partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons

• Published in: Proceedings of the National Academy of Sciences - PNAS 2006-03, Vol.103 (10), p.3834-3839
• Main Authors: Gonzalez, V, Santamaria, R.I, Bustos, P, Hernandez-Gonzalez, I, Medrano-Soto, A, Moreno-Hagelsieb, G, Janga, S.C, Ramirez, M.A, Jimenez-Jacinto, V, Collado-Vides, J
• Format: Article
• Language: English
• Subjects: Bacteria; Bacteriophages; Biological Sciences; Biosynthesis; Chromosomes; Cogs; gene expression regulation; Gene loci; Gene Transfer, Horizontal; Genes; genome; Genome, Bacterial; Genomes; Genomics; Metabolism; Molecular Sequence Data; Multigene Family; nucleotide sequences; Plasmids; Plasmids - genetics; Polysaccharides, Bacterial - biosynthesis; Polysaccharides, Bacterial - genetics; Replicon; Rhizobiaceae - genetics; Rhizobium; Rhizobium etli; Rhizobium etli - genetics; Rhizobium etli - metabolism; Species Specificity; Symbiosis; Symbiosis - genetics; transcription (genetics); Transcription, Genetic
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0508502103

We report the complete 6,530,228-bp genome sequence of the symbiotic nitrogen fixing bacterium Rhizobium etli. Six large plasmids comprise one-third of the total genome size. The chromosome encodes most functions necessary for cell growth, whereas few essential genes or complete metabolic pathways are located in plasmids. Chromosomal synteny is disrupted by genes related to insertion sequences, phages, plasmids, and cell-surface components. Plasmids do not show synteny, and their orthologs are mostly shared by accessory replicons of species with multipartite genomes. Some nodulation genes are predicted to be functionally related with chromosomal loci encoding for the external envelope of the bacterium. Several pieces of evidence suggest an exogenous origin for the symbiotic plasmid (p42d) and p42a. Additional putative horizontal gene transfer events might have contributed to expand the adaptive repertoire of R. etli, because they include genes involved in small molecule metabolism, transport, and transcriptional regulation. Twenty-three putative sigma factors, numerous isozymes, and paralogous families attest to the metabolic redundancy and the genomic plasticity necessary to sustain the lifestyle of R. etli in symbiosis and in the soil.