title: SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa.
abstract: Microbial quiescence and slow growth are ubiquitous physiological states, but their study is complicated by low levels of metabolic activity. To address this issue, we used a time-selective proteome-labeling method [bioorthogonal noncanonical amino acid tagging (BONCAT)] to identify proteins synthesized preferentially, but at extremely low rates, under anaerobic survival conditions by the opportunistic pathogen Pseudomonas aeruginosa. One of these proteins is a transcriptional regulator that has no homology to any characterized protein domains and is posttranscriptionally up-regulated during survival and slow growth. This small, acidic protein associates with RNA polymerase, and chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing suggests that the protein associates with genomic DNA through this interaction. ChIP signal is found both in promoter regions and throughout the coding sequences of many genes and is particularly enriched at ribosomal protein genes and in the promoter regions of rRNA genes. Deletion of the gene encoding this protein affects expression of these and many other genes and impacts biofilm formation, secondary metabolite production, and fitness in fluctuating conditions. On the basis of these observations, we have designated the protein SutA (survival under transitions A).
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125;
authors.forename: Brett M
authors.initials: BM
authors.lastname: Babin
authors.affiliation: Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125;
authors.forename: Megan
authors.initials: M
authors.lastname: Bergkessel
authors.affiliation: Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sweredoski
authors.affiliation: Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125.
authors.forename: Annie
authors.initials: A
authors.lastname: Moradian
authors.affiliation: Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125.
authors.forename: Sonja
authors.initials: S
authors.lastname: Hess
authors.affiliation: Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125; dkn@caltech.edu tirrell@caltech.edu.
authors.forename: Dianne K
authors.initials: DK
authors.lastname: Newman
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; dkn@caltech.edu tirrell@caltech.edu.
authors.forename: David A
authors.initials: DA
authors.lastname: Tirrell
mesh_terms: D000693:Anaerobiosis; D001426:Bacterial Proteins / Q000378:metabolism*; D018441:Biofilms; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D011485:Protein Binding; D011550:Pseudomonas aeruginosa / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D012270:Ribosomes / Q000235:genetics; D014158:Transcription, Genetic; D015854:Up-Regulation
chemical_list: D001426:Bacterial Proteins; D012321:DNA-Directed RNA Polymerases
keywords: BONCAT; Pseudomonas aeruginosa; proteomics; slow growth; transcription