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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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Phylogenetic distribution of RTs in eubacteria (A) and archaea (B). The size of each sector represents the number of sequenced genomes in GenBank as of 31 July 2007, with actual numbers shown in parentheses beside the phyla listed to the right. Sector colors specify the bacterial group classification. Numbers beside each sector indicate unique full-length RTs within each bacterial phylum (Supplementary Table S3 and footnotes).
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Figure 5: Phylogenetic distribution of RTs in eubacteria (A) and archaea (B). The size of each sector represents the number of sequenced genomes in GenBank as of 31 July 2007, with actual numbers shown in parentheses beside the phyla listed to the right. Sector colors specify the bacterial group classification. Numbers beside each sector indicate unique full-length RTs within each bacterial phylum (Supplementary Table S3 and footnotes).

Mentions: To address the phylogenetic distribution in eubacteria, we considered the RT content of 519 completed genomes. Approximately 25% of the genomes have at least one RT, with 9% containing multiple RTs. These numbers are lower estimates, as they are based on a set of nonredundant RTs, such that very closely related RT copies within a genome (i.e. group II introns and UG4) are counted as a single RT. The RTs are widely distributed across taxa, being found in nearly every eubacterial group (11/14 as defined by NCBI) (Figure 5; Supplementary Table S3). Bacterial groups that lack an RT are also underrepresented in GenBank, as indicated by the number of completed genome sequences (Figure 5). Similarly, the number of RTs in each group is roughly proportional to the number of sequenced genomes, although there are exceptions (compare bacteroidetes/chlorobi group versus mollicutes) (Figure 5). We conclude that RTs do not appear to be excluded from particular bacterial groups or have extreme biases in their distribution.Figure 5.


A diversity of uncharacterized reverse transcriptases in bacteria.

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

Phylogenetic distribution of RTs in eubacteria (A) and archaea (B). The size of each sector represents the number of sequenced genomes in GenBank as of 31 July 2007, with actual numbers shown in parentheses beside the phyla listed to the right. Sector colors specify the bacterial group classification. Numbers beside each sector indicate unique full-length RTs within each bacterial phylum (Supplementary Table S3 and footnotes).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: Phylogenetic distribution of RTs in eubacteria (A) and archaea (B). The size of each sector represents the number of sequenced genomes in GenBank as of 31 July 2007, with actual numbers shown in parentheses beside the phyla listed to the right. Sector colors specify the bacterial group classification. Numbers beside each sector indicate unique full-length RTs within each bacterial phylum (Supplementary Table S3 and footnotes).
Mentions: To address the phylogenetic distribution in eubacteria, we considered the RT content of 519 completed genomes. Approximately 25% of the genomes have at least one RT, with 9% containing multiple RTs. These numbers are lower estimates, as they are based on a set of nonredundant RTs, such that very closely related RT copies within a genome (i.e. group II introns and UG4) are counted as a single RT. The RTs are widely distributed across taxa, being found in nearly every eubacterial group (11/14 as defined by NCBI) (Figure 5; Supplementary Table S3). Bacterial groups that lack an RT are also underrepresented in GenBank, as indicated by the number of completed genome sequences (Figure 5). Similarly, the number of RTs in each group is roughly proportional to the number of sequenced genomes, although there are exceptions (compare bacteroidetes/chlorobi group versus mollicutes) (Figure 5). We conclude that RTs do not appear to be excluded from particular bacterial groups or have extreme biases in their distribution.Figure 5.

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