The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature

PLoS Pathog. 2012 Sep;8(9):e1002945. doi: 10.1371/journal.ppat.1002945. Epub 2012 Sep 27.


One of the hallmarks of opportunistic pathogens is their ability to adjust and respond to a wide range of environmental and host-associated conditions. The human pathogen Pseudomonas aeruginosa has an ability to thrive in a variety of hosts and cause a range of acute and chronic infections in individuals with impaired host defenses or cystic fibrosis. Here we report an in-depth transcriptional profiling of this organism when grown at host-related temperatures. Using RNA-seq of samples from P. aeruginosa grown at 28°C and 37°C we detected genes preferentially expressed at the body temperature of mammalian hosts, suggesting that they play a role during infection. These temperature-induced genes included the type III secretion system (T3SS) genes and effectors, as well as the genes responsible for phenazines biosynthesis. Using genome-wide transcription start site (TSS) mapping by RNA-seq we were able to accurately define the promoters and cis-acting RNA elements of many genes, and uncovered new genes and previously unrecognized non-coding RNAs directly controlled by the LasR quorum sensing regulator. Overall we identified 165 small RNAs and over 380 cis-antisense RNAs, some of which predicted to perform regulatory functions, and found that non-coding RNAs are preferentially localized in pathogenicity islands and horizontally transferred regions. Our work identifies regulatory features of P. aeruginosa genes whose products play a role in environmental adaption during infection and provides a reference transcriptional landscape for this pathogen.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Secretion Systems
  • Base Sequence
  • Chromosome Mapping
  • Gene Expression Profiling
  • Humans
  • Phenazines / metabolism
  • Promoter Regions, Genetic
  • Pseudomonas Infections / microbiology
  • Pseudomonas aeruginosa / genetics*
  • Pseudomonas aeruginosa / growth & development
  • Pseudomonas aeruginosa / metabolism
  • RNA, Untranslated / genetics*
  • RNA, Untranslated / isolation & purification
  • Sequence Analysis, DNA
  • Temperature
  • Trans-Activators / genetics
  • Transcriptome*


  • Bacterial Proteins
  • Bacterial Secretion Systems
  • LasR protein, Pseudomonas aeruginosa
  • Phenazines
  • RNA, Untranslated
  • Trans-Activators