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      Cross-species cluster co-conservation: a new method for generating protein interaction networks

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          Abstract

          Cluster Co-Conservation (CCC) has been extended to a method for developing protein interaction networks based on co-conservation between protein pairs across multiple species, Cross-Species Cluster Co-Conservation (CS-CCC).

          Abstract

          Co-conservation (phylogenetic profiles) is a well-established method for predicting functional relationships between proteins. Several publicly available databases use this method and additional clustering strategies to develop networks of protein interactions (cluster co-conservation (CCC)). CCC has previously been limited to interactions within a single target species. We have extended CCC to develop protein interaction networks based on co-conservation between protein pairs across multiple species, cross-species cluster co-conservation.

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          Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.

          M Pellegrini, E Marcotte, M. Thompson … (1999)
          Determining protein functions from genomic sequences is a central goal of bioinformatics. We present a method based on the assumption that proteins that function together in a pathway or structural complex are likely to evolve in a correlated fashion. During evolution, all such functionally linked proteins tend to be either preserved or eliminated in a new species. We describe this property of correlated evolution by characterizing each protein by its phylogenetic profile, a string that encodes the presence or absence of a protein in every known genome. We show that proteins having matching or similar profiles strongly tend to be functionally linked. This method of phylogenetic profiling allows us to predict the function of uncharacterized proteins.
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            Type III protein secretion systems in bacterial pathogens of animals and plants.

            C Hueck (1998)
            Various gram-negative animal and plant pathogens use a novel, sec-independent protein secretion system as a basic virulence mechanism. It is becoming increasingly clear that these so-called type III secretion systems inject (translocate) proteins into the cytosol of eukaryotic cells, where the translocated proteins facilitate bacterial pathogenesis by specifically interfering with host cell signal transduction and other cellular processes. Accordingly, some type III secretion systems are activated by bacterial contact with host cell surfaces. Individual type III secretion systems direct the secretion and translocation of a variety of unrelated proteins, which account for species-specific pathogenesis phenotypes. In contrast to the secreted virulence factors, most of the 15 to 20 membrane-associated proteins which constitute the type III secretion apparatus are conserved among different pathogens. Most of the inner membrane components of the type III secretion apparatus show additional homologies to flagellar biosynthetic proteins, while a conserved outer membrane factor is similar to secretins from type II and other secretion pathways. Structurally conserved chaperones which specifically bind to individual secreted proteins play an important role in type III protein secretion, apparently by preventing premature interactions of the secreted factors with other proteins. The genes encoding type III secretion systems are clustered, and various pieces of evidence suggest that these systems have been acquired by horizontal genetic transfer during evolution. Expression of type III secretion systems is coordinately regulated in response to host environmental stimuli by networks of transcription factors. This review comprises a comparison of the structure, function, regulation, and impact on host cells of the type III secretion systems in the animal pathogens Yersinia spp., Pseudomonas aeruginosa, Shigella flexneri, Salmonella typhimurium, enteropathogenic Escherichia coli, and Chlamydia spp. and the plant pathogens Pseudomonas syringae, Erwinia spp., Ralstonia solanacearum, Xanthomonas campestris, and Rhizobium spp.
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              Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili.

              Leslie A. Pratt, Roberto Kolter (1998)
              We have used Escherichia coli as a model system to investigate the initiation of biofilm formation. Here, we demonstrate that E. coli forms biofilms on multiple abiotic surfaces in a nutrient-dependent fashion. In addition, we have isolated insertion mutations that render this organism defective in biofilm formation. One-half of these mutations was found to perturb normal flagellar function. Using defined fli, flh, mot and che alleles, we show that motility, but not chemotaxis, is critical for normal biofilm formation. Microscopic analyses of these mutants suggest that motility is important for both initial interaction with the surface and for movement along the surface. In addition, we present evidence that type I pili (harbouring the mannose-specific adhesin, FimH) are required for initial surface attachment and that mannose inhibits normal attachment. In light of the observations presented here, a working model is discussed that describes the roles of both motility and type I pili in biofilm development.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2007
                Publication date (Electronic): 5 September 2007
                Volume: 8
                Issue: 9
                Page: R185
                Affiliations
                [1 ]Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
                [2 ]MCD-Biology, University of Colorado, Boulder, CO 80309, USA
                [3 ]Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309, USA
                Article
                Publisher ID: gb-2007-8-9-r185
                DOI: 10.1186/gb-2007-8-9-r185
                PMC ID: 2375023
                PubMed ID: 17803817
                SO-VID: 8e20024b-bc7f-4d43-a71a-3f2ee2d2fd3b
                Copyright © Copyright © 2007 Karimpour-Fard et al.; licensee BioMed Central Ltd.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 5 July 2007
                Date revision received : 30 August 2007
                Date accepted : 5 September 2007
                Categories
                Subject: Method

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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