title: An evolution-based analysis scheme to identify CO2/O2 specificity-determining factors for ribulose 1,5-bisphosphate carboxylase/oxygenase.
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.
authors.affiliation: Computational Biology Institute, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA. yu07_2000@yahoo.com
authors.forename: Gong-Xin
authors.initials: GX
authors.lastname: Yu
authors.forename: Byung-Hoon
authors.initials: BH
authors.lastname: Park
authors.forename: Praveen
authors.initials: P
authors.lastname: Chandramohan
authors.forename: Al
authors.initials: A
authors.lastname: Geist
authors.forename: Nagiza F
authors.initials: NF
authors.lastname: Samatova
mesh_terms: D000595:Amino Acid Sequence; D002245:Carbon Dioxide / Q000378:metabolism*; D019295:Computational Biology; D000458:Cyanobacteria / Q000201:enzymology; D030562:Databases, Protein; D056890:Eukaryota / Q000201:enzymology; D019143:Evolution, Molecular; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D010100:Oxygen / Q000378:metabolism*; D010944:Plants / Q000201:enzymology; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics* / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D002245:Carbon Dioxide; D012273:Ribulose-Bisphosphate Carboxylase; D010100:Oxygen