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      Connecting viral with cellular interactomes

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      Author(s): 1 , 1 , 2
      Publication date (Electronic):
      Journal: Current Opinion in Microbiology
      Publisher: Published by Elsevier Ltd.

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          Abstract

          Genome-scale screens for intraviral and virus–host protein interactions and the analysis of literature-curated datasets are able to provide a novel, comprehensive perspective of viruses, and virus-infected cells. Until now, large-scale interaction screens were predominantly performed with the yeast-two-hybrid (Y2H) system; however, alternative high-throughput technologies detecting binary protein interactions or protein complexes have been developed. Although many of the previous studies suffer from a rather poor validation of the results and few biological implications, these technologies potentially lead to a plethora of novel hypotheses. Here, we will give an overview of current approaches and their technical limitations, present recent examples and novel developments.

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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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              Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.

              Yuen Ho, Albrecht Gruhler, Adrian Heilbut … (2002)
              The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function. To date, generation of large-scale protein-protein interaction maps has relied on the yeast two-hybrid system, which detects binary interactions through activation of reporter gene expression. With the advent of ultrasensitive mass spectrometric protein identification methods, it is feasible to identify directly protein complexes on a proteome-wide scale. Here we report, using the budding yeast Saccharomyces cerevisiae as a test case, an example of this approach, which we term high-throughput mass spectrometric protein complex identification (HMS-PCI). Beginning with 10% of predicted yeast proteins as baits, we detected 3,617 associated proteins covering 25% of the yeast proteome. Numerous protein complexes were identified, including many new interactions in various signalling pathways and in the DNA damage response. Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies. Given the high degree of connectivity observed in this study, even partial HMS-PCI coverage of complex proteomes, including that of humans, should allow comprehensive identification of cellular networks.
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                Author and article information

                Contributors
                SM Bailer
                J Haas
                Journal
                Journal ID (nlm-ta): Curr Opin Microbiol
                Journal ID (iso-abbrev): Curr. Opin. Microbiol
                Title: Current Opinion in Microbiology
                Publisher: Published by Elsevier Ltd.
                ISSN (Print): 1369-5274
                ISSN (Electronic): 1879-0364
                Publication date PMC-release: 24 July 2009
                Publication date (Print): August 2009
                Publication date (Electronic): 24 July 2009
                Volume: 12
                Issue: 4
                Pages: 453-459
                Affiliations
                [1 ]Max-von-Pettenkofer Institut, Ludwig-Maximilians-Universität München, Pettenkoferstrasse 9a, 80336 Muenchen, Germany
                [2 ]Division of Pathway Medicine, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, UK
                Article
                Publisher ID: S1369-5274(09)00073-3
                DOI: 10.1016/j.mib.2009.06.004
                PMC ID: 7108267
                PubMed ID: 19632888
                SO-VID: 78d4e636-6fae-4283-a686-6faf1072a0c5
                Copyright statement: Copyright © 2009 Published by Elsevier Ltd.
                License:

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

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                ScienceOpen disciplines: Microbiology & Virology
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                ScienceOpen disciplines: Microbiology & Virology

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