Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis
The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any prot...
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| description | The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of various organisms, including B.subtilis. The B. halodurans genome contains 112 transposase genes, indicating that transposases have played an important evolutionary role in horizontal gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment. |
| doi_str_mv | 10.1093/nar/28.21.4317 |
| format | Article |
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Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of various organisms, including B.subtilis. The B. halodurans genome contains 112 transposase genes, indicating that transposases have played an important evolutionary role in horizontal gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment.</description><identifier>ISSN: 1362-4962</identifier><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/28.21.4317</identifier><identifier>PMID: 11058132</identifier><identifier>CODEN: NARHAD</identifier><language>eng</language><publisher>England: Oxford Publishing Limited (England)</publisher><subject>Adaptation, Physiological - genetics ; Alkalies - metabolism ; alkaliphilic bacteria ; ATP-Binding Cassette Transporters - genetics ; Bacillus - chemistry ; Bacillus - classification ; Bacillus - genetics ; Bacillus - metabolism ; Bacillus halodurans ; Bacillus subtilis ; Bacillus subtilis - chemistry ; Bacillus subtilis - genetics ; Bacterial Proteins - genetics ; Bacterial Proteins - physiology ; Base Composition ; Biological Transport ; Cell Wall - genetics ; Cell Wall - metabolism ; Conserved Sequence - genetics ; Databases as Topic ; DNA Transposable Elements - genetics ; Energy Metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal - genetics ; Genes, Bacterial - genetics ; Genes, Bacterial - physiology ; Genome, Bacterial ; Molecular Sequence Data ; Open Reading Frames - genetics ; Physical Chromosome Mapping ; Protein Biosynthesis ; Replication Origin - genetics ; RNA, Transfer - genetics ; Sequence Homology ; Sigma Factor - genetics ; Spores, Bacterial - genetics ; Transcription, Genetic - genetics ; transposase ; Transposases - genetics</subject><ispartof>Nucleic acids research, 2000-11, Vol.28 (21), p.4317-4331</ispartof><rights>Copyright Oxford University Press(England) Nov 1, 2000</rights><rights>Copyright © 2000 Oxford University Press 2000</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c443t-52a82af8eff3098bf6c2ba29f5495c6c78328bf8f9003b91a33d9df9515f8ffa3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC113120/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC113120/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,315,729,782,786,887,27933,27934,53800,53802</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11058132$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Takami, H</creatorcontrib><creatorcontrib>Nakasone, K</creatorcontrib><creatorcontrib>Takaki, Y</creatorcontrib><creatorcontrib>Maeno, G</creatorcontrib><creatorcontrib>Sasaki, R</creatorcontrib><creatorcontrib>Masui, N</creatorcontrib><creatorcontrib>Fuji, F</creatorcontrib><creatorcontrib>Hirama, C</creatorcontrib><creatorcontrib>Nakamura, Y</creatorcontrib><creatorcontrib>Ogasawara, N</creatorcontrib><creatorcontrib>Kuhara, S</creatorcontrib><creatorcontrib>Horikoshi, K</creatorcontrib><title>Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of various organisms, including B.subtilis. The B. halodurans genome contains 112 transposase genes, indicating that transposases have played an important evolutionary role in horizontal gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment.</description><subject>Adaptation, Physiological - genetics</subject><subject>Alkalies - metabolism</subject><subject>alkaliphilic bacteria</subject><subject>ATP-Binding Cassette Transporters - genetics</subject><subject>Bacillus - chemistry</subject><subject>Bacillus - classification</subject><subject>Bacillus - genetics</subject><subject>Bacillus - metabolism</subject><subject>Bacillus halodurans</subject><subject>Bacillus subtilis</subject><subject>Bacillus subtilis - chemistry</subject><subject>Bacillus subtilis - genetics</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - physiology</subject><subject>Base Composition</subject><subject>Biological Transport</subject><subject>Cell Wall - genetics</subject><subject>Cell Wall - metabolism</subject><subject>Conserved Sequence - 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genetics</topic><topic>Alkalies - metabolism</topic><topic>alkaliphilic bacteria</topic><topic>ATP-Binding Cassette Transporters - genetics</topic><topic>Bacillus - chemistry</topic><topic>Bacillus - classification</topic><topic>Bacillus - genetics</topic><topic>Bacillus - metabolism</topic><topic>Bacillus halodurans</topic><topic>Bacillus subtilis</topic><topic>Bacillus subtilis - chemistry</topic><topic>Bacillus subtilis - genetics</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - physiology</topic><topic>Base Composition</topic><topic>Biological Transport</topic><topic>Cell Wall - genetics</topic><topic>Cell Wall - metabolism</topic><topic>Conserved Sequence - genetics</topic><topic>Databases as Topic</topic><topic>DNA Transposable Elements - genetics</topic><topic>Energy Metabolism</topic><topic>Evolution, Molecular</topic><topic>Gene Transfer, Horizontal - genetics</topic><topic>Genes, Bacterial - genetics</topic><topic>Genes, Bacterial - physiology</topic><topic>Genome, Bacterial</topic><topic>Molecular Sequence Data</topic><topic>Open Reading Frames - genetics</topic><topic>Physical Chromosome Mapping</topic><topic>Protein Biosynthesis</topic><topic>Replication Origin - genetics</topic><topic>RNA, Transfer - genetics</topic><topic>Sequence Homology</topic><topic>Sigma Factor - genetics</topic><topic>Spores, Bacterial - genetics</topic><topic>Transcription, Genetic - genetics</topic><topic>transposase</topic><topic>Transposases - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Takami, H</creatorcontrib><creatorcontrib>Nakasone, K</creatorcontrib><creatorcontrib>Takaki, Y</creatorcontrib><creatorcontrib>Maeno, G</creatorcontrib><creatorcontrib>Sasaki, R</creatorcontrib><creatorcontrib>Masui, N</creatorcontrib><creatorcontrib>Fuji, F</creatorcontrib><creatorcontrib>Hirama, C</creatorcontrib><creatorcontrib>Nakamura, Y</creatorcontrib><creatorcontrib>Ogasawara, N</creatorcontrib><creatorcontrib>Kuhara, S</creatorcontrib><creatorcontrib>Horikoshi, K</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</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>Takami, H</au><au>Nakasone, K</au><au>Takaki, Y</au><au>Maeno, G</au><au>Sasaki, R</au><au>Masui, N</au><au>Fuji, F</au><au>Hirama, C</au><au>Nakamura, Y</au><au>Ogasawara, N</au><au>Kuhara, S</au><au>Horikoshi, K</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2000-11-01</date><risdate>2000</risdate><volume>28</volume><issue>21</issue><spage>4317</spage><epage>4331</epage><pages>4317-4331</pages><issn>1362-4962</issn><issn>0305-1048</issn><eissn>1362-4962</eissn><coden>NARHAD</coden><abstract>The 4 202 353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066 predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments, 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no match to any protein database. Among the total CDSs, 8.8% match sequences of proteins found only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of various organisms, including B.subtilis. The B. halodurans genome contains 112 transposase genes, indicating that transposases have played an important evolutionary role in horizontal gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact that competence has not been demonstrated experimentally in C-125. There is no paralog of tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an ortholog of tupA cannot be found in the B.subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment.</abstract><cop>England</cop><pub>Oxford Publishing Limited (England)</pub><pmid>11058132</pmid><doi>10.1093/nar/28.21.4317</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adaptation, Physiological - genetics Alkalies - metabolism alkaliphilic bacteria ATP-Binding Cassette Transporters - genetics Bacillus - chemistry Bacillus - classification Bacillus - genetics Bacillus - metabolism Bacillus halodurans Bacillus subtilis Bacillus subtilis - chemistry Bacillus subtilis - genetics Bacterial Proteins - genetics Bacterial Proteins - physiology Base Composition Biological Transport Cell Wall - genetics Cell Wall - metabolism Conserved Sequence - genetics Databases as Topic DNA Transposable Elements - genetics Energy Metabolism Evolution, Molecular Gene Transfer, Horizontal - genetics Genes, Bacterial - genetics Genes, Bacterial - physiology Genome, Bacterial Molecular Sequence Data Open Reading Frames - genetics Physical Chromosome Mapping Protein Biosynthesis Replication Origin - genetics RNA, Transfer - genetics Sequence Homology Sigma Factor - genetics Spores, Bacterial - genetics Transcription, Genetic - genetics transposase Transposases - genetics |
| title | Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis |
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