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Taussig MJ. Protein arrays: issues to be addressed. Comp Funct Genomics 2010; 2:298-300. [PMID: 18629246 PMCID: PMC2448408 DOI: 10.1002/cfg.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2001] [Accepted: 08/06/2001] [Indexed: 11/07/2022] Open
Abstract
Protein arrays are fast becoming established as a means to monitor protein expression
levels and investigate protein interactions and function. They present particular technical
demands that will need to be solved in order to achieve the maximum capability of efficient
and sensitive protein analysis in the high throughput setting of functional genomics. The
following resumé of some major issues around this new technology was made as the
chairperson’s introduction to the workshop session on peptide and protein chips.
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Affiliation(s)
- M J Taussig
- ESF Programme in Integrated Approaches to Functional Genomics, The Babraham Institute, Cambridge CB2 4AT, UK.
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2
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Abstract
Biochemical assay of proteomic libraries derived from the Saccharomyces cerevisiae genome provides a powerful new tool for the assignment of activities to proteins. Particular advantages of this approach include the speed with which a protein can be identified and the generality for any biological activity for which an assay can be developed. We discuss the utility of this approach for the identification of RNA-modifying enzymes using a yeast proteomic library derived from a genomic set of strains expressing GST-ORF fusion proteins. This technique is also broadly applicable to other classes of RNA-protein interactions, including RNA binding and RNA degradation, and can be used with any of the proteomic libraries that are available.
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3
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The spindle positioning protein Kar9p interacts with the sumoylation machinery in Saccharomyces cerevisiae. Genetics 2008; 180:2033-55. [PMID: 18832349 DOI: 10.1534/genetics.108.095042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Accurate positioning of the mitotic spindle is important for the genetic material to be distributed evenly in dividing cells, but little is known about the mechanisms that regulate this process. Here we report that two microtubule-associated proteins important for spindle positioning interact with several proteins in the sumoylation pathway. By two-hybrid analysis, Kar9p and Bim1p interact with the yeast SUMO Smt3p, the E2 enzyme Ubc9p, an E3 Nfi1p, as well as Wss1p, a weak suppressor of a temperature-sensitive smt3 allele. The physical interaction between Kar9p and Ubc9p was confirmed by in vitro binding assays. A single-amino-acid substitution in Kar9p, L304P disrupted its two-hybrid interaction with proteins in the sumoylation pathway, but retained its interactions with the spindle positioning proteins Bim1p, Stu2p, Bik1p, and Myo2p. The kar9-L304P mutant showed defects in positioning the mitotic spindle, with the spindle located more distally than normal. Whereas wild-type Kar9p-3GFP normally localizes to only the bud-directed spindle pole body (SPB), Kar9p-L304P-3GFP was mislocalized to both SPBs. Using a reconstitution assay, Kar9p was sumoylated in vitro. We propose a model in which sumoylation regulates spindle positioning by restricting Kar9p to one SPB. These findings raise the possibility that sumoylation could regulate other microtubule-dependent processes.
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Grelle G, Kostka S, Otto A, Kersten B, Genser KF, Müller EC, Wälter S, Böddrich A, Stelzl U, Hänig C, Volkmer-Engert R, Landgraf C, Alberti S, Höhfeld J, Strödicke M, Wanker EE. Identification of VCP/p97, Carboxyl Terminus of Hsp70-interacting Protein (CHIP), and Amphiphysin II Interaction Partners Using Membrane-based Human Proteome Arrays. Mol Cell Proteomics 2006; 5:234-44. [PMID: 16275660 DOI: 10.1074/mcp.m500198-mcp200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins mediate their biological function through interactions with other proteins. Therefore, the systematic identification and characterization of protein-protein interactions have become a powerful proteomic strategy to understand protein function and comprehensive cellular regulatory networks. For the screening of valosin-containing protein, carboxyl terminus of Hsp70-interacting protein (CHIP), and amphiphysin II interaction partners, we utilized a membrane-based array technology that allows the identification of human protein-protein interactions with crude bacterial cell extracts. Many novel interaction pairs such as valosin-containing protein/autocrine motility factor receptor, CHIP/caytaxin, or amphiphysin II/DLP4 were identified and subsequently confirmed by pull-down, two-hybrid and co-immunoprecipitation experiments. In addition, assays were performed to validate the interactions functionally. CHIP e.g. was found to efficiently polyubiquitinate caytaxin in vitro, suggesting that it might influence caytaxin degradation in vivo. Using peptide arrays, we also identified the binding motifs in the proteins DLP4, XRCC4, and fructose-1,6-bisphosphatase, which are crucial for the association with the Src homology 3 domain of amphiphysin II. Together these studies indicate that our human proteome array technology permits the identification of protein-protein interactions that are functionally involved in neurodegenerative disease processes, the degradation of protein substrates, and the transport of membrane vesicles.
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Affiliation(s)
- Gerlinde Grelle
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany
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5
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Shull NP, Spinelli SL, Phizicky EM. A highly specific phosphatase that acts on ADP-ribose 1''-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae. Nucleic Acids Res 2005; 33:650-60. [PMID: 15684411 PMCID: PMC548356 DOI: 10.1093/nar/gki211] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 01/07/2005] [Accepted: 01/07/2005] [Indexed: 11/21/2022] Open
Abstract
One molecule of ADP-ribose 1'',2''-cyclic phosphate (Appr>p) is formed during each of the approximately 500 000 tRNA splicing events per Saccharomyces cerevisiae generation. The metabolism of Appr>p remains poorly defined. A cyclic phosphodiesterase (Cpd1p) has been shown to convert Appr>p to ADP-ribose-1''-phosphate (Appr1p). We used a biochemical genomics approach to identify two yeast phosphatases that can convert Appr1p to ADP-ribose: the product of ORF YBR022w (now Poa1p), which is completely unrelated to other known phosphatases; and Hal2p, a known 3'-phosphatase of 5',3'-pAp. Poa1p is highly specific for Appr1p, and thus likely acts on this molecule in vivo. Poa1 has a relatively low K(M) for Appr1p (2.8 microM) and a modest kcat (1.7 min(-1)), but no detectable activity on several other substrates. Furthermore, Poa1p is strongly inhibited by ADP-ribose (K(I), 17 microM), modestly inhibited by other nucleotides containing an ADP-ribose moiety and not inhibited at all by other tested molecules. In contrast, Hal2p is much more active on pAp than on Appr1p, and several other tested molecules were Hal2p substrates or inhibitors. poa1-Delta mutants have no obvious growth defect at different temperatures in rich media, and analysis of yeast extracts suggests that approximately 90% of Appr1p processing activity originates from Poa1p.
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Affiliation(s)
- Neil P. Shull
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Sherry L. Spinelli
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Eric M. Phizicky
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine601 Elmwood Avenue, Rochester, NY 14642, USA
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Jansen G, Wu C, Schade B, Thomas DY, Whiteway M. Drag&Drop cloning in yeast. Gene 2004; 344:43-51. [PMID: 15656971 DOI: 10.1016/j.gene.2004.10.016] [Citation(s) in RCA: 152] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Revised: 09/13/2004] [Accepted: 10/14/2004] [Indexed: 11/29/2022]
Abstract
We have developed a set of vectors that have enhanced capabilities for efficiently constructing and expressing differentially tagged fusion proteins using Drag&Drop cloning in the yeast Saccharomyces cerevisiae. The pGREG vectors are based on the pRS series with an additional general kanR selection marker. In vivo homologous recombination is used to introduce genes of interest into galactose-inducible expression vectors (pGREGs), permitting the formation of amino-terminal fusions. The vectors all contain common regions for recombination that flank the stuffer fragment. Introduction of common recombination sequences at the end of PCR fragments will permit the cloning of genes without the need for specific restriction sites. In this process, the selectable stuffer HIS3 gene is replaced by successful gene integration, and a screen for loss of the selection marker identifies potential recombinants. Due to the modular structure of the vectors, genes introduced into one vector can be readily transferred by in vivo recombination to all other members of the vector system, thus permitting rapid and easy Drag&Drop construction of a series of tagged proteins. The pGREG series combines features for expression, tagging, integration, localization and library construction with the advantage of obtaining immediate results from sub-sequent experiments. This Drag&Drop system also allows efficient cloning and expression of heterologous genes in large-scale experiments.
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Affiliation(s)
- Gregor Jansen
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6.
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Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C. Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Trends Cell Biol 2003; 13:344-56. [PMID: 12837605 DOI: 10.1016/s0962-8924(03)00127-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The challenge of large-scale functional genomics projects is to build a comprehensive map of the cell including genome sequence and gene expression data, information on protein localization, structure, function and expression, post-translational modifications, molecular and genetic interactions and phenotypic descriptions. Some of this broad set of functional genomics data has been already assembled for the budding yeast. Even though molecular cartography of the yeast cell is still far from comprehensive, functional genomics has begun to forge connections between disparate cellular events and to foster numerous hypotheses. Here we review several different genomics and proteomics technologies and describe bioinformatics methods for exploring these data to make new discoveries.
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Affiliation(s)
- Gary D Bader
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, 10021, New York, NY, USA
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Abstract
The long-term challenge of proteomics is enormous: to define the identities, quantities, structures and functions of complete complements of proteins, and to characterize how these properties vary in different cellular contexts. One critical step in tackling this goal is the generation of sets of clones that express a representative of each protein of a proteome in a useful format, followed by the analysis of these sets on a genome-wide basis. Such studies enable genetic, biochemical and cell biological technologies to be applied on a systematic level, leading to the assignment of biochemical activities, the construction of protein arrays, the identification of interactions, and the localization of proteins within cellular compartments.
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Affiliation(s)
- Eric Phizicky
- University of Rochester School of Medicine, Department of Biochemistry and Biophysics, Box 712, 601 Elmwood Avenue, Rochester, New York 14642, USA.
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MESH Headings
- Active Transport, Cell Nucleus
- Endoribonucleases/metabolism
- Genes, Fungal
- Mitochondria/metabolism
- Models, Biological
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA Editing
- RNA Processing, Post-Transcriptional
- RNA Splicing
- RNA, Catalytic/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribonuclease P
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
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Affiliation(s)
- Anita K Hopper
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA.
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Phizicky EM, Martzen MR, McCraith SM, Spinelli SL, Xing F, Shull NP, Van Slyke C, Montagne RK, Torres FM, Fields S, Grayhack EJ. Biochemical genomics approach to map activities to genes. Methods Enzymol 2002; 350:546-59. [PMID: 12073335 DOI: 10.1016/s0076-6879(02)50984-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
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11
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2001. [PMCID: PMC2448396 DOI: 10.1002/cfg.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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