title: RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium.
abstract: The opportunistic human pathogen Pseudomonas aeruginosa can thrive under microaerophilic to anaerobic conditions in the lungs of cystic fibrosis patients. RNASeq based comparative RNA profiling of the clinical isolate PA14 cultured in synthetic cystic fibrosis medium was performed after planktonic growth (OD600 = 2.0; P), 30 min after shift to anaerobiosis (A-30) and after anaerobic biofilm growth for 96h (B-96) with the aim to reveal differentially regulated functions impacting on sustained anoxic biofilm formation as well as on tolerance towards different antibiotics. Most notably, functions involved in sulfur metabolism were found to be up-regulated in B-96 cells when compared to A-30 cells. Based on the transcriptome studies a set of transposon mutants were screened, which revealed novel functions involved in anoxic biofilm growth.In addition, these studies revealed a decreased and an increased abundance of the oprD and the mexCD-oprJ operon transcripts, respectively, in B-96 cells, which may explain their increased tolerance towards meropenem and to antibiotics that are expelled by the MexCD-OprD efflux pump. The OprI protein has been implicated as a target for cationic antimicrobial peptides, such as SMAP-29. The transcriptome and subsequent Northern-blot analyses showed that the abundance of the oprI transcript encoding the OprI protein is strongly decreased in B-96 cells. However, follow up studies revealed that the susceptibility of a constructed PA14ΔoprI mutant towards SMAP-29 was indistinguishable from the parental wild-type strain, which questions OprI as a target for this antimicrobial peptide in strain PA14.
authors.affiliation: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
authors.forename: Muralidhar
authors.initials: M
authors.lastname: Tata
authors.affiliation: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.|Institute for Theoretical Chemistry, University of Vienna Währinger Straße 17, 1090 Vienna, Austria.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Wolfinger
authors.affiliation: Department of Chromosome Biology, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.|Institute for Theoretical Chemistry, University of Vienna Währinger Straße 17, 1090 Vienna, Austria.
authors.forename: Fabian
authors.initials: F
authors.lastname: Amman
authors.affiliation: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.|Free University Berlin, Institute of Animal Hygiene and Environmental Health, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany.
authors.forename: Nicole
authors.initials: N
authors.lastname: Roschanski
authors.affiliation: Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Dötsch
authors.affiliation: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Sonnleitner
authors.affiliation: Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.|Institute of Molecular Bacteriology, Twincore, Center for Experimental and Clinical Infection Research, Feodor-Lynen-Straße 7, 30625 Hannover, Germany.
authors.forename: Susanne
authors.initials: S
authors.lastname: Häussler
authors.affiliation: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
authors.forename: Udo
authors.initials: U
authors.lastname: Bläsi
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D018441:Biofilms; D003470:Culture Media; D003550:Cystic Fibrosis / Q000382:microbiology*; D024881:Drug Resistance, Bacterial; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D006801:Humans; D008826:Microbial Sensitivity Tests; D010100:Oxygen / Q000378:metabolism; D011550:Pseudomonas aeruginosa / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D003470:Culture Media; D010100:Oxygen
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