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A diversity of uncharacterized reverse transcriptases in bacteria.

Simon DM, Zimmerly S - Nucleic Acids Res. (2008)

Bottom Line: Here, we present the results of a bioinformatic survey that aims to define the landscape of RTs across eubacterial, archaeal and phage genomes.Surprisingly, a plethora of novel RTs are found that do not belong to characterized classes.The study lays the groundwork for experimental characterization of these highly diverse sequences and has implications for the evolution of retroelements.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

ABSTRACT
Retroelements are usually considered to be eukaryotic elements because of the large number and variety in eukaryotic genomes. By comparison, reverse transcriptases (RTs) are rare in bacteria, with only three characterized classes: retrons, group II introns and diversity-generating retroelements (DGRs). Here, we present the results of a bioinformatic survey that aims to define the landscape of RTs across eubacterial, archaeal and phage genomes. We identify and categorize 1021 RTs, of which the majority are group II introns (73%). Surprisingly, a plethora of novel RTs are found that do not belong to characterized classes. The RTs have 11 domain architectures and are classified into 20 groupings based on sequence similarity, phylogenetic analyses and open reading frame domain structures. Interestingly, group II introns are the only bacterial RTs to exhibit clear evidence for independent mobility, while five other groups have putative functions in defense against phage infection or promotion of phage infection. These examples suggest that additional beneficial functions will be discovered among uncharacterized RTs. The study lays the groundwork for experimental characterization of these highly diverse sequences and has implications for the evolution of retroelements.

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A maximum likelihood tree of group II introns and group II-like (G2L) RTs. Group II introns include representatives of the major intron classes [B–F, mitochondria-like (ML), chloroplast-like (CL)] as well as one that is currently unclassified (G2). Group II-like classes (G2L1–G2L5) are highlighted with gray ovals. Nodes that have a bootstrap value ⩾70 are indicated with black circles. The tree file with GenBank gene identification numbers is available in Supplementary Data S2.
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Figure 2: A maximum likelihood tree of group II introns and group II-like (G2L) RTs. Group II introns include representatives of the major intron classes [B–F, mitochondria-like (ML), chloroplast-like (CL)] as well as one that is currently unclassified (G2). Group II-like classes (G2L1–G2L5) are highlighted with gray ovals. Nodes that have a bootstrap value ⩾70 are indicated with black circles. The tree file with GenBank gene identification numbers is available in Supplementary Data S2.

Mentions: The remaining 146 ORFs were further analyzed by manual alignment and BLASTP searches to confirm that they are bacterial RTs rather than nonspecific BLAST hits. In total, 121 ORFs were alignable with RT motifs, but three of these were discarded as eukaryotic RTs. In the end, 80 RTs were assigned to 14 additional groups based on reciprocal local BLAST best-hits, shared features outside of the RT domains, and in some cases phylogenetic support (Figures 1 and 2). Thirty-eight RTs remain unclassified because they form less convincing groups or groups of two members.Figure 2.


A diversity of uncharacterized reverse transcriptases in bacteria.

Simon DM, Zimmerly S - Nucleic Acids Res. (2008)

A maximum likelihood tree of group II introns and group II-like (G2L) RTs. Group II introns include representatives of the major intron classes [B–F, mitochondria-like (ML), chloroplast-like (CL)] as well as one that is currently unclassified (G2). Group II-like classes (G2L1–G2L5) are highlighted with gray ovals. Nodes that have a bootstrap value ⩾70 are indicated with black circles. The tree file with GenBank gene identification numbers is available in Supplementary Data S2.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2602772&req=5

Figure 2: A maximum likelihood tree of group II introns and group II-like (G2L) RTs. Group II introns include representatives of the major intron classes [B–F, mitochondria-like (ML), chloroplast-like (CL)] as well as one that is currently unclassified (G2). Group II-like classes (G2L1–G2L5) are highlighted with gray ovals. Nodes that have a bootstrap value ⩾70 are indicated with black circles. The tree file with GenBank gene identification numbers is available in Supplementary Data S2.
Mentions: The remaining 146 ORFs were further analyzed by manual alignment and BLASTP searches to confirm that they are bacterial RTs rather than nonspecific BLAST hits. In total, 121 ORFs were alignable with RT motifs, but three of these were discarded as eukaryotic RTs. In the end, 80 RTs were assigned to 14 additional groups based on reciprocal local BLAST best-hits, shared features outside of the RT domains, and in some cases phylogenetic support (Figures 1 and 2). Thirty-eight RTs remain unclassified because they form less convincing groups or groups of two members.Figure 2.

Bottom Line: Here, we present the results of a bioinformatic survey that aims to define the landscape of RTs across eubacterial, archaeal and phage genomes.Surprisingly, a plethora of novel RTs are found that do not belong to characterized classes.The study lays the groundwork for experimental characterization of these highly diverse sequences and has implications for the evolution of retroelements.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

ABSTRACT
Retroelements are usually considered to be eukaryotic elements because of the large number and variety in eukaryotic genomes. By comparison, reverse transcriptases (RTs) are rare in bacteria, with only three characterized classes: retrons, group II introns and diversity-generating retroelements (DGRs). Here, we present the results of a bioinformatic survey that aims to define the landscape of RTs across eubacterial, archaeal and phage genomes. We identify and categorize 1021 RTs, of which the majority are group II introns (73%). Surprisingly, a plethora of novel RTs are found that do not belong to characterized classes. The RTs have 11 domain architectures and are classified into 20 groupings based on sequence similarity, phylogenetic analyses and open reading frame domain structures. Interestingly, group II introns are the only bacterial RTs to exhibit clear evidence for independent mobility, while five other groups have putative functions in defense against phage infection or promotion of phage infection. These examples suggest that additional beneficial functions will be discovered among uncharacterized RTs. The study lays the groundwork for experimental characterization of these highly diverse sequences and has implications for the evolution of retroelements.

Show MeSH
Related in: MedlinePlus