Adaptive Remodeling of the Bacterial Proteome by Specific Ribosomal Modification Regulates <i>Pseudomonas</i> Infection and Niche Colonisation

Post-transcriptional control of protein abundance is a highly important, underexplored regulatory process by which organisms respond to their environments. Here we describe an important and previously unidentified regulatory pathway involving the ribosomal modification protein RimK, its regulator proteins RimA and RimB, and the widespread bacterial second messenger cyclic-di-GMP (cdG). Disruption of rimK affects motility and surface attachment in pathogenic and commensal Pseudomonas species, with rimK deletion significantly compromising rhizosphere colonisation by the commensal soil bacterium P. fluorescens, and plant infection by the pathogens P. syringae and P. aeruginosa. RimK functions as an ATP-dependent glutamyl ligase, adding glutamate residues to the C-terminus of ribosomal protein RpsF and inducing specific effects on both ribosome protein complement and function. Deletion of rimK in P. fluorescens leads to markedly reduced levels of multiple ribosomal proteins, and also of the key translational regulator Hfq. In turn, reduced Hfq levels induce specific downstream proteomic changes, with significant increases in multiple ABC transporters, stress response proteins and non-ribosomal peptide synthetases seen for both ΔrimK and Δhfq mutants. The activity of RimK is itself controlled by interactions with RimA, RimB and cdG. We propose that control of RimK activity represents a novel regulatory mechanism that dynamically influences interactions between bacteria and their hosts; translating environmental pressures into dynamic ribosomal changes, and consequently to an adaptive remodeling of the bacterial proteome.蛋白质丰度的转录后调控是生物体响应环境的一类极为重要但尚未得到充分研究的调控过程。本研究描述了一条重要且此前未被发现的调控通路，该通路涉及核糖体修饰蛋白RimK、其调控蛋白RimA与RimB，以及广泛分布的细菌第二信使环二鸟苷酸（cyclic-di-GMP，cdG）。rimK功能失活会影响致病及共生假单胞菌属物种的运动性与表面附着能力：rimK基因缺失会显著削弱共生土壤细菌荧光假单胞菌（P. fluorescens）的根际定殖能力，同时削弱病原菌丁香假单胞菌（P. syringae）与铜绿假单胞菌（P. aeruginosa）的植物侵染能力。RimK作为ATP依赖型谷氨酰连接酶发挥功能，可向核糖体蛋白RpsF的C端添加谷氨酸残基，并对核糖体蛋白组分与功能产生特异性影响。在荧光假单胞菌中敲除rimK会导致多种核糖体蛋白以及关键翻译调控因子Hfq的表达水平显著降低。反之，Hfq水平下降会诱导特异性的下游蛋白质组变化：ΔrimK与Δhfq突变株中均观察到多种ATP结合盒转运蛋白（ABC转运蛋白）、应激响应蛋白以及非核糖体肽合成酶的表达量显著上调。RimK的活性本身受到与RimA、RimB以及cdG的相互作用调控。本研究提出，对RimK活性的调控代表一种新型调控机制，可动态影响细菌与宿主之间的相互作用；将环境压力转化为动态的核糖体组分变化，进而实现细菌蛋白质组的适应性重塑。