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Zhen Y, Zhu J, Yue M, Mi T. Impacts of phosphoenolpyruvate carboxylase gene silencing on photosynthetic efficiency and carbon fixation in Skeletonema costatum. Gene 2024; 933:148915. [PMID: 39244167 DOI: 10.1016/j.gene.2024.148915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024]
Abstract
Diatoms play a crucial role in marine primary productivity through carbon fixation, which is essential for understanding the operation of marine biological pumps and carbon sinks. This study focuses on the phosphoenolpyruvate carboxylase (PEPC) gene, a key enzyme in the carbon assimilation pathway of diatoms, by investigating the consequences of its silencing in Skeletonemacostatum. Through this approach, we aimed to clarify the distinct contributions of PEPC to the overall carbon fixation process. The mutant strains of S. costatum were subjected to thorough analysis to identify any shifts in physiological behavior, alterations in the gene expression of key carbon-fixing enzymes, and changes in the associated enzyme activities. Notably, the inhibition of the PEPC gene did not significantly affect the growth rate of S. costatum; however, it did have a notable impact on the photosynthetic apparatus, as evidenced by a reduction in the maximal electron transport rate and a decline in light utilization efficiency. A significant decrease was observed in both the enzymatic activity and gene expression of PEPCase. This down-regulation also affected other enzymes integral to the carbon fixation pathway, such as phosphoenolpyruvate carboxykinase and pyruvate-phosphate dikinase, indicating a wider metabolic perturbation. In contrast, the expression and activity of the Rubisco enzyme suggested that some facets of carbon fixation remained resilient. Furthermore, the substantial upregulation of carbonic anhydrase expression and activity probably represented an adaptive mechanism to sustain the inorganic carbon supply necessary for the carboxylation process of Rubisco. This research not only underscores the pivotal role of the PEPC gene in the carbon fixation of S. costatum but also expands our comprehension of carbon fixation mechanisms in diatoms.
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Affiliation(s)
- Yu Zhen
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China.
| | - Jiwei Zhu
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Ming Yue
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Tiezhu Mi
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
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Carrizosa-Carbajal EI, González-Segura L, Muñoz-Clares RA. Two new T-state crystal structures of maize C 4-phosphoenolpyruvate carboxylase reveal and suggest novel structural features of the allosteric regulation and carboxylation step. Int J Biol Macromol 2024; 279:135134. [PMID: 39208913 DOI: 10.1016/j.ijbiomac.2024.135134] [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: 06/09/2024] [Revised: 08/08/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
To get a deeper understanding of the structural bases of the allosteric transition between T and R states of plant and bacterial phosphoenolpyruvate carboxylases (PEPCs), we obtained the first T-state crystal structures of the maize photosynthetic PEPC (ZmPEPC-C4) and exhaustively compared them with the previously reported R-state ZmPEPC-C4 and other T-state structures. We identified previously unrecognized significant conformational changes in the T state: that of the α8-α9 loop, which connects the two kinds of activator allosteric sites with the active site, the conversion of the α30 helix into a 310 helix, leading to the disorganization of the active site lid and activators allosteric sites, and the closure of the inhibitor allosteric-site lid. Additionally, we identified previously overlooked, highly conserved residues of potential interest in the allosteric transition, including two histidines whose protonation might stabilize the T state. The crystal structures reported here also suggest similar tetrameric quaternary arrangements of PEPC enzymes in the R and T states, and the location of the bicarbonate binding site, as well as the conformational changes required for the carboxylation step. Our findings and working hypothesis advance the understanding of the structural features of the allosteric PEPC enzymes and provide a foundation for future experiments.
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Affiliation(s)
- Esdras I Carrizosa-Carbajal
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Lilian González-Segura
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico.
| | - Rosario A Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico.
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3
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Luo Y, Wang X, Zhang D, Zhan L, Li D, Li C, Cong C, Cai H. Overexpression of phosphoenolpyruvate carboxylase kinase gene MsPPCK1 from Medicago sativa L. increased alkali tolerance of alfalfa by enhancing photosynthetic efficiency and promoting nodule development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108764. [PMID: 38879983 DOI: 10.1016/j.plaphy.2024.108764] [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: 03/14/2024] [Revised: 05/02/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024]
Abstract
The phosphoenolpyruvate carboxylase kinase of Medicago sativa L. (MsPPCK1) modulates the phosphorylation status and activity of the C4 pathway phosphoenolpyruvate carboxylase enzyme, which is pivotal for photosynthetic carbon assimilation in plants. This study investigated the role of MsPPCK1 in alfalfa by creating transgenic plants overexpressing MsPPCK1 under the control of the CaMV35S promoter. The enhanced alkali tolerance of transgenic plants indicated an important role of MsPPCK1 gene in regulating plant alkali tolerance. Transgenic plants exhibited heightened antioxidant activity (SOD, POD, and CAT), reduced MDA, H2O2, OFR and REC% content, increased activity of key photosynthetic enzymes (PEPC, PPDK, NADP-ME, and NADP-MDH), and enhanced photosynthetic parameters (Pn, E, Gs, and Ci). Moreover, MsPPCK1 overexpression increased the content of organic acids (oxaloacetic, malic, citric, and succinic acids) in the plants. The upregulation of MsPPCK1 under rhizobial inoculation showcased its other role in nodule development. In transgenic plants, MsDMI2, MsEnod12, and MsNODL4 expression increased, facilitating root nodule development and augmenting plant nodulation. Accelerated root nodule growth positively influences plant growth and yield and enhances alfalfa resistance to alkali stress. This study highlights the pivotal role of MsPPCK1 in fortifying plant alkali stress tolerance and improving yield, underscoring its potential as a key genetic target for developing alkali-tolerant and high-yielding alfalfa varieties.
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Affiliation(s)
- Yaqin Luo
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Xinsheng Wang
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Depeng Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Lifeng Zhan
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Donghuan Li
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Chunxin Li
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Chunlong Cong
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Hua Cai
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China.
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Chéron N. Binding Sites of Bicarbonate in Phosphoenolpyruvate Carboxylase. J Chem Inf Model 2024; 64:3375-3385. [PMID: 38533570 DOI: 10.1021/acs.jcim.3c01830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is used in plant metabolism for fruit maturation or seed development as well as in the C4 and crassulacean acid metabolism (CAM) mechanisms in photosynthesis, where it is used for the capture of hydrated CO2 (bicarbonate). To find the yet unknown binding site of bicarbonate in this enzyme, we have first identified putative binding sites with nonequilibrium molecular dynamics simulations and then ranked these sites with alchemical free energy calculations with corrections of computational artifacts. Fourteen pockets where bicarbonate could bind were identified, with three having realistic binding free energies with differences with the experimental value below 1 kcal/mol. One of these pockets is found far from the active site at 14 Å and predicted to be an allosteric binding site. In the two other binding sites, bicarbonate is in direct interaction with the magnesium ion; neither sequence alignment nor the study of mutant K606N allowed to discriminate between these two pockets, and both are good candidates as the binding site of bicarbonate in phosphoenolpyruvate carboxylase.
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Affiliation(s)
- Nicolas Chéron
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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Xia K, Wu Q, Yang Y, Liu Q, Wang Z, Zhao Z, Li J, He J, Chai S, Qiu S. Drought Stress Induced Different Response Mechanisms in Three Dendrobium Species under Different Photosynthetic Pathways. Int J Mol Sci 2024; 25:2731. [PMID: 38473979 DOI: 10.3390/ijms25052731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/16/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
Many Dendrobium species, which hold a high status and value in traditional Chinese medicine, grow on barks and rocks in the wild, often encountering harsh environments and facing droughts. However, the molecular mechanisms underlying the shift in the photosynthetic pathway induced by drought remain unclear. To address this issue, three Dendrobium species with different photosynthetic pathways were selected for sequencing and transcriptome data analysis after drought treatment. The findings included 134.43 GB of sequencing data, with numerous Differentially Expressed Genes (DEGs) exhibiting different response mechanisms under drought stress. Gene Ontology (GO)-KEGG-based enrichment analysis of DEGs revealed that metabolic pathways contributed to drought tolerance and alterations in photosynthetic pathways. Phosphoenolpyruvate Carboxylase (PEPC) was subjected to phylogenetic tree construction, sequence alignment, and domain analysis. Under drought stress, variations were observed in the PEPC gene structure and expression among different Dendrobium species; the upregulation of Dc_gene2609 expression may be caused by dof-miR-384, which resulted in the shift from C3 photosynthesis to CAM, thereby improving drought tolerance in Dendrobium. This study revealed the expression patterns and roles of PEPC genes in enhancing plant drought tolerance and will provide an important basis for in-depth research on Dendrobium's adaptation mechanisms in arid environments.
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Affiliation(s)
- Ke Xia
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Qiaofen Wu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Yanni Yang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Qiao Liu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Zaihua Wang
- Guangdong Provincial Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhiguo Zhao
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jinxiang He
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Shengfeng Chai
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
| | - Shuo Qiu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences/Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guilin 541006, China
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Wang S, Chen L, Li S, Hu F. Uncovering proteome variations and concomitant quality changes of differently drying-treated rape (Brassica napus) bee pollen by label-free quantitative proteomics. Food Chem 2024; 434:137559. [PMID: 37748288 DOI: 10.1016/j.foodchem.2023.137559] [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: 05/26/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
Abstract
High moisture content of fresh bee pollen makes it difficult to preserve and thus makes drying a necessary process during the bee pollen production. Drying treatment will affect its quality and the effects of sun drying, hot-air drying and freeze drying on the proteome of rape (Brassica napus) bee pollen have been evaluated using label-free quantitative proteomics by liquid chromatography-tandem mass spectrometer (LC-MS/MS). A total of 8377 proteins are identified, among which the most abundant differential proteins were found in freeze drying-treated samples. Also freeze-drying treatment maximizes the content of antioxidant, antibacterial and anemic bioactive pollen protein. Besides, rape bee pollen is found to adjust its metabolism to protect itself during the drying process. These results can be favorable to evaluate the effects of drying treatment on the nutrition and function of processed rape bee pollen and insight into how rape bee pollen proteins respond to dehydration.
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Affiliation(s)
- Shuyue Wang
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Liang Chen
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shanshan Li
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fuliang Hu
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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7
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Li R, Gao X, Wu Y, Wei C, Li MH, Liu DK, Liu ZJ. Identification and Analysis of PEPC Gene Family Reveals Functional Diversification in Orchidaceae and the Regulation of Bacterial-Type PEPC. Int J Mol Sci 2024; 25:2055. [PMID: 38396732 PMCID: PMC10888551 DOI: 10.3390/ijms25042055] [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: 12/05/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) gene family plays a crucial role in both plant growth and response to abiotic stress. Approximately half of the Orchidaceae species are estimated to perform CAM pathway, and the availability of sequenced orchid genomes makes them ideal subjects for investigating the PEPC gene family in CAM plants. In this study, a total of 33 PEPC genes were identified across 15 orchids. Specifically, one PEPC gene was found in Cymbidium goeringii and Platanthera guangdongensis; two in Apostasia shenzhenica, Dendrobium chrysotoxum, D. huoshanense, Gastrodia elata, G. menghaiensis, Phalaenopsis aphrodite, Ph. equestris, and Pl. zijinensis; three in C. ensifolium, C. sinense, D. catenatum, D. nobile, and Vanilla planifolia. These PEPC genes were categorized into four subgroups, namely PEPC-i, PEPC-ii, and PEPC-iii (PTPC), and PEPC-iv (BTPC), supported by the comprehensive analyses of their physicochemical properties, motif, and gene structures. Remarkably, PEPC-iv contained a heretofore unreported orchid PEPC gene, identified as VpPEPC4. Differences in the number of PEPC homolog genes among these species were attributed to segmental duplication, whole-genome duplication (WGD), or gene loss events. Cis-elements identified in promoter regions were predominantly associated with light responsiveness, and circadian-related elements were observed in each PEPC-i and PEPC-ii gene. The expression levels of recruited BTPC, VpPEPC4, exhibited a lower expression level than other VpPEPCs in the tested tissues. The expression analyses and RT-qPCR results revealed diverse expression patterns in orchid PEPC genes. Duplicated genes exhibited distinct expression patterns, suggesting functional divergence. This study offered a comprehensive analysis to unveil the evolution and function of PEPC genes in Orchidaceae.
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Affiliation(s)
- Ruyi Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Xuyong Gao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Yuwei Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Chunyi Wei
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Yamaga-Hatakeyama Y, Okutani M, Hatakeyama Y, Yabiku T, Yukawa T, Ueno O. Photosynthesis and leaf structure of F1 hybrids between Cymbidium ensifolium (C3) and C. bicolor subsp. pubescens (CAM). ANNALS OF BOTANY 2023; 132:895-907. [PMID: 36579478 PMCID: PMC10799985 DOI: 10.1093/aob/mcac157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/17/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS The introduction of crassulacean acid metabolism (CAM) into C3 crops has been considered as a means of improving water-use efficiency. In this study, we investigated photosynthetic and leaf structural traits in F1 hybrids between Cymbidium ensifolium (female C3 parent) and C. bicolor subsp. pubescens (male CAM parent) of the Orchidaceae. METHODS Seven F1 hybrids produced through artificial pollination and in vitro culture were grown in a greenhouse with the parent plants. Structural, biochemical and physiological traits involved in CAM in their leaves were investigated. KEY RESULTS Cymbidium ensifolium accumulated very low levels of malate without diel fluctuation, whereas C. bicolor subsp. pubescens showed nocturnal accumulation and diurnal consumption of malate. The F1s also accumulated malate at night, but much less than C. bicolor subsp. pubescens. This feature was consistent with low nocturnal fixation of atmospheric CO2 in the F1s. The δ13C values of the F1s were intermediate between those of the parents. Leaf thickness was thicker in C. bicolor subsp. pubescens than in C. ensifolium, and those of the F1s were more similar to that of C. ensifolium. This was due to the difference in mesophyll cell size. The chloroplast coverage of mesophyll cell perimeter adjacent to intercellular air spaces of C. bicolor subsp. pubescens was lower than that of C. ensifolium, and that of the F1s was intermediate between them. Interestingly, one F1 had structural and physiological traits more similar to those of C. bicolor subsp. pubescens than the other F1s. Nevertheless, all F1s contained intermediate levels of phosphoenolpyruvate carboxylase but as much pyruvate, Pi dikinase as C. bicolor subsp. pubescens. CONCLUSIONS CAM traits were intricately inherited in the F1 hybrids, the level of CAM expression varied widely among F1 plants, and the CAM traits examined were not necessarily co-ordinately transmitted to the F1s.
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Affiliation(s)
| | - Masamitsu Okutani
- School of Agriculture, Kyushu University, Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yuto Hatakeyama
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takayuki Yabiku
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Museum of Nature and Science, Tsukuba, Ibaraki 305-0005, Japan
| | - Osamu Ueno
- Faculty of Agriculture, Kyushu University, Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Jiang A, Liu J, Gao W, Ma R, Zhang J, Zhang X, Du C, Yi Z, Fang X, Zhang J. Transcriptomic and Metabolomic Analyses Reveal the Key Genes Related to Shade Tolerance in Soybean. Int J Mol Sci 2023; 24:14230. [PMID: 37762532 PMCID: PMC10531609 DOI: 10.3390/ijms241814230] [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: 07/28/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Soybean (Glycine max) is an important crop, rich in proteins, vegetable oils and several other phytochemicals, which is often affected by light during growth. However, the specific regulatory mechanisms of leaf development under shade conditions have yet to be understood. In this study, the transcriptome and metabolome sequencing of leaves from the shade-tolerant soybean 'Nanxiadou 25' under natural light (ND1) and 50% shade rate (SHND1) were carried out, respectively. A total of 265 differentially expressed genes (DEGs) were identified, including 144 down-regulated and 121 up-regulated genes. Meanwhile, KEGG enrichment analysis of DEGs was performed and 22 DEGs were significantly enriched in the top five pathways, including histidine metabolism, riboflavin metabolism, vitamin B6 metabolism, glycerolipid metabolism and cutin, suberine and wax biosynthesis. Among all the enrichment pathways, the most DEGs were enriched in plant hormone signaling pathways with 19 DEGs being enriched. Transcription factors were screened out and 34 differentially expressed TFs (DETFs) were identified. Weighted gene co-expression network analysis (WGCNA) was performed and identified 10 core hub genes. Combined analysis of transcriptome and metabolome screened out 36 DEGs, and 12 potential candidate genes were screened out and validated by quantitative real-time polymerase chain reaction (qRT-PCR) assay, which may be related to the mechanism of shade tolerance in soybean, such as ATP phosphoribosyl transferase (ATP-PRT2), phosphocholine phosphatase (PEPC), AUXIN-RESPONSIVE PROTEIN (IAA17), PURPLE ACID PHOSPHATASE (PAP), etc. Our results provide new knowledge for the identification and function of candidate genes regulating soybean shade tolerance and provide valuable resources for the genetic dissection of soybean shade tolerance molecular breeding.
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Affiliation(s)
- Aohua Jiang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jiaqi Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Weiran Gao
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ronghan Ma
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jijun Zhang
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Xiaochun Zhang
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Chengzhang Du
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Xiaomei Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
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Zhang T, Peng JT, Klair A, Dickinson AJ. Non-canonical and developmental roles of the TCA cycle in plants. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102382. [PMID: 37210789 PMCID: PMC10524895 DOI: 10.1016/j.pbi.2023.102382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/23/2023]
Abstract
Over recent years, our understanding of the tricarboxylic acid cycle (TCAC) in living organisms has expanded beyond its canonical role in cellular energy production. In plants, TCAC metabolites and related enzymes have important roles in physiology, including vacuolar function, chelation of metals and nutrients, photorespiration, and redox regulation. Research in other organisms, including animals, has demonstrated unexpected functions of the TCAC metabolites in a number of biological processes, including signaling, epigenetic regulation, and cell differentiation. Here, we review the recent progress in discovery of non-canonical roles of the TCAC. We then discuss research on these metabolites in the context of plant development, with a focus on research related to tissue-specific functions of the TCAC. Additionally, we review research describing connections between TCAC metabolites and phytohormone signaling pathways. Overall, we discuss the opportunities and challenges in discovering new functions of TCAC metabolites in plants.
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Affiliation(s)
- Tao Zhang
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Jesus T Peng
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Amman Klair
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Alexandra J Dickinson
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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Punyasu N, Kalapanulak S, Saithong T. CO 2 recycling by phospho enolpyruvate carboxylase enables cassava leaf metabolism to tolerate low water availability. FRONTIERS IN PLANT SCIENCE 2023; 14:1159247. [PMID: 37229106 PMCID: PMC10204807 DOI: 10.3389/fpls.2023.1159247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023]
Abstract
Cassava is a staple crop that acclimatizes well to dry weather and limited water availability. The drought response mechanism of quick stomatal closure observed in cassava has no explicit link to the metabolism connecting its physiological response and yield. Here, a genome-scale metabolic model of cassava photosynthetic leaves (leaf-MeCBM) was constructed to study on the metabolic response to drought and stomatal closure. As demonstrated by leaf-MeCBM, leaf metabolism reinforced the physiological response by increasing the internal CO2 and then maintaining the normal operation of photosynthetic carbon fixation. We found that phosphoenolpyruvate carboxylase (PEPC) played a crucial role in the accumulation of the internal CO2 pool when the CO2 uptake rate was limited during stomatal closure. Based on the model simulation, PEPC mechanistically enhanced drought tolerance in cassava by providing sufficient CO2 for carbon fixation by RuBisCO, resulting in high production of sucrose in cassava leaves. The metabolic reprogramming decreased leaf biomass production, which may lead to maintaining intracellular water balance by reducing the overall leaf area. This study indicates the association of metabolic and physiological responses to enhance tolerance, growth, and production of cassava in drought conditions.
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Affiliation(s)
- Nattharat Punyasu
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
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12
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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13
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Behera D, Swain A, Karmakar S, Dash M, Swain P, Baig MJ, Molla KA. Overexpression of Setaria italica phosphoenolpyruvate carboxylase gene in rice positively impacts photosynthesis and agronomic traits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:169-181. [PMID: 36417836 DOI: 10.1016/j.plaphy.2022.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
C4 plants have the inherent capacity to concentrate atmospheric CO2 in the vicinity of RuBisCo, thereby increasing carboxylation, and inhibiting photorespiration. Carbonic anhydrase (CA), the first enzyme of C4 photosynthesis, converts atmospheric CO2 to HCO3-, which is utilized by PEPC to produce C4 acids. Bioengineering of C4 traits into C3 crops is an attractive strategy to increase photosynthesis and water use efficiency. In the present study, we isolated the PEPC gene from the C4 plant Setaria italica and transferred it to C3 rice. Overexpression of SiPEPC resulted in a 2-6-fold increment in PEPC enzyme activity in transgenic lines with respect to non-transformed control. Photosynthetic efficiency was enhanced in transformed plants, which was associated with increased ФPSII, ETR, lower NPQ, and higher chlorophyll accumulation. Water use efficiency was increased by 16-22% in PEPC transgenic rice lines. Increased PEPC activity enhanced quantum yield and carboxylation efficiency of PEPC transgenic lines. Transgenic plants exhibited higher light saturation photosynthesis rate and lower CO2 compensation point, as compared to non-transformed control. An increase in net photosynthesis increased the yield by (23-28.9%) and biomass by (24.1-29%) in transgenic PEPC lines. Altogether, our findings indicate that overexpression of C4-specific SiPEPC enzyme is able to enhance photosynthesis and related parameters in transgenic rice.
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Affiliation(s)
| | - Alaka Swain
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Subhasis Karmakar
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Manaswini Dash
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Padmini Swain
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Mirza J Baig
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India.
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14
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The Production of Pyruvate in Biological Technology: A Critical Review. Microorganisms 2022; 10:microorganisms10122454. [PMID: 36557706 PMCID: PMC9783380 DOI: 10.3390/microorganisms10122454] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Pyruvic acid has numerous applications in the food, chemical, and pharmaceutical industries. The high costs of chemical synthesis have prevented the extensive use of pyruvate for many applications. Metabolic engineering and traditional strategies for mutation and selection have been applied to microorganisms to enhance their ability to produce pyruvate. In the past decades, different microbial strains were generated to enhance their pyruvate production capability. In addition to the development of genetic engineering and metabolic engineering in recent years, the metabolic transformation of wild-type yeast, E. coli, and so on to produce high-yielding pyruvate strains has become a hot spot. The strategy and the understanding of the central metabolism directly related to pyruvate production could provide valuable information for improvements in fermentation products. One of the goals of this review was to collect information regarding metabolically engineered strains and the microbial fermentation processes used to produce pyruvate in high yield and productivity.
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15
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Shen S, Li N, Wang Y, Zhou R, Sun P, Lin H, Chen W, Yu T, Liu Z, Wang Z, Tan X, Zhu C, Feng S, Zhang Y, Song X. High-quality ice plant reference genome analysis provides insights into genome evolution and allows exploration of genes involved in the transition from C3 to CAM pathways. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2107-2122. [PMID: 35838009 PMCID: PMC9616530 DOI: 10.1111/pbi.13892] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/19/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
Ice plant (Mesembryanthemum crystallinum), a member of the Aizoaceae family, is a typical halophyte crop and a model plant for studying the mechanism of transition from C3 photosynthesis to crassulacean acid metabolism (CAM). Here, we report a high-quality chromosome-level ice plant genome sequence. This 98.05% genome sequence is anchored to nine chromosomes, with a total length of 377.97 Mb and an N50 scaffold of 40.45 Mb. Almost half of the genome (48.04%) is composed of repetitive sequences, and 24 234 genes have been annotated. Subsequent to the ancient whole-genome triplication (WGT) that occurred in eudicots, there has been no recent whole-genome duplication (WGD) or WGT in ice plants. However, we detected a novel WGT event that occurred in the same order in Simmondsia chinensis, which was previously overlooked. Our findings revealed that ice plants have undergone chromosome rearrangements and gene removal during evolution. Combined with transcriptome and comparative genomic data and expression verification, we identified several key genes involved in the CAM pathway and constructed a comprehensive network. As the first genome of the Aizoaceae family to be released, this report will provide a rich data resource for comparative and functional genomic studies of Aizoaceae, especially for studies on salt tolerance and C3-to-CAM transitions to improve crop yield and resistance.
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Affiliation(s)
- Shaoqin Shen
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Nan Li
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Yujie Wang
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Rong Zhou
- Department of Food ScienceAarhus UniversityAarhusDenmark
| | - Pengchuan Sun
- Key Laboratory for Bio‐Resource and Eco‐Environment of Ministry of Education, College of Life SciencesSichuan UniversityChengduChina
| | - Hao Lin
- School of Life Science and Technology and Center for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Wei Chen
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
- Innovative Institute of Chinese Medicine and PharmacyChengdu University of Traditional Chinese MedicineChengduChina
| | - Tong Yu
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Zhuo Liu
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Zhiyuan Wang
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Xiao Tan
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Changping Zhu
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Shuyan Feng
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Yu Zhang
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Xiaoming Song
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
- School of Life Science and Technology and Center for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
- Food Science and Technology DepartmentUniversity of Nebraska‐LincolnLincolnNebraskaUSA
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16
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Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proc Natl Acad Sci U S A 2022; 119:e2200014119. [PMID: 36067300 PMCID: PMC9477243 DOI: 10.1073/pnas.2200014119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.
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17
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Conservation and Divergence of Phosphoenolpyruvate Carboxylase Gene Family in Cotton. PLANTS 2022; 11:plants11111482. [PMID: 35684256 PMCID: PMC9182757 DOI: 10.3390/plants11111482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is an important enzyme in plants, which regulates carbon flow through the TCA cycle and controls protein and oil biosynthesis. Although it is important, there is little research on PEPC in cotton, the most important fiber crop in the world. In this study, a total of 125 PEPCs were identified in 15 Gossypium genomes. All PEPC genes in cotton are divided into six groups and each group generally contains one PEPC member in each diploid cotton and two in each tetraploid cotton. This suggests that PEPC genes already existed in cotton before their divergence. There are additional PEPC sub-groups in other plant species, suggesting the different evolution and natural selection during different plant evolution. PEPC genes were independently evolved in each cotton sub-genome. During cotton domestication and evolution, certain PEPC genes were lost and new ones were born to face the new environmental changes and human being needs. The comprehensive analysis of collinearity events and selection pressure shows that genome-wide duplication and fragment duplication are the main methods for the expansion of the PEPC family, and they continue to undergo purification selection during the evolutionary process. PEPC genes were widely expressed with temporal and spatial patterns. The expression patterns of PEPC genes were similar in G. hirsutum and G. barbadense with a slight difference. PEPC2A and 2D were highly expressed in cotton reproductive tissues, including ovule and fiber at all tested developmental stages in both cultivated cottons. However, PEPC1A and 1D were dominantly expressed in vegetative tissues. Abiotic stress also induced the aberrant expression of PEPC genes, in which PEPC1 was induced by both chilling and salinity stresses while PEPC5 was induced by chilling and drought stresses. Each pair (A and D) of PEPC genes showed the similar response to cotton development and different abiotic stress, suggesting the similar function of these PEPCs no matter their origination from A or D sub-genome. However, some divergence was also observed among their origination, such as PEPC5D was induced but PEPC5A was inhibited in G. barbadense during drought treatment, suggesting that a different organized PEPC gene may evolve different functions during cotton evolution. During cotton polyploidization, the homologues genes may refunction and play different roles in different situations.
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18
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Luo S, Lin PP, Nieh LY, Liao GB, Tang PW, Chen C, Liao JC. A cell-free self-replenishing CO2-fixing system. Nat Catal 2022. [DOI: 10.1038/s41929-022-00746-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AbstractBiological CO2 fixation is so far the most effective means for CO2 reduction at scale and accounts for most of the CO2 fixed on Earth. Through this process, carbon is fixed in cellular components and biomass during organismal growth. To uncouple CO2 fixation from growth and cellular regulation, cell-free CO2 fixation systems represent an alternative approach since the rate can be independently manipulated. Here we designed an oxygen-insensitive, self-replenishing CO2 fixation system with opto-sensing. The system comprises a synthetic reductive glyoxylate and pyruvate synthesis (rGPS) cycle and the malyl-CoA-glycerate (MCG) pathway to produce acetyl-coenzyme A (CoA), pyruvate and malate from CO2, which are also intermediates in the cycle. We solved various problems associated with the in vitro system, and implemented opto-sensing modules to control the regeneration of cofactors. We accomplished sustained operation for 6 hours with a CO2-fixing rate comparable to or greater than typical CO2 fixation rates of photosynthetic or lithoautotrophic organisms.
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19
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Shu JP, Yan YH, Wang RJ. Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C 4 and crassulacean acid metabolism plants. PeerJ 2022; 10:e12828. [PMID: 35116203 PMCID: PMC8784020 DOI: 10.7717/peerj.12828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/03/2022] [Indexed: 01/10/2023] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.
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Affiliation(s)
- Jiang-Ping Shu
- Key laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yue-Hong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Jiang Wang
- Key laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China,University of Chinese Academy of Sciences, Beijing, China
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20
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Multiple conformations in solution of the maize C 4-phosphoenolpyruvate carboxylase isozyme. Heliyon 2021; 7:e08464. [PMID: 34888425 PMCID: PMC8637149 DOI: 10.1016/j.heliyon.2021.e08464] [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: 07/24/2021] [Revised: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
The photosynthetic phosphoenolpyruvate carboxylase isozyme from C4 plants (PEPC-C4) has a complex allosteric regulation, involving positive cooperativity in binding the substrate phosphoenolpyruvate as well as positive and negative allosteric effectors. Besides the proposed R- and T-states, previous kinetic results suggested functionally relevant different R-states of the maize enzyme (ZmPEPC-C4) elicited by PEP or its two kinds of activators, glucose 6-phosphate or glycine. To detect these different R-state conformations, we used as conformational probes the fluorescence of 8-anilino-1-naphthalene sulfonate (ANS), near-UV circular dichroism (CD) spectroscopy, and limited proteolysis by trypsin. Phosphoenolpyruvate and malate binding caused distinct concentration-dependent fluorescence changes of ZmPEPC-C4/ANS, suggesting that they elicited conformational states different from that of the free enzyme, while glucose 6-phosphate or glycine binding did not produce fluorescence changes. Differences were also observed in the near UV CD spectra of the enzyme, free or complexed with its substrate or allosteric effectors. Additionally, differences in the trypsin-digestion fragmentation patterns, as well as in the susceptibility of the free and complexed enzyme to digestion and digestion-provoked loss of activity, provided evidence of several ZmPEPC-C4 conformations in solution elicited by the substrate and the allosteric effectors. Using the already reported ZmPEPC-C4 crystal structures and bioinformatics methods, we predicted that the most probable trypsin-cleavage sites are located in superficial flexible regions, which seems relevant for the protein dynamics underlying the function and allosteric regulation of this enzyme. Together, our findings agree with previous kinetic results, shed light on this enzyme's complex allosteric regulation, and place ZmPEPC-C4 in the growing list of allosteric enzymes possessing an ensemble of closely related R-state conformations. PEP or malate binding produce distinct changes in ZmPEPC-C4/ANS fluorescence. Different near-UV CD spectra of the free enzyme or of the enzyme complexes were observed. PEP or effectors binding produce distinctive ZmPEPC-C4 trypsin-fragmentation patterns. Our results support several ligand-induced ZmPEPC-C4 conformational states in solution. Predicted trypsin-cleavage sites are at flexible loops, which probably participate in ZmPEPC-C4 function and regulation.
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21
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Jia YL, Geng SS, Du F, Xu YS, Wang LR, Sun XM, Wang QZ, Li Q. Progress of metabolic engineering for the production of eicosapentaenoic acid. Crit Rev Biotechnol 2021; 42:838-855. [PMID: 34779326 DOI: 10.1080/07388551.2021.1971621] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Eicosapentaenoic Acid (EPA) is an essential ω-3 polyunsaturated fatty acid for human health. Currently, high-quality EPA production is largely dependent on the extraction of fish oil, but this unsustainable approach cannot meet its rising market demand. Biotechnological approaches for EPA production from microorganisms have received increasing attention due to their suitability for large-scale production and independence of the seasonal or climate restrictions. This review summarizes recent research on different microorganisms capable of producing EPA, such as microalgae, bacteria, and fungi, and introduces the different EPA biosynthesis pathways. Notably, some novel engineering strategies have been applied to endow and improve the abilities of microorganisms to synthesize EPA, including the construction and optimization of the EPA biosynthesis pathway, an increase in the acetyl-CoA pool supply, the increase of NADPH and the inhibition of competing pathways. This review aims to provide an updated summary of EPA production.
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Affiliation(s)
- Yu-Lei Jia
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Shan-Shan Geng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Fei Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ying-Shuang Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ling-Ru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Qing-Zhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, People's Republic of China
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22
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Hurtado-Gaitán E, Sellés-Marchart S, Hartwell J, Martínez-Esteso MJ, Bru-Martínez R. Down-Regulation of Phosphoenolpyruvate Carboxylase Kinase in Grapevine Cell Cultures and Leaves Is Linked to Enhanced Resveratrol Biosynthesis. Biomolecules 2021; 11:1641. [PMID: 34827639 PMCID: PMC8615455 DOI: 10.3390/biom11111641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/02/2022] Open
Abstract
In grapevine, trans-Resveratrol (tR) is produced as a defence mechanism against stress or infection. tR is also considered to be important for human health, which increases its interest to the scientific community. Transcriptomic analysis in grapevine cell cultures treated with the defence response elicitor methyl-β-cyclodextrin (CD) revealed that both copies of PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) were down-regulated significantly. A role for PPCK in the defence response pathway has not been proposed previously. We therefore analysed the control of PPCK transcript levels in grapevine cell cultures and leaves elicited with CD. Moreover, phosphoenolpyruvate carboxylase (PPC), stilbene synthase (STS), and the transcription factors MYB14 and WRKY24, which are involved in the activation of STS transcription, were also analysed by RT-qPCR. The results revealed that under CD elicitation conditions PPCK down-regulation, increased stilbene production and loss of PPC activity occurs in both tissues. Moreover, STS transcripts were co-induced with MYB14 and WRKY24 in cell cultures and leaves. These genes have not previously been reported to respond to CD in grape leaves. Our findings thus support the hypothesis that PPCK is involved in diverting metabolism towards stilbene biosynthesis, both for in vitro cell culture and whole leaves. We thus provide new evidence for PEP being redirected between primary and secondary metabolism to support tR production and the stress response.
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Affiliation(s)
- Elías Hurtado-Gaitán
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - Susana Sellés-Marchart
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - James Hartwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK;
| | - Maria José Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
- Instituto de Investigación Sanitaria y Biomédica de Alicante ISABIAL-Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana FISABIO, 03010 Alicante, Spain
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Cao J, Cheng G, Wang L, Maimaitijiang T, Lan H. Genome-Wide Identification and Analysis of the Phosphoenolpyruvate Carboxylase Gene Family in Suaeda aralocaspica, an Annual Halophyte With Single-Cellular C 4 Anatomy. FRONTIERS IN PLANT SCIENCE 2021; 12:665279. [PMID: 34527003 PMCID: PMC8435749 DOI: 10.3389/fpls.2021.665279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) plays pivotal roles in the carbon fixation of photosynthesis and a variety of metabolic and stress pathways. Suaeda aralocaspica belongs to a single-cellular C4 species and carries out a photosynthetic pathway in an unusually elongated chlorenchyma cell, which is expected to have PEPCs with different characteristics. To identify the different isoforms of PEPC genes in S. aralocaspica and comparatively analyze their expression and regulation patterns as well as the biochemical and enzymatic properties in this study, we characterized a bacterial-type PEPC (BTPC; SaPEPC-4) in addition to the two plant-type PEPCs (PTPCs; SaPEPC-1 and SaPEPC-2) using a genome-wide identification. SaPEPC-4 presented a lower expression level in all test combinations with an unknown function; two SaPTPCs showed distinct subcellular localizations and different spatiotemporal expression patterns but positively responded to abiotic stresses. Compared to SaPEPC-2, the expression of SaPEPC-1 specifically in chlorenchyma cell tissues was much more active with the progression of development and under various stresses, particularly sensitive to light, implying the involvement of SaPEPC-1 in a C4 photosynthetic pathway. In contrast, SaPEPC-2 was more like a non-photosynthetic PEPC. The expression trends of two SaPTPCs in response to light, development, and abiotic stresses were also matched with the changes in PEPC activity in vivo (native) or in vitro (recombinant), and the biochemical properties of the two recombinant SaPTPCs were similar in response to various effectors while the catalytic efficiency, substrate affinity, and enzyme activity of SaPEPC-2 were higher than that of SaPEPC-1 in vitro. All the different properties between these two SaPTPCs might be involved in transcriptional (e.g., specific cis-elements), posttranscriptional [e.g., 5'-untranslated region (5'-UTR) secondary structure], or translational (e.g., PEPC phosphorylation/dephosphorylation) regulatory events. The comparative studies on the different isoforms of the PEPC gene family in S. aralocaspica may help to decipher their exact role in C4 photosynthesis, plant growth/development, and stress resistance.
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Gandullo J, Álvarez R, Feria AB, Monreal JA, Díaz I, Vidal J, Echevarría C. A conserved C-terminal peptide of sorghum phosphoenolpyruvate carboxylase promotes its proteolysis, which is prevented by Glc-6P or the phosphorylation state of the enzyme. PLANTA 2021; 254:43. [PMID: 34355288 PMCID: PMC8342391 DOI: 10.1007/s00425-021-03692-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
MAIN CONCLUSION A synthetic peptide from the C-terminal end of C4-phosphoenolpyruvate carboxylase is implicated in the proteolysis of the enzyme, and Glc-6P or phosphorylation of the enzyme modulate this effect. Phosphoenolpyruvate carboxylase (PEPC) is a cytosolic, homotetrameric enzyme that performs a variety of functions in plants. Among them, it is primarily responsible for CO2 fixation in the C4 photosynthesis pathway (C4-PEPC). Here we show that proteolysis of C4-PEPC by cathepsin proteases present in a semi-purified PEPC fraction was enhanced by the presence of a synthetic peptide containing the last 19 amino acids from the C-terminal end of the PEPC subunit (pC19). Threonine (Thr)944 and Thr948 in the peptide are important requirements for the pC19 effect. C4-PEPC proteolysis in the presence of pC19 was prevented by the PEPC allosteric effector glucose 6-phosphate (Glc-6P) and by phosphorylation of the enzyme. The role of these elements in the regulation of PEPC proteolysis is discussed in relation to the physiological context.
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Affiliation(s)
- Jacinto Gandullo
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012, Seville, Spain
| | - Rosario Álvarez
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012, Seville, Spain
| | - Ana-Belén Feria
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012, Seville, Spain
| | - José-Antonio Monreal
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012, Seville, Spain
| | - Isabel Díaz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Autovía M40 (km 38), Pozuelo de Alarcón, 28034, Madrid, Spain
| | - Jean Vidal
- Institut de Biotechnologie des Plantes, UMR8618, Bâtiment 630, Université de Paris-Sud 11, 91405, Orsay, Cedex, France
| | - Cristina Echevarría
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012, Seville, Spain.
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Aslam M, Shehroz M, Ali F, Zia A, Pervaiz S, Shah M, Hussain Z, Nishan U, Zaman A, Afridi SG, Khan A. Chlamydia trachomatis core genome data mining for promising novel drug targets and chimeric vaccine candidates identification. Comput Biol Med 2021; 136:104701. [PMID: 34364258 DOI: 10.1016/j.compbiomed.2021.104701] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022]
Abstract
Chlamydia trachomatis is involved in most sexually transmitted diseases. The species has emerged as a major public health threat due to its multidrug-resistant capabilities, and new therapeutic target inferences have become indispensable to combat its pathogenesis. However, no commercial vaccine is yet available to treat the C. trachomatis infection. In this study, we used the publicly available complete genome sequences of C. trachomatis and performed comparative proteomics and reverse vaccinology analyses to explore novel drug and vaccine targets against this devastating pathogen. We identified 713 core proteins from 71 C. trachomatis complete genome sequences and prioritized them based on their cellular essentiality, virulence, and available antibiotic resistance. The analyses led to the identification of 16 pathogen-specific proteins with no resolved 3D structures, though holding significant druggable potential. The sequences of the three shortlisted candidates' membrane proteins were used for designing vaccine constructs. The antigenicity, toxicity, and solubility profile-based lead epitopes were prioritized for multi-epitope-based vaccine constructs in combination with specific linkers, PADRE sequences, and molecular adjuvants for immunogenicity enhancement. The molecular-level interactions of the prioritized vaccine construct with human immune cells HLA and TLR4/MD were validated by molecular docking and molecular dynamic simulation analyses. Furthermore, the cloning and expression potential of the lead vaccine construct was predicted in the E. coli cloning vector system. Additional testing and experimental validation of these multi-epitope constructs appear promising against C. trachomatis-mediated infection.
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Affiliation(s)
- Muneeba Aslam
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Shehroz
- Department of Biotechnology, Virtual University of Pakistan, Peshawar, Pakistan
| | - Fawad Ali
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Asad Zia
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Sadia Pervaiz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Punjab, Pakistan.
| | - Zahid Hussain
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Aqal Zaman
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Sahib Gul Afridi
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan.
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Abstract
Crassulacean acid metabolism (CAM) has evolved from a C3 ground state to increase water use efficiency of photosynthesis. During CAM evolution, selective pressures altered the abundance and expression patterns of C3 genes and their regulators to enable the trait. The circadian pattern of CO2 fixation and the stomatal opening pattern observed in CAM can be explained largely with a regulatory architecture already present in C3 plants. The metabolic CAM cycle relies on enzymes and transporters that exist in C3 plants and requires tight regulatory control to avoid futile cycles between carboxylation and decarboxylation. Ecological observations and modeling point to mesophyll conductance as a major factor during CAM evolution. The present state of knowledge enables suggestions for genes for a minimal CAM cycle for proof-of-concept engineering, assuming altered regulation of starch synthesis and degradation are not critical elements of CAM photosynthesis and sufficient malic acid export from the vacuole is possible.
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Affiliation(s)
- Katharina Schiller
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
| | - Andrea Bräutigam
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
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27
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Koendjbiharie JG, van Kranenburg R, Kengen SWM. The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiol Rev 2021; 45:fuaa061. [PMID: 33289792 PMCID: PMC8100219 DOI: 10.1093/femsre/fuaa061] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
At the junction between the glycolysis and the tricarboxylic acid cycle-as well as various other metabolic pathways-lies the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate node (PPO-node). These three metabolites form the core of a network involving at least eleven different types of enzymes, each with numerous subtypes. Obviously, no single organism maintains each of these eleven enzymes; instead, different organisms possess different subsets in their PPO-node, which results in a remarkable degree of variation, despite connecting such deeply conserved metabolic pathways as the glycolysis and the tricarboxylic acid cycle. The PPO-node enzymes play a crucial role in cellular energetics, with most of them involved in (de)phosphorylation of nucleotide phosphates, while those responsible for malate conversion are important redox enzymes. Variations in PPO-node therefore reflect the different energetic niches that organisms can occupy. In this review, we give an overview of the biochemistry of these eleven PPO-node enzymes. We attempt to highlight the variation that exists, both in PPO-node compositions, as well as in the roles that the enzymes can have within those different settings, through various recent discoveries in both bacteria and archaea that reveal deviations from canonical functions.
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Affiliation(s)
- Jeroen G Koendjbiharie
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
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28
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Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii. J Bacteriol 2021; 203:JB.00690-20. [PMID: 33558390 DOI: 10.1128/jb.00690-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/28/2021] [Indexed: 12/19/2022] Open
Abstract
The halophilic archaeon Haloferax volcanii has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. Following our previous studies on key enzymes of this pathway, we now focus on the characterization of enzymes involved in 3-phosphoglycerate conversion to pyruvate, in anaplerosis, and in acetyl coenzyme A (acetyl-CoA) formation from pyruvate. These enzymes include phosphoglycerate mutase, enolase, pyruvate kinase, phosphoenolpyruvate carboxylase, and pyruvate-ferredoxin oxidoreductase. The essential function of these enzymes were shown by transcript analyses and growth experiments with respective deletion mutants. Furthermore, we show that H. volcanii-during aerobic growth on glucose-excreted significant amounts of acetate, which was consumed in the stationary phase (acetate switch). The enzyme catalyzing the conversion of acetyl-CoA to acetate as part of the acetate overflow mechanism, an ADP-forming acetyl-CoA synthetase (ACD), was characterized. The functional involvement of ACD in acetate formation and of AMP-forming acetyl-CoA synthetases (ACSs) in activation of excreted acetate was proven by using respective deletion mutants. Together, the data provide a comprehensive analysis of enzymes of the spED pathway and of anaplerosis and report the first genetic evidence of the functional involvement of enzymes of the acetate switch in archaea.IMPORTANCE In this work, we provide a comprehensive analysis of glucose degradation via the semiphosphorylative Entner-Doudoroff pathway in the haloarchaeal model organism Haloferax volcanii The study includes transcriptional analyses, growth experiments with deletion mutants. and characterization of all enzymes involved in the conversion of 3-phosphoglycerate to acetyl coenzyme A (acetyl-CoA) and in anaplerosis. Phylogenetic analyses of several enzymes indicate various lateral gene transfer events from bacteria to haloarchaea. Furthermore, we analyzed the key players involved in the acetate switch, i.e., in the formation (overflow) and subsequent consumption of acetate during aerobic growth on glucose. Together, the data provide novel aspects of glucose degradation, anaplerosis, and acetate switch in H. volcanii and thus expand our understanding of the unusual sugar metabolism in archaea.
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DiMario RJ, Kophs AN, Pathare VS, Schnable JC, Cousins AB. Kinetic variation in grass phosphoenolpyruvate carboxylases provides opportunity to enhance C 4 photosynthetic efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1677-1688. [PMID: 33345397 DOI: 10.1111/tpj.15141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
The high rates of photosynthesis and the carbon-concentrating mechanism (CCM) in C4 plants are initiated by the enzyme phosphoenolpyruvate (PEP) carboxylase (PEPC). The flow of inorganic carbon into the CCM of C4 plants is driven by PEPC's affinity for bicarbonate (KHCO3 ), which can be rate limiting when atmospheric CO2 availability is restricted due to low stomatal conductance. We hypothesize that natural variation in KHCO3 across C4 plants is driven by specific amino acid substitutions to impact rates of C4 photosynthesis under environments such as drought that restrict stomatal conductance. To test this hypothesis, we measured KHCO3 from 20 C4 grasses to compare kinetic properties with specific amino acid substitutions. There was nearly a twofold range in KHCO3 across these C4 grasses (24.3 ± 1.5 to 46.3 ± 2.4 μm), which significantly impacts modeled rates of C4 photosynthesis. Additionally, molecular engineering of a low-HCO3- affinity PEPC identified key domains that confer variation in KHCO3 . This study advances our understanding of PEPC kinetics and builds the foundation for engineering increased-HCO3- affinity and C4 photosynthetic efficiency in important C4 crops.
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Affiliation(s)
- Robert J DiMario
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Ashley N Kophs
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Varsha S Pathare
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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30
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Prokaryotic Expression of Phospho enolpyruvate Carboxylase Fragments from Peanut and Analysis of Osmotic Stress Tolerance of Recombinant Strains. PLANTS 2021; 10:plants10020365. [PMID: 33672856 PMCID: PMC7917721 DOI: 10.3390/plants10020365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 02/08/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a ubiquitous cytosolic enzyme that catalyzes the irreversible β-carboxylation of phosphoenolpyruvate (PEP) in presence of HCO3− to produce oxaloacetate (OAA) during carbon fixation and photosynthesis. It is well accepted that PEPC genes are expressed in plants upon stress. PEPC also supports the biosynthesis of biocompatible osmolytes in many plant species under osmotic stress. There are five isoforms of PEPC found in peanut (Arachis hypogaea L.), namely, AhPEPC1, AhPEPC2, AhPEPC3, AhPEPC4, and AhPEPC5. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that the gene expression patterns of these AhPEPC genes were different in mature seeds, stems, roots, flowers, and leaves. The expression of all the plant type PEPC (PTPCs) (AhPEPC1, AhPEPC2, AhPEPC3, and AhPEPC4) was relatively high in roots, while the bacterial type PEPC (BTPC) (AhPEPC5) showed a remarkable expression level in flowers. Principal component analysis (PCA) result showed that AhPEPC3 and AhPEPC4 are correlated with each other, indicating comparatively associations with roots, and AhPEPC5 have a very close relationship with flowers. In order to investigate the function of these AhPEPCs, the fragments of these five AhPEPC cDNA were cloned and expressed in Escherichia coli (E. coli). The recombinant proteins contained a conserved domain with a histidine site, which is important for enzyme catalysis. Results showed that protein fragments of AhPEPC1, AhPEPC2, and AhPEPC5 had remarkable expression levels in E. coli. These three recombinant strains were more sensitive at pH 9.0, and recombinant strains carrying AhPEPC2 and AhPEPC5 fragments exhibited more growth than the control strain with the presence of PEG6000. Our findings showed that the expression of the AhPEPC fragments may enhance the resistance of transformed E. coli to osmotic stress.
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31
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Ma Z, Wang J, Li C, Ren P, Yao L, Li B, Meng Y, Ma X, Si E, Yang K, Shang X, Wang H. Global Profiling of Phosphorylation Reveals the Barley Roots Response to Phosphorus Starvation and Resupply. FRONTIERS IN PLANT SCIENCE 2021; 12:676432. [PMID: 34335649 PMCID: PMC8317692 DOI: 10.3389/fpls.2021.676432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/09/2021] [Indexed: 05/04/2023]
Abstract
Phosphorus (P) deficiency is a major threat to the crop production, and for understanding the response mechanism of plant roots, P stress may facilitate the development of crops with increased tolerance. Phosphorylation plays a critical role in the regulation of proteins for plant responses to biotic and abiotic stress; however, its functions in P starvation/resupply are largely unknown for barley (Hordeum vulgare) growth. Here, we performed a global review of phosphorylation in barley roots treated by P starvation/resupply. We identified 7,710 phosphorylation sites on 3,373 proteins, of which 76 types of conserved motifs were extracted from 10,428 phosphorylated peptides. Most phosphorylated proteins were located in the nucleus (36%) and chloroplast (32%). Compared with the control, 186 and 131 phosphorylated proteins under P starvation condition and 156 and 111 phosphorylated proteins under P resupply condition showed significant differences at 6 and 48 h, respectively. These proteins mainly participated in carbohydrate metabolism, phytohormones, signal transduction, cell wall stress, and oxidases stress. Moreover, the pathways of the ribosome, RNA binding, protein transport, and metal binding were significantly enriched under P starvation, and only two pathways of ribosome and RNA binding were greatly enriched under Pi resupply according to the protein-protein interaction analysis. The results suggested that the phosphorylation proteins might play important roles in the metabolic processes of barley roots in response to Pi deficiency/resupply. The data not only provide unique access to phosphorylation reprogramming of plant roots under deficiency/resupply but also demonstrate the close cooperation between these phosphorylation proteins and key metabolic functions.
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Affiliation(s)
- Zengke Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Juncheng Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Panrong Ren
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lirong Yao
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Baochun Li
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaxiong Meng
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaole Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Erjing Si
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ke Yang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huajun Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Huajun Wang
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Maurya J, Bandyopadhyay T, Prasad M. Transcriptional regulators of nitrate metabolism: Key players in improving nitrogen use in crops. J Biotechnol 2020; 324:121-133. [PMID: 33031844 DOI: 10.1016/j.jbiotec.2020.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/19/2020] [Accepted: 10/03/2020] [Indexed: 11/30/2022]
Abstract
Green revolution has boosted crop yields by the development of varieties which rely on high fertilizer application. Since then, higher productivity has largely witnessed excessive nitrogen (N) fertilizer application resulting in many environmentally and agronomically unsustainable consequences. One possible solution to this problem is to develop varieties with efficient N use endowed with genetically superior N metabolizing machinery, thereby significantly reducing N loss in soil and facilitating gainful yield performance at lower N conditions. Nitrate (NO3-) is the major form of N acquired by plants in aerobic soils. Hence, its efficient acquisition, transport, assimilation into complex organic compounds, and overall homeostasis is crucial to ensure productivity under optimal and suboptimal N conditions. Transcription factors are prime regulators of these processes, and insights into their mechanism of action and the resultant effect on N metabolism are crucial to generating crops with efficient and durable nitrogen use efficiency. The present review, therefore, presents a comprehensive updated account of major N responsive transcription factor families, their cross-talk with other growth factors, and explores existing and potential areas of their biotechnological application to maximize crop yields.
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Affiliation(s)
- Jyoti Maurya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | | | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Nomura K, Sakurai Y, Dozono M. Molecular Cloning of Novel-Type Phospho enolpyruvate Carboxylase Isoforms in Pitaya ( Hylocereus undatus). PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091241. [PMID: 32967083 PMCID: PMC7569800 DOI: 10.3390/plants9091241] [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: 08/31/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is an important enzyme involved in the initial CO2 fixation of crassulacean acid metabolism (CAM) photosynthesis. To understand the cultivation characteristics of a CAM plant pitaya, it is necessary to clarify the characteristics of PEPC in this species. Here, we cloned three PEPC cDNAs in pitaya, HuPPC1, HuPPC2, and HuPPC3, which encode 942, 934, and 966 amino acid residues, respectively. Phylogenetic analysis indicated that these PEPC belonged to plant-type PEPC (PTPC), although HuPPC1 and HuPPC2 have no Ser-phosphorylation motif in N-terminal region, which is a crucial regulation site in PTPC and contributes to CAM periodicity. HuPPC1 and HuPPC2 phylogenetically unique to the Cactaceae family, whereas HuPPC3 was included in a CAM clade. Two isoforms were partially purified at the protein level and were assigned as HuPPC2 and HuPPC3 using MASCOT analysis. The most distinct difference in enzymatic properties between the two was sensitivity to malate and aspartate, both of which are allosteric inhibitors of PEPC. With 2 mM malate, HuPPC3 was inhibited to 10% of the initial activity, whereas HuPPC2 activity was maintained at 70%. Aspartate inhibited HuPPC3 activity by approximately 50% at 5 mM; however, such inhibition was not observed for HuPPC2 at 10 mM. These results suggest that HuPPC3 corresponds to a general CAM-related PEPC, whereas HuPPC1 and HuPPC2 are related to carbon and/or nitrogen metabolism, with a characteristic regulation mechanism similar to those of Cactaceae plants.
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Affiliation(s)
- Keiichi Nomura
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
| | - Yuho Sakurai
- Faculty of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
| | - Mayu Dozono
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
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Genomic dissection and expression analysis of stress-responsive genes in C4 panicoid models, Setaria italica and Setaria viridis. J Biotechnol 2020; 318:57-67. [DOI: 10.1016/j.jbiotec.2020.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 02/02/2023]
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Structural and biochemical evidence of the glucose 6-phosphate-allosteric site of maize C4-phosphoenolpyruvate carboxylase: its importance in the overall enzyme kinetics. Biochem J 2020; 477:2095-2114. [PMID: 32459324 DOI: 10.1042/bcj20200304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
Activation of phosphoenolpyruvate carboxylase (PEPC) enzymes by glucose 6-phosphate (G6P) and other phospho-sugars is of major physiological relevance. Previous kinetic, site-directed mutagenesis and crystallographic results are consistent with allosteric activation, but the existence of a G6P-allosteric site was questioned and competitive activation-in which G6P would bind to the active site eliciting the same positive homotropic effect as the substrate phosphoenolpyruvate (PEP)-was proposed. Here, we report the crystal structure of the PEPC-C4 isozyme from Zea mays with G6P well bound into the previously proposed allosteric site, unambiguously confirming its existence. To test its functionality, Asp239-which participates in a web of interactions of the protein with G6P-was changed to alanine. The D239A variant was not activated by G6P but, on the contrary, inhibited. Inhibition was also observed in the wild-type enzyme at concentrations of G6P higher than those producing activation, and probably arises from G6P binding to the active site in competition with PEP. The lower activity and cooperativity for the substrate PEP, lower activation by glycine and diminished response to malate of the D239A variant suggest that the heterotropic allosteric activation effects of free-PEP are also abolished in this variant. Together, our findings are consistent with both the existence of the G6P-allosteric site and its essentiality for the activation of PEPC enzymes by phosphorylated compounds. Furthermore, our findings suggest a central role of the G6P-allosteric site in the overall kinetics of these enzymes even in the absence of G6P or other phospho-sugars, because of its involvement in activation by free-PEP.
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Scholl J, Dengler L, Bader L, Forchhammer K. Phosphoenolpyruvate carboxylase from the cyanobacterium Synechocystis sp. PCC 6803 is under global metabolic control by P II signaling. Mol Microbiol 2020; 114:292-307. [PMID: 32274833 DOI: 10.1111/mmi.14512] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/20/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is the second major carbon-fixing enzyme in photoautotrophic organisms. PEPC is required for the synthesis of amino acids of the glutamate and aspartate family by replenishing the TCA cycle. Furthermore, in cyanobacteria, PEPC, together with malate dehydrogenase and malic enzyme, forms a metabolic shunt for the synthesis of pyruvate from PEP. During this process, CO2 is first fixed and later released again. Due to its central metabolic position, it is crucial to fully understand the regulation of PEPC. Here, we identify PEPC from the cyanobacterium Synechocystis sp. PCC 6803 (PEPC) as a novel interaction partner for the global signal transduction protein PII . In addition to an extensive characterization of PEPC, we demonstrate specific PII -PEPC complex formation and its enzymatic consequences. PEPC activity is tuned by the metabolite-sensing properties of PII : Whereas in the absence of PII, PEPC is subjected to ATP inhibition, it is activated beyond its basal activity in the presence of PII . Furthermore, PII -PEPC complex formation is inhibited by ADP and PEPC activation by PII -ATP is mitigated in the presence of 2-OG, linking PEPC regulation to the cell's global carbon/nitrogen status. Finally, physiological relevance of the in vitro measurements was proven by metabolomic analyses of Synechocystis wild-type and PII -deficient cells.
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Affiliation(s)
- Jörg Scholl
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
| | - Lisa Dengler
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
| | - Laura Bader
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
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Ueno Y, Yoshizawa-Kumagaye K, Emura J, Urabe T, Yoshiya T, Furumoto T, Izui K. In Vivo Phosphorylation: Development of Specific Antibodies to Detect the Phosphorylated PEPC Isoform for the C4 Photosynthesis in Zea mays. Methods Mol Biol 2020; 2072:217-240. [PMID: 31541450 DOI: 10.1007/978-1-4939-9865-4_18] [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] [Indexed: 12/14/2022]
Abstract
Phosphoenolpyruvate carboxylases (PEPCs), mostly known as the enzymes responsible for the initial CO2 fixation during C4 photosynthesis, are regulated by reversible phosphorylation in vascular plants. The phosphorylation site on a PEPC molecule is conserved not only among isoforms but also across plant species. An anti-phosphopeptide antibody is a common and powerful tool for detecting phosphorylated target proteins with high specificity. We generated two antibodies, one against a peptide containing a phosphoserine (phosphopeptide) and the other against a peptide containing a phosphoserine mimetic, (S)-2-amino-4-phosphonobutyric acid (phosphonopeptide). The amino acid sequence of the peptide was taken from the site around the phosphorylation site near the N-terminal region of the maize C4-isoform of PEPC. The former antibodies detected almost specifically the phosphorylated C4-isoform of PEPC, whereas the latter antibodies had a broader specificity for the phosphorylated PEPC in various plant species. The following procedures are described herein: (1) preparation of the phosphopeptide and phosphonopeptide; (2) preparation and purification of rabbit antibodies; (3) preparation of cell extracts from leaves for analyses of PEPC phosphorylation with antibodies; and (4) characterization of the obtained antibodies. Finally, (5) two cases involving the application of these antibodies are presented.
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Affiliation(s)
- Yoshihisa Ueno
- Department of Agriculture, Ryukoku University, Shiga, Japan.
| | | | | | | | | | | | - Katsura Izui
- Institute of Advanced Technology, Kindai University, Wakayama, Japan
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Li X, Sanagi M, Lu Y, Nomura Y, Stolze SC, Yasuda S, Saijo Y, Schulze WX, Feil R, Stitt M, Lunn JE, Nakagami H, Sato T, Yamaguchi J. Protein Phosphorylation Dynamics Under Carbon/Nitrogen-Nutrient Stress and Identification of a Cell Death-Related Receptor-Like Kinase in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:377. [PMID: 32308664 PMCID: PMC7145971 DOI: 10.3389/fpls.2020.00377] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/16/2020] [Indexed: 05/03/2023]
Abstract
Nutrient availability, in particular the availability of sugar [carbon (C)] and nitrogen (N), is important for the regulation of plant metabolism and development. In addition to independent utilization of C and N nutrients, plants sense and respond to the balance of C and N nutrients (C/N-nutrient) available to them. High C/low N-nutrient stress has been shown to arrest early post-germinative growth while promoting progression to senescence in Arabidopsis. Although several signaling components of the C/N-nutrient response have been identified, the inclusive molecular basis of plant C/N-nutrient response remains unclear. This proteome analysis evaluated phosphorylation dynamics in response to high C/low N-nutrient stress. Phosphoproteomics under conditions of C/N-nutrient stress showed a global change in the phosphorylation status of proteins, including plasma membrane H+-ATPase, carbon and nitrogen metabolic enzymes and signaling proteins such as protein kinases and transcription factors. Further analyses suggested that SNF1-related protein kinase 1 (SnRK1) is involved in primary C/N-nutrient signal mediation via the transcriptional regulation of C/N-regulatory kinases. We also identified a leucine-rich repeat receptor-like kinase with extracellular malectin-like domain, named as LMK1, which was shown to possess cell death induction activity in plant leaves. These results provide important insight into the C/N-nutrient signaling pathways connecting nutrition stress to various cellular and physiological processes in plants.
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Affiliation(s)
- Xingwen Li
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| | - Miho Sanagi
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| | - Yu Lu
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| | - Yuko Nomura
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Shigetaka Yasuda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yusuke Saijo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Waltraud X. Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - John E. Lunn
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - Hirofumi Nakagami
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- *Correspondence: Hirofumi Nakagami,
| | - Takeo Sato
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
- Takeo Sato,
| | - Junji Yamaguchi
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
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Shahid A, Rehman AU, Usman M, Ashraf MUF, Javed MR, Khan AZ, Gill SS, Mehmood MA. Engineering the metabolic pathways of lipid biosynthesis to develop robust microalgal strains for biodiesel production. Biotechnol Appl Biochem 2020; 67:41-51. [DOI: 10.1002/bab.1812] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/03/2019] [Indexed: 01/29/2023]
Affiliation(s)
- Ayesha Shahid
- Bioenergy Research CenterDepartment of Bioinformatics and BiotechnologyGovernment College University Faisalabad Faisalabad Pakistan
| | - Abd ur Rehman
- Bioenergy Research CenterDepartment of Bioinformatics and BiotechnologyGovernment College University Faisalabad Faisalabad Pakistan
| | - Muhammad Usman
- Bioenergy Research CenterDepartment of Bioinformatics and BiotechnologyGovernment College University Faisalabad Faisalabad Pakistan
| | - Muhammad Umer Farooq Ashraf
- Bioenergy Research CenterDepartment of Bioinformatics and BiotechnologyGovernment College University Faisalabad Faisalabad Pakistan
| | - Muhammad Rizwan Javed
- Bioenergy Research CenterDepartment of Bioinformatics and BiotechnologyGovernment College University Faisalabad Faisalabad Pakistan
| | - Aqib Zafar Khan
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Science and BiotechnologyShanghai Jiao Tong University Shanghai People's Republic of China
| | - Saba Shahid Gill
- Department of Plant and Environmental SciencesNew Mexico State University Las Cruces NM USA
| | - Muhammad Aamer Mehmood
- Bioenergy Research CenterDepartment of Bioinformatics and BiotechnologyGovernment College University Faisalabad Faisalabad Pakistan
- School of BioengineeringSichuan University of Science & Engineering Zigong People's Republic of China
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40
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Ding J, Zhao J, Pan T, Xi L, Zhang J, Zou Z. Comparative Transcriptome Analysis of Gene Expression Patterns in Tomato Under Dynamic Light Conditions. Genes (Basel) 2019; 10:genes10090662. [PMID: 31470680 PMCID: PMC6770952 DOI: 10.3390/genes10090662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 02/02/2023] Open
Abstract
Plants grown under highly variable natural light regimes differ strongly from plants grown under constant light (CL) regimes. Plant phenotype and adaptation responses are important for plant biomass and fitness. However, the underlying regulatory mechanisms are still poorly understood, particularly from a transcriptional perspective. To investigate the influence of different light regimes on tomato plants, three dynamic light (DL) regimes were designed, using a CL regime as control. Morphological, photosynthetic, and transcriptional differences after five weeks of treatment were compared. Leaf area, plant height, shoot /root weight, total chlorophyll content, photosynthetic rate, and stomatal conductance all significantly decreased in response to DL regimes. The biggest expression difference was found between the treatment with the highest light intensity at the middle of the day with a total of 1080 significantly up-/down-regulated genes. A total of 177 common differentially expressed genes were identified between DL and CL conditions. Finally, significant differences were observed in the levels of gene expression between DL and CL treatments in multiple pathways, predominantly of plant–pathogen interactions, plant hormone signal transductions, metabolites, and photosynthesis. These results expand the understanding of plant development and photosynthetic regulations under DL conditions by multiple pathways.
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Affiliation(s)
- Juanjuan Ding
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Jiantao Zhao
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, 67 Allée des Chênes CS 60094, 84143 Montfavet, France
| | - Tonghua Pan
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Linjie Xi
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Jing Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zhirong Zou
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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41
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Mark R, Lyu X, Ng KR, Chen WN. Gene Source Screening as a Tool for Naringenin Production in Engineered Saccharomyces cerevisiae. ACS OMEGA 2019; 4:12872-12879. [PMID: 31460414 PMCID: PMC6682025 DOI: 10.1021/acsomega.9b00364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/24/2019] [Indexed: 06/10/2023]
Abstract
Flavonoids are plant secondary metabolites with great potential in the food industry. Metabolic engineering of Saccharomyces cerevisiae is a sustainable production technique. However, the current naringenin production yield is low because of inefficient enzymatic activity. Hence, this study uses gene source screening as a tool to identify the best gene source for enzymes such as 4-coumarate: coenzyme ligase (4CL) and chalcone synthase (CHS). For the first time, the 4CL gene from Medicago truncatula and the CHS gene from Vitis vinifera were expressed in S. cerevisiae, and this combination provided the highest yield of naringenin, which was 28-fold higher as compared to the reference strain. The combinations obtained similar performance in the Y-28 strains, where the highest production was 28.68 mg/L. Our results demonstrated that the selection and combination of enzymes from the correct gene source could greatly improve naringenin production. For the future, this could help commercialize flavonoid production, which would result in natural food preservatives and additives.
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Alvarez CE, Bovdilova A, Höppner A, Wolff CC, Saigo M, Trajtenberg F, Zhang T, Buschiazzo A, Nagel-Steger L, Drincovich MF, Lercher MJ, Maurino VG. Molecular adaptations of NADP-malic enzyme for its function in C 4 photosynthesis in grasses. NATURE PLANTS 2019; 5:755-765. [PMID: 31235877 DOI: 10.1038/s41477-019-0451-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
In C4 grasses of agronomical interest, malate shuttled into the bundle sheath cells is decarboxylated mainly by nicotinamide adenine dinucleotide phosphate (NADP)-malic enzyme (C4-NADP-ME). The activity of C4-NADP-ME was optimized by natural selection to efficiently deliver CO2 to Rubisco. During its evolution from a plastidic non-photosynthetic NADP-ME, C4-NADP-ME acquired increased catalytic efficiency, tetrameric structure and pH-dependent inhibition by its substrate malate. Here, we identified specific amino acids important for these C4 adaptions based on strict differential conservation of amino acids, combined with solving the crystal structures of maize and sorghum C4-NADP-ME. Site-directed mutagenesis and structural analyses show that Q503, L544 and E339 are involved in catalytic efficiency; E339 confers pH-dependent regulation by malate, F140 is critical for the stabilization of the oligomeric structure and the N-terminal region is involved in tetramerization. Together, the identified molecular adaptations form the basis for the efficient catalysis and regulation of one of the central biochemical steps in C4 metabolism.
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Affiliation(s)
- Clarisa E Alvarez
- Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina
| | - Anastasiia Bovdilova
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Astrid Höppner
- Center for Structural Studies, Hreinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christian-Claus Wolff
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Mariana Saigo
- Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich Heine University, Düsseldorf, Germany
- Institut of Complex Systems, Structural Biochemistry (ICS-6), Jülich, Germany
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Integrative Microbiology of Zoonotic Agents, Department of Microbiology, Institut Pasteur, Paris, France
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich Heine University, Düsseldorf, Germany
- Institut of Complex Systems, Structural Biochemistry (ICS-6), Jülich, Germany
| | - Maria F Drincovich
- Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina
| | - Martin J Lercher
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
- Institute for Computer Science and Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Veronica G Maurino
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany.
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Ceusters N, Luca S, Feil R, Claes JE, Lunn JE, Van den Ende W, Ceusters J. Hierarchical clustering reveals unique features in the diel dynamics of metabolites in the CAM orchid Phalaenopsis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3269-3281. [PMID: 30972416 PMCID: PMC6598073 DOI: 10.1093/jxb/erz170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/01/2019] [Indexed: 05/03/2023]
Abstract
Crassulacean acid metabolism (CAM) is a major adaptation of photosynthesis that involves temporally separated phases of CO2 fixation and accumulation of organic acids at night, followed by decarboxylation and refixation of CO2 by the classical C3 pathway during the day. Transitory reserves such as soluble sugars or starch are degraded at night to provide the phosphoenolpyruvate (PEP) and energy needed for initial carboxylation by PEP carboxylase. The primary photosynthetic pathways in CAM species are well known, but their integration with other pathways of central C metabolism during different phases of the diel light-dark cycle is poorly understood. Gas exchange was measured in leaves of the CAM orchid Phalaenopsis 'Edessa' and leaves were sampled every 2 h during a complete 12-h light-12-h dark cycle for metabolite analysis. A hierarchical agglomerative clustering approach was employed to explore the diel dynamics and relationships of metabolites in this CAM species, and compare these with those in model C3 species. High levels of 3-phosphoglycerate (3PGA) in the light activated ADP-glucose pyrophosphorylase, thereby enhancing production of ADP-glucose, the substrate for starch synthesis. Trehalose 6-phosphate (T6P), a sugar signalling metabolite, was also correlated with ADP-glucose, 3PGA and PEP, but not sucrose, over the diel cycle. Whether or not this indicates a different function of T6P in CAM plants is discussed. T6P levels were low at night, suggesting that starch degradation is regulated primarily by circadian clock-dependent mechanisms. During the lag in starch degradation at dusk, carbon and energy could be supplied by rapid consumption of a large pool of aconitate that accumulates in the light. Our study showed similarities in the diel dynamics and relationships between many photosynthetic metabolites in CAM and C3 plants, but also revealed some major differences reflecting the specialized metabolic fluxes in CAM plants, especially during light-dark transitions and at night.
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Affiliation(s)
- Nathalie Ceusters
- KU Leuven, Department of Biosystems, Division of Crop Biotechnics, Research group for Sustainable Crop Production & Protection, Campus Geel, Kleinhoefstraat, Geel, Belgium
| | - Stijn Luca
- Ghent University, Department of Data Analysis and Mathematical Modelling, Coupure links, Gent, Belgium
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Johan E Claes
- KU Leuven, Department of Microbial and Molecular systems, Bioengineering Technology TC, Campus Geel, Kleinhoefstraat, Geel, Belgium
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Wim Van den Ende
- KU Leuven, Department of Biology, Laboratory of Molecular Plant Biology, Kasteelpark Arenberg, Leuven, Belgium
| | - Johan Ceusters
- KU Leuven, Department of Biosystems, Division of Crop Biotechnics, Research group for Sustainable Crop Production & Protection, Campus Geel, Kleinhoefstraat, Geel, Belgium
- UHasselt, Centre for Environmental Sciences, Environmental Biology, Campus Diepenbeek, Agoralaan Building D, Diepenbeek, Belgium
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Kong F, Yamaoka Y, Ohama T, Lee Y, Li-Beisson Y. Molecular Genetic Tools and Emerging Synthetic Biology Strategies to Increase Cellular Oil Content in Chlamydomonas reinhardtii. PLANT & CELL PHYSIOLOGY 2019; 60:1184-1196. [PMID: 30715500 DOI: 10.1093/pcp/pcz022] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/18/2019] [Indexed: 05/26/2023]
Abstract
Microalgae constitute a highly diverse group of eukaryotic and photosynthetic microorganisms that have developed extremely efficient systems for harvesting and transforming solar energy into energy-rich molecules such as lipids. Although microalgae are considered to be one of the most promising platforms for the sustainable production of liquid oil, the oil content of these organisms is naturally low, and algal oil production is currently not economically viable. Chlamydomonas reinhardtii (Chlamydomonas) is an established algal model due to its fast growth, high transformation efficiency, and well-understood physiology and to the availability of detailed genome information and versatile molecular tools for this organism. In this review, we summarize recent advances in the development of genetic manipulation tools for Chlamydomonas, from gene delivery methods to state-of-the-art genome-editing technologies and fluorescent dye-based high-throughput mutant screening approaches. Furthermore, we discuss practical strategies and toolkits that enhance transgene expression, such as choice of expression vector and background strain. We then provide examples of how advanced genetic tools have been used to increase oil content in Chlamydomonas. Collectively, the current literature indicates that microalgal oil content can be increased by overexpressing key enzymes that catalyze lipid biosynthesis, blocking lipid degradation, silencing metabolic pathways that compete with lipid biosynthesis and modulating redox state. The tools and knowledge generated through metabolic engineering studies should pave the way for developing a synthetic biological approach to enhance lipid productivity in microalgae.
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Affiliation(s)
- Fantao Kong
- Department of Integrative Bioscience & Biotechnology, Pohang University of Science and Technology, Pohang, Korea
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yasuyo Yamaoka
- Department of Integrative Bioscience & Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Takeshi Ohama
- School of Environmental Science and Engineering, Kochi University of Technology (KUT), Tosayamada, Kochi, Japan
| | - Youngsook Lee
- Department of Integrative Bioscience & Biotechnology, Pohang University of Science and Technology, Pohang, Korea
- Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Yonghua Li-Beisson
- Aix-Marseille Univ., CEA, CNRS, BIAM, UMR7265, CEA Cadarache, Saint-Paul-lez Durance F, France
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Gandullo J, Monreal JA, Álvarez R, Díaz I, García-Mauriño S, Echevarría C. Anionic Phospholipids Induce Conformational Changes in Phosphoenolpyruvate Carboxylase to Increase Sensitivity to Cathepsin Proteases. FRONTIERS IN PLANT SCIENCE 2019; 10:582. [PMID: 31143196 PMCID: PMC6521631 DOI: 10.3389/fpls.2019.00582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a cytosolic, homotetrameric enzyme that serves a variety of functions in plants, acting as the primary form of CO2 fixation in the C4 photosynthesis pathway (C4-PEPC). In a previous work we have shown that C4-PEPC bind anionic phospholipids, resulting in PEPC inactivation. Also, we showed that PEPC can associate with membranes and to be partially proteolyzed. However, the mechanism controlling this remains unknown. Using semi purified-PEPC from sorghum leaf and a panel of PEPC-specific antibodies, we analyzed the conformational changes in PEPC induced by anionic phospholipids to cause the inactivation of the enzyme. Conformational changes observed involved the exposure of the C-terminus of PEPC from the native, active enzyme conformation. Investigation of the protease activity associated with PEPC demonstrated that cysteine proteases co-purify with the enzyme, with protease-specific substrates revealing cathepsin B and L as the major protease species present. The anionic phospholipid-induced C-terminal exposed conformation of PEPC appeared highly sensitive to the identified cathepsin protease activity and showed initial proteolysis of the enzyme beginning at the N-terminus. Taken together, these data provide the first evidence that anionic phospholipids promote not only the inactivation of the PEPC enzyme, but also its proteolysis.
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Affiliation(s)
- Jacinto Gandullo
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - José-Antonio Monreal
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Rosario Álvarez
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Isabel Díaz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
| | - Sofía García-Mauriño
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Cristina Echevarría
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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Comparative analysis of proteomic and metabolomic profiles of different species of Paris. J Proteomics 2019; 200:11-27. [PMID: 30890455 DOI: 10.1016/j.jprot.2019.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/12/2019] [Accepted: 02/01/2019] [Indexed: 02/08/2023]
Abstract
An extract prepared from species of Paris is the most widely consumed herbal product in China. The genus Paris includes a variety of genotypes with different medicinal component contents but only two are defined as official sources. Closely related species have different medicinal properties because of differential expression of proteins and metabolites. To better understand the molecular basis of these differences, we examined proteomic and metabolomic changes in rhizomes of P. polyphylla var. chinensis, P. polyphylla var. yunnanensis, and P. fargesii var. fargesii using a technique known as sequential window acquisition of all theoretical mass spectra as well as gas chromatography-time-of-flight mass spectrometry. In total, 419 proteins showed significant abundance changes, and 33 metabolites could be used to discriminate Paris species. A complex analysis of proteomic and metabolomic data revealed a higher efficiency of sucrose utilization and an elevated protein abundance in the sugar metabolic pathway of P. polyphylla var. chinensis. The pyruvate content and efficiency of acetyl-CoA-utilization in saponin biosynthesis were also higher in P. polyphylla var. chinensis than in the other two species. The results expand our understanding of the proteome and metabolome of Paris and offer new insights into the species-specific traits of these herbaceous plants. SIGNIFICANCE: The traditional Chinese medicine Paris is the most widely consumed herbal product for the treatment of joint pain, rheumatoid arthritis and antineoplastic. All Paris species have roughly the same morphological characteristics; however, different members have different medicinal compound contents. Efficient exploitation of genetic diversity is a key factor in the development of rare medicinal plants with improved agronomic traits and malleability to challenging environmental conditions. Nevertheless, only a partial understanding of physiological and molecular mechanisms of different plants of Paris can be achieved without proteomics. To better understand the molecular basis of these differences and facilitate the use of other Paris species, we examine proteomic metabolomic changes in rhizomes of Paris using the technique known as SWATH-MS and GC/TOF-MS. Our research has provided information that can be used in other studies to compare metabolic traits in different Paris species. Our findings can also serve as a theoretical basis for the selection and cultivation of other Paris species with a higher medicinal value.
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Waseem M, Ahmad F. The phosphoenolpyruvate carboxylase gene family identification and expression analysis under abiotic and phytohormone stresses in Solanum lycopersicum L. Gene 2019; 690:11-20. [DOI: 10.1016/j.gene.2018.12.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/12/2018] [Accepted: 12/14/2018] [Indexed: 01/20/2023]
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Zhao Y, Guo A, Wang Y, Hua J. Evolution of PEPC gene family in Gossypium reveals functional diversification and GhPEPC genes responding to abiotic stresses. Gene 2019; 698:61-71. [PMID: 30825597 DOI: 10.1016/j.gene.2019.02.061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 02/10/2019] [Accepted: 02/23/2019] [Indexed: 12/24/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) family genes play important roles in regulating plant growth and abiotic stress response. Based on the sequenced Gossypium genomes, we performed comprehensive analysis of PEPC homolog genes in cotton, which six, six, eleven and ten PEPC genes were identified in Gossypium arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2), respectively. These genes were divided into six subgroups: PEPC-i, PEPC-ii, PEPC-iii, PEPC-iv, PEPC-v and PEPC-vi; PEPC genes in each subgroup displayed conserved gene structure and motifs. Segmental duplication and whole genome duplication (WGD) events yielded the expansion of PEPC genes. Expression assays showed that the duplicated PEPC genes displayed diverse expression patterns, indicating that they experienced functional divergence. Of which, genes in PEPC-iv subgroup played crucial role for substrate distribution in cottonseed. Cis-elements, putative miRNAs and expression analyses showed that GhPEPC homologs might respond to abiotic stresses, expression levels of GhPEPC1 and GhPEPC2/GhPEPC2D genes were larger induced than other GhPEPC genes under cold, heat, salt, and drought stresses, indicating the crucial roles in abiotic stresses response. Present study serves new information to decipher the evolution and function of PEPC genes in Gossypium.
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Affiliation(s)
- Yanpeng Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Anhui Guo
- Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Yumei Wang
- Research Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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Wang Q, Zhang Y, Zheng N, Guo L, Song X, Zhao S, Wang J. Biological System Responses of Dairy Cows to Aflatoxin B1 Exposure Revealed with Metabolomic Changes in Multiple Biofluids. Toxins (Basel) 2019; 11:toxins11020077. [PMID: 30717092 PMCID: PMC6410036 DOI: 10.3390/toxins11020077] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/19/2018] [Accepted: 01/20/2019] [Indexed: 01/28/2023] Open
Abstract
Research on mycotoxins now requires a systematic study of post-exposure organisms. In this study, the effects of aflatoxin B1 (AFB1) on biofluids biomarkers were examined with metabolomics and biochemical tests. The results showed that milk concentration of aflatoxin M1 changed with the addition or removal of AFB1. AFB1 significantly affected serum concentrations of superoxide dismutase (SOD) and malon dialdehyde (MDA), SOD/MDA, and the total antioxidant capacity. Significant differences of volatile fatty acids and NH3-N were detected in the rumen fluid. Eighteen rumen fluid metabolites, 11 plasma metabolites, and 9 milk metabolites were significantly affected by the AFB1. These metabolites are mainly involved in the pathway of amino acids metabolism. Our results suggest that not only is the study of macro-indicators (milk composition and production) important, but that more attention should be paid to micro-indicators (biomarkers) when assessing the risks posed by mycotoxins to dairy cows.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yangdong Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Liya Guo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiaoming Song
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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50
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Learning RuBisCO's birth and subsequent environmental adaptation. Biochem Soc Trans 2018; 47:179-185. [PMID: 30559271 DOI: 10.1042/bst20180449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/08/2018] [Accepted: 11/26/2018] [Indexed: 11/17/2022]
Abstract
It is believed that organisms that first appeared after the formation of the earth lived in a very limited environment, making full use of the limited number of genes. From these early organisms' genes, more were created by replication, mutation, recombination, translocation, and transmission of other organisms' DNA; thus, it became possible for ancient organisms to grow in various environments. The photosynthetic CO2-fixing enzyme RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) began to function in primitive methanogenic archaea and has been evolved as a central CO2-fixing enzyme in response to the large changes in CO2 and O2 concentrations that occurred in the subsequent 4 billion years. In this review, the processes of its adaptation to be specialized for CO2 fixation will be presented from the viewpoint of functions and structures of RuBisCO.
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