Journal Article

Genomic Makeup of the Marine Flavobacterium <i>Nonlabens</i> (<i>Donghaeana</i>) <i>dokdonensis</i> 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 and Jihyun F. Kim

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 5, issue 1, pages 187-199
Published in print January 2013 |
Published online January 2013 | e-ISSN: 1759-6653 | DOI: https://dx.doi.org/10.1093/gbe/evs134

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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.

Keywords: heterotrophic picoplankton; Bacteroidetes; bacteriorhodopsin; xanthorhodopsin; sodium pump; metagenome

Journal Article.  7456 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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