H-NS can facilitate specific DNA-binding by RNA polymerase in AT-rich gene regulatory regions
Extremely AT-rich DNA sequences present a challenging template for specific recognition by RNA polymerase. In bacteria, this is because the promoter -10 hexamer, the major DNA element recognised by RNA polymerase, is itself AT-rich. We show that Histone-like Nucleoid Structuring (H-NS) protein can f...
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| Veröffentlicht in: | PLoS genetics 2013-06, Vol.9 (6), p.e1003589-e1003589 |
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| creator | Singh, Shivani S Grainger, David C |
| description | Extremely AT-rich DNA sequences present a challenging template for specific recognition by RNA polymerase. In bacteria, this is because the promoter -10 hexamer, the major DNA element recognised by RNA polymerase, is itself AT-rich. We show that Histone-like Nucleoid Structuring (H-NS) protein can facilitate correct recognition of a promoter by RNA polymerase in AT-rich gene regulatory regions. Thus, at the Escherichia coli ehxCABD operon, RNA polymerase is unable to distinguish between the promoter -10 element and similar overlapping sequences. This problem is resolved in native nucleoprotein because the overlapping sequences are masked by H-NS. Our work provides mechanistic insight into nucleoprotein structure and its effect on protein-DNA interactions in prokaryotic cells. |
| doi_str_mv | 10.1371/journal.pgen.1003589 |
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In bacteria, this is because the promoter -10 hexamer, the major DNA element recognised by RNA polymerase, is itself AT-rich. We show that Histone-like Nucleoid Structuring (H-NS) protein can facilitate correct recognition of a promoter by RNA polymerase in AT-rich gene regulatory regions. Thus, at the Escherichia coli ehxCABD operon, RNA polymerase is unable to distinguish between the promoter -10 element and similar overlapping sequences. This problem is resolved in native nucleoprotein because the overlapping sequences are masked by H-NS. Our work provides mechanistic insight into nucleoprotein structure and its effect on protein-DNA interactions in prokaryotic cells.</description><identifier>ISSN: 1553-7404</identifier><identifier>ISSN: 1553-7390</identifier><identifier>EISSN: 1553-7404</identifier><identifier>DOI: 10.1371/journal.pgen.1003589</identifier><identifier>PMID: 23818873</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>AT Rich Sequence - genetics ; Biology ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; DNA-Binding Proteins - genetics ; DNA-Directed RNA Polymerases - genetics ; DNA-ligand interactions ; Enzymes ; Escherichia coli - genetics ; Escherichia coli Proteins - genetics ; Fimbriae Proteins - genetics ; Gene Expression Regulation, Bacterial ; Genetic regulation ; Genetics ; Histones - genetics ; Nucleotide sequencing ; Physiological aspects ; Promoter Regions, Genetic ; Proteins ; Regulatory Sequences, Nucleic Acid - genetics ; RNA polymerase ; RNA polymerases ; Transcription, Genetic</subject><ispartof>PLoS genetics, 2013-06, Vol.9 (6), p.e1003589-e1003589</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Singh and Grainger 2013 Singh and Grainger</rights><rights>2013 Singh and Grainger. 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 credited: Singh SS, Grainger DC (2013) H-NS Can Facilitate Specific DNA-binding by RNA Polymerase in AT-rich Gene Regulatory Regions. 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In bacteria, this is because the promoter -10 hexamer, the major DNA element recognised by RNA polymerase, is itself AT-rich. We show that Histone-like Nucleoid Structuring (H-NS) protein can facilitate correct recognition of a promoter by RNA polymerase in AT-rich gene regulatory regions. Thus, at the Escherichia coli ehxCABD operon, RNA polymerase is unable to distinguish between the promoter -10 element and similar overlapping sequences. This problem is resolved in native nucleoprotein because the overlapping sequences are masked by H-NS. 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Grainger, David C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c698t-ac36ffdb44b3ff366fa78bb30a5e7199487ee3d15a225c8b6cd737a5a279b64a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>AT Rich Sequence - genetics</topic><topic>Biology</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>DNA-Binding Proteins - genetics</topic><topic>DNA-Directed RNA Polymerases - genetics</topic><topic>DNA-ligand interactions</topic><topic>Enzymes</topic><topic>Escherichia coli - genetics</topic><topic>Escherichia coli Proteins - genetics</topic><topic>Fimbriae Proteins - genetics</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>Genetic regulation</topic><topic>Genetics</topic><topic>Histones - genetics</topic><topic>Nucleotide sequencing</topic><topic>Physiological aspects</topic><topic>Promoter Regions, Genetic</topic><topic>Proteins</topic><topic>Regulatory Sequences, Nucleic Acid - genetics</topic><topic>RNA polymerase</topic><topic>RNA polymerases</topic><topic>Transcription, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Singh, Shivani S</creatorcontrib><creatorcontrib>Grainger, David C</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Canada</collection><collection>Gale In Context: Science</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Singh, Shivani S</au><au>Grainger, David C</au><au>Burkholder, William F.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>H-NS can facilitate specific DNA-binding by RNA polymerase in AT-rich gene regulatory regions</atitle><jtitle>PLoS genetics</jtitle><addtitle>PLoS Genet</addtitle><date>2013-06-01</date><risdate>2013</risdate><volume>9</volume><issue>6</issue><spage>e1003589</spage><epage>e1003589</epage><pages>e1003589-e1003589</pages><issn>1553-7404</issn><issn>1553-7390</issn><eissn>1553-7404</eissn><abstract>Extremely AT-rich DNA sequences present a challenging template for specific recognition by RNA polymerase. In bacteria, this is because the promoter -10 hexamer, the major DNA element recognised by RNA polymerase, is itself AT-rich. We show that Histone-like Nucleoid Structuring (H-NS) protein can facilitate correct recognition of a promoter by RNA polymerase in AT-rich gene regulatory regions. Thus, at the Escherichia coli ehxCABD operon, RNA polymerase is unable to distinguish between the promoter -10 element and similar overlapping sequences. This problem is resolved in native nucleoprotein because the overlapping sequences are masked by H-NS. Our work provides mechanistic insight into nucleoprotein structure and its effect on protein-DNA interactions in prokaryotic cells.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23818873</pmid><doi>10.1371/journal.pgen.1003589</doi><oa>free_for_read</oa></addata></record> |
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| subjects | AT Rich Sequence - genetics Biology Deoxyribonucleic acid DNA DNA sequencing DNA-Binding Proteins - genetics DNA-Directed RNA Polymerases - genetics DNA-ligand interactions Enzymes Escherichia coli - genetics Escherichia coli Proteins - genetics Fimbriae Proteins - genetics Gene Expression Regulation, Bacterial Genetic regulation Genetics Histones - genetics Nucleotide sequencing Physiological aspects Promoter Regions, Genetic Proteins Regulatory Sequences, Nucleic Acid - genetics RNA polymerase RNA polymerases Transcription, Genetic |
| title | H-NS can facilitate specific DNA-binding by RNA polymerase in AT-rich gene regulatory regions |
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