title: Deep sequencing analyses expands the Pseudomonas aeruginosa AmpR regulon to include small RNA-mediated regulation of iron acquisition, heat shock and oxidative stress response.
abstract: Pathogenicity of Pseudomonas aeruginosa, a major cause of many acute and chronic human infections, is determined by tightly regulated expression of multiple virulence factors. Quorum sensing (QS) controls expression of many of these pathogenic determinants. Previous microarray studies have shown that the AmpC β-lactamase regulator AmpR, a member of the LysR family of transcription factors, also controls non-β-lactam resistance and multiple virulence mechanisms. Using RNA-Seq and complementary assays, this study further expands the AmpR regulon to include diverse processes such as oxidative stress, heat shock and iron uptake. Importantly, AmpR affects many of these phenotypes, in part, by regulating expression of non-coding RNAs such as rgP32, asRgsA, asPrrF1 and rgRsmZ. AmpR positively regulates expression of the major QS regulators LasR, RhlR and MvfR, and genes of the Pseudomonas quinolone system. Chromatin immunoprecipitation (ChIP)-Seq and ChIP-quantitative real-time polymerase chain reaction studies show that AmpR binds to the ampC promoter both in the absence and presence of β-lactams. In addition, AmpR directly binds the lasR promoter, encoding the QS master regulator. Comparison of the AmpR-binding sequences from the transcriptome and ChIP-Seq analyses identified an AT-rich consensus-binding motif. This study further attests to the role of AmpR in regulating virulence and physiological processes in P. aeruginosa.
authors.affiliation: Department of Biological Sciences, College of Arts and Science, Florida International University, Miami, FL 33199, USA, Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA, BioRG, School of Computing and Information Science, College of Engineering and Computing, Florida International University, Miami, FL 33199, USA, Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Deepak
authors.initials: D
authors.lastname: Balasubramanian
authors.forename: Hansi
authors.initials: H
authors.lastname: Kumari
authors.forename: Melita
authors.initials: M
authors.lastname: Jaric
authors.forename: Mitch
authors.initials: M
authors.lastname: Fernandez
authors.forename: Keith H
authors.initials: KH
authors.lastname: Turner
authors.forename: Simon L
authors.initials: SL
authors.lastname: Dove
authors.forename: Giri
authors.initials: G
authors.lastname: Narasimhan
authors.forename: Stephen
authors.initials: S
authors.lastname: Lory
authors.forename: Kalai
authors.initials: K
authors.lastname: Mathee
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D018869:Heat-Shock Response / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D007501:Iron / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D009876:Operon; D018384:Oxidative Stress / Q000235:genetics; D010619:Phenazines / Q000378:metabolism; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D053038:Quorum Sensing; D058727:RNA, Small Untranslated / Q000378:metabolism*; D018085:Regulon; D017423:Sequence Analysis, RNA; D015534:Trans-Activators / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; C080365:LasR protein, Pseudomonas aeruginosa; D010619:Phenazines; D058727:RNA, Small Untranslated; D015534:Trans-Activators; D014157:Transcription Factors; C071526:AmpR protein, Bacteria; D007501:Iron