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SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa

Babin, Brett M. and Bergkessel, Megan and Sweredoski, Michael J. and Moradian, Annie and Hess, Sonja and Newman, Dianne K. and Tirrell, David A. (2016) SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America, 113 (5). E597-E605. ISSN 0027-8424. PMCID PMC4747698. http://resolver.caltech.edu/CaltechAUTHORS:20160120-081453238

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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).


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1073/pnas.1514412113 DOIArticle
http://www.pnas.org/content/113/5/E597PublisherArticle
http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1514412113/-/DCSupplementalPublisherSupporting Information
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747698/PubMed CentralArticle
ORCID:
AuthorORCID
Babin, Brett M.0000-0002-4133-6665
Sweredoski, Michael J.0000-0003-0878-3831
Hess, Sonja0000-0002-5904-9816
Newman, Dianne K.0000-0003-1647-1918
Tirrell, David A.0000-0003-3175-4596
Additional Information:© 2015 National Academy of Sciences. Edited by Lucia B. Rothman-Denes, The University of Chicago, Chicago, IL, and approved December 17, 2015 (received for review July 21, 2015). Published online before print January 19, 2016. We thank Geoff Smith and Roxana Eggleston-Rangel for technical assistance with liquid chromatography–tandem mass spectrometry and Dr. Igor Antoshechkin for assistance with sequencing. We thank Dr. Olaf Schneewind for his gift of the anti-RpoA antibody. We appreciate constructive feedback on the manuscript from members of the D.K.N. and D.A.T. laboratories and Richard Gourse, as well as helpful comments from the editor and reviewers. This work was supported by NIH Grants 5R01HL117328-03 (to D.K.N.) and 1S10RR029594-01A1 (to S.H.), the Institute for Collaborative Biotechnologies through US Army Research Office Grant W911NF-09-0001 (to D.A.T.), Howard Hughes Medical Institute (HHMI), and the Millard and Muriel Jacobs Genetics and Genomics Laboratory at California Institute of Technology (Caltech). The Proteome Exploration Laboratory (M.J.S., A.M., and S.H.) was supported by Gordon and Betty Moore Foundation Grant GBMF775 and by the Beckman Institute at Caltech. D.K.N. is an HHMI Investigator. Author contributions: B.M.B., M.B., M.J.S., A.M., S.H., D.K.N., and D.A.T. designed research; B.M.B. and M.B. performed research; B.M.B., M.B., M.J.S., S.H., D.K.N., and D.A.T. analyzed data; and B.M.B., M.B., M.J.S., S.H., D.K.N., and D.A.T. wrote the paper. The authors declare no conflict of interest. Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE66181). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1514412113/-/DCSupplemental.
Funders:
Funding AgencyGrant Number
NIH5R01HL117328-03
NIH1S10RR029594-01A1
Army Research Office (ARO)W911NF-09-0001
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Millard and Muriel Jacobs Genetics and Genomics LaboratoryUNSPECIFIED
Gordon and Betty Moore FoundationGBMF775
Caltech Beckman InstituteUNSPECIFIED
PubMed Central ID:PMC4747698
Record Number:CaltechAUTHORS:20160120-081453238
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20160120-081453238
Official Citation:Brett M. Babin, Megan Bergkessel, Michael J. Sweredoski, Annie Moradian, Sonja Hess, Dianne K. Newman, and David A. Tirrell SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa PNAS 2016 113 (5) E597-E605; published ahead of print January 19, 2016, doi:10.1073/pnas.1514412113
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:63789
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:20 Jan 2016 16:58
Last Modified:24 Oct 2017 16:44

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