A map of the rubisco biochemical landscape

Abstract

Rubisco is the primary CO₂-fixing enzyme of the biosphere¹, yet it has slow kinetics². 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 failed⁵, although recent results indicate that the functional potential of rubisco has a wider scope than previously known⁶. Here we developed a massively parallel assay, using an engineered Escherichia coli⁷ 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 CO₂ concentration enabled inference of enzyme velocity and apparent CO₂ affinity parameters for thousands of substitutions. This approach identified many highly conserved positions that tolerate mutation and rare mutations that improve CO₂ 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.