Genomic Makeup of the Marine Flavobacterium Nonlabens (Donghaeana) dokdonensis and Identification of a Novel Class of Rhodopsins
Identifieur interne : 000379 ( Ncbi/Merge ); précédent : 000378; suivant : 000380Genomic Makeup of the Marine Flavobacterium Nonlabens (Donghaeana) dokdonensis and Identification of a Novel Class of Rhodopsins
Auteurs : Soon-Kyeong Kwon [Corée du Sud] ; Byung Kwon Kim [Corée du Sud] ; Ju Yeon Song [Corée du Sud] ; Min-Jung Kwak [Corée du Sud] ; Choong Hoon Lee [Corée du Sud] ; Jung-Hoon Yoon [Corée du Sud] ; Tae Kwang Oh [Corée du Sud] ; Jihyun F. Kim [Corée du Sud]Source :
- Genome Biology and Evolution [ 1759-6653 ] ; 2013.
Abstract
Rhodopsin-containing marine microbes such as those in the class
Url:
DOI: 10.1093/gbe/evs134
PubMed: 23292138
PubMed Central: 3595038
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and Identification of a Novel Class of Rhodopsins</title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genomic Makeup of the Marine Flavobacterium <italic>Nonlabens</italic>
(<italic>Donghaeana</italic>
) <italic>dokdonensis</italic>
and Identification of a Novel Class of Rhodopsins</title>
<author><name sortKey="Kwon, Soon Kyeong" sort="Kwon, Soon Kyeong" uniqKey="Kwon S" first="Soon-Kyeong" last="Kwon">Soon-Kyeong Kwon</name>
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<author><name sortKey="Kim, Byung Kwon" sort="Kim, Byung Kwon" uniqKey="Kim B" first="Byung Kwon" last="Kim">Byung Kwon Kim</name>
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<wicri:regionArea>Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul</wicri:regionArea>
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<author><name sortKey="Song, Ju Yeon" sort="Song, Ju Yeon" uniqKey="Song J" first="Ju Yeon" last="Song">Ju Yeon Song</name>
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<author><name sortKey="Kwak, Min Jung" sort="Kwak, Min Jung" uniqKey="Kwak M" first="Min-Jung" last="Kwak">Min-Jung Kwak</name>
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<affiliation wicri:level="1"><nlm:aff id="evs134-AFF2">Biosystems and Bioengineering Program, School of Science, University of Science and Technology, Yuseong-gu, Daejeon, Korea</nlm:aff>
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<author><name sortKey="Lee, Choong Hoon" sort="Lee, Choong Hoon" uniqKey="Lee C" first="Choong Hoon" last="Lee">Choong Hoon Lee</name>
<affiliation wicri:level="3"><nlm:aff id="evs134-AFF3">Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Korea</nlm:aff>
<country xml:lang="fr">Corée du Sud</country>
<wicri:regionArea>Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul</wicri:regionArea>
<placeName><settlement type="city">Séoul</settlement>
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<author><name sortKey="Yoon, Jung Hoon" sort="Yoon, Jung Hoon" uniqKey="Yoon J" first="Jung-Hoon" last="Yoon">Jung-Hoon Yoon</name>
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<country xml:lang="fr">Corée du Sud</country>
<wicri:regionArea>Department of Food Science and Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Jangan-gu, Suwon, Gyeonggi-do</wicri:regionArea>
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<author><name sortKey="Oh, Tae Kwang" sort="Oh, Tae Kwang" uniqKey="Oh T" first="Tae Kwang" last="Oh">Tae Kwang Oh</name>
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<country xml:lang="fr">Corée du Sud</country>
<wicri:regionArea>Systems and Synthetic Biology Research Center, Division of Biosystems Research, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon</wicri:regionArea>
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<affiliation wicri:level="1"><nlm:aff id="evs134-AFF5">21C Frontier Microbial Genomics and Applications Center, Yuseong, Daejeon, Korea</nlm:aff>
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<author><name sortKey="Kim, Jihyun F" sort="Kim, Jihyun F" uniqKey="Kim J" first="Jihyun F." last="Kim">Jihyun F. Kim</name>
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<country xml:lang="fr">Corée du Sud</country>
<wicri:regionArea>Systems and Synthetic Biology Research Center, Division of Biosystems Research, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon</wicri:regionArea>
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<country xml:lang="fr">Corée du Sud</country>
<wicri:regionArea>Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul</wicri:regionArea>
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<front><div type="abstract" xml:lang="en"><p>Rhodopsin-containing marine microbes such as those in the class <italic>Flavobacteriia</italic>
play a pivotal role in the biogeochemical cycle of the euphotic zone (Fuhrman JA, Schwalbach MS, Stingl U. 2008. Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol. 6:488–494). Deciphering the genome information of flavobacteria and accessing the diversity and ecological impact of microbial rhodopsins are important in understanding and preserving the global ecosystems. The genome sequence of the orange-pigmented marine flavobacterium <italic>Nonlabens dokdonensis</italic>
(basonym: <italic>Donghaeana dokdonensis</italic>
) DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its genome physiological features that allow survival in the oligotrophic environments. The sequence analysis also uncovered a gene encoding an unexpected type of microbial rhodopsin containing a unique motif in addition to a proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs of the novel rhodopsin gene were found in other flavobacteria, alphaproteobacteria, a species of <italic>Cytophagia</italic>
, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and form a phylogenetically distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated that it is induced at high NaCl concentrations, as well as in the presence of light and the absence of nutrients. Genomic and metagenomic surveys demonstrate the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the encoding genes among microbial communities inhabiting hypersaline niches, suggesting its involvement in sodium metabolism and the sodium-adapted lifestyle.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol Evol</journal-id>
<journal-id journal-id-type="iso-abbrev">Genome Biol Evol</journal-id>
<journal-id journal-id-type="publisher-id">gbe</journal-id>
<journal-id journal-id-type="hwp">gbe</journal-id>
<journal-title-group><journal-title>Genome Biology and Evolution</journal-title>
</journal-title-group>
<issn pub-type="epub">1759-6653</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23292138</article-id>
<article-id pub-id-type="pmc">3595038</article-id>
<article-id pub-id-type="doi">10.1093/gbe/evs134</article-id>
<article-id pub-id-type="publisher-id">evs134</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Genomic Makeup of the Marine Flavobacterium <italic>Nonlabens</italic>
(<italic>Donghaeana</italic>
) <italic>dokdonensis</italic>
and Identification of a Novel Class of Rhodopsins</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Kwon</surname>
<given-names>Soon-Kyeong</given-names>
</name>
<xref ref-type="aff" rid="evs134-AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="evs134-AFF2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kim</surname>
<given-names>Byung Kwon</given-names>
</name>
<xref ref-type="aff" rid="evs134-AFF3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Song</surname>
<given-names>Ju Yeon</given-names>
</name>
<xref ref-type="aff" rid="evs134-AFF3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kwak</surname>
<given-names>Min-Jung</given-names>
</name>
<xref ref-type="aff" rid="evs134-AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="evs134-AFF2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lee</surname>
<given-names>Choong Hoon</given-names>
</name>
<xref ref-type="aff" rid="evs134-AFF3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yoon</surname>
<given-names>Jung-Hoon</given-names>
</name>
<xref ref-type="aff" rid="evs134-AFF4"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Oh</surname>
<given-names>Tae Kwang</given-names>
</name>
<xref ref-type="aff" rid="evs134-AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="evs134-AFF5"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kim</surname>
<given-names>Jihyun F.</given-names>
</name>
<xref ref-type="aff" rid="evs134-AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="evs134-AFF3"><sup>3</sup>
</xref>
<xref ref-type="corresp" rid="evs134-COR1">*</xref>
</contrib>
</contrib-group>
<aff id="evs134-AFF1"><sup>1</sup>
Systems and Synthetic Biology Research Center, Division of Biosystems Research, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea</aff>
<aff id="evs134-AFF2"><sup>2</sup>
Biosystems and Bioengineering Program, School of Science, University of Science and Technology, Yuseong-gu, Daejeon, Korea</aff>
<aff id="evs134-AFF3"><sup>3</sup>
Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Korea</aff>
<aff id="evs134-AFF4"><sup>4</sup>
Department of Food Science and Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Jangan-gu, Suwon, Gyeonggi-do, Korea</aff>
<aff id="evs134-AFF5"><sup>5</sup>
21C Frontier Microbial Genomics and Applications Center, Yuseong, Daejeon, Korea</aff>
<author-notes><corresp id="evs134-COR1">*Corresponding author: E-mail: <email>jfk1@yonsei.ac.kr</email>
.</corresp>
<fn id="evs134-FN1"><p><bold>Associate editor:</bold>
Bill Martin</p>
</fn>
<fn id="evs134-FN2"><p><bold>Data deposition:</bold>
CP001397</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>3</day>
<month>1</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="collection"><month>1</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>3</day>
<month>1</month>
<year>2013</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
. </pmc-comment>
<volume>5</volume>
<issue>1</issue>
<fpage>187</fpage>
<lpage>199</lpage>
<history><date date-type="accepted"><day>21</day>
<month>12</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</copyright-statement>
<copyright-year>2013</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/">http://creativecommons.org/licenses/by-nc/3.0/</ext-link>
), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><p>Rhodopsin-containing marine microbes such as those in the class <italic>Flavobacteriia</italic>
play a pivotal role in the biogeochemical cycle of the euphotic zone (Fuhrman JA, Schwalbach MS, Stingl U. 2008. Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol. 6:488–494). Deciphering the genome information of flavobacteria and accessing the diversity and ecological impact of microbial rhodopsins are important in understanding and preserving the global ecosystems. The genome sequence of the orange-pigmented marine flavobacterium <italic>Nonlabens dokdonensis</italic>
(basonym: <italic>Donghaeana dokdonensis</italic>
) DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its genome physiological features that allow survival in the oligotrophic environments. The sequence analysis also uncovered a gene encoding an unexpected type of microbial rhodopsin containing a unique motif in addition to a proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs of the novel rhodopsin gene were found in other flavobacteria, alphaproteobacteria, a species of <italic>Cytophagia</italic>
, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and form a phylogenetically distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated that it is induced at high NaCl concentrations, as well as in the presence of light and the absence of nutrients. Genomic and metagenomic surveys demonstrate the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the encoding genes among microbial communities inhabiting hypersaline niches, suggesting its involvement in sodium metabolism and the sodium-adapted lifestyle.</p>
</abstract>
<kwd-group><kwd>heterotrophic picoplankton</kwd>
<kwd><italic>Bacteroidetes</italic>
</kwd>
<kwd>bacteriorhodopsin</kwd>
<kwd>xanthorhodopsin</kwd>
<kwd>sodium pump</kwd>
<kwd>metagenome</kwd>
</kwd-group>
<counts><page-count count="13"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Corée du Sud</li>
</country>
<settlement><li>Séoul</li>
</settlement>
</list>
<tree><country name="Corée du Sud"><noRegion><name sortKey="Kwon, Soon Kyeong" sort="Kwon, Soon Kyeong" uniqKey="Kwon S" first="Soon-Kyeong" last="Kwon">Soon-Kyeong Kwon</name>
</noRegion>
<name sortKey="Kim, Byung Kwon" sort="Kim, Byung Kwon" uniqKey="Kim B" first="Byung Kwon" last="Kim">Byung Kwon Kim</name>
<name sortKey="Kim, Jihyun F" sort="Kim, Jihyun F" uniqKey="Kim J" first="Jihyun F." last="Kim">Jihyun F. Kim</name>
<name sortKey="Kim, Jihyun F" sort="Kim, Jihyun F" uniqKey="Kim J" first="Jihyun F." last="Kim">Jihyun F. Kim</name>
<name sortKey="Kwak, Min Jung" sort="Kwak, Min Jung" uniqKey="Kwak M" first="Min-Jung" last="Kwak">Min-Jung Kwak</name>
<name sortKey="Kwak, Min Jung" sort="Kwak, Min Jung" uniqKey="Kwak M" first="Min-Jung" last="Kwak">Min-Jung Kwak</name>
<name sortKey="Kwon, Soon Kyeong" sort="Kwon, Soon Kyeong" uniqKey="Kwon S" first="Soon-Kyeong" last="Kwon">Soon-Kyeong Kwon</name>
<name sortKey="Lee, Choong Hoon" sort="Lee, Choong Hoon" uniqKey="Lee C" first="Choong Hoon" last="Lee">Choong Hoon Lee</name>
<name sortKey="Oh, Tae Kwang" sort="Oh, Tae Kwang" uniqKey="Oh T" first="Tae Kwang" last="Oh">Tae Kwang Oh</name>
<name sortKey="Oh, Tae Kwang" sort="Oh, Tae Kwang" uniqKey="Oh T" first="Tae Kwang" last="Oh">Tae Kwang Oh</name>
<name sortKey="Song, Ju Yeon" sort="Song, Ju Yeon" uniqKey="Song J" first="Ju Yeon" last="Song">Ju Yeon Song</name>
<name sortKey="Yoon, Jung Hoon" sort="Yoon, Jung Hoon" uniqKey="Yoon J" first="Jung-Hoon" last="Yoon">Jung-Hoon Yoon</name>
</country>
</tree>
</affiliations>
</record>
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