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Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences.

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.

SUBMITTER: Yoo W

PROVIDER: S-EPMC4838527 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences.

Yoo Wonseok W Lim Dongbin D Kim Sangsoo S

Genomics & informatics 20160331 1

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 appli ...[more]

PMID: 27103888

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