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Symbol Bac_rhodopsin
Pfam PF01036
OPM superfamily 6
OPM protein 2l6x

Proteorhodopsin is a photoactive retinylidene protein in marine planktonic bacteria, archaea and eukaryotes.[1][2][3][4] 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 spectra.[5][6][7][8]


Proteorhodopsin was first discovered in 2000.[1] 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.[9] Subsequently, genes of proteorhodopsin variants have been identified in samples from the Mediterranean and Red Seas and the Sargasso Sea and the Sea of Japan.[5] These variants are not spread randomly, but have different distributions of absorption maxima along depth gradients and across locations.[8]

Active site[edit]

In comparison with 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 surface.[10][11]


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 proteorhodopsin 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[10] , 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 bacteriorhodopsin.[10][12][13][14]

Genetic engineering[edit]

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 H+ in the presence of light.[1] It was further demonstrated that the proton gradient generated by proteorhodopsin could be used to generate ATP.[15]


  1. ^ a b c Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF (Sep 2000). "Bacterial rhodopsin: evidence for a new type of phototrophy in the sea". Science 289 (5486): 1902–6. Bibcode:2000Sci...289.1902B. doi:10.1126/science.289.5486.1902. PMID 10988064. 
  2. ^ Lin S, Zhang H, Zhuang Y, Tran B, Gill J (Nov 2010). "Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates". Proceedings of the National Academy of Sciences of the United States of America 107 (46): 20033–8. Bibcode:2010PNAS..10720033L. doi:10.1073/pnas.1007246107. PMID 21041634. 
  3. ^ Slamovits CH, Okamoto N, Burri L, James ER, Keeling PJ (2011). "A bacterial proteorhodopsin proton pump in marine eukaryotes". Nature Communications 2 (2): 183. Bibcode:2011NatCo...2E.183S. doi:10.1038/ncomms1188. PMID 21304512. 
  4. ^ Frigaard NU, Martinez A, Mincer TJ, DeLong EF (Feb 2006). "Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea". Nature 439 (7078): 847–50. Bibcode:2006Natur.439..847F. doi:10.1038/nature04435. PMID 16482157. 
  5. ^ a b Béjà O, Spudich EN, Spudich JL, Leclerc M, DeLong EF (Jun 2001). "Proteorhodopsin phototrophy in the ocean". Nature 411 (6839): 786–9. doi:10.1038/35081051. PMID 11459054. 
  6. ^ Man D, Wang W, Sabehi G, Aravind L, Post AF, Massana R, Spudich EN, Spudich JL, Béjà O (Apr 2003). "Diversification and spectral tuning in marine proteorhodopsins". The EMBO Journal 22 (8): 1725–31. doi:10.1093/emboj/cdg183. PMC 154475. PMID 12682005. 
  7. ^ Kelemen BR, Du M, Jensen RB (Dec 2003). "Proteorhodopsin in living color: diversity of spectral properties within living bacterial cells". Biochimica Et Biophysica Acta 1618 (1): 25–32. doi:10.1016/j.bbamem.2003.10.002. PMID 14643930. 
  8. ^ a b Sabehi G, Kirkup BC, Rozenberg M, Stambler N, Polz MF, Béjà O (May 2007). "Adaptation and spectral tuning in divergent marine proteorhodopsins from the eastern Mediterranean and the Sargasso Seas". The ISME Journal 1 (1): 48–55. doi:10.1038/ismej.2007.10. PMID 18043613. 
  9. ^ 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 (Apr 2004). "Environmental genome shotgun sequencing of the Sargasso Sea". Science 304 (5667): 66–74. Bibcode:2004Sci...304...66V. doi:10.1126/science.1093857. PMID 15001713. 
  10. ^ a b c Dioumaev AK, Brown LS, Shih J, Spudich EN, Spudich JL, Lanyi JK (Apr 2002). "Proton transfers in the photochemical reaction cycle of proteorhodopsin". Biochemistry 41 (17): 5348–58. doi:10.1021/bi025563x. PMID 11969395. 
  11. ^ Partha R, Krebs R, Caterino TL, Braiman MS (Jun 2005). "Weakened coupling of conserved arginine to the proteorhodopsin chromophore and its counterion implies structural differences from bacteriorhodopsin". Biochimica Et Biophysica Acta 1708 (1): 6–12. doi:10.1016/j.bbabio.2004.12.009. PMID 15949979. 
  12. ^ Dioumaev AK, Wang JM, Bálint Z, Váró G, Lanyi JK (Jun 2003). "Proton transport by proteorhodopsin requires that the retinal Schiff base counterion Asp-97 be anionic". Biochemistry 42 (21): 6582–7. doi:10.1021/bi034253r. PMID 12767242. 
  13. ^ Krebs RA, Alexiev U, Partha R, DeVita AM, Braiman MS (Apr 2002). "Detection of fast light-activated H+ release and M intermediate formation from proteorhodopsin". BMC Physiology 2: 5. doi:10.1186/1472-6793-2-5. PMC 103662. PMID 11943070. 
  14. ^ Xiao Y, Partha R, Krebs R, Braiman M (Jan 2005). "Time-resolved FTIR spectroscopy of the photointermediates involved in fast transient H+ release by proteorhodopsin". The Journal of Physical Chemistry. B 109 (1): 634–41. doi:10.1021/jp046314g. PMID 16851056. 
  15. ^ Martinez A, Bradley AS, Waldbauer JR, Summons RE, DeLong EF (2007). "Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host". PNAS 104 (13): 5590–5595. Bibcode:2007PNAS..104.5590M. doi:10.1073/pnas.0611470104. PMC 1838496. PMID 17372221.