title: Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins.
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 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 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, alphaproteobacteria, a species of Cytophagia, 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.
authors.affiliation: Systems and Synthetic Biology Research Center, Division of Biosystems Research, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea.
authors.forename: Soon-Kyeong
authors.initials: SK
authors.lastname: Kwon
authors.forename: Byung Kwon
authors.initials: BK
authors.lastname: Kim
authors.forename: Ju Yeon
authors.initials: JY
authors.lastname: Song
authors.forename: Min-Jung
authors.initials: MJ
authors.lastname: Kwak
authors.forename: Choong Hoon
authors.initials: CH
authors.lastname: Lee
authors.forename: Jung-Hoon
authors.initials: JH
authors.lastname: Yoon
authors.forename: Tae Kwang
authors.initials: TK
authors.lastname: Oh
authors.forename: Jihyun F
authors.initials: JF
authors.lastname: Kim
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D020816:Amino Acid Motifs; D001436:Bacteriorhodopsins / Q000737:chemistry / Q000235:genetics*; D001483:Base Sequence; D017753:Ecosystem; D005417:Flavobacterium / Q000737:chemistry / Q000235:genetics*; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D012623:Seawater; D017422:Sequence Analysis, DNA
chemical_list: D001436:Bacteriorhodopsins