Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins

Soon Kyeong Kwon, Byung Kwon Kim, Ju Yeon Song, Min Jung Kwak, Choong Hoon Lee, Jung Hoon Yoon, Tae Kwang Oh, Jihyun F. Kim

Research output: Contribution to journalArticle

55 Citations (Scopus)

Abstract

Rhodopsin-containing marine microbes such as those in the class Flavobacteriia 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 RevMicrobiol. 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 Nonlabens dokdonensis (basonym: Donghaeana dokdonensis) 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, alphaproteo bacteria, a species of Cytophagia, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and forma phylogenetically distinct group. Expression analysis of this rhodopsin gene inDSW-6indicated 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.

Original languageEnglish
Pages (from-to)187-199
Number of pages13
JournalGenome Biology and Evolution
Volume5
Issue number1
DOIs
Publication statusPublished - 2013 Apr 29

Fingerprint

Flavobacterium
rhodopsin
Rhodopsin
genomics
Microbial Rhodopsins
gene
Genes
Genome
genome
Flavobacteria
Microbial Genes
Cryptochromes
Deoxyribodipyrimidine Photo-Lyase
Sodium
Deinococcus
genes
Metagenomics
Diatoms
sodium
oligotrophic environment

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Kwon, Soon Kyeong ; Kim, Byung Kwon ; Song, Ju Yeon ; Kwak, Min Jung ; Lee, Choong Hoon ; Yoon, Jung Hoon ; Oh, Tae Kwang ; Kim, Jihyun F. / Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins. In: Genome Biology and Evolution. 2013 ; Vol. 5, No. 1. pp. 187-199.
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abstract = "Rhodopsin-containing marine microbes such as those in the class Flavobacteriia 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 RevMicrobiol. 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 Nonlabens dokdonensis (basonym: Donghaeana dokdonensis) 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, alphaproteo bacteria, a species of Cytophagia, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and forma phylogenetically distinct group. Expression analysis of this rhodopsin gene inDSW-6indicated 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.",
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Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins. / Kwon, Soon Kyeong; Kim, Byung Kwon; Song, Ju Yeon; Kwak, Min Jung; Lee, Choong Hoon; Yoon, Jung Hoon; Oh, Tae Kwang; Kim, Jihyun F.

In: Genome Biology and Evolution, Vol. 5, No. 1, 29.04.2013, p. 187-199.

Research output: Contribution to journalArticle

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