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Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment

  1. Joseph P. Bielawski † , ‡ , §,
  2. Katherine A. Dunn †,
  3. Gazalah Sabehi , and
  4. Oded Béjà
  1. †Department of Biology and ‡Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada B3H 4J1; and Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel

  1. Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved August 26, 2004 (received for review June 4, 2004)

Abstract

Proteorhodopsin, a retinal-binding protein, represents a potentially significant source of light-driven energy production in the world's oceans. The distribution of photochemically divergent proteorhodopsins is stratified according to depth. Here, we present evidence that such photochemical diversity was tuned by Darwinian selection. By using a Bayesian method, we identified sites targeted by Darwinian selection and mapped them to three-dimensional models of proteorhodopsins. We suggest that spectral fine-tuning results from the combined effect of amino acids that directly interact with retinal and those that influence the confirmation of the retinal-binding pocket.

Footnotes

  • ↵ § To whom correspondence should be addressed. E-mail: j.bielawski{at}dal.ca.

  • Author contributions: J.P.B. designed research; J.P.B., K.A.D., G.S., and O.B. performed research; J.P.B. and K.A.D. analyzed data; and J.P.B. and K.A.D. wrote the paper.

  • This paper was submitted directly (Track II) to the PNAS office.

  • Abbreviations: BG, background; FG, foreground; LRT, likelihood ratio test; ML, maximum likelihood; PR, proteorhodopsin; G-PR, green-absorbing PR; B-PR, blue-absorbing PR; PS, positive selection.

  • Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AY250714, AY250716, AY250733, AY598757, AY598758, AY601905, and AY728898).

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