Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans
A bacterial transcriptome of the primary etiological agent of human dental caries, Streptococcus mutans, is described here using deep RNA sequencing. Differential expression profiles of the transcriptome in the context of carbohydrate source, and of the presence or absence of the catabolite control...
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| Format: | Online |
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Public Library of Science
2013
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610829/ |
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pubmed-36108292013-04-03 Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans Zeng, Lin Choi, Sang Chul Danko, Charles G. Siepel, Adam Stanhope, Michael J. Burne, Robert A. Research Article A bacterial transcriptome of the primary etiological agent of human dental caries, Streptococcus mutans, is described here using deep RNA sequencing. Differential expression profiles of the transcriptome in the context of carbohydrate source, and of the presence or absence of the catabolite control protein CcpA, revealed good agreement with previously-published DNA microarrays. In addition, RNA-seq considerably expanded the repertoire of DNA sequences that showed statistically-significant changes in expression as a function of the presence of CcpA and growth carbohydrate. Novel mRNAs and small RNAs were identified, some of which were differentially expressed in conditions tested in this study, suggesting that the function of the S. mutans CcpA protein and the influence of carbohydrate sources has a more substantial impact on gene regulation than previously appreciated. Likewise, the data reveal that the mechanisms underlying prioritization of carbohydrate utilization are more diverse than what is currently understood. Collectively, this study demonstrates the validity of RNA-seq as a potentially more-powerful alternative to DNA microarrays in studying gene regulation in S. mutans because of the capacity of this approach to yield a more precise landscape of transcriptomic changes in response to specific mutations and growth conditions. Public Library of Science 2013-03-28 /pmc/articles/PMC3610829/ /pubmed/23555977 http://dx.doi.org/10.1371/journal.pone.0060465 Text en © 2013 Zeng et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Zeng, Lin Choi, Sang Chul Danko, Charles G. Siepel, Adam Stanhope, Michael J. Burne, Robert A. |
| spellingShingle |
Zeng, Lin Choi, Sang Chul Danko, Charles G. Siepel, Adam Stanhope, Michael J. Burne, Robert A. Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans |
| author_facet |
Zeng, Lin Choi, Sang Chul Danko, Charles G. Siepel, Adam Stanhope, Michael J. Burne, Robert A. |
| author_sort |
Zeng, Lin |
| title |
Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans
|
| title_short |
Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans
|
| title_full |
Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans
|
| title_fullStr |
Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans
|
| title_full_unstemmed |
Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans
|
| title_sort |
gene regulation by ccpa and catabolite repression explored by rna-seq in streptococcus mutans |
| description |
A bacterial transcriptome of the primary etiological agent of human dental caries, Streptococcus mutans, is described here using deep RNA sequencing. Differential expression profiles of the transcriptome in the context of carbohydrate source, and of the presence or absence of the catabolite control protein CcpA, revealed good agreement with previously-published DNA microarrays. In addition, RNA-seq considerably expanded the repertoire of DNA sequences that showed statistically-significant changes in expression as a function of the presence of CcpA and growth carbohydrate. Novel mRNAs and small RNAs were identified, some of which were differentially expressed in conditions tested in this study, suggesting that the function of the S. mutans CcpA protein and the influence of carbohydrate sources has a more substantial impact on gene regulation than previously appreciated. Likewise, the data reveal that the mechanisms underlying prioritization of carbohydrate utilization are more diverse than what is currently understood. Collectively, this study demonstrates the validity of RNA-seq as a potentially more-powerful alternative to DNA microarrays in studying gene regulation in S. mutans because of the capacity of this approach to yield a more precise landscape of transcriptomic changes in response to specific mutations and growth conditions. |
| publisher |
Public Library of Science |
| publishDate |
2013 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610829/ |
| _version_ |
1611966092095258624 |