Genomic Makeup of the Marine Flavobacterium Nonlabens (Donghaeana) dokdonensis and Identification of a Novel Class of Rhodopsins
Identifieur interne : 000379 ( Ncbi/Curation ); 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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<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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<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="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>
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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>
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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>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>
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