The RsmA RNA-Binding Proteins in Pseudomonas syringae Exhibit Distinct and Overlapping Roles in Modulating Virulence and Survival Under Different Nutritional Conditions

Abstract

The post-transcriptional regulator RsmA globally controls gene expression in bacteria. Previous studies showed that RsmA2 and RsmA3 played critical roles in regulating type III secretion system (T3SS), motility, syringafactin, and alginate productions in Pseudomonas syringae pv. tomato strain DC3000 (PstDC3000). In this study, we investigated global gene expression profiles of the wild-type PstDC3000, the rsmA3 mutant, and the rsmA2/A3 double mutant in the hrp-inducing minimum medium (HMM) and King’s B (KB) medium. By comparing the rsmA2/A3 and rsmA3 mutants to PstDC3000, a total of 1358 and 1074 differentially expressed genes (DEGs) in HMM, and 870 and 1463 DEGs in KB were uncovered, respectively. When comparing the rsmA2/A3 mutant with the rsmA3 mutant, 277 and 741 DEGs in HMM and KB, respectively, were revealed. Transcriptomic analysis revealed that the rsmY, rsmZ, and rsmX1-5 non-coding small RNAs (ncsRNAs) were positively affected by RsmA2 and RsmA3, while RsmA3 positively regulates the expression of the rsmA2 gene and negatively regulates both rsmA1 and rsmA5 gene expression. Comparative transcriptomic analysis showed that RsmA2 and RsmA3 synergistically influenced the expression of genes involved in T3SS and alginate biosynthesis in HMM and chemotaxis in KB. RsmA2 and RsmA3 inversely affected genes involved in syringafactin production in HMM and ribosomal protein biosynthesis in KB. In addition, RsmA2 played a major role in influencing genes involved in sarcosine and thiamine biosynthesis in HMM and in mannitol and phosphate metabolism in KB. On the other hand, genes involved in fatty acid metabolism, cellulose biosynthesis, signal transduction, and stress responses were mainly impacted by RsmA3 in both HMM and KB; whereas RsmA3 played a major role in controlling genes involved in c-di-GMP, phosphate metabolism, chemotaxis, and capsular polysaccharide in HMM. Furthermore, regulation of syringafactin production and oxidative stress by RsmA2 and RsmA3 was experimentally verified. Our results suggested the potential interplay among the RsmA proteins, which exhibit distinct and overlapping roles in modulating virulence and survival in P. syringae under different nutritional conditions.

In planta transcriptomics reveals conflicts between pattern-triggered immunity and the AlgU sigma factor regulon

“…Another explanation for the environment-specific regulation is that AlgU regulon genes are co-regulated by other transcription factors. Previous studies and our data have shown that the AlgU regulon overlaps with other transcription regulators such as the sigma factors RpoS, RpoN, HrpL, (Markel et al 2016;Yu et al 2014), small RNA regulators RsmA2/A3 (Liu et al 2021), the Fur iron homeostasis regulator (Butcher et al 2011;Nobori et al 2018), and the two-component system CvsSR (Fishman et al 2018).…”

The Escherichia coli two-component signal sensor BarA binds protonated acetate via a conserved hydrophobic-binding pocket

“…This signaling circuitry is highly conserved in γ-proteobacteria ( 42 , 43 , 44 ), preserving most of its general characteristics. However, the genes whose expression are modulated by the BarA/UvrY/CsrA regulatory cascade and hence the physiological response, may vary significantly among bacteria ( 10 , 45 , 46 , 47 , 48 , 49 , 50 , 51 ). Here, we found that the input domain of the BarA/UvrY system of E. coli differs from that of the homologous GacS/GacA of P. aeruginosa, in that the former has evolved to recognize an uncharged signal.…”

Regulation of the Pseudomonas syringae Type III Secretion System by Host Environment Signals

“…RsmA proteins can impact target mRNAs either negatively, i.e., by inhibiting the translation of bound mRNA transcripts, or positively, i.e., by stabilizing the target mRNA [183][184][185][186][187]. DC3000 possesses five distinct RsmA proteins (RsmA1-5), alternatively termed CsrA1-5 in some publications [132,188,189]. In a recent study, both RsmA2 and RsmA3 were required for full T3SS expression and virulence on host tomato [188,189].…”

“…DC3000 possesses five distinct RsmA proteins (RsmA1-5), alternatively termed CsrA1-5 in some publications [132,188,189]. In a recent study, both RsmA2 and RsmA3 were required for full T3SS expression and virulence on host tomato [188,189]. Homologs of RsmA2 and RsmA3 were similarly required for virulence of P. syringae pv.…”

“…The rsm ncRNAs function as molecular sponges to titrate RsmA protein, preventing RsmA interaction with target mRNAs [179,180]. In DC3000, seven rsm ncRNAs (rsmY, rsmX1-5, and rsmZ) are expressed in a GacA-dependent manner [189,192]. Based on the recent characterization of GacA as a negative regulator of T3SS gene expression in DC3000, GacA-mediated expression of rsmXYZ may deactivate RsmA2 and/or RsmA3, preventing these regulatory proteins from activating T3SS expression [140,188,189].…”