title: Isolation of proteorhodopsin-bearing bacterium JL-3 from fresh water and characterization of the proteorhodopsin.
abstract: Proteorhodopsins (PRs), light-driven proton pumps, constitute the largest family of the microbial rhodopsins. PRs are widely distributed in the oceanic environment and freshwater, but no bacteria with PRs have been isolated from freshwater so far. To facilitate isolation of the bacteria with PR genes, we constructed a vector system that can be used to clone potential PR genes and render color changes when overexpressed in Escherichia coli. Using this method, we successfully isolated a strain with PR gene from freshwater and identified it as Exiguobacterium sp. JL-3. The full length PR gene was then cloned using the SEFA PCR method. Protein sequence alignment showed that JL-3_PR shares high sequence identity (84-89%) with the PRs from Exiguobacterium strains, but low sequence identity (< 38%) with other PRs. Surprisingly, we could not detect any proton-pumping activity in the native JL-3 cells and protoplasts, but the recombinant JL-3_PR do pump protons when overexpressed in E. coli. Sequence analysis further revealed that the PRs from Exiguobacterium had an unusual lysine as the proton donor instead of the typical acidic residue. These data suggest that JL-3_PR is a sensory PR rather than a proton pump.
authors.affiliation: Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Zhu
authors.forename: Yanli
authors.initials: Y
authors.lastname: Lan
authors.forename: Xiangdi
authors.initials: X
authors.lastname: Lou
authors.forename: Ning
authors.initials: N
authors.lastname: Han
authors.forename: Tingting
authors.initials: T
authors.lastname: Ran
authors.forename: Langlai
authors.initials: L
authors.lastname: Xu
authors.forename: Dongqing
authors.initials: D
authors.lastname: Xu
authors.forename: Wei-Wu
authors.initials: WW
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D005618:Fresh Water / Q000382:microbiology*; D023061:Gene Order; D005822:Genetic Vectors / Q000235:genetics; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D011522:Protons; D012336:RNA, Ribosomal, 16S; D012243:Rhodopsin / Q000235:genetics / Q000378:metabolism*; D025604:Rhodopsins, Microbial / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D011522:Protons; D012336:RNA, Ribosomal, 16S; D025604:Rhodopsins, Microbial; C413548:proteorhodopsin; D012243:Rhodopsin