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Gionfriddo M, Rhodes T, Whitney SM. Perspectives on improving crop Rubisco by directed evolution. Semin Cell Dev Biol 2024; 155:37-47. [PMID: 37085353 DOI: 10.1016/j.semcdb.2023.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 04/23/2023]
Abstract
Rubisco catalyses the entry of almost all CO2 into the biosphere and is often the rate-limiting step in plant photosynthesis and growth. Its notoriety as the most abundant protein on Earth stems from the slow and error-prone catalytic properties that require plants, cyanobacteria, algae and photosynthetic bacteria to produce it in high amounts. Efforts to improve the CO2-fixing properties of plant Rubisco has been spurred on by the discovery of more effective isoforms in some algae with the potential to significantly improve crop productivity. Incompatibilities between the protein folding machinery of leaf and algae chloroplasts have, so far, prevented efforts to transplant these more effective Rubisco variants into plants. There is therefore increasing interest in improving Rubisco catalysis by directed (laboratory) evolution. Here we review the advances being made in, and the ongoing challenges with, improving the solubility and/or carboxylation activity of differing non-plant Rubisco lineages. We provide perspectives on new opportunities for the directed evolution of crop Rubiscos and the existing plant transformation capabilities available to evaluate the extent to which Rubisco activity improvements can benefit agricultural productivity.
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Affiliation(s)
- Matteo Gionfriddo
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia; Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Timothy Rhodes
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Spencer M Whitney
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.
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2
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Huang Q, Szebenyi DME. Crystal structure of a type III Rubisco in complex with its product 3-phosphoglycerate. Proteins 2023; 91:330-337. [PMID: 36151846 DOI: 10.1002/prot.26431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 02/04/2023]
Abstract
The crystal structure of the complex of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39) from Archaeoglobus fulgidus (afRubisco) with its products 3PGAs has been determined to a resolution of 1.7 Å and is of the closed form. Type III Rubiscos such as afRubisco have 18 out of the 19 essential amino acid residues of canonical Rubisco; the 19th is Tyr rather than Phe. Superposition with the structure of a complex of the similar tkRubisco with the six-carbon intermediate analog 2CABP shows the same conformation of the 19 residues except for Glu46 and Thr51. Glu46 adopts a unique conformation different from that in other Rubiscos and makes two H-bonds with the ligand 3PGA. Similar to other closed state Rubiscos, the backbone of Thr51 is rotated and the side chain makes an H-bond with the ligand 3PGA. Two product 3PGA molecules are bound at the active site, overlapping well with the 2CABP of tkRubisco/2CABP. The positions of the P1 and P2 phosphate groups differ by 0.4 and 0.53 Å, respectively, between 2CABP and the two 3PGAs. This afRubisco/3PGA complex mimics an intermediate stage of the carboxylation reaction which occurs after the production of the two 3PGA products but before the reopening of the active site. The stability of this complex suggests that the Rubisco active site will not reopen before both 3PGA products are formed.
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Affiliation(s)
- Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York, USA
| | - Doletha M E Szebenyi
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York, USA
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3
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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4
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Okude S, Shen J, Hatakeyama M, Nakamura S. Theoretical Study on the Kinetics of the Rubisco Carboxylase Reaction by a Model Based on Quantum Chemistry and Absolute Reaction Rate Theory. ACS OMEGA 2022; 7:30894-30907. [PMID: 36092611 PMCID: PMC9453937 DOI: 10.1021/acsomega.2c02664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
The rate of the Rubisco carboxylase reaction is evaluated by statistical mechanics and hybrid density functional theory (DFT). The Rubisco molecular model given by Kannappan et al. was modified and used in the present calculation. The activation energies of CO2 addition reaction, H2O addition reaction, C2-C3 bond scission, and C2 protonation are estimated. We calculated the turnover number (TON) for each of the four reaction steps based on a revised absolute reaction rate theory, which became applicable to soft matter reactions. The molecular parameters used in TON calculations were obtained by DFT calculations. The TON of the total Rubisco reaction was finally evaluated using rate equations. The calculation in a vacuum gave the total TON to be around 5 × 10-5, which was much lower than the experimental value. The DFT calculation in water solvent gave the total TON to be around 0.1, which agreed reasonably well with experimentally reported values (∼2.71). The rate-limiting process was the scission reaction. The present calculation showed that both the phosphate groups in the substrate accelerate each reaction step. The present calculation showed that a more comprehensive molecular model including enolization and quantum chemical methods is necessary to make a more precise reaction model including the irreversibility of some reactions.
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Affiliation(s)
- Shin’ichiro Okude
- Cluster
for Science, Technology and Innovation Hub, Nakamura Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Junwei Shen
- Cluster
for Science, Technology and Innovation Hub, Nakamura Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Makoto Hatakeyama
- Department
of Pharmacy, Sanyo-Onoda City University, Onoda, Yamaguchi 756-0884, Japan
| | - Shinichiro Nakamura
- Cluster
for Science, Technology and Innovation Hub, Nakamura Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
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5
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Douglas-Gallardo OA, Murillo-López JA, Oller J, Mulholland AJ, Vöhringer-Martinez E. Carbon Dioxide Fixation in RuBisCO Is Protonation-State-Dependent and Irreversible. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Oscar A. Douglas-Gallardo
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Juliana A. Murillo-López
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Javier Oller
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380000, Chile
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
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6
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Possible Steps of the Carboxylation of Ribulose-1,5-biphosphate from Intermediates: 2,3-Enediol versus 1,2-Enol. Int J Mol Sci 2021; 22:ijms22189749. [PMID: 34575912 PMCID: PMC8465432 DOI: 10.3390/ijms22189749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 11/18/2022] Open
Abstract
Ribulose 1,5-bisphosphate (RuBP) undergoes enolization to initiate fixation of atmospheric carbon dioxide in the plant carbon cycle. The known model assumes the binding of RuBP to the Rubisco active site with the subsequent formation of 2,3-enediol (2,3,4-trihydroxypent-2-ene-1,5-diyl diphosphate). In the present study, it is assumed that 1,2-enol (2,3,4-trihydroxypent-1-ene-1,5-diyl diphosphate) can be formed in the enolization step to initiate the carboxylation reaction. We have used Kohn–Sham density functional theory on WB97X-D3/Def2-TZVP levels to compare the reaction barriers in the two ways. We considered the pathways of carboxylation of 1/2-ene (mono/di)ol via the C1 and C2 carbons without taking into account the binding of RuBP to the magnesium ion. Calculations of Gibbs free energies confirm the equal probability of the formation of 2,3-enediol and 1,2-enol. Quantum–chemical modeling of enolization and carboxylation reactions supports the important role of the bridging water molecule and diphosphate groups, which provide proton transfer and lower reaction barriers. The results show that carbon dioxide fixation can occur without a magnesium ion, and binding with C1 can have a lower barrier (~12 kcal/mol) than with C2 (~23 kcal/mol).
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7
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The Mechanism of Rubisco Catalyzed Carboxylation Reaction: Chemical Aspects Involving Acid-Base Chemistry and Functioning of the Molecular Machine. Catalysts 2021. [DOI: 10.3390/catal11070813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In recent years, a great deal of attention has been paid by the scientific community to improving the efficiency of photosynthetic carbon assimilation, plant growth and biomass production in order to achieve a higher crop productivity. Therefore, the primary carboxylase enzyme of the photosynthetic process Rubisco has received considerable attention focused on many aspects of the enzyme function including protein structure, protein engineering and assembly, enzyme activation and kinetics. Based on its fundamental role in carbon assimilation Rubisco is also targeted by the CO2-fertilization effect, which is the increased rate of photosynthesis due to increasing atmospheric CO2-concentration. The aim of this review is to provide a framework, as complete as possible, of the mechanism of the RuBP carboxylation/hydration reaction including description of chemical events occurring at the enzyme “activating” and “catalytic” sites (which involve Broensted acid-base reactions) and the functioning of the complex molecular machine. Important research results achieved over the last few years providing substantial advancement in understanding the enzyme functioning will be discussed.
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8
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Cummins PL. The Coevolution of RuBisCO, Photorespiration, and Carbon Concentrating Mechanisms in Higher Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:662425. [PMID: 34539685 PMCID: PMC8440988 DOI: 10.3389/fpls.2021.662425] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/26/2021] [Indexed: 05/20/2023]
Abstract
Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO) is the carbon-fixing enzyme present in most photosynthetic organisms, converting CO2 into organic matter. Globally, photosynthetic efficiency in terrestrial plants has become increasingly challenged in recent decades due to a rapid increase in atmospheric CO2 and associated changes toward warmer and dryer environments. Well adapted for these new climatic conditions, the C4 photosynthetic pathway utilizes carbon concentrating mechanisms to increase CO2 concentrations surrounding RuBisCO, suppressing photorespiration from the oxygenase catalyzed reaction with O2. The energy efficiency of C3 photosynthesis, from which the C4 pathway evolved, is thought to rely critically on an uninterrupted supply of chloroplast CO2. Part of the homeostatic mechanism that maintains this constancy of supply involves the CO2 produced as a byproduct of photorespiration in a negative feedback loop. Analyzing the database of RuBisCO kinetic parameters, we suggest that in genera (Flaveria and Panicum) for which both C3 and C4 examples are available, the C4 pathway evolved only from C3 ancestors possessing much lower than the average carboxylase specificity relative to that of the oxygenase reaction (S C/O=S C/S O), and hence, the higher CO2 levels required for development of the photorespiratory CO2 pump (C2 photosynthesis) essential in the initial stages of C4 evolution, while in the later stage (final optimization phase in the Flaveria model) increased CO2 turnover may have occurred, which would have been supported by the higher CO2 levels. Otherwise, C4 RuBisCO kinetic traits remain little changed from the ancestral C3 species. At the opposite end of the spectrum, C3 plants (from Limonium) with higher than average S C/O, which may be associated with the ability of increased CO2, relative to O2, affinity to offset reduced photorespiration and chloroplast CO2 levels, can tolerate high stress environments. It is suggested that, instead of inherently constrained by its kinetic mechanism, RuBisCO possesses the extensive kinetic plasticity necessary for adaptation to changes in photorespiration that occur in the homeostatic regulation of CO2 supply under a broad range of abiotic environmental conditions.
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9
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Biophysical analysis of the structural evolution of substrate specificity in RuBisCO. Proc Natl Acad Sci U S A 2020; 117:30451-30457. [PMID: 33199597 DOI: 10.1073/pnas.2018939117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant enzyme on Earth. However, its catalytic rate per molecule of protein is extremely slow and the binding of the primary substrate, CO2, is competitively displaced by O2. Hence, carbon fixation by RuBisCO is highly inefficient; indeed, in higher C3 plants, about 30% of the time the enzyme mistakes CO2 for O2 Using genomic and structural analysis, we identify regions around the catalytic site that play key roles in discriminating between CO2 and O2 Our analysis identified positively charged cavities directly around the active site, which are expanded as the enzyme evolved with higher substrate specificity. The residues that extend these cavities have recently been under selective pressure, indicating that larger charged pockets are a feature of modern RuBisCOs, enabling greater specificity for CO2 This paper identifies a key structural feature that enabled the enzyme to evolve improved CO2 sequestration in an oxygen-rich atmosphere and may guide the engineering of more efficient RuBisCOs.
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10
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Douglas-Gallardo OA, Shepherd I, Bennie SJ, Ranaghan KE, Mulholland AJ, Vöhringer-Martinez E. Electronic structure benchmark calculations of CO 2 fixing elementary chemical steps in RuBisCO using the projector-based embedding approach. J Comput Chem 2020; 41:2151-2157. [PMID: 32640497 DOI: 10.1002/jcc.26380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/13/2020] [Indexed: 11/10/2022]
Abstract
Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is the main enzyme involved in atmospheric carbon dioxide (CO2 ) fixation in the biosphere. This enzyme catalyzes a set of five chemical steps that take place in the same active-site within magnesium (II) coordination sphere. Here, a set of electronic structure benchmark calculations have been carried out on a reaction path proposed by Gready et al. by means of the projector-based embedding approach. Activation and reaction energies for all main steps catalyzed by RuBisCO have been calculated at the MP2, SCS-MP2, CCSD, and CCSD(T)/aug-cc-pVDZ and cc-pVDZ levels of theory. The treatment of the magnesium cation with post-HF methods is explored to determine the nature of its involvement in the mechanism. With the high-level ab initio values as a reference, we tested the performance of a set of density functional theory (DFT) exchange-correlation (xc) functionals in reproducing the reaction energetics of RuBisCO carboxylase activity on a set of model fragments. Different DFT xc-functionals show large variation in activation and reaction energies. Activation and reaction energies computed at the B3LYP level are close to the reference SCS-MP2 results for carboxylation, hydration and protonation reactions. However, for the carbon-carbon bond dissociation reaction, B3LYP and other functionals give results that differ significantly from the ab initio reference values. The results show the applicability of the projector-based embedding approach to metalloenzymes. This technique removes the uncertainty associated with the selection of different DFT xc-functionals and so can overcome some of inherent limitations of DFT calculations, complementing, and potentially adding to modeling of enzyme reaction mechanisms with DFT methods.
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Affiliation(s)
- Oscar A Douglas-Gallardo
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Ian Shepherd
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Simon J Bennie
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
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11
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Cummins PL, Gready JE. Kohn-Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco. J Phys Chem B 2020; 124:3015-3026. [PMID: 32208706 DOI: 10.1021/acs.jpcb.0c01169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ribulose 1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) plays a fundamental role in the carbon cycle by fixing the atmospheric CO2 used in photosynthesis. Rubisco is all the more remarkable because it must catalyze some difficult multistep reaction chemistry involving proton transfers within the one active site. In the present study, we have used Kohn-Sham density functional theory at the B3LYP/6-31G* level with basis set superposition error and dispersion corrections (B3LYP-gCP-D3) to examine the possibility that the proton transfers can take place through molecular wires (including active-site water molecules) via the classical Grotthuss proton-shuttle mechanism. The results support an essential role for water molecules found in the crystal structures of Rubisco complexes as facilitators of proton transport in all the rate-limiting (catalytic) reaction steps through a network of short proton wires within the Rubisco active site. We suggest that completion of the initial product turnover (cycle) requires two excess protons produced in the initial carbamylation that is required for Rubisco activation. By use of proton wires, a large number of reaction steps may be accommodated within a single active site without necessitating the input of excessive conformational strain energy arising from the movement of residue side chains into positions where direct protonation of substrates can occur. The involvement of the identified types of proton wires in the kinetic mechanism is capable of providing a unique explanation for various experimental observations, including deuterium isotope effects and the results of site-directed mutagenesis experiments, and may thus provide a realistic solution to the problem of Rubisco's challenging chemistry.
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Affiliation(s)
- Peter L Cummins
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
| | - Jill E Gready
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
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12
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Cummins PL, Kannappan B, Gready JE. Response: Commentary: Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All. FRONTIERS IN PLANT SCIENCE 2019; 10:1426. [PMID: 31824523 PMCID: PMC6884029 DOI: 10.3389/fpls.2019.01426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 10/15/2019] [Indexed: 05/29/2023]
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13
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Zhou Y, Whitney S. Directed Evolution of an Improved Rubisco; In Vitro Analyses to Decipher Fact from Fiction. Int J Mol Sci 2019; 20:ijms20205019. [PMID: 31658746 PMCID: PMC6834295 DOI: 10.3390/ijms20205019] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 01/01/2023] Open
Abstract
Inaccuracies in biochemically characterizing the amount and CO2-fixing properties of the photosynthetic enzyme Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase continue to hamper an accurate evaluation of Rubisco mutants selected by directed evolution. Here, we outline an analytical pipeline for accurately quantifying Rubisco content and kinetics that averts the misinterpretation of directed evolution outcomes. Our study utilizes a new T7-promoter regulated Rubisco Dependent Escherichia coli (RDE3) screen to successfully select for the first Rhodobacter sphaeroides Rubisco (RsRubisco) mutant with improved CO2-fixing properties. The RsRubisco contains four amino acid substitutions in the large subunit (RbcL) and an improved carboxylation rate (kcatC, up 27%), carboxylation efficiency (kcatC/Km for CO2, increased 17%), unchanged CO2/O2 specificity and a 40% lower holoenzyme biogenesis capacity. Biochemical analysis of RsRubisco chimers coding one to three of the altered amino acids showed Lys-83-Gln and Arg-252-Leu substitutions (plant RbcL numbering) together, but not independently, impaired holoenzyme (L8S8) assembly. An N-terminal Val-11-Ile substitution did not affect RsRubisco catalysis or assembly, while a Tyr-345-Phe mutation alone conferred the improved kinetics without an effect on RsRubisco production. This study confirms the feasibility of improving Rubisco by directed evolution using an analytical pipeline that can identify false positives and reliably discriminate carboxylation enhancing amino acids changes from those influencing Rubisco biogenesis (solubility).
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Affiliation(s)
- Yu Zhou
- Australian Research Council Center of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 0200, Australia.
| | - Spencer Whitney
- Australian Research Council Center of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 0200, Australia.
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14
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Kannappan B, Cummins PL, Gready JE. Mechanism of Oxygenase-Pathway Reactions Catalyzed by Rubisco from Large-Scale Kohn-Sham Density Functional Calculations. J Phys Chem B 2019; 123:2833-2843. [PMID: 30845802 DOI: 10.1021/acs.jpcb.9b00518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco) is the primary carbon-fixing enzyme in photosynthesis, fixing CO2 to a 5-carbon sugar, RuBP, in a series of five reactions. However, it also catalyzes an oxygenase reaction by O2 addition to the same enolized RuBP substrate in an analogous reaction series in the same active site, producing a waste product and loss of photosynthetic efficiency. Starting from RuBP, the reactions are enolization to the enediolate form, addition of CO2 or O2 to form the carboxy or peroxo adduct, hydration to form a gemdiolate, scission of the C2-C3 bond of the original RuBP, and stereospecific or nonstereospecific protonation to form two molecules of the 3-carbon PGA product, or one molecule of PGA, one of 2-carbon PG (waste product), and one water molecule. Reducing the loss of efficiency from the oxygenase reaction is an attractive means to increase crop productivity. However, lack of understanding of key aspects of the catalytic mechanisms for both the carboxylase and oxygenase reactions, particularly those involving proton exchanges and roles of water molecules, has stymied efforts at re-engineering Rubisco to reduce losses from the oxygenation reaction. As the stable form of molecular oxygen is the triplet biradical state (3O2), its reaction with near-universal singlet-state molecules is formally spin forbidden. Although in oxygenase enzymes, 3O2 activation is usually achieved by one-electron transfers using transition-metal ions or organic cofactors, recently, cofactor-less oxygenases in which the substrate itself is the source of the electron for 3O2 activation have been identified, but in all such cases an aromatic ring stabilizes the substrate's negative charge. Here we present the first large-scale Kohn-Sham density functional theory study of the reaction mechanism of the Rubisco oxygenase pathway. First, we show that the enediolate substrate complexed to Mg2+ and its ligands extends the region for charge delocalization and stabilization of its negative charge to allow formation of a caged biradical enediolate-O2 complex. Thus, Rubisco is a unique type of oxygenase without precedent in the literature. Second, for the O2 addition to proceed to the singlet peroxo-adduct intermediate, the system must undergo an intersystem crossing. We found that the presence of protonated LYS334 is required to stabilize this intermediate and that both factors (strongly stabilized anion and protonated LYS334) facilitate a barrier-less activation of 3O2. This finding supports our recent proposal that deoxygenation, that is, reversal of gas binding, is possible. Third, as neither CO2 nor O2 binds to the enzyme, our findings support the proposal from our recent carboxylase study that the observed KC or KO (Michaelis-Menten constants) in the steady-state kinetics reflect the respective adducts, carboxy or peroxo. Fourth, after computing hydration pathways with water addition both syn and anti to C3, we found, in contrast to the results of our carboxylation study indicating anti addition, that in the oxygenation reaction only syn-hydration is capable of producing a stable gemdiolate that facilitates the rate-limiting C2-C3 bond scission to final products. Fifth, we propose that an excess proton we previously found was required in the carboxylation reaction for activating the C2-C3 bond scission is utilized in the oxygenation reaction for the required elimination of a water molecule. In summary, despite its oxygenase handicap, Rubisco's success in directing 75% of its substrate through the carboxylation pathway can be considered impressively effective. Although native C3 Rubiscos are in a fix with unwanted activity of 3O2 hampering its primary carboxylase function, mechanistic differences presented here with findings in our recent carboxylase study for both the gas-addition and subsequent reactions provide some clues as to how creative Rubisco re-engineering may offer a solution to reducing the oxygenase activity.
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Affiliation(s)
- Babu Kannappan
- John Curtin School of Medical Research , The Australian National University , Canberra ACT 0200 , Australia
| | - Peter L Cummins
- John Curtin School of Medical Research , The Australian National University , Canberra ACT 0200 , Australia
| | - Jill E Gready
- John Curtin School of Medical Research , The Australian National University , Canberra ACT 0200 , Australia
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Cummins PL, Kannappan B, Gready JE. Ab Initio Molecular Dynamics Simulation and Energetics of the Ribulose-1,5-biphosphate Carboxylation Reaction Catalyzed by Rubisco: Toward Elucidating the Stereospecific Protonation Mechanism. J Phys Chem B 2019; 123:2679-2686. [DOI: 10.1021/acs.jpcb.8b12088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Babu Kannappan
- John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Jill E. Gready
- John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
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