Complete genomic DNA sequence of the East Asian spotted fever disease agent Rickettsia japonica
Rickettsia japonica is an obligate intracellular alphaproteobacteria that causes tick-borne Japanese spotted fever, which has spread throughout East Asia. We determined the complete genomic DNA sequence of R. japonica type strain YH (VR-1363), which consists of 1,283,087 base pairs (bp) and 971 prot...
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| Veröffentlicht in: | PloS one 2013-09, Vol.8 (9), p.e71861-e71861 |
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| creator | Matsutani, Minenosuke Ogawa, Motohiko Takaoka, Naohisa Hanaoka, Nozomu Toh, Hidehiro Yamashita, Atsushi Oshima, Kenshiro Hirakawa, Hideki Kuhara, Satoru Suzuki, Harumi Hattori, Masahira Kishimoto, Toshio Ando, Shuji Azuma, Yoshinao Shirai, Mutsunori |
| description | Rickettsia japonica is an obligate intracellular alphaproteobacteria that causes tick-borne Japanese spotted fever, which has spread throughout East Asia. We determined the complete genomic DNA sequence of R. japonica type strain YH (VR-1363), which consists of 1,283,087 base pairs (bp) and 971 protein-coding genes. Comparison of the genomic DNA sequence of R. japonica with other rickettsiae in the public databases showed that 2 regions (4,323 and 216 bp) were conserved in a very narrow range of Rickettsia species, and the shorter one was inserted in, and disrupted, a preexisting open reading frame (ORF). While it is unknown how the DNA sequences were acquired in R. japonica genomes, it may be a useful signature for the diagnosis of Rickettsia species. Instead of the species-specific inserted DNA sequences, rickettsial genomes contain Rickettsia-specific palindromic elements (RPEs), which are also capable of locating in preexisting ORFs. Precise alignments of protein and DNA sequences involving RPEs showed that when a gene contains an inserted DNA sequence, each rickettsial ortholog carried an inserted DNA sequence at the same locus. The sequence, ATGAC, was shown to be highly frequent and thus characteristic in certain RPEs (RPE-4, RPE-6, and RPE-7). This finding implies that RPE-4, RPE-6, and RPE-7 were derived from a common inserted DNA sequence. |
| doi_str_mv | 10.1371/journal.pone.0071861 |
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We determined the complete genomic DNA sequence of R. japonica type strain YH (VR-1363), which consists of 1,283,087 base pairs (bp) and 971 protein-coding genes. Comparison of the genomic DNA sequence of R. japonica with other rickettsiae in the public databases showed that 2 regions (4,323 and 216 bp) were conserved in a very narrow range of Rickettsia species, and the shorter one was inserted in, and disrupted, a preexisting open reading frame (ORF). While it is unknown how the DNA sequences were acquired in R. japonica genomes, it may be a useful signature for the diagnosis of Rickettsia species. Instead of the species-specific inserted DNA sequences, rickettsial genomes contain Rickettsia-specific palindromic elements (RPEs), which are also capable of locating in preexisting ORFs. Precise alignments of protein and DNA sequences involving RPEs showed that when a gene contains an inserted DNA sequence, each rickettsial ortholog carried an inserted DNA sequence at the same locus. The sequence, ATGAC, was shown to be highly frequent and thus characteristic in certain RPEs (RPE-4, RPE-6, and RPE-7). This finding implies that RPE-4, RPE-6, and RPE-7 were derived from a common inserted DNA sequence.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0071861</identifier><identifier>PMID: 24039725</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amino Acid Sequence ; Amino acids ; Analysis ; Base pairs ; Base Sequence ; Bioinformatics ; Consensus Sequence ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; DNA, Circular - genetics ; Fever ; Gene sequencing ; Genes ; Genes, Bacterial ; Genome, Bacterial ; Genomes ; Genomics ; Humans ; Immunology ; Infectious diseases ; International conferences ; Life sciences ; Medicine ; Molecular biology ; Molecular Sequence Data ; Nucleotide sequence ; Phylogenetics ; Proteins ; Rickettsia ; Rickettsia - genetics ; Rickettsia Infections - microbiology ; Sequence Analysis, DNA ; Species ; Typhus ; User interface ; Virology ; Wolbachia</subject><ispartof>PloS one, 2013-09, Vol.8 (9), p.e71861-e71861</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Matsutani et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Matsutani et al 2013 Matsutani et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-6acc8ec6976319004072a27e2cb9bb1db1fc219139a3c944bef3fcf5da6ede2a3</citedby><cites>FETCH-LOGICAL-c758t-6acc8ec6976319004072a27e2cb9bb1db1fc219139a3c944bef3fcf5da6ede2a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767692/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767692/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24039725$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Matsutani, Minenosuke</creatorcontrib><creatorcontrib>Ogawa, Motohiko</creatorcontrib><creatorcontrib>Takaoka, Naohisa</creatorcontrib><creatorcontrib>Hanaoka, Nozomu</creatorcontrib><creatorcontrib>Toh, Hidehiro</creatorcontrib><creatorcontrib>Yamashita, Atsushi</creatorcontrib><creatorcontrib>Oshima, Kenshiro</creatorcontrib><creatorcontrib>Hirakawa, Hideki</creatorcontrib><creatorcontrib>Kuhara, Satoru</creatorcontrib><creatorcontrib>Suzuki, Harumi</creatorcontrib><creatorcontrib>Hattori, Masahira</creatorcontrib><creatorcontrib>Kishimoto, Toshio</creatorcontrib><creatorcontrib>Ando, Shuji</creatorcontrib><creatorcontrib>Azuma, Yoshinao</creatorcontrib><creatorcontrib>Shirai, Mutsunori</creatorcontrib><title>Complete genomic DNA sequence of the East Asian spotted fever disease agent Rickettsia japonica</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Rickettsia japonica is an obligate intracellular alphaproteobacteria that causes tick-borne Japanese spotted fever, which has spread throughout East Asia. We determined the complete genomic DNA sequence of R. japonica type strain YH (VR-1363), which consists of 1,283,087 base pairs (bp) and 971 protein-coding genes. Comparison of the genomic DNA sequence of R. japonica with other rickettsiae in the public databases showed that 2 regions (4,323 and 216 bp) were conserved in a very narrow range of Rickettsia species, and the shorter one was inserted in, and disrupted, a preexisting open reading frame (ORF). While it is unknown how the DNA sequences were acquired in R. japonica genomes, it may be a useful signature for the diagnosis of Rickettsia species. Instead of the species-specific inserted DNA sequences, rickettsial genomes contain Rickettsia-specific palindromic elements (RPEs), which are also capable of locating in preexisting ORFs. Precise alignments of protein and DNA sequences involving RPEs showed that when a gene contains an inserted DNA sequence, each rickettsial ortholog carried an inserted DNA sequence at the same locus. The sequence, ATGAC, was shown to be highly frequent and thus characteristic in certain RPEs (RPE-4, RPE-6, and RPE-7). This finding implies that RPE-4, RPE-6, and RPE-7 were derived from a common inserted DNA sequence.</description><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Base pairs</subject><subject>Base Sequence</subject><subject>Bioinformatics</subject><subject>Consensus Sequence</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>DNA, Circular - genetics</subject><subject>Fever</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genes, Bacterial</subject><subject>Genome, Bacterial</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Humans</subject><subject>Immunology</subject><subject>Infectious diseases</subject><subject>International conferences</subject><subject>Life sciences</subject><subject>Medicine</subject><subject>Molecular biology</subject><subject>Molecular Sequence Data</subject><subject>Nucleotide sequence</subject><subject>Phylogenetics</subject><subject>Proteins</subject><subject>Rickettsia</subject><subject>Rickettsia - genetics</subject><subject>Rickettsia Infections - microbiology</subject><subject>Sequence Analysis, DNA</subject><subject>Species</subject><subject>Typhus</subject><subject>User interface</subject><subject>Virology</subject><subject>Wolbachia</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk11v0zAUhiMEYmPwDxBYQkJw0eKvOPENUlUGVJqYND5uLcc5bl3SuMTOBP8eZ82mBu0C-cKW_bzv8Tn2ybLnBM8JK8i7re-7VjfzvW9hjnFBSkEeZKdEMjoTFLOHR-uT7EkIW4xzVgrxODuhHDNZ0Pw0U0u_2zcQAa2h9Ttn0IcvCxTgVw-tAeQtihtA5zpEtAhOtyjsfYxQIwvX0KHaBdABkE7qiK6c-QkxJg5tdbqXM_pp9sjqJsCzcT7Lvn88_7b8PLu4_LRaLi5mpsjLOBPamBKMkIVgRGLMcUE1LYCaSlYVqStiDSWSMKmZkZxXYJk1Nq-1gBqoZmfZy4PvvvFBjbUJinBGCGYszxOxOhC111u179xOd3-U107dbPhurXQXnWlAaVoJWVPgsrAceC7LFIgwU3FqjQGavN6P0fpqB7VJyXe6mZhOT1q3UWt_rVghCiEHgzejQedTqUNUOxcMNI1uwfc392ZUSMF5Ql_9g96f3UitdUrAtdanuGYwVQtelCxnmA5e83uoNGpIT58-knVpfyJ4OxEkJsLvuNZ9CGr19er_2csfU_b1EbsB3cRN8E0fnW_DFOQH0HQ-hA7sXZEJVkMf3FZDDX2gxj5IshfHD3Qnuv347C9GewMD</recordid><startdate>20130909</startdate><enddate>20130909</enddate><creator>Matsutani, Minenosuke</creator><creator>Ogawa, Motohiko</creator><creator>Takaoka, Naohisa</creator><creator>Hanaoka, Nozomu</creator><creator>Toh, Hidehiro</creator><creator>Yamashita, Atsushi</creator><creator>Oshima, Kenshiro</creator><creator>Hirakawa, Hideki</creator><creator>Kuhara, Satoru</creator><creator>Suzuki, Harumi</creator><creator>Hattori, Masahira</creator><creator>Kishimoto, Toshio</creator><creator>Ando, Shuji</creator><creator>Azuma, Yoshinao</creator><creator>Shirai, Mutsunori</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130909</creationdate><title>Complete genomic DNA sequence of the East Asian spotted fever disease agent Rickettsia japonica</title><author>Matsutani, Minenosuke ; Ogawa, Motohiko ; Takaoka, Naohisa ; Hanaoka, Nozomu ; Toh, Hidehiro ; Yamashita, Atsushi ; Oshima, Kenshiro ; Hirakawa, Hideki ; Kuhara, Satoru ; Suzuki, Harumi ; Hattori, Masahira ; Kishimoto, Toshio ; Ando, Shuji ; Azuma, Yoshinao ; Shirai, Mutsunori</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-6acc8ec6976319004072a27e2cb9bb1db1fc219139a3c944bef3fcf5da6ede2a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Amino Acid Sequence</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Base pairs</topic><topic>Base Sequence</topic><topic>Bioinformatics</topic><topic>Consensus Sequence</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>DNA, Circular - 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We determined the complete genomic DNA sequence of R. japonica type strain YH (VR-1363), which consists of 1,283,087 base pairs (bp) and 971 protein-coding genes. Comparison of the genomic DNA sequence of R. japonica with other rickettsiae in the public databases showed that 2 regions (4,323 and 216 bp) were conserved in a very narrow range of Rickettsia species, and the shorter one was inserted in, and disrupted, a preexisting open reading frame (ORF). While it is unknown how the DNA sequences were acquired in R. japonica genomes, it may be a useful signature for the diagnosis of Rickettsia species. Instead of the species-specific inserted DNA sequences, rickettsial genomes contain Rickettsia-specific palindromic elements (RPEs), which are also capable of locating in preexisting ORFs. Precise alignments of protein and DNA sequences involving RPEs showed that when a gene contains an inserted DNA sequence, each rickettsial ortholog carried an inserted DNA sequence at the same locus. The sequence, ATGAC, was shown to be highly frequent and thus characteristic in certain RPEs (RPE-4, RPE-6, and RPE-7). This finding implies that RPE-4, RPE-6, and RPE-7 were derived from a common inserted DNA sequence.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24039725</pmid><doi>10.1371/journal.pone.0071861</doi><tpages>e71861</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2013-09, Vol.8 (9), p.e71861-e71861 |
| issn | 1932-6203 1932-6203 |
| language | eng |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Amino Acid Sequence Amino acids Analysis Base pairs Base Sequence Bioinformatics Consensus Sequence Deoxyribonucleic acid DNA DNA sequencing DNA, Circular - genetics Fever Gene sequencing Genes Genes, Bacterial Genome, Bacterial Genomes Genomics Humans Immunology Infectious diseases International conferences Life sciences Medicine Molecular biology Molecular Sequence Data Nucleotide sequence Phylogenetics Proteins Rickettsia Rickettsia - genetics Rickettsia Infections - microbiology Sequence Analysis, DNA Species Typhus User interface Virology Wolbachia |
| title | Complete genomic DNA sequence of the East Asian spotted fever disease agent Rickettsia japonica |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-08T20%3A44%3A18IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Complete%20genomic%20DNA%20sequence%20of%20the%20East%20Asian%20spotted%20fever%20disease%20agent%20Rickettsia%20japonica&rft.jtitle=PloS%20one&rft.au=Matsutani,%20Minenosuke&rft.date=2013-09-09&rft.volume=8&rft.issue=9&rft.spage=e71861&rft.epage=e71861&rft.pages=e71861-e71861&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0071861&rft_dat=%3Cgale_plos_%3EA478353024%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1431103355&rft_id=info:pmid/24039725&rft_galeid=A478353024&rft_doaj_id=oai_doaj_org_article_a2b69d2e497f4e45985da13cb42fcce2&rfr_iscdi=true |