Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae)
We have investigated the strategy of Halobacterium sp. NRC-1 and other members of the family Halobacteriaceae to survive ultraviolet (UV) irradiation, based on an integrated analysis of various genomic and proteomic features such as dinucleotide composition and distribution of tetranucleotides in th...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2007-07, Vol.90 (1), p.103-109 |
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| container_title | Genomics (San Diego, Calif.) |
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| creator | Zhou, Peng Wen, Ji Oren, Aharon Chen, Ming Wu, Min |
| description | We have investigated the strategy of
Halobacterium sp. NRC-1 and other members of the family Halobacteriaceae to survive ultraviolet (UV) irradiation, based on an integrated analysis of various genomic and proteomic features such as dinucleotide composition and distribution of tetranucleotides in the genome and amino acid composition of the proteins. The low dipyrimidine content may help
Halobacterium reduce formation of photoproducts in its genome. The usage of residues susceptible to reactive oxygen species attack is reduced significantly in
Halobacterium, which helps the organism to minimize protein damage. We then correlated the expression of the
zim gene with the genomic structure to reexamine the importance of the putative mismatch repair pathway proposed previously. Our results showed that
Halobacterium sp. NRC-1 and other haloarchaea (
Haloarcula marismortui,
Haloquadratum walsbyi) have optimized their genomic and proteomic structures to reduce damage induced by UV irradiation, often present at high levels in habitats where these organisms thrive. |
| doi_str_mv | 10.1016/j.ygeno.2007.03.015 |
| format | Article |
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Halobacterium sp. NRC-1 and other members of the family Halobacteriaceae to survive ultraviolet (UV) irradiation, based on an integrated analysis of various genomic and proteomic features such as dinucleotide composition and distribution of tetranucleotides in the genome and amino acid composition of the proteins. The low dipyrimidine content may help
Halobacterium reduce formation of photoproducts in its genome. The usage of residues susceptible to reactive oxygen species attack is reduced significantly in
Halobacterium, which helps the organism to minimize protein damage. We then correlated the expression of the
zim gene with the genomic structure to reexamine the importance of the putative mismatch repair pathway proposed previously. Our results showed that
Halobacterium sp. NRC-1 and other haloarchaea (
Haloarcula marismortui,
Haloquadratum walsbyi) have optimized their genomic and proteomic structures to reduce damage induced by UV irradiation, often present at high levels in habitats where these organisms thrive.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2007.03.015</identifier><identifier>PMID: 17498923</identifier><language>eng</language><publisher>San Diego, CA: Elsevier Inc</publisher><subject>Amino acid composition ; Biological and medical sciences ; CTAG pattern ; Cytosine - chemistry ; Cytosine - radiation effects ; Dipyrimidine composition ; DNA, Archaeal - chemistry ; DNA, Archaeal - radiation effects ; Fundamental and applied biological sciences. Psychology ; Genes. Genome ; Genetics of eukaryotes. Biological and molecular evolution ; Genome, Archaeal - genetics ; Genomic structure ; Haloarcula marismortui ; Halobacteriaceae ; Halobacteriaceae - genetics ; Halobacteriaceae - radiation effects ; Halobacterium ; Molecular and cellular biology ; Molecular genetics ; Radiation Tolerance - genetics ; Thymine - chemistry ; Thymine - radiation effects ; Ultraviolet Rays ; UV tolerance</subject><ispartof>Genomics (San Diego, Calif.), 2007-07, Vol.90 (1), p.103-109</ispartof><rights>2007 Elsevier Inc.</rights><rights>2007 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c418t-d72c7ee0946d1319884c394c4ffd5cd0dda4119107792a78cc4cb54b1b331c13</citedby><cites>FETCH-LOGICAL-c418t-d72c7ee0946d1319884c394c4ffd5cd0dda4119107792a78cc4cb54b1b331c13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ygeno.2007.03.015$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,778,782,3539,27911,27912,45982</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18901264$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17498923$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhou, Peng</creatorcontrib><creatorcontrib>Wen, Ji</creatorcontrib><creatorcontrib>Oren, Aharon</creatorcontrib><creatorcontrib>Chen, Ming</creatorcontrib><creatorcontrib>Wu, Min</creatorcontrib><title>Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae)</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>We have investigated the strategy of
Halobacterium sp. NRC-1 and other members of the family Halobacteriaceae to survive ultraviolet (UV) irradiation, based on an integrated analysis of various genomic and proteomic features such as dinucleotide composition and distribution of tetranucleotides in the genome and amino acid composition of the proteins. The low dipyrimidine content may help
Halobacterium reduce formation of photoproducts in its genome. The usage of residues susceptible to reactive oxygen species attack is reduced significantly in
Halobacterium, which helps the organism to minimize protein damage. We then correlated the expression of the
zim gene with the genomic structure to reexamine the importance of the putative mismatch repair pathway proposed previously. Our results showed that
Halobacterium sp. NRC-1 and other haloarchaea (
Haloarcula marismortui,
Haloquadratum walsbyi) have optimized their genomic and proteomic structures to reduce damage induced by UV irradiation, often present at high levels in habitats where these organisms thrive.</description><subject>Amino acid composition</subject><subject>Biological and medical sciences</subject><subject>CTAG pattern</subject><subject>Cytosine - chemistry</subject><subject>Cytosine - radiation effects</subject><subject>Dipyrimidine composition</subject><subject>DNA, Archaeal - chemistry</subject><subject>DNA, Archaeal - radiation effects</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes. Genome</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genome, Archaeal - genetics</subject><subject>Genomic structure</subject><subject>Haloarcula marismortui</subject><subject>Halobacteriaceae</subject><subject>Halobacteriaceae - genetics</subject><subject>Halobacteriaceae - radiation effects</subject><subject>Halobacterium</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Radiation Tolerance - genetics</subject><subject>Thymine - chemistry</subject><subject>Thymine - radiation effects</subject><subject>Ultraviolet Rays</subject><subject>UV tolerance</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkcFu1DAURS0EotPCFyAhb0CwSHiOPbG9YIEq2iJVYtO95bw8U4-SSbGTkebvcZiRuoONLVnnXdv3MPZOQC1AtF929fEX7ae6AdA1yBrE9gXbCDC2Mq1qX7INGGMqvVXygl3mvAMAK03zml0IrayxjdywcFsixog8L-lARz4Fnun3QnskHsjPS6LMw5T4MszJH-I00Mznsia_InHPH_0w-YSPnjz_FPwYhyO_K2edx5lS9EiePr9hr4IfMr0971fs4eb7w_Vddf_z9sf1t_sKlTBz1esGNRFY1fZCCmuMQmkVqhD6LfbQ914JYQVobRuvDaLCbqs60UkpUMgr9vEU-5Sm8ok8uzFmpGHwe5qW7DS0EkDq_4LC6nKvhQLKE4hpyjlRcE8pjj4dnQC3anA791eDWzU4kK5oKFPvz_FLN1L_PHPuvQAfzoDP6IewthnzM2csiKZVhft64qiUdoiUXMa4yuljIpxdP8V_PuQPw0KoCQ</recordid><startdate>20070701</startdate><enddate>20070701</enddate><creator>Zhou, Peng</creator><creator>Wen, Ji</creator><creator>Oren, Aharon</creator><creator>Chen, Ming</creator><creator>Wu, Min</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>IQODW</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>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20070701</creationdate><title>Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae)</title><author>Zhou, Peng ; Wen, Ji ; Oren, Aharon ; Chen, Ming ; Wu, Min</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c418t-d72c7ee0946d1319884c394c4ffd5cd0dda4119107792a78cc4cb54b1b331c13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Amino acid composition</topic><topic>Biological and medical sciences</topic><topic>CTAG pattern</topic><topic>Cytosine - chemistry</topic><topic>Cytosine - radiation effects</topic><topic>Dipyrimidine composition</topic><topic>DNA, Archaeal - chemistry</topic><topic>DNA, Archaeal - radiation effects</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes. Genome</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genome, Archaeal - genetics</topic><topic>Genomic structure</topic><topic>Haloarcula marismortui</topic><topic>Halobacteriaceae</topic><topic>Halobacteriaceae - genetics</topic><topic>Halobacteriaceae - radiation effects</topic><topic>Halobacterium</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Radiation Tolerance - genetics</topic><topic>Thymine - chemistry</topic><topic>Thymine - radiation effects</topic><topic>Ultraviolet Rays</topic><topic>UV tolerance</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhou, Peng</creatorcontrib><creatorcontrib>Wen, Ji</creatorcontrib><creatorcontrib>Oren, Aharon</creatorcontrib><creatorcontrib>Chen, Ming</creatorcontrib><creatorcontrib>Wu, Min</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhou, Peng</au><au>Wen, Ji</au><au>Oren, Aharon</au><au>Chen, Ming</au><au>Wu, Min</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae)</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2007-07-01</date><risdate>2007</risdate><volume>90</volume><issue>1</issue><spage>103</spage><epage>109</epage><pages>103-109</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>We have investigated the strategy of
Halobacterium sp. NRC-1 and other members of the family Halobacteriaceae to survive ultraviolet (UV) irradiation, based on an integrated analysis of various genomic and proteomic features such as dinucleotide composition and distribution of tetranucleotides in the genome and amino acid composition of the proteins. The low dipyrimidine content may help
Halobacterium reduce formation of photoproducts in its genome. The usage of residues susceptible to reactive oxygen species attack is reduced significantly in
Halobacterium, which helps the organism to minimize protein damage. We then correlated the expression of the
zim gene with the genomic structure to reexamine the importance of the putative mismatch repair pathway proposed previously. Our results showed that
Halobacterium sp. NRC-1 and other haloarchaea (
Haloarcula marismortui,
Haloquadratum walsbyi) have optimized their genomic and proteomic structures to reduce damage induced by UV irradiation, often present at high levels in habitats where these organisms thrive.</abstract><cop>San Diego, CA</cop><pub>Elsevier Inc</pub><pmid>17498923</pmid><doi>10.1016/j.ygeno.2007.03.015</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; ScienceDirect Journals (5 years ago - present) |
| subjects | Amino acid composition Biological and medical sciences CTAG pattern Cytosine - chemistry Cytosine - radiation effects Dipyrimidine composition DNA, Archaeal - chemistry DNA, Archaeal - radiation effects Fundamental and applied biological sciences. Psychology Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Genome, Archaeal - genetics Genomic structure Haloarcula marismortui Halobacteriaceae Halobacteriaceae - genetics Halobacteriaceae - radiation effects Halobacterium Molecular and cellular biology Molecular genetics Radiation Tolerance - genetics Thymine - chemistry Thymine - radiation effects Ultraviolet Rays UV tolerance |
| title | Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae) |
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