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PEDS Advance Access originally published online on October 24, 2005
Protein Engineering Design and Selection 2005 18(12):589-596; doi:10.1093/protein/gzi065
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

An evolution-based analysis scheme to identify CO2/O2 specificity-determining factors for ribulose 1,5-bisphosphate carboxylase/oxygenase

Gong-Xin Yu1,2, Byung-Hoon Park, Praveen Chandramohan, Al Geist and Nagiza F. Samatova2

Computational Biology Institute, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA 1Present address: Virginia Bioinformatics Institute, Washington Street, Blacksburg, VA 24061, USA

2 To whom correspondence should be addressed. E-mail: yu07_2000{at}yahoo.com or samatovan{at}ornl.gov

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) catalyzes a rate-limiting step in photosynthetic carbon assimilation (reacting with CO2) and its competitive photo-respiratory carbon oxidation (reacting with O2). RuBisCo enzyme with an enhanced CO2/O2 specificity would boost the ability to make great progress in agricultural production and environmental management. RuBisCos in marine non-green algae, resulting from an earlier endo-symbiotic event, diverge greatly from those in green plants and cyanobacteria and, further, have the highest CO2/O2 specificity whereas RuBisCos in cyanobacteria have the lowest. We assumed that there exist different levels of CO2/O2 specificity-determining factors, corresponding to different evolutionary events and specificity levels. Based on this assumption, we devised a scheme to identify these substrate-determining factors. From this analysis, we are able to discover different categories of the CO2/O2 specificity-determining factors that show which residue substitutions account for (relatively) small specificity changes, as happened in green plants, or a tremendous enhancement, as observed in marine non-green algae. Therefore, the analysis can improve our understanding of molecular mechanisms in the substrate specificity development and prioritize candidate specificity-determining surface residues for site-directed mutagenesis.

Keywords: chloroplast evolution/CO2/O2 specificity/photosynthesis/photorespiration/ribulose 1,5-bisphosphate carboxylase/oxygenase/RuBisCo/residue substitution pattern

Received July 11, 2005; revised August 13, 2005; accepted September 2, 2005.

Edited by Michael Hecht


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