The TFIIE-related Rpc82 subunit of RNA polymerase III interacts with the TFIIB-related transcription factor Brf1 and the polymerase cleft for transcription initiation
Abstract Rpc82 is a TFIIE-related subunit of the eukaryotic RNA polymerase III (pol III) complex. Rpc82 contains four winged-helix (WH) domains and a C-terminal coiled-coil domain. Structural resolution of the pol III complex indicated that Rpc82 anchors on the clamp domain of the pol III cleft to i...
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| Veröffentlicht in: | Nucleic acids research 2018-02, Vol.46 (3), p.1157-1166 |
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| creator | Khoo, Seok-Kooi Wu, Chih-Chien Lin, Yu-Chun Chen, Hung-Ta |
| description | Abstract
Rpc82 is a TFIIE-related subunit of the eukaryotic RNA polymerase III (pol III) complex. Rpc82 contains four winged-helix (WH) domains and a C-terminal coiled-coil domain. Structural resolution of the pol III complex indicated that Rpc82 anchors on the clamp domain of the pol III cleft to interact with the duplex DNA downstream of the transcription bubble. However, whether Rpc82 interacts with a transcription factor is still not known. Here, we report that a structurally disordered insertion in the third WH domain of Rpc82 is important for cell growth and in vitro transcription activity. Site-specific photo-crosslinking analysis indicated that the WH3 insertion interacts with the TFIIB-related transcription factor Brf1 within the pre-initiation complex (PIC). Moreover, crosslinking and hydroxyl radical probing analyses revealed Rpc82 interactions with the upstream DNA and the protrusion and wall domains of the pol III cleft. Our genetic and biochemical analyses thus provide new molecular insights into the function of Rpc82 in pol III transcription. |
| doi_str_mv | 10.1093/nar/gkx1179 |
| format | Article |
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Rpc82 is a TFIIE-related subunit of the eukaryotic RNA polymerase III (pol III) complex. Rpc82 contains four winged-helix (WH) domains and a C-terminal coiled-coil domain. Structural resolution of the pol III complex indicated that Rpc82 anchors on the clamp domain of the pol III cleft to interact with the duplex DNA downstream of the transcription bubble. However, whether Rpc82 interacts with a transcription factor is still not known. Here, we report that a structurally disordered insertion in the third WH domain of Rpc82 is important for cell growth and in vitro transcription activity. Site-specific photo-crosslinking analysis indicated that the WH3 insertion interacts with the TFIIB-related transcription factor Brf1 within the pre-initiation complex (PIC). Moreover, crosslinking and hydroxyl radical probing analyses revealed Rpc82 interactions with the upstream DNA and the protrusion and wall domains of the pol III cleft. Our genetic and biochemical analyses thus provide new molecular insights into the function of Rpc82 in pol III transcription.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkx1179</identifier><identifier>PMID: 29177422</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Amino Acid Sequence ; Base Sequence ; Benzophenones - chemistry ; Binding Sites ; Cloning, Molecular ; Cross-Linking Reagents - chemistry ; DNA - chemistry ; DNA - genetics ; DNA - metabolism ; DNA, Fungal - chemistry ; DNA, Fungal - genetics ; DNA, Fungal - metabolism ; Gene Expression Regulation, Fungal ; Gene regulation, Chromatin and Epigenetics ; Hydroxyl Radical - chemistry ; Models, Molecular ; Phenylalanine - analogs & derivatives ; Phenylalanine - chemistry ; Plasmids - chemistry ; Plasmids - metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; RNA Polymerase III - chemistry ; RNA Polymerase III - genetics ; RNA Polymerase III - metabolism ; Saccharomyces cerevisiae - genetics ; Saccharomyces cerevisiae - metabolism ; Saccharomyces cerevisiae Proteins - chemistry ; Saccharomyces cerevisiae Proteins - genetics ; Saccharomyces cerevisiae Proteins - metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Transcription Factor TFIIIB - chemistry ; Transcription Factor TFIIIB - genetics ; Transcription Factor TFIIIB - metabolism ; Transcription Initiation, Genetic</subject><ispartof>Nucleic acids research, 2018-02, Vol.46 (3), p.1157-1166</ispartof><rights>The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. 2017</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c412t-ea17e1c13cd8c43dbc8e19568a4883f84aa99705dd598b73f5dc7e979407445a3</citedby><cites>FETCH-LOGICAL-c412t-ea17e1c13cd8c43dbc8e19568a4883f84aa99705dd598b73f5dc7e979407445a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814912/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814912/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29177422$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Khoo, Seok-Kooi</creatorcontrib><creatorcontrib>Wu, Chih-Chien</creatorcontrib><creatorcontrib>Lin, Yu-Chun</creatorcontrib><creatorcontrib>Chen, Hung-Ta</creatorcontrib><title>The TFIIE-related Rpc82 subunit of RNA polymerase III interacts with the TFIIB-related transcription factor Brf1 and the polymerase cleft for transcription initiation</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
Rpc82 is a TFIIE-related subunit of the eukaryotic RNA polymerase III (pol III) complex. Rpc82 contains four winged-helix (WH) domains and a C-terminal coiled-coil domain. Structural resolution of the pol III complex indicated that Rpc82 anchors on the clamp domain of the pol III cleft to interact with the duplex DNA downstream of the transcription bubble. However, whether Rpc82 interacts with a transcription factor is still not known. Here, we report that a structurally disordered insertion in the third WH domain of Rpc82 is important for cell growth and in vitro transcription activity. Site-specific photo-crosslinking analysis indicated that the WH3 insertion interacts with the TFIIB-related transcription factor Brf1 within the pre-initiation complex (PIC). Moreover, crosslinking and hydroxyl radical probing analyses revealed Rpc82 interactions with the upstream DNA and the protrusion and wall domains of the pol III cleft. Our genetic and biochemical analyses thus provide new molecular insights into the function of Rpc82 in pol III transcription.</description><subject>Amino Acid Sequence</subject><subject>Base Sequence</subject><subject>Benzophenones - chemistry</subject><subject>Binding Sites</subject><subject>Cloning, Molecular</subject><subject>Cross-Linking Reagents - chemistry</subject><subject>DNA - chemistry</subject><subject>DNA - genetics</subject><subject>DNA - metabolism</subject><subject>DNA, Fungal - chemistry</subject><subject>DNA, Fungal - genetics</subject><subject>DNA, Fungal - metabolism</subject><subject>Gene Expression Regulation, Fungal</subject><subject>Gene regulation, Chromatin and Epigenetics</subject><subject>Hydroxyl Radical - chemistry</subject><subject>Models, Molecular</subject><subject>Phenylalanine - analogs & derivatives</subject><subject>Phenylalanine - chemistry</subject><subject>Plasmids - chemistry</subject><subject>Plasmids - metabolism</subject><subject>Protein Binding</subject><subject>Protein Conformation, alpha-Helical</subject><subject>Protein Conformation, beta-Strand</subject><subject>Protein Interaction Domains and Motifs</subject><subject>RNA Polymerase III - chemistry</subject><subject>RNA Polymerase III - genetics</subject><subject>RNA Polymerase III - metabolism</subject><subject>Saccharomyces cerevisiae - genetics</subject><subject>Saccharomyces cerevisiae - metabolism</subject><subject>Saccharomyces cerevisiae Proteins - chemistry</subject><subject>Saccharomyces cerevisiae Proteins - genetics</subject><subject>Saccharomyces cerevisiae Proteins - metabolism</subject><subject>Sequence Alignment</subject><subject>Sequence Homology, Amino Acid</subject><subject>Transcription Factor TFIIIB - chemistry</subject><subject>Transcription Factor TFIIIB - genetics</subject><subject>Transcription Factor TFIIIB - metabolism</subject><subject>Transcription Initiation, Genetic</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kUFvFCEYhonR2LV68m44GRMzlm9gFriYtE2rkzSaNOuZsAx00VkYgVH7h_ydUnfdtBdPfITne3iTF6GXQN4BkfQk6HRy8-0XAJeP0ALosm2YXLaP0YJQ0jVAmDhCz3L-Sggw6NhTdNRK4Jy17QL9Xm0sXl32_UWT7KiLHfD1ZESL87yegy84Onz96RRPcbzd2qSzxX3fYx9KvZiS8U9fNrjsJWcHSUk6ZJP8VHwM2FU0JnyWHGAdhr_8PaMZrSvYVeLhmq8BvL4bn6MnTo_Zvtifx-jL5cXq_GNz9flDf3561RgGbWmsBm7BADWDMIwOayMsyG4pNBOCOsG0lpKTbhg6Kdacum4w3EouGeGMdZoeo_c77zSvt3YwNtREo5qS3-p0q6L26uFL8Bt1E3-oTgCT0FbBm70gxe-zzUVtfTZ2HHWwcc4K5FLKGomyir7doSbFnJN1h2-AqLtmVW1W7Zut9Kv7yQ7svyor8HoHxHn6r-kPvM2wKQ</recordid><startdate>20180216</startdate><enddate>20180216</enddate><creator>Khoo, Seok-Kooi</creator><creator>Wu, Chih-Chien</creator><creator>Lin, Yu-Chun</creator><creator>Chen, Hung-Ta</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20180216</creationdate><title>The TFIIE-related Rpc82 subunit of RNA polymerase III interacts with the TFIIB-related transcription factor Brf1 and the polymerase cleft for transcription initiation</title><author>Khoo, Seok-Kooi ; Wu, Chih-Chien ; Lin, Yu-Chun ; Chen, Hung-Ta</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c412t-ea17e1c13cd8c43dbc8e19568a4883f84aa99705dd598b73f5dc7e979407445a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Amino Acid Sequence</topic><topic>Base Sequence</topic><topic>Benzophenones - chemistry</topic><topic>Binding Sites</topic><topic>Cloning, Molecular</topic><topic>Cross-Linking Reagents - chemistry</topic><topic>DNA - chemistry</topic><topic>DNA - genetics</topic><topic>DNA - metabolism</topic><topic>DNA, Fungal - chemistry</topic><topic>DNA, Fungal - genetics</topic><topic>DNA, Fungal - metabolism</topic><topic>Gene Expression Regulation, Fungal</topic><topic>Gene regulation, Chromatin and Epigenetics</topic><topic>Hydroxyl Radical - chemistry</topic><topic>Models, Molecular</topic><topic>Phenylalanine - analogs & derivatives</topic><topic>Phenylalanine - chemistry</topic><topic>Plasmids - chemistry</topic><topic>Plasmids - metabolism</topic><topic>Protein Binding</topic><topic>Protein Conformation, alpha-Helical</topic><topic>Protein Conformation, beta-Strand</topic><topic>Protein Interaction Domains and Motifs</topic><topic>RNA Polymerase III - chemistry</topic><topic>RNA Polymerase III - genetics</topic><topic>RNA Polymerase III - metabolism</topic><topic>Saccharomyces cerevisiae - genetics</topic><topic>Saccharomyces cerevisiae - metabolism</topic><topic>Saccharomyces cerevisiae Proteins - chemistry</topic><topic>Saccharomyces cerevisiae Proteins - genetics</topic><topic>Saccharomyces cerevisiae Proteins - metabolism</topic><topic>Sequence Alignment</topic><topic>Sequence Homology, Amino Acid</topic><topic>Transcription Factor TFIIIB - chemistry</topic><topic>Transcription Factor TFIIIB - genetics</topic><topic>Transcription Factor TFIIIB - metabolism</topic><topic>Transcription Initiation, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Khoo, Seok-Kooi</creatorcontrib><creatorcontrib>Wu, Chih-Chien</creatorcontrib><creatorcontrib>Lin, Yu-Chun</creatorcontrib><creatorcontrib>Chen, Hung-Ta</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Khoo, Seok-Kooi</au><au>Wu, Chih-Chien</au><au>Lin, Yu-Chun</au><au>Chen, Hung-Ta</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The TFIIE-related Rpc82 subunit of RNA polymerase III interacts with the TFIIB-related transcription factor Brf1 and the polymerase cleft for transcription initiation</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2018-02-16</date><risdate>2018</risdate><volume>46</volume><issue>3</issue><spage>1157</spage><epage>1166</epage><pages>1157-1166</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
Rpc82 is a TFIIE-related subunit of the eukaryotic RNA polymerase III (pol III) complex. Rpc82 contains four winged-helix (WH) domains and a C-terminal coiled-coil domain. Structural resolution of the pol III complex indicated that Rpc82 anchors on the clamp domain of the pol III cleft to interact with the duplex DNA downstream of the transcription bubble. However, whether Rpc82 interacts with a transcription factor is still not known. Here, we report that a structurally disordered insertion in the third WH domain of Rpc82 is important for cell growth and in vitro transcription activity. Site-specific photo-crosslinking analysis indicated that the WH3 insertion interacts with the TFIIB-related transcription factor Brf1 within the pre-initiation complex (PIC). Moreover, crosslinking and hydroxyl radical probing analyses revealed Rpc82 interactions with the upstream DNA and the protrusion and wall domains of the pol III cleft. Our genetic and biochemical analyses thus provide new molecular insights into the function of Rpc82 in pol III transcription.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>29177422</pmid><doi>10.1093/nar/gkx1179</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Amino Acid Sequence Base Sequence Benzophenones - chemistry Binding Sites Cloning, Molecular Cross-Linking Reagents - chemistry DNA - chemistry DNA - genetics DNA - metabolism DNA, Fungal - chemistry DNA, Fungal - genetics DNA, Fungal - metabolism Gene Expression Regulation, Fungal Gene regulation, Chromatin and Epigenetics Hydroxyl Radical - chemistry Models, Molecular Phenylalanine - analogs & derivatives Phenylalanine - chemistry Plasmids - chemistry Plasmids - metabolism Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs RNA Polymerase III - chemistry RNA Polymerase III - genetics RNA Polymerase III - metabolism Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - metabolism Saccharomyces cerevisiae Proteins - chemistry Saccharomyces cerevisiae Proteins - genetics Saccharomyces cerevisiae Proteins - metabolism Sequence Alignment Sequence Homology, Amino Acid Transcription Factor TFIIIB - chemistry Transcription Factor TFIIIB - genetics Transcription Factor TFIIIB - metabolism Transcription Initiation, Genetic |
| title | The TFIIE-related Rpc82 subunit of RNA polymerase III interacts with the TFIIB-related transcription factor Brf1 and the polymerase cleft for transcription initiation |
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