Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments

In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.

Automated summary

In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA system positively controls biofilm formation and secondary metabolite production through the synthesis of rsmX, rsmY, and rsmZ. This study reveals genetic amplification of Rsm sRNAs with the discovery of a novel sRNA gene, rsmX-2, and shows that the expression of rsmX-1 and rsmX-2 is GacA-dependent under nutrient-poor conditions. The highest expression levels and longest half-lives of these sRNAs are correlated with nutrient stress, supporting the notion that the Rsm system in P. brassicacearum is likely linked to the stringent response and bacterial adaptation to nutritional stress.