title: Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology.
abstract: The recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of "heterotrophic" bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.
authors.affiliation: Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden jarone.pinhassi@lnu.se.
authors.forename: Jarone
authors.identifier: 0000-0002-6405-1347
authors.initials: J
authors.lastname: Pinhassi
authors.affiliation: Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA Department of Biological Engineering and Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Edward F
authors.initials: EF
authors.lastname: DeLong
authors.affiliation: Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
authors.forename: Oded
authors.initials: O
authors.lastname: Béjà
authors.affiliation: Department of Microbiology, University of La Laguna, La Laguna, Spain.
authors.forename: José M
authors.initials: JM
authors.lastname: González
authors.affiliation: Systems Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Pedrós-Alió
mesh_terms: D059001:Aquatic Organisms / Q000378:metabolism; D001105:Archaea / Q000235:genetics / Q000378:metabolism*; D001419:Bacteria / Q000235:genetics / Q000378:metabolism*; D015870:Gene Expression / Q000235:genetics; D022761:Gene Transfer, Horizontal / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D017136:Ion Transport / Q000502:physiology*; D008027:Light; D025604:Rhodopsins, Microbial / Q000235:genetics / Q000378:metabolism*; D012623:Seawater / Q000382:microbiology; D000254:Sodium-Potassium-Exchanging ATPase / Q000235:genetics / Q000378:metabolism
chemical_list: D025604:Rhodopsins, Microbial; D000254:Sodium-Potassium-Exchanging ATPase