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      • Record: found
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      Is Open Access

      Comparative Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod-Independent Photosynthetic Bradyrhizobia

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          Abstract

          Tropical aquatic species of the legume genus Aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (ND) or a nod gene-independent (NI) pathway to enter into symbiosis with legumes. In this study we used a comparative genomics approach on nine Aeschynomene symbionts representative of their phylogenetic diversity. We produced draft genomes of bradyrhizobial strains representing different phenotypes: five NI photosynthetic strains (STM3809, ORS375, STM3847, STM4509 and STM4523) in addition to the previously sequenced ORS278 and BTAi1 genomes, one photosynthetic strain ORS285 hosting both ND and NI symbiotic systems, and one NI non-photosynthetic strain (STM3843). Comparative genomics allowed us to infer the core, pan and dispensable genomes of Aeschynomene bradyrhizobia, and to detect specific genes and their location in Genomic Islands (GI). Specific gene sets linked to photosynthetic and NI/ND abilities were identified, and are currently being studied in functional analyses.

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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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            Inparanoid: a comprehensive database of eukaryotic orthologs

            Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer (2004)
            The Inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Takifugu rubripes, Gallus gallus, Homo sapiens, Mus musculus, Pan troglodytes, Rattus norvegicus, Oryza sativa, Plasmodium falciparum, Arabidopsis thaliana, Escherichia coli, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Complete proteomes for these genomes were derived from Ensembl and UniProt and compared pairwise using Blast, followed by a clustering step using the Inparanoid program. An Inparanoid cluster is seeded by a reciprocally best-matching ortholog pair, around which inparalogs (should they exist) are gathered independently, while outparalogs are excluded. The ortholog clusters can be searched on the website using Ensembl gene/protein or UniProt identifiers, annotation text or by Blast alignment against our protein datasets. The entire dataset can be downloaded, as can the Inparanoid program itself.
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              The use of gene clusters to infer functional coupling.

              R Overbeek, M Fonstein, M. D'Souza … (1999)
              Previously, we presented evidence that it is possible to predict functional coupling between genes based on conservation of gene clusters between genomes. With the rapid increase in the availability of prokaryotic sequence data, it has become possible to verify and apply the technique. In this paper, we extend our characterization of the parameters that determine the utility of the approach, and we generalize the approach in a way that supports detection of common classes of functionally coupled genes (e.g., transport and signal transduction clusters). Now that the analysis includes over 30 complete or nearly complete genomes, it has become clear that this approach will play a significant role in supporting efforts to assign functionality to the remaining uncharacterized genes in sequenced genomes.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genes (Basel)
                Journal ID (iso-abbrev): Genes (Basel)
                Journal ID (publisher-id): genes
                Title: Genes
                Publisher: MDPI
                ISSN (Electronic): 2073-4425
                Publication date (Electronic): 21 December 2011
                Publication date Collection: March 2012
                Volume: 3
                Issue: 1
                Pages: 35-61
                Affiliations
                [1 ]IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France; E-Mails: dmornico@ 123456genoscope.cns.fr (D.M.); lucie.miche@ 123456univ-provence.fr (L.M.); gilles.bena@ 123456ird.fr (G.B.); nico.nouwen@ 123456ird.fr (N.N.); eric.giraud@ 123456ird.fr (E.G.)
                [2 ]LABGeM, CEA-Genoscope & CNRS-UMR8030, 91057 Evry, France; E-Mails: vallenet@ 123456genoscope.cns.fr (D.V.); asmith@ 123456genoscope.cns.fr (A.A.T.S.); cmedigue@ 123456genoscope.cns.fr (C.M.)
                [3 ]LMBM, Faculté des Sciences, Université Mohammed V-Agdal, Av. Ibn Batouta BP 1014, Rabat, Morocco
                [4 ]Laboratoire de Bioénergétique Cellulaire, CEA Cadarache, DSV, IBEB, 13108 Saint-Paul-lez-Durance, France; E-Mail: andre.vermeglio@ 123456cea.fr
                Author notes
                [* ]Author to whom correspondence should be addressed; E-Mail: lionel.moulin@ 123456ird.fr ; Tel.: +33-4-6759-3763; Fax: +33-4-6759-3802.
                Article
                Publisher ID: genes-03-00035
                DOI: 10.3390/genes3010035
                PMC ID: 3899966
                PubMed ID: 24704842
                SO-VID: 8807aa48-af5f-459a-b81a-8957ccc818bb
                Copyright © © 2012 by the authors; licensee MDPI, Basel, Switzerland.
                License:

                This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/3.0/).

                History
                Date received : 16 September 2011
                Date revision received : 08 November 2011
                Date accepted : 23 November 2011
                Categories
                Subject: Article

                Keywords: rhizobia,genomics,bradyrhizobium,aeschynomene,nod-independent
                Data availability:
                Keywords: rhizobia, genomics, bradyrhizobium, aeschynomene, nod-independent

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