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Zheng X, Li A, Qiu J, Yan G, Ji Y, Wang G. β-N-methylamino-L-alanine production, photosynthesis and transcriptional expression in a possible mutation strain and a wild strain of Thalassiosira minima. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135301. [PMID: 39053058 DOI: 10.1016/j.jhazmat.2024.135301] [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: 04/08/2024] [Revised: 07/02/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The neurotoxin β-N-methylamino-L-alanine (BMAA) produced by marine diatoms has been implicated as an important environmental trigger of neurodegenerative diseases in humans. However, the biosynthesis mechanism of BMAA in marine diatoms is still unknown. In the present study, the strain of diatom Thalassiosira minima almost lost the biosynthesis ability for BMAA after a long-term subculture in our laboratory. The production of BMAA-containing proteins in the mutant strain of T. minima reduced to 18.2 % of that in the wild strain, meanwhile the cell size decreased but pigment content increased in the mutant strain. Take consideration of our previous transcriptional data on the mixed diatom and cyanobacterium cultures, the current transcriptome analysis showed four identical and highly correlated KEGG pathways associated with the accumulation of misfolded proteins in diatom, including ribosome, proteasome, SNARE interactions in vesicle transport, and protein processing in the endoplasmic reticulum. Analysis of amino acids and transcriptional information suggested that amino acid synthesis and degradation are associated with the biosynthesis of BMAA-containing proteins. In addition, a reduction in the precision of ubiquitination-mediated protein hydrolysis and vesicular transport by the COPII system will exacerbate the accumulation of BMAA-containing proteins in diatoms.
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Affiliation(s)
- Xianyao Zheng
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Aifeng Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China.
| | - Jiangbing Qiu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Guowang Yan
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Ying Ji
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Guixiang Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
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2
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Chen S, Qiu G. Physiological and multi-omics analysis reveals the influence of copper on Halophila beccarii Asch. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108785. [PMID: 38824692 DOI: 10.1016/j.plaphy.2024.108785] [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: 02/17/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
High concentrations of copper can pollute coastal waters, primarily from agricultural runoff and mining activities, which can harm marine organisms, including seagrasses. The molecular mechanism of copper toxicity to seagrass currently remains unclear. To determine the response to copper, physiological and multi-omic analyses were conducted to explore the molecular mechanism by which copper affects the global threatened seagrass Halophila beccarii Asch. Excessive copper stress causes oxidative damage and stimulates the activity of the antioxidant enzyme system to remove excess reactive oxygen species (ROS), thereby reducing the damage caused by copper stress. Cu increases the activities of superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), peroxidase (EC 1.11.1.7), ascorbate peroxidase (EC 1.11.1.11), glutathione peroxidase (EC 1.11.1.9), ascorbate oxidase (EC 1.10.3.3), glutathione reductase (EC 1.6.4.2), and dehydroascorbate reductase (EC 1.8.5.1) and the content of malondialdehyde and reduces the activity of monodehydroascorbate reductase (EC 1.6.5.4). Under copper stress, H. beccarii upregulates the metabolic pathways of steroid biosynthesis and cutin, suberin, and wax biosynthesis, downregulates the metabolic pathways of arginine and proline metabolism and fructose and mannose metabolism; the levels of expression of the ribosome-related genes; upregulates the levels of expression of circadian rhythm-related proteins and downregulates the levels of glutathione metabolism and the proteins related to carbon fixation. This study provides new insights into the response of seagrass to copper stress and reports potential candidate metabolites, genes, and proteins that can be considered as biomarkers to improve the protection and management of seagrass meadows.
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Affiliation(s)
- Siting Chen
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Academy of Marine Sciences (Guangxi Mangrove Research Center), Guangxi Academy of Sciences, Beihai, Guangxi, 536007, China.
| | - Guanglong Qiu
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Academy of Marine Sciences (Guangxi Mangrove Research Center), Guangxi Academy of Sciences, Beihai, Guangxi, 536007, China.
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3
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Cheng Y, Yang B, Jia T, Hu X. Rubisco Accumulation Factor1-like (RAFL) interacts with RAF1 to mediate Rubisco assembly in Arabidopsis. Biochem Biophys Res Commun 2024; 701:149609. [PMID: 38316092 DOI: 10.1016/j.bbrc.2024.149609] [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: 01/24/2024] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
Rubisco catalysis a rate-limiting step in photosynthesis. It is a complex of eight large (RbcL) and eight small (RbcS) subunits. The biogenesis of Rubisco requires assembly chaperones. One of the key Rubisco assembly chaperones, Rubisco accumulation factor1 (RAF1), assembled as a dimer, acts downstream of chaperonin-assisted RbcL folding by stabilizing RbcL antiparallel dimers for assembly into RbcL8 complexes. In maize, lacking RAF1 causes Rubisco deficient and seedling lethal. A RAF1 homologue, RAF1-like (RAFL), has been detected in Arabidopsis. We found RAFL shares 61.98 % sequence similarity with RAF1. They have similar conserved domains, predicted 3D structures and gene expression pattern. Phylogenetic tree analysis showed that RAFL and RAF1 only present in analyzed dicots, while only one copy of RAF presented in monocots, mosses and green algae. Combined analysis by three different protein-protein interaction methods showed that RAFL interacts with RAF1 both in vivo and in vitro. Taken together, we conclude that RAFL and RAF1 are close paralogous genes, and they can form heterodimer and/or homodimers to mediate Rubisco assembly in Arabidopsis.
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Affiliation(s)
- Yuting Cheng
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Bing Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Ting Jia
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China.
| | - Xueyun Hu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China.
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4
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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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5
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Zhao L, Cai Z, Li Y, Zhang Y. Engineering Rubisco to enhance CO 2 utilization. Synth Syst Biotechnol 2024; 9:55-68. [PMID: 38273863 PMCID: PMC10809010 DOI: 10.1016/j.synbio.2023.12.006] [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] [Received: 08/28/2023] [Revised: 12/15/2023] [Accepted: 12/25/2023] [Indexed: 01/27/2024] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a pivotal enzyme that mediates the fixation of CO2. As the most abundant protein on earth, Rubisco has a significant impact on global carbon, water, and nitrogen cycles. However, the significantly low carboxylation activity and competing oxygenase activity of Rubisco greatly impede high carbon fixation efficiency. This review first summarizes the current efforts in directly or indirectly modifying plant Rubisco, which has been challenging due to its high conservation and limitations in chloroplast transformation techniques. However, recent advancements in understanding Rubisco biogenesis with the assistance of chaperones have enabled successful heterologous expression of all Rubisco forms, including plant Rubisco, in microorganisms. This breakthrough facilitates the acquisition and evaluation of modified proteins, streamlining the measurement of their activity. Moreover, the establishment of a screening system in E. coli opens up possibilities for obtaining high-performance mutant enzymes through directed evolution. Finally, this review emphasizes the utilization of Rubisco in microorganisms, not only expanding their carbon-fixing capabilities but also holding significant potential for enhancing biotransformation processes.
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Affiliation(s)
- Lei Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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6
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Ito K, Sugawara S, Kageyama S, Sawaguchi N, Hyotani T, Miyazawa SI, Makino A, Suzuki Y. Equisetum praealtum and E. hyemale have abundant Rubisco with a high catalytic turnover rate and low CO 2 affinity. JOURNAL OF PLANT RESEARCH 2024; 137:255-264. [PMID: 38112982 DOI: 10.1007/s10265-023-01514-z] [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: 10/02/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
The kinetic properties of Rubisco, a key enzyme for photosynthesis, have been examined in numerous plant species. However, this information on some plant groups, such as ferns, is scarce. This study examined Rubisco carboxylase activity and leaf Rubisco levels in seven ferns, including four Equisetum plants (E. arvense, E. hyemale, E. praealtum, and E. variegatum), considered living fossils. The turnover rates of Rubisco carboxylation (kcatc) in E. praealtum and E. hyemale were comparable to those in the C4 plants maize (Zea mays) and sorghum (Sorghum bicolor), whose kcatc values are high. Rubisco CO2 affinity, estimated from the percentage of Rubisco carboxylase activity under CO2 unsaturated conditions in kcatc in these Equisetum plants, was low and also comparable to that in maize and sorghum. In contrast, kcatc and CO2 affinities of Rubisco in other ferns, including E. arvense and E. variegatum were comparable with those in C3 plants. The N allocation to Rubisco in the ferns examined was comparable to that in the C3 plants. These results indicate that E. praealtum and E. hyemale have abundant Rubisco with high kcatc and low CO2 affinity, whereas the carboxylase activity and abundance of Rubisco in other ferns were similar to those in C3 plants. Herein, the Rubisco properties of E. praealtum and E. hyemale were discussed regarding their evolution and physiological implications.
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Affiliation(s)
- Kana Ito
- Graduate School of Arts and Sciences, Iwate University, Morioka, Japan
| | | | - Sota Kageyama
- Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Naoki Sawaguchi
- Graduate School of Arts and Sciences, Iwate University, Morioka, Japan
| | - Takuro Hyotani
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | | | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Present address: Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Yuji Suzuki
- Faculty of Agriculture, Iwate University, Morioka, Japan.
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7
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Li P, Wang Z, Wang X, Liu F, Wang H. Changes in Phytohormones and Transcriptomic Reprogramming in Strawberry Leaves under Different Light Qualities. Int J Mol Sci 2024; 25:2765. [PMID: 38474012 DOI: 10.3390/ijms25052765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/18/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Strawberry plants require light for growth, but the frequent occurrence of low-light weather in winter can lead to a decrease in the photosynthetic rate (Pn) of strawberry plants. Light-emitting diode (LED) systems could be used to increase Pn. However, the changes in the phytohormones and transcriptomic reprogramming in strawberry leaves under different light qualities are still unclear. In this study, we treated strawberry plants with sunlight, sunlight covered with a 50% sunshade net, no light, blue light (460 nm), red light (660 nm), and a 50% red/50% blue LED light combination for 3 days and 7 days. Our results revealed that the light quality has an effect on the contents of Chl a and Chl b, the minimal fluorescence (F0), and the Pn of strawberry plants. The light quality also affected the contents of abscisic acid (ABA), auxin (IAA), trans-zeatin-riboside (tZ), jasmonic acid (JA), and salicylic acid (SA). RNA sequencing (RNA-seq) revealed that differentially expressed genes (DEGs) are significantly enriched in photosynthesis antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolisms, carotenoid biosynthesis, tryptophan metabolism, phenylalanine metabolism, zeatin biosynthesis, and linolenic acid metabolism. We then selected the key DEGs based on the results of a weighted gene co-expression network analysis (WGCNA) and drew nine metabolic heatmaps and protein-protein interaction networks to map light regulation.
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Affiliation(s)
- Peng Li
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Zhiqiang Wang
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Xiaodi Wang
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Fengzhi Liu
- Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Haibo Wang
- Institute of Pomology of CAAS, Xingcheng 125100, China
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8
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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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9
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Sun J, Jin L, Li R, Meng X, Jin N, Wang S, Xu Z, Liu Z, Lyu J, Yu J. Effects of Different Forms and Proportions of Nitrogen on the Growth, Photosynthetic Characteristics, and Carbon and Nitrogen Metabolism in Tomato. PLANTS (BASEL, SWITZERLAND) 2023; 12:4175. [PMID: 38140502 PMCID: PMC10748299 DOI: 10.3390/plants12244175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Optimal plant growth in many species is achieved when the two major forms of N are supplied at a particular ratio. This study investigated optimal nitrogen forms and ratios for tomato growth using the 'Jingfan 502' tomato variety. Thirteen treatments were applied with varying proportions of nitrate nitrogen (NN), ammonium nitrogen (AN), and urea nitrogen (UN). Results revealed that the combination of AN and UN inhibited tomato growth and photosynthetic capacity. Conversely, the joint application of NN and UN or NN and AN led to a significant enhancement in tomato plant growth. Notably, the T12 (75%UN:25%NN) and T4 (75%NN:25%AN) treatments significantly increased the gas exchange and chlorophyll fluorescence parameters, thereby promoting the accumulation of photosynthetic products. The contents of fructose, glucose, and sucrose were significantly increased by 121.07%, 206.26%, and 94.64% and by 104.39%, 156.42%, and 61.40%, respectively, compared with those in the control. Additionally, AN favored starch accumulation, while NN and UN favored fructose, sucrose, and glucose accumulation. Gene expression related to nitrogen and sugar metabolism increased significantly in T12 and T4, with T12 showing greater upregulation. Key enzyme activity in metabolism also increased notably. In summary, T12 enhanced tomato growth by upregulating gene expression, increasing enzyme activity, and boosting photosynthesis and sugar accumulation. Growers should consider using NN and UN to reduce AN application in tomato fertilization.
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Affiliation(s)
- Jianhong Sun
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Li Jin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (L.J.); (S.W.)
| | - Ruirui Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Xin Meng
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Ning Jin
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Shuya Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (L.J.); (S.W.)
| | - Zhiqi Xu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Zitong Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
| | - Jian Lyu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (L.J.); (S.W.)
| | - Jinhua Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (R.L.); (X.M.); (N.J.); (Z.X.); (Z.L.)
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (L.J.); (S.W.)
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10
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Rodríguez-Vázquez R, Mesa-Marín J. Plant responses to plant growth promoting bacteria: Insights from proteomics. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154031. [PMID: 37321049 DOI: 10.1016/j.jplph.2023.154031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Affiliation(s)
| | - Jennifer Mesa-Marín
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain.
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11
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Fatma M, Sehar Z, Iqbal N, Alvi AF, Abdi G, Proestos C, Khan NA. Sulfur supplementation enhances nitric oxide efficacy in reversal of chromium-inhibited Calvin cycle enzymes, photosynthetic activity, and carbohydrate metabolism in wheat. Sci Rep 2023; 13:6858. [PMID: 37100855 PMCID: PMC10133275 DOI: 10.1038/s41598-023-33885-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 04/20/2023] [Indexed: 04/28/2023] Open
Abstract
The present study demonstrated that exogenously-sourced nitric oxide (as SNP, sodium nitroprusside; NO donor) and sulfur (S) protected photosynthesis against chromium (Cr) stress in wheat (Triticum aestivum L. cv. HD 2851). Plants grown with 100 µM Cr exhibited higher reactive oxygen species (ROS) production, resulting in photosynthetic damage. The individual application of 50 µM NO increased carbohydrate metabolism as well as photosynthetic parameters, antioxidant system with higher transcriptional gene levels that encode the key enzymes for the Calvin cycle under Cr stress. These effects were more prominent when NO was applied with 1.0 mM SO42-. An increase in the reduced glutathione (GSH) content obtained with NO was further enhanced by S and resulted in higher protection against Cr stress. The protective effect of NO with S against Cr toxicity on photosynthesis was reversed when buthionine sulfoximine (BSO; GSH biosynthetic inhibitor) was used. Application of BSO reversed the impact of NO plus S on photosynthesis under Cr stress, verifying that the ameliorating effect of NO was through S-assimilation and via GSH production. Thus, the availability of S to NO application can help reduce Cr toxicity and protect photosynthetic activity and expression of the Calvin cycle enzymes in leaves through the GSH involvement.
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Affiliation(s)
- Mehar Fatma
- Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Zebus Sehar
- Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Noushina Iqbal
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | | | - Gholamreza Abdi
- Department of Biotechnology, Persian Gulf Research Institute, Persian Gulf University, Bushehr, 75169, Iran.
| | - Charalampos Proestos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15771, Athens, Greece.
| | - Nafees A Khan
- Department of Botany, Aligarh Muslim University, Aligarh, 202002, India.
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12
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Wang RZ, Liu AK, Banda DM, Fischer WW, Shih PM. A Bacterial Form I’ Rubisco Has a Smaller Carbon Isotope Fractionation than Its Form I Counterpart. Biomolecules 2023; 13:biom13040596. [PMID: 37189344 DOI: 10.3390/biom13040596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/14/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Form I rubiscos evolved in Cyanobacteria ≥ 2.5 billion years ago and are enzymatically unique due to the presence of small subunits (RbcS) capping both ends of an octameric large subunit (RbcL) rubisco assembly to form a hexadecameric (L8S8) holoenzyme. Although RbcS was previously thought to be integral to Form I rubisco stability, the recent discovery of a closely related sister clade of octameric rubiscos (Form I’; L8) demonstrates that the L8 complex can assemble without small subunits (Banda et al. 2020). Rubisco also displays a kinetic isotope effect (KIE) where the 3PG product is depleted in 13C relative to 12C. In Cyanobacteria, only two Form I KIE measurements exist, making interpretation of bacterial carbon isotope data difficult. To aid comparison, we measured in vitro the KIEs of Form I’ (Candidatus Promineofilum breve) and Form I (Synechococcus elongatus PCC 6301) rubiscos and found the KIE to be smaller in the L8 rubisco (16.25 ± 1.36‰ vs. 22.42 ± 2.37‰, respectively). Therefore, while small subunits may not be necessary for protein stability, they may affect the KIE. Our findings may provide insight into the function of RbcS and allow more refined interpretation of environmental carbon isotope data.
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13
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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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14
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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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15
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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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16
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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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17
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Badger MR, Sharwood RE. Rubisco, the imperfect winner: it's all about the base. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:562-580. [PMID: 36412307 DOI: 10.1093/jxb/erac458] [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: 06/28/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Rubisco catalysis is complex and includes an activation step through the formation of a carbamate at the conserved active site lysine residue and the formation of a highly reactive enediol that is the key to its catalytic reaction. The formation of this enediol is both the basis of its success and its Achilles' heel, creating imperfections to its catalytic efficiency. While Rubisco originally evolved in an atmosphere of high CO2, the earth's multiple oxidation events provided challenges to Rubisco through the fixation of O2 that competes with CO2 at the active site. Numerous catalytic screens across the Rubisco superfamily have identified significant variation in catalytic properties that have been linked to large and small subunit sequences. Despite this, we still have a rudimentary understanding of Rubisco's catalytic mechanism and how the evolution of kinetic properties has occurred. This review identifies the lysine base that functions both as an activator and a proton abstractor to create the enediol as a key to understanding how Rubisco may optimize its kinetic properties. The ways in which Rubisco and its partners have overcome catalytic and activation imperfections and thrived in a world of high O2, low CO2, and variable climatic regimes is remarkable.
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Affiliation(s)
- Murray R Badger
- Research School of Biology, Building 134 Linnaeus Way, Canberra ACT, 2601, Australia
| | - Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Bourke St, Richmond, NSW, 2753, Australia
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18
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Shen XF, Xu YP, Tong XQ, Huang Q, Zhang S, Gong J, Chu FF, Zeng RJ. The mechanism of carbon source utilization by microalgae when co-cultivated with photosynthetic bacteria. BIORESOURCE TECHNOLOGY 2022; 365:128152. [PMID: 36265788 DOI: 10.1016/j.biortech.2022.128152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Microalgae-photosynthetic bacteria (PSB) co-culture, which is promising for wastewater treatment and lipid production, is lacking of study. In this work, the combinations of 3 microalgae and 3 PSB strains were firstly screened and then different inoculation ratios of the co-cultures were investigated. It was found the best promotion was Chlorella pyrenoidosa/Rhodobacter capsulatus co-culture (1:1), where the biomass productivity, acetate assimilation rate and lipid productivity were 1.64, 1.61 and 2.79 times than that of the sum of pure microalgae and PSB cultures, respectively. Meanwhile, the inoculation ratio significantly affected the growth rate and lipid productivity of co-culture systems. iTRAQ analysis showed that PSB played a positive effect on acetate assimilation, TCA cycle and glyoxylate cycle of microalgae, but decreased the carbon dioxide utilization and photosynthesis, indicating PSB promoted the microalgae metabolism of organic carbon utilization and weakened inorganic carbon utilization. These findings provide in-depth understanding of carbon utilization in microalgae-PSB co-culture.
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Affiliation(s)
- Xiao-Fei Shen
- School of Ecology and Environment, Anhui Normal University, Anhui 241000, PR China
| | - Ya-Ping Xu
- School of Ecology and Environment, Anhui Normal University, Anhui 241000, PR China
| | - Xiao-Qin Tong
- School of Ecology and Environment, Anhui Normal University, Anhui 241000, PR China
| | - Qi Huang
- School of Ecology and Environment, Anhui Normal University, Anhui 241000, PR China
| | - Shuai Zhang
- School of Ecology and Environment, Anhui Normal University, Anhui 241000, PR China
| | - Jing Gong
- School of Ecology and Environment, Anhui Normal University, Anhui 241000, PR China
| | - Fei-Fei Chu
- College of Standardization, China Jiliang University, Zhejiang 310018, PR China
| | - Raymond Jianxiong Zeng
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fujian 350002, PR China.
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19
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Schulz L, Guo Z, Zarzycki J, Steinchen W, Schuller JM, Heimerl T, Prinz S, Mueller-Cajar O, Erb TJ, Hochberg GKA. Evolution of increased complexity and specificity at the dawn of form I Rubiscos. Science 2022; 378:155-160. [PMID: 36227987 DOI: 10.1126/science.abq1416] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that discriminate strongly between their substrate carbon dioxide and the undesired side substrate dioxygen was an important event for photosynthetic organisms adapting to an oxygenated environment. We use ancestral sequence reconstruction to recapitulate this event. We show that Rubisco increased its specificity and carboxylation efficiency through the gain of an accessory subunit before atmospheric oxygen was present. Using structural and biochemical approaches, we retrace how this subunit was gained and became essential. Our work illuminates the emergence of an adaptation to rising ambient oxygen levels, provides a template for investigating the function of interactions that have remained elusive because of their essentiality, and sheds light on the determinants of specificity in Rubisco.
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Affiliation(s)
- Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Zhijun Guo
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany.,Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany
| | - Jan M Schuller
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany.,Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany.,Department of Biology, Philipps University Marburg, 35043 Marburg, Germany
| | - Simone Prinz
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany
| | - Georg K A Hochberg
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany.,Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany.,Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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20
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Singh P, Choudhary KK, Chaudhary N, Gupta S, Sahu M, Tejaswini B, Sarkar S. Salt stress resilience in plants mediated through osmolyte accumulation and its crosstalk mechanism with phytohormones. FRONTIERS IN PLANT SCIENCE 2022; 13:1006617. [PMID: 36237504 PMCID: PMC9552866 DOI: 10.3389/fpls.2022.1006617] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/24/2022] [Indexed: 06/01/2023]
Abstract
Salinity stress is one of the significant abiotic stresses that influence critical metabolic processes in the plant. Salinity stress limits plant growth and development by adversely affecting various physiological and biochemical processes. Enhanced generation of reactive oxygen species (ROS) induced via salinity stress subsequently alters macromolecules such as lipids, proteins, and nucleic acids, and thus constrains crop productivity. Due to which, a decreasing trend in cultivable land and a rising world population raises a question of global food security. In response to salt stress signals, plants adapt defensive mechanisms by orchestrating the synthesis, signaling, and regulation of various osmolytes and phytohormones. Under salinity stress, osmolytes have been investigated to stabilize the osmotic differences between the surrounding of cells and cytosol. They also help in the regulation of protein folding to facilitate protein functioning and stress signaling. Phytohormones play critical roles in eliciting a salinity stress adaptation response in plants. These responses enable the plants to acclimatize to adverse soil conditions. Phytohormones and osmolytes are helpful in minimizing salinity stress-related detrimental effects on plants. These phytohormones modulate the level of osmolytes through alteration in the gene expression pattern of key biosynthetic enzymes and antioxidative enzymes along with their role as signaling molecules. Thus, it becomes vital to understand the roles of these phytohormones on osmolyte accumulation and regulation to conclude the adaptive roles played by plants to avoid salinity stress.
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Affiliation(s)
- Pooja Singh
- Department of Botany, MMV, Banaras Hindu University, Varanasi, India
| | - Krishna Kumar Choudhary
- Department of Botany, MMV, Banaras Hindu University, Varanasi, India
- Department of Botany, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Nivedita Chaudhary
- Department of Environmental Science, School of Earth Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Shweta Gupta
- Department of Botany, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Mamatamayee Sahu
- Department of Botany, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Boddu Tejaswini
- Department of Botany, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Subrata Sarkar
- Department of Botany, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, India
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21
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Song C, Fan Q, Tang Y, Sun Y, Wang L, Wei M, Chang Y. Overexpression of DfRaf from Fragrant Woodfern (Dryopteris fragrans) Enhances High-Temperature Tolerance in Tobacco (Nicotiana tabacum). Genes (Basel) 2022; 13:genes13071212. [PMID: 35885995 PMCID: PMC9321628 DOI: 10.3390/genes13071212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/03/2022] [Accepted: 06/27/2022] [Indexed: 01/25/2023] Open
Abstract
Heat stress seriously affects medicinal herbs’ growth and yield. Rubisco accumulation factor (Raf) is a key mediator regulating the activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), which plays important roles in carbon assimilation and the Calvin cycle in plants. Raf has been studied in many plants, but has rarely been studied in the important medicinal plant fragrant woodfern (Dryopteris fragrans). The aim of this study was to analyze the effects of Raf on carbohydrate metabolism and the response to heat stress in medicinal plants. In this study, high temperature treatment upregulated the expression of DfRaf, which was significantly higher than that of phosphoribokinase (DfPRK), Rubisco small subunits (DfRbcS), Rubisco large subunits (DfRbcL) and Rubisco activase (DfRCA). The subcellular localization showed that the DfRaf proteins were primarily located in the nucleus; DfPRK, DfRbcS, DfRbcL and DfRCA proteins were primarily located in the chloroplast. We found that overexpression of DfRaf led to increased activity of Rubisco, RCA and PRK under high-temperature stress. The H2O2, O2− and MDA content of the DfRaf-OV-L2 and DfRaf-OV-L6 transgenic lines were significantly lower than those of WT and VC plants under high-temperature stress. The photosynthetic pigments, proline, soluble sugar content and ROS-scavenging ability of the DfRaf-OV-L2 and DfRaf-OV-L6 transgenic lines were higher than those of WT and VC plants under high-temperature stress. The results showed that overexpression of the DfRaf gene increased the Rubisco activity, which enhanced the high-temperature tolerance of plants.
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Affiliation(s)
| | | | | | | | | | | | - Ying Chang
- Correspondence: ; Tel.: +86-(0451)-5519-0410
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22
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Sutter M, Kerfeld CA, Scott KM. Atypical Carboxysome Loci: JEEPs or Junk? Front Microbiol 2022; 13:872708. [PMID: 35668770 PMCID: PMC9164163 DOI: 10.3389/fmicb.2022.872708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Carboxysomes, responsible for a substantial fraction of CO2 fixation on Earth, are proteinaceous microcompartments found in many autotrophic members of domain Bacteria, primarily from the phyla Proteobacteria and Cyanobacteria. Carboxysomes facilitate CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle, particularly under conditions where the CO2 concentration is variable or low, or O2 is abundant. These microcompartments are composed of an icosahedral shell containing the enzymes ribulose 1,5-carboxylase/oxygenase (RubisCO) and carbonic anhydrase. They function as part of a CO2 concentrating mechanism, in which cells accumulate HCO3 - in the cytoplasm via active transport, HCO3 - enters the carboxysomes through pores in the carboxysomal shell proteins, and carboxysomal carbonic anhydrase facilitates the conversion of HCO3 - to CO2, which RubisCO fixes. Two forms of carboxysomes have been described: α-carboxysomes and β-carboxysomes, which arose independently from ancestral microcompartments. The α-carboxysomes present in Proteobacteria and some Cyanobacteria have shells comprised of four types of proteins [CsoS1 hexamers, CsoS4 pentamers, CsoS2 assembly proteins, and α-carboxysomal carbonic anhydrase (CsoSCA)], and contain form IA RubisCO (CbbL and CbbS). In the majority of cases, these components are encoded in the genome near each other in a gene locus, and transcribed together as an operon. Interestingly, genome sequencing has revealed some α-carboxysome loci that are missing genes encoding one or more of these components. Some loci lack the genes encoding RubisCO, others lack a gene encoding carbonic anhydrase, some loci are missing shell protein genes, and in some organisms, genes homologous to those encoding the carboxysome-associated carbonic anhydrase are the only carboxysome-related genes present in the genome. Given that RubisCO, assembly factors, carbonic anhydrase, and shell proteins are all essential for carboxysome function, these absences are quite intriguing. In this review, we provide an overview of the most recent studies of the structural components of carboxysomes, describe the genomic context and taxonomic distribution of atypical carboxysome loci, and propose functions for these variants. We suggest that these atypical loci are JEEPs, which have modified functions based on the presence of Just Enough Essential Parts.
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Affiliation(s)
| | | | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kathleen M. Scott
- Integrative Biology Department, University of South Florida, Tampa, FL, United States
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23
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Li S, Chen S, Zhang Z, Huang Y, Li G, Li Y, Deng X, Li J. Short-term exposure to silver nano-particles alters the physiology and induces stress-related gene expression in Nelumbo nucifera. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 177:38-45. [PMID: 35245773 DOI: 10.1016/j.plaphy.2022.02.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Lotus (Nelumbo nucifera) was used as model plant in this study to explore its physiology and molecular response upon short-term exposure to silver nano-particles (AgNPs). Accumulation patterns demonstrated a potential uptake of AgNPs by roots and transport to the leaves as a likely key translocation route in lotus. AgNPs exposure was negatively correlated with lotus growth, including germination rate and petiole length in a concentration-dependent manner. Synthesis of chloroplast pigments in lotus leaves was enhanced by low AgNPs concentration, but were inhibited at high concentration. Hydrogen peroxide (H2O2) was detected in lotus leaves after AgNPs treatment. Proline accumulation in lotus leaves was induced with the increase in AgNPs concentration and exposure time. Antioxidant enzyme activities of superoxide dismutase (SOD), peroxidase (POD) as well as catalase (CAT) were enhanced after the first day of AgNPs exposure, but declined with increased exposure time, indicating a time-dependent toxicity of AgNPs. In addition, real-time PCR revealed that two detoxification-related genes, GSH1 and GST, could be activated on the first day of AgNPs exposure, but down-regulated with prolonged AgNPs treatment. Photosynthesis-related RbcS gene was up-regulated, however, no obvious difference in the expression of RbcL was observed after the first day of AgNPs exposure. Moreover, WRKY70a and WRKY70b transcription factors exhibited similar expression patterns, with the highest induction after a 5 mg/L AgNPs exposure on the first day, which decreased with prolonged exposure time. This study provides useful references for further evaluation of the toxic mechanism of AgNPs and their bio-effects on aquatic plants and ecosystems.
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Affiliation(s)
- Shang Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China
| | - Simeng Chen
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China
| | - Zeyu Zhang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China
| | - Yufei Huang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China
| | - Guoqian Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China
| | - Yi Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China
| | - Xianbao Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jing Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China.
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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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ElSayed AI, Mohamed AH, Rafudeen MS, Omar AA, Awad MF, Mansour E. Polyamines mitigate the destructive impacts of salinity stress by enhancing photosynthetic capacity, antioxidant defense system and upregulation of calvin cycle-related genes in rapeseed (Brassica napus L.). Saudi J Biol Sci 2022; 29:3675-3686. [PMID: 35844395 PMCID: PMC9280241 DOI: 10.1016/j.sjbs.2022.02.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/24/2022] [Accepted: 02/27/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Abdelaleim I. ElSayed
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt
| | - Azza H. Mohamed
- Agricultural Chemistry Department, Faculty of Agriculture, Mansoura University, Mansoura 35516, Egypt
- Citrus Research and Education Center, University of Florida, IFAS, Lake Alfred, FL 33850, USA
| | - Mohammed Suhail Rafudeen
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
| | - Ahmad A. Omar
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt
- Citrus Research and Education Center, University of Florida, IFAS, Lake Alfred, FL 33850, USA
| | - Mohamed F. Awad
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Elsayed Mansour
- Department of Crop Science, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt
- Corresponding author.
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New Insight into the Effects of Various Parameters on the Crystallization of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RuBisCO) from Alcaligenes eutrophus. CRYSTALS 2022. [DOI: 10.3390/cryst12020196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Crystallization remains a bottleneck for determining the three-dimensional X-ray structure of proteins. Many parameters influence the complexity of protein crystallization. Therefore, it is not easy to systematically examine all of these parameters individually during crystallization because of a limited quantity of purified protein. We studied several factors that influence crystallization including protein concentration, pH, temperature, age, volume of crystallization, inhibitors, metal ions, seeding, and precipitating agents on RuBisCO samples from Alcaligenes eutrophus which are not only freshly purified, but are also dissolved both individually and in combination from microcrystals and precipitated droplets of recycled RuBisCO. Single-, twin-, and/or microcrystals are dependent upon the concentration of RuBisCO by both RuBisCO samples. The morphology, either orthorhombic- or monoclinic-space group, depends upon pH. Furthermore, ammonium sulfate((NH4)2SO4) concentration at 20 °C (22% saturated) and/or at 4 °C (28% saturated) affected the crystallization of RuBisCO differently from one another. Finally, the age of RuBisCO also affected more uniformity and forming sharp edge during crystallization. Unexpected surprising monoclinic RuBisCO crystals were grown from dissolved microcrystals and precipitated droplets recycled RuBisCO samples. This quaternary RuBisCO single crystal, which contained Mg2+ and HCO3 for an activated ternary complex and is inhibited with a transition substrate analogue, CABP (2-carboxyarabinitol-1,5-bisphosphate)−, diffracts better than 2.2 Å. It is different from Hansen S. et al. reported RuBisCO crystals which were grown ab initio in absence of Mg2+, HCO3− and CABP, a structure which was determined at 2.7 Å resolution.
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ElSayed AI, Rafudeen MS, Gomaa AM, Hasanuzzaman M. Exogenous melatonin enhances the reactive oxygen species metabolism, antioxidant defense-related gene expression, and photosynthetic capacity of Phaseolus vulgaris L. to confer salt stress tolerance. PHYSIOLOGIA PLANTARUM 2021; 173:1369-1381. [PMID: 33619766 DOI: 10.1111/ppl.13372] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 05/03/2023]
Abstract
Melatonin (MT) has been reported to regulate certain plant physiological processes and promote tolerance to different environmental stresses such as salinity. Green bean (Phaseolus vulgaris L. cv. Royal Nel) seedlings were exposed to 200 mM NaCl with or without pre-treatment with 150 μM MT. Salt stress led to a lower chlorophyll content, a reduced photosynthetic activity, increased reactive oxygen species (ROS) contents, and decreased photosystem II (PSII) activity. The application of exogenous MT to green bean seedlings under salt stress improved photosynthetic activity and alleviated the oxidative damages by enhancing the activity of antioxidant enzymes. The expression of catalase (CAT1), glutathione reductase (GR), superoxide dismutase (CuZnSOD1), ascorbate peroxidase (APX), Peroxiredoxin Q (PrxQ), and 2-cysteine peroxiredoxin (2-Cys-Prx) encoding genes was significantly increased under salt stress in green bean seedling compared with the untreated control. However, plants treated with exogenous MT and NaCl had 28.8, 21.1, 26.1, 20, 26.2, and 22.4% higher CuZnSOD, CAT1, APX, GR, PrxQ, and 2-Cys-Prx transcript levels, respectively, compared to NaCl stress alone. Our study revealed the protective mechanisms mediated by exogenous MT application in NaCl stress alleviation and our findings could be used in the management of green bean cultivation in salinity-prone soils.
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Affiliation(s)
| | | | - Ayman M Gomaa
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
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28
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Tcherkez G, Farquhar GD. Rubisco catalytic adaptation is mostly driven by photosynthetic conditions - Not by phylogenetic constraints. JOURNAL OF PLANT PHYSIOLOGY 2021; 267:153554. [PMID: 34749030 DOI: 10.1016/j.jplph.2021.153554] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The prevalence of phylogenetic constraints in Rubisco evolution has been emphasised recently by (Bouvier et al., 2021), who argued that phylogenetic inheritance limits Rubisco adaptation much more than the biochemical trade-off between specificity, CO2 affinity and turn-over. In this Opinion, we have critically examined how a phylogenetic signal can be computed with Rubisco kinetic properties and phylogenetic trees, and we arrive at a different conclusion. In particular, Rubisco's adaptation is partly driven by C4 vs. C3 photosynthetic conditions in Angiosperms, apparent phylogenetic signals being mostly due to either homoplasy, computation artefacts or the use of nearly identical sister species. While phylogenetic inheritance of an ancestral enzyme form probably has some role in Rubisco's adaptation landscape, it is a minor player, at least compared to microenvironmental conditions such as CO2 and O2 concentrations.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Recherche and Horticulture et Semences, INRAe Angers, Université D'Angers, 42 Rue Georges Morel, 49070, Beaucouzé, France; Research School of Biology, ANU College of Science, Australian National University, 2601, Canberra ACT, Australia.
| | - Graham D Farquhar
- Research School of Biology, ANU College of Science, Australian National University, 2601, Canberra ACT, Australia
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Hussain S, Ulhassan Z, Brestic M, Zivcak M, Allakhverdiev SI, Yang X, Safdar ME, Yang W, Liu W. Photosynthesis research under climate change. PHOTOSYNTHESIS RESEARCH 2021; 150:5-19. [PMID: 34235625 DOI: 10.1007/s11120-021-00861-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/28/2021] [Indexed: 05/13/2023]
Abstract
Increasing global population and climate change uncertainties have compelled increased photosynthetic efficiency and yields to ensure food security over the coming decades. Potentially, genetic manipulation and minimization of carbon or energy losses can be ideal to boost photosynthetic efficiency or crop productivity. Despite significant efforts, limited success has been achieved. There is a need for thorough improvement in key photosynthetic limiting factors, such as stomatal conductance, mesophyll conductance, biochemical capacity combined with Rubisco, the Calvin-Benson cycle, thylakoid membrane electron transport, nonphotochemical quenching, and carbon metabolism or fixation pathways. In addition, the mechanistic basis for the enhancement in photosynthetic adaptation to environmental variables such as light intensity, temperature and elevated CO2 requires further investigation. This review sheds light on strategies to improve plant photosynthesis by targeting these intrinsic photosynthetic limitations and external environmental factors.
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Affiliation(s)
- Sajad Hussain
- College of Agronomy, Sichuan Agricultural University, 211-Huimin Road, Wenjiang District, Chengdu, 611130, People's Republic of China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Zaid Ulhassan
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, 94976, Nitra, Slovakia
| | - Marek Zivcak
- Department of Plant Physiology, Slovak University of Agriculture, 94976, Nitra, Slovakia
| | - Suleyman I Allakhverdiev
- К.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya St. 35, Moscow, Russia, 127276
| | - Xinghong Yang
- Department of Plant Physiology, College of Life Sciences, Shandong Agricultural University, Daizong Road No. 61, 271018, Taian, People's Republic of China
| | | | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, 211-Huimin Road, Wenjiang District, Chengdu, 611130, People's Republic of China.
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, People's Republic of China.
| | - Weiguo Liu
- College of Agronomy, Sichuan Agricultural University, 211-Huimin Road, Wenjiang District, Chengdu, 611130, People's Republic of China.
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, People's Republic of China.
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30
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Liu LN. Advances in the bacterial organelles for CO 2 fixation. Trends Microbiol 2021; 30:567-580. [PMID: 34802870 DOI: 10.1016/j.tim.2021.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
Carboxysomes are a family of bacterial microcompartments (BMCs), present in all cyanobacteria and some proteobacteria, which encapsulate the primary CO2-fixing enzyme, Rubisco, within a virus-like polyhedral protein shell. Carboxysomes provide significantly elevated levels of CO2 around Rubisco to maximize carboxylation and reduce wasteful photorespiration, thus functioning as the central CO2-fixation organelles of bacterial CO2-concentration mechanisms. Their intriguing architectural features allow carboxysomes to make a vast contribution to carbon assimilation on a global scale. In this review, we discuss recent research progress that provides new insights into the mechanisms of how carboxysomes are assembled and functionally maintained in bacteria and recent advances in synthetic biology to repurpose the metabolic module in diverse applications.
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Affiliation(s)
- Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 266003 Qingdao, China.
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31
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Komatsu S, Maruyama J, Furuya T, Yin X, Yamaguchi H, Hitachi K, Miyashita N, Tsuchida K, Tani M. Proteomic and Biological Analyses Reveal the Effect on Growth under Flooding Stress of Chickpea Irradiated with Millimeter Waves. J Proteome Res 2021; 20:4718-4727. [PMID: 34455783 DOI: 10.1021/acs.jproteome.1c00368] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chickpea cultivated on marginal lands in arid and semiarid tropics is one of the food legumes, and its growth is reduced by flooding stress. Millimeter-wave irradiation has influences on organisms, and it improves the growth of plants such as soybean. To reveal the dynamic effects of millimeter-wave irradiation on chickpea under flooding, gel- and label-free proteomic analysis was conducted. Millimeter-wave irradiation improved chickpea growth and its tolerance to flooding stress. According to functional categorization, oppositely changed proteins were correlated with photosynthesis, fermentation, and protein degradation. Immunoblot analysis confirmed that RuBisCO activase and large subunits decreased in leaves under flooding; however, they are recovered in irradiated chickpea even if it was in this condition. The activity and accumulation of alcohol dehydrogenase increased in roots under flooding; however, this followed the same pattern. Cell death was significantly increased and decreased by flooding on unirradiated and irradiated chickpeas, respectively. These findings suggest that irradiation with millimeter waves on chickpea seeds improves the recovery of plant growth through regulation of photosynthesis in leaves and fermentation in roots. Furthermore, millimeter-wave irradiation might promote chickpea tolerance under flooding via the regulation of cell death.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Junya Maruyama
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Takashi Furuya
- Research Center for Development of Far-Infrared Region, University of Fukui, Fukui 910-8507, Japan
| | - Xiaojian Yin
- Department of Pharmacognosy, China Pharmaceutical University, Nanjing 211198, China
| | - Hisateru Yamaguchi
- Department of Medical Technology, Yokkaichi Nursing and Medical Care University, Yokkaichi 512-8045, Japan
| | - Keisuke Hitachi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Natsuki Miyashita
- Research Center for Development of Far-Infrared Region, University of Fukui, Fukui 910-8507, Japan
| | - Kunihiro Tsuchida
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Masahiko Tani
- Research Center for Development of Far-Infrared Region, University of Fukui, Fukui 910-8507, Japan
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Hassanein RA, Hussein OS, Abdelkader AF, Farag IA, Hassan YE, Ibrahim M. Metabolic activities and molecular investigations of the ameliorative impact of some growth biostimulators on chilling-stressed coriander (Coriandrum sativum L.) plant. BMC PLANT BIOLOGY 2021; 21:361. [PMID: 34364372 PMCID: PMC8349021 DOI: 10.1186/s12870-021-03021-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 05/10/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Priming of seed prior chilling is regarded as one of the methods to promote seeds germination, whole plant growth, and yield components. The application of biostimulants was reported as beneficial for protecting many plants from biotic or abiotic stresses. Their value was as important to be involved in improving the growth parameters of plants. Also, they were practiced in the regulation of various metabolic pathways to enhance acclimation and tolerance in coriander against chilling stress. To our knowledge, little is deciphered about the molecular mechanisms underpinning the ameliorative impact of biostimulants in the context of understanding the link and overlap between improved morphological characters, induced metabolic processes, and upregulated gene expression. In this study, the ameliorative effect(s) of potassium silicate, HA, and gamma radiation on acclimation of coriander to tolerate chilling stress was evaluated by integrating the data of growth, yield, physiological and molecular aspects. RESULTS Plant growth, yield components, and metabolic activities were generally diminished in chilling-stressed coriander plants. On the other hand, levels of ABA and soluble sugars were increased. Alleviation treatment by humic acid, followed by silicate and gamma irradiation, has notably promoted plant growth parameters and yield components in chilling-stressed coriander plants. This improvement was concomitant with a significant increase in phytohormones, photosynthetic pigments, carbohydrate contents, antioxidants defense system, and induction of large subunit of RuBisCO enzyme production. The assembly of Toc complex subunits was maintained, and even their expression was stimulated (especially Toc75 and Toc 34) upon alleviation of the chilling stress by applied biostimulators. Collectively, humic acid was the best the element to alleviate the adverse effects of chilling stress on growth and productivity of coriander. CONCLUSIONS It could be suggested that the inducing effect of the pretreatments on hormonal balance triggered an increase in IAA + GA3/ABA hormonal ratio. This ratio could be linked and engaged with the protection of cellular metabolic activities from chilling injury against the whole plant life cycle. Therefore, it was speculated that seed priming in humic acid is a powerful technique that can benefit the chilled along with non-chilled plants and sustain the economic importance of coriander plant productivity.
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Affiliation(s)
- Raifa A Hassanein
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, 11355, Egypt
| | - Omaima S Hussein
- Department of Natural Products, National Center for Radiation Research and Technology, Atomic Energy Authority, P.O. 29, Cairo, Nasr City, Egypt
| | - Amal F Abdelkader
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, 11355, Egypt
| | - Iman A Farag
- Department of Natural Products, National Center for Radiation Research and Technology, Atomic Energy Authority, P.O. 29, Cairo, Nasr City, Egypt
| | - Yousra E Hassan
- Department of Natural Products, National Center for Radiation Research and Technology, Atomic Energy Authority, P.O. 29, Cairo, Nasr City, Egypt
| | - Mohamed Ibrahim
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, 11355, Egypt.
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The Mechanism of Rubisco Catalyzed Carboxylation Reaction: Chemical Aspects Involving Acid-Base Chemistry and Functioning of the Molecular Machine. Catalysts 2021. [DOI: 10.3390/catal11070813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In recent years, a great deal of attention has been paid by the scientific community to improving the efficiency of photosynthetic carbon assimilation, plant growth and biomass production in order to achieve a higher crop productivity. Therefore, the primary carboxylase enzyme of the photosynthetic process Rubisco has received considerable attention focused on many aspects of the enzyme function including protein structure, protein engineering and assembly, enzyme activation and kinetics. Based on its fundamental role in carbon assimilation Rubisco is also targeted by the CO2-fertilization effect, which is the increased rate of photosynthesis due to increasing atmospheric CO2-concentration. The aim of this review is to provide a framework, as complete as possible, of the mechanism of the RuBP carboxylation/hydration reaction including description of chemical events occurring at the enzyme “activating” and “catalytic” sites (which involve Broensted acid-base reactions) and the functioning of the complex molecular machine. Important research results achieved over the last few years providing substantial advancement in understanding the enzyme functioning will be discussed.
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34
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Leitão ST, Santos C, Araújo SDS, Rubiales D, Vaz Patto MC. Shared and tailored common bean transcriptomic responses to combined fusarium wilt and water deficit. HORTICULTURE RESEARCH 2021; 8:149. [PMID: 34193847 PMCID: PMC8245569 DOI: 10.1038/s41438-021-00583-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
Common bean (Phaseolus vulgaris L.), one of the most consumed food legumes worldwide, is threatened by two main constraints that are found frequently together in nature, water deficit (WD) and fusarium wilt (Fop). To understand the shared and unique responses of common bean to Fop and WD, we analyzed the transcriptomic changes and phenotypic responses in two accessions, one resistant and one susceptible to both stresses, exposed to single and combined stresses. Physiological responses (photosynthetic performance and pigments quantification) and disease progression were also assessed. The combined FopWD imposition negatively affected the photosynthetic performance and increased the susceptible accession disease symptoms. The susceptible accession revealed a higher level of transcriptional changes than the resistant one, and WD single stress triggered the highest transcriptional changes. While 89 differentially expressed genes were identified exclusively in combined stresses for the susceptible accession, 35 were identified in the resistant one. These genes belong mainly to "stress", "signaling", "cell wall", "hormone metabolism", and "secondary metabolism" functional categories. Among the up-regulated genes with higher expression in the resistant accession, the cysteine-rich secretory, antigen 5 and Pr-1 (CAP) superfamily protein, a ribulose bisphosphate carboxylase family protein, and a chitinase A seem promising targets for multiple stress breeding.
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Affiliation(s)
- Susana T Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Carmen Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Association BLC3 - Technology and Innovation Campus, Centre Bio R&D Unit, Lagares da Beira, Portugal
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Combined Proteomic and Physiological Analysis of Chloroplasts Reveals Drought and Recovery Response Mechanisms in Nicotiana benthamiana. PLANTS 2021; 10:plants10061127. [PMID: 34199332 PMCID: PMC8228571 DOI: 10.3390/plants10061127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022]
Abstract
Chloroplasts play essential roles in plant metabolic processes and stress responses by functioning as environmental sensors. Understanding chloroplast responses to drought stress and subsequent recovery will help the ability to improve stress tolerance in plants. Here, a combined proteomic and physiological approach was used to investigate the response mechanisms of Nicotiana benthamiana chloroplasts to drought stress and subsequent recovery. Early in the stress response, changes in stomatal movement were accompanied by immediate changes in protein synthesis to sustain the photosynthetic process. Thereafter, increasing drought stress seriously affected photosynthetic efficiency and led to altered expression of photosynthesis- and carbon-fixation-related proteins to protect the plants against photo-oxidative damage. Additional repair mechanisms were activated at the early stage of recovery to restore physiological functions and repair drought-induced damages, even while the negative effects of drought stress were still ongoing. Prolonging the re-watering period led to the gradual recovery of photosynthesis at both physiological and protein levels, indicating that a long repair process is required to restore plant function. Our findings provide a precise view of drought and recovery response mechanisms in N. benthamiana and serve as a reference for further investigation into the physiological and molecular mechanisms underlying plant drought tolerance.
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36
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Nagamalla SS, Alaparthi MD, Mellacheruvu S, Gundeti R, Earrawandla JPS, Sagurthi SR. Morpho-Physiological and Proteomic Response of Bt-Cotton and Non-Bt Cotton to Drought Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:663576. [PMID: 34040622 PMCID: PMC8143030 DOI: 10.3389/fpls.2021.663576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Drought stress impacts cotton plant growth and productivity across countries. Plants can initiate morphological, cellular, and proteomic changes to adapt to unfavorable conditions. However, our knowledge of how cotton plants respond to drought stress at the proteome level is limited. Herein, we elucidated the molecular coordination underlining the drought tolerance of two inbred cotton varieties, Bacillus thuringiensis-cotton [Bt-cotton + Cry1 Ac gene and Cry 2 Ab gene; NCS BG II BT (BTCS/BTDS)] and Hybrid cotton variety [Non-Bt-cotton; (HCS/HDS)]. Our morphological observations and biochemical experiments showed a different tolerance level between two inbred lines to drought stress. Our proteomic analysis using 2D-DIGE revealed that the changes among them were not obviously in respect to their controls apart from under drought stress, illustrating the differential expression of 509 and 337 proteins in BTDS and HDS compared to their controls. Among these, we identified eight sets of differentially expressed proteins (DEPs) and characterized them using MALDI-TOF/TOF mass spectrometry. Furthermore, the quantitative real-time PCR analysis was carried out with the identified drought-related proteins and confirmed differential expressions. In silico analysis of DEPs using Cytoscape network finds ATPB, NAT9, ERD, LEA, and EMB2001 to be functionally correlative to various drought-responsive genes LEA, AP2/ERF, WRKY, and NAC. These proteins play a vital role in transcriptomic regulation under stress conditions. The higher drought response in Bt cotton (BTCS/BTDS) attributed to the overexpression of photosynthetic proteins enhanced lipid metabolism, increased cellular detoxification and activation chaperones, and reduced synthesis of unwanted proteins. Thus, the Bt variety had enhanced photosynthesis, elevated water retention potential, balanced leaf stomata ultrastructure, and substantially increased antioxidant activity than the Non-Bt cotton. Our results may aid breeders and provide further insights into developing new drought-tolerant and high-yielding cotton hybrid varieties.
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Perdomo JA, Buchner P, Carmo-Silva E. The relative abundance of wheat Rubisco activase isoforms is post-transcriptionally regulated. PHOTOSYNTHESIS RESEARCH 2021; 148:47-56. [PMID: 33796933 PMCID: PMC8154801 DOI: 10.1007/s11120-021-00830-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/11/2021] [Indexed: 06/06/2023]
Abstract
Diurnal rhythms and light availability affect transcription-translation feedback loops that regulate the synthesis of photosynthetic proteins. The CO2-fixing enzyme Rubisco is the most abundant protein in the leaves of major crop species and its activity depends on interaction with the molecular chaperone Rubisco activase (Rca). In Triticum aestivum L. (wheat), three Rca isoforms are present that differ in their regulatory properties. Here, we tested the hypothesis that the relative abundance of the redox-sensitive and redox-insensitive Rca isoforms could be differentially regulated throughout light-dark diel cycle in wheat. While TaRca1-β expression was consistently negligible throughout the day, transcript levels of both TaRca2-β and TaRca2-α were higher and increased at the start of the day, with peak levels occurring at the middle of the photoperiod. Abundance of TaRca-β protein was maximal 1.5 h after the peak in TaRca2-β expression, but the abundance of TaRca-α remained constant during the entire photoperiod. The redox-sensitive TaRca-α isoform was less abundant, representing 85% of the redox-insensitive TaRca-β at the transcript level and 12.5% at the protein level. Expression of Rubisco large and small subunit genes did not show a consistent pattern throughout the diel cycle, but the abundance of Rubisco decreased by up to 20% during the dark period in fully expanded wheat leaves. These results, combined with a lack of correlation between transcript and protein abundance for both Rca isoforms and Rubisco throughout the entire diel cycle, suggest that the abundance of these photosynthetic enzymes is post-transcriptionally regulated.
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Affiliation(s)
| | - Peter Buchner
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
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Lesharadevi K, Parthasarathi T, Muneer S. Silicon biology in crops under abiotic stress: A paradigm shift and cross-talk between genomics and proteomics. J Biotechnol 2021; 333:21-38. [PMID: 33933485 DOI: 10.1016/j.jbiotec.2021.04.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 01/26/2023]
Abstract
Silicon is a beneficial element to improve the biological process, growth, development, and crop productivity. The review mainly focuses on the advantage of crops supplemented with silicon, how Si alleviate abiotic stress as well as regulate the genes and proteins involved in metabolic and biological functions in plants. Abiotic stress causes damage to the proteins, nucleic acids, affect transpiration rate, stomatal conductance, alter the nutrient balance, and cell desiccation which could reduce the growth and development of the plants. To overcome from this problem researchers, focus on beneficial element like silicon to protect the plants against various abiotic stresses. The previous review reports are based on the application of silicon on salinity and drought stress, plant defense mechanism, the elevation of plant metabolism, enhancement of the biochemical and physiological properties, regulation of secondary metabolites and plant hormone. Here, we discuss about the silicon uptake and accumulation in plants, and silicon regulates the reactive oxygen species under abiotic stress, further we mainly focus on the genes and proteins which play a vital role in plants with silicon supplementation. The study can help the researchers to focus further on plants to improve the advancement in them under abiotic stress.
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Affiliation(s)
- Kuppan Lesharadevi
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Tamil Nadu, India; School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India; Plant Genomics and Biochemistry Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Tamil-Nadu, India
| | - Theivasigamani Parthasarathi
- Plant Genomics and Biochemistry Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Tamil-Nadu, India.
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Tamil Nadu, India.
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Matsuzaki R, Suzuki S, Yamaguchi H, Kawachi M, Kanesaki Y, Yoshikawa H, Mori T, Nozaki H. The Rubisco small subunits in the green algal genus Chloromonas provide insights into evolutionary loss of the eukaryotic carbon-concentrating organelle, the pyrenoid. BMC Ecol Evol 2021; 21:11. [PMID: 33514317 PMCID: PMC7853309 DOI: 10.1186/s12862-020-01733-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/10/2020] [Indexed: 12/14/2022] Open
Abstract
Background Pyrenoids are protein microcompartments composed mainly of Rubisco that are localized in the chloroplasts of many photosynthetic organisms. Pyrenoids contribute to the CO2-concentrating mechanism. This organelle has been lost many times during algal/plant evolution, including with the origin of land plants. The molecular basis of the evolutionary loss of pyrenoids is a major topic in evolutionary biology. Recently, it was hypothesized that pyrenoid formation is controlled by the hydrophobicity of the two helices on the surface of the Rubisco small subunit (RBCS), but the relationship between hydrophobicity and pyrenoid loss during the evolution of closely related algal/plant lineages has not been examined. Here, we focused on, the Reticulata group of the unicellular green algal genus Chloromonas, within which pyrenoids are present in some species, although they are absent in the closely related species. Results Based on de novo transcriptome analysis and Sanger sequencing of cloned reverse transcription-polymerase chain reaction products, rbcS sequences were determined from 11 strains of two pyrenoid-lacking and three pyrenoid-containing species of the Reticulata group. We found that the hydrophobicity of the RBCS helices was roughly correlated with the presence or absence of pyrenoids within the Reticulata group and that a decrease in the hydrophobicity of the RBCS helices may have primarily caused pyrenoid loss during the evolution of this group. Conclusions Although we suggest that the observed correlation may only exist for the Reticulata group, this is still an interesting study that provides novel insight into a potential mechanism determining initial evolutionary steps of gain and loss of the pyrenoid.
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Affiliation(s)
- Ryo Matsuzaki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Shigekatsu Suzuki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.,NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Toshiyuki Mori
- Department of Tropical Medicine and Parasitology, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Donovan S, Mao Y, Orr DJ, Carmo-Silva E, McCormick AJ. CRISPR-Cas9-Mediated Mutagenesis of the Rubisco Small Subunit Family in Nicotiana tabacum. Front Genome Ed 2020; 2:605614. [PMID: 34713229 PMCID: PMC8525408 DOI: 10.3389/fgeed.2020.605614] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
Engineering the small subunit of the key CO2-fixing enzyme Rubisco (SSU, encoded by rbcS) in plants currently poses a significant challenge, as many plants have polyploid genomes and SSUs are encoded by large multigene families. Here, we used CRISPR-Cas9-mediated genome editing approach to simultaneously knock-out multiple rbcS homologs in the model tetraploid crop tobacco (Nicotiana tabacum cv. Petit Havana). The three rbcS homologs rbcS_S1a, rbcS_S1b and rbcS_T1 account for at least 80% of total rbcS expression in tobacco. In this study, two multiplexing guide RNAs (gRNAs) were designed to target homologous regions in these three genes. We generated tobacco mutant lines with indel mutations in all three genes, including one line with a 670 bp deletion in rbcS-T1. The Rubisco content of three selected mutant lines in the T1 generation was reduced by ca. 93% and mutant plants accumulated only 10% of the total biomass of wild-type plants. As a second goal, we developed a proof-of-principle approach to simultaneously introduce a non-native rbcS gene while generating the triple SSU knockout by co-transformation into a wild-type tobacco background. Our results show that CRISPR-Cas9 is a viable tool for the targeted mutagenesis of rbcS families in polyploid species and will contribute to efforts aimed at improving photosynthetic efficiency through expression of superior non-native Rubisco enzymes in plants.
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Affiliation(s)
- Sophie Donovan
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yuwei Mao
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Douglas J. Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | | | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Matsumura H, Shiomi K, Yamamoto A, Taketani Y, Kobayashi N, Yoshizawa T, Tanaka SI, Yoshikawa H, Endo M, Fukayama H. Hybrid Rubisco with Complete Replacement of Rice Rubisco Small Subunits by Sorghum Counterparts Confers C 4 Plant-like High Catalytic Activity. MOLECULAR PLANT 2020; 13:1570-1581. [PMID: 32882392 DOI: 10.1016/j.molp.2020.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/28/2020] [Accepted: 08/22/2020] [Indexed: 05/25/2023]
Abstract
Photosynthetic rate at the present atmospheric condition is limited by the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) because of its extremely low catalytic rate (kcat) and poor affinity for CO2 (Kc) and specificity for CO2 (Sc/o). Rubisco in C4 plants generally shows higher kcat than that in C3 plants. Rubisco consists of eight large subunits and eight small subunits (RbcS). Previously, the chimeric incorporation of sorghum C4-type RbcS significantly increased the kcat of Rubisco in a C3 plant, rice. In this study, we knocked out rice RbcS multigene family using the CRISPR-Cas9 technology and completely replaced rice RbcS with sorghum RbcS in rice Rubisco. Obtained hybrid Rubisco showed almost C4 plant-like catalytic properties, i.e., higher kcat, higher Kc, and lower Sc/o. Transgenic lines expressing the hybrid Rubisco accumulated reduced levels of Rubisco, whereas they showed slightly but significantly higher photosynthetic capacity and similar biomass production under high CO2 condition compared with wild-type rice. High-resolution crystal structural analysis of the wild-type Rubisco and hybrid Rubisco revealed the structural differences around the central pore of Rubisco and the βC-βD hairpin in RbcS. We propose that such differences, particularly in the βC-βD hairpin, may impact the flexibility of Rubisco catalytic site and change its catalytic properties.
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Affiliation(s)
- Hiroyoshi Matsumura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu 525-8577, Japan.
| | - Keita Shiomi
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-tyou, Nada-ku, Kobe 657-8501, Japan
| | - Akito Yamamoto
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-tyou, Nada-ku, Kobe 657-8501, Japan
| | - Yuri Taketani
- Faculty of Agriculture, Kobe University, 1-1 Rokkodai-tyou, Nada-ku, Kobe 657-8501, Japan
| | - Noriyuki Kobayashi
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-tyou, Nada-ku, Kobe 657-8501, Japan
| | - Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu 525-8577, Japan
| | - Shun-Ichi Tanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu 525-8577, Japan
| | - Hiroki Yoshikawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu 525-8577, Japan
| | - Masaki Endo
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba 305-8634, Japan
| | - Hiroshi Fukayama
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-tyou, Nada-ku, Kobe 657-8501, Japan.
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Lin MT, Stone WD, Chaudhari V, Hanson MR. Small subunits can determine enzyme kinetics of tobacco Rubisco expressed in Escherichia coli. NATURE PLANTS 2020; 6:1289-1299. [PMID: 32929197 DOI: 10.1038/s41477-020-00761-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/28/2020] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) catalyses the first step in carbon fixation and is a strategic target for improving photosynthetic efficiency. In plants, Rubisco is composed of eight large and eight small subunits, and its biogenesis requires multiple chaperones. Here, we optimized a system to produce tobacco Rubisco in Escherichia coli by coexpressing chaperones in autoinduction medium. We successfully assembled tobacco Rubisco in E. coli with each small subunit that is normally encoded by the nuclear genome. Even though each enzyme carries only a single type of small subunit in E. coli, the enzymes exhibit carboxylation kinetics that are very similar to the carboxylation kinetics of the native Rubisco. Tobacco Rubisco assembled with a recently discovered trichome small subunit has a higher catalytic rate and a lower CO2 affinity compared with Rubisco complexes that are assembled with other small subunits. Our E. coli expression system will enable the analysis of features of both subunits of Rubisco that affect its kinetic properties.
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Affiliation(s)
- Myat T Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - William D Stone
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, USA
| | | | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E, Adams PD, Banfield JF, Shih PM. Novel bacterial clade reveals origin of form I Rubisco. NATURE PLANTS 2020; 6:1158-1166. [PMID: 32868887 DOI: 10.1038/s41477-020-00762-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/28/2020] [Indexed: 05/12/2023]
Abstract
Rubisco sustains the biosphere through the fixation of CO2 into biomass. In plants and cyanobacteria, form I Rubisco is structurally comprised of large and small subunits, whereas all other Rubisco forms lack small subunits. The rise of the form I complex through the innovation of small subunits represents a key, yet poorly understood, transition in Rubisco's evolution. Through metagenomic analyses, we discovered a previously uncharacterized clade sister to form I Rubisco that evolved without small subunits. This clade diverged before the evolution of cyanobacteria and the origin of the small subunit; thus, it provides a unique reference point to advance our understanding of form I Rubisco evolution. Structural and kinetic data presented here reveal how a proto-form I Rubisco assembled and functioned without the structural stability imparted from small subunits. Our findings provide insight into a key evolutionary transition of the most abundant enzyme on Earth and the predominant entry point for nearly all global organic carbon.
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Affiliation(s)
- Douglas M Banda
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jose H Pereira
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Albert K Liu
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christine He
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Martin A J Parry
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | | | - Paul D Adams
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.
- Genome Center, University of California, Davis, Davis, CA, USA.
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Goudet MMM, Orr DJ, Melkonian M, Müller KH, Meyer MT, Carmo-Silva E, Griffiths H. Rubisco and carbon-concentrating mechanism co-evolution across chlorophyte and streptophyte green algae. THE NEW PHYTOLOGIST 2020; 227:810-823. [PMID: 32249430 DOI: 10.1111/nph.16577] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/23/2020] [Indexed: 05/19/2023]
Abstract
Green algae expressing a carbon-concentrating mechanism (CCM) are usually associated with a Rubisco-containing micro-compartment, the pyrenoid. A link between the small subunit (SSU) of Rubisco and pyrenoid formation in Chlamydomonas reinhardtii has previously suggested that specific RbcS residues could explain pyrenoid occurrence in green algae. A phylogeny of RbcS was used to compare the protein sequence and CCM distribution across the green algae and positive selection in RbcS was estimated. For six streptophyte algae, Rubisco catalytic properties, affinity for CO2 uptake (K0.5 ), carbon isotope discrimination (δ13 C) and pyrenoid morphology were compared. The length of the βA-βB loop in RbcS provided a phylogenetic marker discriminating chlorophyte from streptophyte green algae. Rubisco kinetic properties in streptophyte algae have responded to the extent of inducible CCM activity, as indicated by changes in inorganic carbon uptake affinity, δ13 C and pyrenoid ultrastructure between high and low CO2 conditions for growth. We conclude that the Rubisco catalytic properties found in streptophyte algae have coevolved and reflect the strength of any CCM or degree of pyrenoid leakiness, and limitations to inorganic carbon in the aquatic habitat, whereas Rubisco in extant land plants reflects more recent selective pressures associated with improved diffusive supply of the terrestrial environment.
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Affiliation(s)
- Myriam M M Goudet
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Michael Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, 50674, Cologne, Germany
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, 45141, Essen, Germany
| | - Karin H Müller
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Moritz T Meyer
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | | | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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Li C, Li N, Huang R, Chen C, Guo J, Yang X, Zhang X, Sun C, Deng X, Wang P. A single nucleotide substitution at the 3'-end of SBPase gene involved in Calvin cycle severely affects plant growth and grain yield in rice. BMC PLANT BIOLOGY 2020; 20:345. [PMID: 32698774 PMCID: PMC7374905 DOI: 10.1186/s12870-020-02541-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Calvin cycle plays a crucial role in carbon fixation which provides the precursors of organic macromolecules for plant growth and development. Currently, no gene involved in Calvin cycle has been identified in monocotyledonous plants through mutant or/and map-based cloning approach. RESULTS Here, we isolated a low-tillering mutant, c6635, in rice (Oryza sativa). The mutant displayed light green leaves and intensely declined pigment contents and photosynthetic capacity at early growth stage. Moreover, its individual plant showed a much smaller size, and most individuals produced only two tillers. At mature stage, its productive panicles, grain number and seed setting rate were significantly decreased, which lead to a sharp reduction of the grain yield. We confirmed that a single nucleotide mutation in LOC_Os04g16680 gene encoding sedoheptulose 1,7-bisphosphatase (SBPase) involved in Calvin cycle was responsible for the mutant phenotype of c6635 through map-based cloning, MutMap analysis and complementation experiments. Sequence analysis suggested that the point mutation caused an amino acid change from Gly-364 to Asp at the C-terminal of SBPase. In addition, OsSBPase gene was mainly expressed in leaf, and the encoded protein was located in chloroplast. The mutation of OsSBPase could significantly affect expression levels of some key genes involved in Calvin cycle. CONCLUSIONS We successfully identified a SBPase gene in monocotyledonous plants. Meanwhile, we demonstrated that a single nucleotide substitution at the 3'-end of this gene severely affects plant growth and grain yield, implying that the Gly-364 at the C-terminal of SBPase could play an important role in SBPase function in rice.
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Affiliation(s)
- Chun Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Na Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Rui Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Congping Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Jia Guo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiaorong Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiangyu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China.
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Rubisco accumulation factor 1 (Raf1) plays essential roles in mediating Rubisco assembly and carboxysome biogenesis. Proc Natl Acad Sci U S A 2020; 117:17418-17428. [PMID: 32636267 PMCID: PMC7382273 DOI: 10.1073/pnas.2007990117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Carboxysomes are membrane-free organelles for carbon assimilation in cyanobacteria. The carboxysome consists of a proteinaceous shell that structurally resembles virus capsids and internal enzymes including ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), the primary carbon-fixing enzyme in photosynthesis. The formation of carboxysomes requires hierarchical self-assembly of thousands of protein subunits, initiated from Rubisco assembly and packaging to shell encapsulation. Here we study the role of Rubisco assembly factor 1 (Raf1) in Rubisco assembly and carboxysome formation in a model cyanobacterium, Synechococcus elongatus PCC7942 (Syn7942). Cryo-electron microscopy reveals that Raf1 facilitates Rubisco assembly by mediating RbcL dimer formation and dimer-dimer interactions. Syn7942 cells lacking Raf1 are unable to form canonical intact carboxysomes but generate a large number of intermediate assemblies comprising Rubisco, CcaA, CcmM, and CcmN without shell encapsulation and a low abundance of carboxysome-like structures with reduced dimensions and irregular shell shapes and internal organization. As a consequence, the Raf1-depleted cells exhibit reduced Rubisco content, CO2-fixing activity, and cell growth. Our results provide mechanistic insight into the chaperone-assisted Rubisco assembly and biogenesis of carboxysomes. Advanced understanding of the biogenesis and stepwise formation process of the biogeochemically important organelle may inform strategies for heterologous engineering of functional CO2-fixing modules to improve photosynthesis.
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Zhuang K, Wang J, Jiao B, Chen C, Zhang J, Ma N, Meng Q. WHIRLY1 maintains leaf photosynthetic capacity in tomato by regulating the expression of RbcS1 under chilling stress. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3653-3663. [PMID: 32189001 DOI: 10.1093/jxb/eraa145] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Rubisco, which consists of eight large subunits (RBCLs) and eight small subunits (RBCSs), is a major photosynthetic enzyme that is sensitive to chilling stress. However, it is largely unclear how plants maintain high Rubisco content under low temperature conditions. Here, we report that tomato WHIRLY1 (SlWHY1) positively regulates the Rubisco level under chilling stress by directly binding to the promoter region of SlRbcS1, resulting in the activation of SlRbcS1 expression. SlRbcS1-overexpressing lines had higher Rubisco contents and were more resistant to chilling stress compared with the wild type. Quantitative real-time PCR analyses showed that, among the five RbcS genes, only SlRbcS1 expression is up-regulated by chilling treatment. These results indicate that SlWHIRLY1 specifically enhances the levels of SlRbcS1 and confers tolerance to chilling stress. The amino acid sequence of SlRBCS1 shows 92.67% identity with those of another two RBCS proteins and three residues are specifically found in SlRBCS1. However, mutation of these residues to alanine in SlRBCS1 does not influence its function during cold adaptation. Thus, we conclude that high levels of Rubisco, but not the specific residues in SlRBCS1, play important roles in tolerance to chilling stress in tomato.
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Affiliation(s)
- Kunyang Zhuang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, Shandong, China
| | - Jieyu Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, Shandong, China
| | - Baozhen Jiao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, Shandong, China
| | - Chong Chen
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, Shandong, China
| | - Junjie Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, Shandong, China
| | - Nana Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, Shandong, China
| | - Qingwei Meng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai' an, Shandong, China
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48
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Jiang T, Moriwaki K, Kobayashi O, Ishimura K, Danielache SO, Nanbu S. Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO. J Comput Chem 2020; 41:1116-1123. [PMID: 31984537 DOI: 10.1002/jcc.26156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/21/2019] [Accepted: 01/11/2020] [Indexed: 11/10/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) fixes atmospheric carbon dioxide into bioavailable sugar molecules. It is also well known that a kinetic isotope effect (KIE; CO2 carbon atoms) accompanies the carboxylation process. To describe the reaction and the KIE α, two different types of molecular dynamics (MD) simulations (ab initio MD and classical MD) have been performed with an Own N-layered Integrated molecular Orbitals and molecular Mechanics (ONIOM)-hybrid model. A channel structure for CO2 transport has been observed during the MD simulation in RubisCO, and assuming the reaction path from the inlet to the product through the coordinate complex with Mg2+ , simulations have been performed on several molecular configuration models fixing several distances between CO2 and ribulose-1,5-bisphosphate along the channel. Free energy analysis and diffusion coefficient analysis have been evaluated for different phases of the process. It is confirmed that the isotopic fractionation effect for CO2 containing either 13 C or 12 C would appear through the transiting path in the channel structure identified in RubisCO. The estimated isotope fractionation constant was quite close to the experimental value.
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Affiliation(s)
- Tianlong Jiang
- Department of Materials and Life Sciences, Sophia University, Tokyo, Japan
| | - Kenta Moriwaki
- Department of Materials and Life Sciences, Sophia University, Tokyo, Japan
| | - Osamu Kobayashi
- Department of Materials and Life Sciences, Sophia University, Tokyo, Japan.,Department of Nanosystem Science, Yokohama City University, Yokohama, Japan
| | - Kazuya Ishimura
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Japan
| | | | - Shinkoh Nanbu
- Department of Materials and Life Sciences, Sophia University, Tokyo, Japan
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49
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Iñiguez C, Capó-Bauçà S, Niinemets Ü, Stoll H, Aguiló-Nicolau P, Galmés J. Evolutionary trends in RuBisCO kinetics and their co-evolution with CO 2 concentrating mechanisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:897-918. [PMID: 31820505 DOI: 10.1111/tpj.14643] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/15/2019] [Accepted: 11/27/2019] [Indexed: 05/19/2023]
Abstract
RuBisCO-catalyzed CO2 fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5-bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen-rich atmosphere promoted the appearance of CO2 concentrating mechanisms (CCMs) and/or the evolution of a more CO2 -specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO2 /O2 concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co-evolution of RuBisCO and CCMs. Trade-offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO2 specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.
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Affiliation(s)
- Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
- Estonian Academy of Sciences, Kohtu 6, 10130, Tallinn, Estonia
| | - Heather Stoll
- Department of Earth Sciences, ETH Zürich, Sonnegstrasse 5, 8092, Zürich, Switzerland
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
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50
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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: 92] [Impact Index Per Article: 23.0] [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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