title: Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments.
abstract: Proteorhodopsins are light-energy-harvesting transmembrane proteins encoded by genes recently discovered in the surface waters of the world's oceans. Metagenomic data from the Global Ocean Sampling expedition (GOS) recovered 2674 proteorhodopsin-related sequences from 51 aquatic samples. Four of these samples were from non-marine environments, specifically, Lake Gatun within the Panama Canal, Delaware Bay and Chesapeake Bay and the Punta Cormorant Lagoon in Ecuador. Rhodopsins related to but phylogenetically distinct from most sequences designated proteorhodopsins were present at all four of these non-marine sites and comprised three different clades that were almost completely absent from marine samples. Phylogenomic analyses of genes adjacent to those encoding these novel rhodopsins suggest affiliation to the Actinobacteria, and hence we propose to name these divergent, non-marine rhodopsins 'actinorhodopsins'. Actinorhodopsins conserve the acidic amino acid residues critical for proton pumping and their genes lack genomic association with those encoding photo-sensory transducer proteins, thus supporting a putative ion pumping function. The ratio of recA and radA to rhodopsin genes in the different environment types sampled within the GOS indicates that rhodopsins of one type or another are abundant in microbial communities in freshwater, estuarine and lagoon ecosystems, supporting an important role for these photosystems in all aquatic environments influenced by sunlight.
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax, Nova Scotia, Canada, B3H 1X5. aksharma@dal.ca
authors.forename: Adrian K
authors.initials: AK
authors.lastname: Sharma
authors.forename: Olga
authors.initials: O
authors.lastname: Zhaxybayeva
authors.forename: R Thane
authors.initials: RT
authors.lastname: Papke
authors.forename: W Ford
authors.initials: WF
authors.lastname: Doolittle
mesh_terms: D039903:Actinobacteria / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D003691:Delaware; D004484:Ecuador; D005618:Fresh Water / Q000382:microbiology; D016623:Ion Pumps / Q000378:metabolism; D008396:Maryland; D010177:Panama Canal Zone; D010802:Phylogeny; D011938:Rec A Recombinases / Q000235:genetics; D025604:Rhodopsins, Microbial / Q000235:genetics*; D012988:Soil Microbiology; D014871:Water Microbiology
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D016623:Ion Pumps; C100901:RadA protein, bacteria; C089760:RecA protein, Acinetobacter calcoaceticus; D025604:Rhodopsins, Microbial; D011938:Rec A Recombinases