Skip Navigation



PEDS Advance Access published online on October 24, 2005
Protein Engineering Design and Selection, doi:10.1093/protein/gzi065
This Article
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
18/12/589    most recent
gzi065v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Yu, G.-X.
Right arrow Articles by Samatova, N. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yu, G.-X.
Right arrow Articles by Samatova, N. F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org
Received July 11, 2005
Revised August 13, 2005
Accepted September 2, 2005

Article

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

Gong-Xin Yu 1*, Byung-Hoon Park 2, Praveen Chandramohan 2, Al Geist 2, and Nagiza F. Samatova 2

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

* To whom correspondence should be addressed.
Gong-Xin Yu, E-mail: yu07_2000{at}yahoo.com


  Abstract

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.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
P.-A. Christin, N. Salamin, A. M. Muasya, E. H. Roalson, F. Russier, and G. Besnard
Evolutionary Switch and Genetic Convergence on rbcL following the Evolution of C4 Photosynthesis
Mol. Biol. Evol., November 1, 2008; 25(11): 2361 - 2368.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
T. J. Barkman, T. R. Martins, E. Sutton, and J. T. Stout
Positive Selection for Single Amino Acid Change Promotes Substrate Discrimination of a Plant Volatile-Producing Enzyme
Mol. Biol. Evol., June 1, 2007; 24(6): 1320 - 1329.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.