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

Abstract

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. multireplicon genome ͉ rhizobiales ͉ symbiosis ͉ horizontal transfer

Structural Adaptation of a Thermostable Biotin-binding Protein in a Psychrophilic Environment

“…Each originates from a different host bacterium which inhabits a distinctive environment. Whereas rhizavidin from R. etli is found in the soil rhizosphere habitat (27), shwanavidin is found in the deep Gotland basin region of the Baltic Sea, at a depth of 120 -130 m (26). Furthermore, both rhizavidin and shwanavidin are unique proteins in their families, where no other species of Shewanella or Rhizobium is known to exhibit another avidin-like sequence in its genome.…”

“…One of these sequences, identified from the Gram-negative bacterium Shewanella denitrificans (26), is termed herein shwanavidin. Whereas rhizavidin from R. etli and streptavidin from Streptomyces avidinii inhabit the soil rhizosphere (27), S. denitrificans is found at 120 -130 m depths of the Baltic Sea at low temperatures (28), and shwanavidin exhibits a high degree of sequence similarity to other avidins (Fig. 1B).…”

Rhizobium cellulase CelC2 is essential for primary symbiotic infection of legume host roots

“…AM236080) (25), 85% to celC from R. etli CFN42 (GenBank accession no. CP000133) (26), and 69% to Smed 5210 from Sinorhizobium medicae WSM419 (GenBank accession no. CP000740).…”

Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains

“…In addition to symbiotic plasmids, several rhizobial strains also contain one or more smaller, accessory plasmids, also termed non-symbiotic plasmids (Mercado-Blanco and Toro, 1996;Gonzalez et al, 2006;Stiens et al, 2006;Young et al, 2006). Some of these plasmids have been shown to transfer between populations of indigenous rhizobia (Mercado-Blanco and Toro, 1996).…”