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      Quantitative nature of overexpression experiments

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      Author(s): 1
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      Publication date (Print):
      Journal: Molecular Biology of the Cell
      Publisher: The American Society for Cell Biology

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          Abstract

          Overexpression experiments are sometimes considered as qualitative experiments designed to identify novel proteins and study their function. However, in order to draw conclusions regarding protein overexpression through association analyses using large-scale biological data sets, we need to recognize the quantitative nature of overexpression experiments. Here I discuss the quantitative features of two different types of overexpression experiment: absolute and relative. I also introduce the four primary mechanisms involved in growth defects caused by protein overexpression: resource overload, stoichiometric imbalance, promiscuous interactions, and pathway modulation associated with the degree of overexpression.

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          A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.

          Peter Uetz, Loic Giot, Gerard Cagney … (2000)
          Two large-scale yeast two-hybrid screens were undertaken to identify protein-protein interactions between full-length open reading frames predicted from the Saccharomyces cerevisiae genome sequence. In one approach, we constructed a protein array of about 6,000 yeast transformants, with each transformant expressing one of the open reading frames as a fusion to an activation domain. This array was screened by a simple and automated procedure for 192 yeast proteins, with positive responses identified by their positions in the array. In a second approach, we pooled cells expressing one of about 6,000 activation domain fusions to generate a library. We used a high-throughput screening procedure to screen nearly all of the 6,000 predicted yeast proteins, expressed as Gal4 DNA-binding domain fusion proteins, against the library, and characterized positives by sequence analysis. These approaches resulted in the detection of 957 putative interactions involving 1,004 S. cerevisiae proteins. These data reveal interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes. The results of these screens are shown here.
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            A comprehensive two-hybrid analysis to explore the yeast protein interactome.

            T Ito, T Chiba, R Ozawa … (2001)
            Protein-protein interactions play crucial roles in the execution of various biological functions. Accordingly, their comprehensive description would contribute considerably to the functional interpretation of fully sequenced genomes, which are flooded with novel genes of unpredictable functions. We previously developed a system to examine two-hybrid interactions in all possible combinations between the approximately 6,000 proteins of the budding yeast Saccharomyces cerevisiae. Here we have completed the comprehensive analysis using this system to identify 4,549 two-hybrid interactions among 3,278 proteins. Unexpectedly, these data do not largely overlap with those obtained by the other project [Uetz, P., et al. (2000) Nature (London) 403, 623-627] and hence have substantially expanded our knowledge on the protein interaction space or interactome of the yeast. Cumulative connection of these binary interactions generates a single huge network linking the vast majority of the proteins. Bioinformatics-aided selection of biologically relevant interactions highlights various intriguing subnetworks. They include, for instance, the one that had successfully foreseen the involvement of a novel protein in spindle pole body function as well as the one that may uncover a hitherto unidentified multiprotein complex potentially participating in the process of vesicular transport. Our data would thus significantly expand and improve the protein interaction map for the exploration of genome functions that eventually leads to thorough understanding of the cell as a molecular system.
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              Effects of aneuploidy on cellular physiology and cell division in haploid yeast.

              Eduardo M Torres, Tanya Sokolsky, Cheryl M. Tucker … (2007)
              Aneuploidy is a condition frequently found in tumor cells, but its effect on cellular physiology is not known. We have characterized one aspect of aneuploidy: the gain of extra chromosomes. We created a collection of haploid yeast strains that each bear an extra copy of one or more of almost all of the yeast chromosomes. Their characterization revealed that aneuploid strains share a number of phenotypes, including defects in cell cycle progression, increased glucose uptake, and increased sensitivity to conditions interfering with protein synthesis and protein folding. These phenotypes were observed only in strains carrying additional yeast genes, which indicates that they reflect the consequences of additional protein production as well as the resulting imbalances in cellular protein composition. We conclude that aneuploidy causes not only a proliferative disadvantage but also a set of phenotypes that is independent of the identity of the individual extra chromosomes.
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                Author and article information

                Contributors
                Orna Cohen-Fix: Role: Monitoring Editor
                Journal
                Journal ID (nlm-ta): Mol Biol Cell
                Journal ID (iso-abbrev): Mol. Biol. Cell
                Journal ID (hwp): molbiolcell
                Journal ID (pmc): mbc
                Journal ID (publisher-id): Mol. Bio. Cell
                Title: Molecular Biology of the Cell
                Publisher: The American Society for Cell Biology
                ISSN (Print): 1059-1524
                ISSN (Electronic): 1939-4586
                Publication date (Print): 05 November 2015
                Volume: 26
                Issue: 22
                Pages: 3932-3939
                Affiliations
                [1]Research Core for Interdisciplinary Sciences, Okayama University, Okayama 700-8530, Japan
                National Institutes of Health
                Author notes
                1Address correspondence to: Hisao Moriya ( hisaom@ 123456cc.okayama-u.ac.jp ).
                Article
                Publisher ID: E15-07-0512
                DOI: 10.1091/mbc.E15-07-0512
                PMC ID: 4710226
                PubMed ID: 26543202
                SO-VID: cd9b3512-12af-4d07-8d3e-9931133350fc
                Copyright © © 2015 Moriya. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License ( http://creativecommons.org/licenses/by-nc-sa/3.0).
                License:

                “ASCB®,” “The American Society for Cell Biology®,” and “Molecular Biology of the Cell®” are registered trademarks of The American Society for Cell Biology.

                History
                Date received : 17 July 2015
                Date revision received : 09 September 2015
                Date accepted : 14 September 2015
                Categories
                Subject: Perspectives

                ScienceOpen disciplines: Molecular biology
                Data availability:
                ScienceOpen disciplines: Molecular biology

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