Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from Gram-positive bacteria
Abstract Most small plasmids of Gram-positive bacteria use the rolling-circle mechanism of replication and several of these have been studied in considerable detail at the DNA level and for the function of their genes. Although most of the common laboratory Bacillus subtilis 168 strains do not conta...
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| Veröffentlicht in: | FEMS microbiology reviews 1998-02, Vol.21 (4), p.337-368 |
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| creator | Meijer, Wilfried J.J. Wisman, G. Bea A. Terpstra, Peter Thorsted, Peter B. Thomas, Chris M. Holsappel, S. Venema, Gerard Bron, Sierd |
| description | Abstract
Most small plasmids of Gram-positive bacteria use the rolling-circle mechanism of replication and several of these have been studied in considerable detail at the DNA level and for the function of their genes. Although most of the common laboratory Bacillus subtilis 168 strains do not contain plasmids, several industrial strains and natural soil isolates do contain rolling-circle replicating (RCR) plasmids. So far, knowledge about these plasmids was mainly limited to: (i) a classification into seven groups, based on size and restriction patterns; and (ii) DNA sequences of the replication region of a limited number of them. To increase the knowledge, also with respect to other functions specified by these plasmids, we have determined the complete DNA sequence of four plasmids, representing different groups, and performed computer-assisted and experimental analyses on the possible function of their genes. The plasmids analyzed are pTA1015 (5.8 kbp), pTA1040 (7.8 kbp), pTA1050 (8.4 kbp), and pTA1060 (8.7 kbp). These plasmids have a structural organization similar to most other known RCR plasmids. They contain highly related replication functions, both for leading and lagging strand synthesis. pTA1015 and pTA1060 contain a mobilization gene enabling their conjugative transfer. Strikingly, in addition to the conserved replication modules, these plasmids contain unique module(s) with genes which are not present on known RCR plasmids of other Gram-positive bacteria. Examples are genes encoding a type I signal peptidase and genes encoding proteins belonging to the family of response regulator aspartate phosphatases. The latter are likely to be involved in the regulation of post-exponential phase processes. The presence of these modules on plasmids may reflect an adaptation to the special conditions to which the host cells were exposed. |
| doi_str_mv | 10.1111/j.1574-6976.1998.tb00357.x |
| format | Article |
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Most small plasmids of Gram-positive bacteria use the rolling-circle mechanism of replication and several of these have been studied in considerable detail at the DNA level and for the function of their genes. Although most of the common laboratory Bacillus subtilis 168 strains do not contain plasmids, several industrial strains and natural soil isolates do contain rolling-circle replicating (RCR) plasmids. So far, knowledge about these plasmids was mainly limited to: (i) a classification into seven groups, based on size and restriction patterns; and (ii) DNA sequences of the replication region of a limited number of them. To increase the knowledge, also with respect to other functions specified by these plasmids, we have determined the complete DNA sequence of four plasmids, representing different groups, and performed computer-assisted and experimental analyses on the possible function of their genes. The plasmids analyzed are pTA1015 (5.8 kbp), pTA1040 (7.8 kbp), pTA1050 (8.4 kbp), and pTA1060 (8.7 kbp). These plasmids have a structural organization similar to most other known RCR plasmids. They contain highly related replication functions, both for leading and lagging strand synthesis. pTA1015 and pTA1060 contain a mobilization gene enabling their conjugative transfer. Strikingly, in addition to the conserved replication modules, these plasmids contain unique module(s) with genes which are not present on known RCR plasmids of other Gram-positive bacteria. Examples are genes encoding a type I signal peptidase and genes encoding proteins belonging to the family of response regulator aspartate phosphatases. The latter are likely to be involved in the regulation of post-exponential phase processes. The presence of these modules on plasmids may reflect an adaptation to the special conditions to which the host cells were exposed.</description><identifier>ISSN: 0168-6445</identifier><identifier>ISSN: 1574-6976</identifier><identifier>EISSN: 1574-6976</identifier><identifier>DOI: 10.1111/j.1574-6976.1998.tb00357.x</identifier><identifier>PMID: 9532747</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Bacillus subtilis ; Bacillus subtilis - genetics ; Bacteria ; Bacteriology ; Biological and medical sciences ; Deoxyribonucleic acid ; DNA ; DNA biosynthesis ; DNA Replication ; Fundamental and applied biological sciences. Psychology ; Gene sequencing ; Genes ; Genes, Bacterial - genetics ; Genetics ; Gram-positive bacteria ; Gram-Positive Bacteria - genetics ; Industrial strains ; Microbiology ; Mobilization ; Modules ; Molecular Sequence Data ; Nucleotide sequence ; Nucleotides ; Plasmids ; Plasmids - genetics ; Replication ; Replication module ; Response aspartate phosphatase ; Rolling‐circle plasmid ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Signal peptidase ; Soil isolates ; Strains (organisms)</subject><ispartof>FEMS microbiology reviews, 1998-02, Vol.21 (4), p.337-368</ispartof><rights>1998 Federation of European Microbiological Societies. 1998</rights><rights>1998 INIST-CNRS</rights><rights>1998 Federation of European Microbiological Societies.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4047-8298c3fc4203db783919ff8b8b43d1a9a66bffbe42314f8c273c591c35f920033</citedby><cites>FETCH-LOGICAL-c4047-8298c3fc4203db783919ff8b8b43d1a9a66bffbe42314f8c273c591c35f920033</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1574-6976.1998.tb00357.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1574-6976.1998.tb00357.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=2232520$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/9532747$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Meijer, Wilfried J.J.</creatorcontrib><creatorcontrib>Wisman, G. Bea A.</creatorcontrib><creatorcontrib>Terpstra, Peter</creatorcontrib><creatorcontrib>Thorsted, Peter B.</creatorcontrib><creatorcontrib>Thomas, Chris M.</creatorcontrib><creatorcontrib>Holsappel, S.</creatorcontrib><creatorcontrib>Venema, Gerard</creatorcontrib><creatorcontrib>Bron, Sierd</creatorcontrib><title>Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from Gram-positive bacteria</title><title>FEMS microbiology reviews</title><addtitle>FEMS Microbiol Rev</addtitle><description>Abstract
Most small plasmids of Gram-positive bacteria use the rolling-circle mechanism of replication and several of these have been studied in considerable detail at the DNA level and for the function of their genes. Although most of the common laboratory Bacillus subtilis 168 strains do not contain plasmids, several industrial strains and natural soil isolates do contain rolling-circle replicating (RCR) plasmids. So far, knowledge about these plasmids was mainly limited to: (i) a classification into seven groups, based on size and restriction patterns; and (ii) DNA sequences of the replication region of a limited number of them. To increase the knowledge, also with respect to other functions specified by these plasmids, we have determined the complete DNA sequence of four plasmids, representing different groups, and performed computer-assisted and experimental analyses on the possible function of their genes. The plasmids analyzed are pTA1015 (5.8 kbp), pTA1040 (7.8 kbp), pTA1050 (8.4 kbp), and pTA1060 (8.7 kbp). These plasmids have a structural organization similar to most other known RCR plasmids. They contain highly related replication functions, both for leading and lagging strand synthesis. pTA1015 and pTA1060 contain a mobilization gene enabling their conjugative transfer. Strikingly, in addition to the conserved replication modules, these plasmids contain unique module(s) with genes which are not present on known RCR plasmids of other Gram-positive bacteria. Examples are genes encoding a type I signal peptidase and genes encoding proteins belonging to the family of response regulator aspartate phosphatases. The latter are likely to be involved in the regulation of post-exponential phase processes. The presence of these modules on plasmids may reflect an adaptation to the special conditions to which the host cells were exposed.</description><subject>Bacillus subtilis</subject><subject>Bacillus subtilis - genetics</subject><subject>Bacteria</subject><subject>Bacteriology</subject><subject>Biological and medical sciences</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA biosynthesis</subject><subject>DNA Replication</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genes, Bacterial - genetics</subject><subject>Genetics</subject><subject>Gram-positive bacteria</subject><subject>Gram-Positive Bacteria - genetics</subject><subject>Industrial strains</subject><subject>Microbiology</subject><subject>Mobilization</subject><subject>Modules</subject><subject>Molecular Sequence Data</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Plasmids</subject><subject>Plasmids - genetics</subject><subject>Replication</subject><subject>Replication module</subject><subject>Response aspartate phosphatase</subject><subject>Rolling‐circle plasmid</subject><subject>Sequence Analysis, DNA</subject><subject>Sequence Homology, Amino Acid</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Signal peptidase</subject><subject>Soil isolates</subject><subject>Strains (organisms)</subject><issn>0168-6445</issn><issn>1574-6976</issn><issn>1574-6976</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1998</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqVUVFv1SAUJkYz59WfYELU-GSvUKCUPZjMxU2TGZNlPhNKYXJDS4XW7f5K_5J0be7Dog-SED4433fO4XwAvMJoi_N6v9tixmlRCV5tsRD1dmwQIoxv7x6B40PoMThGuKqLilL2FDxLaYcQYoKxI3AkGCk55cfg91Xw3vU3hXZRewMHr1Ln2gRtDB38qLTzfkowTc3ovEsnUIdu8GY0sJ8yP4yuNTCZn5PptUlQ9W3eyu9TvgQLb0y_gOH6FCPM3i2AohUwdC-5x1V-nC9zBRVdCn2Ct278AaPxajTtg94uouqKISQ3ul8GNkqPJjr1HDyxyifzYj034Pv5p-uzz8Xlt4svZ6eXhaaI8qIuRa2J1bREpG14TQQW1tZN3VDSYiVUVTXWNoaWBFNb65ITzQTWhFlR5lmTDXi75B1iyJ9Po-xc0sZ71ZswJckF56RGOBNfPyDuwhTziJIsCSFViWglMutkYekYUorGyiG6TsW9xEjOnsudnI2Vs7Fy9lyunsu7LH65lpiazrQH6Wpyjr9Z4ypp5W1UvXbpQCtLUrI8hw34sNBunTf7_2hAnn-9ImSuw5YEYRr-IS_-1v8fQCbY3g</recordid><startdate>199802</startdate><enddate>199802</enddate><creator>Meijer, Wilfried J.J.</creator><creator>Wisman, G. Bea A.</creator><creator>Terpstra, Peter</creator><creator>Thorsted, Peter B.</creator><creator>Thomas, Chris M.</creator><creator>Holsappel, S.</creator><creator>Venema, Gerard</creator><creator>Bron, Sierd</creator><general>Blackwell Publishing Ltd</general><general>Blackwell</general><general>Oxford University Press</general><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>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>199802</creationdate><title>Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from Gram-positive bacteria</title><author>Meijer, Wilfried J.J. ; Wisman, G. Bea A. ; Terpstra, Peter ; Thorsted, Peter B. ; Thomas, Chris M. ; Holsappel, S. ; Venema, Gerard ; Bron, Sierd</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4047-8298c3fc4203db783919ff8b8b43d1a9a66bffbe42314f8c273c591c35f920033</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1998</creationdate><topic>Bacillus subtilis</topic><topic>Bacillus subtilis - genetics</topic><topic>Bacteria</topic><topic>Bacteriology</topic><topic>Biological and medical sciences</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA biosynthesis</topic><topic>DNA Replication</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genes, Bacterial - genetics</topic><topic>Genetics</topic><topic>Gram-positive bacteria</topic><topic>Gram-Positive Bacteria - genetics</topic><topic>Industrial strains</topic><topic>Microbiology</topic><topic>Mobilization</topic><topic>Modules</topic><topic>Molecular Sequence Data</topic><topic>Nucleotide sequence</topic><topic>Nucleotides</topic><topic>Plasmids</topic><topic>Plasmids - genetics</topic><topic>Replication</topic><topic>Replication module</topic><topic>Response aspartate phosphatase</topic><topic>Rolling‐circle plasmid</topic><topic>Sequence Analysis, DNA</topic><topic>Sequence Homology, Amino Acid</topic><topic>Sequence Homology, Nucleic Acid</topic><topic>Signal peptidase</topic><topic>Soil isolates</topic><topic>Strains (organisms)</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Meijer, Wilfried J.J.</creatorcontrib><creatorcontrib>Wisman, G. Bea A.</creatorcontrib><creatorcontrib>Terpstra, Peter</creatorcontrib><creatorcontrib>Thorsted, Peter B.</creatorcontrib><creatorcontrib>Thomas, Chris M.</creatorcontrib><creatorcontrib>Holsappel, S.</creatorcontrib><creatorcontrib>Venema, Gerard</creatorcontrib><creatorcontrib>Bron, Sierd</creatorcontrib><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>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>FEMS microbiology reviews</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Meijer, Wilfried J.J.</au><au>Wisman, G. Bea A.</au><au>Terpstra, Peter</au><au>Thorsted, Peter B.</au><au>Thomas, Chris M.</au><au>Holsappel, S.</au><au>Venema, Gerard</au><au>Bron, Sierd</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from Gram-positive bacteria</atitle><jtitle>FEMS microbiology reviews</jtitle><addtitle>FEMS Microbiol Rev</addtitle><date>1998-02</date><risdate>1998</risdate><volume>21</volume><issue>4</issue><spage>337</spage><epage>368</epage><pages>337-368</pages><issn>0168-6445</issn><issn>1574-6976</issn><eissn>1574-6976</eissn><abstract>Abstract
Most small plasmids of Gram-positive bacteria use the rolling-circle mechanism of replication and several of these have been studied in considerable detail at the DNA level and for the function of their genes. Although most of the common laboratory Bacillus subtilis 168 strains do not contain plasmids, several industrial strains and natural soil isolates do contain rolling-circle replicating (RCR) plasmids. So far, knowledge about these plasmids was mainly limited to: (i) a classification into seven groups, based on size and restriction patterns; and (ii) DNA sequences of the replication region of a limited number of them. To increase the knowledge, also with respect to other functions specified by these plasmids, we have determined the complete DNA sequence of four plasmids, representing different groups, and performed computer-assisted and experimental analyses on the possible function of their genes. The plasmids analyzed are pTA1015 (5.8 kbp), pTA1040 (7.8 kbp), pTA1050 (8.4 kbp), and pTA1060 (8.7 kbp). These plasmids have a structural organization similar to most other known RCR plasmids. They contain highly related replication functions, both for leading and lagging strand synthesis. pTA1015 and pTA1060 contain a mobilization gene enabling their conjugative transfer. Strikingly, in addition to the conserved replication modules, these plasmids contain unique module(s) with genes which are not present on known RCR plasmids of other Gram-positive bacteria. Examples are genes encoding a type I signal peptidase and genes encoding proteins belonging to the family of response regulator aspartate phosphatases. The latter are likely to be involved in the regulation of post-exponential phase processes. The presence of these modules on plasmids may reflect an adaptation to the special conditions to which the host cells were exposed.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>9532747</pmid><doi>10.1111/j.1574-6976.1998.tb00357.x</doi><tpages>32</tpages></addata></record> |
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| ispartof | FEMS microbiology reviews, 1998-02, Vol.21 (4), p.337-368 |
| issn | 0168-6445 1574-6976 1574-6976 |
| language | eng |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Access via Wiley Online Library; Oxford Journals Open Access Collection; Alma/SFX Local Collection |
| subjects | Bacillus subtilis Bacillus subtilis - genetics Bacteria Bacteriology Biological and medical sciences Deoxyribonucleic acid DNA DNA biosynthesis DNA Replication Fundamental and applied biological sciences. Psychology Gene sequencing Genes Genes, Bacterial - genetics Genetics Gram-positive bacteria Gram-Positive Bacteria - genetics Industrial strains Microbiology Mobilization Modules Molecular Sequence Data Nucleotide sequence Nucleotides Plasmids Plasmids - genetics Replication Replication module Response aspartate phosphatase Rolling‐circle plasmid Sequence Analysis, DNA Sequence Homology, Amino Acid Sequence Homology, Nucleic Acid Signal peptidase Soil isolates Strains (organisms) |
| title | Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from Gram-positive bacteria |
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