A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria

The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
PLoS ONE (Impact Factor: 3.23). 02/2008; 3(7):e2567. DOI: 10.1371/journal.pone.0002567
Source: PubMed Central


This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

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Available from: Santiago Castillo-Ramírez
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    • "that are highly expressed by rhizobia on plant roots [33]. On the other hand, plasmids are highly variable and confer adaptive traits, such as nodulation and nitrogen fixation in legumes [6] [8] [19] [26] [29] [38] [43] [49] [51], or they may be transferred between bacteria [30] [31] [40]. "
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    ABSTRACT: Genomics has provided data for defining bacterial-species limits from estimates of gene conservation, synteny, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH). Phylogenomic analyses that allowed a more accurate definition of rhizobial relationships showed two major superclades within the family Rhizobiaceae that corresponded to the Rhizobium/Agrobacterium and Shinella/Ensifer groups. Within the Rhizobium/Agrobacterium group, four highly-supported clades were evident that could correspond to distinct genera. The Shinella/Ensifer group encompassed not only the genera Shinella and Ensifer but also a separate clade containing the type strain of R. giardinii. Ensifer adhaerens (Casida AT) was an outlier within its group, separated from the rest of the Ensifer (formerly Sinorhizobium) strains. The phylogenomic analysis presented provided support for the revival of Allorhizobium as a bona fide genus within the Rhizobiaceae, the distinctiveness of Agrobacterium and the recently proposed Neorhizobium genus, and suggested that R. giardinii may be transferred to a novel genus. ANI reference values are becoming the gold standard in rhizobial taxonomy and are being used to recognize novel rhizobial lineages and species that seem to be biologically coherent, as shown in this study.
    Full-text · Article · Jan 2015 · Systematic and Applied Microbiology
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    • "The same symbiovar may be present in distinct species as a consequence of the lateral transfer of symbiotic plasmids or islands. Symbiotic genes and other genes associated with niche adaptation may have evolutionary histories independent of the evolution of the chromosomal genes [8]. Two symbiovars are recognized in Rhizobium etli: phaseoli (conferring the ability to nodulate Phaseolus vulgaris) and mimosae (involved in nodulating mimosas and P. vulgaris, [9]). "
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    ABSTRACT: Background Symbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium. Rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. In Rhizobium etli or in Rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodules in Phaseolus vulgaris while symbiovar mimosae confers a broad host range including different mimosa trees. Results We report on the genome of R. etli symbiovar mimosae strain Mim1 and its comparison to that from R. etli symbiovar phaseoli strain CFN42. Differences were found in plasmids especially in the symbiosis plasmid, not only in nod gene sequences but in nod gene content. Differences in Nod factors deduced from the presence of nod genes, in secretion systems or ACC-deaminase could help explain the distinct host specificity. Genes involved in P. vulgaris exudate uptake were not found in symbiovar mimosae but hup genes (involved in hydrogen uptake) were found. Plasmid pRetCFN42a was partially contained in Mim1 and a plasmid (pRetMim1c) was found only in Mim1. Chromids were well conserved. Conclusions The genomic differences between the two symbiovars, mimosae and phaseoli may explain different host specificity. With the genomic analysis presented, the term symbiovar is validated. Furthermore, our data support that the generalist symbiovar mimosae may be older than the specialist symbiovar phaseoli. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-575) contains supplementary material, which is available to authorized users.
    Full-text · Article · Jul 2014 · BMC Genomics
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    • "In contrast to chromosomes , plasmids are considered as usually poorly conserved, flexible and heterogeneous in size and gene content. Variations in the location of chromosomal and extrachromosomal genes can be observed even in small rhizobial populations (Crossman et al. 2008; Mazur et al. 2011b; López-Guerrero et al. 2012). Some of the rhizobial extrachromosomal replicons referred to as chromids are characterised by a plasmid-type replication system but differ from plasmids in their GC content and codon usage, which are similar to those of the chromosome. "
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    ABSTRACT: Rhizobium leguminosarum bv. trifolii TA1 (RtTA1) is a soil bacterium establishing a highly specific symbiotic relationship with clover, which is based on the exchange of molecular signals between the host plant and the microsymbiont. The RtTA1 genome is large and multipartite, composed of a chromosome and four plasmids, which comprise approximately 65 % and 35 % of the total genome, respectively. Extrachromosomal replicons were previously shown to confer significant metabolic versatility to bacteria, which is important for their adaptation in the soil and nodulation competitiveness. To investigate the contribution of individual RtTA1 plasmids to the overall cell phenotype, metabolic properties and symbiotic performance, a transposon-based elimination strategy was employed. RtTA1 derivatives cured of pRleTA1b or pRleTA1d and deleted in pRleTA1a were obtained. In contrast to the in silico predictions of pRleTA1b and pRleTA1d, which were described as chromid-like replicons, both appeared to be completely curable. On the other hand, for pRleTA1a (symbiotic plasmid) and pRleTA1c, which were proposed to be unessential for RtTA1 viability, it was not possible to eliminate them at all (pRleTA1c) or entirely (pRleTA1a). Analyses of the phenotypic traits of the RtTA1 derivatives obtained revealed the functional significance of individual plasmids and their indispensability for growth, certain metabolic pathways, production of surface polysaccharides, autoaggregation, biofilm formation, motility and symbiotic performance. Moreover, the results allow us to suggest broad functional cooperation among the plasmids in shaping the phenotypic properties and symbiotic capabilities of rhizobia. Electronic supplementary material The online version of this article (doi:10.1007/s13353-014-0220-2) contains supplementary material, which is available to authorized users.
    Full-text · Article · May 2014 · Journal of applied genetics
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