Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103

Weidner, Stefan; Becker, Anke; Bonilla, Ildefonso; Jaenicke, Sebastian; Lloret, Javier; Margaret, Isabel; Pühler, Alfred; Ruíz-Sainz, José E.; Schneiker-Bekel, Susanne; Szczepanowski, Rafael; Vinardell, José‐María; Zehner, Susanne; Göttfert, Michael

doi:10.1128/jb.06729-11

Cited by 44 publications

(35 citation statements)

References 11 publications

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“…4), the tree showed that both the engA and tRNA arg genes were located on the main chromosome, except in the case of all sequenced S. meliloti strains (15 strains) and S. medicae WSM419 (16,43,44,54,55). Furthermore, both the engA and tRNA arg genes were located on the chromosome for Sinorhizobium fredii strains NGR234, USDA257, and HH103 (45)(46)(47) and nine recently sequenced Sinorhizobium strains (seven S. fredii strains, one Sinorhizobium sojae strain, and one Sinorhizobium sp. strain [56]).…”

Section: Figmentioning

confidence: 97%

“…Genome sequences were downloaded from GenBank, and the corresponding accession numbers are as follows: AL591688.1 (S. meliloti 1021 chromosome) (41), AL591985.1 (S. meliloti 1021/pSymB) (15), CP001832.1 (S. meliloti SM11/pSmeSM11d) (42), CP002782.1 and CP002742.1 (S. meliloti AK83 chromosome 2 and S. meliloti BL225C/ pSINMEB02) (43), CP000738.1 and CP000739.1 (Sinorhizobium medicae WSM419 chromosome and pSMED01) (44), CP001389.1 and CP000874.1 (Sinorhizobium fredii NGR234 chromosome and pNGR234b) (45), NC_016812.1 (S. fredii HH103 chromosome) (46), and CP003563.1 (S. fredii USDA 257) (47).…”

Section: Methodsmentioning

confidence: 99%

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The tRNA ^arg Gene and engA Are Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

et al. 2013

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Bacterial genomes with two (or more) chromosome-like replicons are known, and these appear to be particularly frequent in alphaproteobacteria. The genome of the N 2 -fixing alfalfa symbiont Sinorhizobium meliloti 1021 contains a 3.7-Mb chromosome and 1.4-Mb (pSymA) and 1.7-Mb (pSymB) megaplasmids. In this study, the tRNA arg and engA genes, located on the pSymB megaplasmid, are shown to be essential for growth. These genes could be deleted from pSymB when copies were previously integrated into the chromosome. However, in the closely related strain Sinorhizobium fredii NGR234, the tRNA arg and engA genes are located on the chromosome, in a 69-kb region designated the engA-tRNA arg -rmlC region. This region includes bacA, a gene that is important for intracellular survival during host-bacterium interactions for S. meliloti and the related alphaproteobacterium Brucella abortus. The engA-tRNA arg -rmlC region lies between the kdgK and dppF2 (NGR_c24410) genes on the S. fredii chromosome. Synteny analysis showed that kdgK and dppF2 orthologues are adjacent to each other on the chromosomes of 15 sequenced strains of S. meliloti and Sinorhizobium medicae, whereas the 69-kb engA-tRNA arg -rmlC region is present on the pSymB-equivalent megaplasmids. This and other evidence strongly suggests that the engA-tRNA arg -rmlC region translocated from the chromosome to the progenitor of pSymB in an ancestor common to S. meliloti and S. medicae. To our knowledge, this work represents one of the first experimental demonstrations that essential genes are present on a megaplasmid.

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Section: Figmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 99%

The tRNA ^arg Gene and engA Are Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

et al. 2013

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“…Both strains are the best-studied model organisms with respect to host range. The analysis of the recently published complete genome of S. fredii NGR234 and the genome of the broad-host-range strain S. fredii HH103 suggested that these three strains share a high degree of synteny in their genomes (3,5,6). The complete genome sequence of USDA257 therefore significantly increases our knowledge of molecular mechanisms involved in the determination of host range in the interaction of plants with microbes.…”

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confidence: 97%

Complete Genome Sequence of the Broad-Host-Range Strain Sinorhizobium fredii USDA257

et al. 2012

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Here we announce the complete genome sequence of the symbiotic and nitrogen-fixing bacterium Sinorhizobium fredii USDA257. The genome shares a high degree of sequence similarity with the closely related broad-host-range strains S. fredii NGR234 and HH103. Most strikingly, the USDA257 genome encodes a wealth of secretory systems. Sinorhizobium fredii USDA257 is a Gram-negative soil bacterium that fixes nitrogen in symbiosis with legume plants. It was originally isolated from wild soybean cultivars (1) and has an extremely broad host range, comprising 79 legume plant genera (4). Only the closely related S. fredii NGR234 strain reveals a wider host range, being able to nodulate 112 plant genera (4). Both strains are the best-studied model organisms with respect to host range. The analysis of the recently published complete genome of S. fredii NGR234 and the genome of the broad-host-range strain S. fredii HH103 suggested that these three strains share a high degree of synteny in their genomes (3,5,6). The complete genome sequence of USDA257 therefore significantly increases our knowledge of molecular mechanisms involved in the determination of host range in the interaction of plants with microbes.

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“…Man is also present in the genome of S. fredii strains (CCBAU 45436/ HH103) (17,40). However, the ptsI and ptsH mutants were not impaired in symbiotic performance in terms of the relative chlorophyll concentration and shoot dry weight of soybean ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Genetic Analysis Reveals the Essential Role of Nitrogen Phosphotransferase System Components in Sinorhizobium fredii CCBAU 45436 Symbioses with Soybean and Pigeonpea Plants

Wang

Feng

et al. 2016

Appl Environ Microbiol

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The nitrogen phosphotransferase system (PTS Ntr ) consists of EI Ntr , NPr, and EIIA Ntr . The active phosphate moiety derived from phosphoenolpyruvate is transferred through EI Ntr and NPr to EIIA Ntr . Sinorhizobium fredii can establish a nitrogen-fixing symbiosis with the legume crops soybean (as determinate nodules) and pigeonpea (as indeterminate nodules). In this study, S. fredii strains with mutations in ptsP and ptsO (encoding EI Ntr and NPr, respectively) formed ineffective nodules on soybeans, while a strain with a ptsN mutation (encoding EIIA Ntr ) was not defective in symbiosis with soybeans. Notable reductions in the numbers of bacteroids within each symbiosome and of poly-␤-hydroxybutyrate granules in bacteroids were observed in nodules infected by the ptsP or ptsO mutant strains but not in those infected with the ptsN mutant strain. However, these defects of the ptsP and ptsO mutant strains were recovered in ptsP ptsN and ptsO ptsN double-mutant strains, implying a negative role of unphosphorylated EIIA Ntr in symbiosis. Moreover, the symbiotic defect of the ptsP mutant was also recovered by expressing EI Ntr with or without the GAF domain, indicating that the putative glutamine-sensing domain GAF is dispensable in symbiotic interactions. The critical role of PTS Ntr in symbiosis was also observed when related PTS Ntr mutant strains of S. fredii were inoculated on pigeonpea plants. Furthermore, nodule occupancy and carbon utilization tests suggested that multiple outputs could be derived from components of PTS Ntr in addition to the negative role of unphosphorylated EIIA Ntr . In bacteria, the phosphotransferase system (PTS) is important for transport and signal transduction in cellular metabolism (1). Two general types of PTSs have been identified (Fig. 1): the sugar PTS, dedicated to carbohydrate transport, and the nitrogen PTS (PTS Ntr ), which exerts regulatory functions (2). In the canonical model of both PTSs, described in Gram-negative bacteria, the active phosphate moiety derived from phosphoenolpyruvate (PEP) is transferred through two general phosphotransferase proteins: enzyme I (EI, or EI Ntr ) and histidine protein (HPr or NPr) (2, 3). In the sugar PTS, HPr can then phosphorylate sugar-specific EIIA, which will pass the phosphate to the corresponding EIICB transport protein, allowing uptake of the sugar (3). With PTS Ntr , NPr can phosphorylate EIIA Ntr , which is a homolog of EIIA but is not active in sugar transport, as the required EIIB-and EIIC-like domains are lacking (2). Accumulating evidence has suggested that EIIA Ntr seems to exclusively serve regulatory functions. In Escherichia coli, for example, unphosphorylated EIIA Ntr directly binds the TrkA subunit of the low-affinity potassium transporter, thereby inhibiting uptake of potassium at high concentrations, while it stimulates autophosphorylation of KdpD through protein-protein interactions when the potassium level is low, enhancing the transcription of kdpFABC, which encode the high-affinity potassium transporter (4, 5). ...

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Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103

Cited by 44 publications

References 11 publications

The tRNA ^arg Gene and engA Are Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

The tRNA ^arg Gene and engA Are Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

Complete Genome Sequence of the Broad-Host-Range Strain Sinorhizobium fredii USDA257

Genetic Analysis Reveals the Essential Role of Nitrogen Phosphotransferase System Components in Sinorhizobium fredii CCBAU 45436 Symbioses with Soybean and Pigeonpea Plants

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Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103

Cited by 44 publications

References 11 publications

The tRNA arg Gene and engA Are Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

The tRNA arg Gene and engA Are Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

Complete Genome Sequence of the Broad-Host-Range Strain Sinorhizobium fredii USDA257

Genetic Analysis Reveals the Essential Role of Nitrogen Phosphotransferase System Components in Sinorhizobium fredii CCBAU 45436 Symbioses with Soybean and Pigeonpea Plants

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The tRNA ^arg Gene and engA Are Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

The tRNA ^arg Gene and engA Are Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain