Second messenger control of mRNA translation by dynamic ribosome modification

Pseudomonas species employ complex, dynamic signalling networks to fine-tune responses to changing environments, with regulation taking place at the transcriptional, post-transcriptional and post-translational levels. Control of mRNA translation and hence protein abundance is a crucial element of this regulatory network. Previously, we identified the ribosomal modification protein RimK, which influences the transition between active and sessile bacterial lifestyles. RimK is an ATP-dependent glutamyl ligase that adds glutamate residues to the C-terminus of ribosomal protein RpsF. This in-turn induces specific changes in ribosome function and translational output. RimK activity is itself under complex, multifactorial control: by the bacterial second messenger cyclic-di-GMP; a phosphodiesterase trigger enzyme (RimA); and a polyglutamate-specific protease (RimB). Deletion of the rim operon affects phenotypes including attachment, motility and cytotoxicity, severely compromising rhizosphere colonisation by the soil bacterium Pseudomonas fluorescens. Using a combination of protein biochemistry, quantitative proteomics and ribosomal profiling experiments, we examined the relationship between ribosomal modification and downstream changes in the P. fluorescens proteome. RimK activity leads to active proteome remodelling by two main routes; indirectly, through changes in the abundance of the global translational regulator Hfq and directly, with translation of surface attachment factors, amino acid transporters and key secreted molecules linked specifically to RpsF modification. Our findings suggest post-translational ribosomal modification as a rapid-response mechanism to tune global gene translation and thereby protein abundance in response to environmental signals.