Complete Genome Sequence of the Alfalfa Symbiont
            <i>Sinorhizobium</i>
            /Ensifer meliloti Strain GR4

Martı́nez-Abarca, Francisco; Martínez-Rodríguez, Laura; López-Contreras, José Antonio; Jiménez‐Zurdo, José I.; Toro, Nicolás

doi:10.1128/genomea.00174-12

Cited by 29 publications

(22 citation statements)

References 13 publications

(11 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%

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%

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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“…Phylogenies of the species of interest were constructed with the MEGA 5.2.2 package (Tamura et al, 2011), multiple sequence alignments were constructed with MUSCLE (Edgar, 2004) and phylogenetic trees were produced from the resulting alignments as described. All accession numbers for the genomes/ contigs used in this study are listed in Table S5 (Galibert et al, 2001;González et al, 2006;Reeve et al, 2006;2010;Schmeisser et al, 2009;Galardini et al, 2011;Schneiker-Bekel et al, 2011;Schuldes et al, 2012;Weidner et al, 2012;Martínez-Abarca et al, 2013;Sallet et al, 2013;Mora et al, 2014;Rudder et al, 2014;Toro et al, 2014).…”

Section: Sequence Analysis Of the Etr Regionmentioning

confidence: 99%

Genomic resources for identification of the minimal N₂‐fixing symbiotic genome

diCenzo

Zamani

Milunovic

et al. 2016

Environmental Microbiology

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The lack of an appropriate genomic platform has precluded the use of gain-of-function approaches to study the rhizobium-legume symbiosis, preventing the establishment of the genes necessary and sufficient for symbiotic nitrogen fixation (SNF) and potentially hindering synthetic biology approaches aimed at engineering this process. Here, we describe the development of an appropriate system by reverse engineering Sinorhizobium meliloti. Using a novel in vivo cloning procedure, the engA-tRNA-rmlC (ETR) region, essential for cell viability and symbiosis, was transferred from Sinorhizobium fredii to the ancestral location on the S. meliloti chromosome, rendering the ETR region on pSymB redundant. A derivative of this strain lacking both the large symbiotic replicons (pSymA and pSymB) was constructed. Transfer of pSymA and pSymB back into this strain restored symbiotic capabilities with alfalfa. To delineate the location of the single-copy genes essential for SNF on these replicons, we screened a S. meliloti deletion library, representing > 95% of the 2900 genes of the symbiotic replicons, for their phenotypes with alfalfa. Only four loci, accounting for < 12% of pSymA and pSymB, were essential for SNF. These regions will serve as our preliminary target of the minimal set of horizontally acquired genes necessary and sufficient for SNF.

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“…The sequencing of S. meliloti strain GR4, 38 the host in which RmInt1 was first identified and from which it was isolated, showed there to be 10 copies of this intron present in three of the five replicons of this strain. Additionally, we identified several copies of a related element (72% nucleotide identity), hereafter referred as to RmInt2.…”

Section: Resultsmentioning

confidence: 98%

Insights into the strategies used by related group II introns to adapt successfully for the colonisation of a bacterial genome

et al. 2014

Self Cite

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Abbreviations: IEP, intron encoded protein; RNP, ribonucleoprotein; EBS, exon binding site; IBS, intron binding site;RT, reverse transcriptaseGroup II introns are self-splicing RNAs and site-specific mobile retroelements found in bacterial and organellar genomes. The group II intron RmInt1 is present at high copy number in Sinorhizobium meliloti species, and has a multifunctional intron-encoded protein (IEP) with reverse transcriptase/maturase activities, but lacking the DNA-binding and endonuclease domains. We characterized two RmInt1-related group II introns RmInt2 from S. meliloti strain GR4 and Sr.md.I1 from S. medicae strain WSM419 in terms of splicing and mobility activities. We used both wild-type and engineered intron-donor constructs based on ribozyme DORF-coding sequence derivatives, and we determined the DNA target requirements for RmInt2, the element most distantly related to RmInt1. The excision and mobility patterns of intron-donor constructs expressing different combinations of IEP and intron RNA provided experimental evidence for the co-operation of IEPs and intron RNAs from related elements in intron splicing and, in some cases, in intron homing. We were also able to identify the DNA target regions recognized by these IEPs lacking the DNA endonuclease domain. Our results provide new insight into the versatility of related group II introns and the possible co-operation between these elements to facilitate the colonization of bacterial genomes.

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Complete Genome Sequence of the Alfalfa Symbiont Sinorhizobium /Ensifer meliloti Strain GR4

Cited by 29 publications

References 13 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

Genomic resources for identification of the minimal N₂‐fixing symbiotic genome

Insights into the strategies used by related group II introns to adapt successfully for the colonisation of a bacterial genome

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Complete Genome Sequence of the Alfalfa Symbiont Sinorhizobium /Ensifer meliloti Strain GR4

Cited by 29 publications

References 13 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

Genomic resources for identification of the minimal N2‐fixing symbiotic genome

Insights into the strategies used by related group II introns to adapt successfully for the colonisation of a bacterial genome

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Genomic resources for identification of the minimal N₂‐fixing symbiotic genome