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

Abstract

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.

Bacterial pathogenesis of plants: future challenges from a microbial perspective

“…When bacteria were directly applied to cut petioles (Tans‐Kersten et al ., ), or when the requirement for apoplastic penetration was bypassed by syringe infiltration of bacteria (Pfeilmeier et al ., ), no loss of virulence was seen in either case. Interestingly, the deletion of several signalling genes [ P. syringae rimK (Little et al ., ), rpfS from Xcc (An et al ., ) and xbmR from X. citri ssp. citri (Yaryura et al ., )] produces similar, conditional effects, with virulence defects only seen on bacterial application to leaf surfaces.…”

“…cdG-regulated systems control multiple important aspects of phytopathogenic Pseudomonas behaviour, and affect the virulence of various species and pathovars (Engl et al, 2014;Perez-Mendoza et al, 2014;Pfeilmeier et al, 2016). A specific role of cdG has been suggested in the regulation of flagellum and T3SS activity (Trampari et al, 2015), and the control of proteome composition through ribosomal modification (Little et al, 2016). The Gac-Rsm network, which controls secretion systems, biofilm formation and QS, as well as siderophore and toxin production (Vakulskas et al, 2015), affects cdG levels by manipulating PDE/DGC production (Moscoso et al, 2014(Moscoso et al, , 2011.…”

Environment‐driven changes of mRNA and protein levels in Pseudomonas aeruginosa

“…The complex network of transcriptional regulators and sigma factors guarantees fine-tuned regulation of the optimized geneexpression-based systems in the opportunistic pathogen. However, recent studies also indicated that a number of post-transcriptional regulatory processes are responsible for changes in the protein profile and the phenotype (Martínez and Vadyvaloo, 2014;Krueger et al, 2016;Little et al, 2016;Ouidir et al, 2016;Grenga et al, 2017). In this study, we obtained extensive proteome datasets under several different environmental conditions that in their entirety allowed a comparison of RNA to protein ratios for each individual gene.…”

Interrogation of genes controlling biofilm formation using CRISPR interference in Pseudomonas fluorescens

“…C-di-GMP also regulates alginate synthesis through binding to the PilZtype domain of alginate co-polymerase Alg44. Additional levels of regulation involve the PDE protein RimA which modulates the activity of RimK, an enzyme that modifies the ribosomal protein RpsF by adding glutamate residues to its C terminus, thus altering ribosome abundance and function 40,41 . Altogether, these studies reveal that c-di-GMP-binding enzymes and proteins act in a coordinated manner to control the various stages of the planktonic-to-biofilm transition, altering motility, promoting cell adhesion, producing EPS and shaping biofilm architecture.…”