A map of the rubisco biochemical landscape

Prywes, Noam [University of California, Berkeley, CA (United States)] (ORCID:0000000325262392); Phillips, Naiya R. [University of California, Berkeley, CA (United States)] (ORCID:0000000318365182); Oltrogge, Luke M. [University of California, Berkeley, CA (United States)] (ORCID:0000000157169980); Lindner, Sebastian [Heidelberg University (Germany)] (ORCID:0009000982512758); Taylor-Kearney, Leah J. [University of California, Berkeley, CA (United States)] (ORCID:0000000175307670); Tsai, Yi-Chin Candace [Nanyang Technological University (Singapore)]; de Pins, Benoit [University of Naples Federico II (Italy)]; Cowan, Aidan E. [University of California, Berkeley, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Emeryville, CA (United States)]; Chang, Hana A. [University of California, Berkeley, CA (United States)] (ORCID:0009000519190363); Wang, Renée Z. [University of California, Berkeley, CA (United States)] (ORCID:0000000339943244); Hall, Laina N. [University of California, Berkeley, CA (United States)] (ORCID:000000033135332X); Bellieny-Rabelo, Daniel [University of California, Berkeley, CA (United States)] (ORCID:0000000325447899); Nisonoff, Hunter M. [University of California, Berkeley, CA (United States)] (ORCID:0000000313578111); Weissman, Rachel F. [University of California, Berkeley, CA (United States)]; Flamholz, Avi I. [California Institute of Technology (CalTech), Pasadena, CA (United States)]; Ding, David [University of California, Berkeley, CA (United States)]; Bhatt, Abhishek Y. [University of California, Berkeley, CA (United States); University of California, San Diego, CA (United States)]; Mueller-Cajar, Oliver [Nanyang Technological University (Singapore)] (ORCID:0000000328665963); Shih, Patrick M. [University of California, Berkeley, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000221193345); Milo, Ron [Weizmann Institute of Science, Rehovot (Israel)]; Savage, David F. [University of California, Berkeley, CA (United States)] (ORCID:0000000300422257)

doi:10.1038/s41586-024-08455-0

DOE OSTI · 2565869

A map of the rubisco biochemical landscape

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Abstract

Rubisco is the primary CO 2 -fixing enzyme of the biosphere, yet it has slow kinetics. The roles of evolution and chemical mechanism in constraining its biochemical function remain debated. Engineering efforts aimed at adjusting the biochemical parameters of rubisco have largely failed, although recent results indicate that the functional potential of rubisco has a wider scope than previously known. Here we developed a massively parallel assay, using an engineered Escherichia coli 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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Prywes, Noam [University of California, Berkeley, CA (United States)] (ORCID:0000000325262392), Phillips, Naiya R. [University of California, Berkeley, CA (United States)] (ORCID:0000000318365182), Oltrogge, Luke M. [University of California, Berkeley, CA (United States)] (ORCID:0000000157169980), Lindner, Sebastian [Heidelberg University (Germany)] (ORCID:0009000982512758), Taylor-Kearney, Leah J. [University of California, Berkeley, CA (United States)] (ORCID:0000000175307670), Tsai, Yi-Chin Candace [Nanyang Technological University (Singapore)], de Pins, Benoit [University of Naples Federico II (Italy)], Cowan, Aidan E. [University of California, Berkeley, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Emeryville, CA (United States)], Chang, Hana A. [University of California, Berkeley, CA (United States)] (ORCID:0009000519190363), Wang, Renée Z. [University of California, Berkeley, CA (United States)] (ORCID:0000000339943244), Hall, Laina N. [University of California, Berkeley, CA (United States)] (ORCID:000000033135332X), Bellieny-Rabelo, Daniel [University of California, Berkeley, CA (United States)] (ORCID:0000000325447899), Nisonoff, Hunter M. [University of California, Berkeley, CA (United States)] (ORCID:0000000313578111), Weissman, Rachel F. [University of California, Berkeley, CA (United States)], Flamholz, Avi I. [California Institute of Technology (CalTech), Pasadena, CA (United States)], Ding, David [University of California, Berkeley, CA (United States)], Bhatt, Abhishek Y. [University of California, Berkeley, CA (United States); University of California, San Diego, CA (United States)], Mueller-Cajar, Oliver [Nanyang Technological University (Singapore)] (ORCID:0000000328665963), Shih, Patrick M. [University of California, Berkeley, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000221193345), Milo, Ron [Weizmann Institute of Science, Rehovot (Israel)], Savage, David F. [University of California, Berkeley, CA (United States)] (ORCID:0000000300422257). 2025-01-22. A map of the rubisco biochemical landscape. https://doi.org/10.1038/s41586-024-08455-0

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