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Friedrichs N, Shokouhi D, Heyer AG. Flux Calculation for Primary Metabolism Reveals Changes in Allocation of Nitrogen to Different Amino Acid Families When Photorespiratory Activity Changes. Int J Mol Sci 2024; 25:8394. [PMID: 39125964 PMCID: PMC11313221 DOI: 10.3390/ijms25158394] [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: 06/30/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
Photorespiration, caused by oxygenation of the enzyme Rubisco, is considered a wasteful process, because it reduces photosynthetic carbon gain, but it also supplies amino acids and is involved in amelioration of stress. Here, we show that a sudden increase in photorespiratory activity not only reduced carbon acquisition and production of sugars and starch, but also affected diurnal dynamics of amino acids not obviously involved in the process. Flux calculations based on diurnal metabolite profiles suggest that export of proline from leaves increases, while aspartate family members accumulate. An immense increase is observed for turnover in the cyclic reaction of glutamine synthetase/glutamine-oxoglutarate aminotransferase (GS/GOGAT), probably because of increased production of ammonium in photorespiration. The hpr1-1 mutant, defective in peroxisomal hydroxypyruvate reductase, shows substantial alterations in flux, leading to a shift from the oxoglutarate to the aspartate family of amino acids. This is coupled to a massive export of asparagine, which may serve in exchange for serine between shoot and root.
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Affiliation(s)
| | | | - Arnd G. Heyer
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany (D.S.)
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Chaturvedi S, Khan S, Thakur N, Jangra A, Tiwari S. Genome-wide identification and gene expression analysis of GHMP kinase gene family in banana cv. Rasthali. Mol Biol Rep 2023; 50:9061-9072. [PMID: 37731027 DOI: 10.1007/s11033-023-08743-4] [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: 10/28/2022] [Accepted: 08/08/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND The GHMP kinase gene family encompasses ATP-dependent kinases, significantly involved in the biosynthesis of isoprenes, amino acids, and metabolism of carbohydrates. Banana is a staple tropical crop that is globally consumed but known for high sensitivity to salt, cold, and drought stresses. The GHMP kinases are known to play a significant role during abiotic stresses in plants. The present study emphasizes the role of GHMP kinases in various abiotic stress conditions in banana. METHODS AND RESULTS We identified 12 GHMP kinase (MaGHMP kinase) genes in the banana genome database and witnessed the presence of the conserved Pro-X-X-X-Gly-Leu-X-Ser-Ser-Ala domain in their protein sequences. All genes were found to be involved in ATP-binding and carried kinase activity confronting their biological roles in the isoprene (27%) and amino acid (20%) biosyntheses. The expression analysis of genes during cold, drought, and salt stress conditions in tissue culture grown banana cultivar Rasthali plants showed a significant involvement of MaGHMP kinase genes in these stress conditions. The highest expression of MaGHMP kinase3 (8.5 fold) was noted during cold stress, while MaGHMP kinase1 (25 fold and 40.01 fold) showed maximum expression during drought and salt stress conditions in leaf tissue of Rasthali. CONCLUSION Our findings suggested that MaGHMP kinase1 (MaHSK) and MaGHMP kinase3 (MaGlcAK) could be considered promising candidates for thwarting the abiotic stresses in banana.
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Affiliation(s)
- Siddhant Chaturvedi
- Plant Tissue Culture and Genetic Engineering Lab, Department of Biotechnology, S.A.S. Nagar, Ministry of Science and Technology (Government of India), National Agri-Food Biotechnology Institute (NABI), Sector 81, Knowledge City, Mohali, Punjab, 140306, India
- Department of Biotechnology, Panjab University, Chandigarh, 160014, India
- Department of Botany, Goswami Tulsidas Government Post Graduate College (Bundelkhand University, Jhansi), Karwi, Chitrakoot, Uttar Pradesh, 210205, India
| | - Shahirina Khan
- Plant Tissue Culture and Genetic Engineering Lab, Department of Biotechnology, S.A.S. Nagar, Ministry of Science and Technology (Government of India), National Agri-Food Biotechnology Institute (NABI), Sector 81, Knowledge City, Mohali, Punjab, 140306, India
- Department of Botany, Central University of Punjab, Bathinda, Punjab, 151001, India
| | - Neha Thakur
- Plant Tissue Culture and Genetic Engineering Lab, Department of Biotechnology, S.A.S. Nagar, Ministry of Science and Technology (Government of India), National Agri-Food Biotechnology Institute (NABI), Sector 81, Knowledge City, Mohali, Punjab, 140306, India
| | - Alka Jangra
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, Department of Biotechnology, S.A.S. Nagar, Ministry of Science and Technology (Government of India), National Agri-Food Biotechnology Institute (NABI), Sector 81, Knowledge City, Mohali, Punjab, 140306, India.
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Kitashova A, Brodsky V, Chaturvedi P, Pierides I, Ghatak A, Weckwerth W, Nägele T. Quantifying the impact of dynamic plant-environment interactions on metabolic regulation. JOURNAL OF PLANT PHYSIOLOGY 2023; 290:154116. [PMID: 37839392 DOI: 10.1016/j.jplph.2023.154116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth, development and resilience towards adverse conditions. Although genome sequencing technologies and applications have experienced triumphantly rapid development during the last decades, enabling nowadays a fast and cheap sequencing of full genomes, prediction of metabolic phenotypes from genotype × environment interactions remains, at best, very incomplete. The main reasons are a lack of understanding of how different levels of molecular organisation depend on each other, and how they are constituted and expressed within a setup of growth conditions. Phenotypic plasticity, e.g., of the genetic model plant Arabidopsis thaliana, has provided important insights into plant-environment interactions and the resulting genotype x phenotype relationships. Here, we summarize previous and current findings about plant development in a changing environment and how this might be shaped and reflected in metabolism and its regulation. We identify current challenges in the study of plant development and metabolic regulation and provide an outlook of how methodological workflows might support the application of findings made in model systems to crops and their cultivation.
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Affiliation(s)
- Anastasia Kitashova
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Vladimir Brodsky
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Palak Chaturvedi
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Iro Pierides
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Arindam Ghatak
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Wolfram Weckwerth
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Thomas Nägele
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
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Vanderwall M, Gendron JM. HEXOKINASE1 and glucose-6-phosphate fuel plant growth and development. Development 2023; 150:dev202346. [PMID: 37842778 PMCID: PMC10617624 DOI: 10.1242/dev.202346] [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] [Indexed: 10/17/2023]
Abstract
As photoautotrophic organisms, plants produce an incredible spectrum of pigments, anti-herbivory compounds, structural materials and energic intermediates. These biosynthetic routes help plants grow, reproduce and mitigate stress. HEXOKINASE1 (HXK1), a metabolic enzyme and glucose sensor, catalyzes the phosphorylation of hexoses, a key introductory step for many of these pathways. However, previous studies have largely focused on the glucose sensing and signaling functions of HXK1, and the importance of the enzyme's catalytic function is only recently being connected to plant development. In this brief Spotlight, we describe the developmental significance of plant HXK1 and its role in plant metabolic pathways, specifically in glucose-6-phosphate production. Furthermore, we describe the emerging connections between metabolism and development and suggest that HXK1 signaling and catalytic activity regulate discrete areas of plant development.
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Affiliation(s)
- Morgan Vanderwall
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Joshua M. Gendron
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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Oh SW, Imran M, Kim EH, Park SY, Lee SG, Park HM, Jung JW, Ryu TH. Approach strategies and application of metabolomics to biotechnology in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1192235. [PMID: 37636096 PMCID: PMC10451086 DOI: 10.3389/fpls.2023.1192235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
Metabolomics refers to the technology for the comprehensive analysis of metabolites and low-molecular-weight compounds in a biological system, such as cells or tissues. Metabolites play an important role in biological phenomena through their direct involvement in the regulation of physiological mechanisms, such as maintaining cell homeostasis or signal transmission through protein-protein interactions. The current review aims provide a framework for how the integrated analysis of metabolites, their functional actions and inherent biological information can be used to understand biological phenomena related to the regulation of metabolites and how this information can be applied to safety assessments of crops created using biotechnology. Advancement in technology and analytical instrumentation have led new ways to examine the convergence between biology and chemistry, which has yielded a deeper understanding of complex biological phenomena. Metabolomics can be utilized and applied to safety assessments of biotechnology products through a systematic approach using metabolite-level data processing algorithms, statistical techniques, and database development. The integration of metabolomics data with sequencing data is a key step towards improving additional phenotypical evidence to elucidate the degree of environmental affects for variants found in genome associated with metabolic processes. Moreover, information analysis technology such as big data, machine learning, and IT investment must be introduced to establish a system for data extraction, selection, and metabolomic data analysis for the interpretation of biological implications of biotechnology innovations. This review outlines the integrity of metabolomics assessments in determining the consequences of genetic engineering and biotechnology in plants.
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Liu Y, Jiang Y, Liu X, Cheng H, Han Y, Zhang D, Wu J, Liu L, Yan M, Que Y, Zhou D. Identification and Expression Analysis of Hexokinases Family in Saccharum spontaneum L. under Drought and Cold Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:1215. [PMID: 36986904 PMCID: PMC10056587 DOI: 10.3390/plants12061215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/28/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
In plants, the multi-gene family of dual-function hexokinases (HXKs) plays an important role in sugar metabolism and sensing, that affects growth and stress adaptation. Sugarcane is an important sucrose crop and biofuel crop. However, little is known about the HXK gene family in sugarcane. A comprehensive survey of sugarcane HXKs, including physicochemical properties, chromosomal distribution, conserved motifs, and gene structure was conducted, identifying 20 members of the SsHXK gene family that were located on seven of the 32 Saccharum spontaneum L. chromosomes. Phylogenetic analysis showed that the SsHXK family could be divided into three subfamilies (group I, II and III). Motifs and gene structure were related to the classification of SsHXKs. Most SsHXKs contained 8-11 introns which was consistent with other monocots. Duplication event analysis indicated that HXKs in S. spontaneum L. primarily originated from segmental duplication. We also identified putative cis-elements in the SsHXK promoter regions which were involved in phytohormone, light and abiotic stress responses (drought, cold et al.). During normal growth and development, 17 SsHXKs were constitutively expressed in all ten tissues. Among them, SsHXK2, SsHXK12 and SsHXK14 had similar expression patterns and were more highly expressed than other genes at all times. The RNA-seq analysis showed that 14/20 SsHXKs had the highest expression level after cold stress for 6 h, especially SsHXK15, SsHXK16 and SsHXK18. As for drought treatment, 7/20 SsHXKs had the highest expression level after drought stress for 10 days, 3/20 (SsHKX1, SsHKX10 and SsHKX11) had the highest expression level after 10 days of recovery. Overall, our results revealed the potential biological function of SsHXKs, which may provide information for in-depth functional verification.
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Affiliation(s)
- Ying Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yaolan Jiang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xiaolan Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Hefen Cheng
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yuekun Han
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Dawei Zhang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Jinfeng Wu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Lili Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Mingli Yan
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410000, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/National Engineering Research Center for Sugarcane, Ministry of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dinggang Zhou
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/National Engineering Research Center for Sugarcane, Ministry of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
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Wu Y, Ma L, Zhang L, Zhang Y, Zhou H, Wang Y, Liu Y. Photosynthetic carbon and nitrogen metabolism of Camellia oleifera Abel during acclimation to low light conditions. JOURNAL OF PLANT PHYSIOLOGY 2022; 278:153814. [PMID: 36179398 DOI: 10.1016/j.jplph.2022.153814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Tea-oil tree (Camellia oleifera Abel) is an important woody oil crop with high economic value. However, it has low photosynthetic production considering the low light intensity of its growth environment. To understand the acclimation mechanism of tea-oil trees to low light conditions, three light intensity treatments were conducted: high light (450-500 μmol. m-2. s-1), medium light (180-200 μmol. m-2. s-1), and low light (45-50 μmol. m-2. s-1). The carbon (C) and nitrogen (N) metabolism network were constructed by investigating the leaf anatomy, photosynthetic characteristics, N partitioning, transcriptome and metabolome. Results demonstrated that a larger proportion light energy was used for photochemical reactions in an environment with lower light intensity, which resulted in an increase in photosystem II photochemical efficiency and instantaneous light use efficiency (LUE) at the leaf level. As the light intensity increased, decreased electron transfer and carboxylation efficiencies, photorespiration and dark respiration rates, LUE at plant level, and N use efficiency (PNUE) were observed. Leaves trended to harvest more light using higher expression levels of light-harvesting protein genes, higher chlorophyll content, more granum and more tightly stacked granum lamella under lower light intensity. At transcriptional and metabolic levels, the TCA cycle, and the synthesis of starch and saccharides were weakened as light intensity decreased, while the Calvin cycle did not show the regularity between different treatments. Less N was distributed in Rubisco, respiration, and cell wall proteins as light decreased. Storage N was prominently accumulated in forms of amino acids (especially L-arginine) and amino acid derivatives as under medium and low light environments, to make up for C deficiency. Therefore, tea-oil trees actively improve light-harvesting capacity and enlarges the storage N pool to adapt to a low light environment, at the cost of a decrease of photosynthetic C assimilation and PNUE.
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Affiliation(s)
- Yang Wu
- Institute of Jiangxi Oil-tea Camellia, Jiujiang University, Jiujiang, Jiangxi Province, 332005, China
| | - Lin Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lisha Zhang
- Institute of Jiangxi Oil-tea Camellia, Jiujiang University, Jiujiang, Jiangxi Province, 332005, China
| | - Yan Zhang
- Institute of Jiangxi Oil-tea Camellia, Jiujiang University, Jiujiang, Jiangxi Province, 332005, China
| | - Huiwen Zhou
- Institute of Jiangxi Oil-tea Camellia, Jiujiang University, Jiujiang, Jiangxi Province, 332005, China.
| | - Yongjun Wang
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, Jilin Province, 130033, China.
| | - Yanan Liu
- Institute of Jiangxi Oil-tea Camellia, Jiujiang University, Jiujiang, Jiangxi Province, 332005, China
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Han M, Xu X, Xiong Y, Wei H, Yao K, Huang T, Long Y, Su T. Genome-Wide Survey and Expression Analyses of Hexokinase Family in Poplar (Populus trichocarpa). PLANTS 2022; 11:plants11152025. [PMID: 35956502 PMCID: PMC9370503 DOI: 10.3390/plants11152025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022]
Abstract
Hexokinase (HXK) family proteins exert critical roles in catalyzing hexose phosphorylation, sugar sensing, and modulation of plant growth and stress adaptation. Nevertheless, a large amount remains unknown about the molecular profile of HXK enzymes in Populus trichocarpa, a woody model tree species. A genome-wide survey of HXK-encoding genes, including phylogenies, genomic structures, exon/intron organization, chromosomal distribution, and conserved features, was conducted, identifying six putative HXK isogenes (PtHXK1-6) in the Populus genome. The evolutionary tree demonstrated that 135 homologous HXKs between 17 plant species were categorized into four major subfamilies (type A, B, C, and D), clustering one plastidic (PtHXK3) and five mitochondrial PtHXKs grouped into type A and B, respectively. The in silico deduction prompted the presence of the conserved sugar-binding core (motif 4), phosphorylation sites (motif 2 and 3), and adenosine-binding domains (motif 7). The transcriptomic sequencing (RNA-seq) and the quantitative real-time PCR (qRT-PCR) assays revealed that three isogenes (PtHXK2, 3, and 6) were abundantly expressed in leaves, stems, and roots, while others appeared to be dominantly expressed in the reproductive tissues. Under the stress exposure, PtHXK2 and 6 displayed a significant induction upon the pathogenic fungi (Fusarium solani) infection and marked promotions by glucose feeding in roots. In contrast, the PtHXK3 and 6 are ABA-responsive genes, following a dose-dependent manner. The comprehensive analyses of the genomic patterns and expression profiling provide theoretical clues and lay a foundation for unraveling the physiological and signaling roles underlying the fine-tuned PtHXKs responding to diverse stressors.
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Affiliation(s)
- Mei Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
| | - Xianglei Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
| | - Yuan Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
| | - Haikun Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
| | - Kejun Yao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
| | - Tingting Huang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
| | - Yingle Long
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
| | - Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (X.X.); (Y.X.); (H.W.); (K.Y.); (T.H.); (Y.L.)
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel.: +86-1589-598-3381
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Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology. Int J Mol Sci 2022; 23:ijms23136985. [PMID: 35805979 PMCID: PMC9266571 DOI: 10.3390/ijms23136985] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.
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Seydel C, Kitashova A, Fürtauer L, Nägele T. Temperature-induced dynamics of plant carbohydrate metabolism. PHYSIOLOGIA PLANTARUM 2022; 174:e13602. [PMID: 34802152 DOI: 10.1111/ppl.13602] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Carbohydrates are direct products of photosynthetic CO2 assimilation. Within a changing temperature regime, both photosynthesis and carbohydrate metabolism need tight regulation to prevent irreversible damage of plant tissue and to sustain energy metabolism, growth and development. Due to climate change, plants are and will be exposed to both long-term and short-term temperature changes with increasing amplitude. Particularly sudden fluctuations, which might comprise a large temperature amplitude from low to high temperature, pose a challenge for plants from the cellular to the ecosystem level. A detailed understanding of fundamental regulatory processes, which link photosynthesis and carbohydrate metabolism under such fluctuating environmental conditions, is essential for an estimate of climate change consequences. Further, understanding these processes is important for biotechnological application, breeding and engineering. Environmental light and temperature regimes are sensed by a molecular network that comprises photoreceptors and molecular components of the circadian clock. Photosynthetic efficiency and plant productivity then critically depend on enzymatic regulation and regulatory circuits connecting plant cells with their environment and re-stabilising photosynthetic efficiency and carbohydrate metabolism after temperature-induced deflection. This review summarises and integrates current knowledge about re-stabilisation of photosynthesis and carbohydrate metabolism after perturbation by changing temperature (heat and cold).
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Affiliation(s)
- Charlotte Seydel
- Faculty of Biology, Plant Development, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Anastasia Kitashova
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Lisa Fürtauer
- Institute for Biology III, Unit of Plant Molecular Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Thomas Nägele
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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Qin S, Zhang Y, Tian Y, Xu F, Zhang P. Subcellular metabolomics: Isolation, measurement, and applications. J Pharm Biomed Anal 2021; 210:114557. [PMID: 34979492 DOI: 10.1016/j.jpba.2021.114557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/26/2022]
Abstract
Metabolomics, a technique that profiles global small molecules in biological samples, has been a pivotal tool for disease diagnosis and mechanism research. The sample type in metabolomics covers a wide range, including a variety of body fluids, tissues, and cells. However, little attention was paid to the smaller, relatively independent partition systems in cells, namely the organelles. The organelles are specific compartments/places where diverse metabolic activities are happening in an orderly manner. Metabolic disorders of organelles were found to occur in various pathological conditions such as inherited metabolic diseases, diabetes, cancer, and neurodegenerative diseases. However, at the cellular level, the metabolic outcomes of organelles and cytoplasm are superimposed interactively, making it difficult to describe the changes in subcellular compartments. Therefore, characterizing the metabolic pool in the compartmentalized system is of great significance for understanding the role of organelles in physiological functions and diseases. So far, there are very few research articles or reviews related to subcellular metabolomics. In this review, subcellular fractionation and metabolite analysis methods, as well as the application of subcellular metabolomics in the physiological and pathological studies are systematically reviewed, as a practical reference to promote the continued advancement in subcellular metabolomics.
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Affiliation(s)
- Siyuan Qin
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yuxin Zhang
- Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, PR China
| | - Yuan Tian
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China
| | - Fengguo Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Pei Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China.
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Funck D, Baumgarten L, Stift M, von Wirén N, Schönemann L. Differential Contribution of P5CS Isoforms to Stress Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:565134. [PMID: 33101333 PMCID: PMC7545825 DOI: 10.3389/fpls.2020.565134] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/09/2020] [Indexed: 05/24/2023]
Abstract
Proline accumulation is a widespread response of plants to salt stress as well as drought and cold stress. In most plant species, two isoforms of pyrroline-5-carboxylate synthetase (P5CS) catalyze the first step in proline biosynthesis from glutamate. In Arabidopsis, these isoforms differ in their spatial and temporal expression patterns, suggesting sub-functionalization. P5CS1 has been identified as the major contributor to stress-induced proline accumulation, whereas P5CS2 has been considered important for embryo development and growth. In contrast to previous results, our analysis of P5CS1- and P5CS2-GFP fusion proteins indicates that both enzymes were exclusively localized in the cytosol. The comparison of the susceptibility of p5cs1 and p5cs2 mutants to infection with Pseudomonas syringae and salt stress provided novel information on the contribution of the two P5CS isoforms to proline accumulation and stress tolerance. In agreement with previous studies, salt-stressed p5cs1 mutants accumulated very little proline, indicating that P5CS1 contributed more to stress-induced proline accumulation, whereas its impact on stress tolerance was rather weak. Germination and establishment of p5cs2 mutants were impaired under ambient conditions, further supporting that P5CS2 is most important for growth and development, whereas its contribution to stress-induced proline accumulation was smaller than that of P5CS1. In contrast to p5cs1 mutants or wildtype plants, p5cs2 mutants were only weakly affected by sudden exposure to a high NaCl concentration. These findings show that proline content, which was intermediate in leaves of p5cs2 mutants, was not directly correlated with stress tolerance in our experiments. In rosettes of NaCl-exposed p5cs2 mutants, nearly no accumulation of Na+ was observed, and the plants showed neither chlorosis nor reduction of photosynthesis. Based on these data, we suggest a function of P5CS2 or P5CS2-mediated proline synthesis in regulating Na+ accumulation in leaves and thereby salt stress tolerance.
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Affiliation(s)
- Dietmar Funck
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Lukas Baumgarten
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Marc Stift
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Luise Schönemann
- Department of Biology, University of Konstanz, Konstanz, Germany
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Indications for a Central Role of Hexokinase Activity in Natural Variation of Heat Acclimation in Arabidopsis thaliana. PLANTS 2020; 9:plants9070819. [PMID: 32610673 PMCID: PMC7411702 DOI: 10.3390/plants9070819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 01/06/2023]
Abstract
Diurnal and seasonal changes of abiotic environmental factors shape plant performance and distribution. Changes of growth temperature and light intensity may vary significantly on a diurnal, but also on a weekly or seasonal scale. Hence, acclimation to a changing temperature and light regime is essential for plant survival and propagation. In the present study, we analyzed photosynthetic CO2 assimilation and metabolic regulation of the central carbohydrate metabolism in two natural accessions of Arabidopsis thaliana that originate from north western Russia and south Italy during exposure to heat and a combination of heat and high light. Our findings indicate that it is hardly possible to predict photosynthetic capacities under combined stress from single stress experiments. Further, capacities of hexose phosphorylation were found to be significantly lower in the Italian than in the Russian accession, which could explain an inverted sucrose-to-hexose ratio. Together with the finding of significantly stronger accumulation of anthocyanins under heat/high light, these observations indicate a central role of hexokinase activity in the stabilization of photosynthesis and carbohydrate metabolism during environmental changes.
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Lee K, Kang H. Roles of Organellar RNA-Binding Proteins in Plant Growth, Development, and Abiotic Stress Responses. Int J Mol Sci 2020; 21:ijms21124548. [PMID: 32604726 PMCID: PMC7352785 DOI: 10.3390/ijms21124548] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Organellar gene expression (OGE) in chloroplasts and mitochondria is primarily modulated at post-transcriptional levels, including RNA processing, intron splicing, RNA stability, editing, and translational control. Nucleus-encoded Chloroplast or Mitochondrial RNA-Binding Proteins (nCMRBPs) are key regulatory factors that are crucial for the fine-tuned regulation of post-transcriptional RNA metabolism in organelles. Although the functional roles of nCMRBPs have been studied in plants, their cellular and physiological functions remain largely unknown. Nevertheless, existing studies that have characterized the functions of nCMRBP families, such as chloroplast ribosome maturation and splicing domain (CRM) proteins, pentatricopeptide repeat (PPR) proteins, DEAD-Box RNA helicase (DBRH) proteins, and S1-domain containing proteins (SDPs), have begun to shed light on the role of nCMRBPs in plant growth, development, and stress responses. Here, we review the latest research developments regarding the functional roles of organellar RBPs in RNA metabolism during growth, development, and abiotic stress responses in plants.
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Affiliation(s)
- Kwanuk Lee
- Plant Molecular Biology (Botany), Department of Biology I, Ludwig-Maximilians-University München, 82152 Martinsried, Germany
- Correspondence: (K.L.); (H.K.); Tel.: +49-157-8852-8990 (K.L.); +82-62-530-2181 (H.K.); Fax: +82-62-530-2079 (H.K.)
| | - Hunseung Kang
- Department of Applied Biology and AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju 61186, Korea
- Correspondence: (K.L.); (H.K.); Tel.: +49-157-8852-8990 (K.L.); +82-62-530-2181 (H.K.); Fax: +82-62-530-2079 (H.K.)
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Fürtauer L, Weiszmann J, Weckwerth W, Nägele T. Dynamics of Plant Metabolism during Cold Acclimation. Int J Mol Sci 2019; 20:E5411. [PMID: 31671650 PMCID: PMC6862541 DOI: 10.3390/ijms20215411] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/26/2022] Open
Abstract
Plants have evolved strategies to tightly regulate metabolism during acclimation to a changing environment. Low temperature significantly constrains distribution, growth and yield of many temperate plant species. Exposing plants to low but non-freezing temperature induces a multigenic processes termed cold acclimation, which eventually results in an increased freezing tolerance. Cold acclimation comprises reprogramming of the transcriptome, proteome and metabolome and affects communication and signaling between subcellular organelles. Carbohydrates play a central role in this metabolic reprogramming. This review summarizes current knowledge about the role of carbohydrate metabolism in plant cold acclimation with a focus on subcellular metabolic reprogramming, its thermodynamic constraints under low temperature and mathematical modelling of metabolism.
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Affiliation(s)
- Lisa Fürtauer
- Plant Evolutionary Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Bavaria, Germany.
| | - Jakob Weiszmann
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna 1090, Austria.
- Vienna Metabolomics Center, University of Vienna, Vienna 1090, Austria.
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna 1090, Austria.
- Vienna Metabolomics Center, University of Vienna, Vienna 1090, Austria.
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Bavaria, Germany.
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