Genomic arrangement of regulons in bacterial genomes.
Regulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arran...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3250446?pdf=render |
| _version_ | 1818776915270434816 |
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| author | Han Zhang Yanbin Yin Victor Olman Ying Xu |
| author_facet | Han Zhang Yanbin Yin Victor Olman Ying Xu |
| author_sort | Han Zhang |
| collection | DOAJ |
| description | Regulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arranged in a bacterial genome. We present a computational study to elucidate of the organizational principles of regulons in a bacterial genome, based on the experimentally validated regulons of E. coli and B. subtilis. Our results indicate that (1) genomic locations of transcriptional factors (TFs) are under stronger evolutionary constraints than those of the operons they regulate so changing a TF's genomic location will have larger impact to the bacterium than changing the genomic position of any of its target operons; (2) operons of regulons are generally not uniformly distributed in the genome but tend to form a few closely located clusters, which generally consist of genes working in the same metabolic pathways; and (3) the global arrangement of the component operons of all the regulons in a genome tends to minimize a simple scoring function, indicating that the global arrangement of regulons follows simple organizational principles. |
| first_indexed | 2024-12-18T11:20:31Z |
| format | Article |
| id | doaj.art-e19cbf4f184c4ba1a9f2722a6f1459d8 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-18T11:20:31Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-e19cbf4f184c4ba1a9f2722a6f1459d82022-12-21T21:09:50ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0171e2949610.1371/journal.pone.0029496Genomic arrangement of regulons in bacterial genomes.Han ZhangYanbin YinVictor OlmanYing XuRegulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arranged in a bacterial genome. We present a computational study to elucidate of the organizational principles of regulons in a bacterial genome, based on the experimentally validated regulons of E. coli and B. subtilis. Our results indicate that (1) genomic locations of transcriptional factors (TFs) are under stronger evolutionary constraints than those of the operons they regulate so changing a TF's genomic location will have larger impact to the bacterium than changing the genomic position of any of its target operons; (2) operons of regulons are generally not uniformly distributed in the genome but tend to form a few closely located clusters, which generally consist of genes working in the same metabolic pathways; and (3) the global arrangement of the component operons of all the regulons in a genome tends to minimize a simple scoring function, indicating that the global arrangement of regulons follows simple organizational principles.http://europepmc.org/articles/PMC3250446?pdf=render |
| spellingShingle | Han Zhang Yanbin Yin Victor Olman Ying Xu Genomic arrangement of regulons in bacterial genomes. PLoS ONE |
| title | Genomic arrangement of regulons in bacterial genomes. |
| title_full | Genomic arrangement of regulons in bacterial genomes. |
| title_fullStr | Genomic arrangement of regulons in bacterial genomes. |
| title_full_unstemmed | Genomic arrangement of regulons in bacterial genomes. |
| title_short | Genomic arrangement of regulons in bacterial genomes. |
| title_sort | genomic arrangement of regulons in bacterial genomes |
| url | http://europepmc.org/articles/PMC3250446?pdf=render |
| work_keys_str_mv | AT hanzhang genomicarrangementofregulonsinbacterialgenomes AT yanbinyin genomicarrangementofregulonsinbacterialgenomes AT victorolman genomicarrangementofregulonsinbacterialgenomes AT yingxu genomicarrangementofregulonsinbacterialgenomes |