Intergenic regions of <it>Borrelia </it>plasmids contain phylogenetically conserved RNA secondary structure motifs
<p>Abstract</p> <p>Background</p> <p><it>Borrelia </it>species are unusual in that they contain a large number of linear and circular plasmids. Many of these plasmids have long intergenic regions. These regions have many fragmented genes, repeated sequences...
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| Format: | Article |
| Language: | English |
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BMC
2009-03-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/10/101 |
| _version_ | 1818119200695123968 |
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| author | Delihas Nicholas |
| author_facet | Delihas Nicholas |
| author_sort | Delihas Nicholas |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Borrelia </it>species are unusual in that they contain a large number of linear and circular plasmids. Many of these plasmids have long intergenic regions. These regions have many fragmented genes, repeated sequences and appear to be in a state of flux, but they may serve as reservoirs for evolutionary change and/or maintain stable motifs such as small RNA genes.</p> <p>Results</p> <p>In an in silico study, intergenic regions of <it>Borrelia </it>plasmids were scanned for phylogenetically conserved stem loop structures that may represent functional units at the RNA level. Five repeat sequences were found that could fold into stable RNA-type stem loop structures, three of which are closely linked to protein genes, one of which is a member of the <it>Borrelia </it>lipoprotein_1 super family genes and another is the complement regulator-acquiring surface protein_1 (CRASP-1) family. Modeled secondary structures of repeat sequences display numerous base-pair compensatory changes in stem regions, including C-G→A-U transversions when orthologous sequences are compared. Base-pair compensatory changes constitute strong evidence for phylogenetic conservation of secondary structure.</p> <p>Conclusion</p> <p>Intergenic regions of <it>Borrelia </it>species carry evolutionarily stable RNA secondary structure motifs. Of major interest is that some motifs are associated with protein genes that show large sequence variability. The cell may conserve these RNA motifs whereas allow a large flux in amino acid sequence, possibly to create new virulence factors but with associated RNA motifs intact.</p> |
| first_indexed | 2024-12-11T05:06:25Z |
| format | Article |
| id | doaj.art-e7f84b26b77a47deba0fd94f013fd090 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-11T05:06:25Z |
| publishDate | 2009-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e7f84b26b77a47deba0fd94f013fd0902022-12-22T01:20:01ZengBMCBMC Genomics1471-21642009-03-0110110110.1186/1471-2164-10-101Intergenic regions of <it>Borrelia </it>plasmids contain phylogenetically conserved RNA secondary structure motifsDelihas Nicholas<p>Abstract</p> <p>Background</p> <p><it>Borrelia </it>species are unusual in that they contain a large number of linear and circular plasmids. Many of these plasmids have long intergenic regions. These regions have many fragmented genes, repeated sequences and appear to be in a state of flux, but they may serve as reservoirs for evolutionary change and/or maintain stable motifs such as small RNA genes.</p> <p>Results</p> <p>In an in silico study, intergenic regions of <it>Borrelia </it>plasmids were scanned for phylogenetically conserved stem loop structures that may represent functional units at the RNA level. Five repeat sequences were found that could fold into stable RNA-type stem loop structures, three of which are closely linked to protein genes, one of which is a member of the <it>Borrelia </it>lipoprotein_1 super family genes and another is the complement regulator-acquiring surface protein_1 (CRASP-1) family. Modeled secondary structures of repeat sequences display numerous base-pair compensatory changes in stem regions, including C-G→A-U transversions when orthologous sequences are compared. Base-pair compensatory changes constitute strong evidence for phylogenetic conservation of secondary structure.</p> <p>Conclusion</p> <p>Intergenic regions of <it>Borrelia </it>species carry evolutionarily stable RNA secondary structure motifs. Of major interest is that some motifs are associated with protein genes that show large sequence variability. The cell may conserve these RNA motifs whereas allow a large flux in amino acid sequence, possibly to create new virulence factors but with associated RNA motifs intact.</p>http://www.biomedcentral.com/1471-2164/10/101 |
| spellingShingle | Delihas Nicholas Intergenic regions of <it>Borrelia </it>plasmids contain phylogenetically conserved RNA secondary structure motifs BMC Genomics |
| title | Intergenic regions of <it>Borrelia </it>plasmids contain phylogenetically conserved RNA secondary structure motifs |
| title_full | Intergenic regions of <it>Borrelia </it>plasmids contain phylogenetically conserved RNA secondary structure motifs |
| title_fullStr | Intergenic regions of <it>Borrelia </it>plasmids contain phylogenetically conserved RNA secondary structure motifs |
| title_full_unstemmed | Intergenic regions of <it>Borrelia </it>plasmids contain phylogenetically conserved RNA secondary structure motifs |
| title_short | Intergenic regions of <it>Borrelia </it>plasmids contain phylogenetically conserved RNA secondary structure motifs |
| title_sort | intergenic regions of it borrelia it plasmids contain phylogenetically conserved rna secondary structure motifs |
| url | http://www.biomedcentral.com/1471-2164/10/101 |
| work_keys_str_mv | AT delihasnicholas intergenicregionsofitborreliaitplasmidscontainphylogeneticallyconservedrnasecondarystructuremotifs |