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A map of the rubisco biochemical landscape.
Prywes, Noam; Philips, Naiya R; Oltrogge, Luke M; Lindner, Sebastian; Candace Tsai, Yi-Chin; de Pins, Benoit; Cowan, Aidan E; Taylor-Kearney, Leah J; Chang, Hana A; Hall, Laina N; Bellieny-Rabelo, Daniel; Nisonoff, Hunter M; Weissman, Rachel F; Flamholz, Avi I; Ding, David; Bhatt, Abhishek Y; Shih, Patrick M; Mueller-Cajar, Oliver; Milo, Ron; Savage, David F.
Affiliation
  • Prywes N; Innovative Genomics Institute, University of California; Berkeley, California 94720, USA.
  • Philips NR; Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA.
  • Oltrogge LM; Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA.
  • Lindner S; Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA.
  • Candace Tsai YC; Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA.
  • de Pins B; University of Heidelberg; 69047 Heidelberg, Germany.
  • Cowan AE; School of Biological Sciences, Nanyang Technological University; Singapore 637551, Singapore.
  • Taylor-Kearney LJ; Department of Plant and Environmental Sciences, Weizmann Institute of Science; Rehovot 76100, Israel.
  • Chang HA; Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA.
  • Hall LN; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory; Emeryville, CA 94608, USA.
  • Bellieny-Rabelo D; Department of Plant and Microbial Biology, University of California, Berkeley; Berkeley, CA 94720, USA.
  • Nisonoff HM; Department of Plant and Microbial Biology, University of California, Berkeley; Berkeley, CA 94720, USA.
  • Weissman RF; Biophysics, University of California, Berkeley; Berkeley, CA 94720, USA.
  • Flamholz AI; Innovative Genomics Institute, University of California; Berkeley, California 94720, USA.
  • Ding D; California Institute for Quantitative Biosciences (QB3), University of California; Berkeley, CA 94720, USA.
  • Bhatt AY; Center for Computational Biology, University of California, Berkeley; Berkeley, CA, USA.
  • Shih PM; Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA.
  • Mueller-Cajar O; Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125.
  • Milo R; Innovative Genomics Institute, University of California; Berkeley, California 94720, USA.
  • Savage DF; Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA.
bioRxiv ; 2024 Apr 11.
Article in En | MEDLINE | ID: mdl-38645011
ABSTRACT
Rubisco is the primary CO2 fixing enzyme of the biosphere yet has slow kinetics. The roles of evolution and chemical mechanism in constraining the sequence landscape of rubisco remain debated. In order to map sequence to function, we developed a massively parallel assay for rubisco using an engineered E. coli where enzyme function is coupled to growth. By assaying >99% of single amino acid mutants across CO2 concentrations, we inferred enzyme velocity and CO2 affinity for thousands of substitutions. We identified many highly conserved positions that tolerate mutation and rare mutations that improve CO2 affinity. These data suggest that non-trivial kinetic improvements are readily accessible and provide a comprehensive sequence-to-function mapping for enzyme engineering efforts.
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Full text: 1 Database: MEDLINE Language: En Year: 2024 Type: Article
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Full text: 1 Database: MEDLINE Language: En Year: 2024 Type: Article