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Huang C, Huang J, Xiao J, Li X, He HS, Liang Y, Chen F, Tian H. Global convergence in terrestrial gross primary production response to atmospheric vapor pressure deficit. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2016-2025. [PMID: 38733513 DOI: 10.1007/s11427-023-2475-9] [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: 08/14/2023] [Accepted: 10/23/2023] [Indexed: 05/13/2024]
Abstract
Atmospheric vapor pressure deficit (VPD) increases with climate warming and may limit plant growth. However, gross primary production (GPP) responses to VPD remain a mystery, offering a significant source of uncertainty in the estimation of global terrestrial ecosystems carbon dynamics. In this study, in-situ measurements, satellite-derived data, and Earth System Models (ESMs) simulations were analysed to show that the GPP of most ecosystems has a similar threshold in response to VPD: first increasing and then declining. When VPD exceeds these thresholds, atmospheric drought stress reduces soil moisture and stomatal conductance, thereby decreasing the productivity of terrestrial ecosystems. Current ESMs underscore CO2 fertilization effects but predict significant GPP decline in low-latitude ecosystems when VPD exceeds the thresholds. These results emphasize the impacts of climate warming on VPD and propose limitations to future ecosystems productivity caused by increased atmospheric water demand. Incorporating VPD, soil moisture, and canopy conductance interactions into ESMs enhances the prediction of terrestrial ecosystem responses to climate change.
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Affiliation(s)
- Chao Huang
- Key Laboratory of National Forestry and Grassland Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Jingfeng Huang
- Institute of Applied Remote Sensing & Information Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
- Key Laboratory of Agricultural Remote Sensing and Information Systems, Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
| | - Jingfeng Xiao
- Earth Systems Research Center, Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, NH, 03824, USA
| | - Xing Li
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hong S He
- School of Natural Resources, University of Missouri, 203 ABNR Building, Columbia, MO, 65211, USA
| | - Yu Liang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Fusheng Chen
- Key Laboratory of National Forestry and Grassland Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Hanqin Tian
- Schiller Institute for Integrated Science and Society, Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, MA, 02467, USA
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2
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Eshenour K, Hotto A, Michel EJS, Oh ZG, Stern DB. Transgenic expression of Rubisco accumulation factor2 and Rubisco subunits increases photosynthesis and growth in maize. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4024-4037. [PMID: 38696303 DOI: 10.1093/jxb/erae186] [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: 11/01/2023] [Accepted: 05/01/2024] [Indexed: 05/04/2024]
Abstract
Carbon assimilation by Rubisco is often a limitation to photosynthesis and therefore plant productivity. We have previously shown that transgenic co-expression of the Rubisco large (LS) and small (SS) subunits along with an essential Rubisco accumulation factor, Raf1, leads to faster growth, increased photosynthesis, and enhanced chilling tolerance in maize (Zea mays). Maize also requires Rubisco accumulation factor2 (Raf2) for full accumulation of Rubisco. Here we have analyzed transgenic maize lines with increased expression of Raf2 or Raf2 plus LS and SS. We show that increasing Raf2 expression alone had minor effects on photosynthesis, whereas expressing Raf2 with Rubisco subunits led to increased Rubisco content, more rapid carbon assimilation, and greater plant height, most notably in plants at least 6 weeks of age. The magnitude of the effects was similar to what was observed previously for expression of Raf1 together with Rubisco subunits. Taken together, this suggests that increasing the amount of either assembly factor with Rubisco subunits can independently enhance Rubisco abundance and some aspects of plant performance. These results could also imply either synergy or a degree of functional redundancy for Raf1 and Raf2, the latter of whose precise role in Rubisco assembly is currently unknown.
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Affiliation(s)
| | - Amber Hotto
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA
| | | | - Zhen Guo Oh
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - David B Stern
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA
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3
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Chen H, Song Y, Wang Y, Wang H, Ding Z, Fan K. Zno nanoparticles: improving photosynthesis, shoot development, and phyllosphere microbiome composition in tea plants. J Nanobiotechnology 2024; 22:389. [PMID: 38956645 PMCID: PMC11221027 DOI: 10.1186/s12951-024-02667-2] [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: 03/06/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Nanotechnology holds revolutionary potential in the field of agriculture, with zinc oxide nanoparticles (ZnO NPs) demonstrating advantages in promoting crop growth. Enhanced photosynthetic efficiency is closely linked to improved vigor and superior quality in tea plants, complemented by the beneficial role of phyllosphere microorganisms in maintaining plant health. However, the effects of ZnO NPs on the photosynthesis of tea plants, the sprouting of new shoots, and the community of phyllosphere microorganisms have not been fully investigated. RESULTS This study investigated the photosynthetic physiological parameters of tea plants under the influence of ZnO NPs, the content of key photosynthetic enzymes such as RubisCO, chlorophyll content, chlorophyll fluorescence parameters, transcriptomic and extensive targeted metabolomic profiles of leaves and new shoots, mineral element composition in these tissues, and the epiphytic and endophytic microbial communities within the phyllosphere. The results indicated that ZnO NPs could enhance the photosynthesis of tea plants, upregulate the expression of some genes related to photosynthesis, increase the accumulation of photosynthetic products, promote the development of new shoots, and alter the content of various mineral elements in the leaves and new shoots of tea plants. Furthermore, the application of ZnO NPs was observed to favorably influence the microbial community structure within the phyllosphere of tea plants. This shift in microbial community dynamics suggests a potential for ZnO NPs to contribute to plant health and productivity by modulating the phyllosphere microbiome. CONCLUSION This study demonstrates that ZnO NPs have a positive impact on the photosynthesis of tea plants, the sprouting of new shoots, and the community of phyllosphere microorganisms, which can improve the growth condition of tea plants. These findings provide new scientific evidence for the application of ZnO NPs in sustainable agricultural development and contribute to advancing research in nanobiotechnology aimed at enhancing crop yield and quality.
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Affiliation(s)
- Hao Chen
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yujie Song
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yu Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Huan Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhaotang Ding
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Kai Fan
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
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Li A, Cao X, Fu R, Guo S, Fei Q. Biocatalysis of CO 2 and CH 4: Key enzymes and challenges. Biotechnol Adv 2024; 72:108347. [PMID: 38527656 DOI: 10.1016/j.biotechadv.2024.108347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/10/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
Mitigating greenhouse gas emissions is a critical challenge for promoting global sustainability. The utilization of CO2 and CH4 as substrates for the production of valuable products offers a promising avenue for establishing an eco-friendly economy. Biocatalysis, a sustainable process utilizing enzymes to facilitate biochemical reactions, plays a significant role in upcycling greenhouse gases. This review provides a comprehensive overview of the enzymes and associated reactions involved in the biocatalytic conversion of CO2 and CH4. Furthermore, the challenges facing the field are discussed, paving the way for future research directions focused on developing robust enzymes and systems for the efficient fixation of CO2 and CH4.
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Affiliation(s)
- Aipeng Li
- Xi'an Key Laboratory of C1 Compound Bioconversion Technology, School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xupeng Cao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Rongzhan Fu
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an 710069, China
| | - Shuqi Guo
- Xi'an Key Laboratory of C1 Compound Bioconversion Technology, School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Qiang Fei
- Xi'an Key Laboratory of C1 Compound Bioconversion Technology, School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
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5
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Faisal M, Sarnaik AP, Kannoju N, Hajinajaf N, Asad MJ, Davis RW, Varman AM. RuBisCO activity assays: a simplified biochemical redox approach for in vitro quantification and an RNA sensor approach for in vivo monitoring. Microb Cell Fact 2024; 23:83. [PMID: 38486280 PMCID: PMC10938803 DOI: 10.1186/s12934-024-02357-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant soluble protein in nature. Extensive studies have been conducted for improving its activity in photosynthesis through approaches like protein engineering. Concurrently, multiple biochemical and radiolabeling assays have been developed for determining its activity. Although these existing assays yield reliable results, they require addition of multiple external components, rendering them less convenient and expensive. Therefore, in this study, we have developed two relatively cheaper, convenient, and easily reproducible assays for quantitative and qualitative estimation of RuBisCO activity. RESULTS We simplified a contemporary NADH based spectrophotometric RuBisCO assay by using cyanobacterial cell lysate as the source for Calvin cycle enzymes. We analyzed the influence of inorganic carbon substrates, CO2 and NaHCO3, and varying protein concentrations on RuBisCO activity. Ribulose-1,5-bisphosphate (RuBP) consumption rates for the cultures grown under 5% CO2 were 5-7 times higher than the ones grown with 20 mM NaHCO3, at different protein concentrations. The difference could be due to the impaired activity of carbonic anhydrase in the cell lysate, which is required for the conversion of HCO3- to CO2. The highest RuBisCO activity of 2.13 nmol of NAD+/ µg of Chl-a/ min was observed with 50 µg of protein and 5% CO2. Additionally, we developed a novel RNA-sensor based fluorescence assay that is based on the principle of tracking the kinetics of ATP hydrolysis to ADP during the conversion of 3-phosphoglycerate (3-PG) to 1,3-bisphosphoglycerate (1,3-BPG) in the Calvin cycle. Under in vitro conditions, the fluorometric assay exhibited ~ 3.4-fold slower reaction rate (0.37 min-1) than the biochemical assay when using 5% CO2. We also confirmed the in vivo application of this assay, where increase in the fluorescence was observed with the recombinant strain of Synechocystis sp. PCC 6803 (SSL142) expressing the ADP-specific RNA sensor, compared to the WT. In addition, SSL142 exhibited three-fold higher fluorescence when supplemented with 20 mM NaHCO3 as compared to the cells that were grown without NaHCO3 supplementation. CONCLUSIONS Overall, we have developed a simplified biochemical assay for monitoring RuBisCO activity and demonstrated that it can provide reliable results as compared to the prior literature. Furthermore, the biochemical assay using 5% CO2 (100% relative activity) provided faster RuBP consumption rate compared to the biochemical assay utilizing 20 mM NaHCO3 (30.70% relative activity) and the in vitro fluorometric assay using 5% CO2 (29.64% relative activity). Therefore, the absorbance-based biochemical assay using 5% CO2 or higher would be suitable for in vitro quantification of the RuBisCO activity. On the other hand, the RNA-sensor based in vivo fluorometric assay can be applied for qualitative analysis and be used for high-throughput screening of RuBisCO variants. As RuBisCO is an enzyme shared amongst all the photoautotrophs, the assays developed in this study can easily be extended for analyzing the RuBisCO activities even in microalgae and higher plants.
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Affiliation(s)
- Muhammad Faisal
- Chemical Engineering, School for Engineering of Matter, Transport and Energy (SEMTE), Arizona State University, Tempe, AZ, 85281, USA
- University Institute of Biochemistry and Biotechnology, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, 46000, Pakistan
| | - Aditya P Sarnaik
- Chemical Engineering, School for Engineering of Matter, Transport and Energy (SEMTE), Arizona State University, Tempe, AZ, 85281, USA
| | - Nandini Kannoju
- Chemical Engineering, School for Engineering of Matter, Transport and Energy (SEMTE), Arizona State University, Tempe, AZ, 85281, USA
| | - Nima Hajinajaf
- Chemical Engineering, School for Engineering of Matter, Transport and Energy (SEMTE), Arizona State University, Tempe, AZ, 85281, USA
| | - Muhammad Javaid Asad
- University Institute of Biochemistry and Biotechnology, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, 46000, Pakistan
| | - Ryan W Davis
- Sandia National Laboratories, Livermore, CA, USA
| | - Arul M Varman
- Chemical Engineering, School for Engineering of Matter, Transport and Energy (SEMTE), Arizona State University, Tempe, AZ, 85281, USA.
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6
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Bouvier JW, Emms DM, Kelly S. Rubisco is evolving for improved catalytic efficiency and CO 2 assimilation in plants. Proc Natl Acad Sci U S A 2024; 121:e2321050121. [PMID: 38442173 PMCID: PMC10945770 DOI: 10.1073/pnas.2321050121] [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: 11/30/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024] Open
Abstract
Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of the molecular and kinetic evolution of Form I rubisco we uncover the evolutionary trajectory of rubisco kinetic evolution in angiosperms. We show that rbcL is among the 1% of slowest-evolving genes and enzymes on Earth, accumulating one nucleotide substitution every 0.9 My and one amino acid mutation every 7.2 My. Despite this, rubisco catalysis has been continually evolving toward improved CO2/O2 specificity, carboxylase turnover, and carboxylation efficiency. Consistent with this kinetic adaptation, increased rubisco evolution has led to a concomitant improvement in leaf-level CO2 assimilation. Thus, rubisco has been slowly but continually evolving toward improved catalytic efficiency and CO2 assimilation in plants.
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Affiliation(s)
- Jacques W Bouvier
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - David M Emms
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Steven Kelly
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
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7
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Aguirre-Bottger C, Zolla G. The best of both worlds: photosynthesis and Solanaceae biodiversity seeking a sustainable food and cosmetic industry. FRONTIERS IN PLANT SCIENCE 2024; 15:1362814. [PMID: 38434437 PMCID: PMC10904534 DOI: 10.3389/fpls.2024.1362814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Affiliation(s)
| | - Gaston Zolla
- Grupo de Investigation en Fisiología Molecular de Plantas, Facultad de Agronomia, Universidad Nacional Agraria La Molina, Lima, Peru
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Lupo Y, Moshelion M. The balance of survival: Comparative drought response in wild and domesticated tomatoes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111928. [PMID: 37992898 DOI: 10.1016/j.plantsci.2023.111928] [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: 09/03/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Plants have the ability to undergo reversible behavioral, morphological, or physiological changes in response to environmental conditions. This plasticity enables plants to cope with uncertain environmental conditions, such as drought. A primary plastic trait is the rate of stomatal response to changes in ambient conditions, which determines the amount of water lost via transpiration, as well as levels of CO2 absorption, growth, and productivity. Here, we examined the differences between domesticated (S. lycopersicum cv. M82) and wild tomato (S. pennellii) species and their responses to drought stress. The plants were grown in pots in a functional phenotyping platform (FPP) in a semi-controlled environment greenhouse. We found that the domesticated tomato had a higher transpiration rate (E) and higher stomatal conductance (gs). The domesticated tomato also had greater biomass and greater leaf area under drought conditions, as compared to the wild tomato. Despite the domesticated tomato's higher E and higher gs, there was no difference between the photosynthetic rates (An) of the two lines. Moreover, the wild tomato had a higher maximum rate of rubisco activity (Vcmax), which might explain its greater leaf level and whole canopy water-use efficiency. The domesticated tomato's higher E and greater leaf area led to its earlier exposure to drought stress, as compared to the wild tomato, which maintained higher levels of soil water, enabling it to maintain steady rates of whole-canopy stomatal conductance (gsc) for extended periods. The wild tomato was also more sensitive to soil water availability and lowered its maximum transpiration rate (Emax) at a higher soil-water-content (SWC) level compared to the domesticated species. Our results suggest that the domestication of tomatoes favored morphological/anatomical performance traits over physiological efficiency.
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Affiliation(s)
- Yaniv Lupo
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel; French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boker, Israel
| | - Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
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9
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Liu AK, Kaeser B, Chen L, West-Roberts J, Taylor-Kearney LJ, Lavy A, Günzing D, Li WJ, Hammel M, Nogales E, Banfield JF, Shih PM. Deep-branching evolutionary intermediates reveal structural origins of form I rubisco. Curr Biol 2023; 33:5316-5325.e3. [PMID: 37979578 PMCID: PMC11309020 DOI: 10.1016/j.cub.2023.10.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 11/20/2023]
Abstract
The enzyme rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyzes the majority of biological carbon fixation on Earth. Although the vast majority of rubiscos across the tree of life assemble as homo-oligomers, the globally predominant form I enzyme-found in plants, algae, and cyanobacteria-forms a unique hetero-oligomeric complex. The recent discovery of a homo-oligomeric sister group to form I rubisco (named form I') has filled a key gap in our understanding of the enigmatic origins of the form I clade. However, to elucidate the series of molecular events leading to the evolution of form I rubisco, we must examine more distantly related sibling clades to contextualize the molecular features distinguishing form I and form I' rubiscos. Here, we present a comparative structural study retracing the evolutionary history of rubisco that reveals a complex structural trajectory leading to the ultimate hetero-oligomerization of the form I clade. We structurally characterize the oligomeric states of deep-branching form Iα and I'' rubiscos recently discovered from metagenomes, which represent key evolutionary intermediates preceding the form I clade. We further solve the structure of form I'' rubisco, revealing the molecular determinants that likely primed the enzyme core for the transition from a homo-oligomer to a hetero-oligomer. Our findings yield new insight into the evolutionary trajectory underpinning the adoption and entrenchment of the prevalent assembly of form I rubisco, providing additional context when viewing the enzyme family through the broader lens of protein evolution.
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Affiliation(s)
- Albert K Liu
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA; Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Benjamin Kaeser
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - LinXing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob West-Roberts
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Leah J Taylor-Kearney
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Adi Lavy
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Damian Günzing
- Department of Physics, University of Duisburg-Essen, 47057 Duisburg, Germany
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, P.R. China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, P.R. China
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA; School of Geography, Earth and Atmospheric Sciences, University of Melbourne, Melbourne, VIC 3053, Australia; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA.
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10
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Nicoll CR, Massari M, Fraaije MW, Mascotti ML, Mattevi A. Impact of ancestral sequence reconstruction on mechanistic and structural enzymology. Curr Opin Struct Biol 2023; 82:102669. [PMID: 37544113 DOI: 10.1016/j.sbi.2023.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
Abstract
Ancestral sequence reconstruction (ASR) provides insight into the changes within a protein sequence across evolution. More specifically, it can illustrate how specific amino acid changes give rise to different phenotypes within a protein family. Over the last few decades it has established itself as a powerful technique for revealing molecular common denominators that govern enzyme function. Here, we describe the strength of ASR in unveiling catalytic mechanisms and emerging phenotypes for a range of different proteins, also highlighting biotechnological applications the methodology can provide.
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Affiliation(s)
- Callum R Nicoll
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marta Massari
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, the Netherlands. https://twitter.com/fraaije1
| | - Maria Laura Mascotti
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, D5700HHW, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.
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11
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Zhou Y, Gunn LH, Birch R, Andersson I, Whitney SM. Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth. NATURE PLANTS 2023; 9:978-986. [PMID: 37291398 DOI: 10.1038/s41477-023-01436-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Improving the carboxylation properties of Rubisco has primarily arisen from unforeseen amino acid substitutions remote from the catalytic site. The unpredictability has frustrated rational design efforts to enhance plant Rubisco towards the prized growth-enhancing carboxylation properties of red algae Griffithsia monilis GmRubisco. To address this, we determined the crystal structure of GmRubisco to 1.7 Å. Three structurally divergent domains were identified relative to the red-type bacterial Rhodobacter sphaeroides RsRubisco that, unlike GmRubisco, are expressed in Escherichia coli and plants. Kinetic comparison of 11 RsRubisco chimaeras revealed that incorporating C329A and A332V substitutions from GmRubisco Loop 6 (corresponding to plant residues 328 and 331) into RsRubisco increased the carboxylation rate (kcatc) by 60%, the carboxylation efficiency in air by 22% and the CO2/O2 specificity (Sc/o) by 7%. Plastome transformation of this RsRubisco Loop 6 mutant into tobacco enhanced photosynthesis and growth up to twofold over tobacco producing wild-type RsRubisco. Our findings demonstrate the utility of RsRubisco for the identification and in planta testing of amino acid grafts from algal Rubisco that can enhance the enzyme's carboxylase potential.
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Affiliation(s)
- Yu Zhou
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Laura H Gunn
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Rosemary Birch
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Norwegian College of Fisheries Sciences, UiT Arctic University of Norway, Tromsø, Norway
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Biocev, Vestec, Czech Republic
| | - Spencer M Whitney
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.
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12
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Wei S, Li F, Zhu N, Wei X, Wu P, Dang Z. Biomass production of Chlorella pyrenoidosa by filled sphere carrier reactor: Performance and mechanism. BIORESOURCE TECHNOLOGY 2023:129195. [PMID: 37207699 DOI: 10.1016/j.biortech.2023.129195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
Microalgae-based Carbon Capture, Utilization and Storage is vital for mitigating global climate change. A filled sphere carrier reactor was developed to achieve high biomass production and carbon sequestration rate of Chlorella pyrenoidosa. By introducing air (0.04% CO2) into the reactor, the dry biomass production achieved 8.26 g/L with the optimized parameters of polyester carrier, 80% packing density, 5-fold concentrated nutrient combining 0.2 mol/L phosphate buffer. At simulated flue gas CO2 concentration of 7%, the dry biomass yield and carbon sequestration rate reached up to 9.98 g/L and 18.32 g/L/d in one day, which were as high as 249.5 and 79.65 times comparing with those of suspension culture at day 1, respectively. The mechanism was mainly attributed to the obvious intensification of electron transfer rate and remarkable increase of RuBisCO enzyme activity in the photosynthetic chloroplast matrix. This work provided a novel approach for potential microalgae-based carbon capture and storage.
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Affiliation(s)
- Sijing Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Fei Li
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Nengwu Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters of Ministry of Education, Guangzhou 510006, PR China; Guangdong Environmental Protection Key Laboratory of Solid Waste Treatment and Recycling, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, PR China.
| | - Xiaorong Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Pingxiao Wu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters of Ministry of Education, Guangzhou 510006, PR China; Guangdong Environmental Protection Key Laboratory of Solid Waste Treatment and Recycling, Guangzhou 510006, PR China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters of Ministry of Education, Guangzhou 510006, PR China; Guangdong Environmental Protection Key Laboratory of Solid Waste Treatment and Recycling, Guangzhou 510006, PR China
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13
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Recent developments in the engineering of Rubisco activase for enhanced crop yield. Biochem Soc Trans 2023; 51:627-637. [PMID: 36929563 DOI: 10.1042/bst20221281] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023]
Abstract
Rubisco activase (RCA) catalyzes the release of inhibitory sugar phosphates from ribulose-1,6-biphosphate carboxylase/oxygenase (Rubisco) and can play an important role in biochemical limitations of photosynthesis under dynamic light and elevated temperatures. There is interest in increasing RCA activity to improve crop productivity, but a lack of understanding about the regulation of photosynthesis complicates engineering strategies. In this review, we discuss work relevant to improving RCA with a focus on advances in understanding the structural cause of RCA instability under heat stress and the regulatory interactions between RCA and components of photosynthesis. This reveals substantial variation in RCA thermostability that can be influenced by single amino acid substitutions, and that engineered variants can perform better in vitro and in vivo under heat stress. In addition, there are indications RCA activity is controlled by transcriptional, post-transcriptional, post-translational, and spatial regulation, which may be important for balancing between carbon fixation and light capture. Finally, we provide an overview of findings from recent field experiments and consider the requirements for commercial validation as part of efforts to increase crop yields in the face of global climate change.
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14
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Capó-Bauçà S, Whitney S, Iñiguez C, Serrano O, Rhodes T, Galmés J. The trajectory in catalytic evolution of Rubisco in Posidonia seagrass species differs from terrestrial plants. PLANT PHYSIOLOGY 2023; 191:946-956. [PMID: 36315095 PMCID: PMC9922400 DOI: 10.1093/plphys/kiac492] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The CO2-fixing enzyme Ribulose bisphosphate carboxylase-oxygenase (Rubisco) links the inorganic and organic phases of the global carbon cycle. In aquatic systems, the catalytic adaptation of algae Rubiscos has been more expansive and followed an evolutionary pathway that appears distinct to terrestrial plant Rubisco. Here, we extend this survey to differing seagrass species of the genus Posidonia to reveal how their disjunctive geographical distribution and diverged phylogeny, along with their CO2 concentrating mechanisms (CCMs) effectiveness, have impacted their Rubisco kinetic properties. The Rubisco from Posidonia species showed lower carboxylation efficiencies and lower sensitivity to O2 inhibition than those measured for terrestrial C3 and C4-plant Rubiscos. Compared with the Australian Posidonia species, Rubisco from the Mediterranean Posidonia oceanica had 1.5-2-fold lower carboxylation and oxygenation efficiencies, coinciding with effective CCMs and five Rubisco large subunit amino acid substitutions. Among the Australian Posidonia species, CCM effectiveness was higher in Posidonia sinuosa and lower in the deep-living Posidonia angustifolia, likely related to the 20%-35% lower Rubisco carboxylation efficiency in P. sinuosa and the two-fold higher Rubisco content in P. angustifolia. Our results suggest that the catalytic evolution of Posidonia Rubisco has been impacted by the low CO2 availability and gas exchange properties of marine environments, but with contrasting Rubisco kinetics according to the time of diversification among the species. As a result, the relationships between maximum carboxylation rate and CO2- and O2-affinities of Posidonia Rubiscos follow an alternative path to that characteristic of terrestrial angiosperm Rubiscos.
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Affiliation(s)
- Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions. Universitat de les Illes Balears-INAGEA, Palma 07122, Spain
| | - Spencer Whitney
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions. Universitat de les Illes Balears-INAGEA, Palma 07122, Spain
| | - Oscar Serrano
- Centro de Estudios Avanzados de Blanes, Consejo Superior de Investigaciones Cientificas (CEAB-CISC), Blanes 17300, Spain
- School of Science, Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Timothy Rhodes
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions. Universitat de les Illes Balears-INAGEA, Palma 07122, Spain
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15
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Jin K, Chen G, Yang Y, Zhang Z, Lu T. Strategies for manipulating Rubisco and creating photorespiratory bypass to boost C 3 photosynthesis: Prospects on modern crop improvement. PLANT, CELL & ENVIRONMENT 2023; 46:363-378. [PMID: 36444099 DOI: 10.1111/pce.14500] [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: 09/15/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 06/16/2023]
Abstract
Photosynthesis is a process that uses solar energy to fix CO2 in the air and converts it into sugar, and ultimately powers almost all life activities on the earth. C3 photosynthesis is the most common form of photosynthesis in crops. Current efforts of increasing crop yields in response to growing global food requirement are mostly focused on improving C3 photosynthesis. In this review, we summarized the strategies of C3 photosynthesis improvement in terms of Rubisco properties and photorespiratory limitation. Potential engineered targets include Rubisco subunits and their catalytic sites, Rubisco assembly chaperones, and Rubisco activase. In addition, we reviewed multiple photorespiratory bypasses built by strategies of synthetic biology to reduce the release of CO2 and ammonia and minimize energy consumption by photorespiration. The potential strategies are suggested to enhance C3 photosynthesis and boost crop production.
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Affiliation(s)
- Kaining Jin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- Department of Plant Sciences, Centre for Crop Systems Analysis, Wageningen University & Research, Wageningen, The Netherlands
| | - Guoxin Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yirong Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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16
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Cavanagh AP, Slattery R, Kubien DS. Temperature-induced changes in Arabidopsis Rubisco activity and isoform expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:651-663. [PMID: 36124740 PMCID: PMC9833042 DOI: 10.1093/jxb/erac379] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/16/2022] [Indexed: 06/06/2023]
Abstract
In many plant species, expression of the nuclear encoded Rubisco small subunit (SSu) varies with environmental changes, but the functional role of any changes in expression remains unclear. In this study, we investigated the impact of differential expression of Rubisco SSu isoforms on carbon assimilation in Arabidopsis. Using plants grown at contrasting temperatures (10 °C and 30 °C), we confirm the previously reported temperature response of the four RbcS genes and extend this to protein expression, finding that warm-grown plants produce Rubisco containing ~65% SSu-B and cold-grown plants produce Rubisco with ~65% SSu-A as a proportion of the total pool of subunits. We find that these changes in isoform concentration are associated with kinetic changes to Rubisco in vitro: warm-grown plants produce a Rubisco having greater CO2 affinity (i.e. higher SC/O and lower KC) but lower kcatCO2 at warm measurement temperatures. Although warm-grown plants produce 38% less Rubisco than cold-grown plants on a leaf area basis, warm-grown plants can maintain similar rates of photosynthesis to cold-grown plants at ambient CO2 and 30 °C, indicating that the carboxylation capacity of warm-grown Rubisco is enhanced at warmer measurement temperatures, and is able to compensate for the lower Rubisco content in warm-grown plants. This association between SSu isoform expression and maintenance of Rubisco activity at high temperature suggests that SSu isoform expression could impact the temperature response of C3 photosynthesis.
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Affiliation(s)
| | - Rebecca Slattery
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David S Kubien
- Department of Biology, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
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17
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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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18
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Mao Y, Catherall E, Díaz-Ramos A, Greiff GRL, Azinas S, Gunn L, McCormick AJ. The small subunit of Rubisco and its potential as an engineering target. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:543-561. [PMID: 35849331 PMCID: PMC9833052 DOI: 10.1093/jxb/erac309] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/07/2022] [Indexed: 05/06/2023]
Abstract
Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.
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Affiliation(s)
| | | | - Aranzazú Díaz-Ramos
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
| | - George R L Greiff
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stavros Azinas
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Laura Gunn
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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19
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Iqbal WA, Lisitsa A, Kapralov MV. Predicting plant Rubisco kinetics from RbcL sequence data using machine learning. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:638-650. [PMID: 36094849 PMCID: PMC9833099 DOI: 10.1093/jxb/erac368] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is responsible for the conversion of atmospheric CO2 to organic carbon during photosynthesis, and often acts as a rate limiting step in the later process. Screening the natural diversity of Rubisco kinetics is the main strategy used to find better Rubisco enzymes for crop engineering efforts. Here, we demonstrate the use of Gaussian processes (GPs), a family of Bayesian models, coupled with protein encoding schemes, for predicting Rubisco kinetics from Rubisco large subunit (RbcL) sequence data. GPs trained on published experimentally obtained Rubisco kinetic datasets were applied to over 9000 sequences encoding RbcL to predict Rubisco kinetic parameters. Notably, our predicted kinetic values were in agreement with known trends, e.g. higher carboxylation turnover rates (Kcat) for Rubisco enzymes from C4 or crassulacean acid metabolism (CAM) species, compared with those found in C3 species. This is the first study demonstrating machine learning approaches as a tool for screening and predicting Rubisco kinetics, which could be applied to other enzymes.
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Affiliation(s)
- Wasim A Iqbal
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Alexei Lisitsa
- Department of Computer Science, University of Liverpool, Liverpool, L69 3BX, United Kingdom
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20
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Buck S, Rhodes T, Gionfriddo M, Skinner T, Yuan D, Birch R, Kapralov MV, Whitney SM. Escherichia coli expressing chloroplast chaperones as a proxy to test heterologous Rubisco production in leaves. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:664-676. [PMID: 36322613 DOI: 10.1093/jxb/erac435] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Rubisco is a fundamental enzyme in photosynthesis and therefore for life. Efforts to improve plant Rubisco performance have been hindered by the enzymes' complex chloroplast biogenesis requirements. New Synbio approaches, however, now allow the production of some plant Rubisco isoforms in Escherichia coli. While this enhances opportunities for catalytic improvement, there remain limitations in the utility of the expression system. Here we generate, optimize, and test a robust Golden Gate cloning E. coli expression system incorporating the protein folding machinery of tobacco chloroplasts. By comparing the expression of different plant Rubiscos in both E. coli and plastome-transformed tobacco, we show that the E. coli expression system can accurately predict high level Rubisco production in chloroplasts but poorly forecasts the biogenesis potential of isoforms with impaired production in planta. We reveal that heterologous Rubisco production in E. coli and tobacco plastids poorly correlates with Rubisco large subunit phylogeny. Our findings highlight the need to fully understand the factors governing Rubisco biogenesis if we are to deliver an efficient, low-cost screening tool that can accurately emulate chloroplast expression.
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Affiliation(s)
- Sally Buck
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Tim Rhodes
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Matteo Gionfriddo
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Tanya Skinner
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Ding Yuan
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Rosemary Birch
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
| | - Maxim V Kapralov
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Spencer M Whitney
- ARC Centre of Excellence in Translational Photosynthesis, Australian National University, Canberra 2000, Australia
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21
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Manning T, Birch R, Stevenson T, Nugent G, Whitney S. Bacterial Form II Rubisco can support wild-type growth and productivity in Solanum tuberosum cv. Desiree (potato) under elevated CO 2. PNAS NEXUS 2023; 2:pgac305. [PMID: 36743474 PMCID: PMC9896143 DOI: 10.1093/pnasnexus/pgac305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/22/2022] [Indexed: 02/05/2023]
Abstract
The last decade has seen significant advances in the development of approaches for improving both the light harvesting and carbon fixation pathways of photosynthesis by nuclear transformation, many involving multigene synthetic biology approaches. As efforts to replicate these accomplishments from tobacco into crops gather momentum, similar diversification is needed in the range of transgenic options available, including capabilities to modify crop photosynthesis by chloroplast transformation. To address this need, here we describe the first transplastomic modification of photosynthesis in a crop by replacing the native Rubisco in potato with the faster, but lower CO2-affinity and poorer CO2/O2 specificity Rubisco from the bacterium Rhodospirillum rubrum. High level production of R. rubrum Rubisco in the potRr genotype (8 to 10 µmol catalytic sites m2) allowed it to attain wild-type levels of productivity, including tuber yield, in air containing 0.5% (v/v) CO2. Under controlled environment growth at 25°C and 350 µmol photons m2 PAR, the productivity and leaf biochemistry of wild-type potato at 0.06%, 0.5%, or 1.5% (v/v) CO2 and potRr at 0.5% or 1.5% (v/v) CO2 were largely indistinguishable. These findings suggest that increasing the scope for enhancing productivity gains in potato by improving photosynthate production will necessitate improvement to its sink-potential, consistent with current evidence productivity gains by eCO2 fertilization for this crop hit a ceiling around 560 to 600 ppm CO2.
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Affiliation(s)
- Tahnee Manning
- School of Science, RMIT University, Bundoora, VIC 3083, Australia
| | - Rosemary Birch
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 0200, Australia
| | - Trevor Stevenson
- School of Science, RMIT University, Bundoora, VIC 3083, Australia
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22
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Li C, Wang R, Wang J, Liu L, Li H, Zheng H, Ni J. A Highly Compatible Phototrophic Community for Carbon-Negative Biosynthesis. Angew Chem Int Ed Engl 2023; 62:e202215013. [PMID: 36378012 DOI: 10.1002/anie.202215013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
Abstract
CO2 sequestration engineering is promising for carbon-negative biosynthesis, and artificial communities can solve more complex problems than monocultures. However, obtaining an ideal photosynthetic community is still a great challenge. Herein, we describe the development of a highly compatible photosynthetic community (HCPC) by integrating a sucrose-producing CO2 sequestration module and a super-coupled module. The cyanobacteria CO2 sequestration module was obtained using stepwise metabolic engineering and then coupled with the efficient sucrose utilization module Vibrio natriegens. Integrated omics analysis indicated that enhanced photosynthetic electron transport and extracellular vesicles promote intercellular communication. Additionally, the HCPC was used to channel CO2 into valuable chemicals, enabling the overall release of -22.27 to -606.59 kgCO2 e kg-1 in the end products. This novel light-driven community could facilitate circular economic implementation in the future.
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Affiliation(s)
- Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ruoyu Wang
- School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
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23
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Nasar J, Wang GY, Zhou FJ, Gitari H, Zhou XB, Tabl KM, Hasan ME, Ali H, Waqas MM, Ali I, Jahan MS. Nitrogen fertilization coupled with foliar application of iron and molybdenum improves shade tolerance of soybean under maize-soybean intercropping. FRONTIERS IN PLANT SCIENCE 2022; 13:1014640. [PMID: 36267939 PMCID: PMC9577300 DOI: 10.3389/fpls.2022.1014640] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/15/2022] [Indexed: 06/01/2023]
Abstract
Maize-soybean intercropping is practiced worldwide because of some of the anticipated advantages such as high crop yield and better utilization of resources (i.e., water, light, nutrients and land). However, the shade of the maize crop has a detrimental effect on the growth and yield of soybean under the maize-soybean intercropping system. Hence, this experiment was conducted to improve the shade tolerance of such soybean crops with optimal nitrogen (N) fertilization combined with foliar application of iron (Fe) and molybdenum (Mo). The treatments comprised five (5) maize-soybean intercropping practices: without fertilizer application (F0), with N fertilizer application (F1), with N fertilizer combined with foliar application of Fe (F2), with N fertilizer coupled with foliar application of Mo (F3) and with N fertilizer combined with foliar application of Fe and Mo (F4). The findings of this study showed that maize-soybean intercropping under F4 treatment had significantly (p< 0.05) increased growth indices such as leaf area (cm2), plant height (cm), stem diameter (mm), stem strength (g pot-1), and internode length (cm) and yield indices (i.e., No of pods plant-1, grain yield (g plant-1), 100-grain weight (g), and biomass dry matter (g plant-1)) of the soybean crop. Moreover, intercropping under F4 treatment enhanced the chlorophyll SPAD values by 26% and photosynthetic activities such as Pn by 30%, gs by 28%, and Tr by 28% of the soybean crops, but reduced its CO2 by 11%. Furthermore, maize-soybean intercropping under F4 treatment showed improved efficiency of leaf chlorophyll florescence parameters of soybean crops such as Fv/Fm (26%), qp (17%), ϕPSII (20%), and ETR (17%), but reduced NPQ (12%). In addition, the rubisco activity and soluble protein content of the soybean crop increased by 18% in maize-soybean intercropping under F4 treatment. Thus, this suggested that intercropping under optimal N fertilization combined with foliar application of Fe and Mo can improve the shade tolerance of soybean crops by regulating their chlorophyll content, photosynthetic activities, and the associated enzymes, thereby enhancing their yield and yield traits.
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Affiliation(s)
- Jamal Nasar
- Guangxi Key Laboratory of Agro-environment and Agro-products Safety, Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Agricultural College of Guangxi University, Nanning, China
| | - Gui Yang Wang
- Guangxi Key Laboratory of Agro-environment and Agro-products Safety, Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Agricultural College of Guangxi University, Nanning, China
| | - Feng Jue Zhou
- Guangxi Key Laboratory of Agro-environment and Agro-products Safety, Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Agricultural College of Guangxi University, Nanning, China
| | - Harun Gitari
- Department of Agricultural Science and Technology, School of Agriculture and Enterprise Development, Kenyatta University, Nairobi, Kenya
| | - Xun Bo Zhou
- Guangxi Key Laboratory of Agro-environment and Agro-products Safety, Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Agricultural College of Guangxi University, Nanning, China
| | - Karim M. Tabl
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Mohamed E. Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Habib Ali
- Khwaja Fareed University of Engineering and Information Technology, Rahim, Yar Khan, Pakistan
| | - Muhammad Mohsin Waqas
- Khwaja Fareed University of Engineering and Information Technology, Rahim, Yar Khan, Pakistan
| | - Izhar Ali
- Guangxi Key Laboratory of Agro-environment and Agro-products Safety, Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Agricultural College of Guangxi University, Nanning, China
| | - Mohammad Shah Jahan
- Department of Horticulture, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
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