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. https://resolver.caltech.edu/CaltechAUTHORS:20160120-081453238
![]() |
PDF
- Published Version
See Usage Policy. 1165Kb |
![]() |
PDF
- Supplemental Material
See Usage Policy. 1049Kb |
![]() |
MS Excel (Dataset_S01)
- Supplemental Material
See Usage Policy. 81Kb |
![]() |
MS Excel (Dataset_S02)
- Supplemental Material
See Usage Policy. 22Kb |
![]() |
MS Excel (Dataset_S03)
- Supplemental Material
See Usage Policy. 1906Kb |
![]() |
MS Excel (Dataset_S04)
- Supplemental Material
See Usage Policy. 18Kb |
![]() |
MS Excel (Dataset_S05)
- Supplemental Material
See Usage Policy. 17Mb |
![]() |
MS Excel (Dataset_S06)
- Supplemental Material
See Usage Policy. 279Kb |
Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20160120-081453238
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: |
| ||||||||||||||||
ORCID: |
| ||||||||||||||||
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: |
| ||||||||||||||||
Issue or Number: | 5 | ||||||||||||||||
PubMed Central ID: | PMC4747698 | ||||||||||||||||
Record Number: | CaltechAUTHORS:20160120-081453238 | ||||||||||||||||
Persistent URL: | https://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: | 09 Mar 2020 13:18 |
Repository Staff Only: item control page