Control of mRNA translation by dynamic ribosome modification

Control of mRNA translation is a crucial regulatory mechanism used by bacteria to respond to their environment. In the soil bacterium Pseudomonas fluorescens, RimK modifies the C-terminus of ribosomal protein RpsF to influence important aspects of rhizosphere colonisation through proteome remodelling. In this study, we show that RimK activity is itself under complex, multifactorial control by the co-transcribed phosphodiesterase trigger enzyme (RimA) and a polyglutamate-specific protease (RimB). Furthermore, biochemical experimentation and mathematical modelling reveal a role for the nucleotide second messenger cyclic-di-GMP in coordinating these activities. Active ribosome regulation by RimK occurs 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 show that post-translational ribosomal modification functions as a rapid-response mechanism that tunes global gene translation in response to environmental signals. Author summary In the soil bacterium Pseudomonas fluorescens, root colonisation is controlled by RimK, a glutamate ligase found in many different bacterial species. By modifying the ribosomal protein RpsF, RimK changes the translation of a range of different colonisation-related genes. This in turn enables bacteria to effectively adapt to the root environment. In this study, we first unravel the regulation of RimK by the signalling molecule cyclic-di-GMP (cdG) and the enzymes RimA and RimB. We show how interactions between cdG, the RimA phosphodiesterase, the RimB protease and the RimK ligase produce an elegant regulatory circuit that translates cdG concentration into the proportion of cellular ribosomes that are modified by RimK activity. Next we examine the consequences of this ribosomal modification for mRNA translation and bacterial behaviour. RimK activity indirectly controls the abundance of the global translational regulator Hfq. This leads to the regulation of a range of root colonisation genes. Furthermore, the RimK ribosomal modification directly affects translation of a second set of genes, with secreted molecules, surface attachment factors and amino acid transporters rapidly responding to changes in ribosomal modification. Thus, RimK ribosomal modification enables bacterial gene translation to rapidly adapt to changing environmental signals in the complex root environment.