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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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RTs identified in eubacterial, archaeal and phage genomes. RTs were classified based on limited phylogenetic analyses, BLAST scores and sequence examination for synapomorphies. The number of RTs per group is indicated in parentheses and by triangle size. Domain structures are depicted in black (alignable with group II introns), gray (uncertain alignment) and white (lack of alignability). Additional domains, including domains of unknown function (DUFs), are in light gray squares, with parentheses indicating that some members lack the domain. In this figure, the designation of an extension as a DUF indicates that the amino acid sequence is conserved within the group. Groups corresponding to lineages in Kojima and Kanehisa (38) are as follows: G2L1 [H1, H2, H3 in (38)]; G2L2, (H4); UG1 (F1); UG3 (G); UG5 (F2); UG6 (E); UG8 (G); UG9 (D); retrons (A); and DGRs (B, C).
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Figure 1: RTs identified in eubacterial, archaeal and phage genomes. RTs were classified based on limited phylogenetic analyses, BLAST scores and sequence examination for synapomorphies. The number of RTs per group is indicated in parentheses and by triangle size. Domain structures are depicted in black (alignable with group II introns), gray (uncertain alignment) and white (lack of alignability). Additional domains, including domains of unknown function (DUFs), are in light gray squares, with parentheses indicating that some members lack the domain. In this figure, the designation of an extension as a DUF indicates that the amino acid sequence is conserved within the group. Groups corresponding to lineages in Kojima and Kanehisa (38) are as follows: G2L1 [H1, H2, H3 in (38)]; G2L2, (H4); UG1 (F1); UG3 (G); UG5 (F2); UG6 (E); UG8 (G); UG9 (D); retrons (A); and DGRs (B, C).

Mentions: Classification of Abi RTs is problematic because the three elements reported to have abortive infection properties (AbiA, AbiK and Abi-P2) are distantly related, with only three RT domains alignable between them (Figure 1). One possibility is that Abi elements constitute an extremely diverse but monophyletic lineage of RTs involved in phage abortive infection. Alternatively, multiple lineages of RTs may have evolved roles in abortive infection. In either case, one cannot confidently conclude which other RTs in the set might have abortive infection properties. Hence, we assign only three close relatives as belonging to the AbiK group and eight to the Abi-P2 group, while AbiA has no close relatives.Figure 1.


A diversity of uncharacterized reverse transcriptases in bacteria.

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

RTs identified in eubacterial, archaeal and phage genomes. RTs were classified based on limited phylogenetic analyses, BLAST scores and sequence examination for synapomorphies. The number of RTs per group is indicated in parentheses and by triangle size. Domain structures are depicted in black (alignable with group II introns), gray (uncertain alignment) and white (lack of alignability). Additional domains, including domains of unknown function (DUFs), are in light gray squares, with parentheses indicating that some members lack the domain. In this figure, the designation of an extension as a DUF indicates that the amino acid sequence is conserved within the group. Groups corresponding to lineages in Kojima and Kanehisa (38) are as follows: G2L1 [H1, H2, H3 in (38)]; G2L2, (H4); UG1 (F1); UG3 (G); UG5 (F2); UG6 (E); UG8 (G); UG9 (D); retrons (A); and DGRs (B, C).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: RTs identified in eubacterial, archaeal and phage genomes. RTs were classified based on limited phylogenetic analyses, BLAST scores and sequence examination for synapomorphies. The number of RTs per group is indicated in parentheses and by triangle size. Domain structures are depicted in black (alignable with group II introns), gray (uncertain alignment) and white (lack of alignability). Additional domains, including domains of unknown function (DUFs), are in light gray squares, with parentheses indicating that some members lack the domain. In this figure, the designation of an extension as a DUF indicates that the amino acid sequence is conserved within the group. Groups corresponding to lineages in Kojima and Kanehisa (38) are as follows: G2L1 [H1, H2, H3 in (38)]; G2L2, (H4); UG1 (F1); UG3 (G); UG5 (F2); UG6 (E); UG8 (G); UG9 (D); retrons (A); and DGRs (B, C).
Mentions: Classification of Abi RTs is problematic because the three elements reported to have abortive infection properties (AbiA, AbiK and Abi-P2) are distantly related, with only three RT domains alignable between them (Figure 1). One possibility is that Abi elements constitute an extremely diverse but monophyletic lineage of RTs involved in phage abortive infection. Alternatively, multiple lineages of RTs may have evolved roles in abortive infection. In either case, one cannot confidently conclude which other RTs in the set might have abortive infection properties. Hence, we assign only three close relatives as belonging to the AbiK group and eight to the Abi-P2 group, while AbiA has no close relatives.Figure 1.

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