title: The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature.
abstract: 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.
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Omri
authors.initials: O
authors.lastname: Wurtzel
authors.forename: Deborah R
authors.initials: DR
authors.lastname: Yoder-Himes
authors.forename: Kook
authors.initials: K
authors.lastname: Han
authors.forename: Ajai A
authors.initials: AA
authors.lastname: Dandekar
authors.forename: Sarit
authors.initials: S
authors.lastname: Edelheit
authors.forename: E Peter
authors.initials: EP
authors.lastname: Greenberg
authors.forename: Rotem
authors.initials: R
authors.lastname: Sorek
authors.forename: Stephen
authors.initials: S
authors.lastname: Lory
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D058947:Bacterial Secretion Systems; D001483:Base Sequence; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D006801:Humans; D010619:Phenazines / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011552:Pseudomonas Infections / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D013696:Temperature; D015534:Trans-Activators / Q000235:genetics; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D058947:Bacterial Secretion Systems; C080365:LasR protein, Pseudomonas aeruginosa; D010619:Phenazines; D022661:RNA, Untranslated; D015534:Trans-Activators