Role of Interactions of the CRE Region of Escherichia coli RNA Polymerase with Nontemplate DNA during Promoter Escape
RNA polymerase (RNAP) recognizes promoter DNA through many interactions that determine specificity of transcription initiation. In addition to the dedicated transcription initiation σ factor in bacteria, the core enzyme of RNAP can also participate in promoter recognition. In particular, guanine res...
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| Veröffentlicht in: | Biochemistry (Moscow) 2020-07, Vol.85 (7), p.792-800 |
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| creator | Petushkov, I. V. Kulbachinskiy, A. V. |
| description | RNA polymerase (RNAP) recognizes promoter DNA through many interactions that determine specificity of transcription initiation. In addition to the dedicated transcription initiation σ factor in bacteria, the core enzyme of RNAP can also participate in promoter recognition. In particular, guanine residue at the +2 position (+2G) of the nontemplate DNA strand is bound in the CRE pocket formed by the RNAP β subunit. Here, we analyzed the role of these contacts in the process of promoter escape by RNAP by studying point mutations in the β subunit of
Escherichia coli
RNAP that disrupted these interactions. We found that the presence of +2G in the promoter slowed down the rate of promoter escape and increased proportion of inactive complexes. Amino acid substitutions in the CRE pocket decreased the promoter complex stability and changed the pattern of short RNA products synthesized during initiation, but did not significantly affect the rate of transition to elongation, regardless of the presence of +2G. Thus, the contacts of the CRE pocket with +2G do not make a significant contribution to the kinetics of promoter escape by RNAP, while the observed changes in the efficiency of abortive synthesis are not directly related to the rate of promoter escape. |
| doi_str_mv | 10.1134/S000629792007007X |
| format | Article |
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Escherichia coli
RNAP that disrupted these interactions. We found that the presence of +2G in the promoter slowed down the rate of promoter escape and increased proportion of inactive complexes. Amino acid substitutions in the CRE pocket decreased the promoter complex stability and changed the pattern of short RNA products synthesized during initiation, but did not significantly affect the rate of transition to elongation, regardless of the presence of +2G. Thus, the contacts of the CRE pocket with +2G do not make a significant contribution to the kinetics of promoter escape by RNAP, while the observed changes in the efficiency of abortive synthesis are not directly related to the rate of promoter escape.</description><identifier>ISSN: 0006-2979</identifier><identifier>EISSN: 1608-3040</identifier><identifier>DOI: 10.1134/S000629792007007X</identifier><identifier>PMID: 33040723</identifier><language>eng</language><publisher>Moscow: Pleiades Publishing</publisher><subject>Amino acids ; Analysis ; Biochemistry ; Biomedical and Life Sciences ; Biomedicine ; Bioorganic Chemistry ; Deoxyribonucleic acid ; DNA ; DNA - metabolism ; DNA, Bacterial - metabolism ; DNA-directed RNA polymerase ; DNA-Directed RNA Polymerases - genetics ; DNA-Directed RNA Polymerases - metabolism ; E coli ; Elongation ; Escherichia coli ; Escherichia coli - genetics ; Escherichia coli - metabolism ; Escherichia coli Proteins - genetics ; Escherichia coli Proteins - metabolism ; Ethylenediaminetetraacetic acid ; Genetic transcription ; Guanine ; Life Sciences ; Microbiology ; Mutation ; Promoter Regions, Genetic - genetics ; Ribonucleic acid ; RNA ; RNA - metabolism ; RNA polymerase ; RNA polymerases ; Sigma Factor - genetics ; Transcription, Genetic - genetics</subject><ispartof>Biochemistry (Moscow), 2020-07, Vol.85 (7), p.792-800</ispartof><rights>Pleiades Publishing, Ltd. 2020</rights><rights>COPYRIGHT 2020 Springer</rights><rights>Pleiades Publishing, Ltd. 2020.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c354X-cd18d2575c74f174691981d3bcda6aedfe7089f3f3d0df052789b6c265b548093</citedby><cites>FETCH-LOGICAL-c354X-cd18d2575c74f174691981d3bcda6aedfe7089f3f3d0df052789b6c265b548093</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1134/S000629792007007X$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1134/S000629792007007X$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27922,27923,41486,42555,51317</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33040723$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Petushkov, I. V.</creatorcontrib><creatorcontrib>Kulbachinskiy, A. V.</creatorcontrib><title>Role of Interactions of the CRE Region of Escherichia coli RNA Polymerase with Nontemplate DNA during Promoter Escape</title><title>Biochemistry (Moscow)</title><addtitle>Biochemistry Moscow</addtitle><addtitle>Biochemistry (Mosc)</addtitle><description>RNA polymerase (RNAP) recognizes promoter DNA through many interactions that determine specificity of transcription initiation. In addition to the dedicated transcription initiation σ factor in bacteria, the core enzyme of RNAP can also participate in promoter recognition. In particular, guanine residue at the +2 position (+2G) of the nontemplate DNA strand is bound in the CRE pocket formed by the RNAP β subunit. Here, we analyzed the role of these contacts in the process of promoter escape by RNAP by studying point mutations in the β subunit of
Escherichia coli
RNAP that disrupted these interactions. We found that the presence of +2G in the promoter slowed down the rate of promoter escape and increased proportion of inactive complexes. Amino acid substitutions in the CRE pocket decreased the promoter complex stability and changed the pattern of short RNA products synthesized during initiation, but did not significantly affect the rate of transition to elongation, regardless of the presence of +2G. Thus, the contacts of the CRE pocket with +2G do not make a significant contribution to the kinetics of promoter escape by RNAP, while the observed changes in the efficiency of abortive synthesis are not directly related to the rate of promoter escape.</description><subject>Amino acids</subject><subject>Analysis</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Bioorganic Chemistry</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - metabolism</subject><subject>DNA, Bacterial - metabolism</subject><subject>DNA-directed RNA polymerase</subject><subject>DNA-Directed RNA Polymerases - genetics</subject><subject>DNA-Directed RNA Polymerases - metabolism</subject><subject>E coli</subject><subject>Elongation</subject><subject>Escherichia coli</subject><subject>Escherichia coli - genetics</subject><subject>Escherichia coli - metabolism</subject><subject>Escherichia coli Proteins - genetics</subject><subject>Escherichia coli Proteins - metabolism</subject><subject>Ethylenediaminetetraacetic acid</subject><subject>Genetic transcription</subject><subject>Guanine</subject><subject>Life Sciences</subject><subject>Microbiology</subject><subject>Mutation</subject><subject>Promoter Regions, Genetic - genetics</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA - metabolism</subject><subject>RNA polymerase</subject><subject>RNA polymerases</subject><subject>Sigma Factor - genetics</subject><subject>Transcription, Genetic - genetics</subject><issn>0006-2979</issn><issn>1608-3040</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp1kdtrFDEUxoNY7Fr9A3yRgC--TJvLXB-Xda2F0pZVoW9DNjnZTZmZjMkM0v--J2yteCkJhJzz-75cPkLecXbKuczPvjLGStFUjWCswnn7gix4yepMspy9JIvUzlL_mLyO8Q63gjXyFTmWCaiEXJB54zug3tKLYYKg9OT8ENN-2gNdbdZ0Azsspco66j0Ep_dOUe07RzdXS3rju_sehRHoTzft6ZVHn37s1AT0E_bNHNywozfB9x4PSCZqhDfkyKouwtvH9YR8_7z-tvqSXV6fX6yWl5mWRX6bacNrI4qq0FVueZWXDW9qbuRWG1UqMBYqVjdWWmmYsawQVd1sSy3KYlvkNT71hHw8-I7B_5ghTm3vooauUwP4ObYiL_BTciET-uEv9M7PYcDbISWkzHmJyxO1Ux20brB-wk9Lpu0Sk0BCVCVSp_-hcBjonfYDWIf1PwT8INDBxxjAtmNwvQr3LWdtirr9J2rUvH-88LztwTwpfmWLgDgAcUwZQPj9ouddHwB5ea-T</recordid><startdate>20200701</startdate><enddate>20200701</enddate><creator>Petushkov, I. 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V. ; Kulbachinskiy, A. V.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c354X-cd18d2575c74f174691981d3bcda6aedfe7089f3f3d0df052789b6c265b548093</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Amino acids</topic><topic>Analysis</topic><topic>Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedicine</topic><topic>Bioorganic Chemistry</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA - metabolism</topic><topic>DNA, Bacterial - metabolism</topic><topic>DNA-directed RNA polymerase</topic><topic>DNA-Directed RNA Polymerases - genetics</topic><topic>DNA-Directed RNA Polymerases - metabolism</topic><topic>E coli</topic><topic>Elongation</topic><topic>Escherichia coli</topic><topic>Escherichia coli - genetics</topic><topic>Escherichia coli - metabolism</topic><topic>Escherichia coli Proteins - genetics</topic><topic>Escherichia coli Proteins - metabolism</topic><topic>Ethylenediaminetetraacetic acid</topic><topic>Genetic transcription</topic><topic>Guanine</topic><topic>Life Sciences</topic><topic>Microbiology</topic><topic>Mutation</topic><topic>Promoter Regions, Genetic - genetics</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA - metabolism</topic><topic>RNA polymerase</topic><topic>RNA polymerases</topic><topic>Sigma Factor - genetics</topic><topic>Transcription, Genetic - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Petushkov, I. 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V.</au><au>Kulbachinskiy, A. V.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Role of Interactions of the CRE Region of Escherichia coli RNA Polymerase with Nontemplate DNA during Promoter Escape</atitle><jtitle>Biochemistry (Moscow)</jtitle><stitle>Biochemistry Moscow</stitle><addtitle>Biochemistry (Mosc)</addtitle><date>2020-07-01</date><risdate>2020</risdate><volume>85</volume><issue>7</issue><spage>792</spage><epage>800</epage><pages>792-800</pages><issn>0006-2979</issn><eissn>1608-3040</eissn><abstract>RNA polymerase (RNAP) recognizes promoter DNA through many interactions that determine specificity of transcription initiation. In addition to the dedicated transcription initiation σ factor in bacteria, the core enzyme of RNAP can also participate in promoter recognition. In particular, guanine residue at the +2 position (+2G) of the nontemplate DNA strand is bound in the CRE pocket formed by the RNAP β subunit. Here, we analyzed the role of these contacts in the process of promoter escape by RNAP by studying point mutations in the β subunit of
Escherichia coli
RNAP that disrupted these interactions. We found that the presence of +2G in the promoter slowed down the rate of promoter escape and increased proportion of inactive complexes. Amino acid substitutions in the CRE pocket decreased the promoter complex stability and changed the pattern of short RNA products synthesized during initiation, but did not significantly affect the rate of transition to elongation, regardless of the presence of +2G. Thus, the contacts of the CRE pocket with +2G do not make a significant contribution to the kinetics of promoter escape by RNAP, while the observed changes in the efficiency of abortive synthesis are not directly related to the rate of promoter escape.</abstract><cop>Moscow</cop><pub>Pleiades Publishing</pub><pmid>33040723</pmid><doi>10.1134/S000629792007007X</doi><tpages>9</tpages></addata></record> |
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| subjects | Amino acids Analysis Biochemistry Biomedical and Life Sciences Biomedicine Bioorganic Chemistry Deoxyribonucleic acid DNA DNA - metabolism DNA, Bacterial - metabolism DNA-directed RNA polymerase DNA-Directed RNA Polymerases - genetics DNA-Directed RNA Polymerases - metabolism E coli Elongation Escherichia coli Escherichia coli - genetics Escherichia coli - metabolism Escherichia coli Proteins - genetics Escherichia coli Proteins - metabolism Ethylenediaminetetraacetic acid Genetic transcription Guanine Life Sciences Microbiology Mutation Promoter Regions, Genetic - genetics Ribonucleic acid RNA RNA - metabolism RNA polymerase RNA polymerases Sigma Factor - genetics Transcription, Genetic - genetics |
| title | Role of Interactions of the CRE Region of Escherichia coli RNA Polymerase with Nontemplate DNA during Promoter Escape |
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