title: Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.
abstract: Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.
authors.affiliation: Helmholtz-Centre for Infection Research, Braunschweig, Germany. Thomas.Riedel@helmholtz-hzi.de
authors.forename: Thomas
authors.initials: T
authors.lastname: Riedel
authors.forename: Laura
authors.initials: L
authors.lastname: Gómez-Consarnau
authors.forename: Jürgen
authors.initials: J
authors.lastname: Tomasch
authors.forename: Madeleine
authors.initials: M
authors.lastname: Martin
authors.forename: Michael
authors.initials: M
authors.lastname: Jarek
authors.forename: José M
authors.initials: JM
authors.lastname: González
authors.forename: Stefan
authors.initials: S
authors.lastname: Spring
authors.forename: Meike
authors.initials: M
authors.lastname: Rohlfs
authors.forename: Thorsten
authors.initials: T
authors.lastname: Brinkhoff
authors.forename: Heribert
authors.initials: H
authors.lastname: Cypionka
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
authors.forename: Anne
authors.initials: A
authors.lastname: Fiebig
authors.forename: Johannes
authors.initials: J
authors.lastname: Klein
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Jed A
authors.initials: JA
authors.lastname: Fuhrman
authors.forename: Irene
authors.initials: I
authors.lastname: Wagner-Döbler
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D002338:Carotenoids / Q000096:biosynthesis / Q000235:genetics; D041965:Flavobacteriaceae / Q000145:classification / Q000235:genetics* / Q000502:physiology*; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D010802:Phylogeny; D012172:Retinaldehyde / Q000096:biosynthesis / Q000235:genetics; D012243:Rhodopsin / Q000235:genetics*; D025604:Rhodopsins, Microbial / Q000235:genetics*; D012623:Seawater / Q000382:microbiology; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D025604:Rhodopsins, Microbial; C413548:proteorhodopsin; D002338:Carotenoids; D012243:Rhodopsin; D012172:Retinaldehyde