New criteria for selecting the origin of DNA replication in <it>Wolbachia </it>and closely related bacteria
<p>Abstract</p> <p>Background</p> <p>The annotated genomes of two closely related strains of the intracellular bacterium <it>Wolbachia pipientis </it>have been reported without the identifications of the putative origin of replication (<it>ori</it&g...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2007-06-01
|
| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/8/182 |
| _version_ | 1811295102520262656 |
|---|---|
| author | Baldo Laura Bordenstein Seth R Tsiamis Georgios Siozios Stefanos Sapountzis Panagiotis Hotopp Julie Ioannidis Panagiotis Werren John H Bourtzis Kostas |
| author_facet | Baldo Laura Bordenstein Seth R Tsiamis Georgios Siozios Stefanos Sapountzis Panagiotis Hotopp Julie Ioannidis Panagiotis Werren John H Bourtzis Kostas |
| author_sort | Baldo Laura |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The annotated genomes of two closely related strains of the intracellular bacterium <it>Wolbachia pipientis </it>have been reported without the identifications of the putative origin of replication (<it>ori</it>). Identifying the <it>ori </it>of these bacteria and related alpha-Proteobacteria as well as their patterns of sequence evolution will aid studies of cell replication and cell density, as well as the potential genetic manipulation of these widespread intracellular bacteria.</p> <p>Results</p> <p>Using features that have been previously experimentally verified in the alpha-Proteobacterium <it>Caulobacter crescentus</it>, the origin of DNA replication (<it>ori</it>) regions were identified <it>in silico </it>for <it>Wolbachia </it>strains and eleven other related bacteria belonging to <it>Ehrlichia</it>, <it>Anaplasma</it>, and <it>Rickettsia </it>genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in <it>C. crescentus</it>. The <it>Wolbachia ori </it>boundary genes were found to be <it>hemE </it>and COG1253 protein (CBS domain protein). Comparisons of the putative <it>ori </it>region among related <it>Wolbachia </it>strains showed higher conservation of bases within binding sites.</p> <p>Conclusion</p> <p>The sequences of the <it>ori </it>regions described here are only similar among closely related bacteria while fundamental characteristics like presence of DnaA and IHF binding sites as well as the boundary genes are more widely conserved. The relative paucity of CtrA binding sites in the <it>ori </it>regions, as well as the absence of key enzymes associated with DNA replication in the respective genomes, suggest that several of these obligate intracellular bacteria may have altered replication mechanisms. Based on these analyses, criteria are set forth for identifying the <it>ori </it>region in genome sequencing projects.</p> |
| first_indexed | 2024-04-13T05:27:31Z |
| format | Article |
| id | doaj.art-5abe3a4874e34282bb307d95fa2bb16b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T05:27:31Z |
| publishDate | 2007-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-5abe3a4874e34282bb307d95fa2bb16b2022-12-22T03:00:32ZengBMCBMC Genomics1471-21642007-06-018118210.1186/1471-2164-8-182New criteria for selecting the origin of DNA replication in <it>Wolbachia </it>and closely related bacteriaBaldo LauraBordenstein Seth RTsiamis GeorgiosSiozios StefanosSapountzis PanagiotisHotopp JulieIoannidis PanagiotisWerren John HBourtzis Kostas<p>Abstract</p> <p>Background</p> <p>The annotated genomes of two closely related strains of the intracellular bacterium <it>Wolbachia pipientis </it>have been reported without the identifications of the putative origin of replication (<it>ori</it>). Identifying the <it>ori </it>of these bacteria and related alpha-Proteobacteria as well as their patterns of sequence evolution will aid studies of cell replication and cell density, as well as the potential genetic manipulation of these widespread intracellular bacteria.</p> <p>Results</p> <p>Using features that have been previously experimentally verified in the alpha-Proteobacterium <it>Caulobacter crescentus</it>, the origin of DNA replication (<it>ori</it>) regions were identified <it>in silico </it>for <it>Wolbachia </it>strains and eleven other related bacteria belonging to <it>Ehrlichia</it>, <it>Anaplasma</it>, and <it>Rickettsia </it>genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in <it>C. crescentus</it>. The <it>Wolbachia ori </it>boundary genes were found to be <it>hemE </it>and COG1253 protein (CBS domain protein). Comparisons of the putative <it>ori </it>region among related <it>Wolbachia </it>strains showed higher conservation of bases within binding sites.</p> <p>Conclusion</p> <p>The sequences of the <it>ori </it>regions described here are only similar among closely related bacteria while fundamental characteristics like presence of DnaA and IHF binding sites as well as the boundary genes are more widely conserved. The relative paucity of CtrA binding sites in the <it>ori </it>regions, as well as the absence of key enzymes associated with DNA replication in the respective genomes, suggest that several of these obligate intracellular bacteria may have altered replication mechanisms. Based on these analyses, criteria are set forth for identifying the <it>ori </it>region in genome sequencing projects.</p>http://www.biomedcentral.com/1471-2164/8/182 |
| spellingShingle | Baldo Laura Bordenstein Seth R Tsiamis Georgios Siozios Stefanos Sapountzis Panagiotis Hotopp Julie Ioannidis Panagiotis Werren John H Bourtzis Kostas New criteria for selecting the origin of DNA replication in <it>Wolbachia </it>and closely related bacteria BMC Genomics |
| title | New criteria for selecting the origin of DNA replication in <it>Wolbachia </it>and closely related bacteria |
| title_full | New criteria for selecting the origin of DNA replication in <it>Wolbachia </it>and closely related bacteria |
| title_fullStr | New criteria for selecting the origin of DNA replication in <it>Wolbachia </it>and closely related bacteria |
| title_full_unstemmed | New criteria for selecting the origin of DNA replication in <it>Wolbachia </it>and closely related bacteria |
| title_short | New criteria for selecting the origin of DNA replication in <it>Wolbachia </it>and closely related bacteria |
| title_sort | new criteria for selecting the origin of dna replication in it wolbachia it and closely related bacteria |
| url | http://www.biomedcentral.com/1471-2164/8/182 |
| work_keys_str_mv | AT baldolaura newcriteriaforselectingtheoriginofdnareplicationinitwolbachiaitandcloselyrelatedbacteria AT bordensteinsethr newcriteriaforselectingtheoriginofdnareplicationinitwolbachiaitandcloselyrelatedbacteria AT tsiamisgeorgios newcriteriaforselectingtheoriginofdnareplicationinitwolbachiaitandcloselyrelatedbacteria AT sioziosstefanos newcriteriaforselectingtheoriginofdnareplicationinitwolbachiaitandcloselyrelatedbacteria AT sapountzispanagiotis newcriteriaforselectingtheoriginofdnareplicationinitwolbachiaitandcloselyrelatedbacteria AT hotoppjulie newcriteriaforselectingtheoriginofdnareplicationinitwolbachiaitandcloselyrelatedbacteria AT ioannidispanagiotis newcriteriaforselectingtheoriginofdnareplicationinitwolbachiaitandcloselyrelatedbacteria AT werrenjohnh newcriteriaforselectingtheoriginofdnareplicationinitwolbachiaitandcloselyrelatedbacteria AT bourtziskostas newcriteriaforselectingtheoriginofdnareplicationinitwolbachiaitandcloselyrelatedbacteria |