Wurtzel, OmriYoder-Himes, DeborahHan, KookDandekar, Ajai A.Edelheit, SaritGreenberg, E. PeterSorek, RotemLory, Stephen2013-04-102012Wurtzel, Omri, Deborah R. Yoder-Himes, Kook Han, Ajai A. Dandekar, Sarit Edelheit, E. Peter Greenberg, Rotem Sorek, and Stephen Lory. 2012. The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature. PLoS Pathogens 8(9): e1002945.1553-7366http://nrs.harvard.edu/urn-3:HUL.InstRepos:10522928One 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.en-USBiologyMicrobiologyMedicineInfectious DiseasesJournal Article2013-04-1010.1371/journal.ppat.1002945