The complete nucleotide sequence of a plant root-inducing (Ri) plasmid indicates its chimeric structure and evolutionary relationship between tumor-inducing (Ti) and symbiotic (Sym) plasmids in rhizobiaceae11Edited by N.-H. Chua

Moriguchi, Kazuki; Maeda, Y.; Satou, Megumi; Hardayani, Niken S.N; Kataoka, Mikiko; Tanaka, Nobukazu; Yoshida, Kazuo

doi:10.1006/jmbi.2001.4488

Cited by 94 publications

(78 citation statements)

References 43 publications

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“…The plasmids p42a and p42d are the poorest conserved replicons of the R. etli genome but show some highly conserved regions shared with plasmids of Agrobacterium (i.e., pTiC58, pTi-Sakura, and pRi1724), Rhizobium spp (pNGR234a), and M. loti (pMLa) (5,11,22,23) (Fig. 1).…”

Section: Cog Distribution Among Repliconsmentioning

confidence: 99%

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

González

Santamaría

Bustos

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

343

315

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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

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Section: Cog Distribution Among Repliconsmentioning

confidence: 99%

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

González

Santamaría

Bustos

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

343

315

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“…The complete nucleotide sequence of the mikimopine-type Ri plasmid pRi1724 has been determined previously (16) and has been shown to have close similarity to the cucumopinetype plasmid pRi2659, a known RMA pRi (32). The conjugal transfer (tra) system of pRi1724 shows closer similarity to the tra system of the sequenced Sinorhizobium Sym plasmid pNGR234 (6) and to some plasmids in R. leguminosarum (29) than to the tra systems in several Ti plasmids (16).…”

Section: Discussionmentioning

confidence: 96%

“…The conjugal transfer (tra) system of pRi1724 shows closer similarity to the tra system of the sequenced Sinorhizobium Sym plasmid pNGR234 (6) and to some plasmids in R. leguminosarum (29) than to the tra systems in several Ti plasmids (16). The plasmid replication genes of Agrobacterium plasmids are also related to those of rhizobia (21).…”

Section: Discussionmentioning

confidence: 97%

Acquisition of an Agrobacterium Ri Plasmid and Pathogenicity by Other α- Proteobacteria in Cucumber and Tomato Crops Affected by Root Mat

Weller¹,

Stead²,

Young

2004

Appl Environ Microbiol

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Root mat of cucumbers and tomatoes has previously been shown to be caused by Agrobacterium radiobacter strains harboring a root-inducing Ri plasmid (pRi). Nine other pRi-harboring ␣-Proteobacteria have subsequently been isolated from root mat-infected crops. Fatty acid profiling and partial 16S rRNA sequence analysis identified three of these strains as being in the genus Ochrobactrum, five as being in the genus Rhizobium, and one as being in the genus Sinorhizobium. An in vitro pathogenicity test involving inoculation of cucumber cotyledons was developed. All pRi-harboring ␣-Proteobacteria induced typical root mat symptoms from the cotyledons. Average transformation rates for rhizogenic Ochrobactrum (46%) and Rhizobium (44%) strains were lower than those observed for rhizogenic A. radiobacter strains (64%). However, individual strains from these three genera all had transformation rates comparable to those observed from cotyledons inoculated with a rhizogenic Sinorhizobium strain (75%

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“…70,71 The symbiotic genes from rhizobia are codified in plasmids in fast and some middle growing species and in symbiotic islands in the middle and slow growing ones. [72][73][74][75][76][77][78][79][80][81][82][83][84][85] From these genes, the most studied in rhizobia are nodD, nodA, nodC and nifH. 25,70,[86][87][88][89][90] Nevertheless, the symbiotic genes are not useful in taxonomy because due to their ability to be transferred in nature 91,92 from plasmids to islands, 93 from bacteria to plants 95 and among bacteria.…”

Section: Recent Changes In the Taxonomy Of Rhizobiamentioning

confidence: 99%

Taxonomy of Bacteria Nodulating Legumes

2009

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Over the years, the term "rhizobia" has come to be used for all the bacteria that are capable of nodulation and nitrogen fixation in association with legumes but the taxonomy of rhizobia has changed considerably over the last 30 year. Recently, several nonrhizobial species belonging to alpha and beta subgroup of Proteobacteria have been identified as nitrogen-fixing legume symbionts. Here we provide an overview of the history of the rhizobia and the widespread phylogenetic diversity of nitrogen-fixing legume symbionts.

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The complete nucleotide sequence of a plant root-inducing (Ri) plasmid indicates its chimeric structure and evolutionary relationship between tumor-inducing (Ti) and symbiotic (Sym) plasmids in rhizobiaceae11Edited by N.-H. Chua

Cited by 94 publications

References 43 publications

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

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

Acquisition of an Agrobacterium Ri Plasmid and Pathogenicity by Other α- Proteobacteria in Cucumber and Tomato Crops Affected by Root Mat

Taxonomy of Bacteria Nodulating Legumes

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