1. Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti
- Author
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Alessio Mengoni, Jan Fang Cheng, Lynne Goodwin, Miriam Land, Antonella Fioravanti, Marco Galardini, Natalia Mikhailova, J. Chris Detter, Tanja Woyke, Francesco Pini, Marco Bazzicalupo, Roxanne Tapia, Susan Lucas, Hazuki Teshima, Sam Pitluck, Emanuele G. Biondi, Cliff Han, Loren Hauser, Matteo Brilli, Hajnalka E. Daligault, Stefano Mocali, David Bruce, Alla Lapidus, Natalia Ivanova, Dipartimento di Biologia Evoluzionistica 'Leo Pardi', Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Rheumatology Unit [Siena], Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] (IRI), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Droit et Santé-Université de Lille, Sciences et Technologies, Università degli Studi di Firenze = University of Florence (UniFI), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), Department of Bio-engineering Sciences, and Faculty of Economic and Social Sciences and Solvay Business School
- Subjects
pangenome ,lcsh:QH426-470 ,lcsh:Biotechnology ,Genomics ,comparative genomics ,Regulon ,Genome ,03 medical and health sciences ,Plasmid ,Species Specificity ,Nitrogen Fixation ,lcsh:TP248.13-248.65 ,Genetic variation ,Genetics ,panregulon ,nodulation ,Gene ,030304 developmental biology ,Comparative genomics ,0303 health sciences ,Sinorhizobium meliloti ,biology ,030306 microbiology ,food and beverages ,Pan-genome ,Molecular Sequence Annotation ,biology.organism_classification ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,symbiosis ,lcsh:Genetics ,Phenotype ,Genes, Bacterial ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,Genome, Bacterial ,Research Article ,Transcription Factors ,Biotechnology - Abstract
Background Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains. Results With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains. Conclusions In conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.
- Published
- 2011