Proteorhodopsin

Proteorhodopsin is a photoactive retinylidene protein in marine bacterioplanktons. Just like the homologous pigment bacteriorhodopsin found in some archaea, it consists of a transmembrane protein bound to a retinal molecule and functions as a light-driven proton pump. Some members of the family (of more than 800 types) are believed to have sensory functions. Members are known to have different absorption spectracite journal |author=Kelemen BR, Du M, Jensen RB |title=Proteorhodopsin in living color: diversity of spectral properties within living bacterial cells |journal=Biochim. Biophys. Acta |volume=1618 |year=2003 |pages=25–32 |pmid=14643930 |doi=10.1016/j.bbamem.2003.10.002] .

Proteorhodopsin was first discovered in 2000cite journal |author=Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF |title=Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea |journal=Science |volume=289 |pages=1902–1904 |year=2000 |pmid= 10988064 |doi=10.1126/science.289.5486.1902] . It was found in the genomes of several species of uncultivated marine γ-proteobacteria present in the Eastern Pacific Ocean, Central North Pacific Ocean and Southern Ocean, Antarctica [cite journal |author=Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW,Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO |title=Environmental genome shotgun sequencing of the Sargasso Sea |journal=Science |volume=304 |year=2004 |pages=66–74 |pmid=15001713 |doi=10.1126/science.1093857] . Subsequently, genes of proteorhodopsin variants have been identified in samples from the Mediterranean and Red Seas and the Sargasso Sea and the Sea of Japancite journal |author=Béjà O, Spudich EN, Spudich JL, Leclerc M, DeLong EF |title=Proteorhodopsin phototrophy in the ocean |journal=Nature |volume=411 |year=2001 |pages=786–789 |pmid=11459054 |doi=10.1038/35081051] . These variants are not spread randomly, but have different distributions of absorption maxima along depth gradients and across locations cite journal |journal=The ISME Journal |year=2007 |author = Sabehi G, Kirkup BC, Rosenberg M, Stambler N, Polz MF, Béjà O |title= Adaptation and spectral tuning in divergent marine proteorhodopsins from the eastern Mediterranean and the Sargasso Seas |volume=1 |issue=1 |pages=8–55 |doi= 10.1038/ismej.2007.10] .

On comparison to its better-known archaeal homolog bacteriorhodopsin, most of the active site residues of known importance to the bacteriorhodopsin mechanism are conserved in proteorhodopsin. Homologues of the active site residues Arg82, Asp85 (the primary proton acceptor), Asp212 and Lys216 (the retinal Schiff base binding site) in bacteriorhodopsin are conserved as Arg94, Asp97, Asp227 and Lys231 in proteorhodopsin. However, in proteorhodopsin, there are no carboxylic acid residues directly homologous to Glu194 or Glu204 of bacteriorhodopsin, which are thought to be involved in the proton release pathway at the extracellular surfacecite journal |author=Partha R, Krebs R, Caterino TL, Braiman MS |title=Weakened coupling of conserved arginine to the proteorhodopsin chromophore and its counterion implies structural differences from bacteriorhodopsin |journal=Bioch. Biophys. Acta. |year=2005 |volume=1708 |issue=1 |pages=6–12 |pmid= 15949979 |doi=10.1016/j.bbabio.2004.12.009] .

It seems likely that proteorhodopsin functions throughout the Earth's oceans as a light-driven H+ pump, by a mechanism similar to that of bacteriorhodopsin. As in bacteriorhodopsin, the retinal chromophore of bacteriorhodopsin is covalently bound to the apoprotein via a protonated Schiff base at Lys231. The configuration of the retinal chromophore in unphotolyzed proteorhodopsin is predominantly all-trans, and changes to 13-cis upon illumination with light. Several models of the complete proteorhodopsin photocycle have been proposed, based on FTIR and UV–visible spectroscopy; they resemble established photocycle models for bacteriorhodopsincite journal |author = Krebs RA, Alexiev U, Partha R, DeVita AM, Braiman MS |title= Detection of fast light-activated H+ release and M intermediate formation from proteorhodopsin |journal=BMC Physiol. |volume=2 |year=2002 |pages=5 |pmid =11943070 |doi= 10.1186/1472-6793-2-5] cite journal |author=Xiao Y, Partha R, Krebs R, Braiman MS |title=Time-Resolved FTIR Spectroscopy of the Photointermediates Involved in Fast Transient H+ Release by Proteorhodopsin |journal=J. Phys. Chem. B |year=2005 |volume=109 |issue=1 |pages=634–641 |doi=10.1021/jp046314g] .

Genetic Engineering with Proteorhodopsins

If the gene for proteorhodopsin is inserted into "E. coli" and retinal is given to these modified bacteria, then they will incorporate the pigment into their cell membrane and will pump protons in the presence of light cite journal |author=Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF |title=Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea |journal=Science |volume=289 |pages=1902–1904 |year=2000 |pmid= 10988064 |doi=10.1126/science.289.5486.1902] . It was further demonstrated that the proton gradient generated by proteorhodopsin could be used to generate ATP cite journal |author=Martinez A, Bradley AS, Waldbauer JR, Summons RE, DeLong EF |title=Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host |journal=PNAS |volume=104 |pages=5590-5595 |year=2007 |PMID= 17372221 |doi: 10.1073/pnas.0611470104] .

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