Gcs1. Finally, we present evidence supporting a role for ArfGAP protein in the generation of COPI retrograde transport vesicles.
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Affiliation(s)
- Stephen M Lewis
- Departments of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
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29
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Abstract
COPII vesicles transport proteins destined for secretion from the ER to the Golgi apparatus. A recent study has shown that, in budding yeast, the formation of COPII vesicles requires Yip1p, an effector protein of a Rab GTPase.
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Affiliation(s)
- Anne Spang
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, D-72076, Tuebingen, Germany.
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