Manipulation of Rubisco: the amount, activity, function and regulation

Parry, M. A. J.; Andralojc, P. J.; Mitchell, R. A. C.; Madgwick, P. J.; Keys, A. J.

doi:10.1093/jxb/erg141

Cited by 327 publications

(218 citation statements)

References 127 publications

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“…This destabilization could directly alter the catalytic parameters by allowing more flexibility in loop 6, thus affecting the opening and closing of the active site (16). Extensive studies of this loop region in algal and cyanobacterial RubisCOs have shown that catalytic parameters are sensitive to its modification even if the mutated residues have no direct interaction with substrates (30). L270I is located directly beneath H298, which interacts with the P5 phosphate in the preactivated state.…”

Section: Analysis Of Mutations Occurring During Evolution and Their Ementioning

confidence: 99%

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO

Studer

Christin

Williams

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

153

143

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A well-known case of evolutionary adaptation is that of ribulose-1,5-bisphosphate carboxylase (RubisCO), the enzyme responsible for fixation of CO 2 during photosynthesis. Although the majority of plants use the ancestral C 3 photosynthetic pathway, many flowering plants have evolved a derived pathway named C 4 photosynthesis. The latter concentrates CO 2 , and C 4 RubisCOs consequently have lower specificity for, and faster turnover of, CO 2 . The C 4 forms result from convergent evolution in multiple clades, with substitutions at a small number of sites under positive selection. To understand the physical constraints on these evolutionary changes, we reconstructed in silico ancestral sequences and 3D structures of RubisCO from a large group of related C 3 and C 4 species. We were able to precisely track their past evolutionary trajectories, identify mutations on each branch of the phylogeny, and evaluate their stability effect. We show that RubisCO evolution has been constrained by stability-activity tradeoffs similar in character to those previously identified in laboratory-based experiments. The C 4 properties require a subset of several ancestral destabilizing mutations, which from their location in the structure are inferred to mainly be involved in enhancing conformational flexibility of the open-closed transition in the catalytic cycle. These mutations are near, but not in, the active site or at intersubunit interfaces. The C 3 to C 4 transition is preceded by a sustained period in which stability of the enzyme is increased, creating the capacity to accept the functionally necessary destabilizing mutations, and is immediately followed by compensatory mutations that restore global stability.T he adaptive diversification of organisms often requires the evolution of novel enzymatic properties. The evolutionary shift from one enzymatic function to another involves crossing an energetic barrier in a fitness landscape (1). The number of mutations that confer advantageous function during such a shift is consequently limited. Some residues are critical for maintaining the stability of the protein fold, others are important for the catalytic activity itself. Due to the multiple roles of amino acids in proteins, the adaptation of one physical parameter of an enzyme is likely to affect other properties (2). As proteins usually form thermodynamically stable structures, their evolutionary trajectories are constrained to a narrow range of stability (3). Stability and activity are likely to be negatively correlated. Most possible amino acid changes in native proteins are destabilizing and, consequently, mutations that lead to a more favorable enzyme activity are likely to decrease the stability of the protein (2, 4). Compensatory mutations are then needed to restore global stability. These processes are referred to as stability-activity tradeoffs (5-7). Furthermore, proteins with higher stability confer greater evolvability, because there is more scope to accept destabilizing yet functionally beneficial changes (8). Wh...

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Section: Analysis Of Mutations Occurring During Evolution and Their Ementioning

confidence: 99%

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO

Studer

Christin

Williams

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

153

143

View full text Add to dashboard Cite

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“…Many agriculturally important crops, including cereals such as rice (Oryza sativa) and most woody perennials, are classified as C 3 plants. Their photosynthetic rate at present atmospheric CO 2 level is limited by the activity of Rubisco because of its extremely low catalytic turnover rate (k cat ) and competing oxygenase reaction, which initiates wasteful photorespiration (von Caemmerer and Quick, 2000;Parry et al, 2003). To compensate for these detrimental enzymatic properties, C 3 plants invest 15% to 35% of total leaf nitrogen in this single enzyme (Evans, 1989;Makino et al, 1992).…”

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confidence: 99%

Functional Incorporation of Sorghum Small Subunit Increases the Catalytic Turnover Rate of Rubisco in Transgenic Rice

et al. 2011

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Rubisco limits photosynthetic CO 2 fixation because of its low catalytic turnover rate (k cat ) and competing oxygenase reaction. Previous attempts to improve the catalytic efficiency of Rubisco by genetic engineering have gained little progress. Here we demonstrate that the introduction of the small subunit (RbcS) of high k cat Rubisco from the C 4 plant sorghum (Sorghum bicolor) significantly enhances k cat of Rubisco in transgenic rice (Oryza sativa). Three independent transgenic lines expressed sorghum RbcS at a high level, accounting for 30%, 44%, and 79% of the total RbcS. Rubisco was likely present as a chimera of sorghum and rice RbcS, and showed 1.32-to 1.50-fold higher k cat than in nontransgenic rice. Rubisco from transgenic lines showed a higher K m for CO 2 and slightly lower specificity for CO 2 than nontransgenic controls. These results suggest that Rubisco in rice transformed with sorghum RbcS partially acquires the catalytic properties of sorghum Rubisco. Rubisco content in transgenic lines was significantly increased over wild-type levels but Rubisco activation was slightly decreased. The expression of sorghum RbcS did not affect CO 2 assimilation rates under a range of CO 2 partial pressures. The J max /V cmax ratio was significantly lower in transgenic line compared to the nontransgenic plants. These observations suggest that the capacity of electron transport is not sufficient to support the increased Rubisco capacity in transgenic rice. Although the photosynthetic rate was not enhanced, the strategy presented here opens the way to engineering Rubisco for improvement of photosynthesis and productivity in the future.

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“…In Arabidopsis, per gm fresh weight, leaves have higher amount of protein content than roots, flowers and siliques mostly due to the presence of rubisco which accounts for 50 % of total protein. (Parry et al 2003). The higher demand of huge amount of nitrogen is met by the nitrogen and sulfur assimilation pathway operating chiefly in leaves.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic analysis and photoregulation of siroheme biosynthesis genes: uroporphyrinogen III methyltransferase and sirohydrochlorin ferrochelatase of Arabidopsis thaliana

Garai

Joshi

Tripathy

2016

Physiol Mol Biol Plants

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Uroporphyrinogen III methyl transferase (UPM1) and Sirohydrochlorin ferrochelatase (SIRB) are the important genes involved in the biosynthesis of siroheme, the prosthetic group of nitrite reductases (NiR) and sulfite reductases (SiR) involved in nitrogen and sulfur assimilation. Both UPM1 and SIRB could be potential candidate genes targeted for sustainable agriculture especially in N-deficient soil. The phylogenetic analysis revealed that these genes are highly conserved among algae, bryophytes and vascular plants including dicots and monocots. The Arabidopsis proteins UPM1 and SIRB have close similarity with Camelina sativa followed by Brassica napus, Brassica rapa, and Brassica oleracea of the family brassicaceae. The tissue specific expression studies revealed that both the gene are expressed in stem, flower and silique and have highest expression in leaves where the protein content is quite high. The in silico promoter analysis revealed the presence of several light-responsive elements like GATA box, G box, I box, SORLIP2, SORLIP5, SORLREP3 and SORLREP4. Therefore, expression of both the genes was minimal in etiolated seedlings and was upregulated in light. Photo-regulation of transcript abundance of UPM1 and SIRB involved in the biosynthesis of siroheme the cofactor involved in 6 electron reduction of NO 2 -and SO 3 2-by NiR and SiR is crucial as the gene expression of latter two enzymes along with other N and S assimilatory enzymes are also modulated by light.

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Manipulation of Rubisco: the amount, activity, function and regulation

Cited by 327 publications

References 127 publications

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO

Functional Incorporation of Sorghum Small Subunit Increases the Catalytic Turnover Rate of Rubisco in Transgenic Rice

Phylogenetic analysis and photoregulation of siroheme biosynthesis genes: uroporphyrinogen III methyltransferase and sirohydrochlorin ferrochelatase of Arabidopsis thaliana

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