Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage
Deinococcus radiodurans R1 (DR) survives conditions of extreme desiccation, irradiation and exposure to genotoxic chemicals, due to efficient DNA breaks repair, also through Mn2+ protection of DNA repair enzymes. Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinform...
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| Veröffentlicht in: | Biochimica et biophysica acta. General subjects 2019-01, Vol.1863 (1), p.118-129 |
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| creator | Ferrandi, Alex Castani, Federica Pitaro, Mauro Tagliaferri, Sara de la Tour, Claire Bouthier Alduina, Rosa Sommer, Suzanne Fasano, Mauro Barbieri, Paola Mancini, Monica Bonapace, Ian Marc |
| description | Deinococcus radiodurans R1 (DR) survives conditions of extreme desiccation, irradiation and exposure to genotoxic chemicals, due to efficient DNA breaks repair, also through Mn2+ protection of DNA repair enzymes.
Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinformatic analysis. The gene was cloned and expressed as fusion protein. Band-shift assays of Shp or the SRA and HNH domains were performed on oligonucleotides, genomic DNA from E. coli and DR. shp knock-out mutant was generated by homologous recombination with a kanamycin resistance cassette.
DR1533 contains an N-terminal SRA domain and a C-terminal HNH motif (SRA-HNH Protein, Shp). Through its SRA domain, Shp binds double-strand oligonucleotides containing 5mC and 5hmC, but also unmethylated and mismatched cytosines in presence of Mn2+. Shp also binds to Escherichia coli dcm+ genomic DNA, and to cytosine unmethylated DR and E. coli dcm− genomic DNAs, but only in presence of Mn2+. Under these binding conditions, Shp displays DNAse activity through its HNH domain. Shp KO enhanced >100 fold the number of spontaneous mutants, whilst the treatment with DNA double strand break inducing agents enhanced up to 3-log the number of survivors.
The SRA-HNH containing protein Shp binds to and cuts 5mC DNA, and unmethylated DNA in a Mn2+ dependent manner, and might be involved in faithful genome inheritance maintenance following DNA damage.
Our results provide evidence for a potential role of DR Shp protein for genome integrity maintenance, following DNA double strand breaks induced by genotoxic agents.
•Dr1533 protein of D. radiodurans R1 (DR) contains a SRA and a HNH domain (Shp).•Shp binds to and cuts unmethylated E. coli and DR genomic DNA in presence of Mn2+.•shp-KO (Δshp) enhances DR survival after DNA damage induced by genotoxic agents.•Δshp increases the number of mutants in DR exposed to genotoxic agents. |
| doi_str_mv | 10.1016/j.bbagen.2018.09.020 |
| format | Article |
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Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinformatic analysis. The gene was cloned and expressed as fusion protein. Band-shift assays of Shp or the SRA and HNH domains were performed on oligonucleotides, genomic DNA from E. coli and DR. shp knock-out mutant was generated by homologous recombination with a kanamycin resistance cassette.
DR1533 contains an N-terminal SRA domain and a C-terminal HNH motif (SRA-HNH Protein, Shp). Through its SRA domain, Shp binds double-strand oligonucleotides containing 5mC and 5hmC, but also unmethylated and mismatched cytosines in presence of Mn2+. Shp also binds to Escherichia coli dcm+ genomic DNA, and to cytosine unmethylated DR and E. coli dcm− genomic DNAs, but only in presence of Mn2+. Under these binding conditions, Shp displays DNAse activity through its HNH domain. Shp KO enhanced >100 fold the number of spontaneous mutants, whilst the treatment with DNA double strand break inducing agents enhanced up to 3-log the number of survivors.
The SRA-HNH containing protein Shp binds to and cuts 5mC DNA, and unmethylated DNA in a Mn2+ dependent manner, and might be involved in faithful genome inheritance maintenance following DNA damage.
Our results provide evidence for a potential role of DR Shp protein for genome integrity maintenance, following DNA double strand breaks induced by genotoxic agents.
•Dr1533 protein of D. radiodurans R1 (DR) contains a SRA and a HNH domain (Shp).•Shp binds to and cuts unmethylated E. coli and DR genomic DNA in presence of Mn2+.•shp-KO (Δshp) enhances DR survival after DNA damage induced by genotoxic agents.•Δshp increases the number of mutants in DR exposed to genotoxic agents.</description><identifier>ISSN: 0304-4165</identifier><identifier>EISSN: 1872-8006</identifier><identifier>DOI: 10.1016/j.bbagen.2018.09.020</identifier><identifier>PMID: 30308220</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Amino Acid Sequence ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; CCAAT-Enhancer-Binding Proteins - metabolism ; Cloning, Molecular ; Computational Biology ; Cytosine - metabolism ; Deinococcus - genetics ; Deinococcus - metabolism ; DNA cytosine-methylation ; DNA Damage ; DNA Methylation ; DNA Repair ; DNA, Bacterial - genetics ; DR1533 locus ; Drug Resistance, Bacterial ; Escherichia coli - genetics ; Escherichia coli - metabolism ; Genome, Bacterial ; Genotoxic agents ; Humans ; Kanamycin - chemistry ; Life Sciences ; Mn2 ; Mutagens - chemistry ; Mutation ; Protein Domains ; SRA domain</subject><ispartof>Biochimica et biophysica acta. General subjects, 2019-01, Vol.1863 (1), p.118-129</ispartof><rights>2018 Elsevier B.V.</rights><rights>Copyright © 2018 Elsevier B.V. All rights reserved.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c396t-34bdbc88c6b9f792abec96af6c332f0a2f48eab8320352986bdc0ec7253305283</citedby><cites>FETCH-LOGICAL-c396t-34bdbc88c6b9f792abec96af6c332f0a2f48eab8320352986bdc0ec7253305283</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0304416518303088$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,776,780,881,3537,4010,27900,27901,27902,65534</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30308220$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-02170785$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Ferrandi, Alex</creatorcontrib><creatorcontrib>Castani, Federica</creatorcontrib><creatorcontrib>Pitaro, Mauro</creatorcontrib><creatorcontrib>Tagliaferri, Sara</creatorcontrib><creatorcontrib>de la Tour, Claire Bouthier</creatorcontrib><creatorcontrib>Alduina, Rosa</creatorcontrib><creatorcontrib>Sommer, Suzanne</creatorcontrib><creatorcontrib>Fasano, Mauro</creatorcontrib><creatorcontrib>Barbieri, Paola</creatorcontrib><creatorcontrib>Mancini, Monica</creatorcontrib><creatorcontrib>Bonapace, Ian Marc</creatorcontrib><title>Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage</title><title>Biochimica et biophysica acta. General subjects</title><addtitle>Biochim Biophys Acta Gen Subj</addtitle><description>Deinococcus radiodurans R1 (DR) survives conditions of extreme desiccation, irradiation and exposure to genotoxic chemicals, due to efficient DNA breaks repair, also through Mn2+ protection of DNA repair enzymes.
Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinformatic analysis. The gene was cloned and expressed as fusion protein. Band-shift assays of Shp or the SRA and HNH domains were performed on oligonucleotides, genomic DNA from E. coli and DR. shp knock-out mutant was generated by homologous recombination with a kanamycin resistance cassette.
DR1533 contains an N-terminal SRA domain and a C-terminal HNH motif (SRA-HNH Protein, Shp). Through its SRA domain, Shp binds double-strand oligonucleotides containing 5mC and 5hmC, but also unmethylated and mismatched cytosines in presence of Mn2+. Shp also binds to Escherichia coli dcm+ genomic DNA, and to cytosine unmethylated DR and E. coli dcm− genomic DNAs, but only in presence of Mn2+. Under these binding conditions, Shp displays DNAse activity through its HNH domain. Shp KO enhanced >100 fold the number of spontaneous mutants, whilst the treatment with DNA double strand break inducing agents enhanced up to 3-log the number of survivors.
The SRA-HNH containing protein Shp binds to and cuts 5mC DNA, and unmethylated DNA in a Mn2+ dependent manner, and might be involved in faithful genome inheritance maintenance following DNA damage.
Our results provide evidence for a potential role of DR Shp protein for genome integrity maintenance, following DNA double strand breaks induced by genotoxic agents.
•Dr1533 protein of D. radiodurans R1 (DR) contains a SRA and a HNH domain (Shp).•Shp binds to and cuts unmethylated E. coli and DR genomic DNA in presence of Mn2+.•shp-KO (Δshp) enhances DR survival after DNA damage induced by genotoxic agents.•Δshp increases the number of mutants in DR exposed to genotoxic agents.</description><subject>Amino Acid Sequence</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>CCAAT-Enhancer-Binding Proteins - metabolism</subject><subject>Cloning, Molecular</subject><subject>Computational Biology</subject><subject>Cytosine - metabolism</subject><subject>Deinococcus - genetics</subject><subject>Deinococcus - metabolism</subject><subject>DNA cytosine-methylation</subject><subject>DNA Damage</subject><subject>DNA Methylation</subject><subject>DNA Repair</subject><subject>DNA, Bacterial - genetics</subject><subject>DR1533 locus</subject><subject>Drug Resistance, Bacterial</subject><subject>Escherichia coli - genetics</subject><subject>Escherichia coli - metabolism</subject><subject>Genome, Bacterial</subject><subject>Genotoxic agents</subject><subject>Humans</subject><subject>Kanamycin - chemistry</subject><subject>Life Sciences</subject><subject>Mn2</subject><subject>Mutagens - chemistry</subject><subject>Mutation</subject><subject>Protein Domains</subject><subject>SRA domain</subject><issn>0304-4165</issn><issn>1872-8006</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9UU2P0zAQtRCILQv_ACHf2D2kjO182BekagsUqVokFs6WYztbV4ld7KSI38EfxiHLHvFlRuM3783MQ-g1gTUBUr87rttW3Vu_pkD4GsQaKDxBK8IbWnCA-ilaAYOyKEldXaAXKR0hv0pUz9EFyz-cUlih31vrfNBB6ynhqIwLZorKp7f47uum2N3usAmDch7r4Mccnb_HpxjG3IXvDid8tY2kYuwau4SdP4f-bE1OcKfceOimHucJw2Bz6WCjG5XXFs98o_V_8y70ffg5s25vN9ioIa_0Ej3rVJ_sq4d4ib5__PDtZlfsv3z6fLPZF5qJeixY2ZpWc67rVnSNoKq1WtSqqzVjtANFu5Jb1XJGgVVU8Lo1GqxuaJ4XKsrZJbpeeA-ql6foBhV_yaCc3G32cq4BJQ00vDqTjL1asHn5H5NNoxxc0rbvlbdhSpISIgQVom4ytFygOoaUou0euQnI2Tp5lIt1crZOgshCkNvePChM7WDNY9M_rzLg_QKw-SZnZ6NM2tl8ROOi1aM0wf1f4Q8RDau0</recordid><startdate>201901</startdate><enddate>201901</enddate><creator>Ferrandi, Alex</creator><creator>Castani, Federica</creator><creator>Pitaro, Mauro</creator><creator>Tagliaferri, Sara</creator><creator>de la Tour, Claire Bouthier</creator><creator>Alduina, Rosa</creator><creator>Sommer, Suzanne</creator><creator>Fasano, Mauro</creator><creator>Barbieri, Paola</creator><creator>Mancini, Monica</creator><creator>Bonapace, Ian Marc</creator><general>Elsevier B.V</general><general>Elsevier</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>1XC</scope></search><sort><creationdate>201901</creationdate><title>Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage</title><author>Ferrandi, Alex ; Castani, Federica ; Pitaro, Mauro ; Tagliaferri, Sara ; de la Tour, Claire Bouthier ; Alduina, Rosa ; Sommer, Suzanne ; Fasano, Mauro ; Barbieri, Paola ; Mancini, Monica ; Bonapace, Ian Marc</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c396t-34bdbc88c6b9f792abec96af6c332f0a2f48eab8320352986bdc0ec7253305283</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Amino Acid Sequence</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - metabolism</topic><topic>CCAAT-Enhancer-Binding Proteins - metabolism</topic><topic>Cloning, Molecular</topic><topic>Computational Biology</topic><topic>Cytosine - metabolism</topic><topic>Deinococcus - genetics</topic><topic>Deinococcus - metabolism</topic><topic>DNA cytosine-methylation</topic><topic>DNA Damage</topic><topic>DNA Methylation</topic><topic>DNA Repair</topic><topic>DNA, Bacterial - genetics</topic><topic>DR1533 locus</topic><topic>Drug Resistance, Bacterial</topic><topic>Escherichia coli - genetics</topic><topic>Escherichia coli - metabolism</topic><topic>Genome, Bacterial</topic><topic>Genotoxic agents</topic><topic>Humans</topic><topic>Kanamycin - chemistry</topic><topic>Life Sciences</topic><topic>Mn2</topic><topic>Mutagens - chemistry</topic><topic>Mutation</topic><topic>Protein Domains</topic><topic>SRA domain</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ferrandi, Alex</creatorcontrib><creatorcontrib>Castani, Federica</creatorcontrib><creatorcontrib>Pitaro, Mauro</creatorcontrib><creatorcontrib>Tagliaferri, Sara</creatorcontrib><creatorcontrib>de la Tour, Claire Bouthier</creatorcontrib><creatorcontrib>Alduina, Rosa</creatorcontrib><creatorcontrib>Sommer, Suzanne</creatorcontrib><creatorcontrib>Fasano, Mauro</creatorcontrib><creatorcontrib>Barbieri, Paola</creatorcontrib><creatorcontrib>Mancini, Monica</creatorcontrib><creatorcontrib>Bonapace, Ian Marc</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>Hyper Article en Ligne (HAL)</collection><jtitle>Biochimica et biophysica acta. General subjects</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ferrandi, Alex</au><au>Castani, Federica</au><au>Pitaro, Mauro</au><au>Tagliaferri, Sara</au><au>de la Tour, Claire Bouthier</au><au>Alduina, Rosa</au><au>Sommer, Suzanne</au><au>Fasano, Mauro</au><au>Barbieri, Paola</au><au>Mancini, Monica</au><au>Bonapace, Ian Marc</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage</atitle><jtitle>Biochimica et biophysica acta. General subjects</jtitle><addtitle>Biochim Biophys Acta Gen Subj</addtitle><date>2019-01</date><risdate>2019</risdate><volume>1863</volume><issue>1</issue><spage>118</spage><epage>129</epage><pages>118-129</pages><issn>0304-4165</issn><eissn>1872-8006</eissn><abstract>Deinococcus radiodurans R1 (DR) survives conditions of extreme desiccation, irradiation and exposure to genotoxic chemicals, due to efficient DNA breaks repair, also through Mn2+ protection of DNA repair enzymes.
Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinformatic analysis. The gene was cloned and expressed as fusion protein. Band-shift assays of Shp or the SRA and HNH domains were performed on oligonucleotides, genomic DNA from E. coli and DR. shp knock-out mutant was generated by homologous recombination with a kanamycin resistance cassette.
DR1533 contains an N-terminal SRA domain and a C-terminal HNH motif (SRA-HNH Protein, Shp). Through its SRA domain, Shp binds double-strand oligonucleotides containing 5mC and 5hmC, but also unmethylated and mismatched cytosines in presence of Mn2+. Shp also binds to Escherichia coli dcm+ genomic DNA, and to cytosine unmethylated DR and E. coli dcm− genomic DNAs, but only in presence of Mn2+. Under these binding conditions, Shp displays DNAse activity through its HNH domain. Shp KO enhanced >100 fold the number of spontaneous mutants, whilst the treatment with DNA double strand break inducing agents enhanced up to 3-log the number of survivors.
The SRA-HNH containing protein Shp binds to and cuts 5mC DNA, and unmethylated DNA in a Mn2+ dependent manner, and might be involved in faithful genome inheritance maintenance following DNA damage.
Our results provide evidence for a potential role of DR Shp protein for genome integrity maintenance, following DNA double strand breaks induced by genotoxic agents.
•Dr1533 protein of D. radiodurans R1 (DR) contains a SRA and a HNH domain (Shp).•Shp binds to and cuts unmethylated E. coli and DR genomic DNA in presence of Mn2+.•shp-KO (Δshp) enhances DR survival after DNA damage induced by genotoxic agents.•Δshp increases the number of mutants in DR exposed to genotoxic agents.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>30308220</pmid><doi>10.1016/j.bbagen.2018.09.020</doi><tpages>12</tpages></addata></record> |
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| source | MEDLINE; Elsevier ScienceDirect Journals Complete |
| subjects | Amino Acid Sequence Bacterial Proteins - genetics Bacterial Proteins - metabolism CCAAT-Enhancer-Binding Proteins - metabolism Cloning, Molecular Computational Biology Cytosine - metabolism Deinococcus - genetics Deinococcus - metabolism DNA cytosine-methylation DNA Damage DNA Methylation DNA Repair DNA, Bacterial - genetics DR1533 locus Drug Resistance, Bacterial Escherichia coli - genetics Escherichia coli - metabolism Genome, Bacterial Genotoxic agents Humans Kanamycin - chemistry Life Sciences Mn2 Mutagens - chemistry Mutation Protein Domains SRA domain |
| title | Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage |
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