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Liu B, Lin B, Su H, Sheng X. Quantum chemical studies of the reaction mechanisms of enzymatic CO 2 conversion. Phys Chem Chem Phys 2024. [PMID: 39347748 DOI: 10.1039/d4cp03049d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Enzymatic capture and conversion of carbon dioxide (CO2) into value-added chemicals are of great interest in the field of biocatalysis and have a positive impact on climate change. The quantum chemical methods, recognized as valuable tools for studying reaction mechanisms, have been widely employed in investigating the reaction mechanisms of the enzymes involved in CO2 utilization. In this perspective, we review the mechanistic studies of representative enzymes that are either currently used or have the potential for converting CO2, utilizing the quantum chemical cluster approach and the quantum mechanical/molecular mechanical (QM/MM) method. We begin by summarizing current trends in enzymatic CO2 conversion, followed by a brief description of the computational details of quantum chemical methods. Then, a series of representative examples of the computational modeling of biocatalytic CO2 conversion are presented, including the reduction of CO2 to C1 species (carbon monoxide and formate), and the fixation of CO2 to form aliphatic and aromatic carboxylic acids. The microscopic views of reaction mechanisms obtained from these studies are helpful in guiding the rational design of current enzymes and the discovery of novel enzymes with enhanced performance in converting CO2. Additionally, they provide key information for the de novo design of new-to-nature enzymes. To conclude, we present a perspective on the potential combination of machine learning with quantum description in the study of enzymatic conversion of CO2.
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Affiliation(s)
- Baoyan Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Beibei Lin
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Hao Su
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Xiang Sheng
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
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Mrnjavac N, Nagies FSP, Wimmer JLE, Kapust N, Knopp MR, Trost K, Modjewski L, Bremer N, Mentel M, Esposti MD, Mizrahi I, Allen JF, Martin WF. The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third. FEBS Lett 2024; 598:1692-1714. [PMID: 38750628 PMCID: PMC7616280 DOI: 10.1002/1873-3468.14906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 07/15/2024]
Abstract
Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD+, pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.
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Affiliation(s)
- Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Falk S P Nagies
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Jessica L E Wimmer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nils Kapust
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Michael R Knopp
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Katharina Trost
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Luca Modjewski
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nico Bremer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and The National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, UK
| | - William F Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
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3
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Atkinson N, Stringer R, Mitchell SR, Seung D, McCormick AJ. SAGA1 and SAGA2 promote starch formation around proto-pyrenoids in Arabidopsis chloroplasts. Proc Natl Acad Sci U S A 2024; 121:e2311013121. [PMID: 38241434 PMCID: PMC10823261 DOI: 10.1073/pnas.2311013121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/11/2023] [Indexed: 01/21/2024] Open
Abstract
The pyrenoid is a chloroplastic microcompartment in which most algae and some terrestrial plants condense the primary carboxylase, Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) as part of a CO2-concentrating mechanism that improves the efficiency of CO2 capture. Engineering a pyrenoid-based CO2-concentrating mechanism (pCCM) into C3 crop plants is a promising strategy to enhance yield capacities and resilience to the changing climate. Many pyrenoids are characterized by a sheath of starch plates that is proposed to act as a barrier to limit CO2 diffusion. Recently, we have reconstituted a phase-separated "proto-pyrenoid" Rubisco matrix in the model C3 plant Arabidopsis thaliana using proteins from the alga with the most well-studied pyrenoid, Chlamydomonas reinhardtii [N. Atkinson, Y. Mao, K. X. Chan, A. J. McCormick, Nat. Commun. 11, 6303 (2020)]. Here, we describe the impact of introducing the Chlamydomonas proteins StArch Granules Abnormal 1 (SAGA1) and SAGA2, which are associated with the regulation of pyrenoid starch biogenesis and morphology. We show that SAGA1 localizes to the proto-pyrenoid in engineered Arabidopsis plants, which results in the formation of atypical spherical starch granules enclosed within the proto-pyrenoid condensate and adjacent plate-like granules that partially cover the condensate, but without modifying the total amount of chloroplastic starch accrued. Additional expression of SAGA2 further increases the proportion of starch synthesized as adjacent plate-like granules that fully encircle the proto-pyrenoid. Our findings pave the way to assembling a diffusion barrier as part of a functional pCCM in vascular plants, while also advancing our understanding of the roles of SAGA1 and SAGA2 in starch sheath formation and broadening the avenues for engineering starch morphology.
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Affiliation(s)
- Nicky Atkinson
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
- Centre of Engineering Biology, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
| | - Rhea Stringer
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, NorwichNR4 7UH, United Kingdom
| | - Stephen R. Mitchell
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
| | - David Seung
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, NorwichNR4 7UH, United Kingdom
| | - Alistair J. McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
- Centre of Engineering Biology, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
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Jämsä T, Tervasmäki P, Pitkänen JP, Salusjärvi L. Inactivation of poly(3-hydroxybutyrate) (PHB) biosynthesis in 'Knallgas' bacterium Xanthobacter sp. SoF1. AMB Express 2023; 13:75. [PMID: 37452197 PMCID: PMC10349022 DOI: 10.1186/s13568-023-01577-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
Aerobic hydrogen-oxidizing 'Knallgas' bacteria are promising candidates for microbial cell factories due to their ability to use hydrogen and carbon dioxide as the sole energy and carbon sources, respectively. These bacteria can convert atmospheric CO2 to chemicals which could help to mitigate climate change by replacing fossil fuel-based chemicals. A known method to enhance the product yield is to disrupt competing metabolic pathways in the host organism. One such pathway in many 'Knallgas' bacteria is polyhydroxybutyrate (PHB) biosynthesis. In this study, the PHB biosynthesis genes of a non-model 'Knallgas' bacterium Xanthobacter sp. SoF1 were identified. Consequently, the phaA, phaB and phaC genes were individually deleted and the resulting knockouts were evaluated for their ability to produce PHB in autotrophic shake flask and small-scale bioreactor cultivations. The results demonstrate that PHB production was inactivated in the phaC1 knockout strain, which advances the development of Xanthobacter sp. SoF1 as a production host.
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Affiliation(s)
- Tytti Jämsä
- VTT Technical Research Centre of Finland Ltd., 02150, Espoo, Finland.
| | | | | | - Laura Salusjärvi
- VTT Technical Research Centre of Finland Ltd., 02150, Espoo, Finland
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J. Erb
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K. Winkler
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M. Glueck
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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6
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Meng Y, Liu R, Wang L, Li F, Tian Y, Lu H. Binding affinity and conformational change predictions for a series of inhibitors with RuBisCO in a carbon dioxide gas and water environment by multiple computational methods. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Qu Y, Mueller-Cajar O, Yamori W. Improving plant heat tolerance through modification of Rubisco activase in C3 plants to secure crop yield and food security in a future warming world. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:591-599. [PMID: 35981868 DOI: 10.1093/jxb/erac340] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
The world's population may reach 10 billion by 2050, but 10% still suffer from food shortages. At the same time, global warming threatens food security by decreasing crop yields, so it is necessary to develop crops with enhanced resistance to high temperatures in order to secure the food supply. In this review, the role of Rubisco activase as an important factor in plant heat tolerance is summarized, based on the conclusions of recent findings. Rubisco activase is a molecular chaperone determining the activation of Rubisco, whose heat sensitivity causes reductions of photosynthesis at high temperatures. Thus, the thermostability of Rubisco activase is considered to be critical for improving plant heat tolerance. It has been shown that the introduction of thermostable Rubisco activase through gene editing into Arabidopsis thaliana and from heat-adapted wild Oryza species or C4Zea mays into Oryza sativa improves Rubisco activation, photosynthesis, and plant growth at high temperatures. We propose that developing a universal thermostable Rubisco activase could be a promising direction for further studies.
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Affiliation(s)
- Yuchen Qu
- Graduate School of Agricultural and Life Sciences, Institute for Sustainable Agri-ecosystem Services, The University of Tokyo, Tokyo, Japan
| | | | - Wataru Yamori
- Graduate School of Agricultural and Life Sciences, Institute for Sustainable Agri-ecosystem Services, The University of Tokyo, Tokyo, Japan
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8
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Laisk A. Prying into the green black-box. PHOTOSYNTHESIS RESEARCH 2022; 154:89-112. [PMID: 36114436 DOI: 10.1007/s11120-022-00960-5] [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: 02/09/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Life-long efforts of the Tartu photosynthesis research group have been summarized. The measurements were facilitated by self-designed instruments, distinct in multifunctionality and fastresponse time. The black-box type kinetical analysis on intact leaves has revealed several physiologically significant features of leaf photosynthesis. Rubisco studies reflected competition for the active site between the substrates and products, linearizing in vivo kinetics compared with the low-Km in vitro responses. Rubisco Activase usually activates only a small part of the Rubisco, making the rest of it a storage protein. Precisely quantifying absorbed photons and the responding transmittance changes, electron flow rates through cytochrome b6f, plastocyanin and photosystem I were measured, revealing competition between the proton-uncoupled cyclic electron flow from PSI to Cyt b6f to P700+ and the proton-coupled linear flow from PSII to Cyt b6f to P700+. Analyzing responses of O2 evolution and Chl fluorescence to ms-length light pulses we concluded that explanation of the sigmoidal fluorescence induction by excitonic connectivity between PSII units is a misconception. Each PSII processes excitation from its own antenna, but the sigmoidicity is caused by rise of the fluorescence yield of the QA-reduced PSII units after their QB site becomes occupied by reduced plastoquinone (or diuron). Unlike respiration, photosynthetic electrons must prepare their acceptor by coupled synthesis of 3ATP/4e-. Feedback regulation of this ratio leads to oscillations under saturating light and CO2, when the rate is Pi-limited. The slow oscillations (period 60s) indicate that the magnitudes of the deflections in the 3ATP/4e- ratio, corrected by regulating cyclic and alternative electron flow (including the Mehler type O2 reduction), are only a fraction of a per cent. The Pi limitation causes slip in the ATP synthase, slightly increasing the basic 12H+/3ATP requirement.
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Affiliation(s)
- Agu Laisk
- Institute of Technology, University of Tartu, W. Ostwaldi 1, 51011, Tartu, Estonia.
- Estonian Academy of Sciences, Kohtu 6, 10130, Tallinn, Estonia.
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Adler L, Díaz-Ramos A, Mao Y, Pukacz KR, Fei C, McCormick AJ. New horizons for building pyrenoid-based CO2-concentrating mechanisms in plants to improve yields. PLANT PHYSIOLOGY 2022; 190:1609-1627. [PMID: 35961043 PMCID: PMC9614477 DOI: 10.1093/plphys/kiac373] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/06/2022] [Indexed: 05/06/2023]
Abstract
Many photosynthetic species have evolved CO2-concentrating mechanisms (CCMs) to improve the efficiency of CO2 assimilation by Rubisco and reduce the negative impacts of photorespiration. However, the majority of plants (i.e. C3 plants) lack an active CCM. Thus, engineering a functional heterologous CCM into important C3 crops, such as rice (Oryza sativa) and wheat (Triticum aestivum), has become a key strategic ambition to enhance yield potential. Here, we review recent advances in our understanding of the pyrenoid-based CCM in the model green alga Chlamydomonas reinhardtii and engineering progress in C3 plants. We also discuss recent modeling work that has provided insights into the potential advantages of Rubisco condensation within the pyrenoid and the energetic costs of the Chlamydomonas CCM, which, together, will help to better guide future engineering approaches. Key findings include the potential benefits of Rubisco condensation for carboxylation efficiency and the need for a diffusional barrier around the pyrenoid matrix. We discuss a minimal set of components for the CCM to function and that active bicarbonate import into the chloroplast stroma may not be necessary for a functional pyrenoid-based CCM in planta. Thus, the roadmap for building a pyrenoid-based CCM into plant chloroplasts to enhance the efficiency of photosynthesis now appears clearer with new challenges and opportunities.
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Affiliation(s)
- Liat Adler
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Aranzazú Díaz-Ramos
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Yuwei Mao
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Krzysztof Robin Pukacz
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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Abstract
Carbon dioxide is a major greenhouse gas, and its fixation and transformation are receiving increasing attention. Biofixation of CO2 is an eco–friendly and efficient way to reduce CO2, and six natural CO2 fixation pathways have been identified in microorganisms and plants. In this review, the six pathways along with the most recent identified variant pathway were firstly comparatively characterized. The key metabolic process and enzymes of the CO2 fixation pathways were also summarized. Next, the enzymes of Rubiscos, biotin-dependent carboxylases, CO dehydrogenase/acetyl-CoA synthase, and 2-oxoacid:ferredoxin oxidoreductases, for transforming inorganic carbon (CO2, CO, and bicarbonate) to organic chemicals, were specially analyzed. Then, the factors including enzyme properties, CO2 concentrating, energy, and reducing power requirements that affect the efficiency of CO2 fixation were discussed. Recent progress in improving CO2 fixation through enzyme and metabolic engineering was then summarized. The artificial CO2 fixation pathways with thermodynamical and/or energetical advantages or benefits and their applications in biosynthesis were included as well. The challenges and prospects of CO2 biofixation and conversion are discussed.
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Blake LI, Cann MJ. Carbon Dioxide and the Carbamate Post-Translational Modification. Front Mol Biosci 2022; 9:825706. [PMID: 35300111 PMCID: PMC8920986 DOI: 10.3389/fmolb.2022.825706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/03/2022] [Indexed: 01/10/2023] Open
Abstract
Carbon dioxide is essential for life. It is at the beginning of every life process as a substrate of photosynthesis. It is at the end of every life process as the product of post-mortem decay. Therefore, it is not surprising that this gas regulates such diverse processes as cellular chemical reactions, transport, maintenance of the cellular environment, and behaviour. Carbon dioxide is a strategically important research target relevant to crop responses to environmental change, insect vector-borne disease and public health. However, we know little of carbon dioxide’s direct interactions with the cell. The carbamate post-translational modification, mediated by the nucleophilic attack by carbon dioxide on N-terminal α-amino groups or the lysine ɛ-amino groups, is one mechanism by which carbon dioxide might alter protein function to form part of a sensing and signalling mechanism. We detail known protein carbamates, including the history of their discovery. Further, we describe recent studies on new techniques to isolate this problematic post-translational modification.
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12
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Graiff A, Karsten U. Antioxidative Properties of Baltic Sea Keystone Macroalgae (Fucus vesiculosus, Phaeophyceae) under Ocean Warming and Acidification in a Seasonally Varying Environment. BIOLOGY 2021; 10:biology10121330. [PMID: 34943245 PMCID: PMC8698884 DOI: 10.3390/biology10121330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The brown seaweed Fucus vesiculosus is the dominant and the most ecologically crucial primary producer and habitat founder in the Baltic Sea. In the shallow coastal zone, F. vesiculosus is particularly exposed to strongly and rapidly changing environmental conditions due to global change. This study examines how single and joint effects of elevated seawater temperature and pCO2 levels influence F. vesiculosus in all four seasons, using benthic mesocosms. The antioxidative properties and the sensitivity of F. vesiculosus photosynthetic performance to oxidative stress under different global change scenarios were assessed. F. vesiculosus tolerated strong hydrogen peroxide stress in all seasons, as reflected in high antioxidative enzyme activities and a low degree of membrane lipid peroxidation. Forecasted warming affected the antioxidative properties of F. vesiculosus stronger than acidification, causing significantly increased lipid peroxidation under elevated temperatures in all seasons. However, pCO2 levels modulated the oxidative stress of F. vesiculosus under warming. Overall, summer heatwaves reaching lethal temperatures in shallow waters will most likely determine the persistence of Baltic F. vesiculosus. Abstract The keystone macroalga Fucus vesiculosus (Phaeophyceae), dominating shallow hard bottom zones, encounters a strongly and rapidly changing environment due to anthropogenic change over the last decades in the Baltic Sea. Thus, in four successive benthic mesocosm experiments, the single and joint effects of increased temperature (Δ + 5 °C) and pCO2 (1100 ppm) under ambient irradiances were experimentally tested on the antioxidative properties of western Baltic F. vesiculosus in all seasons. The antioxidative properties (superoxide dismutase activity and lipid peroxidation) as well as the sensitivity of F. vesiculosus photosynthetic performance (i.e., effective quantum yield) to oxidative stress under these global change scenarios were seasonally examined. F. vesiculosus exhibited high and relatively constant photosynthetic performance under artificial hydrogen peroxide (H2O2) stress in all seasons. High activities of superoxide dismutase and a relatively low degree of the biomarker for lipid peroxidation (malondialdehyde concentration) were found in F. vesiculosus. Thus, Baltic F. vesiculosus is equipped with a high antioxidative potential to tolerate strong oxidative stress for at least short periods. Antioxidative properties of F. vesiculosus were more strongly affected by warming than by acidification, resulting in significantly increased malondialdehyde concentrations under elevated temperature levels in all seasons. Oxidative stress was enhanced in F. vesiculosus under warming but seem to be modulated by seasonally varying environmental conditions (e.g., high and low irradiances) and pCO2 levels. However, more frequent summer heatwaves reaching and surpassing lethal temperatures in shallow coastal waters may determine the F. vesiculosus population’s overall persistence in the Baltic Sea.
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Affiliation(s)
- Angelika Graiff
- Correspondence: ; Tel.: +49-381-4986101; Fax: +49-381-4986072
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13
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The CbbQO-type rubisco activases encoded in carboxysome gene clusters can activate carboxysomal form IA rubiscos. J Biol Chem 2021; 298:101476. [PMID: 34890642 PMCID: PMC8718961 DOI: 10.1016/j.jbc.2021.101476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/15/2023] Open
Abstract
The CO2-fixing enzyme rubisco is responsible for almost all carbon fixation. This process frequently requires rubisco activase (Rca) machinery, which couples ATP hydrolysis to the removal of inhibitory sugar phosphates, including the rubisco substrate ribulose 1,5-bisphosphate (RuBP). Rubisco is sometimes compartmentalized in carboxysomes, bacterial microcompartments that enable a carbon dioxide concentrating mechanism (CCM). Characterized carboxysomal rubiscos, however, are not prone to inhibition, and often no activase machinery is associated with these enzymes. Here, we characterize two carboxysomal rubiscos of the form IAC clade that are associated with CbbQO-type Rcas. These enzymes release RuBP at a much lower rate than the canonical carboxysomal rubisco from Synechococcus PCC6301. We found that CbbQO-type Rcas encoded in carboxysome gene clusters can remove RuBP and the tight-binding transition state analog carboxy-arabinitol 1,5-bisphosphate from cognate rubiscos. The Acidithiobacillus ferrooxidans genome encodes two form IA rubiscos associated with two sets of cbbQ and cbbO genes. We show that the two CbbQO activase systems display specificity for the rubisco enzyme encoded in the same gene cluster, and this property can be switched by substituting the C-terminal three residues of the large subunit. Our findings indicate that the kinetic and inhibitory properties of proteobacterial form IA rubiscos are diverse and predict that Rcas may be necessary for some α-carboxysomal CCMs. These findings will have implications for efforts aiming to introduce biophysical CCMs into plants and other hosts for improvement of carbon fixation of crops.
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14
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Morelli AM, Chiantore M, Ravera S, Scholkmann F, Panfoli I. Myelin sheath and cyanobacterial thylakoids as concentric multilamellar structures with similar bioenergetic properties. Open Biol 2021; 11:210177. [PMID: 34905702 PMCID: PMC8670949 DOI: 10.1098/rsob.210177] [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] [Indexed: 01/07/2023] Open
Abstract
There is a surprisingly high morphological similarity between multilamellar concentric thylakoids in cyanobacteria and the myelin sheath that wraps the nerve axons. Thylakoids are multilamellar structures, which express photosystems I and II, cytochromes and ATP synthase necessary for the light-dependent reaction of photosynthesis. Myelin is a multilamellar structure that surrounds many axons in the nervous system and has long been believed to act simply as an insulator. However, it has been shown that myelin has a trophic role, conveying nutrients to the axons and producing ATP through oxidative phosphorylation. Therefore, it is tempting to presume that both membranous structures, although distant in the evolution tree, share not only a morphological but also a functional similarity, acting in feeding ATP synthesized by the ATP synthase to the centre of the multilamellar structure. Therefore, both molecular structures may represent a convergent evolution of life on Earth to fulfill fundamentally similar functions.
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Affiliation(s)
| | - Mariachiara Chiantore
- Department of Earth, Environment and Life Sciences, University of Genova, Genova, Italy
| | - Silvia Ravera
- Experimental Medicine Department, University of Genova, Genova, Italy
| | - Felix Scholkmann
- Biomedical Optics Research Laboratory, Department of Neonatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Isabella Panfoli
- Experimental Medicine Department, University of Genova, Genova, Italy
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15
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Stitt M, Luca Borghi G, Arrivault S. Targeted metabolite profiling as a top-down approach to uncover interspecies diversity and identify key conserved operational features in the Calvin-Benson cycle. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5961-5986. [PMID: 34473300 PMCID: PMC8411860 DOI: 10.1093/jxb/erab291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/21/2021] [Indexed: 05/02/2023]
Abstract
Improving photosynthesis is a promising avenue to increase crop yield. This will be aided by better understanding of natural variance in photosynthesis. Profiling of Calvin-Benson cycle (CBC) metabolites provides a top-down strategy to uncover interspecies diversity in CBC operation. In a study of four C4 and five C3 species, principal components analysis separated C4 species from C3 species and also separated different C4 species. These separations were driven by metabolites that reflect known species differences in their biochemistry and pathways. Unexpectedly, there was also considerable diversity between the C3 species. Falling atmospheric CO2 and changing temperature, nitrogen, and water availability have driven evolution of C4 photosynthesis in multiple lineages. We propose that analogous selective pressures drove lineage-dependent evolution of the CBC in C3 species. Examples of species-dependent variation include differences in the balance between the CBC and the light reactions, and in the balance between regulated steps in the CBC. Metabolite profiles also reveal conserved features including inactivation of enzymes in low irradiance, and maintenance of CBC metabolites at relatively high levels in the absence of net CO2 fixation. These features may be important for photosynthetic efficiency in low light, fluctuating irradiance, and when stomata close due to low water availability.
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Affiliation(s)
- Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Gian Luca Borghi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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16
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Moore CE, Meacham-Hensold K, Lemonnier P, Slattery RA, Benjamin C, Bernacchi CJ, Lawson T, Cavanagh AP. The effect of increasing temperature on crop photosynthesis: from enzymes to ecosystems. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2822-2844. [PMID: 33619527 PMCID: PMC8023210 DOI: 10.1093/jxb/erab090] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/19/2021] [Indexed: 05/03/2023]
Abstract
As global land surface temperature continues to rise and heatwave events increase in frequency, duration, and/or intensity, our key food and fuel cropping systems will likely face increased heat-related stress. A large volume of literature exists on exploring measured and modelled impacts of rising temperature on crop photosynthesis, from enzymatic responses within the leaf up to larger ecosystem-scale responses that reflect seasonal and interannual crop responses to heat. This review discusses (i) how crop photosynthesis changes with temperature at the enzymatic scale within the leaf; (ii) how stomata and plant transport systems are affected by temperature; (iii) what features make a plant susceptible or tolerant to elevated temperature and heat stress; and (iv) how these temperature and heat effects compound at the ecosystem scale to affect crop yields. Throughout the review, we identify current advancements and future research trajectories that are needed to make our cropping systems more resilient to rising temperature and heat stress, which are both projected to occur due to current global fossil fuel emissions.
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Affiliation(s)
- Caitlin E Moore
- School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
- Institute for Sustainability, Energy & Environment, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Katherine Meacham-Hensold
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | | | - Rebecca A Slattery
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Claire Benjamin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Carl J Bernacchi
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture–Agricultural Research Service, Urbana, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, UK
| | - Amanda P Cavanagh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
- School of Life Sciences, University of Essex, Colchester, UK
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17
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Whitney SM, Sharwood RE. Rubisco Engineering by Plastid Transformation and Protocols for Assessing Expression. Methods Mol Biol 2021; 2317:195-214. [PMID: 34028770 DOI: 10.1007/978-1-0716-1472-3_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The assimilation of CO2 within chloroplasts is catalyzed by the bifunctional enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase, Rubisco. Within higher plants the Rubisco large subunit gene, rbcL, is encoded in the plastid genome, while the Rubisco small subunit gene, RbcS is coded in the nucleus by a multigene family. Rubisco is considered a poor catalyst due to its slow turnover rate and its additional fixation of O2 that can result in wasteful loss of carbon through the energy requiring photorespiratory cycle. Improving the carboxylation efficiency and CO2/O2 selectivity of Rubisco within higher plants has been a long term goal which has been greatly advanced in recent times using plastid transformation techniques. Here we present experimental methodologies for efficiently engineering Rubisco in the plastids of a tobacco master line and analyzing leaf Rubisco content.
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Affiliation(s)
- Spencer M Whitney
- Plant Sciences, Research School of Biology, College of Science, The Australian National University, Acton, ACT, Australia.
| | - Robert E Sharwood
- Plant Sciences, Research School of Biology, College of Science, The Australian National University, Acton, ACT, Australia
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18
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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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19
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Heuschkel I, Dagini R, Karande R, Bühler K. The Impact of Glass Material on Growth and Biocatalytic Performance of Mixed-Species Biofilms in Capillary Reactors for Continuous Cyclohexanol Production. Front Bioeng Biotechnol 2020; 8:588729. [PMID: 33042983 PMCID: PMC7522790 DOI: 10.3389/fbioe.2020.588729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 08/25/2020] [Indexed: 11/21/2022] Open
Abstract
In this study, the growth and catalytic performance of mixed-species biofilms consisting of photoautotrophic Synechocystis sp. PCC 6803 and chemoheterotrophic Pseudomonas sp. VLB120 was investigated. Both strains contained a cytochrome P450 monooxygenase enzyme system catalyzing the oxyfunctionalization of cyclohexane to cyclohexanol. Biofilm cultivation was performed in capillary glass reactors made of either, borosilicate glass (Duran) or quartz glass, in different flow regimes. Consequently, four phases could be distinguished for mixed-species biofilm growth and development in the glass-capillaries. The first phase represents the limited growth of mixed-species biofilm in the single-phase flow condition. The second phase includes a rapid increase in biofilm spatial coverage after the start of air-segments. The third phase starts with the sloughing of large biofilm patches from well-grown biofilms, and the final stage consists of biofilm regrowth and the expansion of the spatial coverage. The catalytic performance of the mixed-species biofilm after the detachment process was compared to a well-grown biofilm. With an increase in the biofilm surface coverage, the cyclohexanol production rate improved from 1.75 to 6.4 g m–2 d–1, resulting in comparable production rates to the well-grown biofilms. In summary, high productivities can be reached for biofilms cultivated in glass capillaries, but stable product formation was disturbed by sloughing events.
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Affiliation(s)
- Ingeborg Heuschkel
- Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Rakesh Dagini
- Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Rohan Karande
- Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Katja Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
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20
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Bathellier C, Yu LJ, Farquhar GD, Coote ML, Lorimer GH, Tcherkez G. Ribulose 1,5-bisphosphate carboxylase/oxygenase activates O 2 by electron transfer. Proc Natl Acad Sci U S A 2020; 117:24234-24242. [PMID: 32934141 PMCID: PMC7533879 DOI: 10.1073/pnas.2008824117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the cornerstone of atmospheric CO2 fixation by the biosphere. It catalyzes the addition of CO2 onto enolized ribulose 1,5-bisphosphate (RuBP), producing 3-phosphoglycerate which is then converted to sugars. The major problem of this reaction is competitive O2 addition, which forms a phosphorylated product (2-phosphoglycolate) that must be recycled by a series of biochemical reactions (photorespiratory metabolism). However, the way the enzyme activates O2 is still unknown. Here, we used isotope effects (with 2H, 25Mg, and 18O) to monitor O2 activation and assess the influence of outer sphere atoms, in two Rubisco forms of contrasted O2/CO2 selectivity. Neither the Rubisco form nor the use of solvent D2O and deuterated RuBP changed the 16O/18O isotope effect of O2 addition, in clear contrast with the 12C/13C isotope effect of CO2 addition. Furthermore, substitution of light magnesium (24Mg) by heavy, nuclear magnetic 25Mg had no effect on O2 addition. Therefore, outer sphere protons have no influence on the reaction and direct radical chemistry (intersystem crossing with triplet O2) does not seem to be involved in O2 activation. Computations indicate that the reduction potential of enolized RuBP (near 0.49 V) is compatible with superoxide (O2•-) production, must be insensitive to deuteration, and yields a predicted 16O/18O isotope effect and energy barrier close to observed values. Overall, O2 undergoes single electron transfer to form short-lived superoxide, which then recombines to form a peroxide intermediate.
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Affiliation(s)
- Camille Bathellier
- Elementar France, Spectrométrie de Masse Isotopique, 69428 Lyon Cedex 3, France
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601 Canberra ACT, Australia
| | - Li-Juan Yu
- Australian Research Council Centre of Excellence for Electromaterials Science, Research School of Chemistry, ANU Joint College of Sciences, Australian National University, 2601 Canberra ACT, Australia
| | - Graham D Farquhar
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601 Canberra ACT, Australia;
| | - Michelle L Coote
- Australian Research Council Centre of Excellence for Electromaterials Science, Research School of Chemistry, ANU Joint College of Sciences, Australian National University, 2601 Canberra ACT, Australia
| | - George H Lorimer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Guillaume Tcherkez
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601 Canberra ACT, Australia;
- Institut de Recherche en Horticulture et Semences, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAe), Université d'Angers, 49070 Beaucouzé, France
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21
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Sales CRG, da Silva AB, Carmo-Silva E. Measuring Rubisco activity: challenges and opportunities of NADH-linked microtiter plate-based and 14C-based assays. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5302-5312. [PMID: 32728715 PMCID: PMC7501812 DOI: 10.1093/jxb/eraa289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/22/2020] [Indexed: 05/28/2023]
Abstract
Rubisco is central to carbon assimilation, and efforts to improve the efficiency and sustainability of crop production have spurred interest in phenotyping Rubisco activity. We tested the hypothesis that microtiter plate-based methods provide comparable results to those obtained with the radiometric assay that measures the incorporation of 14CO2 into 3-phosphoglycerate (3-PGA). Three NADH-linked assays were tested that use alternative coupling enzymes: glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and glycerolphosphate dehydrogenase (GlyPDH); phosphoenolpyruvate carboxylase (PEPC) and malate dehydrogenase (MDH); and pyruvate kinase (PK) and lactate dehydrogenase (LDH). To date there has been no thorough evaluation of their reliability by comparison with the 14C-based method. The three NADH-linked assays were used in parallel to estimate (i) the 3-PGA concentration-response curve of NADH oxidation, (ii) the Michaelis-Menten constant for ribulose-1,5-bisphosphate, (iii) fully active and inhibited Rubisco activities, and (iv) Rubisco initial and total activities in fully illuminated and shaded leaves. All three methods correlated strongly with the 14C-based method, and the PK-LDH method showed a strong correlation and was the cheapest method. PEPC-MDH would be a suitable option for situations in which ADP/ATP might interfere with the assay. GAPDH-GlyPDH proved more laborious than the other methods. Thus, we recommend the PK-LDH method as a reliable, cheaper, and higher throughput method to phenotype Rubisco activity for crop improvement efforts.
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Affiliation(s)
- Cristina R G Sales
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, UK
| | - Anabela Bernardes da Silva
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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22
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von Caemmerer S. Rubisco carboxylase/oxygenase: From the enzyme to the globe: A gas exchange perspective. JOURNAL OF PLANT PHYSIOLOGY 2020; 252:153240. [PMID: 32707452 DOI: 10.1016/j.jplph.2020.153240] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 07/12/2020] [Indexed: 05/28/2023]
Abstract
Rubisco is the primary carboxylase of the photosynthetic process, the most abundant enzyme in the biosphere, and also one of the best-characterized enzymes. Rubisco also functions as an oxygenase, a discovery made 50 years ago by Bill Ogren. Carboxylation of ribulose bisphosphate (RuBP) is the first step of the photosynthetic carbon reduction cycle and leads to the assimilation of CO2, whereas the oxygenase activity necessitates the recycling of phosphoglycolate through the photorespiratory carbon oxidation cycle with concomitant loss of CO2. Since the discovery of Rubisco's dual function, the biochemical properties of Rubisco have underpinned the mechanistic mathematical models of photosynthetic CO2 fixation which link Rubisco kinetic properties to gas exchange of leaves. This has allowed assessments of global CO2 exchange and predictions of how Rubisco has and will shape the environmental responses of crop and global photosynthesis in future climates. Rubisco's biochemical properties, including its slow catalytic turnover and poor affinity for CO2, constrain crop growth and therefore improving its activity and regulation and minimising photorespiration are key targets for crop improvement.
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Affiliation(s)
- Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, 2601, Australia.
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23
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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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24
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Busch FA. Photorespiration in the context of Rubisco biochemistry, CO 2 diffusion and metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:919-939. [PMID: 31910295 DOI: 10.1111/tpj.14674] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 05/11/2023]
Abstract
Photorespiratory metabolism is essential for plants to maintain functional photosynthesis in an oxygen-containing environment. Because the oxygenation reaction of Rubisco is followed by the loss of previously fixed carbon, photorespiration is often considered a wasteful process and considerable efforts are aimed at minimizing the negative impact of photorespiration on the plant's carbon uptake. However, the photorespiratory pathway has also many positive aspects, as it is well integrated within other metabolic processes, such as nitrogen assimilation and C1 metabolism, and it is important for maintaining the redox balance of the plant. The overall effect of photorespiratory carbon loss on the net CO2 fixation of the plant is also strongly influenced by the physiology of the leaf related to CO2 diffusion. This review outlines the distinction between Rubisco oxygenation and photorespiratory CO2 release as a basis to evaluate the costs and benefits of photorespiration.
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Affiliation(s)
- Florian A Busch
- Research School of Biology and ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Acton, ACT, 2601, Australia
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25
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Insights into the mechanism and regulation of the CbbQO-type Rubisco activase, a MoxR AAA+ ATPase. Proc Natl Acad Sci U S A 2019; 117:381-387. [PMID: 31848241 DOI: 10.1073/pnas.1911123117] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The vast majority of biological carbon dioxide fixation relies on the function of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). In most cases the enzyme exhibits a tendency to become inhibited by its substrate RuBP and other sugar phosphates. The inhibition is counteracted by diverse molecular chaperones known as Rubisco activases (Rcas). In some chemoautotrophic bacteria, the CbbQO-type Rca Q2O2 repairs inhibited active sites of hexameric form II Rubisco. The 2.2-Å crystal structure of the MoxR AAA+ protein CbbQ2 from Acidithiobacillus ferrooxidans reveals the helix 2 insert (H2I) that is critical for Rca function and forms the axial pore of the CbbQ hexamer. Negative-stain electron microscopy shows that the essential CbbO adaptor protein binds to the conserved, concave side of the CbbQ2 hexamer. Site-directed mutagenesis supports a model in which adenosine 5'-triphosphate (ATP)-powered movements of the H2I are transmitted to CbbO via the concave residue L85. The basal ATPase activity of Q2O2 Rca is repressed but strongly stimulated by inhibited Rubisco. The characterization of multiple variants where this repression is released indicates that binding of inhibited Rubisco to the C-terminal CbbO VWA domain initiates a signal toward the CbbQ active site that is propagated via elements that include the CbbQ α4-β4 loop, pore loop 1, and the presensor 1-β hairpin (PS1-βH). Detailed mechanistic insights into the enzyme repair chaperones of the highly diverse CO2 fixation machinery of Proteobacteria will facilitate their successful implementation in synthetic biology ventures.
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26
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Desmarais JJ, Flamholz AI, Blikstad C, Dugan EJ, Laughlin TG, Oltrogge LM, Chen AW, Wetmore K, Diamond S, Wang JY, Savage DF. DABs are inorganic carbon pumps found throughout prokaryotic phyla. Nat Microbiol 2019; 4:2204-2215. [PMID: 31406332 PMCID: PMC10184468 DOI: 10.1038/s41564-019-0520-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/13/2019] [Accepted: 06/20/2019] [Indexed: 12/30/2022]
Abstract
Bacterial autotrophs often rely on CO2 concentrating mechanisms (CCMs) to assimilate carbon. Although many CCM proteins have been identified, a systematic screen of the components of CCMs is lacking. Here, we performed a genome-wide barcoded transposon screen to identify essential and CCM-related genes in the γ-proteobacterium Halothiobacillus neapolitanus. Screening revealed that the CCM comprises at least 17 and probably no more than 25 genes, most of which are encoded in 3 operons. Two of these operons (DAB1 and DAB2) contain a two-gene locus that encodes a domain of unknown function (Pfam: PF10070) and a putative cation transporter (Pfam: PF00361). Physiological and biochemical assays demonstrated that these proteins-which we name DabA and DabB, for DABs accumulate bicarbonate-assemble into a heterodimeric complex, which contains a putative β-carbonic anhydrase-like active site and functions as an energy-coupled inorganic carbon (Ci) pump. Interestingly, DAB operons are found in a diverse range of bacteria and archaea. We demonstrate that functional DABs are present in the human pathogens Bacillus anthracis and Vibrio cholerae. On the basis of these results, we propose that DABs constitute a class of energized Ci pumps and play a critical role in the metabolism of Ci throughout prokaryotic phyla.
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Affiliation(s)
- John J Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Avi I Flamholz
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Eli J Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Allen W Chen
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Kelly Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Joy Y Wang
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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27
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Flamholz AI, Prywes N, Moran U, Davidi D, Bar-On YM, Oltrogge LM, Alves R, Savage D, Milo R. Revisiting Trade-offs between Rubisco Kinetic Parameters. Biochemistry 2019; 58:3365-3376. [PMID: 31259528 PMCID: PMC6686151 DOI: 10.1021/acs.biochem.9b00237] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Rubisco
is the primary carboxylase of the Calvin cycle, the most
abundant enzyme in the biosphere, and one of the best-characterized
enzymes. On the basis of correlations between Rubisco kinetic parameters,
it is widely posited that constraints embedded in the catalytic mechanism
enforce trade-offs between CO2 specificity, SC/O, and maximum carboxylation rate, kcat,C. However, the reasoning that established this view
was based on data from ≈20 organisms. Here, we re-examine models
of trade-offs in Rubisco catalysis using a data set from ≈300
organisms. Correlations between kinetic parameters are substantially
attenuated in this larger data set, with the inverse relationship
between kcat,C and SC/O being a key example. Nonetheless, measured kinetic parameters
display extremely limited variation, consistent with a view of Rubisco
as a highly constrained enzyme. More than 95% of kcat,C values are between 1 and 10 s–1, and no measured kcat,C exceeds 15 s–1. Similarly, SC/O varies
by only 30% among Form I Rubiscos and <10% among C3 plant
enzymes. Limited variation in SC/O forces
a strong positive correlation between the catalytic efficiencies (kcat/KM) for carboxylation
and oxygenation, consistent with a model of Rubisco catalysis in which
increasing the rate of addition of CO2 to the enzyme–substrate
complex requires an equal increase in the O2 addition rate.
Altogether, these data suggest that Rubisco evolution is tightly constrained
by the physicochemical limits of CO2/O2 discrimination.
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Affiliation(s)
- Avi I Flamholz
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
| | - Noam Prywes
- Innovative Genomics Institute , University of California , Berkeley , California 94704 , United States
| | - Uri Moran
- Department of Plant and Environmental Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
| | - Rui Alves
- Institute of Biomedical Research of Lleida , IRBLleida , 25198 Lleida , Catalunya , Spain.,Departament de Ciències Mèdiques Bàsiques , University of Lleida , 25198 Lleida , Catalunya , Spain
| | - David Savage
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
| | - Ron Milo
- Department of Plant and Environmental Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
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Wang S, Alseekh S, Fernie AR, Luo J. The Structure and Function of Major Plant Metabolite Modifications. MOLECULAR PLANT 2019; 12:899-919. [PMID: 31200079 DOI: 10.1016/j.molp.2019.06.001] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/27/2019] [Accepted: 06/04/2019] [Indexed: 05/23/2023]
Abstract
Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality.
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Affiliation(s)
- Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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29
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Boyd RA, Cavanagh AP, Kubien DS, Cousins AB. Temperature response of Rubisco kinetics in Arabidopsis thaliana: thermal breakpoints and implications for reaction mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:231-242. [PMID: 30403800 PMCID: PMC6305185 DOI: 10.1093/jxb/ery355] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/09/2018] [Indexed: 05/04/2023]
Abstract
Enhancement of Rubisco kinetics could improve photosynthetic efficiency, ultimately resulting in increased crop yield. However, imprecise knowledge of the reaction mechanism and the individual rate constants limits our ability to optimize the enzyme. Membrane inlet mass spectrometry (MIMS) may offer benefits over traditional methods for determining individual rate constants of the Rubisco reaction mechanism, as it can directly monitor concentration changes in CO2, O2, and their isotopologs during assays. However, a direct comparison of MIMS with the traditional radiolabel method of determining Rubisco kinetic parameters has not been made. Here, the temperature responses of Rubisco kinetic parameters from Arabidopsis thaliana were measured using radiolabel and MIMS methods. The two methods provided comparable parameters above 25 °C, but temperature responses deviated at low temperature as MIMS-derived catalytic rates of carboxylation, oxygenation, and CO2/O2 specificity showed thermal breakpoints. Here, we discuss the variability and uncertainty surrounding breakpoints in the Rubisco temperature response and the relevance of individual rate constants of the reaction mechanisms to potential breakpoints.
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Affiliation(s)
- Ryan A Boyd
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Amanda P Cavanagh
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - David S Kubien
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Asaph B Cousins
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA
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30
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Kim SM, Lim HS, Lee SB. Discovery of a RuBisCO-like Protein that Functions as an Oxygenase in the Novel d-Hamamelose Pathway. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0305-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Shimakawa G, Miyake C. Oxidation of P700 Ensures Robust Photosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:1617. [PMID: 30459798 PMCID: PMC6232666 DOI: 10.3389/fpls.2018.01617] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/18/2018] [Indexed: 05/18/2023]
Abstract
In the light, photosynthetic cells can potentially suffer from oxidative damage derived from reactive oxygen species. Nevertheless, a variety of oxygenic photoautotrophs, including cyanobacteria, algae, and plants, manage their photosynthetic systems successfully. In the present article, we review previous research on how these photoautotrophs safely utilize light energy for photosynthesis without photo-oxidative damage to photosystem I (PSI). The reaction center chlorophyll of PSI, P700, is kept in an oxidized state in response to excess light, under high light and low CO2 conditions, to tune the light utilization and dissipate the excess photo-excitation energy in PSI. Oxidation of P700 is co-operatively regulated by a number of molecular mechanisms on both the electron donor and acceptor sides of PSI. The strategies to keep P700 oxidized are diverse among a variety of photoautotrophs, which are evolutionarily optimized for their ecological niche.
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Affiliation(s)
- Ginga Shimakawa
- Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Chikahiro Miyake
- Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- Core Research for Environmental Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
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32
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Mahounga DM, Sun H, Jiang YL. Crystal structure of the effector-binding domain of Synechococcus elongatus CmpR in complex with ribulose 1,5-bisphosphate. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2018; 74:506-511. [PMID: 30084400 DOI: 10.1107/s2053230x18008841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/16/2018] [Indexed: 11/10/2022]
Abstract
The CO2-concentrating mechanism (CCM) has evolved to improve the efficiency of photosynthesis in autotrophic cyanobacteria. CmpR, a LysR-type transcriptional regulator (LTTR) from Synechococcus elongatus PCC 7942, was found to regulate CCM-related genes under low-CO2 conditions. Here, the dimeric structure of the effector-binding domain of CmpR (CmpR-EBD) in complex with the co-activator ribulose 1,5-bisphosphate (RuBP) is reported at 2.15 Å resolution. One RuBP molecule binds to the inter-domain cleft between the two subunits of the CmpR-EBD dimer. Structural comparison combined with sequence analyses demonstrated that CmpR-EBD has an overall structure similar to those of LTTRs of known structure, but possesses a distinctly different effector-binding pattern.
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Affiliation(s)
- Didel M Mahounga
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Hui Sun
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Yong Liang Jiang
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
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33
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Bloom AJ, Lancaster KM. Manganese binding to Rubisco could drive a photorespiratory pathway that increases the energy efficiency of photosynthesis. NATURE PLANTS 2018; 4:414-422. [PMID: 29967515 DOI: 10.1038/s41477-018-0191-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 06/01/2018] [Indexed: 05/18/2023]
Abstract
Most plants, contrary to popular belief, do not waste over 30% of their photosynthate in a futile cycle called photorespiration. Rather, the photorespiratory pathway generates additional malate in the chloroplast that empowers many energy-intensive chemical reactions, such as those involved in nitrate assimilation. Thus, the balance between carbon fixation and photorespiration determines the plant carbon-nitrogen balance and protein concentrations. Plant protein concentrations, in turn, depend not only on the relative concentrations of carbon dioxide and oxygen in the chloroplast but also on the relative activities of magnesium and manganese, which are metals that associate with several key enzymes in the photorespiratory pathway and alter their function. Understanding the regulation of these processes is critical for sustaining food quality under rising CO2 atmospheres.
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Affiliation(s)
- Arnold J Bloom
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA.
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
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34
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Increasing metabolic potential: C-fixation. Essays Biochem 2018; 62:109-118. [PMID: 29653967 DOI: 10.1042/ebc20170014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/17/2018] [Accepted: 02/18/2018] [Indexed: 01/30/2023]
Abstract
Due to the growing world population, crop yields must increase to meet the rising demand. Crop plants also require adaptation to optimize performance in the changing environments caused by climate change. Improving photosynthetic carbon fixation is a promising, albeit technically challenging, strategy whose potential has only just begun to be considered in breeding programmes. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), a fundamental enzyme of carbon fixation, is extremely inefficient and many strategies to improve photosynthesis focus on overcoming the limitations of this enzyme, either by improving Rubisco activity and regulation or by improving the supply of substrates. Although progress is being made, the need to tailor solutions for each crop and their respective environments has been highlighted. Even so, continuing research will be required to achieve these objectives and to grow crops more sustainably in the future.
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35
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Bathellier C, Tcherkez G, Lorimer GH, Farquhar GD. Rubisco is not really so bad. PLANT, CELL & ENVIRONMENT 2018; 41:705-716. [PMID: 29359811 DOI: 10.1111/pce.13149] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the most widespread carboxylating enzyme in autotrophic organisms. Its kinetic and structural properties have been intensively studied for more than half a century. Yet important aspects of the catalytic mechanism remain poorly understood, especially the oxygenase reaction. Because of its relatively modest turnover rate (a few catalytic events per second) and the competitive inhibition by oxygen, Rubisco is often viewed as an inefficient catalyst for CO2 fixation. Considerable efforts have been devoted to improving its catalytic efficiency, so far without success. In this review, we re-examine Rubisco's catalytic performance by comparison with other chemically related enzymes. We find that Rubisco is not especially slow. Furthermore, considering both the nature and the complexity of the chemical reaction, its kinetic properties are unremarkable. Although not unique to Rubisco, oxygenation is not systematically observed in enolate and enamine forming enzymes and cannot be considered as an inevitable consequence of the mechanism. It is more likely the result of a compromise between chemical and metabolic imperatives. We argue that a better description of Rubisco mechanism is still required to better understand the link between CO2 and O2 reactivity and the rationale of Rubisco diversification and evolution.
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Affiliation(s)
- Camille Bathellier
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| | - Guillaume Tcherkez
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| | - George H Lorimer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 27042, USA
| | - Graham D Farquhar
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
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36
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Wilson RH, Martin-Avila E, Conlan C, Whitney SM. An improved Escherichia coli screen for Rubisco identifies a protein-protein interface that can enhance CO 2-fixation kinetics. J Biol Chem 2018; 293:18-27. [PMID: 28986448 PMCID: PMC5766918 DOI: 10.1074/jbc.m117.810861] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/28/2017] [Indexed: 01/03/2023] Open
Abstract
An overarching goal of photosynthesis research is to identify how components of the process can be improved to benefit crop productivity, global food security, and renewable energy storage. Improving carbon fixation has mostly focused on enhancing the CO2 fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). This grand challenge has mostly proved ineffective because of catalytic mechanism constraints and required chaperone complementarity that hinder Rubisco biogenesis in alternative hosts. Here we refashion Escherichia coli metabolism by expressing a phosphoribulokinase-neomycin phosphotransferase fusion protein to produce a high-fidelity, high-throughput Rubisco-directed evolution (RDE2) screen that negates false-positive selection. Successive evolution rounds using the plant-like Te-Rubisco from the cyanobacterium Thermosynechococcus elongatus BP1 identified two large subunit and six small subunit mutations that improved carboxylation rate, efficiency, and specificity. Structural analysis revealed the amino acids clustered in an unexplored subunit interface of the holoenzyme. To study its effect on plant growth, the Te-Rubisco was transformed into tobacco by chloroplast transformation. As previously seen for Synechocccus PCC6301 Rubisco, the specialized folding and assembly requirements of Te-Rubisco hinder its heterologous expression in leaf chloroplasts. Our findings suggest that the ongoing efforts to improve crop photosynthesis by integrating components of a cyanobacteria CO2-concentrating mechanism will necessitate co-introduction of the ancillary molecular components required for Rubisco biogenesis.
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Affiliation(s)
- Robert H Wilson
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Elena Martin-Avila
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Carly Conlan
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Spencer M Whitney
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia.
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37
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Flexas J, Cano FJ, Carriquí M, Coopman RE, Mizokami Y, Tholen D, Xiong D. CO2 Diffusion Inside Photosynthetic Organs. THE LEAF: A PLATFORM FOR PERFORMING PHOTOSYNTHESIS 2018. [DOI: 10.1007/978-3-319-93594-2_7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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Cummins PL, Kannappan B, Gready JE. Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All. FRONTIERS IN PLANT SCIENCE 2018; 9:183. [PMID: 29545812 PMCID: PMC5838012 DOI: 10.3389/fpls.2018.00183] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/31/2018] [Indexed: 05/19/2023]
Abstract
The ubiquitous enzyme Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) fixes atmospheric carbon dioxide within the Calvin-Benson cycle that is utilized by most photosynthetic organisms. Despite this central role, RuBisCO's efficiency surprisingly struggles, with both a very slow turnover rate to products and also impaired substrate specificity, features that have long been an enigma as it would be assumed that its efficiency was under strong evolutionary pressure. RuBisCO's substrate specificity is compromised as it catalyzes a side-fixation reaction with atmospheric oxygen; empirical kinetic results show a trend to tradeoff between relative specificity and low catalytic turnover rate. Although the dominant hypothesis has been that the active-site chemistry constrains the enzyme's evolution, a more recent study on RuBisCO stability and adaptability has implicated competing selection pressures. Elucidating these constraints is crucial for directing future research on improving photosynthesis, as the current literature casts doubt on the potential effectiveness of site-directed mutagenesis to improve RuBisCO's efficiency. Here we use regression analysis to quantify the relationships between kinetic parameters obtained from empirical data sets spanning a wide evolutionary range of RuBisCOs. Most significantly we found that the rate constant for dissociation of CO2 from the enzyme complex was much higher than previous estimates and comparable with the corresponding catalytic rate constant. Observed trends between relative specificity and turnover rate can be expressed as the product of negative and positive correlation factors. This provides an explanation in simple kinetic terms of both the natural variation of relative specificity as well as that obtained by reported site-directed mutagenesis results. We demonstrate that the kinetic behaviour shows a lesser rather than more constrained RuBisCO, consistent with growing empirical evidence of higher variability in relative specificity. In summary our analysis supports an explanation for the origin of the tradeoff between specificity and turnover as due to competition between protein stability and activity, rather than constraints between rate constants imposed by the underlying chemistry. Our analysis suggests that simultaneous improvement in both specificity and turnover rate of RuBisCO is possible.
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39
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Ślesak I, Ślesak H, Kruk J. RubisCO Early Oxygenase Activity: A Kinetic and Evolutionary Perspective. Bioessays 2017; 39. [PMID: 28976010 DOI: 10.1002/bies.201700071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/10/2017] [Indexed: 11/09/2022]
Abstract
RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase) is Earth's main enzyme responsible for CO2 fixation via carboxylation of ribulose-1,5-bisphosphate (RuBP) into organic matter. Besides the carboxylation reaction, RubisCO also catalyzes the oxygenation of RuBP by O2 , which is probably as old as its carboxylation properties. Based on molecular phylogeny, the occurrence of the reactive oxygen species (ROS)-removing system and kinetic properties of different RubisCO forms, we postulated that RubisCO oxygenase activity appeared in local microoxic areas, yet before the appearance of oxygenic photosynthesis. Here, in reviewing the literature, we present a novel hypothesis: the RubisCO early oxygenase activity hypothesis. This hypothesis may be compared with the exaptation hypothesis, according to which latent RubisCO oxygenase properties emerged later during the oxygenation of the Earth's atmosphere. The reconstruction of ancestral RubisCO forms using ancestral sequence reconstruction (ASR) techniques, as a promising way for testing of RubisCO early oxygenase activity hypothesis, is presented.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, Kraków 30-239, Poland
| | - Halina Ślesak
- Institute of Botany, Jagiellonian University, Gronostajowa 9, Kraków 30-387, Poland
| | - Jerzy Kruk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
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40
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Ogbaga CC, Stepien P, Athar HUR, Ashraf M. Engineering Rubisco activase from thermophilic cyanobacteria into high-temperature sensitive plants. Crit Rev Biotechnol 2017; 38:559-572. [DOI: 10.1080/07388551.2017.1378998] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chukwuma C. Ogbaga
- Department of Biological Sciences, Nile University of Nigeria, Abuja, Nigeria
| | - Piotr Stepien
- Department of Plant Nutrition, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Habib-Ur-Rehman Athar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
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41
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Heureux AMC, Young JN, Whitney SM, Eason-Hubbard MR, Lee RBY, Sharwood RE, Rickaby REM. The role of Rubisco kinetics and pyrenoid morphology in shaping the CCM of haptophyte microalgae. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3959-3969. [PMID: 28582571 PMCID: PMC5853415 DOI: 10.1093/jxb/erx179] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/15/2017] [Indexed: 05/18/2023]
Abstract
The haptophyte algae are a cosmopolitan group of primary producers that contribute significantly to the marine carbon cycle and play a major role in paleo-climate studies. Despite their global importance, little is known about carbon assimilation in haptophytes, in particular the kinetics of their Form 1D CO2-fixing enzyme, Rubisco. Here we examine Rubisco properties of three haptophytes with a range of pyrenoid morphologies (Pleurochrysis carterae, Tisochrysis lutea, and Pavlova lutheri) and the diatom Phaeodactylum tricornutum that exhibit contrasting sensitivities to the trade-offs between substrate affinity (Km) and turnover rate (kcat) for both CO2 and O2. The pyrenoid-containing T. lutea and P. carterae showed lower Rubisco content and carboxylation properties (KC and kCcat) comparable with those of Form 1D-containing non-green algae. In contrast, the pyrenoid-lacking P. lutheri produced Rubisco in 3-fold higher amounts, and displayed a Form 1B Rubisco kCcat-KC relationship and increased CO2/O2 specificity that, when modeled in the context of a C3 leaf, supported equivalent rates of photosynthesis to higher plant Rubisco. Correlation between the differing Rubisco properties and the occurrence and localization of pyrenoids with differing intracellular CO2:O2 microenvironments has probably influenced the divergent evolution of Form 1B and 1D Rubisco kinetics.
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Affiliation(s)
- Ana M C Heureux
- University of Oxford, Department of Earth Sciences, South Parks Road, Oxford, UK
| | - Jodi N Young
- University of Washington, School of Oceanography, Seattle, WA, USA
| | - Spencer M Whitney
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra ACT, Australia
| | | | - Renee B Y Lee
- University of Oxford, Department of Earth Sciences, South Parks Road, Oxford, UK
- University of Reading, School of Biological Sciences, Reading, Berkshire, UK
| | - Robert E Sharwood
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra ACT, Australia
| | - Rosalind E M Rickaby
- University of Oxford, Department of Earth Sciences, South Parks Road, Oxford, UK
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42
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Mueller-Cajar O. The Diverse AAA+ Machines that Repair Inhibited Rubisco Active Sites. Front Mol Biosci 2017; 4:31. [PMID: 28580359 PMCID: PMC5437159 DOI: 10.3389/fmolb.2017.00031] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/29/2017] [Indexed: 11/13/2022] Open
Abstract
Gaseous carbon dioxide enters the biosphere almost exclusively via the active site of the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). This highly conserved catalyst has an almost universal propensity to non-productively interact with its substrate ribulose 1,5-bisphosphate, leading to the formation of dead-end inhibited complexes. In diverse autotrophic organisms this tendency has been counteracted by the recruitment of dedicated AAA+ (ATPases associated with various cellular activities) proteins that all use the energy of ATP hydrolysis to remodel inhibited Rubisco active sites leading to release of the inhibitor. Three evolutionarily distinct classes of these Rubisco activases (Rcas) have been discovered so far. Green and red-type Rca are mostly found in photosynthetic eukaryotes of the green and red plastid lineage respectively, whereas CbbQO is associated with chemoautotrophic bacteria. Ongoing mechanistic studies are elucidating how the various motors are utilizing both similar and contrasting strategies to ultimately perform their common function of cracking the inhibited Rubisco active site. The best studied mechanism utilized by red-type Rca appears to involve transient threading of the Rubisco large subunit C-terminal peptide, reminiscent of the action performed by Clp proteases. As well as providing a fascinating example of convergent molecular evolution, Rca proteins can be considered promising crop-improvement targets. Approaches aiming to replace Rubisco in plants with improved enzymes will need to ensure the presence of a compatible Rca protein. The thermolability of the Rca protein found in crop plants provides an opportunity to fortify photosynthesis against high temperature stress. Photosynthesis also appears to be limited by Rca when light conditions are fluctuating. Synthetic biology strategies aiming to enhance the autotrophic CO2 fixation machinery will need to take into consideration the requirement for Rubisco activases as well as their properties.
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Affiliation(s)
- Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological UniversitySingapore, Singapore
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Bracher A, Whitney SM, Hartl FU, Hayer-Hartl M. Biogenesis and Metabolic Maintenance of Rubisco. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:29-60. [PMID: 28125284 DOI: 10.1146/annurev-arplant-043015-111633] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) mediates the fixation of atmospheric CO2 in photosynthesis by catalyzing the carboxylation of the 5-carbon sugar ribulose-1,5-bisphosphate (RuBP). Rubisco is a remarkably inefficient enzyme, fixing only 2-10 CO2 molecules per second. Efforts to increase crop yields by bioengineering Rubisco remain unsuccessful, owing in part to the complex cellular machinery required for Rubisco biogenesis and metabolic maintenance. The large subunit of Rubisco requires the chaperonin system for folding, and recent studies have shown that assembly of hexadecameric Rubisco is mediated by specific assembly chaperones. Moreover, Rubisco function can be inhibited by a range of sugar-phosphate ligands, including RuBP. Metabolic repair depends on remodeling of Rubisco by the ATP-dependent Rubisco activase and hydrolysis of inhibitory sugar phosphates by specific phosphatases. Here, we review our present understanding of the structure and function of these auxiliary factors and their utilization in efforts to engineer more catalytically efficient Rubisco enzymes.
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Affiliation(s)
- Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ; , ,
| | - Spencer M Whitney
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia;
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ; , ,
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ; , ,
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Sharwood RE, Ghannoum O, Kapralov MV, Gunn LH, Whitney SM. Temperature responses of Rubisco from Paniceae grasses provide opportunities for improving C 3 photosynthesis. NATURE PLANTS 2016; 2:16186. [PMID: 27892943 DOI: 10.1038/nplants.2016.186] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/27/2016] [Indexed: 05/03/2023]
Abstract
Enhancing the catalytic properties of the CO2-fixing enzyme Rubisco is a target for improving agricultural crop productivity. Here, we reveal extensive diversity in the kinetic response between 10 and 37 °C by Rubisco from C3 and C4 species within the grass tribe Paniceae. The CO2 fixation rate (kcatc) for Rubisco from the C4 grasses with nicotinamide adenine dinucleotide (NAD) phosphate malic enzyme (NADP-ME) and phosphoenolpyruvate carboxykinase (PCK) photosynthetic pathways was twofold greater than the kcatc of Rubisco from NAD-ME species across all temperatures. The declining response of CO2/O2 specificity with increasing temperature was less pronounced for PCK and NADP-ME Rubisco, which would be advantageous in warmer climates relative to the NAD-ME grasses. Modelled variation in the temperature kinetics of Paniceae C3 Rubisco and PCK Rubisco differentially stimulated C3 photosynthesis relative to tobacco above and below 25 °C under current and elevated CO2. Amino acid substitutions in the large subunit that could account for the catalytic variation among Paniceae Rubisco are identified; however, incompatibilities with Paniceae Rubisco biogenesis in tobacco hindered their mutagenic testing by chloroplast transformation. Circumventing these bioengineering limitations is critical to tailoring the properties of crop Rubisco to suit future climates.
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Affiliation(s)
- Robert E Sharwood
- Research School of Biology, Australian National University, Canberra Australian Capital Territory 2601, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra Australian Capital Territory 2601, Australia
| | - Oula Ghannoum
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra Australian Capital Territory 2601, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales 2753, Australia
| | - Maxim V Kapralov
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Laura H Gunn
- Research School of Biology, Australian National University, Canberra Australian Capital Territory 2601, Australia
| | - Spencer M Whitney
- Research School of Biology, Australian National University, Canberra Australian Capital Territory 2601, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Canberra Australian Capital Territory 2601, Australia
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Betti M, Bauwe H, Busch FA, Fernie AR, Keech O, Levey M, Ort DR, Parry MAJ, Sage R, Timm S, Walker B, Weber APM. Manipulating photorespiration to increase plant productivity: recent advances and perspectives for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2977-88. [PMID: 26951371 DOI: 10.1093/jxb/erw076] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Recycling of the 2-phosphoglycolate generated by the oxygenase reaction of Rubisco requires a complex and energy-consuming set of reactions collectively known as the photorespiratory cycle. Several approaches aimed at reducing the rates of photorespiratory energy or carbon loss have been proposed, based either on screening for natural variation or by means of genetic engineering. Recent work indicates that plant yield can be substantially improved by the alteration of photorespiratory fluxes or by engineering artificial bypasses to photorespiration. However, there is also evidence indicating that, under certain environmental and/or nutritional conditions, reduced photorespiratory capacity may be detrimental to plant performance. Here we summarize recent advances obtained in photorespiratory engineering and discuss prospects for these advances to be transferred to major crops to help address the globally increasing demand for food and biomass production.
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Affiliation(s)
- Marco Betti
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, 41012 Sevilla, Spain
| | - Hermann Bauwe
- Plant Physiology Department, University of Rostock, D-18051 Rostock, Germany
| | - Florian A Busch
- Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Alisdair R Fernie
- Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden
| | - Myles Levey
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Donald R Ort
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture/Agricultural Research Service, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Martin A J Parry
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Rowan Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada, M5S 3B2
| | - Stefan Timm
- Plant Physiology Department, University of Rostock, D-18051 Rostock, Germany
| | - Berkley Walker
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture/Agricultural Research Service, Urbana, IL 61801, USA Carl Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, 40225 Düsseldorf, Germany
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Young JN, Heureux AMC, Sharwood RE, Rickaby REM, Morel FMM, Whitney SM. Large variation in the Rubisco kinetics of diatoms reveals diversity among their carbon-concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3445-56. [PMID: 27129950 PMCID: PMC4892730 DOI: 10.1093/jxb/erw163] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
While marine phytoplankton rival plants in their contribution to global primary productivity, our understanding of their photosynthesis remains rudimentary. In particular, the kinetic diversity of the CO2-fixing enzyme, Rubisco, in phytoplankton remains unknown. Here we quantify the maximum rates of carboxylation (k cat (c)), oxygenation (k cat (o)), Michaelis constants (K m) for CO2 (K C) and O2 (K O), and specificity for CO2 over O2 (SC/O) for Form I Rubisco from 11 diatom species. Diatom Rubisco shows greater variation in K C (23-68 µM), SC/O (57-116mol mol(-1)), and K O (413-2032 µM) relative to plant and algal Rubisco. The broad range of K C values mostly exceed those of C4 plant Rubisco, suggesting that the strength of the carbon-concentrating mechanism (CCM) in diatoms is more diverse, and more effective than previously predicted. The measured k cat (c) for each diatom Rubisco showed less variation (2.1-3.7s(-1)), thus averting the canonical trade-off typically observed between K C and k cat (c) for plant Form I Rubisco. Uniquely, a negative relationship between K C and cellular Rubisco content was found, suggesting variation among diatom species in how they allocate their limited cellular resources between Rubisco synthesis and their CCM. The activation status of Rubisco in each diatom was low, indicating a requirement for Rubisco activase. This work highlights the need to better understand the correlative natural diversity between the Rubisco kinetics and CCM of diatoms and the underpinning mechanistic differences in catalytic chemistry among the Form I Rubisco superfamily.
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Affiliation(s)
- Jodi N Young
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Ana M C Heureux
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Robert E Sharwood
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - François M M Morel
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Spencer M Whitney
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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Kreel NE, Tabita FR. Serine 363 of a Hydrophobic Region of Archaeal Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from Archaeoglobus fulgidus and Thermococcus kodakaraensis Affects CO2/O2 Substrate Specificity and Oxygen Sensitivity. PLoS One 2015; 10:e0138351. [PMID: 26381513 PMCID: PMC4575112 DOI: 10.1371/journal.pone.0138351] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/28/2015] [Indexed: 11/18/2022] Open
Abstract
Archaeal ribulose 1, 5-bisphospate carboxylase/oxygenase (RubisCO) is differentiated from other RubisCO enzymes and is classified as a form III enzyme, as opposed to the form I and form II RubisCOs typical of chemoautotrophic bacteria and prokaryotic and eukaryotic phototrophs. The form III enzyme from archaea is particularly interesting as several of these proteins exhibit unusual and reversible sensitivity to molecular oxygen, including the enzyme from Archaeoglobus fulgidus. Previous studies with A. fulgidus RbcL2 had shown the importance of Met-295 in oxygen sensitivity and pointed towards the potential significance of another residue (Ser-363) found in a hydrophobic pocket that is conserved in all RubisCO proteins. In the current study, further structure/function studies have been performed focusing on Ser-363 of A. fulgidus RbcL2; various changes in this and other residues of the hydrophobic pocket point to and definitively establish the importance of Ser-363 with respect to interactions with oxygen. In addition, previous findings had indicated discrepant CO2/O2 specificity determinations of the Thermococcus kodakaraensis RubisCO, a close homolog of A. fulgidus RbcL2. It is shown here that the T. kodakaraensis enzyme exhibits a similar substrate specificity as the A. fulgidus enzyme and is also oxygen sensitive, with equivalent residues involved in oxygen interactions.
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Affiliation(s)
- Nathan E. Kreel
- The Ohio State University Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio, 43210–1292, United States of America
| | - F. Robert Tabita
- The Ohio State University Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio, 43210–1292, United States of America
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio, 43210–1292, United States of America
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