Overcoming the limitations of Rubisco: fantasy or realistic prospect?

Orr, Douglas J.; Parry, M. A. J.

doi:10.1016/j.jplph.2020.153285

Cited by 7 publications

(3 citation statements)

References 16 publications

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“…While photorespiration may play a regulatory role in carbon and nitrogen metabolism ( Flügel et al , 2017 ; Busch et al , 2018 ; Busch, 2020 ; Timm, 2020 ; Shi and Bloom, 2021 ), it is generally considered an energetically wasteful process that results in the loss of previously fixed CO 2 , and reduces the overall efficiency of photosynthesis and crop yield potential ( Zhu et al , 2010 ). As such, Rubisco and the proteins associated with its assembly and regulation (the so-called ‘Rubiscosome’) have been key targets for crop improvement for several decades ( Parry et al , 2013 ; Erb and Zarzycki, 2018 ; Orr and Parry, 2020 ; von Caemmerer, 2020 ; Taylor et al , 2022 ).…”

Section: Introductionmentioning

confidence: 99%

The small subunit of Rubisco and its potential as an engineering target

Mao

Catherall

Díaz-Ramos

et al. 2022

Journal of Experimental Botany

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Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.

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Section: Introductionmentioning

confidence: 99%

The small subunit of Rubisco and its potential as an engineering target

Mao

Catherall

Díaz-Ramos

et al. 2022

Journal of Experimental Botany

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“…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 ). Specifically, RbcS enhances the stability and assembly of the holoenzyme complex ( 21 , 37 – 42 ), improves the efficiency of CO 2 binding ( 43 ), and is thought to act as a reservoir for CO 2 accumulation ( 44 ).…”

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confidence: 99%

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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“…Improving Rubisco kinetic traits is therefore a target for improving plant carbon uptake and crop yield. One strategy of doing this is screening the natural diversity of Rubisco kinetics and replacing native Rubisco enzymes in plants with catalytically more efficient enzymes ( Ort et al , 2015 ; Hermida-Carrera et al , 2016 ; Orr et al , 2016 ; Sharwood et al , 2016 ; Galmés et al , 2019 ; Orr and Parry, 2020 ; Von Caemmerer, 2020 ; Iqbal et al , 2021 ; Johnson, 2022 ; Lin et al , 2022 ). Although there has been some progress with this strategy, direct replacement of Rubisco in crops is currently challenging, due to both limited capacity to mass-screen Rubisco kinetics, and Rubisco chaperone incompatibilities between distant species ( Kanevski et al , 1999 ; Whitney et al , 2011 , 2015 ; Wilson et al , 2016 , 2018 ; Sharwood, 2017 ; Zhou and Whitney, 2019 ; Gunn et al , 2020 ; Martin-Avila et al , 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Predicting plant Rubisco kinetics from RbcL sequence data using machine learning

Iqbal

Lisitsa

Kapralov

2022

Journal of Experimental Botany

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Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is responsible for the conversion of atmospheric CO2 to organic carbon during photosynthesis and often acts as a rate limiting step in the later process. Screening the natural diversity of Rubisco kinetics is the main strategy used to find better Rubiscos for crop engineering efforts. Here, we demonstrate the use of Gaussian processes (GPs), a family of Bayesian models, coupled with protein encoding schemes for predicting Rubisco kinetics from Rubisco large subunit (RbcL) sequence data. GPs trained on published experimentally obtained Rubisco kinetic datasets were applied to over 9,000 sequences encoding RbcL to predict Rubisco kinetic parameters. Notably, our predicted kinetic values were in agreement with known trends, e.g. higher carboxylation turnover rates (Kcat) for Rubiscos from C4 or Crassulacean acid metabolism (CAM) species compared to ones found in C3 species. This is the first study demonstrating machine learning approaches as a tool for screening and predicting Rubisco kinetics, and our approach could be applied to other enzymes.

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Overcoming the limitations of Rubisco: fantasy or realistic prospect?

Cited by 7 publications

References 16 publications

The small subunit of Rubisco and its potential as an engineering target

The small subunit of Rubisco and its potential as an engineering target

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

Predicting plant Rubisco kinetics from RbcL sequence data using machine learning

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Overcoming the limitations of Rubisco: fantasy or realistic prospect?

Cited by 7 publications

References 16 publications

The small subunit of Rubisco and its potential as an engineering target

The small subunit of Rubisco and its potential as an engineering target

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

Predicting plant Rubisco kinetics from RbcL sequence data using machine learning

Contact Info

Product

Resources

About

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