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Capó-Bauçà S, Iñiguez C, Galmés J. The diversity and coevolution of Rubisco and CO 2 concentrating mechanisms in marine macrophytes. THE NEW PHYTOLOGIST 2024; 241:2353-2365. [PMID: 38197185 DOI: 10.1111/nph.19528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024]
Abstract
The kinetic properties of Rubisco, the most important carbon-fixing enzyme, have been assessed in a small fraction of the estimated existing biodiversity of photosynthetic organisms. Until recently, one of the most significant gaps of knowledge in Rubisco kinetics was marine macrophytes, an ecologically relevant group including brown (Ochrophyta), red (Rhodophyta) and green (Chlorophyta) macroalgae and seagrasses (Streptophyta). These organisms express various Rubisco types and predominantly possess CO2 -concentrating mechanisms (CCMs), which facilitate the use of bicarbonate for photosynthesis. Since bicarbonate is the most abundant form of dissolved inorganic carbon in seawater, CCMs allow marine macrophytes to overcome the slow gas diffusion and low CO2 availability in this environment. The present review aims to compile and integrate recent findings on the biochemical diversity of Rubisco and CCMs in the main groups of marine macrophytes. The Rubisco kinetic data provided demonstrate a more relaxed relationship among catalytic parameters than previously reported, uncovering a variability in Rubisco catalysis that has been hidden by a bias in the literature towards terrestrial vascular plants. The compiled data indicate the existence of convergent evolution between Rubisco and biophysical CCMs across the polyphyletic groups of marine macrophytes and suggest a potential role for oxygen in shaping such relationship.
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Affiliation(s)
- Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, 07122, Palma, Balearic Islands, Spain
| | - Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, 07122, Palma, Balearic Islands, Spain
- Department of Ecology, Faculty of Sciences, University of Malaga, Boulevard Louis Pasteur s/n, 29010, Málaga, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, 07122, Palma, Balearic Islands, Spain
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2
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Bouvier JW. Evolution: Unearthing missing links in the origin of our planet's primary carbon-fixing enzyme. Curr Biol 2023; 33:R1301-R1303. [PMID: 38113844 DOI: 10.1016/j.cub.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Form I rubisco underpins life on Earth, but the origins of its anomalous and highly complex multimeric structure have long proven elusive. New research helps to unravel this enigma by uncovering key missing links in the enzyme's evolutionary history.
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Affiliation(s)
- Jacques W Bouvier
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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3
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Smith EN, van Aalst M, Tosens T, Niinemets Ü, Stich B, Morosinotto T, Alboresi A, Erb TJ, Gómez-Coronado PA, Tolleter D, Finazzi G, Curien G, Heinemann M, Ebenhöh O, Hibberd JM, Schlüter U, Sun T, Weber APM. Improving photosynthetic efficiency toward food security: Strategies, advances, and perspectives. MOLECULAR PLANT 2023; 16:1547-1563. [PMID: 37660255 DOI: 10.1016/j.molp.2023.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
Photosynthesis in crops and natural vegetation allows light energy to be converted into chemical energy and thus forms the foundation for almost all terrestrial trophic networks on Earth. The efficiency of photosynthetic energy conversion plays a crucial role in determining the portion of incident solar radiation that can be used to generate plant biomass throughout a growth season. Consequently, alongside the factors such as resource availability, crop management, crop selection, maintenance costs, and intrinsic yield potential, photosynthetic energy use efficiency significantly influences crop yield. Photosynthetic efficiency is relevant to sustainability and food security because it affects water use efficiency, nutrient use efficiency, and land use efficiency. This review focuses specifically on the potential for improvements in photosynthetic efficiency to drive a sustainable increase in crop yields. We discuss bypassing photorespiration, enhancing light use efficiency, harnessing natural variation in photosynthetic parameters for breeding purposes, and adopting new-to-nature approaches that show promise for achieving unprecedented gains in photosynthetic efficiency.
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Affiliation(s)
- Edward N Smith
- Faculty of Science and Engineering, Molecular Systems Biology - Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Marvin van Aalst
- Institute of Quantitative and Theoretical Biology, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Tiina Tosens
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | | | | | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry & Synthetic Metabolism, 35043 Marburg, Germany
| | - Paul A Gómez-Coronado
- Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry & Synthetic Metabolism, 35043 Marburg, Germany
| | - Dimitri Tolleter
- Interdisciplinary Research Institute of Grenoble, IRIG-LPCV, Grenoble Alpes University, CNRS, CEA, INRAE, 38000 Grenoble, France
| | - Giovanni Finazzi
- Interdisciplinary Research Institute of Grenoble, IRIG-LPCV, Grenoble Alpes University, CNRS, CEA, INRAE, 38000 Grenoble, France
| | - Gilles Curien
- Interdisciplinary Research Institute of Grenoble, IRIG-LPCV, Grenoble Alpes University, CNRS, CEA, INRAE, 38000 Grenoble, France
| | - Matthias Heinemann
- Faculty of Science and Engineering, Molecular Systems Biology - Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Oliver Ebenhöh
- Institute of Quantitative and Theoretical Biology, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Julian M Hibberd
- Molecular Physiology, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Urte Schlüter
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Tianshu Sun
- Molecular Physiology, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Andreas P M Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
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4
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Ishida A, Yamaji K, Nakano T, Ladpala P, Popradit A, Yoshimura K, Saiki ST, Maeda T, Yoshimura J, Koyama K, Diloksumpun S, Marod D. Comparative physiology of canopy tree leaves in evergreen and deciduous forests in lowland Thailand. Sci Data 2023; 10:601. [PMID: 37684226 PMCID: PMC10491629 DOI: 10.1038/s41597-023-02468-6] [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: 02/10/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
The typical seasonally dry forests in Southeast Asia are the mixed deciduous forest (MDF), dry dipterocarp (deciduous) forest (DDF), and dry evergreen forest (DEF). We obtained 21 physiological traits in the top/sunlit leaves of 107, 65 and 51 tree species in MDF, DEF and DDF, respectively. Approximately 70%, 95% and 95% of canopy tree species which consist of MDF, DEF and DDF are sampled, respectively. Light-saturated photosynthetic rates (Asat) exhibit a positive correlation with foliar nitrogen (N) and phosphorus (P) on leaf mass and area bases across tree species. Decreased leaf mass-based P reduces the positive slope of the mass-based N and Asat relationship across species and habitats. The differences in nutrient and water use and leaf habits are well matched to the variation in soil properties among the forest types, highlighting the reliability of this comprehensive database for revealing the mechanism of niche segregation based on edaphic factors.
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Affiliation(s)
- Atsushi Ishida
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan.
| | - Keiko Yamaji
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-0006, Japan
| | - Takashi Nakano
- Yamanashi Mount Fuji Research Institute, Kami-Yoshida, Fuji-Yoshida, Yamanashi, 403-0005, Japan
| | - Phanumard Ladpala
- Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, 10900, Thailand
| | - Ananya Popradit
- College of Innovation Management, Valaya Alongkorn University under the Royal Patronage, Klongluang, Pathum Thani, 13180, Thailand
| | - Kenichi Yoshimura
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, 997-8555, Japan
| | - Shin-Taro Saiki
- Department of Forest Ecology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
| | - Takahisa Maeda
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8569, Japan
| | - Jin Yoshimura
- Institute of Tropical Medicine, Nagasaki University, Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
- Faculty of Science, Tokyo Metropolitan University, Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
- The University Museum, The University of Tokyo, Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Kohei Koyama
- Asahikawa campus, Hokkaido University of Education, Asahikawa, Hokkaido, 070-8621, Japan
| | - Sapit Diloksumpun
- Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Dokrak Marod
- Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
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Bouvier JW, Kelly S. Response to Tcherkez and Farquhar: Rubisco adaptation is more limited by phylogenetic constraint than by catalytic trade-off. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154021. [PMID: 37392528 DOI: 10.1016/j.jplph.2023.154021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
Rubisco is the primary entry point for carbon into the biosphere. It has been widely proposed that rubisco is highly constrained by catalytic trade-offs due to correlations between the enzyme's kinetic traits across species. In previous work, we have shown that the strength of these correlations, and thus the strength of catalytic trade-offs, have been overestimated due to the presence of phylogenetic signal in the kinetic trait data (Bouvier et al., 2021). We demonstrated that only the trade-offs between the Michaelis constant for CO2 and carboxylase turnover, and between the Michaelis constants for CO2 and O2 were robust to phylogenetic effects. We further demonstrated that phylogenetic constraints have limited rubisco adaptation to a greater extent than the combined action of catalytic trade-offs. Recently, however, our claims have been contested by Tcherkez and Farquhar (2021), who have argued that the phylogenetic signal we detect in rubisco kinetic traits is an artefact of species sampling, the use of rbcL-based trees for phylogenetic inference, laboratory-to-laboratory variability in kinetic measurements, and homoplasy of the C4 trait. In the present article, we respond to these criticisms on a point-by-point basis and conclusively show that all are unfounded. As such, we stand by our original conclusions. Namely, although rubisco kinetic evolution has been limited by biochemical trade-offs, these are not absolute and have been previously overestimated due to phylogenetic biases. Instead, rubisco adaptation has in fact been more limited by phylogenetic constraint.
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Affiliation(s)
- Jacques W Bouvier
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom
| | - Steven Kelly
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom.
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Oh ZG, Askey B, Gunn LH. Red Rubiscos and opportunities for engineering green plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:520-542. [PMID: 36055563 PMCID: PMC9833100 DOI: 10.1093/jxb/erac349] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Nature's vital, but notoriously inefficient, CO2-fixing enzyme Rubisco often limits the growth of photosynthetic organisms including crop species. Form I Rubiscos comprise eight catalytic large subunits and eight auxiliary small subunits and can be classified into two distinct lineages-'red' and 'green'. While red-type Rubiscos (Form IC and ID) are found in rhodophytes, their secondary symbionts, and certain proteobacteria, green-type Rubiscos (Form IA and IB) exist in terrestrial plants, chlorophytes, cyanobacteria, and other proteobacteria. Eukaryotic red-type Rubiscos exhibit desirable kinetic properties, namely high specificity and high catalytic efficiency, with certain isoforms outperforming green-type Rubiscos. However, it is not yet possible to functionally express a high-performing red-type Rubisco in chloroplasts to boost photosynthetic carbon assimilation in green plants. Understanding the molecular and evolutionary basis for divergence between red- and green-type Rubiscos could help us to harness the superior CO2-fixing power of red-type Rubiscos. Here we review our current understanding about red-type Rubisco distribution, biogenesis, and sequence-structure, and present opportunities and challenges for utilizing red-type Rubisco kinetics towards crop improvements.
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Affiliation(s)
- Zhen Guo Oh
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Bryce Askey
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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Bathellier C, Tcherkez G. Experimental evidence for extra proton exchange in ribulose 1,5-bisphosphate carboxylase/oxygenase catalysis. Commun Integr Biol 2022; 15:68-74. [PMID: 35186179 PMCID: PMC8855871 DOI: 10.1080/19420889.2022.2039431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Despite considerable advances in the past 50 y, the mechanism of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalysis is still not well understood. In particular, the movement and exchange of protons within the active site is not well documented: typically, kinetics of H exchange during the first steps of catalysis, i.e. abstraction of the H3 atom of ribulose 1,5-bisphosphate (RuBP) and enolization, are not clearly established. Here, we took advantage of reaction assays run in heavy water (2H2O) to monitor the appearance of deuterated RuBP and deuterated products (3-phosphoglycerate and 2-phosphoglycolate) with exact mass LC-MS. Enolization was reversible such that de-enolization generated not only monodeuterated RuBP (2H-[H-3]-ribulose 1,5-bisphosphate) but also dideuterated RuBP (2H2-[H-3,O-3]-ribulose 1,5-bisphosphate). Carboxylation yielded about one half deuterated 3-phosphoglycerate (2H-[H-2]-3-phosphoglycerate) and also a small proportion of dideuterated 3-phosphoglycerate (2H2-[H-2,O-2]-3-phosphoglycerate). Oxygenation generated a small amount of monodeuterated, but no dideuterated, products. (Di)deuterated isotopologue abundance depended negatively on gas concentration. We conclude that in addition to the first step of proton exchange at H3 occurring before gas addition (and thus influenced by the competition between de-enolization and gas addition), there is another proton exchange step between solvent water, active site residues, and the 2,3-enediol(ate) leading to deuterated OH groups in products.
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Affiliation(s)
| | - Guillaume Tcherkez
- Research School of Biology, Australian National University, Canberra, Australia.,Institut de Recherche en Horticulture et Semences, Université d'Angers, INRAe, Beaucouzé, France
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