Genomics Inform.  2016 Mar;14(1):29-33. 10.5808/GI.2016.14.1.29.

Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences

• Yoo W
• Lim D
• Kim S

• KMID: 2166537
• DOI: http://doi.org/10.5808/GI.2016.14.1.29

Abstract

A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and applied it to scan National Center for Biotechnology Information (NCBI) RefSeq bacterial genome sequences. Among 16,844 bacterial sequences possessing a retron-type RT domain, we identified 48 unique types of msDNA. Currently, the biological role of msDNA is not well understood. Our work will be a useful tool in studying the distribution, evolution, and physiological role of msDNA.

Keyword

msDNA; retron; reverse transcriptase; RNA secondary structure

MeSH Terms

Biotechnology
Chimera
DNA
DNA, Single-Stranded*
Genome, Bacterial*
Retroelements
Reverse Transcription
RNA
RNA-Directed DNA Polymerase
DNA
DNA, Single-Stranded
RNA
RNA-Directed DNA Polymerase
Retroelements