Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011

Sallet, Erika; Roux, Brice Le; Sauviac, Laurent; Jardinaud, Marie-Françoise; Carrère, Sébastien; Faraut, Thomas; Carvalho-Niebel, Fernanda de; Gouzy, Jérôme; Gamas, Pascal; Capela, Delphine; Bruand, Claude; Schiex, Thomas

doi:10.1093/dnares/dst014

Cited by 83 publications

(111 citation statements)

References 91 publications

(106 reference statements)

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“…syrM, nodD3, and syrA appear to be universal in the Sinorhizobium genus based on published genome sequences (95)(96)(97)(98)(99)(100)(101)(102)(103)(104). Among S. meliloti and S. medicae strains, the orthologous proteins are nearly identical, and the gene arrangement is syntenic to S. meliloti Rm1021 (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Rm1021 lacks functional genes encoding NolR, a nod gene repressor (109), ExpR, an LuxR-family global regulator of population-based behavior (6), EcfRI, which regulates sulfite metabolism (110), PstC, involved in high-affinity phosphate transport (111), and perhaps others (99,102). NolR of S. meliloti Rm41 represses expression of nodD1 and nodD2 but probably not nodD3 and syrM (112); NolR may also regulate genes involved in bacterial growth, survival, and conjugative plasmid transfer (113).…”

Section: Discussionmentioning

confidence: 99%

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The Sinorhizobium meliloti SyrM Regulon: Effects on Global Gene Expression Are Mediated by syrA and nodD3

Barnett

Long

2015

J Bacteriol

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In Sinorhizobium meliloti, three NodD transcriptional regulators activate bacterial nodulation (nod) gene expression. NodD1 and NodD2 require plant compounds to activate nod genes. The NodD3 protein does not require exogenous compounds to activate nod gene expression; instead, another transcriptional regulator, SyrM, activates nodD3 expression. In addition, NodD3 can activate syrM expression. SyrM also activates expression of another gene, syrA, which when overexpressed causes a dramatic increase in exopolysaccharide production. In a previous study, we identified more than 200 genes with altered expression in a strain overexpressing nodD3. In this work, we define the transcriptomes of strains overexpressing syrM or syrA. The syrM, nodD3, and syrA overexpression transcriptomes share similar gene expression changes; analyses imply that nodD3 and syrA are the only targets directly activated by SyrM. We propose that most of the gene expression changes observed when nodD3 is overexpressed are due to NodD3 activation of syrM expression, which in turn stimulates SyrM activation of syrA expression. The subsequent increase in SyrA abundance results in broad changes in gene expression, most likely mediated by the ChvI-ExoS-ExoR regulatory circuit. IMPORTANCESymbioses with bacteria are prevalent across the animal and plant kingdoms. Our system of study, the rhizobium-legume symbiosis (Sinorhizobium meliloti and Medicago spp.), involves specific host-microbe signaling, differentiation in both partners, and metabolic exchange of bacterial fixed nitrogen for host photosynthate. During this complex developmental process, both bacteria and plants undergo profound changes in gene expression. The S. meliloti SyrM-NodD3-SyrA and ChvI-ExoS-ExoR regulatory circuits affect gene expression and are important for optimal symbiosis. In this study, we defined the transcriptomes of S. meliloti overexpressing SyrM or SyrA. In addition to identifying new targets of the SyrM-NodD3-SyrA regulatory circuit, our work further suggests how it is linked to the ChvI-ExoS-ExoR regulatory circuit. The symbiotic soil alphaproteobacterium Sinorhizobium meliloti forms nitrogen-fixing nodules on the roots of leguminous plants such as Medicago sativa (alfalfa) and Medicago truncatula (barrel medic). The earliest stages of the symbiosis involve an exchange of molecular signals: plant roots exude compounds that induce transcription of bacterial nod genes, which encode enzymes that synthesize lipochitooligosaccharide Nod factors (NF) (1, 2). These bacterial NF trigger early plant responses such as root hair curling, calcium spiking, and root cortical cell divisions to form the nodule organ (2). Bacteria trapped in curled root hairs penetrate the root hair through an infection thread (IT), an ingrowth of plant cell membrane and wall (3). As the IT elongates into the root, the bacteria at the tip are actively dividing.Bacterial polysaccharides, such as cyclic ␤-glucans and exopolysaccharide I (EPS-I; also known as succinoglycan), are essential for bacte...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The Sinorhizobium meliloti SyrM Regulon: Effects on Global Gene Expression Are Mediated by syrA and nodD3

Barnett

Long

2015

J Bacteriol

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“…LM21 (17), Sinorhizobium sp. strain M14 (18), Sinorhizobium meliloti 1021 (19), S. meliloti 2011 (20), and S. meliloti SM11 (21).…”

Section: Methodsmentioning

confidence: 99%

Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity

Dziewit

Oscik

Bartosik

et al. 2014

J Virol

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ABSTRACT⌽LM21 is a temperate phage isolated from Sinorhizobium sp. strain LM21 (Alphaproteobacteria). Genomic analysis and electron microscopy suggested that ⌽LM21 is a member of the family Siphoviridae. The phage has an isometric head and a long noncontractile tail. The genome of ⌽LM21 has 50,827 bp of linear double-stranded DNA encoding 72 putative proteins, including proteins responsible for the assembly of the phage particles, DNA packaging, transcription, replication, and lysis. Virion proteins were characterized using mass spectrometry, leading to the identification of the major capsid and tail components, tape measure, and a putative portal protein. We have confirmed the activity of two gene products, a lytic enzyme (a putative chitinase) and a DNA methyltransferase, sharing sequence specificity with the cell cycle-regulating methyltransferase (CcrM) of the bacterial host. Interestingly, the genome of Sinorhizobium phage ⌽LM21 shows very limited similarity to other known phage genome sequences and is thus considered unique. IMPORTANCEProphages are known to play an important role in the genomic diversification of bacteria via horizontal gene transfer. The influence of prophages on pathogenic bacteria is very well documented. However, our knowledge of the overall impact of prophages on the survival of their lysogenic, nonpathogenic bacterial hosts is still limited. In particular, information on prophages of the agronomically important Sinorhizobium species is scarce. In this study, we describe the isolation and molecular characterization of a novel temperate bacteriophage, ⌽LM21, of Sinorhizobium sp. LM21. Since we have not found any similar sequences, we propose that this bacteriophage is a novel species. We conducted a functional analysis of selected proteins. We have demonstrated that the phage DNA methyltransferase has the same sequence specificity as the cell cycle-regulating methyltransferase CcrM of its host. We point out that this phenomenon of mimicking the host regulatory mechanisms by viruses is quite common in bacteriophages.

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“…The mutant strains are referred to here as 2011rne and 2011rnj, respectively. Strain 2011 is closely related to strain 1021, the S. meliloti strain with the first sequenced genome and both strains are expR mutants [43,50,51]. Bacterial strains and plasmids are listed in Table S1 (available in the online Supplementary Material).…”

Section: Strains Plasmids Cultivation and Cloningmentioning

confidence: 99%

RNase E and RNase J are needed for S-adenosylmethionine homeostasis in Sinorhizobium meliloti

Baumgardt

Melior²,

Madhugiri

et al. 2017

Microbiology

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The ribonucleases (RNases) E and J play major roles in E. coli and Bacillus subtilis, respectively, and co-exist in Sinorhizobium meliloti. We analysed S. meliloti 2011 mutants with mini-Tn5 insertions in the corresponding genes rne and rnj and found many overlapping effects. We observed similar changes in mRNA levels, including lower mRNA levels of the motility and chemotaxis related genes flaA, flgB and cheR and higher levels of ndvA (important for glucan export). The acyl-homoserine lactone (AHL) levels were also higher during exponential growth in both RNase mutants, despite no increase in the expression of the sinI AHL synthase gene. Furthermore, several RNAs from both mutants migrated aberrantly in denaturing gels at 300 V but not under stronger denaturing conditions at 1300 V. The similarities between the two mutants could be explained by increased levels of the key methyl donor S-adenosylmethionine (SAM), since this may result in faster AHL synthesis leading to higher AHL accumulation as well as in uncontrolled methylation of macromolecules including RNA, which may strengthen RNA secondary structures. Indeed, we found that in both mutants the N 6 -methyladenosine content was increased almost threefold and the SAM level was increased at least sevenfold. Complementation by induced ectopic expression of the respective RNase restored the AHL and SAM levels in each of the mutants. In summary, our data show that both RNase E and RNase J are needed for SAM homeostasis in S. meliloti.

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Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011

Cited by 83 publications

References 91 publications

The Sinorhizobium meliloti SyrM Regulon: Effects on Global Gene Expression Are Mediated by syrA and nodD3

The Sinorhizobium meliloti SyrM Regulon: Effects on Global Gene Expression Are Mediated by syrA and nodD3

Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity

RNase E and RNase J are needed for S-adenosylmethionine homeostasis in Sinorhizobium meliloti

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