Bacteria of the genus Pseudomonas are ubiquitous on Earth due to their great metabolic versatility and adaptation to fluctuating environments and different hosts. Some groups are important animal/human and plant pathogens, whereas others are studied for their biotechnological applications, including bioremediation, biological control of phytopathogens and plant growth promotion. Notably, their adaptability is mediated by various signal transduction systems, with the post-transcriptional Gac-Rsm cascade playing a key role. This pervasive Pseudomonas pathway controls major transitions at the population level, such as motile/sessile lifestyle, primary/secondary metabolism or replicative/infective behaviour. A hallmark of the Gac-Rsm cascade is the participation of small, regulatory, non-coding RNAs of the Rsm clan. These RNAs are synthetised in response to cell-density-dependent autoinducer signals channelled through the GacS/GacA two-component system, and they counteract, by molecular mimicry, the translational control that RNA-binding proteins of the RsmA family exert over hundreds of mRNAs. Rsm RNAs have been investigated in a few Pseudomonas model species, evidencing the presence of a variable number and families of genes depending on the taxonomic clade. However, the global picture of the distribution of these riboregulators at the genus level was unknown until now. We have undertaken a comprehensive survey and annotation of the vast array of gene sequences encoding members of the Rsm RNA clan in 245 complete genomes that cover 28 phylogenomic clades across the entire genus. The properties of the different families of rsm genes, their phylogenetic radiation, as well as the features of their promoters and adjacent regions, are discussed. The novel insights presented in our manuscript will significantly boost research on the biology of these prevalent RNAs in understudied species of the genus Pseudomonas and closely related genera.

中文翻译：

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假单胞菌中 rsm 氏族的小调节 RNA


假单胞菌属的细菌在地球上无处不在，因为它们具有很强的代谢多功能性和对波动环境和不同宿主的适应性。一些组是重要的动物/人类和植物病原体，而另一些组则因其生物技术应用而受到研究，包括生物修复、植物病原体的生物控制和植物生长促进。值得注意的是，它们的适应性是由各种信号转导系统介导的，其中转录后 Gac-Rsm 级联反应起着关键作用。这种普遍的假单胞菌通路控制着种群水平的主要转变，例如运动/无柄生活方式、初级/次级代谢或复制/感染行为。Gac-Rsm 级联反应的一个标志是 Rsm 家族的小的、调节性的、非编码的 RNA 的参与。这些 RNA 是在响应通过 GacS/GacA 双组分系统传递的细胞密度依赖性自诱导信号时合成的，它们通过分子模拟抵消 RsmA 家族的 RNA 结合蛋白对数百个 mRNA 施加的翻译控制。已在一些假单胞菌模型物种中研究了 RSM RNA，证明了根据分类分支存在可变数量的基因和家族。然而，直到现在，这些核糖调节因子在属水平上的分布的全球情况尚不清楚。我们对 245 个完整基因组中编码 Rsm RNA 氏族成员的大量基因序列进行了全面调查和注释，这些基因组涵盖了整个属的 28 个系统发育分支。 讨论了 rsm 基因不同家族的特性、它们的系统发育辐射以及它们的启动子和相邻区域的特征。我们手稿中提出的新见解将显着促进对假单胞菌属和密切相关属中研究不足的这些普遍 RNA 的生物学研究。