A map of the rubisco biochemical landscape
2025/01/22 by Noam Prywes, Naiya R. Phillips, Luke M. Oltrogge +18 · 1 voice · 66 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · #Biochemistry #Biology #Chemistry #Computational biology #Directed evolution #Enzyme #Function (biology) #Gene #Genetics #Microbial Metabolic Engineering and Bioproduction #Mutant #Mutation #Photosynthetic Processes and Mechanisms #Plant biochemistry and biosynthesis #Protein engineering #RuBisCO
paper · pdf · doi:10.1038/s41586-024-08455-0
published in Nature 638(8051), 823-828 (Nature Portfolio)
openalex publication_date 2025/01/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06
Abstract
Abstract Rubisco is the primary CO 2 -fixing enzyme of the biosphere 1 , yet it has slow kinetics 2 . The roles of evolution and chemical mechanism in constraining its biochemical function remain debated 3,4 . Engineering efforts aimed at adjusting the biochemical parameters of rubisco have largely failed 5 , although recent results indicate that the functional potential of rubisco has a wider scope than previously known 6 . Here we developed a massively parallel assay, using an engineered Escherichia coli 7 in which enzyme activity is coupled to growth, to systematically map the sequence–function landscape of rubisco. Composite assay of more than 99% of single-amino acid mutants versus CO 2 concentration enabled inference of enzyme velocity and apparent CO 2 affinity parameters for thousands of substitutions. This approach identified many highly conserved positions that tolerate mutation and rare mutations that improve CO 2 affinity. These data indicate that non-trivial biochemical changes are readily accessible and that the functional distance between rubiscos from diverse organisms can be traversed, laying the groundwork for further enzyme engineering efforts.
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- Harnessing natural variation for photosynthetic improvement in next‐generation crop breeding
- Calvin cycle driven autotrophic CO2-fixation traits and autotrophic microbial communities in paddy (Anthrosol) and upland (Vertisol) soils: rhizosphere effects and impacts of biochar
- Pyrenoid Structure, Function, Evolution, and Characterization Across Diverse Lineages
- Atomic resolution structure of spinach rubisco reveals protons and dynamics
- Mutational scanning of TnpB reveals latent activity for genome editing
- Aerobic syngas conversion: opportunities, challenges, and solutions
- The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations
- Understanding carboxysomes to enhance carbon fixation in crops. [europepmc]
- A Cyanobacterial Screening Platform for Rubisco Mutant Variants. [europepmc]
- Approaches for regulating enzyme activities: Recent advances in experiment and computation. [europepmc]
- Directed evolution of a plant Rubisco chaperone with altered client recognition. [europepmc]
- Molecular Mechanisms of Herbicide Resistance in Rapeseed: Current Status and Future Prospects for Resistant Germplasm Development. [europepmc]
- Harnessing plant agriculture to mitigate climate change: A framework to evaluate synthetic biology (and other) interventions. [europepmc]
- Rubisco is slow across the tree of life. [europepmc]
- High-Throughput Detection of Cyanobacterial Form I Rubisco Assembly. [europepmc]
- Reprogramme the E. coli metabolism by engineering a functional carbon-fixation pathway. [europepmc]
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications. [europepmc]
- Continuous Directed Evolution of a Short-Lived Plant Histidinol Dehydrogenase. [europepmc]
- AI-enabled protein design facilitates future plant research and crop breeding. [europepmc]
- Scalable and cost-efficient custom gene library assembly from oligopools. [europepmc]
- Engineering and Biological Mechanisms of Microalgal CO 2 Fixation: A Review from Molecular Regulation to System Optimization. [europepmc]
- RuBisCO-based CO2 fixation improves glutamate production in Corynebacterium glutamicum [europepmc]
- Origin of chaperone dependence and assembly complexity in Rubisco’s biogenesis [europepmc]
- Reprogramme the E. coli metabolism by engineering a functional carbon-fixation pathway [europepmc]
- Form IF Rubiscos include highly active, specific, and small subunit-independent enzymes [europepmc]
- Rubisco is slow across the tree of life [europepmc]
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