Functional characterization of bacterial sRNAs using a network biology approach
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. 1073/pnas.1104318108/-/DCSupplemental.
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| Format: | Article |
| Language: | en_US |
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Proceedings of the National Academy of Sciences (PNAS)
2012
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| Online Access: | http://hdl.handle.net/1721.1/70019 https://orcid.org/0000-0001-7243-8261 |
| _version_ | 1826203409164795904 |
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| author | Walker, Graham C. Modia, Sheetal R. Camacho, Diogo M. Kohanski, Michael A. Collins, James J. |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Walker, Graham C. Modia, Sheetal R. Camacho, Diogo M. Kohanski, Michael A. Collins, James J. |
| author_sort | Walker, Graham C. |
| collection | MIT |
| description | This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.
1073/pnas.1104318108/-/DCSupplemental. |
| first_indexed | 2024-09-23T12:36:30Z |
| format | Article |
| id | mit-1721.1/70019 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T12:36:30Z |
| publishDate | 2012 |
| publisher | Proceedings of the National Academy of Sciences (PNAS) |
| record_format | dspace |
| spelling | mit-1721.1/700192022-09-28T08:56:57Z Functional characterization of bacterial sRNAs using a network biology approach Walker, Graham C. Modia, Sheetal R. Camacho, Diogo M. Kohanski, Michael A. Collins, James J. Massachusetts Institute of Technology. Department of Biology Walker, Graham C. Walker, Graham C. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. 1073/pnas.1104318108/-/DCSupplemental. Small RNAs (sRNAs) are important components of posttranscriptional regulation. These molecules are prevalent in bacterial and eukaryotic organisms, and involved in a variety of responses to environmental stresses. The functional characterization of sRNAs is challenging and requires highly focused and extensive experimental procedures. Here, using a network biology approach and a compendium of gene expression profiles, we predict functional roles and regulatory interactions for sRNAs in Escherichia coli. We experimentally validate predictions for three sRNAs in our inferred network: IsrA, GlmZ, and GcvB. Specifically, we validate a predicted role for IsrA and GlmZ in the SOS response, and we expand on current knowledge of the GcvB sRNA, demonstrating its broad role in the regulation of amino acid metabolism and transport. We also show, using the inferred network coupled with experiments, that GcvB and Lrp, a transcription factor, repress each other in a mutually inhibitory network. This work shows that a network-based approach can be used to identify the cellular function of sRNAs and characterize the relationship between sRNAs and transcription factors. Howard Hughes Medical Institute National Institutes of Health (U.S.). Pioneer Award National Institutes of Health (U.S.) (Grant CA21615) National Institutes of Health (U.S.) (Grant GM31030) 2012-04-13T16:44:31Z 2012-04-13T16:44:31Z 2011-08 2011-03 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/70019 Modi, S. R. et al. “Functional Characterization of Bacterial sRNAs Using a Network Biology Approach.” Proceedings of the National Academy of Sciences 108.37 (2011): 15522–15527. Web. 13 Apr. 2012. https://orcid.org/0000-0001-7243-8261 en_US http://dx.doi.org/10.1073/pnas.1104318108 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Proceedings of the National Academy of Sciences (PNAS) PNAS |
| spellingShingle | Walker, Graham C. Modia, Sheetal R. Camacho, Diogo M. Kohanski, Michael A. Collins, James J. Functional characterization of bacterial sRNAs using a network biology approach |
| title | Functional characterization of bacterial sRNAs using a network biology approach |
| title_full | Functional characterization of bacterial sRNAs using a network biology approach |
| title_fullStr | Functional characterization of bacterial sRNAs using a network biology approach |
| title_full_unstemmed | Functional characterization of bacterial sRNAs using a network biology approach |
| title_short | Functional characterization of bacterial sRNAs using a network biology approach |
| title_sort | functional characterization of bacterial srnas using a network biology approach |
| url | http://hdl.handle.net/1721.1/70019 https://orcid.org/0000-0001-7243-8261 |
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