Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences
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 s...
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BioMed Central
2016-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-14-29.pdf |
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| author | Wonseok Yoo Dongbin Lim Sangsoo Kim |
| author_facet | Wonseok Yoo Dongbin Lim Sangsoo Kim |
| author_sort | Wonseok Yoo |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-a30b07c9c3344087b44f4c2a4b80b09e |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2016-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-a30b07c9c3344087b44f4c2a4b80b09e2025-02-02T00:04:20ZengBioMed CentralGenomics & Informatics1598-866X2234-07422016-03-01141293310.5808/GI.2016.14.1.29186Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome SequencesWonseok Yoo0Dongbin Lim1Sangsoo Kim2Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea.Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea.Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea.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.http://genominfo.org/upload/pdf/gni-14-29.pdfmsDNAretronreverse transcriptaseRNA secondary structure |
| spellingShingle | Wonseok Yoo Dongbin Lim Sangsoo Kim Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences Genomics & Informatics msDNA retron reverse transcriptase RNA secondary structure |
| title | Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences |
| title_full | Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences |
| title_fullStr | Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences |
| title_full_unstemmed | Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences |
| title_short | Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences |
| title_sort | compiling multicopy single stranded dna sequences from bacterial genome sequences |
| topic | msDNA retron reverse transcriptase RNA secondary structure |
| url | http://genominfo.org/upload/pdf/gni-14-29.pdf |
| work_keys_str_mv | AT wonseokyoo compilingmulticopysinglestrandeddnasequencesfrombacterialgenomesequences AT dongbinlim compilingmulticopysinglestrandeddnasequencesfrombacterialgenomesequences AT sangsookim compilingmulticopysinglestrandeddnasequencesfrombacterialgenomesequences |