Mutation design of a thermophilic Rubisco based on three-dimensional structure enhances its activity at ambient temperature

Proteins. 2016 Oct;84(10):1339-46. doi: 10.1002/prot.25080. Epub 2016 Jun 24.

Abstract

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) plays a central role in carbon dioxide fixation on our planet. Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk-Rubisco) shows approximately twenty times the activity of spinach Rubisco at high temperature, but only one-eighth the activity at ambient temperature. We have tried to improve the activity of Tk-Rubisco at ambient temperature, and have successfully constructed several mutants which showed higher activities than the wild-type enzyme both in vitro and in vivo. Here, we designed new Tk-Rubisco mutants based on its three-dimensional structure and a sequence comparison of thermophilic and mesophilic plant Rubiscos. Four mutations were introduced to generate new mutants based on this strategy, and one of the four mutants, T289D, showed significantly improved activity compared to that of the wild-type enzyme. The crystal structure of the Tk-Rubisco T289D mutant suggested that the increase in activity was due to mechanisms distinct from those involved in the improvement in activity of Tk-Rubisco SP8, a mutant protein previously reported to show the highest activity at ambient temperature. Combining the mutations of T289D and SP8 successfully generated a mutant protein (SP8-T289D) with the highest activity to date both in vitro and in vivo. The improvement was particularly pronounced for the in vivo activity of SP8-T289D when introduced into the mesophilic, photosynthetic bacterium Rhodopseudomonas palustris, which resulted in a strain with nearly two-fold higher specific growth rates compared to that of a strain harboring the wild-type enzyme at ambient temperature. Proteins 2016; 84:1339-1346. © 2016 Wiley Periodicals, Inc.

Keywords: carbon dioxide fixation; crystal structure; protein engineering; protein-ligand complex; ribulose-1,5-bisphosphate carboxylase/oxygenase.

MeSH terms

  • Amino Acid Sequence
  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Kinetics
  • Models, Molecular
  • Mutation*
  • Plant Proteins / chemistry*
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Plasmids / chemistry
  • Plasmids / metabolism
  • Protein Engineering
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Rhodopseudomonas / chemistry
  • Rhodopseudomonas / enzymology
  • Rhodopseudomonas / genetics
  • Ribulose-Bisphosphate Carboxylase / chemistry*
  • Ribulose-Bisphosphate Carboxylase / genetics
  • Ribulose-Bisphosphate Carboxylase / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Spinacia oleracea / chemistry
  • Spinacia oleracea / enzymology
  • Spinacia oleracea / genetics
  • Structure-Activity Relationship
  • Thermococcus / chemistry
  • Thermococcus / enzymology
  • Thermococcus / genetics

Substances

  • Archaeal Proteins
  • Bacterial Proteins
  • Plant Proteins
  • Recombinant Proteins
  • Ribulose-Bisphosphate Carboxylase