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Nucleic Acids Research Advance Access originally published online on November 12, 2008
Nucleic Acids Research 2008 36(22):7219-7229; doi:10.1093/nar/gkn867
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Nucleic Acids Research, 2008, Vol. 36, No. 22 7219-7229
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

A diversity of uncharacterized reverse transcriptases in bacteria

Dawn M. Simon and Steven Zimmerly*

Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4

*To whom correspondence should be addressed. Tel: +1 403 220 7933; Fax: +1 403 289 9311; Email: zimmerly{at}ucalgary.ca

Received July 5, 2008. Revised October 16, 2008. Accepted October 17, 2008.

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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