A map of the rubisco biochemical landscape
Noam Prywes, Naiya R. Phillips, Luke M. Oltrogge, Sebastian Lindner, Leah J. Taylor‐Kearney, Yi-Chin Candace Tsai, Benoit de Pins, Aidan E. Cowan, Hana A. Chang, Renée Z. Wang, L Hall, Daniel Bellieny‐Rabelo, Hunter Nisonoff, Rachel F. Weissman, Avi I. Flamholz, David Ding, Abhishek Bhatt, Oliver Mueller‐Cajar, Patrick M. Shih, Ron Milo, David F. Savage
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.