Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas

Abstract

Gene expression is adjusted according to cellular needs through a combination of mechanisms acting at different layers of the flow of genetic information. At the posttranscriptional level, RNA-binding proteins are key factors controlling the fate of nascent and mature mRNAs. Among them, the members of the CsrA family are small dimeric proteins with heterogeneous distribution across the bacterial tree of life, that act as global regulators of gene expression because they recognize characteristic sequence/structural motifs (short hairpins with GGA triplets in the loop) present in hundreds of mRNAs. The regulatory output of CsrA binding to mRNAs is counteracted in most cases by molecular mimic, non-protein coding RNAs that titrate the CsrA dimers away from the target mRNAs. In γ-proteobacteria, the regulatory modules composed by CsrA homologs and the corresponding antagonistic sRNAs, are mastered by two-component systems of the GacS-GacA type, which control the transcription and the abundance of the sRNAs, thus constituting the rather linear cascade Gac-Rsm that responds to environmental or cellular signals to adjust and coordinate the expression of a set of target genes posttranscriptionally. Within the γ-proteobacteria, the genus Pseudomonas has been shown to contain species with different number of active CsrA (RsmA) homologs and of molecular mimic sRNAs. Here, with the help of the increasing availability of genomic data we provide a comprehensive state-of-the-art picture of the remarkable multiplicity of CsrA lineages, including novel yet uncharacterized paralogues, and discuss evolutionary aspects of the CsrA subfamilies of the genus Pseudomonas, and implications of the striking presence of csrA alleles in natural mobile genetic elements (phages and plasmids).

Two Homologues of the Global Regulator Csr/Rsm Redundantly Control Phaseolotoxin Biosynthesis and Virulence in the Plant Pathogen Pseudomonas amygdali pv. phaseolicola 1448A

“…The ability of free-living bacteria to respond and adapt to environmental changes relies on various interconnected regulatory networks, from which the Csr/Rsm (carbon storage regulator/ repressor of stationary-phase metabolites) is one of the most intensively studied post-transcriptional regulatory systems [ 1 , 2 , 3 ]. This system is widely present and conserved among nearly 3,000 species of bacteria and act as a global regulator of gene expression of hundreds of genes including, among others, those supporting robust growth and a diverse collection of virulence genes in animal and plant pathogens.…”

“…The central component of the Csr/Rsm system is CsrA, which is also called RsmA and various other names in different bacteria [ 1 , 2 ]. For clarity, we will refer collectively to these proteins as Csr/Rsm proteins, and to the corresponding genes as csr / rsm , but in the main text we will use the proposed uniform nomenclature for the nine Rsm subfamilies for Pseudomonas [ 2 ]. Csr/Rsm is a small protein of 50-150 amino acids acting as a homodimer to bind RNAs at a 12 nt sequence containing a highly conserved GGA motif typically included in a stem-and-loop structure.…”

“…The vast majority of the genomes examined contain a single copy of a csr / rsm gene. However, several bacterial lineages, particularly from Legionella, Pseudomonas and Xanthomonas , contain two to seven functional csr / rsm homologues, which are often carried by mobile genetic elements [ 2 ]. The homologues show variable levels of sequence identity, and within Pseudomonas can be classified into nine different protein subfamilies plus a group of unassigned proteins.…”

“…The homologues show variable levels of sequence identity, and within Pseudomonas can be classified into nine different protein subfamilies plus a group of unassigned proteins. Homologues of RsmA (CsrA2) and RsmE (CsrA3) are present in many, but not all bacteria containing a Csr/Rsm system; members of the other Rsm subfamilies, however, have a rather patchy distribution [ 2 ]. Although the exact role of the different homologues is often unclear, some of them were shown to be redundant and/or have unique regulatory roles, which likely provide genetic flexibility and helps to fine-tune the regulatory responses [ 6 , 7 , 8 , 9 , 10 ].…”

“…The levels of these small RNAs are in turn regulated by several factors, of which a main activator is the two-component signal transduction system GacS/GacA ( g lobal a ctivator of antibiotic and c yanide production) [ 3 , 11 ]. This system was first described in P. syringae and P. fluorescens and shown to participate in virulence, ecological fitness, and antifungal activity, and is widely conserved among Gammaproteobacteria [ 2 ]. The GacS/GacA signaling is activated by various metabolites, including short-chain carboxylates and citrate, leading to autophosphorylation of the transmembrane sensor histidine kinase GacS, which in turn phosphorylates GacA for activation [ 1 , 3 ].…”