ArticleGenome biology and evolution2013
Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed, 86 citations in OpenAlex.
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- Review
- Characterization of symbiotic and nitrogen fixing bacteria.AMB Express · 2022Review
- Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice.Microorganisms · 2022Article
- Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile.PloS one · 2021Article
- The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants.The Journal of biological chemistry · 2020Article
- Omega Rhodopsins: A Versatile Class of Microbial Rhodopsins.Journal of microbiology and biotechnology · 2020Review
- High-resolution structural insights into the heliorhodopsin family.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Unique structure and function of viral rhodopsins.Nature communications · 2019Article
- Engineered Passive Potassium Conductance in the KR2 Sodium Pump.Biophysical journal · 2019Article
- Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency.The Journal of biological chemistry · 2019Article
- Distribution and Diversity of Rhodopsin-Producing Microbes in the Chesapeake Bay.Applied and environmental microbiology · 2018Article
- Electrical properties, substrate specificity and optogenetic potential of the engineered light-driven sodium pump eKR2.Scientific reports · 2018Article
- Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5.Journal of microbiology (Seoul, Korea) · 2017Article
- Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus.Journal of microbiology (Seoul, Korea) · 2017Article
- Microbial Rhodopsins: Diversity, Mechanisms, and Optogenetic Applications.Annual review of biochemistry · 2017Review
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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