Comprehensive phylogenetic analysis of bacterial reverse transcriptases.
Much less is known about reverse transcriptases (RTs) in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like se...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4244168?pdf=render |
| _version_ | 1818063824687726592 |
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| author | Nicolás Toro Rafael Nisa-Martínez |
| author_facet | Nicolás Toro Rafael Nisa-Martínez |
| author_sort | Nicolás Toro |
| collection | DOAJ |
| description | Much less is known about reverse transcriptases (RTs) in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center) platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity) per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs), Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L), and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology. |
| first_indexed | 2024-12-10T14:26:15Z |
| format | Article |
| id | doaj.art-834410eaeb1b4dde8b4766637c1f4753 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T14:26:15Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-834410eaeb1b4dde8b4766637c1f47532022-12-22T01:45:05ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-01911e11408310.1371/journal.pone.0114083Comprehensive phylogenetic analysis of bacterial reverse transcriptases.Nicolás ToroRafael Nisa-MartínezMuch less is known about reverse transcriptases (RTs) in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center) platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity) per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs), Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L), and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology.http://europepmc.org/articles/PMC4244168?pdf=render |
| spellingShingle | Nicolás Toro Rafael Nisa-Martínez Comprehensive phylogenetic analysis of bacterial reverse transcriptases. PLoS ONE |
| title | Comprehensive phylogenetic analysis of bacterial reverse transcriptases. |
| title_full | Comprehensive phylogenetic analysis of bacterial reverse transcriptases. |
| title_fullStr | Comprehensive phylogenetic analysis of bacterial reverse transcriptases. |
| title_full_unstemmed | Comprehensive phylogenetic analysis of bacterial reverse transcriptases. |
| title_short | Comprehensive phylogenetic analysis of bacterial reverse transcriptases. |
| title_sort | comprehensive phylogenetic analysis of bacterial reverse transcriptases |
| url | http://europepmc.org/articles/PMC4244168?pdf=render |
| work_keys_str_mv | AT nicolastoro comprehensivephylogeneticanalysisofbacterialreversetranscriptases AT rafaelnisamartinez comprehensivephylogeneticanalysisofbacterialreversetranscriptases |