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Prywes N, Philips NR, Oltrogge LM, Lindner S, Candace Tsai YC, de Pins B, Cowan AE, Taylor-Kearney LJ, Chang HA, Hall LN, Bellieny-Rabelo D, Nisonoff HM, Weissman RF, Flamholz AI, Ding D, Bhatt AY, Shih PM, Mueller-Cajar O, Milo R, Savage DF. A map of the rubisco biochemical landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.27.559826. [PMID: 38645011 PMCID: PMC11030240 DOI: 10.1101/2023.09.27.559826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
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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Affiliation(s)
- Noam Prywes
- Innovative Genomics Institute, University of California; Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA
| | - Naiya R. Philips
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
| | - Luke M. Oltrogge
- Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
| | | | - Yi-Chin Candace Tsai
- School of Biological Sciences, Nanyang Technological University; Singapore 637551, Singapore
| | - Benoit de Pins
- Department of Plant and Environmental Sciences, Weizmann Institute of Science; Rehovot 76100, Israel
| | - Aidan E. Cowan
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory; Emeryville, CA 94608, USA
| | - Leah J. Taylor-Kearney
- Department of Plant and Microbial Biology, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Hana A. Chang
- Department of Plant and Microbial Biology, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Laina N. Hall
- Biophysics, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Daniel Bellieny-Rabelo
- Innovative Genomics Institute, University of California; Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California; Berkeley, CA 94720, USA
| | - Hunter M. Nisonoff
- Center for Computational Biology, University of California, Berkeley; Berkeley, CA, USA
| | - Rachel F. Weissman
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
| | - Avi I. Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125
| | - David Ding
- Innovative Genomics Institute, University of California; Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA
| | - Abhishek Y. Bhatt
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
- School of Medicine, University of California, San Diego; La Jolla, CA 92092, USA
| | - Patrick M. Shih
- Innovative Genomics Institute, University of California; Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley; Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory; Berkeley, CA 94720, USA
- Feedstocks Division, Joint BioEnergy Institute; Emeryville, CA 94608, USA
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University; Singapore 637551, Singapore
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science; Rehovot 76100, Israel
| | - David F. Savage
- Innovative Genomics Institute, University of California; Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
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Kinetic characterization of OmcA and MtrC, terminal reductases involved in respiratory electron transfer for dissimilatory iron reduction in Shewanella oneidensis MR-1. Appl Environ Microbiol 2009; 75:5218-26. [PMID: 19542342 DOI: 10.1128/aem.00544-09] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have used scaling kinetics and the concept of kinetic competence to elucidate the role of hemeproteins OmcA and MtrC in iron reduction by Shewanella oneidensis MR-1. Second-order rate constants for OmcA and MtrC were determined by single-turnover experiments. For soluble iron species, a stopped-flow apparatus was used, and for the less reactive iron oxide goethite, a conventional spectrophotometer was used to measure rates. Steady-state experiments were performed to obtain molecular rate constants by quantifying the OmcA and MtrC contents of membrane fractions and whole cells by Western blot analysis. For reduction of soluble iron, rates determined from transient-state experiments were able to account for rates obtained from steady-state experiments. However, this was not true with goethite; rate constants determined from transient-state experiments were 100 to 1,000 times slower than those calculated from steady-state experiments with membrane fractions and whole cells. In contrast, addition of flavins to the goethite experiments resulted in rates that were consistent with both transient- and steady-state experiments. Kinetic simulations of steady-state results with kinetic constants obtained from transient-state experiments supported flavin involvement. Therefore, we show for the first time that OmcA and MtrC are kinetically competent to account for catalysis of soluble iron reduction in whole Shewanella cells but are not responsible for electron transfer via direct contact alone with insoluble iron-containing minerals. This work supports the hypothesis that electron shuttles are important participants in the reduction of solid Fe phases by this organism.
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Portis AR, Parry MAJ. Discoveries in Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase): a historical perspective. PHOTOSYNTHESIS RESEARCH 2007; 94:121-43. [PMID: 17665149 DOI: 10.1007/s11120-007-9225-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 07/04/2007] [Indexed: 05/16/2023]
Abstract
Historic discoveries and key observations related to Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase), from 1947 to 2006, are presented. Currently, around 200 papers describing Rubisco research are published each year and the literature contains more than 5000 manuscripts on the subject. While trying to ensure that all the major events over this period are recorded, this analysis will inevitably be incomplete and will reflect the areas of particular interest to the authors.
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Affiliation(s)
- Archie R Portis
- Photosynthesis Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA.
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Cleland WW, Andrews TJ, Gutteridge S, Hartman FC, Lorimer GH. Mechanism of Rubisco: The Carbamate as General Base. Chem Rev 1998; 98:549-562. [PMID: 11848907 DOI: 10.1021/cr970010r] [Citation(s) in RCA: 279] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- W. Wallace Cleland
- The Institute for Enzyme Research, University of Wisconsin, Madison, Wisconsin 53705, Research School of Biological Sciences, Australian National University, Canberra 2601, Australia, Central Research and Development Department, Dupont Company, Experimental Station, Wilmington, Delaware 19880-0402, and Protein Engineering Program, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-8077
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Wang ZY, Luo S, Sato K, Kobayashi M, Nozawa T. In situ measurements of ribulose-1,5-bisphosphate carboxylase activity by nuclear magnetic resonance. Anal Biochem 1998; 257:26-32. [PMID: 9512768 DOI: 10.1006/abio.1997.2521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
High-resolution NMR spectroscopy is demonstrated to be capable of monitoring in situ the carboxylation reaction catalyzed by ribulose-1,5-bisphosphate carboxylase. Specific activities are determined for three enzymes from different sources containing higher plant and photosynthetic bacteria, and they are in agreement with those measured by other methods. Several important features of the reaction have been confirmed at the atomic level. A decrease in activity with time after the reaction started has also been observed for both enzymes with L8S8 and L2 structures from photosynthetic bacteria and higher plants, suggesting that the "fallover" of activity may be a more general phenomenon. 1H spectra obtained with H2O as solvent provide the most efficient quantitative measurement of the reaction product, 3-phosphoglycerate. 31P spectra give essentially the same result as 1H NMR but have the advantage of showing the degree of reaction at any time during the reaction. The incorporated carbon atom is unequivocally identified as the C-1 carbon of 3-phosphoglycerate from the 13C spectrum.
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Affiliation(s)
- Z Y Wang
- Department of Biochemistry and Engineering, Faculty of Engineering, Tohoku University, Sendai, Japan
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Abstract
The structural genes for three forms of Rubisco have been isolated from bacteria and introduced into various plasmids. Apart from details of the sequences which have been obtained from these constructs, they are now being exploited for mutagenesis to determine the identity and specific function of the individual amino acid residues that compose the active site. These methods have been applied to a plasmid that contains the structural gene for the simplest form of Rubisco from
Rhodospirillum rubrum
to obtain mutant enzymes with altered activity. The construct pRR2119 is also expressed to very high levels in
Escherichia coli
and enough recombinant protein of both the wild-type and m utant enzymes can be obtained for detailed physico-chemical studies. Other vectors have now been constructed, containing the genes of prokaryotic Rubisco that assemble into an active form I enzyme. The levels of expression are acceptable and the product is similar to the authentic enzyme. These constructs are now being used for mutagenesis
in vitro
to attempt to alter the relative rates of the oxygenase and carboxylase activities.
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Newman J, Gutteridge S. Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate. Structure 1994; 2:495-502. [PMID: 7922027 DOI: 10.1016/s0969-2126(00)00050-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyzes the addition of CO2 to ribulose 1,5-bisphosphate in all photosynthetic organisms. During catalysis, the bisphosphate is depleted by reactions other than carboxylation and some of the products are potent inhibitors of rubisco. We have used one of these, xylulose 1,5-bisphosphate as an analogue of the natural substrate and co-crystallized it with the enzyme. RESULTS We have solved the crystal structure of Synechococcus rubisco with bound xylulose 1,5-bisphosphate to 2.3 A and compared it with the previously solved 2'-carboxylarabinitol 1,5-bisphosphate (2CABP) enzyme quaternary complex. Unlike 2CABP, xylulose 1,5-bisphosphate forms a binary complex with no activating CO2 or essential metal present. Five flexible elements that restrict access to the active site in the 2CABP complex also close off the active site in the xylulose 1,5-bisphosphate complex, stabilized by interactions with the hydrated form of the analogue. CONCLUSIONS Xylulose 1,5-bisphosphate induces closure of critical loops of the protein without essential cofactors resident at the active site. In the case of rubisco in one species, catalysis is completely inhibited.
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Affiliation(s)
- J Newman
- Department of Molecular Biology, Biomedical Centre, Uppsala, Sweden
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Janson K, Brändén R. A spectrometric study of the Co(2+)-activated ribulose-1,5-bisphosphate carboxylase reaction during turnover and at different pH. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1080:40-4. [PMID: 1657177 DOI: 10.1016/0167-4838(91)90109-d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
EPR as well as optical absorption studies of the Co(2+)-activated ribulose-1,5-bisphosphate carboxylase/oxygenase under turnover conditions show that the formation of the two detectable intermediates are pH dependent. The amount of one of them, which earlier has been proposed to be a metal coordinated endiol of ribulose-1,5-bisphosphate (Brändén et al. (1987) Biochim. Biophys. Acta 916, 298-303), increased with increasing pH. Distinct optical absorption bands could be assigned to this intermediate and a pH profile could be made. It is therefore proposed that a base with a pKa value of about 8 is responsible for the enzyme-catalysed abstraction of a proton from ribulose-1,5-bisphosphate in order to form the metal coordinated endiol of ribulose-1,5-bisphosphate.
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Affiliation(s)
- K Janson
- Department of Biochemistry and Biophysics, University of Göteborg, Sweden
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