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MBE Advance Access published online on August 3, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl079
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted July 12, 2006

Research Article

Conservation of Distantly Related Membrane Proteins: Photosynthetic Reaction Centers Share a Common Structural Core

Sumedha Sadekar 1, Jason Raymond 2, and Robert E. Blankenship 3 *

1 Computational Biosciences Program, Arizona State University, Tempe, AZ 85287-1604 USA
2 Microbial Systems Division, Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
3 Departments of Biology and Chemistry, Washington University, St. Louis, MO 63130 USA

* To whom correspondence should be addressed.
Robert E. Blankenship, E-mail: blankenship{at}wustl.edu


  Abstract

Photosynthesis was established on the Earth more than 3 billion years ago. All available evidence suggests that the earliest photosynthetic organisms were anoxygenic and that oxygen-evolving photosynthesis is a more recent development. The reaction center complexes that form the heart of the energy storage process are integral membrane pigment-proteins that span the membrane in vectorial fashion to carry out electron transfer. The origin and extent of distribution of these proteins has been perplexing from a phylogenetic point of view, mostly because of extreme sequence divergence. A series of integral membrane proteins of known structure and varying degrees of sequence identity have been compared using combinatorial extension-Monte Carlo methods. The proteins include photosynthetic reaction centers from proteobacteria and cyanobacterial photosystems I and II, as well as cytochrome oxidase, bacteriorhodopsin and cytochrome b. The reaction center complexes show a remarkable conservation of the core structure of five transmembrane helices, strongly implying common ancestry, even though the residual sequence identity is less than 10%, while the other proteins have structures that are unrelated. A relationship of sequence with structure was derived from the reaction center structures; with characteristic decay length of 1.6 Å. Phylogenetic trees derived from the structural alignments give insights into the earliest photosynthetic reaction center, strongly suggesting that it was a homodimeric complex that did not evolve oxygen.

Keywords: Photosynthesis; evolution; reaction center; protein structure.
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