Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine
Abstract Derivatives of 5-hydroxyuridine (ho5U), such as 5-methoxyuridine (mo5U) and 5-oxyacetyluridine (cmo5U), are ubiquitous modifications of the wobble position of bacterial tRNA that are believed to enhance translational fidelity by the ribosome. In gram-negative bacteria, the last step in the...
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| Veröffentlicht in: | Nucleic acids research 2018-09, Vol.46 (17), p.9160-9169 |
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| creator | Ryu, Huijeong Grove, Tyler L Almo, Steven C Kim, Jungwook |
| description | Abstract
Derivatives of 5-hydroxyuridine (ho5U), such as 5-methoxyuridine (mo5U) and 5-oxyacetyluridine (cmo5U), are ubiquitous modifications of the wobble position of bacterial tRNA that are believed to enhance translational fidelity by the ribosome. In gram-negative bacteria, the last step in the biosynthesis of cmo5U from ho5U involves the unique metabolite carboxy S-adenosylmethionine (Cx-SAM) and the carboxymethyl transferase CmoB. However, the equivalent position in the tRNA of Gram-positive bacteria is instead mo5U, where the methyl group is derived from SAM and installed by an unknown methyltransferase. By utilizing a cmoB-deficient strain of Escherichia coli as a host and assaying for the formation of mo5U in total RNA isolates with methyltransferases of unknown function from Bacillus subtilis, we found that this modification is installed by the enzyme TrmR (formerly known as YrrM). Furthermore, X-ray crystal structures of TrmR with and without the anticodon stemloop of tRNAAla have been determined, which provide insight into both sequence and structure specificity in the interactions of TrmR with tRNA. |
| doi_str_mv | 10.1093/nar/gky592 |
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Derivatives of 5-hydroxyuridine (ho5U), such as 5-methoxyuridine (mo5U) and 5-oxyacetyluridine (cmo5U), are ubiquitous modifications of the wobble position of bacterial tRNA that are believed to enhance translational fidelity by the ribosome. In gram-negative bacteria, the last step in the biosynthesis of cmo5U from ho5U involves the unique metabolite carboxy S-adenosylmethionine (Cx-SAM) and the carboxymethyl transferase CmoB. However, the equivalent position in the tRNA of Gram-positive bacteria is instead mo5U, where the methyl group is derived from SAM and installed by an unknown methyltransferase. By utilizing a cmoB-deficient strain of Escherichia coli as a host and assaying for the formation of mo5U in total RNA isolates with methyltransferases of unknown function from Bacillus subtilis, we found that this modification is installed by the enzyme TrmR (formerly known as YrrM). Furthermore, X-ray crystal structures of TrmR with and without the anticodon stemloop of tRNAAla have been determined, which provide insight into both sequence and structure specificity in the interactions of TrmR with tRNA.</description><identifier>ISSN: 0305-1048</identifier><identifier>ISSN: 1362-4962</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gky592</identifier><identifier>PMID: 29982645</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Bacillus subtilis - enzymology ; Bacillus subtilis - genetics ; Bacillus subtilis - metabolism ; Cloning, Molecular ; Crystallography, X-Ray ; Methyltransferases - chemistry ; Methyltransferases - genetics ; Methyltransferases - isolation & purification ; Methyltransferases - metabolism ; RNA and RNA-protein complexes ; RNA, Bacterial - chemistry ; RNA, Bacterial - metabolism ; RNA, Transfer - chemistry ; RNA, Transfer - metabolism ; S-Adenosylmethionine - metabolism ; Uridine - analogs & derivatives ; Uridine - biosynthesis ; Uridine - metabolism</subject><ispartof>Nucleic acids research, 2018-09, Vol.46 (17), p.9160-9169</ispartof><rights>The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c474t-bd9cf51707e30f7d99ea26c793be9734e00682411e2cfa0a390549fad62dc02a3</citedby><cites>FETCH-LOGICAL-c474t-bd9cf51707e30f7d99ea26c793be9734e00682411e2cfa0a390549fad62dc02a3</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/PMC6158493/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158493/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,1605,27928,27929,53795,53797</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29982645$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ryu, Huijeong</creatorcontrib><creatorcontrib>Grove, Tyler L</creatorcontrib><creatorcontrib>Almo, Steven C</creatorcontrib><creatorcontrib>Kim, Jungwook</creatorcontrib><title>Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
Derivatives of 5-hydroxyuridine (ho5U), such as 5-methoxyuridine (mo5U) and 5-oxyacetyluridine (cmo5U), are ubiquitous modifications of the wobble position of bacterial tRNA that are believed to enhance translational fidelity by the ribosome. In gram-negative bacteria, the last step in the biosynthesis of cmo5U from ho5U involves the unique metabolite carboxy S-adenosylmethionine (Cx-SAM) and the carboxymethyl transferase CmoB. However, the equivalent position in the tRNA of Gram-positive bacteria is instead mo5U, where the methyl group is derived from SAM and installed by an unknown methyltransferase. By utilizing a cmoB-deficient strain of Escherichia coli as a host and assaying for the formation of mo5U in total RNA isolates with methyltransferases of unknown function from Bacillus subtilis, we found that this modification is installed by the enzyme TrmR (formerly known as YrrM). Furthermore, X-ray crystal structures of TrmR with and without the anticodon stemloop of tRNAAla have been determined, which provide insight into both sequence and structure specificity in the interactions of TrmR with tRNA.</description><subject>Bacillus subtilis - enzymology</subject><subject>Bacillus subtilis - genetics</subject><subject>Bacillus subtilis - metabolism</subject><subject>Cloning, Molecular</subject><subject>Crystallography, X-Ray</subject><subject>Methyltransferases - chemistry</subject><subject>Methyltransferases - genetics</subject><subject>Methyltransferases - isolation & purification</subject><subject>Methyltransferases - metabolism</subject><subject>RNA and RNA-protein complexes</subject><subject>RNA, Bacterial - chemistry</subject><subject>RNA, Bacterial - metabolism</subject><subject>RNA, Transfer - chemistry</subject><subject>RNA, Transfer - metabolism</subject><subject>S-Adenosylmethionine - metabolism</subject><subject>Uridine - analogs & derivatives</subject><subject>Uridine - biosynthesis</subject><subject>Uridine - metabolism</subject><issn>0305-1048</issn><issn>1362-4962</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kV1LHDEUhkNR6qq96Q-Q3BREmG4-ZzY3BZF-CKJQ6nXIZE52Y2eS7SSzOv_eWXYVe-NVDuQ5zzmHF6HPlHylRPF5MP18-XeUin1AM8pLVghVsgM0I5zIghKxOELHKT0QQgWV4iM6YkotWCnkDK2uGwjZO29N9jHg6LDBIW6gxfn37SV-jHXdAh563_gAuIuNd6MPS2xs9hufR-wDzivAtY9pDFOVfNpaZNFBXsWncd96ig6daRN82r8n6P7H9z9Xv4qbu5_XV5c3hRWVyEXdKOskrUgFnLiqUQoMK22leA2q4gIIKRdMUArMOkMMV0QK5UxTssYSZvgJ-rbzroe6g8ZO1_Wm1eved6YfdTRe__8T_Eov40aXVC6E4pPgfC_o478BUtadTxba1gSIQ9KMlBVliio5oRc71PYxpR7c6xhK9DYaPUWjd9FM8NnbxV7Rlywm4MsOiMP6PdEzB8uaXA</recordid><startdate>20180928</startdate><enddate>20180928</enddate><creator>Ryu, Huijeong</creator><creator>Grove, Tyler L</creator><creator>Almo, Steven C</creator><creator>Kim, Jungwook</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>20180928</creationdate><title>Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine</title><author>Ryu, Huijeong ; Grove, Tyler L ; Almo, Steven C ; Kim, Jungwook</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c474t-bd9cf51707e30f7d99ea26c793be9734e00682411e2cfa0a390549fad62dc02a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Bacillus subtilis - enzymology</topic><topic>Bacillus subtilis - genetics</topic><topic>Bacillus subtilis - metabolism</topic><topic>Cloning, Molecular</topic><topic>Crystallography, X-Ray</topic><topic>Methyltransferases - chemistry</topic><topic>Methyltransferases - genetics</topic><topic>Methyltransferases - isolation & purification</topic><topic>Methyltransferases - metabolism</topic><topic>RNA and RNA-protein complexes</topic><topic>RNA, Bacterial - chemistry</topic><topic>RNA, Bacterial - metabolism</topic><topic>RNA, Transfer - chemistry</topic><topic>RNA, Transfer - metabolism</topic><topic>S-Adenosylmethionine - metabolism</topic><topic>Uridine - analogs & derivatives</topic><topic>Uridine - biosynthesis</topic><topic>Uridine - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ryu, Huijeong</creatorcontrib><creatorcontrib>Grove, Tyler L</creatorcontrib><creatorcontrib>Almo, Steven C</creatorcontrib><creatorcontrib>Kim, Jungwook</creatorcontrib><collection>Access via Oxford University Press (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>Ryu, Huijeong</au><au>Grove, Tyler L</au><au>Almo, Steven C</au><au>Kim, Jungwook</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2018-09-28</date><risdate>2018</risdate><volume>46</volume><issue>17</issue><spage>9160</spage><epage>9169</epage><pages>9160-9169</pages><issn>0305-1048</issn><issn>1362-4962</issn><eissn>1362-4962</eissn><abstract>Abstract
Derivatives of 5-hydroxyuridine (ho5U), such as 5-methoxyuridine (mo5U) and 5-oxyacetyluridine (cmo5U), are ubiquitous modifications of the wobble position of bacterial tRNA that are believed to enhance translational fidelity by the ribosome. In gram-negative bacteria, the last step in the biosynthesis of cmo5U from ho5U involves the unique metabolite carboxy S-adenosylmethionine (Cx-SAM) and the carboxymethyl transferase CmoB. However, the equivalent position in the tRNA of Gram-positive bacteria is instead mo5U, where the methyl group is derived from SAM and installed by an unknown methyltransferase. By utilizing a cmoB-deficient strain of Escherichia coli as a host and assaying for the formation of mo5U in total RNA isolates with methyltransferases of unknown function from Bacillus subtilis, we found that this modification is installed by the enzyme TrmR (formerly known as YrrM). Furthermore, X-ray crystal structures of TrmR with and without the anticodon stemloop of tRNAAla have been determined, which provide insight into both sequence and structure specificity in the interactions of TrmR with tRNA.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>29982645</pmid><doi>10.1093/nar/gky592</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Bacillus subtilis - enzymology Bacillus subtilis - genetics Bacillus subtilis - metabolism Cloning, Molecular Crystallography, X-Ray Methyltransferases - chemistry Methyltransferases - genetics Methyltransferases - isolation & purification Methyltransferases - metabolism RNA and RNA-protein complexes RNA, Bacterial - chemistry RNA, Bacterial - metabolism RNA, Transfer - chemistry RNA, Transfer - metabolism S-Adenosylmethionine - metabolism Uridine - analogs & derivatives Uridine - biosynthesis Uridine - metabolism |
| title | Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine |
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