Isolation and Regulation of
            <i>Sinorhizobium meliloti</i>
            1021 Loci Induced by Oxygen Limitation

Trzebiatowski, Jodi R.; Ragatz, D.; Bruijn, Frans J. de

doi:10.1128/aem.67.8.3728-3731.2001

Cited by 17 publications

(33 citation statements)

References 23 publications

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“…Seven of these genes (SMa1447, SMb20238, SMb20481, SMb20482, SMb21441, SMc04299, and SMc03247) were not induced under microoxic conditions in our study. This result may be explained by a slightly different genetic background, shorter exposure to a low oxygen concentration (2 h instead of 6 or 8 h in the former studies [9,48]), or a low level of induction of these genes (48) which did not allow us to detect their induction in microarray experiments. However, the gene cyoC, encoding a ubiquinol oxidase subunit protein, was shown to be induced independently of FixJ in our study as well as in a previous one (48).…”

Section: Vol 188 2006mentioning

confidence: 48%

“…One gene displayed a sevenfold increase in its level of expression and encodes a putative twocomponent receiver domain (SMc01504). Eight genes had been shown previously to be induced by microoxic conditions independently of FixJ (9,24,48). Seven of these genes (SMa1447, SMb20238, SMb20481, SMb20482, SMb21441, SMc04299, and SMc03247) were not induced under microoxic conditions in our study.…”

Section: Vol 188 2006mentioning

confidence: 57%

“…Once phosphorylated, FixJ activates transcription of the nifA and fixK genes, encoding two intermediate regulators which induce expression of nif and fix genes involved in respiration and nitrogen fixation (44). In total, about 35 FixJ targets (direct or indirect) have been described, including FixM, a flavoprotein whose physiological function is yet unknown (14), and two homologues of ORF277 (Bradyrhizobium japonicum and Rhodobacter capsulatus) presenting homology with the family of universal stress protein (48). FixJ also controls, via FixK, the expression of a gene, fixT, that negatively affects expression of FixLJ-dependent genes by inhibiting FixL autophosphorylation (29).…”

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confidence: 99%

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FixJ: a Major Regulator of the Oxygen Limitation Response and Late Symbiotic Functions of Sinorhizobium meliloti

2006

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Sinorhizobium meliloti exists either in a free-living state in the soil or in symbiosis within legume nodules, where the bacteria differentiate into nitrogen-fixing bacteroids. Expression of genes involved in nitrogen fixation and associated respiration is governed by two intermediate regulators, NifA and FixK, respectively, which are controlled by a two-component regulatory system FixLJ in response to low-oxygen conditions. In order to identify the FixLJ regulon, gene expression profiles were determined in microaerobic free-living cells as well as during the symbiotic life of the bacterium for the wild type and a fixJ null-mutant strain. We identified 122 genes activated by FixJ in either state, including 87 novel targets. FixJ controls 74% of the genes induced in microaerobiosis (2% oxygen) and the majority of genes expressed in mature bacteroids. Ninetyseven percent of FixJ-activated genes are located on the symbiotic plasmid pSymA. Transcriptome profiles of a nifA and a fixK mutant showed that NifA activates a limited number of genes, all specific to the symbiotic state, whereas FixK controls more than 90 genes, involved in free-living and/or symbiotic life. This study also revealed that FixJ has no other direct targets besides those already known. FixJ is involved in the regulation of functions such as denitrification or amino acid/polyamine metabolism and transport. Mutations in selected novel FixJ targets did not affect the ability of the bacteria to form nitrogen-fixing nodules on Medicago sativa roots. From these results, we propose an updated model of the FixJ regulon.

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Section: Vol 188 2006mentioning

confidence: 48%

Section: Vol 188 2006mentioning

confidence: 57%

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confidence: 99%

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FixJ: a Major Regulator of the Oxygen Limitation Response and Late Symbiotic Functions of Sinorhizobium meliloti

2006

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“…Other genes have been shown to be regulated by oxygen in a FixJ-independent fashion, such as the asnO gene, which encodes an asparagine synthetase homologue (Bergès et al, 2001), and the six loe-2, loe-3, loe-5, loe-6, loe-8 and loe-9 loci (Trzebiatowski et al, 2001). Furthermore, microaerobic induction of nifA appears not to be solely regulated by the FixLJ system (Kahn & Ditta, 1991).…”

Section: Fixj-independent Microaerobic Gene Inductionmentioning

confidence: 99%

FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti

et al. 2004

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The FixLJ two-component system of Sinorhizobium meliloti is a global regulator, turning on nitrogen-fixation genes in microaerobiosis. Up to now, nifA and fixK were the only genes known to be directly regulated by FixJ. We used a genomic SELEX approach in order to isolate new FixJ targets in the genome. This led to the identification of 22 FixJ binding sites, including the known sites in the fixK1 and fixK2 promoters. FixJ binding sites are unevenly distributed among the three replicons constituting the S. meliloti genome: a majority are carried either by pSymA or by a short chromosomal region of non-chromosomal origin. Thus FixJ binding sites appear to be preferentially associated with the pSymA replicon, which carries the fixJ gene. Functional analysis of FixJ targets led to the discovery of two new FixJ-regulated genes, smc03253 and proB2. This FixJ-dependent regulation appears to be mediated by a duplication of the whole fixK promoter region, including the beginning of the fixK gene. Similar duplications were previously reported for the nifH promoter. By systematic comparison of all promoter regions we found 17 such duplications throughout the genome, indicating that promoter duplication is a common mechanism for the evolution of regulatory pathways in S. meliloti.

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“…Recent studies have focused on understanding how rhizobia adapt to these unique environments, especially at the level of gene expression (6,13,62). For the symbiosis to occur, expression of a subset of genes, such as the nod and nif genes, must be tightly regulated (reviewed in reference 22).…”

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confidence: 99%

The RNA Polymerase α Subunit from Sinorhizobium meliloti Can Assemble with RNA Polymerase Subunits from Escherichia coli and Function in Basal and Activated Transcription both In Vivo and In Vitro

et al. 2002

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Sinorhizobium meliloti, a gram-negative soil bacterium, forms a nitrogen-fixing symbiotic relationship with members of the legume family. To facilitate our studies of transcription in S. meliloti, we cloned and characterized the gene for the ␣ subunit of RNA polymerase (RNAP). S. meliloti rpoA encodes a 336-amino-acid, 37-kDa protein. Sequence analysis of the region surrounding rpoA identified six open reading frames that are found in the conserved gene order secY (SecY)-adk (Adk)-rpsM (S13)-rpsK (S11)-rpoA (␣)-rplQ (L17) found in the ␣-proteobacteria. In vivo, S. meliloti rpoA expressed in Escherichia coli complemented a temperature sensitive mutation in E. coli rpoA, demonstrating that S. meliloti ␣ supports RNAP assembly, sequence-specific DNA binding, and interaction with transcriptional activators in the context of E. coli. In vitro, we reconstituted RNAP holoenzyme from S. meliloti ␣ and E. coli ␤, ␤, and subunits. Similar to E. coli RNAP, the hybrid RNAP supported transcription from an E. coli core promoter and responded to both upstream (UP) elementand Fis-dependent transcription activation. We obtained similar results using purified RNAP from S. meliloti. Our results demonstrate that S. meliloti ␣ functions are conserved in heterologous host E. coli even though the two ␣ subunits are only 51% identical. The ability to utilize E. coli as a heterologous system in which to study the regulation of S. meliloti genes could provide an important tool for our understanding and manipulation of these processes.The ␣-proteobacterium Sinorhizobium meliloti is able to live either as a soil saprophyte or in a symbiotic relationship with members of the legume family, such as alfalfa. Recent studies have focused on understanding how rhizobia adapt to these unique environments, especially at the level of gene expression (6,13,62). For the symbiosis to occur, expression of a subset of genes, such as the nod and nif genes, must be tightly regulated (reviewed in reference 22). As is the case with other bacteria, much of the gene regulation occurs at the level of initiation of transcription (28). To facilitate our studies of transcription and its regulation in S. meliloti, we must understand RNA polymerase (RNAP) structure and function.Previous work demonstrated that RNAP from S. meliloti displays the characteristic ␣ 2 ␤␤Ј core subunit structure found in most bacteria (23,45). In addition 70 , 54 , and 72 homologs have been cloned from S. meliloti (47, 48, 52, 55). These results are consistent with the evidence that bacterial RNAPs display overall sequence and functional similarities, although they can exhibit some differences in individual steps during transcription such as promoter recognition and promoter escape (4). Since only a limited number of S. meliloti promoters have been characterized, the cis-acting elements are not yet as well defined as in Escherichia coli promoters (7,23,55). Nevertheless, S. meliloti RNAP can initiate transcription at typical E. coli promoters (19, 23). However, most S. meliloti promoters t...

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Isolation and Regulation of Sinorhizobium meliloti 1021 Loci Induced by Oxygen Limitation

Cited by 17 publications

References 23 publications

FixJ: a Major Regulator of the Oxygen Limitation Response and Late Symbiotic Functions of Sinorhizobium meliloti

FixJ: a Major Regulator of the Oxygen Limitation Response and Late Symbiotic Functions of Sinorhizobium meliloti

FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti

The RNA Polymerase α Subunit from Sinorhizobium meliloti Can Assemble with RNA Polymerase Subunits from Escherichia coli and Function in Basal and Activated Transcription both In Vivo and In Vitro

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