Probing the sRNA regulatory landscape of P. aeruginosa: post-transcriptional control of determinants of pathogenicity and antibiotic susceptibility

Mol Microbiol. 2017 Dec;106(6):919-937. doi: 10.1111/mmi.13857. Epub 2017 Nov 2.

Abstract

During environmental adaptation bacteria use small regulatory RNAs (sRNAs) to repress or activate expression of a large fraction of their proteome. We extended the use of the in vivo RNA proximity ligation method toward probing global sRNA interactions with their targets in Pseudomonas aeruginosa and verified the method with a known regulon controlled by the PrrF1 sRNA. We also identified two sRNAs (Sr0161 and ErsA) that interact with the mRNA encoding the major porin OprD responsible for the uptake of carbapenem antibiotics. These two sRNAs base pair with the 5' UTR of oprD leading to increase in resistance of the bacteria to meropenem. Additional proximity ligation experiments and enrichment for Sr0161 targets identified the mRNA for the regulator of type III secretion system. Interaction between the exsA mRNA and Sr0161 leads to a block in the synthesis of a component of the T3SS apparatus and an effector. Another sRNA, Sr006, positively regulates, without Hfq, the expression of PagL, an enzyme responsible for deacylation of lipid A, reducing its pro-inflammatory property and resulting in polymyxin resistance. Therefore, an analysis of global sRNA-mRNA interactions can lead to discoveries of novel pathways controlling gene expression that are likely integrated into larger regulatory networks.

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Carbapenems / metabolism
  • Drug Resistance, Bacterial / genetics*
  • Gene Expression Regulation, Bacterial*
  • Genes, Regulator / physiology
  • Host Factor 1 Protein / metabolism
  • Lipid A / metabolism
  • Meropenem
  • Polymyxins / pharmacology
  • Porins / genetics
  • Porins / metabolism
  • Pseudomonas aeruginosa / drug effects*
  • Pseudomonas aeruginosa / genetics
  • Pseudomonas aeruginosa / pathogenicity*
  • RNA, Messenger / metabolism
  • RNA, Small Untranslated / genetics*
  • RNA, Small Untranslated / metabolism
  • Regulon
  • Thienamycins / pharmacology
  • Trans-Activators / genetics
  • Trans-Activators / metabolism
  • Type III Secretion Systems / genetics
  • Type III Secretion Systems / metabolism

Substances

  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Carbapenems
  • ExsA protein, Pseudomonas aeruginosa
  • Host Factor 1 Protein
  • Lipid A
  • Polymyxins
  • Porins
  • RNA, Messenger
  • RNA, Small Untranslated
  • Thienamycins
  • Trans-Activators
  • Type III Secretion Systems
  • OprD protein, Pseudomonas aeruginosa
  • Meropenem