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Insight into the Human DNA Primase Interaction with Template-Primer
DNA replication in almost all organisms depends on the activity of DNA primase, a DNA-dependent RNA polymerase that synthesizes short RNA primers of defined size for DNA polymerases. Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large accessory subunits, both of...
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| Published in: | The Journal of biological chemistry 2016-02, Vol.291 (9), p.4793-4802 |
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| container_end_page | 4802 |
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| container_title | The Journal of biological chemistry |
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| creator | Baranovskiy, Andrey G. Zhang, Yinbo Suwa, Yoshiaki Gu, Jianyou Babayeva, Nigar D. Pavlov, Youri I. Tahirov, Tahir H. |
| description | DNA replication in almost all organisms depends on the activity of DNA primase, a DNA-dependent RNA polymerase that synthesizes short RNA primers of defined size for DNA polymerases. Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large accessory subunits, both of which are necessary for the activity. The mode of interaction of primase subunits with substrates during the various steps of primer synthesis that results in the counting of primer length is not clear. Here we show that the C-terminal domain of the large subunit (p58C) plays a major role in template-primer binding and also defines the elements of the DNA template and the RNA primer that interact with p58C. The specific mode of interaction with a template-primer involving the terminal 5′-triphosphate of RNA and the 3′-overhang of DNA results in a stable complex between p58C and the DNA/RNA duplex. Our results explain how p58C participates in RNA synthesis and primer length counting and also indicate that the binding site for initiating NTP is located on p58C. These findings provide notable insight into the mechanism of primase function and are applicable for DNA primases from other species. |
| doi_str_mv | 10.1074/jbc.M115.704064 |
| format | article |
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Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large accessory subunits, both of which are necessary for the activity. The mode of interaction of primase subunits with substrates during the various steps of primer synthesis that results in the counting of primer length is not clear. Here we show that the C-terminal domain of the large subunit (p58C) plays a major role in template-primer binding and also defines the elements of the DNA template and the RNA primer that interact with p58C. The specific mode of interaction with a template-primer involving the terminal 5′-triphosphate of RNA and the 3′-overhang of DNA results in a stable complex between p58C and the DNA/RNA duplex. Our results explain how p58C participates in RNA synthesis and primer length counting and also indicate that the binding site for initiating NTP is located on p58C. These findings provide notable insight into the mechanism of primase function and are applicable for DNA primases from other species.</description><identifier>ISSN: 0021-9258</identifier><identifier>EISSN: 1083-351X</identifier><identifier>DOI: 10.1074/jbc.M115.704064</identifier><identifier>PMID: 26710848</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>5′-triphosphate ; Binding Sites ; DNA and Chromosomes ; DNA primase ; DNA Primase - chemistry ; DNA Primase - genetics ; DNA Primase - metabolism ; DNA replication ; DNA, Single-Stranded - chemistry ; DNA, Single-Stranded - metabolism ; DNA-Directed DNA Polymerase - chemistry ; DNA-Directed DNA Polymerase - genetics ; DNA-Directed DNA Polymerase - metabolism ; DNA-protein interaction ; Electrophoretic Mobility Shift Assay ; Fluorescence Polarization ; Fluorescent Dyes - chemistry ; gel electrophoresis ; human ; Humans ; Kinetics ; Models, Molecular ; Multifunctional Enzymes - chemistry ; Multifunctional Enzymes - genetics ; Multifunctional Enzymes - metabolism ; Nucleic Acid Conformation ; p58 subunit ; Peptide Fragments - chemistry ; Peptide Fragments - genetics ; Peptide Fragments - metabolism ; primase activity ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Recombinant Proteins - chemistry ; Recombinant Proteins - metabolism ; RNA - chemistry ; RNA - metabolism ; RNA primer length counting ; RNA synthesis ; RNA/DNA duplex ; Transcription, Genetic</subject><ispartof>The Journal of biological chemistry, 2016-02, Vol.291 (9), p.4793-4802</ispartof><rights>2016 © 2016 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology.</rights><rights>2016 by The American Society for Biochemistry and Molecular Biology, Inc.</rights><rights>2016 by The American Society for Biochemistry and Molecular Biology, Inc. 2016 The American Society for Biochemistry and Molecular Biology, Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c443t-bbb28131bced90b4c931c9a32b9ec51734ffe464e4b8d1b1ea14e2e72f7e81d53</citedby><cites>FETCH-LOGICAL-c443t-bbb28131bced90b4c931c9a32b9ec51734ffe464e4b8d1b1ea14e2e72f7e81d53</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/PMC4813500/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813500/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,315,733,786,790,891,27957,27958,53827,53829</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26710848$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Baranovskiy, Andrey G.</creatorcontrib><creatorcontrib>Zhang, Yinbo</creatorcontrib><creatorcontrib>Suwa, Yoshiaki</creatorcontrib><creatorcontrib>Gu, Jianyou</creatorcontrib><creatorcontrib>Babayeva, Nigar D.</creatorcontrib><creatorcontrib>Pavlov, Youri I.</creatorcontrib><creatorcontrib>Tahirov, Tahir H.</creatorcontrib><title>Insight into the Human DNA Primase Interaction with Template-Primer</title><title>The Journal of biological chemistry</title><addtitle>J Biol Chem</addtitle><description>DNA replication in almost all organisms depends on the activity of DNA primase, a DNA-dependent RNA polymerase that synthesizes short RNA primers of defined size for DNA polymerases. Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large accessory subunits, both of which are necessary for the activity. The mode of interaction of primase subunits with substrates during the various steps of primer synthesis that results in the counting of primer length is not clear. Here we show that the C-terminal domain of the large subunit (p58C) plays a major role in template-primer binding and also defines the elements of the DNA template and the RNA primer that interact with p58C. The specific mode of interaction with a template-primer involving the terminal 5′-triphosphate of RNA and the 3′-overhang of DNA results in a stable complex between p58C and the DNA/RNA duplex. Our results explain how p58C participates in RNA synthesis and primer length counting and also indicate that the binding site for initiating NTP is located on p58C. These findings provide notable insight into the mechanism of primase function and are applicable for DNA primases from other species.</description><subject>5′-triphosphate</subject><subject>Binding Sites</subject><subject>DNA and Chromosomes</subject><subject>DNA primase</subject><subject>DNA Primase - chemistry</subject><subject>DNA Primase - genetics</subject><subject>DNA Primase - metabolism</subject><subject>DNA replication</subject><subject>DNA, Single-Stranded - chemistry</subject><subject>DNA, Single-Stranded - metabolism</subject><subject>DNA-Directed DNA Polymerase - chemistry</subject><subject>DNA-Directed DNA Polymerase - genetics</subject><subject>DNA-Directed DNA Polymerase - metabolism</subject><subject>DNA-protein interaction</subject><subject>Electrophoretic Mobility Shift Assay</subject><subject>Fluorescence Polarization</subject><subject>Fluorescent Dyes - chemistry</subject><subject>gel electrophoresis</subject><subject>human</subject><subject>Humans</subject><subject>Kinetics</subject><subject>Models, Molecular</subject><subject>Multifunctional Enzymes - chemistry</subject><subject>Multifunctional Enzymes - genetics</subject><subject>Multifunctional Enzymes - metabolism</subject><subject>Nucleic Acid Conformation</subject><subject>p58 subunit</subject><subject>Peptide Fragments - chemistry</subject><subject>Peptide Fragments - genetics</subject><subject>Peptide Fragments - metabolism</subject><subject>primase activity</subject><subject>Protein Conformation</subject><subject>Protein Interaction Domains and Motifs</subject><subject>Protein Multimerization</subject><subject>Recombinant Proteins - chemistry</subject><subject>Recombinant Proteins - metabolism</subject><subject>RNA - chemistry</subject><subject>RNA - metabolism</subject><subject>RNA primer length counting</subject><subject>RNA synthesis</subject><subject>RNA/DNA duplex</subject><subject>Transcription, Genetic</subject><issn>0021-9258</issn><issn>1083-351X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><recordid>eNp1kE1P4zAQhq3Vom0pe-aGctxLiid26uSyEioLVOLrANLeLNuZtEaJ07VdVvx7XBUqODCXOcwz74weQo6BToEKfvqkzfQGoJwKyumMfyNjoBXLWQl_v5MxpQXkdVFWI3IYwhNNxWv4QUbFTCSOV2MyX7hgl6uYWReHLK4wu9r0ymXnt2fZvbe9CpgtXESvTLSDy_7buMoesF93KmK-JdAfkYNWdQF_vvUJebz48zC_yq_vLhfzs-vccM5irrUuKmCgDTY11dzUDEytWKFrNCUIxtsW-Ywj11UDGlABxwJF0QqsoCnZhPze5a43usfGoItedXK9fdO_yEFZ-Xni7Eouh2fJ09mS0hTw6y3AD_82GKLsbTDYdcrhsAkSxKwqS1EJltDTHWr8EILHdn8GqNyql0m93KqXO_Vp4-Tjd3v-3XUC6h2AydGzRS-DseiSDevRRNkM9svwV8rJk8U</recordid><startdate>20160226</startdate><enddate>20160226</enddate><creator>Baranovskiy, Andrey G.</creator><creator>Zhang, Yinbo</creator><creator>Suwa, Yoshiaki</creator><creator>Gu, Jianyou</creator><creator>Babayeva, Nigar D.</creator><creator>Pavlov, Youri I.</creator><creator>Tahirov, Tahir H.</creator><general>Elsevier Inc</general><general>American Society for Biochemistry and Molecular Biology</general><scope>6I.</scope><scope>AAFTH</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>20160226</creationdate><title>Insight into the Human DNA Primase Interaction with Template-Primer</title><author>Baranovskiy, Andrey G. ; Zhang, Yinbo ; Suwa, Yoshiaki ; Gu, Jianyou ; Babayeva, Nigar D. ; Pavlov, Youri I. ; Tahirov, Tahir H.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c443t-bbb28131bced90b4c931c9a32b9ec51734ffe464e4b8d1b1ea14e2e72f7e81d53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>5′-triphosphate</topic><topic>Binding Sites</topic><topic>DNA and Chromosomes</topic><topic>DNA primase</topic><topic>DNA Primase - chemistry</topic><topic>DNA Primase - genetics</topic><topic>DNA Primase - metabolism</topic><topic>DNA replication</topic><topic>DNA, Single-Stranded - chemistry</topic><topic>DNA, Single-Stranded - metabolism</topic><topic>DNA-Directed DNA Polymerase - chemistry</topic><topic>DNA-Directed DNA Polymerase - genetics</topic><topic>DNA-Directed DNA Polymerase - metabolism</topic><topic>DNA-protein interaction</topic><topic>Electrophoretic Mobility Shift Assay</topic><topic>Fluorescence Polarization</topic><topic>Fluorescent Dyes - chemistry</topic><topic>gel electrophoresis</topic><topic>human</topic><topic>Humans</topic><topic>Kinetics</topic><topic>Models, Molecular</topic><topic>Multifunctional Enzymes - chemistry</topic><topic>Multifunctional Enzymes - genetics</topic><topic>Multifunctional Enzymes - metabolism</topic><topic>Nucleic Acid Conformation</topic><topic>p58 subunit</topic><topic>Peptide Fragments - chemistry</topic><topic>Peptide Fragments - genetics</topic><topic>Peptide Fragments - metabolism</topic><topic>primase activity</topic><topic>Protein Conformation</topic><topic>Protein Interaction Domains and Motifs</topic><topic>Protein Multimerization</topic><topic>Recombinant Proteins - chemistry</topic><topic>Recombinant Proteins - metabolism</topic><topic>RNA - chemistry</topic><topic>RNA - metabolism</topic><topic>RNA primer length counting</topic><topic>RNA synthesis</topic><topic>RNA/DNA duplex</topic><topic>Transcription, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Baranovskiy, Andrey G.</creatorcontrib><creatorcontrib>Zhang, Yinbo</creatorcontrib><creatorcontrib>Suwa, Yoshiaki</creatorcontrib><creatorcontrib>Gu, Jianyou</creatorcontrib><creatorcontrib>Babayeva, Nigar D.</creatorcontrib><creatorcontrib>Pavlov, Youri I.</creatorcontrib><creatorcontrib>Tahirov, Tahir H.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</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>The Journal of biological chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Baranovskiy, Andrey G.</au><au>Zhang, Yinbo</au><au>Suwa, Yoshiaki</au><au>Gu, Jianyou</au><au>Babayeva, Nigar D.</au><au>Pavlov, Youri I.</au><au>Tahirov, Tahir H.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Insight into the Human DNA Primase Interaction with Template-Primer</atitle><jtitle>The Journal of biological chemistry</jtitle><addtitle>J Biol Chem</addtitle><date>2016-02-26</date><risdate>2016</risdate><volume>291</volume><issue>9</issue><spage>4793</spage><epage>4802</epage><pages>4793-4802</pages><issn>0021-9258</issn><eissn>1083-351X</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><notes>Both authors contributed equally.</notes><abstract>DNA replication in almost all organisms depends on the activity of DNA primase, a DNA-dependent RNA polymerase that synthesizes short RNA primers of defined size for DNA polymerases. Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large accessory subunits, both of which are necessary for the activity. The mode of interaction of primase subunits with substrates during the various steps of primer synthesis that results in the counting of primer length is not clear. Here we show that the C-terminal domain of the large subunit (p58C) plays a major role in template-primer binding and also defines the elements of the DNA template and the RNA primer that interact with p58C. The specific mode of interaction with a template-primer involving the terminal 5′-triphosphate of RNA and the 3′-overhang of DNA results in a stable complex between p58C and the DNA/RNA duplex. Our results explain how p58C participates in RNA synthesis and primer length counting and also indicate that the binding site for initiating NTP is located on p58C. These findings provide notable insight into the mechanism of primase function and are applicable for DNA primases from other species.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>26710848</pmid><doi>10.1074/jbc.M115.704064</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | The Journal of biological chemistry, 2016-02, Vol.291 (9), p.4793-4802 |
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| source | BACON - Elsevier - GLOBAL_SCIENCEDIRECT-OPENACCESS; PubMed Central |
| subjects | 5′-triphosphate Binding Sites DNA and Chromosomes DNA primase DNA Primase - chemistry DNA Primase - genetics DNA Primase - metabolism DNA replication DNA, Single-Stranded - chemistry DNA, Single-Stranded - metabolism DNA-Directed DNA Polymerase - chemistry DNA-Directed DNA Polymerase - genetics DNA-Directed DNA Polymerase - metabolism DNA-protein interaction Electrophoretic Mobility Shift Assay Fluorescence Polarization Fluorescent Dyes - chemistry gel electrophoresis human Humans Kinetics Models, Molecular Multifunctional Enzymes - chemistry Multifunctional Enzymes - genetics Multifunctional Enzymes - metabolism Nucleic Acid Conformation p58 subunit Peptide Fragments - chemistry Peptide Fragments - genetics Peptide Fragments - metabolism primase activity Protein Conformation Protein Interaction Domains and Motifs Protein Multimerization Recombinant Proteins - chemistry Recombinant Proteins - metabolism RNA - chemistry RNA - metabolism RNA primer length counting RNA synthesis RNA/DNA duplex Transcription, Genetic |
| title | Insight into the Human DNA Primase Interaction with Template-Primer |
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