title: Identification of the alternative sigma factor SigX regulon and its implications for Pseudomonas aeruginosa pathogenicity.
abstract: Pseudomonas aeruginosa is distinguished by its broad metabolic diversity and its remarkable capability for adaptation, which relies on a large collection of transcriptional regulators and alternative sigma (σ) factors. The largest group of alternative σ factors is that of the extracytoplasmic function (ECF) σ factors, which control key transduction pathways for maintenance of envelope homeostasis in response to external stress and cell growth. In addition, there are specific roles of alternative σ factors in regulating the expression of virulence and virulence-associated genes. Here, we analyzed a deletion mutant of the ECF σ factor SigX and applied mRNA profiling to define the SigX-dependent regulon in P. aeruginosa in response to low-osmolarity-medium conditions. Furthermore, the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) led to the identification of the DNA binding motif of SigX. Genome-wide mapping of SigX-binding regions revealed enrichment of downstream genes involved in fatty acid biosynthesis, type III secretion, swarming and cyclic di-GMP (c-di-GMP) signaling. In accordance, a sigX deletion mutant exhibited altered fatty acid composition of the cell membrane, reduced cytotoxicity, impaired swarming activity, elevated c-di-GMP levels, and increased biofilm formation. In conclusion, a combination of ChIP-seq with transcriptional profiling and bioinformatic approaches to define consensus DNA binding sequences proved to be effective for the elucidation of the regulon of the alternative σ factor SigX, revealing its role in complex virulence-associated phenotypes in P. aeruginosa.
authors.affiliation: Institute for Molecular Bacteriology, Twincore GmbH, Center of Clinical and Experimental Infection Research, Hannover, Germany.
authors.forename: Andrea
authors.initials: A
authors.lastname: Blanka
authors.forename: Sebastian
authors.initials: S
authors.lastname: Schulz
authors.forename: Denitsa
authors.initials: D
authors.lastname: Eckweiler
authors.forename: Raimo
authors.initials: R
authors.lastname: Franke
authors.forename: Agata
authors.initials: A
authors.lastname: Bielecka
authors.forename: Tanja
authors.initials: T
authors.lastname: Nicolai
authors.forename: Fiordiligie
authors.initials: F
authors.lastname: Casilag
authors.forename: Juliane
authors.initials: J
authors.lastname: Düvel
authors.forename: Wolf-Rainer
authors.initials: WR
authors.lastname: Abraham
authors.forename: Volkhard
authors.initials: V
authors.lastname: Kaever
authors.forename: Susanne
authors.initials: S
authors.lastname: Häussler
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D003470:Culture Media / Q000737:chemistry; D017353:Gene Deletion; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D009997:Osmotic Pressure; D011485:Protein Binding; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000472:pathogenicity*; D018085:Regulon; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism*; D037521:Virulence Factors / Q000096:biosynthesis*
chemical_list: D003470:Culture Media; D012808:Sigma Factor; D037521:Virulence Factors