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

Abstract

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...

Genome‐wide identification of genes directly regulated by ChvI and a consensus sequence for ChvI binding in Sinorhizobium meliloti

“…Previous transcriptome studies identified numerous genes that appeared to be transcriptionally regulated by ExoS/ChvI (Yao et al, ; Chen et al, ; Wells et al, ; Barnett and Long, ). However, of the ChvI‐regulated genes identified in those previous studies, only ropB1 , SMb21440 and the SMc01580 ‐ SMc01581 operon (Chen et al, ) and the SMb21188 ‐ msbA2 operon (Bélanger and Charles, ) were shown to be directly regulated by ChvI, using EMSA to detect binding between purified ChvI protein and the upstream regions of these genes.…”

“…Notable ChvI direct targets identified in this study include chvI itself (Group 2), the exoY and exoH operons encoding enzymes involved in succinoglycan synthesis (Group 1), and rem , encoding a key regulator that activates expression of the class II flagellar assembly and motility genes (Group 1) (Rotter et al, ). While ChvI had been proposed to play a role in coordinating EPS‐I production and motility, evidence that motility/chemotaxis genes were directly regulated by ChvI was lacking until now (Yao et al, ; Wells et al, ; Chen et al, ; Barnett and Long, ; Barnett and Long, ). The effect of ChvI on rem transcription is negative, rather than positive as on the exo genes, and further work is needed to understand the mechanism by which ChvI down‐regulates promoter activity.…”

Sinorhizobium fredii HH103 syrM inactivation affects the expression of a large number of genes, impairs nodulation with soybean and extends the host‐range to Lotus japonicus

“…Part of the genes whose expression was activated by NodD1 and genistein lacked the promoter sequences recognized by NodD1 or TtsI (NB and TB, respectively), suggesting that other transcriptional regulators could be involved in the regulation of their expression. One of the obvious candidates was SyrM, since its orthologues participate in the nod regulon in S. meliloti and S. fredii NGR234 (Kobayashi et al, 2004;Barnett and Long, 2015). The expression of syrM is induced by NodD1 and genistein through NB19, and well conserved SyrM boxes were found upstream of two operons (psfHH103d_322-psfHH103d_319 and psfHH103d_306-psfHH103d_311) that were highly induced by genistein and lacked functional NB or TB (Pérez-Montaño et al, 2016).…”

The Absence of the N-acyl-homoserine-lactone Autoinducer Synthase Genes traI and ngrI Increases the Copy Number of the Symbiotic Plasmid in Sinorhizobium fredii NGR234

“…Thereby, the plant-released polyphenols and the betaines are highly specific signals that are perceived by the bacterial NodD or SyrM receptor and activator proteins, which in turn activate transcription of many symbiosis related genes (Hartwig et al, 1990; Swanson et al, 1993; Barnett and Long, 2015). The nod and nol genes encode for the strain-specific biosynthesis of chito-lipo-oligosaccharides, commonly called Nod factors.…”