Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs
Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity pro...
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| Veröffentlicht in: | Nucleic acids research 2017-09, Vol.45 (17), p.10306-10320 |
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| creator | Michalska, Karolina Gucinski, Grant C Garza-Sánchez, Fernando Johnson, Parker M Stols, Lucy M Eschenfeldt, William H Babnigg, Gyorgy Low, David A Goulding, Celia W Joachimiak, Andrzej Hayes, Christopher S |
| description | Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxin specifically cleaves substrate in the context of GTP·EF-Tu·aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP·EF-Tu·aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a β-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Together, these observations suggest that the toxin remodels GTP·EF-Tu·aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site. |
| doi_str_mv | 10.1093/nar/gkx700 |
| format | Article |
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Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxin specifically cleaves substrate in the context of GTP·EF-Tu·aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP·EF-Tu·aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a β-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Together, these observations suggest that the toxin remodels GTP·EF-Tu·aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkx700</identifier><identifier>PMID: 28973472</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>60 APPLIED LIFE SCIENCES ; Bacterial Toxins - chemistry ; Bacterial Toxins - metabolism ; BASIC BIOLOGICAL SCIENCES ; Crystallography, X-Ray ; Escherichia coli - genetics ; Escherichia coli - metabolism ; Escherichia coli Proteins - metabolism ; Guanine - metabolism ; immunity ; Models, Molecular ; nuclease ; Nucleic Acid Conformation ; peptide elongation factor tu ; Peptide Elongation Factor Tu - metabolism ; Protein Conformation ; Protein Domains ; Recombinant Fusion Proteins - metabolism ; RNA, Bacterial - metabolism ; RNA, Transfer - metabolism ; Structural Biology ; Structure-Activity Relationship ; Substrate Specificity ; toxins ; transfer rna</subject><ispartof>Nucleic acids research, 2017-09, Vol.45 (17), p.10306-10320</ispartof><rights>The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><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-c405t-917211f8c61d132dbee1fb23bd317f84543f0ef1ed211b5ad73081509d41067e3</citedby><cites>FETCH-LOGICAL-c405t-917211f8c61d132dbee1fb23bd317f84543f0ef1ed211b5ad73081509d41067e3</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/PMC5737660/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737660/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28973472$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1393513$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Michalska, Karolina</creatorcontrib><creatorcontrib>Gucinski, Grant C</creatorcontrib><creatorcontrib>Garza-Sánchez, Fernando</creatorcontrib><creatorcontrib>Johnson, Parker M</creatorcontrib><creatorcontrib>Stols, Lucy M</creatorcontrib><creatorcontrib>Eschenfeldt, William H</creatorcontrib><creatorcontrib>Babnigg, Gyorgy</creatorcontrib><creatorcontrib>Low, David A</creatorcontrib><creatorcontrib>Goulding, Celia W</creatorcontrib><creatorcontrib>Joachimiak, Andrzej</creatorcontrib><creatorcontrib>Hayes, Christopher S</creatorcontrib><creatorcontrib>Argonne National Laboratory (ANL), Argonne, IL (United States)</creatorcontrib><title>Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxin specifically cleaves substrate in the context of GTP·EF-Tu·aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP·EF-Tu·aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a β-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Together, these observations suggest that the toxin remodels GTP·EF-Tu·aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site.</description><subject>60 APPLIED LIFE SCIENCES</subject><subject>Bacterial Toxins - chemistry</subject><subject>Bacterial Toxins - metabolism</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Crystallography, X-Ray</subject><subject>Escherichia coli - genetics</subject><subject>Escherichia coli - metabolism</subject><subject>Escherichia coli Proteins - metabolism</subject><subject>Guanine - metabolism</subject><subject>immunity</subject><subject>Models, Molecular</subject><subject>nuclease</subject><subject>Nucleic Acid Conformation</subject><subject>peptide elongation factor tu</subject><subject>Peptide Elongation Factor Tu - metabolism</subject><subject>Protein Conformation</subject><subject>Protein Domains</subject><subject>Recombinant Fusion Proteins - metabolism</subject><subject>RNA, Bacterial - metabolism</subject><subject>RNA, Transfer - metabolism</subject><subject>Structural Biology</subject><subject>Structure-Activity Relationship</subject><subject>Substrate Specificity</subject><subject>toxins</subject><subject>transfer rna</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkV1rFDEUhoNY7Fq98QdI8KoIY3MmmcnMjVCKX1Ba0HodMpmT3Wg2WZPMsv33RrYWvToX5-E9L-ch5BWwd8BGfhF0ulj_PEjGnpAV8L5txNi3T8mKcdY1wMRwSp7n_IMxENCJZ-S0HUbJhWxXxH8raTFlSUijpZqGuEdPdShu0qZgctrTEg8u0LLRheJh56MrmaKPYa2Li4HaCsZE75YKUuNR75HmHRpnnaEl6ZAtJvr15jK_ICdW-4wvH-YZ-f7xw93V5-b69tOXq8vrxgjWlWYE2QLYwfQwA2_nCRHs1PJp5iDtIDrBLUMLOFds6vQsORugY-MsgPUS-Rl5f8zdLdMWZ4Oh1vBql9xWp3sVtVP_b4LbqHXcq05y2fesBrw5BsRcnMrGFTQbE0NAUxTwkXfAK3T-cCXFXwvmorYuG_ReB4xLVjAKyUZZP17Rt0fUpJhzQvvYBZj641BVh-rosMKv_23_iP6Vxn8Dm4uaaw</recordid><startdate>20170929</startdate><enddate>20170929</enddate><creator>Michalska, Karolina</creator><creator>Gucinski, Grant C</creator><creator>Garza-Sánchez, Fernando</creator><creator>Johnson, Parker M</creator><creator>Stols, Lucy M</creator><creator>Eschenfeldt, William H</creator><creator>Babnigg, Gyorgy</creator><creator>Low, David A</creator><creator>Goulding, Celia W</creator><creator>Joachimiak, Andrzej</creator><creator>Hayes, Christopher S</creator><general>Oxford University Press</general><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>OIOZB</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20170929</creationdate><title>Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs</title><author>Michalska, Karolina ; Gucinski, Grant C ; Garza-Sánchez, Fernando ; Johnson, Parker M ; Stols, Lucy M ; Eschenfeldt, William H ; Babnigg, Gyorgy ; Low, David A ; Goulding, Celia W ; Joachimiak, Andrzej ; Hayes, Christopher S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c405t-917211f8c61d132dbee1fb23bd317f84543f0ef1ed211b5ad73081509d41067e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>60 APPLIED LIFE SCIENCES</topic><topic>Bacterial Toxins - chemistry</topic><topic>Bacterial Toxins - metabolism</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Crystallography, X-Ray</topic><topic>Escherichia coli - genetics</topic><topic>Escherichia coli - metabolism</topic><topic>Escherichia coli Proteins - metabolism</topic><topic>Guanine - metabolism</topic><topic>immunity</topic><topic>Models, Molecular</topic><topic>nuclease</topic><topic>Nucleic Acid Conformation</topic><topic>peptide elongation factor tu</topic><topic>Peptide Elongation Factor Tu - metabolism</topic><topic>Protein Conformation</topic><topic>Protein Domains</topic><topic>Recombinant Fusion Proteins - metabolism</topic><topic>RNA, Bacterial - metabolism</topic><topic>RNA, Transfer - metabolism</topic><topic>Structural Biology</topic><topic>Structure-Activity Relationship</topic><topic>Substrate Specificity</topic><topic>toxins</topic><topic>transfer rna</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Michalska, Karolina</creatorcontrib><creatorcontrib>Gucinski, Grant C</creatorcontrib><creatorcontrib>Garza-Sánchez, Fernando</creatorcontrib><creatorcontrib>Johnson, Parker M</creatorcontrib><creatorcontrib>Stols, Lucy M</creatorcontrib><creatorcontrib>Eschenfeldt, William H</creatorcontrib><creatorcontrib>Babnigg, Gyorgy</creatorcontrib><creatorcontrib>Low, David A</creatorcontrib><creatorcontrib>Goulding, Celia W</creatorcontrib><creatorcontrib>Joachimiak, Andrzej</creatorcontrib><creatorcontrib>Hayes, Christopher S</creatorcontrib><creatorcontrib>Argonne National Laboratory (ANL), Argonne, IL (United States)</creatorcontrib><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>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</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>Michalska, Karolina</au><au>Gucinski, Grant C</au><au>Garza-Sánchez, Fernando</au><au>Johnson, Parker M</au><au>Stols, Lucy M</au><au>Eschenfeldt, William H</au><au>Babnigg, Gyorgy</au><au>Low, David A</au><au>Goulding, Celia W</au><au>Joachimiak, Andrzej</au><au>Hayes, Christopher S</au><aucorp>Argonne National Laboratory (ANL), Argonne, IL (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2017-09-29</date><risdate>2017</risdate><volume>45</volume><issue>17</issue><spage>10306</spage><epage>10320</epage><pages>10306-10320</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxin specifically cleaves substrate in the context of GTP·EF-Tu·aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP·EF-Tu·aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a β-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Together, these observations suggest that the toxin remodels GTP·EF-Tu·aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>28973472</pmid><doi>10.1093/nar/gkx700</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 60 APPLIED LIFE SCIENCES Bacterial Toxins - chemistry Bacterial Toxins - metabolism BASIC BIOLOGICAL SCIENCES Crystallography, X-Ray Escherichia coli - genetics Escherichia coli - metabolism Escherichia coli Proteins - metabolism Guanine - metabolism immunity Models, Molecular nuclease Nucleic Acid Conformation peptide elongation factor tu Peptide Elongation Factor Tu - metabolism Protein Conformation Protein Domains Recombinant Fusion Proteins - metabolism RNA, Bacterial - metabolism RNA, Transfer - metabolism Structural Biology Structure-Activity Relationship Substrate Specificity toxins transfer rna |
| title | Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs |
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