Response to Tcherkez and Farquhar: Rubisco adaptation is more limited by phylogenetic constraint than by catalytic trade-off

Bouvier, Jacques W.; Kelly, Steven

doi:10.1016/j.jplph.2023.154021

Cited by 4 publications

(13 citation statements)

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“…Within Form I rubisco the active site is located in RbcL ( 16 , 20 , 21 ). As a result, interspecific differences in Form I kinetics are primarily attributable to sequence variation in RbcL ( 22 – 33 ). Despite not playing a direct role in catalysis, RbcS influences the function of rubisco ( 34 , 35 ) and its incorporation in the holoenzyme enables its higher kinetic efficiency ( 36 ).…”

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confidence: 99%

“…Moreover, there is increasing recognition of the importance of both environment ( 59 ) and organ-specific ( 60 , 61 ) differences in plant RbcS isoform expression on holoenzyme catalysis. However, even though RbcS influences holoenzyme function, sequence variation in RbcL remains the primary determinant of variation in kinetics ( 22 – 33 ).…”

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confidence: 99%

“…Specifically, analysis of larger species sets have revealed that kinetic trait correlations are not strong ( 83 – 85 ). In addition, phylogenetic signal in rubisco kinetics causes kinetic trait correlations to be overestimated unless phylogenetic comparative methods are employed ( 22 , 23 ). Thus, when larger datasets are analyzed with phylogenetic methods, the strength of catalytic trade-offs are substantially reduced ( 22 , 23 ).…”

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confidence: 99%

“…In addition, phylogenetic signal in rubisco kinetics causes kinetic trait correlations to be overestimated unless phylogenetic comparative methods are employed ( 22 , 23 ). Thus, when larger datasets are analyzed with phylogenetic methods, the strength of catalytic trade-offs are substantially reduced ( 22 , 23 ). Instead, phylogenetic constraints have had a larger impact on limiting enzyme adaptation compared to catalytic trade-offs ( 22 , 23 ).…”

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confidence: 99%

“…Thus, when larger datasets are analyzed with phylogenetic methods, the strength of catalytic trade-offs are substantially reduced ( 22 , 23 ). Instead, phylogenetic constraints have had a larger impact on limiting enzyme adaptation compared to catalytic trade-offs ( 22 , 23 ). These recent findings motivate a revaluation of the rubisco paradox, and an investigation of whether rubisco is evolving for improved catalysis and CO 2 assimilation in plants.…”

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Rubisco is evolving for improved catalytic efficiency and CO ₂ assimilation in plants

Bouvier,

Emms,

Kelly

2024

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

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Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of the molecular and kinetic evolution of Form I rubisco we uncover the evolutionary trajectory of rubisco kinetic evolution in angiosperms. We show that rbcL is among the 1% of slowest-evolving genes and enzymes on Earth, accumulating one nucleotide substitution every 0.9 My and one amino acid mutation every 7.2 My. Despite this, rubisco catalysis has been continually evolving toward improved CO 2 /O 2 specificity, carboxylase turnover, and carboxylation efficiency. Consistent with this kinetic adaptation, increased rubisco evolution has led to a concomitant improvement in leaf-level CO 2 assimilation. Thus, rubisco has been slowly but continually evolving toward improved catalytic efficiency and CO 2 assimilation in plants.

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confidence: 99%

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confidence: 99%

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confidence: 99%

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Rubisco is evolving for improved catalytic efficiency and CO ₂ assimilation in plants

Bouvier,

Emms,

Kelly

2024

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

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Evolution: Unearthing missing links in the origin of our planet’s primary carbon-fixing enzyme

Bouvier

2023

Current Biology

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Rubisco is evolving for improved catalytic efficiency and CO₂assimilation in plants

Bouvier

Emms

Kelly

2022

Preprint

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Rubisco assimilates CO2 to form the sugars that fuel life on Earth. Although rubisco is the source of most carbon in the biosphere, it is a surprisingly inefficient catalyst with a modest carboxylase turnover rate and a competing oxygenase activity which results in the loss of fixed CO2. These apparent shortcomings of rubisco present a puzzling evolutionary paradox: why does the enzyme appear well suited to the high CO2 low O2 conditions of its origin, rather than the low CO2 high O2 conditions of the present day? To help answer this question, we perform a phylogenetically resolved analysis of the molecular and kinetic evolution of Form I rubisco. We discover that rubisco is among the slowest evolving genes on Earth. Specifically, we find that the rubisco catalytic large subunit evolves substantially slower than its cognate small subunit, and is slower than >98% of all other genes and enzymes across the tree of life. Next, through simultaneous analysis of rubisco molecular and kinetic evolution in C3 angiosperms, we demonstrate that despite its slow molecular evolution, rubisco kinetics have evolved, and are continuing to evolve, to improve CO2/O2 specificity, carboxylase turnover and overall carboxylation efficiency. Thus, slow molecular evolution has severely limited rubisco kinetic optimisation, resulting in the present enzyme that is poorly adapted for current conditions.

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Response to Tcherkez and Farquhar: Rubisco adaptation is more limited by phylogenetic constraint than by catalytic trade-off

Cited by 4 publications

References 74 publications

Rubisco is evolving for improved catalytic efficiency and CO ₂ assimilation in plants

Rubisco is evolving for improved catalytic efficiency and CO ₂ assimilation in plants

Evolution: Unearthing missing links in the origin of our planet’s primary carbon-fixing enzyme

Rubisco is evolving for improved catalytic efficiency and CO₂assimilation in plants

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Response to Tcherkez and Farquhar: Rubisco adaptation is more limited by phylogenetic constraint than by catalytic trade-off

Cited by 4 publications

References 74 publications

Rubisco is evolving for improved catalytic efficiency and CO 2 assimilation in plants

Rubisco is evolving for improved catalytic efficiency and CO 2 assimilation in plants

Evolution: Unearthing missing links in the origin of our planet’s primary carbon-fixing enzyme

Rubisco is evolving for improved catalytic efficiency and CO2assimilation in plants

Contact Info

Product

Resources

About

Rubisco is evolving for improved catalytic efficiency and CO ₂ assimilation in plants

Rubisco is evolving for improved catalytic efficiency and CO ₂ assimilation in plants

Rubisco is evolving for improved catalytic efficiency and CO₂assimilation in plants