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

Gong Xin Yu; Byung Hoon Park; Praveen Chandramohan; Al Geist; Nagiza F. Samatova

doi:10.1093/protein/gzi065

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

Gong Xin Yu, Byung Hoon Park, Praveen Chandramohan, Al Geist, Nagiza F. Samatova

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

Abstract

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) catalyzes a rate-limiting step in photosynthetic carbon assimilation (reacting with CO ₂) and its competitive photo-respiratory carbon oxidation (reacting with O₂). RuBisCo enzyme with an enhanced CO₂/O ₂ 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 CO ₂/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 CO ₂/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.

Original language	English
Pages (from-to)	589-596
Number of pages	8
Journal	Protein Engineering, Design and Selection
Volume	18
Issue number	12
DOIs	https://doi.org/10.1093/protein/gzi065
State	Published - Dec 2005

Funding

This work was funded by the US Department of Energy’s Genomes to Life program (www.doegenomestolife.org) under the project ‘Carbon Sequestration in Synechococcus sp.: from Molecular Machines to Hierarchical Modeling’ (www.genomes-to-life.org). The work of N.F.S. was sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory. This research used resources of the Center for Computational Sciences and the eXtreme TORC cluster at Oak Ridge National Laboratory.

Funders	Funder number
U.S. Department of Energy
Oak Ridge National Laboratory

Keywords

CO
Chloroplast evolution
O specificity
Oxygenase
Photorespiration
Photosynthesis
Residue substitution pattern
Ribulose 1,5-bisphosphate carboxylase
RuBisCo

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1093/protein/gzi065

Cite this

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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 CO 2) and its competitive photo-respiratory carbon oxidation (reacting with O2). RuBisCo enzyme with an enhanced CO2/O 2 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 CO 2/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 CO 2/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 = "CO, Chloroplast evolution, O specificity, Oxygenase, Photorespiration, Photosynthesis, Residue substitution pattern, Ribulose 1,5-bisphosphate carboxylase, RuBisCo",

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AU - Yu, Gong Xin

AU - Park, Byung Hoon

AU - Chandramohan, Praveen

AU - Geist, Al

AU - Samatova, Nagiza F.

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N2 - Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) catalyzes a rate-limiting step in photosynthetic carbon assimilation (reacting with CO 2) and its competitive photo-respiratory carbon oxidation (reacting with O2). RuBisCo enzyme with an enhanced CO2/O 2 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 CO 2/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 CO 2/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.

AB - Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) catalyzes a rate-limiting step in photosynthetic carbon assimilation (reacting with CO 2) and its competitive photo-respiratory carbon oxidation (reacting with O2). RuBisCo enzyme with an enhanced CO2/O 2 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 CO 2/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 CO 2/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.

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