Quick change: post-transcriptional regulation in Pseudomonas

Abstract

Pseudomonas species have evolved dynamic and intricate regulatory networks to fine-tune gene expression, with complex regulation occurring at every stage in the processing of genetic information. This approach enables Pseudomonas to generate precise individual responses to the environment in order to improve their fitness and resource economy. The weak correlations we observe between RNA and protein abundance highlight the significant regulatory contribution of a series of intersecting post-transcriptional pathways, influencing mRNA stability, translational activity and ribosome function, to Pseudomonas environmental responses. This review examines our current understanding of three major post-transcriptional regulatory systems in Pseudomonas spp.; Gac/Rsm, Hfq and RimK, and presents an overview of new research frontiers, emerging genome-wide methodologies, and their potential for the study of global regulatory responses in Pseudomonas.

The global regulator Crc orchestrates the metabolic robustness underlying oxidative stress resistance in Pseudomonas aeruginosa

“…Sophisticated regulatory networks in Pseudomonads control the physiological responses to these stressful conditions, including both local and global regulators that adjust transcriptional levels according to environmental cues (Tribelli et al, 2013;Balasubramanian et al, 2015;Arce-Rodríguez et al, 2016;Udaondo et al, 2018). Carbon catabolite repression, governed by the Crc protein, is a major player among these regulatory systems in Pseudomonas species (Wolff et al, 1991;Collier et al, 1996;Velázquez et al, 2004;Rojo, 2010;Grenga et al, 2017;Liu et al, 2017;Wirebrand et al, 2018). Crc is a global regulator that exerts its influence at the post-transcriptional level by binding (together with the Hfq protein, the actual RNA-binding protein in the complex) a cognate region of target mRNAs (Kambara et al, 2018), thus blocking translation (Moreno et al, 2009;Milojevic et al, 2013;Moreno et al, 2015).…”

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

“…In response to environmental stimuli, GacS phosphorylates and activates of the response regulator GacA leading to the upregulation of the expression of regulatory small RNAs. These sRNAs bind to the global regulator RsmA, releasing its repression of genes necessary for biofilm formation 20,40 . The decrease in biofilm formation observed upon CRISPRimediated silencing of gacS is in agreement with the regulatory model and with phenotypes observed in gacS mutants in various Pseudomonas 17,18,25,40,68 .…”

“…These sRNAs bind to the global regulator RsmA, releasing its repression of genes necessary for biofilm formation 20,40 . The decrease in biofilm formation observed upon CRISPRimediated silencing of gacS is in agreement with the regulatory model and with phenotypes observed in gacS mutants in various Pseudomonas 17,18,25,40,68 . In SBW25, GacS is also regulating genes involved in oxidative stress response, and the gacS::Tn5 mutant has a reduced capacity to survive exposure to sub-lethal doses of H2O2 25 .…”

“…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.…”