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Balcke GU, Vahabi K, Giese J, Finkemeier I, Tissier A. Coordinated metabolic adaptation of Arabidopsis thaliana to high light. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:387-405. [PMID: 39175460 DOI: 10.1111/tpj.16992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/03/2024] [Accepted: 08/05/2024] [Indexed: 08/24/2024]
Abstract
SUMMARYIn plants, exposure to high light irradiation induces various stress responses, which entail complex metabolic rearrangements. To explore these dynamics, we conducted time‐course experiments spanning 2 min to 72 h with Arabidopsis thaliana under high and control light. Comparative metabolomics, transcriptomics, redox proteomics, and stable isotope labeling on leaf rosettes identified a series of synchronous and successive responses that provide a deeper insight into well‐orchestrated mechanisms contributing to high‐light acclimation. We observed transient transcriptome downregulation related to light harvesting and electron flow before the profound remodeling of the photosynthetic apparatus. Throughout the entire time course, redox homeostasis is tightly balanced between downregulation of production and enhanced transformation of NADPH accompanied by redistribution of reducing equivalents across several subcellular compartments. In both light conditions, C4 acids such as malate and fumarate are produced via anaplerosis. In carbon units, their accumulation in vacuoles surpasses plastidic levels of starch and intensifies notably under high light. In parallel, citrate synthesis from pyruvate is significantly hindered diurnally. Isotopic labeling in 2‐oxoglutarate and glutamate suggests a moderate de novo synthesis of C5 acids from a vacuolar citrate reservoir during the light phase while they are largely renewed during the night. In the absence of a diurnal clockwise flow through the tricarboxylic acid (TCA) cycle, increased oxidation of photorespiratory glycine takes over as a source of reductants to fuel mitochondrial ATP production. These findings, along with previous research, contribute to a model integrating redox balance and linking increased carbon assimilation and nitrogen metabolism, especially in the context of an incomplete TCA cycle.
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Affiliation(s)
- Gerd Ulrich Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Khabat Vahabi
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Jonas Giese
- Institute for Plant Biology and Biotechnology (IBBP), University of Muenster, Schlossplatz 7, D-48149, Münster, Germany
| | - Iris Finkemeier
- Institute for Plant Biology and Biotechnology (IBBP), University of Muenster, Schlossplatz 7, D-48149, Münster, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
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2
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Wang C, Lu C, Wang J, Liu X, Wei Z, Qin Y, Zhang H, Wang X, Wei B, Lv W, Mu G. Molecular mechanisms regulating glucose metabolism in quinoa (Chenopodium quinoa Willd.) seeds under drought stress. BMC PLANT BIOLOGY 2024; 24:796. [PMID: 39174961 PMCID: PMC11342610 DOI: 10.1186/s12870-024-05510-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND Abiotic stress seriously affects the growth and yield of crops. It is necessary to search and utilize novel abiotic stress resistant genes for 2.0 breeding programme in quinoa. In this study, the impact of drought stress on glucose metabolism were investigated through transcriptomic and metabolomic analyses in quinoa seeds. Candidate drought tolerance genes on glucose metabolism pathway were verified by qRT-PCR combined with yeast expression system. RESULTS From 70 quinoa germplasms, drought tolerant material M059 and drought sensitive material M024 were selected by comprehensive evaluation of drought resistance. 7042 differentially expressed genes (DEGs) were indentified through transcriptomic analyses. Gene Ontology (GO) analysis revealed that these DEGs were closely related to carbohydrate metabolic process, phosphorus-containing groups, and intracellular membrane-bounded organelles. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis detected that DEGs were related to pathways involving carbohydrate metabolisms, glycolysis and gluconeogenesis. Twelve key differentially accumulated metabolites (DAMs), (D-galactose, UDP-glucose, succinate, inositol, D-galactose, D-fructose-6-phosphate, D-glucose-6-phosphate, D-glucose-1-phosphate, dihydroxyacetone phosphate, ribulose-5-phosphate, citric acid and L-malate), and ten key candidate DEGs (CqAGAL2, CqINV, CqFrK7, CqCELB, Cqbg1x, CqFBP, CqALDO, CqPGM, CqIDH3, and CqSDH) involved in drought response were identified. CqSDH, CqAGAL2, and Cqβ-GAL13 were candidate genes that have been validated in both transcriptomics and yeast expression screen system. CONCLUSION These findings provide a foundation for elucidating the molecular regulatory mechanisms governing glucose metabolism in quinoa seeds under drought stress, providing insights for future research exploring responses to drought stress in quinoa.
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Affiliation(s)
- Chunmei Wang
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Chuan Lu
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Junling Wang
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Xiaoqing Liu
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Zhimin Wei
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals(Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, The Key Research Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Yan Qin
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Huilong Zhang
- Shijiazhuang Fubao Ecological Technology Co., LTD, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Xiaoxia Wang
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Boxiang Wei
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Wei Lv
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, 050000, Hebei Province, P. R. China.
| | - Guojun Mu
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China.
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China.
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3
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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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4
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Miao F, Wang Y, Haq NU, Lyu MJA, Zhu XG. Rewiring of primary metabolism for ammonium recycling under short-term low CO 2 treatment - its implication for C 4 evolution. FRONTIERS IN PLANT SCIENCE 2024; 15:1322261. [PMID: 39148616 PMCID: PMC11324553 DOI: 10.3389/fpls.2024.1322261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 07/04/2024] [Indexed: 08/17/2024]
Abstract
The dramatic decrease in atmospheric CO2 concentration during Oligocene was proposed as directly linked to C4 evolution. However, it remains unclear how the decreased CO2 concentration directly facilitate C4 evolution, besides its role as a selection pressure. We conducted a systematic transcriptomics and metabolomics analysis under short-term low CO2 condition and found that Arabidopsis grown under this condition showed 1) increased expression of most genes encoding C4-related enzymes and transporters; 2) increased expression of genes involved in photorespiration and pathways related to carbon skeleton generation for ammonium refixation; 3) increased expression of genes directly involved in ammonium refixation. Furthermore, we found that in vitro treatment of leaves with NH4 + induced a similar pattern of changes in C4 related genes and genes involved in ammonium refixation. These data support the view that Arabidopsis grown under short-term low CO2 conditions rewired its metabolism to supply carbon skeleton for ammonium recycling, during which process the expression of C4 genes were up-regulated as a result of a hitchhiking process. This study provides new insights into the adaptation of the C3 model plant Arabidopsis under low CO2 conditions and suggests that low CO2 can facilitate the evolution of C4 photosynthesis beyond the commonly assumed role of being a selection pressure.
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Affiliation(s)
- Fenfen Miao
- University of Chinese Academy of Sciences (UCAS), Beijing, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Ying Wang
- University of Chinese Academy of Sciences (UCAS), Beijing, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Noor Ui Haq
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber-Pakhtunkhwa, Pakistan
| | - Ming-Ju Amy Lyu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xin-Guang Zhu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
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5
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Zha L, Wei S, Huang D, Zhang J. Multi-Omics Analyses of Lettuce ( Lactuca sativa) Reveals Primary Metabolism Reorganization Supporting Distinct Features of Secondary Metabolism Induced by Supplementing UV-A Radiation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15498-15511. [PMID: 38950542 DOI: 10.1021/acs.jafc.4c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
UV can serve as an effective light spectrum for regulating plant secondary metabolites, while relevant studies on UV-A are much less extensive than those on UV-B. A comprehensive understanding of the selective effects of UV-A on different secondary metabolites and the specific features of primary metabolism that drive these effects is still lacking. To address this knowledge gap, we conducted a study to analyze the dynamic changes in the metabolome and transcriptome of lettuce leaves irradiated with red plus UV-A light (monochromatic red light as control). Generally, UV-A promoted the synthesis of most phenylpropanoids and terpenoids originating from the shikimate and methylerythritol phosphate (MEP) pathway in plastids but sacrificed the synthesis of terpenoids derived from the mevalonate (MVA) pathway, particularly sesquiterpenes. Increased precursors supply for the shikimate and MEP pathway under UV-A was directly supported by the activation of the Calvin-Benson cycle and phosphoenolpyruvate transport. Whereas, along with phosphoenolpyruvate transport, the TCA cycle was restrained, causing deprivation of the MVA pathway precursor. In addition, UV-A also activated the plastidic oxidative branch of the pentose phosphate pathway, photorespiration, and malate shuttle, to ensure a sufficient supply of nitrogen, circulation homeostasis of the Calvin-Benson cycle, and energy balance, thus indirectly supporting UV-A-induced specific secondary metabolic output. This study provides a comprehensive framework for understanding the flexible primary-secondary metabolism interactions that are able to produce specific metabolites favorable for adaptation to environmental stimuli.
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Affiliation(s)
- Lingyan Zha
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiwei Wei
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Danfeng Huang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingjin Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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6
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Pastor-Fernández J, Sanmartín N, Manresa-Grao M, Cassan C, Pétriacq P, Gibon Y, Gamir J, Romero-Rodriguez B, Castillo AG, Cerezo M, Flors V, Sánchez-Bel P. Deciphering molecular events behind Systemin-induced resistance to Botrytis cinerea in tomato plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4111-4127. [PMID: 38581374 DOI: 10.1093/jxb/erae146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 04/05/2024] [Indexed: 04/08/2024]
Abstract
Plant defence peptides are paramount endogenous danger signals secreted after a challenge, intensifying the plant immune response. The peptidic hormone Systemin (Sys) was shown to participate in resistance in several plant pathosystems, although the mechanisms behind Sys-induced resistance when exogenously applied remain elusive. We performed proteomic, metabolomic, and enzymatic studies to decipher the Sys-induced changes in tomato plants in either the absence or the presence of Botrytis cinerea infection. Sys treatments triggered direct proteomic rearrangement mostly involved in carbon metabolism and photosynthesis. However, the final induction of defence proteins required concurrent challenge, triggering priming of pathogen-targeted proteins. Conversely, at the metabolomic level, Sys-treated plants showed an alternative behaviour following a general priming profile. Of the primed metabolites, the flavonoids rutin and isorhamnetin and two alkaloids correlated with the proteins 4-coumarate-CoA-ligase and chalcone-flavanone-isomerase triggered by Sys treatment. In addition, proteomic and enzymatic analyses revealed that Sys conditioned the primary metabolism towards the production of available sugars that could be fuelling the priming of callose deposition in Sys-treated plants; furthermore, PR1 appeared as a key element in Sys-induced resistance. Collectively, the direct induction of proteins and priming of specific secondary metabolites in Sys-treated plants indicated that post-translational protein regulation is an additional component of priming against necrotrophic fungi.
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Affiliation(s)
- Julia Pastor-Fernández
- Plant Immunity and Biochemistry Laboratory, Biochemistry and Molecular Biology Section, Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, Avd Vicente Sos Baynat s/n 12071 Castellón, Spain
| | - Neus Sanmartín
- Plant Immunity and Biochemistry Laboratory, Biochemistry and Molecular Biology Section, Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, Avd Vicente Sos Baynat s/n 12071 Castellón, Spain
| | - Maria Manresa-Grao
- Plant Immunity and Biochemistry Laboratory, Biochemistry and Molecular Biology Section, Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, Avd Vicente Sos Baynat s/n 12071 Castellón, Spain
| | - Cédric Cassan
- Univ Bordeaux, INRAE, UMR1332 BFP, 33882 Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140 Villenave d'Ornon, France
| | - Pierre Pétriacq
- Univ Bordeaux, INRAE, UMR1332 BFP, 33882 Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140 Villenave d'Ornon, France
| | - Yves Gibon
- Univ Bordeaux, INRAE, UMR1332 BFP, 33882 Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140 Villenave d'Ornon, France
| | - Jordi Gamir
- Plant Immunity and Biochemistry Laboratory, Biochemistry and Molecular Biology Section, Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, Avd Vicente Sos Baynat s/n 12071 Castellón, Spain
| | - Beatriz Romero-Rodriguez
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM 'La Mayora'), Universidad de Málaga-Consejo Superior de Investigaciones Cientificas (UMA-CSIC), Campus Teatinos, 29010 Málaga, Spain
| | - Araceli G Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM 'La Mayora'), Universidad de Málaga-Consejo Superior de Investigaciones Cientificas (UMA-CSIC), Campus Teatinos, 29010 Málaga, Spain
| | - Miguel Cerezo
- Plant Immunity and Biochemistry Laboratory, Biochemistry and Molecular Biology Section, Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, Avd Vicente Sos Baynat s/n 12071 Castellón, Spain
| | - Victor Flors
- Plant Immunity and Biochemistry Laboratory, Biochemistry and Molecular Biology Section, Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, Avd Vicente Sos Baynat s/n 12071 Castellón, Spain
| | - Paloma Sánchez-Bel
- Plant Immunity and Biochemistry Laboratory, Biochemistry and Molecular Biology Section, Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, Avd Vicente Sos Baynat s/n 12071 Castellón, Spain
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7
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Tcherkez G, Abadie C, Dourmap C, Lalande J, Limami AM. Leaf day respiration: More than just catabolic CO 2 production in the light. PLANT, CELL & ENVIRONMENT 2024; 47:2631-2639. [PMID: 38528759 DOI: 10.1111/pce.14904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/08/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
Summary statementDay respiration is a net flux resulting from several CO2‐generating and CO2‐fixing reactions, not only related to catabolism but also to anabolism. We review pieces of evidence that decarboxylating reactions are partly fed by carbon sources disconnected from current photosynthesis and how they reflect various metabolic pathways.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de recherche en horticulture et semences, Université d'Angers, INRAe, Beaucouzé, France
- Research school of biology, ANU College of Science, Australian National University, Canberra, Australia
| | - Cyril Abadie
- Institut de recherche en horticulture et semences, Université d'Angers, INRAe, Beaucouzé, France
- Ecophysiologie et génomique fonctionnelle de la vigne, Institut des Sciences de la Vigne et du Vin, INRAe, Université de Bordeaux, Villenave-d'Ornon, France
| | - Corentin Dourmap
- Institut de recherche en horticulture et semences, Université d'Angers, INRAe, Beaucouzé, France
| | - Julie Lalande
- Institut de recherche en horticulture et semences, Université d'Angers, INRAe, Beaucouzé, France
| | - Anis M Limami
- Institut de recherche en horticulture et semences, Université d'Angers, INRAe, Beaucouzé, France
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8
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Timm S, Klaas N, Niemann J, Jahnke K, Alseekh S, Zhang Y, Souza PVL, Hou LY, Cosse M, Selinski J, Geigenberger P, Daloso DM, Fernie AR, Hagemann M. Thioredoxins o1 and h2 jointly adjust mitochondrial dihydrolipoamide dehydrogenase-dependent pathways towards changing environments. PLANT, CELL & ENVIRONMENT 2024; 47:2542-2560. [PMID: 38518065 DOI: 10.1111/pce.14899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/24/2024]
Abstract
Thioredoxins (TRXs) are central to redox regulation, modulating enzyme activities to adapt metabolism to environmental changes. Previous research emphasized mitochondrial and microsomal TRX o1 and h2 influence on mitochondrial metabolism, including photorespiration and the tricarboxylic acid (TCA) cycle. Our study aimed to compare TRX-based regulation circuits towards environmental cues mainly affecting photorespiration. Metabolite snapshots, phenotypes and CO2 assimilation were compared among single and multiple TRX mutants in the wild-type and the glycine decarboxylase T-protein knockdown (gldt1) background. Our analyses provided evidence for additive negative effects of combined TRX o1 and h2 deficiency on growth and photosynthesis. Especially metabolite accumulation patterns suggest a shared regulation mechanism mainly on mitochondrial dihydrolipoamide dehydrogenase (mtLPD1)-dependent pathways. Quantification of pyridine nucleotides, in conjunction with 13C-labelling approaches, and biochemical analysis of recombinant mtLPD1 supported this. It also revealed mtLPD1 inhibition by NADH, pointing at an additional measure to fine-tune it's activity. Collectively, we propose that lack of TRX o1 and h2 perturbs the mitochondrial redox state, which impacts on other pathways through shifts in the NADH/NAD+ ratio via mtLPD1. This regulation module might represent a node for simultaneous adjustments of photorespiration, the TCA cycle and branched chain amino acid degradation under fluctuating environmental conditions.
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Affiliation(s)
- Stefan Timm
- Plant Physiology Department, University of Rostock, Rostock, Germany
| | - Nicole Klaas
- Plant Physiology Department, University of Rostock, Rostock, Germany
| | - Janice Niemann
- Plant Physiology Department, University of Rostock, Rostock, Germany
| | - Kathrin Jahnke
- Plant Physiology Department, University of Rostock, Rostock, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - Youjun Zhang
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Paulo V L Souza
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Liang-Yu Hou
- Department Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Maike Cosse
- Department of Plant Cell Biology, Botanical Institute, Christian-Albrechts University Kiel, Kiel, Germany
| | - Jennifer Selinski
- Department of Plant Cell Biology, Botanical Institute, Christian-Albrechts University Kiel, Kiel, Germany
| | - Peter Geigenberger
- Department Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Danilo M Daloso
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Martin Hagemann
- Plant Physiology Department, University of Rostock, Rostock, Germany
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9
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Tiepo AN, Coutinho ID, de Oliveira Machado G, Calzavara AK, Hertel MF, Pimenta JA, de Oliveira ALM, Colnago LA, Henning LMM, Oliveira HC, Stolf-Moreira R. Influence of plant growth-promoting bacteria on leaf carbon and nitrogen metabolism of two drought-stressed neotropical tree species: a metabolomic approach. PLANTA 2024; 260:31. [PMID: 38888604 DOI: 10.1007/s00425-024-04460-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 06/07/2024] [Indexed: 06/20/2024]
Abstract
Deforestation of Atlantic Forest has caused prolonged drought events in the last decades. The need for reforestation is growing, and the development of native seedlings that are more tolerant to drought stress is necessary. A biotechnological tool that improves plant tolerance is the use of plant growth-promoting bacteria (PGPB) as inoculants. Two species of PGPB were inoculated in drought-stressed seedlings of two neotropical tree species that have been used in environmental restoration programs: Cecropia pachystachya and Cariniana estrellensis. Biometrical, physiological, and metabolomic parameters from carbon and nitrogen pathways were evaluated. We found that the PGPB positively influenced photosynthesis and growth parameters in both trees under drought. The enzymes activities, the tricarboxylic acid cycle intermediates, the amino acids, and protein contents were also influenced by the PGPB treatments. The results allowed us to find the specific composition of secondary metabolites of each plant species. This study provides evidence that there is not a single mechanism involved in drought tolerance and that the inoculation with PGPB promotes a broad-spectrum tolerance response in Neotropical trees. The inoculation with PGPB appears as an important strategy to improve drought tolerance in Atlantic Forest native trees and enhance environmental restoration programs' success. MAIN CONCLUSION: The association with plant growth-promoting bacteria improved the tolerance to drought in Neotropical trees through biochemical, physiological, and biometrical parameters. This can enhance the success of forest restoration programs.
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Affiliation(s)
- Angelica Nunes Tiepo
- Department of Animal and Plant Biology, Center of Biological Sciences, State University of Londrina-UEL, Rodovia Celso Garcia Cid-PR445, Km 380, Campus Universitário, Londrina, PR, 86057-970, Brazil.
| | - Isabel Duarte Coutinho
- Embrapa Instrumentação, Rua XV de Novembro, São Carlos, São Paulo, 1452, 13560-970, Brazil
| | | | - Anderson Kikuchi Calzavara
- Department of Animal and Plant Biology, Center of Biological Sciences, State University of Londrina-UEL, Rodovia Celso Garcia Cid-PR445, Km 380, Campus Universitário, Londrina, PR, 86057-970, Brazil
| | - Mariana Fernandes Hertel
- Department of Animal and Plant Biology, Center of Biological Sciences, State University of Londrina-UEL, Rodovia Celso Garcia Cid-PR445, Km 380, Campus Universitário, Londrina, PR, 86057-970, Brazil
| | - José Antonio Pimenta
- Department of Animal and Plant Biology, Center of Biological Sciences, State University of Londrina-UEL, Rodovia Celso Garcia Cid-PR445, Km 380, Campus Universitário, Londrina, PR, 86057-970, Brazil
| | | | - Luiz Alberto Colnago
- Embrapa Instrumentação, Rua XV de Novembro, São Carlos, São Paulo, 1452, 13560-970, Brazil
| | | | - Halley Caixeta Oliveira
- Department of Animal and Plant Biology, Center of Biological Sciences, State University of Londrina-UEL, Rodovia Celso Garcia Cid-PR445, Km 380, Campus Universitário, Londrina, PR, 86057-970, Brazil
| | - Renata Stolf-Moreira
- Department of Animal and Plant Biology, Center of Biological Sciences, State University of Londrina-UEL, Rodovia Celso Garcia Cid-PR445, Km 380, Campus Universitário, Londrina, PR, 86057-970, Brazil.
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10
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Khan Z, Jan R, Asif S, Farooq M, Kim KM. Exogenous GABA Enhances Copper Stress Resilience in Rice Plants via Antioxidant Defense Mechanisms, Gene Regulation, Mineral Uptake, and Copper Homeostasis. Antioxidants (Basel) 2024; 13:700. [PMID: 38929139 PMCID: PMC11200589 DOI: 10.3390/antiox13060700] [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: 05/09/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
The importance of gamma-aminobutyric acid (GABA) in plants has been highlighted due to its critical role in mitigating metal toxicity, specifically countering the inhibitory effects of copper stress on rice plants. This study involved pre-treating rice plants with 1 mM GABA for one week, followed by exposure to varying concentrations of copper at 50 μM, 100 μM, and 200 μM. Under copper stress, particularly at 100 μM and 200 μM, plant height, biomass, chlorophyll content, relative water content, mineral content, and antioxidant activity decreased significantly compared to control conditions. However, GABA treatment significantly alleviated the adverse effects of copper stress. It increased plant height by 13%, 18%, and 32%; plant biomass by 28%, 52%, and 60%; chlorophyll content by 12%, 30%, and 24%; and relative water content by 10%, 24%, and 26% in comparison to the C50, C100, and C200 treatments. Furthermore, GABA treatment effectively reduced electrolyte leakage by 11%, 34%, and 39%, and the concentration of reactive oxygen species, such as malondialdehyde (MDA), by 9%, 22%, and 27%, hydrogen peroxide (H2O2) by 12%, 38%, and 30%, and superoxide anion content by 8%, 33, and 39% in comparison to C50, C100, and C200 treatments. Additionally, GABA supplementation led to elevated levels of glutathione by 69% and 80%, superoxide dismutase by 22% and 125%, ascorbate peroxidase by 12% and 125%, and catalase by 75% and 100% in the C100+G and C200+G groups as compared to the C100 and C200 treatments. Similarly, GABA application upregulated the expression of GABA shunt pathway-related genes, including gamma-aminobutyric transaminase (OsGABA-T) by 38% and 80% and succinic semialdehyde dehydrogenase (OsSSADH) by 60% and 94% in the C100+G and C200+G groups, respectively, as compared to the C100 and C200 treatments. Conversely, the expression of gamma-aminobutyric acid dehydrogenase (OsGAD) was downregulated. GABA application reduced the absorption of Cu2+ by 54% and 47% in C100+G and C200+G groups as compared to C100, and C200 treatments. Moreover, GABA treatment enhanced the uptake of Ca2+ by 26% and 82%, Mg2+ by 12% and 67%, and K+ by 28% and 128% in the C100+G and C200+G groups as compared to C100, and C200 treatments. These findings underscore the pivotal role of GABA-induced enhancements in various physiological and molecular processes, such as plant growth, chlorophyll content, water content, antioxidant capacity, gene regulation, mineral uptake, and copper sequestration, in enhancing plant tolerance to copper stress. Such mechanistic insights offer promising implications for the advancement of safe and sustainable food production practices.
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Affiliation(s)
- Zakirullah Khan
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea; (Z.K.); (S.A.); (M.F.)
| | - Rahmatullah Jan
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea; (Z.K.); (S.A.); (M.F.)
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Saleem Asif
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea; (Z.K.); (S.A.); (M.F.)
| | - Muhammad Farooq
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea; (Z.K.); (S.A.); (M.F.)
| | - Kyung-Min Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea; (Z.K.); (S.A.); (M.F.)
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
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11
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Xu Y, Schmiege SC, Sharkey TD. The oxidative pentose phosphate pathway in photosynthesis: a tale of two shunts. THE NEW PHYTOLOGIST 2024; 242:2453-2463. [PMID: 38567702 DOI: 10.1111/nph.19730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/17/2024] [Indexed: 05/24/2024]
Abstract
CO2 release in the light (RL) and its presumed source, oxidative pentose phosphate pathways, were found to be insensitive to CO2 concentration. The oxidative pentose phosphate pathways form glucose 6-phosphate (G6P) shunts that bypass the nonoxidative pentose phosphate reactions of the Calvin-Benson cycle. Using adenosine diphosphate glucose and uridine diphosphate glucose as proxies for labeling of G6P in the stroma and cytosol respectively, it was found that only the cytosolic shunt was active. Uridine diphosphate glucose, a proxy for cytosolic G6P, and 6-phosphogluconate (6PG) were significantly less labeled than Calvin-Benson cycle intermediates in the light. But ADP glucose, a proxy for stromal G6P, is labeled to the same degree as Calvin-Benson cycle intermediates and much greater than 6PG. A metabolically inert pool of sedoheptulose bisphosphate can slowly equilibrate keeping the label in sedoheptulose lower than in other stromal metabolites. Finally, phosphorylation of fructose 6-phosphate (F6P) in the cytosol can allow some unlabeled carbon in cytosolic F6P to dilute label in phosphenolpyruvate. The results clearly show that there is oxidative pentose phosphate pathway activity in the cytosol that provides a shunt around the nonoxidative pentose phosphate pathway reactions of the Calvin-Benson cycle and is not strongly CO2-sensitive.
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Affiliation(s)
- Yuan Xu
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Stephanie C Schmiege
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biology, Western University, London, ON, N6A 5B7, Canada
| | - Thomas D Sharkey
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
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12
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Mi C, Zhang Y, Zhao Y, Lin L. Mechanisms of low nighttime temperature promote oil accumulation in Brassica napus L. based on in-depth transcriptome analysis. PHYSIOLOGIA PLANTARUM 2024; 176:e14372. [PMID: 38812077 DOI: 10.1111/ppl.14372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/08/2024] [Indexed: 05/31/2024]
Abstract
Rape (Brassica napus L.; AACC) is an important oil-bearing crop worldwide. Temperature significantly affects the production of oil crops; however, the mechanisms underlying temperature-promoted oil biosynthesis remain largely unknown. In this study, we found that a temperature-sensitive cultivar (O) could accumulate higher seed oil content under low nighttime temperatures (LNT,13°C) compared with a temperature-insensitive cultivar (S). We performed an in-depth transcriptome analysis of seeds from both cultivars grown under different nighttime temperatures. We found that low nighttime temperatures induced significant changes in the transcription patterns in the seeds of both cultivars. In contrast, the expression of genes associated with fatty acid and lipid pathways was higher in the O cultivar than in the S cultivar under low nighttime temperatures. Among these genes, we identified 14 genes associated with oil production, especially BnLPP and ACAA1, which were remarkably upregulated in the O cultivar in response to low nighttime temperatures compared to S. Further, a WGCNA analysis and qRT-PCR verification revealed that these genes were mainly regulated by five transcription factors, WRKY20, MYB86, bHLH144, bHLH95, and NAC12, whose expression was also increased in O compared to S under LNT. These results allowed the elucidation of the probable molecular mechanism of oil accumulation under LNT conditions in the O cultivar. Subsequent biochemical assays verified that BnMYB86 transcriptionally activated BnLPP expression, contributing to oil accumulation. Meanwhile, at LNT, the expression levels of these genes in the O plants were higher than at high nighttime temperatures, DEGs (SUT, PGK, PK, GPDH, ACCase, SAD, KAS II, LACS, FAD2, FAD3, KCS, KAR, ECR, GPAT, LPAAT, PAP, DGAT, STERO) related to lipid biosynthesis were also upregulated, most of which are used in oil accumulation.
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Affiliation(s)
- Chao Mi
- Agricultural Research Institute, Xizang Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Yusong Zhang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yanning Zhao
- Vegetable Research Institute, Xizang Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Liangbin Lin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
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13
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Han B, Yan J, Wu T, Yang X, Wang Y, Ding G, Hammond J, Wang C, Xu F, Wang S, Shi L. Proteomics reveals the significance of vacuole Pi transporter in the adaptability of Brassica napus to Pi deprivation. FRONTIERS IN PLANT SCIENCE 2024; 15:1340867. [PMID: 38590751 PMCID: PMC11000671 DOI: 10.3389/fpls.2024.1340867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 03/04/2024] [Indexed: 04/10/2024]
Abstract
Vacuolar Pi transporters (VPTs) have recently been identified as important regulators of cellular Pi status in Arabidopsis thaliana and Oryza sativa. In the oil crop Brassica napus, BnA09PHT5;1a and BnC09PHT5;1a are two homologs of AtPHT5;1, the vacuolar Pi influx transporter in Arabidopsis. Here, we show that Pi deficiency induces the transcription of both homologs of PHT5;1a genes in B. napus leaves. Brassica PHT5;1a double mutants (DM) had smaller shoots and higher cellular Pi concentrations than wild-type (WT, Westar 10), suggesting the potential role of BnPHT5;1a in modulating cellular Pi status in B. napus. A proteomic analysis was performed to estimate the role of BnPHT5;1a in Pi fluctuation. Results show that Pi deprivation disturbs the abundance of proteins in the physiological processes involved in carbohydrate metabolism, response to stimulus and stress in B. napus, while disruption of BnPHT5;1a genes may exacerbate these processes. Besides, the processes of cell redox homeostasis, lipid metabolic and proton transmembrane transport are supposed to be unbalanced in BnPHT5;1a DM under the -Pi condition. Noteworthy, disruption of BnPHT5;1a genes severely alters the abundance of proteins related to ATP biosynthesis, and proton/inorganic cation transmembrane under normal Pi condition, which might contribute to B. napus growth limitations. Additionally, seven new protein markers of Pi homeostasis are identified in B. napus. Taken together, this study characterizes the important regulatory role of BnPHT5;1a genes as vacuolar Pi influx transporters in Pi homeostasis in B. napus.
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Affiliation(s)
- Bei Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Junjun Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Tao Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, China
| | - Yajie Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, China
| | - John Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Chuang Wang
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan, China
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14
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Cheng T, Zhou X, Lin J, Zhou X, Wang H, Chen T. Transcriptomic and Metabolomic Analyses Reveal the Response Mechanism of Ophiopogon japonicus to Waterlogging Stress. BIOLOGY 2024; 13:197. [PMID: 38534466 DOI: 10.3390/biology13030197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Ophiopogon japonicus, a plant that thrives in river alluvial dams, often faces waterlogging stress due to sustained rainfall and flood seasons, which significantly impacts its growth and development. Currently, the mechanisms of waterlogging tolerance in Ophiopogon japonicus are still unclear. This study analyzed the transcriptome and metabolome data for Ophiopogon japonicus in the Sichuan region (referred to as CMD) under varying degrees of waterlogging stress: mild, moderate, and severe. The results indicate that the group exposed to flooding stress exhibited a higher number of differentially expressed genes (DEGs) compared to the control group. Notably, most DEGs were downregulated and primarily enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction pathways. A total of 5151 differentially accumulated metabolites (DAMs) were identified, with significantly upregulated DAMs annotated to two clusters, namely flavonoids such as apiin, pelargonin, and others. Furthermore, our study revealed significant upregulation in the expression of C2H2 (C2H2 zinc finger proteins) and AP2/ERF-ERF (the subfamily ERF proteins of APETALA2/ethylene-responsive element binding factors) transcription factors in CMD under flooding stress, suggesting their critical roles in enabling CMD to adapt to these conditions. In conclusion, this research provides insights into the intricate molecular mechanisms underlying CMD's response to flooding stress and reports valuable genetic data for the development of transgenic plants with improved waterlogging tolerance.
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Affiliation(s)
- Tingting Cheng
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Xia Zhou
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Juan Lin
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Xianjian Zhou
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Hongsu Wang
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Tiezhu Chen
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
- Sichuan Provincial Key Laboratory of Quality and Innovation Research of Chinese Materia Medica, Chengdu 610041, China
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15
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Fedorin DN, Eprintsev AT, Igamberdiev AU. The role of promoter methylation of the genes encoding the enzymes metabolizing di- and tricarboxylic acids in the regulation of plant respiration by light. JOURNAL OF PLANT PHYSIOLOGY 2024; 294:154195. [PMID: 38377939 DOI: 10.1016/j.jplph.2024.154195] [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: 11/23/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
We discuss the role of epigenetic changes at the level of promoter methylation of the key enzymes of carbon metabolism in the regulation of respiration by light. While the direct regulation of enzymes via modulation of their activity and post-translational modifications is fast and readily reversible, the role of cytosine methylation is important for providing a prolonged response to environmental changes. In addition, adenine methylation can play a role in the regulation of transcription of genes. The mitochondrial and extramitochondrial forms of several enzymes participating in the tricarboxylic acid cycle and associated reactions are regulated via promoter methylation in opposite ways. The mitochondrial forms of citrate synthase, aconitase, fumarase, NAD-malate dehydrogenase are inhibited while the cytosolic forms of aconitase, fumarase, NAD-malate dehydrogenase, and the peroxisomal form of citrate synthase are activated. It is concluded that promoter methylation represents a universal mechanism of the regulation of activity of respiratory enzymes in plant cells by light. The role of the regulation of the mitochondrial and cytosolic forms of respiratory enzymes in the operation of malate and citrate valves and in controlling the redox state and balancing the energy level of photosynthesizing plant cells is discussed.
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Affiliation(s)
- Dmitry N Fedorin
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018, Voronezh, Russia.
| | - Alexander T Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018, Voronezh, Russia.
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada.
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16
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Liu H, Jiao P, Guan L, Wang C, Zhang XX, Ma L. Functional traits and health implications of the global household drinking-water microbiome retrieved using an integrative genome-centric approach. WATER RESEARCH 2024; 250:121094. [PMID: 38183799 DOI: 10.1016/j.watres.2023.121094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/15/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
The biological safety of drinking water plays a crucial role in public health protection. However, research on the drinking water microbiome remains in its infancy, especially little is known about the potentially pathogenic bacteria in and functional characteristics of the microbiome in household tap water that people are directly exposed to. In this study, we used a genomic-centric approach to construct a genetic catalogue of the drinking water microbiome by analysing 116 metagenomic datasets of household tap water worldwide, spanning nine countries/regions on five continents. We reconstructed 859 high-quality metagenome-assembled genomes (MAGs) spanning 27 bacterial and 2 archaeal phyla, and found that the core MAGs belonging to the phylum Proteobacteria encoded the highest metabolic functional diversity of the 33 key complete metabolic modules. In particular, we found that two core MAGs of Brevibacillus and Methylomona encoded genes for methane metabolism, which may support the growth of heterotrophic organisms observed in the oligotrophic ecosystem. Four MAGs of complete ammonia oxidation (comammox) Nitrospira were identified and functional metabolic analysis suggested these may enable mixotrophic growth and encode genes for reactive oxygen stress defence and arsenite reduction that could aid survival in the environment of oligotrophic drinking water systems. Four MAGs were annotated as potentially pathogenic bacteria (PPB) and thus represented a possible public health concern. They belonged to the genera Acinetobacter (n = 3) and Mycobacterium (n = 1), with a total relative abundance of 1.06 % in all samples. The genomes of PPB A. junii and A. ursingii were discovered to contain antibiotic resistance genes and mobile genetic elements that could contribute to antimicrobial dissemination in drinking water. Further network analysis suggested that symbiotic microbes which support the growth of pathogenic bacteria can be targets for future surveillance and removal.
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Affiliation(s)
- Huafeng Liu
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Pengbo Jiao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Lei Guan
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Chen Wang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Liping Ma
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai 200062, PR China.
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17
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Páez-Watson T, van Loosdrecht MCM, Wahl SA. From metagenomes to metabolism: Systematically assessing the metabolic flux feasibilities for "Candidatus Accumulibacter" species during anaerobic substrate uptake. WATER RESEARCH 2024; 250:121028. [PMID: 38128304 DOI: 10.1016/j.watres.2023.121028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/06/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
Abstract
With the rapid growing availability of metagenome assembled genomes (MAGs) and associated metabolic models, the identification of metabolic potential in individual community members has become possible. However, the field still lacks an unbiassed systematic evaluation of the generated metagenomic information to uncover not only metabolic potential, but also feasibilities of these models under specific environmental conditions. In this study, we present a systematic analysis of the metabolic potential in species of "Candidatus Accumulibacter", a group of polyphosphate-accumulating organisms (PAOs). We constructed a metabolic model of the central carbon metabolism and compared the metabolic potential among available MAGs for "Ca. Accumulibacter" species. By combining Elementary Flux Modes Analysis (EFMA) with max-min driving force (MDF) optimization, we obtained all possible flux distributions of the metabolic network and calculated their individual thermodynamic feasibility. Our findings reveal significant variations in the metabolic potential among "Ca. Accumulibacter" MAGs, particularly in the presence of anaplerotic reactions. EFMA revealed 700 unique flux distributions in the complete metabolic model that enable the anaerobic uptake of acetate and its conversion into polyhydroxyalkanoates (PHAs), a well-known phenotype of "Ca. Accumulibacter". However, thermodynamic constraints narrowed down this solution space to 146 models that were stoichiometrically and thermodynamically feasible (MDF > 0 kJ/mol), of which only 8 were strongly feasible (MDF > 7 kJ/mol). Notably, several novel flux distributions for the metabolic model were identified, suggesting putative, yet unreported, functions within the PAO communities. Overall, this work provides valuable insights into the metabolic variability among "Ca. Accumulibacter" species and redefines the anaerobic metabolic potential in the context of phosphate removal. More generally, the integrated workflow presented in this paper can be applied to any metabolic model obtained from a MAG generated from microbial communities to objectively narrow the expected phenotypes from community members.
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Affiliation(s)
- Timothy Páez-Watson
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| | | | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
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18
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Ramírez CF, Cavieres LA, Sanhueza C, Vallejos V, Gómez-Espinoza O, Bravo LA, Sáez PL. Ecophysiology of Antarctic Vascular Plants: An Update on the Extreme Environment Resistance Mechanisms and Their Importance in Facing Climate Change. PLANTS (BASEL, SWITZERLAND) 2024; 13:449. [PMID: 38337983 PMCID: PMC10857404 DOI: 10.3390/plants13030449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 02/12/2024]
Abstract
Antarctic flowering plants have become enigmatic because of their unique capability to colonize Antarctica. It has been shown that there is not a single trait that makes Colobanthus quitensis and Deschampsia antarctica so special, but rather a set of morphophysiological traits that coordinately confer resistance to one of the harshest environments on the Earth. However, both their capacity to inhabit Antarctica and their uniqueness remain not fully explained from a biological point of view. These aspects have become more relevant due to the climatic changes already impacting Antarctica. This review aims to compile and update the recent advances in the ecophysiology of Antarctic vascular plants, deepen understanding of the mechanisms behind their notable resistance to abiotic stresses, and contribute to understanding their potential responses to environmental changes. The uniqueness of Antarctic plants has prompted research that emphasizes the role of leaf anatomical traits and cell wall properties in controlling water loss and CO2 exchange, the role of Rubisco kinetics traits in facilitating efficient carbon assimilation, and the relevance of metabolomic pathways in elucidating key processes such as gas exchange, nutrient uptake, and photoprotection. Climate change is anticipated to have significant and contrasting effects on the morphophysiological processes of Antarctic species. However, more studies in different locations outside Antarctica and using the latitudinal gradient as a natural laboratory to predict the effects of climate change are needed. Finally, we raise several questions that should be addressed, both to unravel the uniqueness of Antarctic vascular species and to understand their potential responses to climate change.
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Affiliation(s)
- Constanza F. Ramírez
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción 4030000, Chile; (C.F.R.); (V.V.)
- Instituto de Ecología y Biodiversidad-IEB, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Lohengrin A. Cavieres
- Instituto de Ecología y Biodiversidad-IEB, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
- ECOBIOSIS, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4030000, Chile
| | - Carolina Sanhueza
- Laboratorio de Fisiología Vegetal, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4030000, Chile;
| | - Valentina Vallejos
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción 4030000, Chile; (C.F.R.); (V.V.)
- Instituto de Ecología y Biodiversidad-IEB, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Olman Gómez-Espinoza
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile; (O.G.-E.) (L.A.B.)
| | - León A. Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile; (O.G.-E.) (L.A.B.)
| | - Patricia L. Sáez
- Instituto de Ecología y Biodiversidad-IEB, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile; (O.G.-E.) (L.A.B.)
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Sankar TV, Saharay M, Santhosh D, Menon S, Raran-Kurussi S, Padmasree K. Biomolecular interaction of purified recombinant Arabidopsis thaliana's alternative oxidase 1A with TCA cycle metabolites: Biophysical and molecular docking studies. Int J Biol Macromol 2024; 258:128814. [PMID: 38114006 DOI: 10.1016/j.ijbiomac.2023.128814] [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: 04/14/2023] [Revised: 11/08/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
In higher plants, the mitochondrial alternative oxidase (AOX) pathway plays an essential role in maintaining the TCA cycle/cellular carbon and energy balance under various physiological and stress conditions. Though the activation of AOX pathway upon exogenous addition of α-ketoacids/TCA cycle metabolites [pyruvate, α-ketoglutarate (α-KG), oxaloacetic acid (OAA), succinate and malic acid] to isolated mitochondria is known, the molecular mechanism of interaction of these metabolites with AOX protein is limited. The present study is designed to understand the biomolecular interaction of pure recombinant Arabidopsis thaliana AOX1A with TCA cycle metabolites under in vitro conditions using various biophysical and molecular docking studies. The binding of α-KG, fumaric acid and OAA to rAtAOX1A caused conformational change in the microenvironment of tryptophan residues as evidenced by red shift in the synchronous fluorescence spectra (∆λ = 60 nm). Besides, a decrease in conventional fluorescence emission spectra, tyrosine specific synchronous fluorescence spectra (∆λ = 15 nm) and α-helical content of CD spectra revealed the conformation changes in rAtAOX1A structure associated with binding of various TCA cycle metabolites. Further, surface plasmon resonance (SPR) and microscale thermophoresis (MST) studies revealed the binding affinity, while docking studies identified binding pocket residues, respectively, for these metabolites on rAtAOX1A.
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Affiliation(s)
- Tadiboina Veera Sankar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Moumita Saharay
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Dharawath Santhosh
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Saji Menon
- Senior Field Application Scientist, Nanotemper Technologies GmbH, India
| | - Sreejith Raran-Kurussi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 500107, India
| | - Kollipara Padmasree
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India.
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20
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Garcia-Molina A, Pastor V. Systemic analysis of metabolome reconfiguration in Arabidopsis after abiotic stressors uncovers metabolites that modulate defense against pathogens. PLANT COMMUNICATIONS 2024; 5:100645. [PMID: 37403356 PMCID: PMC10811363 DOI: 10.1016/j.xplc.2023.100645] [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: 03/08/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/06/2023]
Abstract
Understanding plant immune responses is complex because of the high interdependence among biological processes in homeostatic networks. Hence, the integration of environmental cues causes network rewiring that interferes with defense responses. Similarly, plants retain molecular signatures configured under abiotic stress periods to rapidly respond to recurrent stress, and these can alter immunity. Metabolome changes imposed by abiotic stressors are persistent, although their impact on defense remains to be clarified. In this study, we profiled metabolomes of Arabidopsis plants under several abiotic stress treatments applied individually or simultaneously to capture temporal trajectories in metabolite composition during adverse conditions and recovery. Further systemic analysis was performed to address the relevance of metabolome changes and extract central features to be tested in planta. Our results demonstrate irreversibility in major fractions of metabolome changes as a general pattern in response to abiotic stress periods. Functional analysis of metabolomes and co-abundance networks points to convergence in the reconfiguration of organic acid and secondary metabolite metabolism. Arabidopsis mutant lines for components related to these metabolic pathways showed altered defense capacities against different pathogens. Collectively, our data suggest that sustained metabolome changes configured in adverse environments can act as modulators of immune responses and provide evidence for a new layer of regulation in plant defense.
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Affiliation(s)
- Antoni Garcia-Molina
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, C/Vall Moronta, Edifici CRAG, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain.
| | - Victoria Pastor
- Department of Biology, Biochemistry, and Natural Sciences, School of Technology and Experimental Sciences, Universitat Jaume I, 12006 Castelló de la Plana, Spain
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21
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Zhang Y, Hu J, Zhong Y, Liu S, Liu L, Mu X, Chen C, Yang S, Li G, Zhang D, Huang X, Yang J, Huang X, Bian S, Nie S. Insoluble/soluble fraction ratio determines effects of dietary fiber on gut microbiota and serum metabolites in healthy mice. Food Funct 2024; 15:338-354. [PMID: 38088096 DOI: 10.1039/d3fo04068b] [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: 01/03/2024]
Abstract
Both soluble dietary fiber (SDF) and insoluble dietary fiber (IDF) play pivotal roles in maintaining gut microbiota homeostasis; whether the effects of the different ratios of IDF and SDF are consistent remains unclear. Consequently, we selected SDFs and IDFs from six representative foods (apple, celery, kale, black fungus, oats, and soybeans) and formulated nine dietary fiber recipes composed of IDF and SDF with a ratio from 1 : 9 to 9 : 1 (NDFR) to compare their impact on microbial effects with healthy mice. We discovered that NDFR treatment decreased the abundance of Proteobacteria and the ratio of Firmicutes/Bacteroidetes at the phylum level. The α diversity and relative richness of Parabacteroides and Prevotella at the genus level showed an upward trend along with the ratio of IDF increasing, while the relative abundance of Akkermansia at the genus level and the production of acetic acid and propionic acid exhibited an increased trend along with the ratio of SDF increasing. The relative abundance of Parabacteroides and Prevotella in the I9S1DF group (the ratio of IDF and SDF was 9 : 1) was 1.72 times and 5.92 times higher than that in the I1S9DF group (the ratio of IDF and SDF was 1 : 9), respectively. The relative abundance of Akkermansia in the I1S9DF group was 17.18 times higher than that in the I9S1DF group. Moreover, a high ratio of SDF (SDF reaches 60% or more) enriched the glycerophospholipid metabolism pathway; however, a high ratio of IDF (IDF reaches 80% or more) regulated the tricarboxylic acid cycle. These findings are helpful in the development of dietary fiber supplements based on gut microbiota and metabolites.
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Affiliation(s)
- Yanli Zhang
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Jielun Hu
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Yadong Zhong
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Shuai Liu
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Liandi Liu
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Xinyi Mu
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Chunhua Chen
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Shenji Yang
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Guohao Li
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Duoduo Zhang
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Xinru Huang
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Jinrui Yang
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Xiaojun Huang
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Shuigen Bian
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Shaoping Nie
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
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22
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Dellero Y, Berardocco S, Bouchereau A. U- 13C-glucose incorporation into source leaves of Brassica napus highlights light-dependent regulations of metabolic fluxes within central carbon metabolism. JOURNAL OF PLANT PHYSIOLOGY 2024; 292:154162. [PMID: 38103478 DOI: 10.1016/j.jplph.2023.154162] [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: 07/07/2023] [Revised: 11/07/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
Plant central carbon metabolism comprises several important metabolic pathways acting together to support plant growth and yield establishment. Despite the emergence of 13C-based dynamic approaches, the regulation of metabolic fluxes between light and dark conditions has not yet received sufficient attention for agronomically relevant plants. Here, we investigated the impact of light/dark conditions on carbon allocation processes within central carbon metabolism of Brassica napus after U-13C-glucose incorporation into leaf discs. Leaf gas-exchanges and metabolite contents were weakly impacted by the leaf disc method and the incorporation of glucose. 13C-analysis by GC-MS showed that U-13C-glucose was converted to fructose for de novo biosynthesis of sucrose at similar rates in both light and dark conditions. However, light conditions led to a reduced commitment of glycolytic carbons towards respiratory substrates (pyruvate, alanine, malate) and TCA cycle intermediates compared to dark conditions. Analysis of 13C-enrichment at the isotopologue level and metabolic pathway isotopic tracing reconstructions identified the contribution of multiple pathways to serine biosynthesis in light and dark conditions. However, the direct contribution of the glucose-6-phosphate shunt to serine biosynthesis was not observed. Our results also provided isotopic evidences for an active metabolic connection between the TCA cycle, glycolysis and photorespiration in light conditions through a rapid reallocation of TCA cycle decarboxylations back to the TCA cycle through photorespiration and glycolysis. Altogether, these results suggest the active coordination of core metabolic pathways across multiple compartments to reorganize C-flux modes.
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Affiliation(s)
- Younès Dellero
- INRAE, Université Rennes, Institut Agro, IGEPP-UMR1349, P2M2-MetaboHUB, Le Rheu, 35653, France.
| | - Solenne Berardocco
- INRAE, Université Rennes, Institut Agro, IGEPP-UMR1349, P2M2-MetaboHUB, Le Rheu, 35653, France
| | - Alain Bouchereau
- INRAE, Université Rennes, Institut Agro, IGEPP-UMR1349, P2M2-MetaboHUB, Le Rheu, 35653, France
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23
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Marín-Peña AJ, Vega-Mas I, Busturia I, de la Osa C, González-Moro MB, Monreal JA, Marino D. Root phosphoenolpyruvate carboxylase activity is essential for Sorghum bicolor tolerance to ammonium nutrition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108312. [PMID: 38154297 DOI: 10.1016/j.plaphy.2023.108312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/05/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) is an enzyme family with pivotal roles in plant carbon and nitrogen metabolism. A main role for non-photosynthetic PEPC is as anaplerotic enzyme to load tricarboxylic acid (TCA) cycle with carbon skeletons that compensate the intermediates diverted for biomolecule synthesis such as amino acids. When plants are grown under ammonium (NH4+) nutrition, the excessive uptake of NH4+ often provokes a stress situation. When plants face NH4+ stress, N assimilation is greatly induced and thus, requires the supply of carbon skeletons coming from TCA cycle. In this work, we addressed the importance of root PEPC and TCA cycle for sorghum (Sorghum bicolor L. Moench), a C4 cereal crop, grown under ammonium nutrition. To do so, we used RNAi sorghum lines that display a decrease expression of SbPPC3 (Ppc3 lines), the main root PEPC isoform, and reduced root PEPC activity. SbPPC3 silencing provoked ammonium hypersensitivity, meaning lower biomass accumulation in Ppc3 respect to WT plants when growing under ammonium nutrition. The silenced plants presented a deregulation of primary metabolism as highlighted by the accumulation of NH4+ in the root and the alteration of normal TCA functioning, which was evidenced by the accumulation of organic acids in the root under ammonium nutrition. Altogether, our work evidences the importance of non-photosynthetic PEPC, and root TCA cycle, in sorghum to deal with high external NH4+ availability.
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Affiliation(s)
- A J Marín-Peña
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - I Vega-Mas
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - I Busturia
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - C de la Osa
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, 41012, Sevilla, Spain
| | - M B González-Moro
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - J A Monreal
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, 41012, Sevilla, Spain.
| | - D Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain.
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24
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Göttlinger T, Lohaus G. Origin and Function of Amino Acids in Nectar and Nectaries of Pitcairnia Species with Particular Emphasis on Alanine and Glutamine. PLANTS (BASEL, SWITZERLAND) 2023; 13:23. [PMID: 38202331 PMCID: PMC10780904 DOI: 10.3390/plants13010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Floral nectar contains sugars and numerous other compounds, including amino acids, but little is known about their function and origin in nectar. Therefore, the amino acid, sugar, and inorganic ion concentrations, as well as the activity of alanine aminotransferase (AlaAT) and glutamine synthetase (GS) in nectar, nectaries, and leaves were analyzed in 30 Pitcairnia species. These data were compared with various floral traits, the pollinator type, and the phylogenetic relationships of the species to find possible causes for the high amino acid concentrations in the nectar of some species. The highest concentrations of amino acids (especially alanine) in nectar were found in species with reddish flowers. Furthermore, the concentration of amino acids in nectar and nectaries is determined through analyzing flower color/pollination type rather than phylogenetic relations. This study provides new insights into the origin of amino acids in nectar. The presence of almost all amino acids in nectar is mainly due to their transport in the phloem to the nectaries, with the exception of alanine, which is partially produced in nectaries. In addition, active regulatory mechanisms are required in nectaries that retain most of the amino acids and allow the selective secretion of specific amino acids, such as alanine.
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Affiliation(s)
- Thomas Göttlinger
- Molecular Plant Science and Plant Biochemistry, University of Wuppertal, 42119 Wuppertal, Germany;
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25
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O'Lone CE, Juhász A, Nye-Wood M, Dunn H, Moody D, Ral JP, Colgrave ML. Proteomic exploration reveals a metabolic rerouting due to low oxygen during controlled germination of malting barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1305381. [PMID: 38186599 PMCID: PMC10771735 DOI: 10.3389/fpls.2023.1305381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/20/2023] [Indexed: 01/09/2024]
Abstract
Barley (Hordeum vulgare L.) is used in malt production for brewing applications. Barley malting involves a process of controlled germination that modifies the grain by activating enzymes to solubilize starch and proteins for brewing. Initially, the grain is submerged in water to raise grain moisture, requiring large volumes of water. Achieving grain modification at reduced moisture levels can contribute to the sustainability of malting practices. This study combined proteomics, bioinformatics, and biochemical phenotypic analysis of two malting barley genotypes with observed differences in water uptake and modification efficiency. We sought to reveal the molecular mechanisms at play during controlled germination and explore the roles of protein groups at 24 h intervals across the first 72 h. Overall, 3,485 protein groups were identified with 793 significant differentially abundant (DAP) within and between genotypes, involved in various biological processes, including protein synthesis, carbohydrate metabolism, and hydrolysis. Functional integration into metabolic pathways, such as glycolysis, pyruvate, starch and sucrose metabolism, revealed a metabolic rerouting due to low oxygen enforced by submergence during controlled germination. This SWATH-MS study provides a comprehensive proteome reference, delivering new insights into the molecular mechanisms underlying the impacts of low oxygen during controlled germination. It is concluded that continued efficient modification of malting barley subjected to submergence is largely due to the capacity to reroute energy to maintain vital processes, particularly protein synthesis.
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Affiliation(s)
- Clare E. O'Lone
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, Joondalup, WA, Australia
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, ACT, Canberra, ACT, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, Joondalup, WA, Australia
| | - Mitchell Nye-Wood
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, Joondalup, WA, Australia
| | - Hugh Dunn
- Pilot Malting Australia, Edith Cowan University, School of Science, Joondalup, WA, Australia
| | - David Moody
- Barley Breeding, InterGrain Pty Ltd, Bibra Lake, WA, Australia
| | - Jean-Philippe Ral
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, ACT, Canberra, ACT, Australia
| | - Michelle L. Colgrave
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, Joondalup, WA, Australia
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Brisbane, QLD, Australia
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26
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Baker CR, Cocuron JC, Alonso AP, Niyogi KK. Time-resolved systems analysis of the induction of high photosynthetic capacity in Arabidopsis during acclimation to high light. THE NEW PHYTOLOGIST 2023; 240:2335-2352. [PMID: 37849025 DOI: 10.1111/nph.19324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
Induction of high photosynthetic capacity is a key acclimation response to high light (HL) for many herbaceous dicot plants; however, the signaling pathways that control this response remain largely unknown. Here, a systems biology approach was utilized to characterize the induction of high photosynthetic capacity in strongly and weakly acclimating Arabidopsis thaliana accessions. Plants were grown for 5 wk in a low light (LL) regime, and time-resolved photosynthetic physiological, metabolomic, and transcriptomic responses were measured during subsequent exposure to HL. The induction of high nitrogen (N) assimilation rates early in the HL shift was strongly predictive of the induction of photosynthetic capacity later in the HL shift. Accelerated N assimilation rates depended on the mobilization of existing organic acid (OA) reserves and increased de novo OA synthesis during the induction of high photosynthetic capacity. Enhanced sucrose biosynthesis capacity increased in tandem with the induction of high photosynthetic capacity, and increased starch biosynthetic capacity was balanced by increased starch catabolism. This systems analysis supports a model in which the efficient induction of N assimilation early in the HL shift begins the cascade of events necessary for the induction of high photosynthetic capacity acclimation in HL.
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Affiliation(s)
- Christopher R Baker
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
| | | | - Ana Paula Alonso
- BioAnalytical Facility, University of North Texas, Denton, TX, 76201, USA
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76201, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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27
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Igamberdiev AU, Gordon R. Macroevolution, differentiation trees, and the growth of coding systems. Biosystems 2023; 234:105044. [PMID: 37783374 DOI: 10.1016/j.biosystems.2023.105044] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023]
Abstract
An open process of evolution of multicellular organisms is based on the rearrangement and growth of the program of differentiation that underlies biological morphogenesis. The maintenance of the final (adult) stable non-equilibrium state (stasis) of a developmental system determines the direction of the evolutionary process. This state is achieved via the sequence of differentiation events representable as differentiation trees. A special type of morphogenetic code, acting as a metacode governing gene expression, may include electromechanical signals appearing as differentiation waves. The excessive energy due to the incorporation of mitochondria in eukaryotic cells resulted not only in more active metabolism but also in establishing the differentiation code for interconnecting cells and forming tissues, which fueled the evolutionary process. The "invention" of "continuing differentiation" distinguishes multicellular eukaryotes from other organisms. The Janus-faced control, involving both top-down control by differentiation waves and bottom-up control via the mechanical consequences of cell differentiations, underlies the process of morphogenesis and results in the achievement of functional stable final states. Duplications of branches of the differentiation tree may be the basis for continuing differentiation and macroevolution, analogous to gene duplication permitting divergence of genes. Metamorphoses, if they are proven to be fusions of disparate species, may be classified according to the topology of fusions of two differentiation trees. In the process of unfolding of morphogenetic structures, microevolution can be defined as changes of the differentiation tree that preserve topology of the tree, while macroevolution represents any change that alters the topology of the differentiation tree.
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Affiliation(s)
- Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.
| | - Richard Gordon
- Gulf Specimen Marine Laboratory & Aquarium, 222 Clark Drive, Panacea, FL, 32346, USA.
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28
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Li G, Tang Y, Khan KY, Son Y, Jung J, Qiu X, Zhao X, Iqbal B, Stoffella PJ, Kim GJ, Du D. The toxicological effect on pak choi of co-exposure to degradable and non-degradable microplastics with oxytetracycline in the soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 268:115707. [PMID: 37988994 DOI: 10.1016/j.ecoenv.2023.115707] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]
Abstract
Microplastics and antibiotics are emerging as ubiquitous contaminants in farmland soil, harming crop quality and yield, and thus threatening global food security and human health. However, few studies have examined the individual and joint effects of degradable and/or non-degradable microplastics and antibiotics on crop plants. This study examined the individual and joint effects of polyethylene (PE) and polylactic acid (PLA) microplastics and the antibiotic oxytetracycline (OTC) on pak choi by measuring its growth, photosynthesis, antioxidant enzyme activity, and metabolite levels. Microplastics and/or oxytetracycline adversely affected root weight, photosynthesis, and antioxidant enzyme (superoxide dismutase, catalase, and ascorbate peroxidase) activities. The levels of leaf metabolites were significantly altered, causing physiological changes. Biosynthesis of plant secondary metabolites and amino acids was altered, and plant hormones pathways were disrupted. Separately and together, OTC, PE, and PLA exerted phytotoxic and antagonistic effects on pak choi. Separately and together with OTC, degradable microplastics altered the soil properties, thus causing more severe impacts on plant performance than non-degradable microplastics. This study elucidates the effects on crop plants of toxicity caused by co-exposure to degradable or non-degradable microplastic and antibiotics contamination and suggests mechanisms.
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Affiliation(s)
- Guanlin Li
- School of Emergency Management, Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu Province Engineering Research Center of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, Zhenjiang 212013, People's Republic of China; Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China; Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Yi Tang
- School of Emergency Management, Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu Province Engineering Research Center of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Kiran Yasmin Khan
- School of Emergency Management, Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu Province Engineering Research Center of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, Zhenjiang 212013, People's Republic of China.
| | - Yowhan Son
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jinho Jung
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Xuchun Qiu
- School of Emergency Management, Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu Province Engineering Research Center of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Xin Zhao
- Department of Civil and Environmental Engineering, College of Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Babar Iqbal
- School of Emergency Management, Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu Province Engineering Research Center of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, Zhenjiang 212013, People's Republic of China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, People's Republic of China
| | - Peter Joseph Stoffella
- Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL 34945, United States
| | - Gwang-Jung Kim
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Daolin Du
- School of Emergency Management, Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu Province Engineering Research Center of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, Zhenjiang 212013, People's Republic of China.
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Zhao M, Li C, Zhang C, Zhao Y, Wang X, Cao B, Xu L, Zhang J, Wang J, Zuo Q, Chen Y, Zou G. Under flooding conditions, controlled-release fertiliser coated microplastics affect the growth and accumulation of cadmium in rice by increasing the fluidity of cadmium and interfering with metabolic pathways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166434. [PMID: 37598965 DOI: 10.1016/j.scitotenv.2023.166434] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/05/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
The combined pollution of microplastics (MPs) and Cd can affect plant growth and development and Cd accumulation, with most studies focusing on dryland soil. However, the effects of polyurethane (PU) controlled-release fertiliser coated MPs (PU MPs), which widely exist in rice systems, coupled with Cd on plant growth and Cd accumulation under flooding conditions are still unknown. Therefore, in the present study, in situ techniques were used to systematically study the effects of PU MPs and Cd coupling on the physiological and biochemical performance, metabolomics characteristics, rhizosphere bacterial community, and Cd bioavailability of rice in different soil types (red soil/cinnamon soil). The results showed that the effects of PU MPs on rice growth and Cd accumulation were concentration-dependent, especially in red soil. High PU concentration (1 %) inhibited rice root growth significantly (44 %). The addition of PU MPs inhibited photosynthetically active radiation, net photosynthesis, and transpiration rate of rice, mainly with low concentration (0.1 %) in red soil and high concentration (1 %) in cinnamon soil. PU MPs can enhance the expression of Cd resistance genes (cadC and copA) in soil, enhance the mobility of Cd, and affect the metabolic pathways of metabolites in the rhizosphere soil (red soil: fatty acid metabolism; cinnamon soil: amino acid degradation, heterobiodegradation, and nucleotide metabolism) to promote Cd absorption in rice. Especially in red soil, Cd accumulation in the root and aboveground parts of rice after the addition of high concentration PU (1 %) was 1.7 times and 1.3 times, respectively, that of the control (p < 0.05). Simultaneously, microorganisms can affect rice growth and Cd bioavailability by affecting functional bacteria related to carbon, iron, sulfur, and manganese. The results of the present study provide novel insights into the potential effects of PU MPs coupled with Cd on plants, rhizosphere bacterial communities, and Cd bioavailability.
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Affiliation(s)
- Meng Zhao
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Congping Li
- Qujing City Agricultural Environmental Protection Monitoring Station, Yunnan 655000, China
| | - Cheng Zhang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Yujie Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xuexia Wang
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Bing Cao
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Li Xu
- Institute of Quality Standard and Testing Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jiajia Zhang
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jiachen Wang
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Qiang Zuo
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanhua Chen
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Guoyuan Zou
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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30
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Ladd SN, Daber LE, Bamberger I, Kübert A, Kreuzwieser J, Purser G, Ingrisch J, Deleeuw J, van Haren J, Meredith LK, Werner C. Leaf-level metabolic changes in response to drought affect daytime CO2 emission and isoprenoid synthesis pathways. TREE PHYSIOLOGY 2023; 43:1917-1932. [PMID: 37552065 PMCID: PMC10643046 DOI: 10.1093/treephys/tpad094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/28/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
In the near future, climate change will cause enhanced frequency and/or severity of droughts in terrestrial ecosystems, including tropical forests. Drought responses by tropical trees may affect their carbon use, including production of volatile organic compounds (VOCs), with implications for carbon cycling and atmospheric chemistry that are challenging to predict. It remains unclear how metabolic adjustments by mature tropical trees in response to drought will affect their carbon fluxes associated with daytime CO2 production and VOC emission. To address this gap, we used position-specific 13C-pyruvate labeling to investigate leaf CO2 and VOC fluxes from four tropical species before and during a controlled drought in the enclosed rainforest of Biosphere 2 (B2). Overall, plants that were more drought-sensitive had greater reductions in daytime CO2 production. Although daytime CO2 production was always dominated by non-mitochondrial processes, the relative contribution of CO2 from the tricarboxylic acid cycle tended to increase under drought. A notable exception was the legume tree Clitoria fairchildiana R.A. Howard, which had less anabolic CO2 production than the other species even under pre-drought conditions, perhaps due to more efficient refixation of CO2 and anaplerotic use for amino acid synthesis. The C. fairchildiana was also the only species to allocate detectable amounts of 13C label to VOCs and was a major source of VOCs in B2. In C. fairchildiana leaves, our data indicate that intermediates from the mevalonic acid (MVA) pathway are used to produce the volatile monoterpene trans-β-ocimene, but not isoprene. This apparent crosstalk between the MVA and methylerythritol phosphate pathways for monoterpene synthesis declined with drought. Finally, although trans-β-ocimene emissions increased under drought, it was increasingly sourced from stored intermediates and not de novo synthesis. Unique metabolic responses of legumes may play a disproportionate role in the overall changes in daytime CO2 and VOC fluxes in tropical forests experiencing drought.
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Affiliation(s)
- S Nemiah Ladd
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Georges–Köhler–Allee 053/054, Freiburg 79110, Germany
- Department of Environmental Sciences, University of Basel, Bernoullistrasse 30, Basel 4056, Switzerland
| | - L Erik Daber
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Georges–Köhler–Allee 053/054, Freiburg 79110, Germany
| | - Ines Bamberger
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Georges–Köhler–Allee 053/054, Freiburg 79110, Germany
- Atmospheric Chemistry Group, University of Bayreuth (BayCEER), Dr–Hans–Frisch–Straße 1–3, Bayreuth 95448, Germany
| | - Angelika Kübert
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Georges–Köhler–Allee 053/054, Freiburg 79110, Germany
- Institute for Atmospheric and Earth System Research, University of Helsinki, Pietari Kalmin katu 5, Helsinki 00014, Finland
| | - Jürgen Kreuzwieser
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Georges–Köhler–Allee 053/054, Freiburg 79110, Germany
| | - Gemma Purser
- School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
- UK Centre for Ecology & Hydrology, Bush Estate, Penicuik EH26 0QB, UK
| | - Johannes Ingrisch
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Georges–Köhler–Allee 053/054, Freiburg 79110, Germany
- Department of Ecology, University of Innsbruck, Sternwartestrasse 15, Innsbruck 6020, Austria
| | - Jason Deleeuw
- Biosphere 2, University of Arizona, 32540 S. Biosphere Rd, Oracle, AZ 85739, USA
| | - Joost van Haren
- Biosphere 2, University of Arizona, 32540 S. Biosphere Rd, Oracle, AZ 85739, USA
- Honors College, University of Arizona, 1101 E. Mabel Street, Tucson, AZ 85719, USA
| | - Laura K Meredith
- Biosphere 2, University of Arizona, 32540 S. Biosphere Rd, Oracle, AZ 85739, USA
- School of Natural Resources and the Environment, University of Arizona, 1064 E. Lowell St., Tucson, AZ, 85721, USA
| | - Christiane Werner
- Ecosystem Physiology, Faculty of Environment and Natural Resources, University of Freiburg, Georges–Köhler–Allee 053/054, Freiburg 79110, Germany
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31
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von Bismarck T, Wendering P, Perez de Souza L, Ruß J, Strandberg L, Heyneke E, Walker BJ, Schöttler MA, Fernie AR, Nikoloski Z, Armbruster U. Growth in fluctuating light buffers plants against photorespiratory perturbations. Nat Commun 2023; 14:7052. [PMID: 37923709 PMCID: PMC10624928 DOI: 10.1038/s41467-023-42648-x] [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: 04/26/2023] [Accepted: 10/12/2023] [Indexed: 11/06/2023] Open
Abstract
Photorespiration (PR) is the pathway that detoxifies the product of the oxygenation reaction of Rubisco. It has been hypothesized that in dynamic light environments, PR provides a photoprotective function. To test this hypothesis, we characterized plants with varying PR enzyme activities under fluctuating and non-fluctuating light conditions. Contrasting our expectations, growth of mutants with decreased PR enzyme levels was least affected in fluctuating light compared with wild type. Results for growth, photosynthesis and metabolites combined with thermodynamics-based flux analysis revealed two main causal factors for this unanticipated finding: reduced rates of photosynthesis in fluctuating light and complex re-routing of metabolic fluxes. Only in non-fluctuating light, mutants lacking the glutamate:glyoxylate aminotransferase 1 re-routed glycolate processing to the chloroplast, resulting in photooxidative damage through H2O2 production. Our results reveal that dynamic light environments buffer plant growth and metabolism against photorespiratory perturbations.
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Affiliation(s)
- Thekla von Bismarck
- Molecular Photosynthesis, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany.
| | - Philipp Wendering
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Jeremy Ruß
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Linnéa Strandberg
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Elmien Heyneke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Berkley J Walker
- DOE-Plant Research Laboratory, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd Rm 212, East Lansing, MI, 48823, USA
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Ute Armbruster
- Molecular Photosynthesis, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany.
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Yu J, Wang X, Yuan Q, Shi J, Cai J, Li Z, Ma H. Elucidating the impact of in vitro cultivation on Nicotiana tabacum metabolism through combined in silico modeling and multiomics analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1281348. [PMID: 38023876 PMCID: PMC10655011 DOI: 10.3389/fpls.2023.1281348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
The systematical characterization and understanding of the metabolic behaviors are the basis of the efficient plant metabolic engineering and synthetic biology. Genome-scale metabolic networks (GSMNs) are indispensable tools for the comprehensive characterization of overall metabolic profile. Here we first constructed a GSMN of tobacco, which is one of the most widely used plant chassis, and then combined the tobacco GSMN and multiomics analysis to systematically elucidate the impact of in-vitro cultivation on the tobacco metabolic network. In-vitro cultivation is a widely used technique for plant cultivation, not only in the field of basic research but also for the rapid propagation of valuable horticultural and pharmaceutical plants. However, the systemic effects of in-vitro cultivation on overall plant metabolism could easily be overlooked and are still poorly understood. We found that in-vitro tobacco showed slower growth, less biomass and suppressed photosynthesis than soil-grown tobacco. Many changes of metabolites and metabolic pathways between in-vitro and soil-grown tobacco plants were identified, which notably revealed a significant increase of the amino acids content under in-vitro condition. The in silico investigation showed that in-vitro tobacco downregulated photosynthesis and primary carbon metabolism, while significantly upregulated the GS/GOGAT cycle, as well as producing more energy and less NADH/NADPH to acclimate in-vitro growth demands. Altogether, the combination of experimental and in silico analyses offers an unprecedented view of tobacco metabolism, with valuable insights into the impact of in-vitro cultivation, enabling more efficient utilization of in-vitro techniques for plant propagation and metabolic engineering.
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Affiliation(s)
- Jing Yu
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiaowei Wang
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qianqian Yuan
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiaxin Shi
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jingyi Cai
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhichao Li
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Iglesias-Moya J, Abreu AC, Alonso S, Torres-García MT, Martínez C, Fernández I, Jamilena M. Physiological and metabolomic responses of the ethylene insensitive squash mutant etr2b to drought. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111853. [PMID: 37659732 DOI: 10.1016/j.plantsci.2023.111853] [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: 05/10/2023] [Revised: 07/24/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
The squash gain-of-function mutant etr2b disrupts the ethylene-binding domain of ethylene receptor CpETR2B, conferring partial ethylene insensitivity, changes in flower and fruit development, and enhanced salt tolerance. In this paper, we found that etr2b also confers a growth advantage as well as a physiological and metabolomic response that make the mutant better adapted to drought. Mutant plants had a higher root and leaf biomass than WT under both well-watered and drought conditions, but the reduction in growth parameters in response to drought was similar in WT and etr2b. Water deficit reduced all gas-exchange parameters in both WT and etr2b, but under moderate drought the mutant increased photosynthesis rate in comparison with control conditions, and showed a higher leaf CO2 concentration, transpiration rate, and stomata conductance than WT. The response of etr2b to drought indicates that ethylene is a negative regulator of plant growth under both control and drought. Since etr2b increased ABA content in well-watered plant, but prevented the induction of ABA production in response to drought, it is likely that the etr2b response under drought is not mediated by ABA. A 1H NMR metabolomic analysis revealed that etr2b enhances the accumulation of osmolytes (soluble sugars and trigonelline), unsaturated and polyunsaturated fatty acids, and phenolic compounds under drought, concomitantly with a reduction of malic- and fumaric-acid. The role of CpETR2B and ethylene in the regulation of these drought-protective metabolites is discussed.
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Affiliation(s)
- Jessica Iglesias-Moya
- Department of Biology and Geology, CIAIMBITAL Research Centers. University of Almería, 04120 Almería, Spain
| | - Ana Cristina Abreu
- Department of Chemistry and Physics, CAESCG Research Centers. University of Almería, 04120 Almería, Spain
| | - Sonsoles Alonso
- Department of Biology and Geology, CIAIMBITAL Research Centers. University of Almería, 04120 Almería, Spain
| | - María Trinidad Torres-García
- Department of Biology and Geology, CIAIMBITAL Research Centers. University of Almería, 04120 Almería, Spain; CAESCG Research Centers. University of Almería, 04120 Almería, Spain
| | - Cecilia Martínez
- Department of Biology and Geology, CIAIMBITAL Research Centers. University of Almería, 04120 Almería, Spain
| | - Ignacio Fernández
- Department of Chemistry and Physics, CAESCG Research Centers. University of Almería, 04120 Almería, Spain.
| | - Manuel Jamilena
- Department of Biology and Geology, CIAIMBITAL Research Centers. University of Almería, 04120 Almería, Spain.
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Giese J, Eirich J, Walther D, Zhang Y, Lassowskat I, Fernie AR, Elsässer M, Maurino VG, Schwarzländer M, Finkemeier I. The interplay of post-translational protein modifications in Arabidopsis leaves during photosynthesis induction. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1172-1193. [PMID: 37522418 DOI: 10.1111/tpj.16406] [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: 05/10/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
Diurnal dark to light transition causes profound physiological changes in plant metabolism. These changes require distinct modes of regulation as a unique feature of photosynthetic lifestyle. The activities of several key metabolic enzymes are regulated by light-dependent post-translational modifications (PTM) and have been studied at depth at the level of individual proteins. In contrast, a global picture of the light-dependent PTMome dynamics is lacking, leaving the response of a large proportion of cellular function undefined. Here, we investigated the light-dependent metabolome and proteome changes in Arabidopsis rosettes in a time resolved manner to dissect their kinetic interplay, focusing on phosphorylation, lysine acetylation, and cysteine-based redox switches. Of over 24 000 PTM sites that were detected, more than 1700 were changed during the transition from dark to light. While the first changes, as measured 5 min after onset of illumination, occurred mainly in the chloroplasts, PTM changes at proteins in other compartments coincided with the full activation of the Calvin-Benson cycle and the synthesis of sugars at later timepoints. Our data reveal connections between metabolism and PTM-based regulation throughout the cell. The comprehensive multiome profiling analysis provides unique insight into the extent by which photosynthesis reprograms global cell function and adds a powerful resource for the dissection of diverse cellular processes in the context of photosynthetic function.
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Affiliation(s)
- Jonas Giese
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Jürgen Eirich
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Dirk Walther
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, Potsdam, D-14476, Germany
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, Potsdam, D-14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Ines Lassowskat
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, Potsdam, D-14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Marlene Elsässer
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Veronica G Maurino
- Institute of Cellular and Molecular Botany (IZMB), Rheinische Friedrich-Wilhelms-Universität Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
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Grayson C, Mailloux RJ. Coenzyme Q 10 and nicotinamide nucleotide transhydrogenase: Sentinels for mitochondrial hydrogen peroxide signaling. Free Radic Biol Med 2023; 208:260-271. [PMID: 37573896 DOI: 10.1016/j.freeradbiomed.2023.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/21/2023] [Accepted: 08/08/2023] [Indexed: 08/15/2023]
Abstract
Mitochondria use hydrogen peroxide (H2O2) as a mitokine for cell communication. H2O2 output for signaling depends on its rate of production and degradation, both of which are strongly affected by the redox state of the coenzyme Q10 (CoQ) pool and NADPH availability. Here, we propose the CoQ pool and nicotinamide nucleotide transhydrogenase (NNT) have evolved to be central modalities for mitochondrial H2O2 signaling. Both factors play opposing yet equally important roles in dictating H2O2 availability because they are connected to one another by two central parameters in bioenergetics: electron supply and Δp. The CoQ pool is the central point of convergence for electrons from various dehydrogenases and the electron transport chain (ETC). The increase in Δp creates a significant amount of protonic backpressure on mitochondria to promote H2O2 genesis through CoQ pool reduction. These same factors also drive the activity of NNT, which uses electrons and the Δp to eliminate H2O2. In this way, electron supply and the magnitude of the Δp manifests as a redox connection between the two sentinels, CoQ and NNT, which serve as opposing yet equally important forces required for budgeting H2O2. Taken together, CoQ and NNT are sentinels linked through mitochondrial bioenergetics to manage H2O2 availability for interorganelle and intercellular redox signaling.
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Affiliation(s)
- Cathryn Grayson
- The School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Ste.-Anne-de-Bellevue, Quebec, Canada
| | - Ryan J Mailloux
- The School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Ste.-Anne-de-Bellevue, Quebec, Canada.
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Yang H, Zhang J, Li H. Strategies of NaCl Tolerance in Saline-Alkali-Tolerant Green Microalga Monoraphidium dybowskii LB50. PLANTS (BASEL, SWITZERLAND) 2023; 12:3495. [PMID: 37836235 PMCID: PMC10575140 DOI: 10.3390/plants12193495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023]
Abstract
Studying how freshwater cells modify metabolism and membrane lipids in response to salt stress is important for understanding how freshwater organisms adapt to salt stress and investigating new osmoregulatory ways. Physiological, biochemical, metabolic, and proteomic analyses were applied in a novel saline-alkali-tolerant microalga Monoraphidium dybowskii LB50 under different NaCl concentrations. Cells adopt a variety of strategies to adapt to salt stress, including increasing ion transport and osmolytes, regulating cell cycle and life history, and accumulating triacylglycerol (TAG). A large number of metabolic activities point to TAG accumulation. With increasing NaCl concentration, the C resource for TAG accumulation went from photosynthetically fixed C and a small amount of lipid remodeling to macromolecule degradation and a mass of lipid remodeling, respectively. The energy for TAG accumulation went from linear electron transfer and oxidative phosphate pentose pathway to cyclic electron flow, substrate phosphorylation, oxidation phosphorylation, and FA oxidation. Additionally, digalacturonic acid and amino acids of the N-acetyl group, which usually were the osmotica for marine organisms, were important for M. dybowskii LB50. Freshwater organisms evolved many biological ways to adapt to salt stress. This insight enriches our understanding of the adaptation mechanisms underlying abiotic stress.
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Affiliation(s)
- Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
| | - Jing Zhang
- Analysis and Testing Center of Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Hua Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
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Wrobel TJ, Brilhaus D, Stefanski A, Stühler K, Weber APM, Linka N. Mapping the castor bean endosperm proteome revealed a metabolic interaction between plastid, mitochondria, and peroxisomes to optimize seedling growth. FRONTIERS IN PLANT SCIENCE 2023; 14:1182105. [PMID: 37868318 PMCID: PMC10588648 DOI: 10.3389/fpls.2023.1182105] [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: 03/08/2023] [Accepted: 08/07/2023] [Indexed: 10/24/2023]
Abstract
In this work, we studied castor-oil plant Ricinus communis as a classical system for endosperm reserve breakdown. The seeds of castor beans consist of a centrally located embryo with the two thin cotyledons surrounded by the endosperm. The endosperm functions as major storage tissue and is packed with nutritional reserves, such as oil, proteins, and starch. Upon germination, mobilization of the storage reserves requires inter-organellar interplay of plastids, mitochondria, and peroxisomes to optimize growth for the developing seedling. To understand their metabolic interactions, we performed a large-scale organellar proteomic study on castor bean endosperm. Organelles from endosperm of etiolated seedlings were isolated and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). Computer-assisted deconvolution algorithms were applied to reliably assign the identified proteins to their correct subcellular localization and to determine the abundance of the different organelles in the heterogeneous protein samples. The data obtained were used to build a comprehensive metabolic model for plastids, mitochondria, and peroxisomes during storage reserve mobilization in castor bean endosperm.
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Affiliation(s)
- Thomas J. Wrobel
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Dominik Brilhaus
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum (BMFZ), Universitätsklinikum, Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum (BMFZ), Universitätsklinikum, Düsseldorf, Germany
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Nicole Linka
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
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Papadopoulou A, Ainalidou A, Mellidou I, Karamanoli K. Metabolome and transcriptome reprogramming underlying tomato drought resistance triggered by a Pseudomonas strain. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108080. [PMID: 37812990 DOI: 10.1016/j.plaphy.2023.108080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/05/2023] [Accepted: 10/03/2023] [Indexed: 10/11/2023]
Abstract
Although amelioration of drought stress by Plant Growth Promoting Rhizobacteria (PGPR) is a well-documented phenomenon, the combined molecular and metabolic mechanisms governing this process remain unclear. In these lines, the present study aimed to provide new insights in the underlying drought attenuating mechanisms of tomato plants inoculated with a PGP Pseudomonas putida strain, by using a combination of metabolomic and transcriptomic approaches. Following Differentially Expressed Gene analysis, it became evident that inoculation resulted in a less disturbed plant transcriptome upon drought stress. Untargeted metabolomics highlighted the differential metabolite accumulation upon inoculation, as well as the less metabolic reprograming and the lower accumulation of stress-related metabolites for inoculated stressed plants. These findings were in line with morpho-physiological evidence of drought stress mitigation in the inoculated plants. The redox state modulation, the more efficient nitrogen assimilation, as well as the differential changes in amino acid metabolism, and the induction of the phenylpropanoid biosynthesis pathway, were the main drought-attenuating mechanisms in the SAESo11-inoculated plants. Shifts in pathways related to hormonal signaling were also evident upon inoculation at a transcript level and in conjunction with carbon metabolism regulation, possibly contributed to a drought-attenuation preconditioning. The identified signatory molecules of SAESo11-mediated priming against drought included aspartate, myo-inositol, glutamate, along with key genes related to trehalose, tryptophan and cysteine synthesis. Taken together, SAESo11-inoculation provides systemic effects encompassing both metabolic and regulatory functions, supporting both seedling growth and drought stress amelioration.
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Affiliation(s)
- Anastasia Papadopoulou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Aggeliki Ainalidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER, Thermi, Greece
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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Lamm CE, Rabbi IY, Medeiros DB, Rosado-Souza L, Pommerrenig B, Dahmani I, Rüscher D, Hofmann J, van Doorn AM, Schlereth A, Neuhaus HE, Fernie AR, Sonnewald U, Zierer W. Efficient sugar utilization and transition from oxidative to substrate-level phosphorylation in high starch storage roots of African cassava genotypes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:38-57. [PMID: 37329210 DOI: 10.1111/tpj.16357] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023]
Abstract
Cassava's storage roots represent one of the most important sources of nutritional carbohydrates worldwide. Particularly, smallholder farmers in sub-Saharan Africa depend on this crop plant, where resilient and yield-improved varieties are of vital importance to support steadily increasing populations. Aided by a growing understanding of the plant's metabolism and physiology, targeted improvement concepts already led to visible gains in recent years. To expand our knowledge and to contribute to these successes, we investigated storage roots of eight cassava genotypes with differential dry matter content from three successive field trials for their proteomic and metabolic profiles. At large, the metabolic focus in storage roots transitioned from cellular growth processes toward carbohydrate and nitrogen storage with increasing dry matter content. This is reflected in higher abundance of proteins related to nucleotide synthesis, protein turnover, and vacuolar energization in low starch genotypes, while proteins involved in sugar conversion and glycolysis were more prevalent in high dry matter genotypes. This shift in metabolic orientation was underlined by a clear transition from oxidative- to substrate-level phosphorylation in high dry matter genotypes. Our analyses highlight metabolic patterns that are consistently and quantitatively associated with high dry matter accumulation in cassava storage roots, providing fundamental understanding of cassava's metabolism as well as a data resource for targeted genetic improvement.
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Affiliation(s)
- Christian E Lamm
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Ismail Y Rabbi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Laise Rosado-Souza
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Ismail Dahmani
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - David Rüscher
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Jörg Hofmann
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Anna M van Doorn
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Armin Schlereth
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Uwe Sonnewald
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Wolfgang Zierer
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
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Pavlovic T, Margarit E, Müller GL, Saenz E, Ruzzo AI, Drincovich MF, Borrás L, Saigo M, Wheeler MCG. Differential metabolic reprogramming in developing soybean embryos in response to nutritional conditions and abscisic acid. PLANT MOLECULAR BIOLOGY 2023; 113:89-103. [PMID: 37702897 DOI: 10.1007/s11103-023-01377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Seed storage compound deposition is influenced by both maternal and filial tissues. Within this framework, we analyzed strategies that operate during the development and filling of soybean embryos, using in vitro culture systems combined with metabolomics and proteomics approaches. The carbon:nitrogen ratio (C:N) of the maternal supply and the hormone abscisic acid (ABA) are specific and interacting signals inducing differential metabolic reprogrammings linked to changes in the accumulation of storage macromolecules like proteins or oils. Differences in the abundance of sugars, amino acids, enzymes, transporters, transcription factors, and proteins involved in signaling were detected. Embryos adapted to the nutritional status by enhancing the metabolism of both carbon and nitrogen under lower C:N ratio condition or only carbon under higher C:N ratio condition. ABA turned off multiple pathways especially in high availability of amino acids, prioritizing the storage compounds biosynthesis. Common responses induced by ABA involved increased sucrose uptake (to increase the sink force) and oleosin (oil body structural component) accumulation. In turn, ABA differentially promoted protein degradation under lower nitrogen supply in order to sustain the metabolic demands. Further, the operation of a citrate shuttle was suggested by transcript quantification and enzymatic activity measurements. The results obtained are useful to help define biotechnological tools and technological approaches to improve oil and protein yields, with direct impact on human and animal nutrition as well as in green chemistry.
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Affiliation(s)
- Tatiana Pavlovic
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina
| | - Ezequiel Margarit
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina
| | - Gabriela Leticia Müller
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina
| | - Ezequiel Saenz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino CC14, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Andrés Iván Ruzzo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina
| | - María Fabiana Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina
| | - Lucas Borrás
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino CC14, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Mariana Saigo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina.
| | - Mariel Claudia Gerrard Wheeler
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina.
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41
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Ooka H, Chiba Y, Nakamura R. Thermodynamic principle to enhance enzymatic activity using the substrate affinity. Nat Commun 2023; 14:4860. [PMID: 37620340 PMCID: PMC10449852 DOI: 10.1038/s41467-023-40471-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Understanding how to tune enzymatic activity is important not only for biotechnological applications, but also to elucidate the basic principles guiding the design and optimization of biological systems in nature. So far, the Michaelis-Menten equation has provided a fundamental framework of enzymatic activity. However, there is still no concrete guideline on how the parameters should be optimized towards higher activity. Here, we demonstrate that tuning the Michaelis-Menten constant ([Formula: see text]) to the substrate concentration ([Formula: see text]) enhances enzymatic activity. This guideline ([Formula: see text]) was obtained mathematically by assuming that thermodynamically favorable reactions have higher rate constants, and that the total driving force is fixed. Due to the generality of these thermodynamic considerations, we propose [Formula: see text] as a general concept to enhance enzymatic activity. Our bioinformatic analysis reveals that the [Formula: see text] and in vivo substrate concentrations are consistent across a dataset of approximately 1000 enzymes, suggesting that even natural selection follows the principle [Formula: see text].
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Affiliation(s)
- Hideshi Ooka
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Yoko Chiba
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Faculty of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, 2-12-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
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42
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Zhang Y, Fernie AR. The Role of TCA Cycle Enzymes in Plants. Adv Biol (Weinh) 2023; 7:e2200238. [PMID: 37341441 DOI: 10.1002/adbi.202200238] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 04/29/2023] [Indexed: 06/22/2023]
Abstract
As one of the iconic pathways in plant metabolism, the tricarboxylic acid (TCA) cycle is commonly thought to not only be responsible for the oxidization of respiratory substrate to drive ATP synthesis but also provide carbon skeletons to anabolic processes and contribute to carbon-nitrogen interaction and biotic stress responses. The functions of the TCA cycle enzymes are characterized by a saturation transgenesis approach, whereby the constituent expression of proteins is knocked out or reduced in order to investigate their function in vivo. The alteration of TCA cycle enzyme expression results in changed plant growth and photosynthesis under controlled conditions. Moreover, improvements in plant performance and postharvest properties are reported by overexpression of either endogenous forms or heterologous genes of a number of the enzymes. Given the importance of the TCA cycle in plant metabolism regulation, here, the function of each enzyme and its roles in different tissues are discussed. This article additionally highlights the recent finding that the plant TCA cycle, like that of mammals and microbes, dynamically assembles functional substrate channels or metabolons and discusses the implications of this finding to the current understanding of the metabolic regulation of the plant TCA cycle.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
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Du J, Li Y, Lu X, Geng Z, Yuan Y, Liu Y, Li J, Wang M, Wang J. Metabolomics-based study on the changes of endogenous metabolites during adventitious bud formation from leaf margin of Bryophyllum pinnatum (Lam.) Oken. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107845. [PMID: 37364508 DOI: 10.1016/j.plaphy.2023.107845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/21/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
Bryophyllum pinnatum (Lam.) Oken is an ornamental and ethno-medicine plant, which can grow a circle of adventitious bud around the leaf margin. The dynamic change of metabolites during the development of B. pinnatum remains poorly understood. Here, leaves from B. pinnatum at four developmental stages were sampled based on morphological characteristics. A non-targeted metabolomics approach was used to evaluate the changes of endogenous metabolites during adventitious bud formation in B. pinnatum. The results showed that differential metabolites were mainly enriched in sphingolipid metabolism, flavone and flavonol biosynthesis, phenylalanine metabolism, and tricarboxylic acid cycle pathway. The metabolites assigned to amino acids, flavonoids, sphingolipids, and the plant hormone jasmonic acid decreased from period Ⅰ to Ⅱ, and then increased from period Ⅲ to Ⅳ with the emergence of adventitious bud (period Ⅲ). While the metabolites related to the tricarboxylic acid cycle showed a trend of first increasing and then decreasing during the four observation periods. Depending on the metabolite changes, leaves may provide conditions similar to in vitro culture for adventitious bud to occur, thus enabling adventitious bud to grow at the leaf edge. Our results provide a basis for illustrating the regulatory mechanisms of adventitious bud in B. pinnatum.
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Affiliation(s)
- Jialin Du
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Yi Li
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Xu Lu
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Zhaopeng Geng
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Yuanyuan Yuan
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Yue Liu
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Juanling Li
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Minjuan Wang
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Junli Wang
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China.
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Young T, Gale SL, Ragg NLC, Sander SG, Burritt DJ, Benedict B, Le DV, Villas-Bôas SG, Alfaro AC. Metabolic Regulation of Copper Toxicity during Marine Mussel Embryogenesis. Metabolites 2023; 13:838. [PMID: 37512545 PMCID: PMC10385052 DOI: 10.3390/metabo13070838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The development of new tools for assessing the health of cultured shellfish larvae is crucial for aquaculture industries to develop and refine hatchery methodologies. We established a large-volume ecotoxicology/health stressor trial, exposing mussel (Perna canaliculus) embryos to copper in the presence of ethylenediaminetetraacetic acid (EDTA). GC/MS-based metabolomics was applied to identify potential biomarkers for monitoring embryonic/larval health and to characterise mechanisms of metal toxicity. Cellular viability, developmental abnormalities, larval behaviour, mortality, and a targeted analysis of proteins involved in the regulation of reactive oxygen species were simultaneously evaluated to provide a complementary framework for interpretative purposes and authenticate the metabolomics data. Trace metal analysis and speciation modelling verified EDTA as an effective copper chelator. Toxicity thresholds for P. canaliculus were low, with 10% developmental abnormalities in D-stage larvae being recorded upon exposure to 1.10 μg·L-1 bioavailable copper for 66 h. Sublethal levels of bioavailable copper (0.04 and 1.10 μg·L-1) caused coordinated fluctuations in metabolite profiles, which were dependent on development stage, treatment level, and exposure duration. Larvae appeared to successfully employ various mechanisms involving the biosynthesis of antioxidants and a restructuring of energy-related metabolism to alleviate the toxic effects of copper on cells and developing tissues. These results suggest that regulation of trace metal-induced toxicity is tightly linked with metabolism during the early ontogenic development of marine mussels. Lethal-level bioavailable copper (50.3 μg·L-1) caused severe metabolic dysregulation after 3 h of exposure, which worsened with time, substantially delayed embryonic development, induced critical oxidative damage, initiated the apoptotic pathway, and resulted in cell/organism death shortly after 18 h of exposure. Metabolite profiling is a useful approach to (1) assess the health status of marine invertebrate embryos and larvae, (2) detect early warning biomarkers for trace metal contamination, and (3) identify novel regulatory mechanisms of copper-induced toxicity.
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Affiliation(s)
- Tim Young
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | | | | | - Sylvia G. Sander
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
- Marine Mineral Resources Group, Research Division 4: Dynamics of the Ocean Floor, Magmatic and Hydrothermal Systems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148 Kiel, Germany
| | - David J. Burritt
- Department of Botany, University of Otago, 464 Great King St, Dunedin 9016, New Zealand
| | - Billy Benedict
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9010, New Zealand
| | - Dung V. Le
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- Faculty of Fisheries, Vietnam National University of Agriculture, Hanoi 000084, Vietnam
| | - Silas G. Villas-Bôas
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Andrea C. Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
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Han SY, Kim WY, Kim JS, Hwang I. Comparative transcriptomics reveals the role of altered energy metabolism in the establishment of single-cell C 4 photosynthesis in Bienertia sinuspersici. FRONTIERS IN PLANT SCIENCE 2023; 14:1202521. [PMID: 37476170 PMCID: PMC10354284 DOI: 10.3389/fpls.2023.1202521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 05/31/2023] [Indexed: 07/22/2023]
Abstract
Single-cell C4 photosynthesis (SCC4) in terrestrial plants without Kranz anatomy involves three steps: initial CO2 fixation in the cytosol, CO2 release in mitochondria, and a second CO2 fixation in central chloroplasts. Here, we investigated how the large number of mechanisms underlying these processes, which occur in three different compartments, are orchestrated in a coordinated manner to establish the C4 pathway in Bienertia sinuspersici, a SCC4 plant. Leaves were subjected to transcriptome analysis at three different developmental stages. Functional enrichment analysis revealed that SCC4 cycle genes are coexpressed with genes regulating cyclic electron flow and amino/organic acid metabolism, two key processes required for the production of energy molecules in C3 plants. Comparative gene expression profiling of B. sinuspersici and three other species (Suaeda aralocaspica, Amaranthus hypochondriacus, and Arabidopsis thaliana) showed that the direction of metabolic flux was determined via an alteration in energy supply in peripheral chloroplasts and mitochondria via regulation of gene expression in the direction of the C4 cycle. Based on these results, we propose that the redox homeostasis of energy molecules via energy metabolism regulation is key to the establishment of the SCC4 pathway in B. sinuspersici.
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Affiliation(s)
- Sang-Yun Han
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21+) and Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Jung Sun Kim
- Genomic Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
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Sun L, Wang J, Cui Y, Cui R, Kang R, Zhang Y, Wang S, Zhao L, Wang D, Lu X, Fan Y, Han M, Chen C, Chen X, Guo L, Ye W. Changes in terpene biosynthesis and submergence tolerance in cotton. BMC PLANT BIOLOGY 2023; 23:330. [PMID: 37344795 DOI: 10.1186/s12870-023-04334-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
BACKGROUND Flooding is among the most severe abiotic stresses in plant growth and development. The mechanism of submergence tolerance of cotton in response to submergence stress is unknown. RESULTS The transcriptome results showed that a total of 6,893 differentially expressed genes (DEGs) were discovered under submergence stress. Gene Ontology (GO) enrichment analysis showed that DEGs were involved in various stress or stimulus responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs related to plant hormone signal transduction, starch and sucrose metabolism, glycolysis and the biosynthesis of secondary metabolites were regulated by submergence stress. Eight DEGs related to ethylene signaling and 3 ethylene synthesis genes were identified in the hormone signal transduction. For respiratory metabolism, alcohol dehydrogenase (ADH, GH_A02G0728) and pyruvate decarboxylase (PDC, GH_D09G1778) were significantly upregulated but 6-phosphofructokinase (PFK, GH_D05G0280), phosphoglycerate kinase (PGK, GH_A01G0945 and GH_D01G0967) and sucrose synthase genes (SUS, GH_A06G0873 and GH_D06G0851) were significantly downregulated in the submergence treatment. Terpene biosynthetic pathway-related genes in the secondary metabolites were regulated in submergence stress. CONCLUSIONS Regulation of terpene biosynthesis by respiratory metabolism may play a role in enhancing the tolerance of cotton to submergence under flooding. Our findings showed that the mevalonate pathway, which occurs in the cytoplasm of the terpenoid backbone biosynthesis pathway (ko00900), may be the main response to submergence stress.
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Affiliation(s)
- Liangqing Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
- Cotton Research Institute of Jiangxi Province, Jiujiang, 332105, Jiangxi, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Yupeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Ruifeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Ruiqing Kang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.
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47
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Ofoe R, Thomas RH, Abbey L. Coordinated Regulation of Central Carbon Metabolism in Pyroligneous Acid-Treated Tomato Plants under Aluminum Stress. Metabolites 2023; 13:770. [PMID: 37367927 DOI: 10.3390/metabo13060770] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023] Open
Abstract
Aluminum (Al) toxicity is a major threat to global crop production in acidic soils, which can be mitigated by natural substances such as pyroligneous acid (PA). However, the effect of PA in regulating plant central carbon metabolism (CCM) under Al stress is unknown. In this study, we investigated the effects of varying PA concentrations (0, 0.25 and 1% PA/ddH2O (v/v)) on intermediate metabolites involved in CCM in tomato (Solanum lycopersicum L., 'Scotia') seedlings under varying Al concentrations (0, 1 and 4 mM AlCl3). A total of 48 differentially expressed metabolites of CCM were identified in the leaves of both control and PA-treated plants under Al stress. Calvin-Benson cycle (CBC) and pentose phosphate pathway (PPP) metabolites were considerably reduced under 4 mM Al stress, irrespective of the PA treatment. Conversely, the PA treatment markedly increased glycolysis and tricarboxylic acid cycle (TCA) metabolites compared to the control. Although glycolysis metabolites in the 0.25% PA-treated plants under Al stress were comparable to the control, the 1% PA-treated plants exhibited the highest accumulation of glycolysis metabolites. Furthermore, all PA treatments increased TCA metabolites under Al stress. Electron transport chain (ETC) metabolites were higher in PA-treated plants alone and under 1 mM, Al but were reduced under a higher Al treatment of 4 mM. Pearson correlation analysis revealed that CBC metabolites had a significantly strong positive (r = 0.99; p < 0.001) association with PPP metabolites. Additionally, glycolysis metabolites showed a significantly moderate positive association (r = 0.76; p < 0.05) with TCA metabolites, while ETC metabolites exhibited no association with any of the determined pathways. The coordinated association between CCM pathway metabolites suggests that PA can stimulate changes in plant metabolism to modulate energy production and biosynthesis of organic acids under Al stress conditions.
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Affiliation(s)
- Raphael Ofoe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, 50 Pictou Road, Bible Hill, NS B2N 5E3, Canada
| | - Raymond H Thomas
- Department of Biology, Faculty of Science, Western University 2025E Biological & Geological Sciences Building, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Lord Abbey
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, 50 Pictou Road, Bible Hill, NS B2N 5E3, Canada
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48
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Eprintsev AT, Fedorin DN, Igamberdiev AU. Light-Dependent Expression and Promoter Methylation of the Genes Encoding Succinate Dehydrogenase, Fumarase, and NAD-Malate Dehydrogenase in Maize ( Zea mays L.) Leaves. Int J Mol Sci 2023; 24:10211. [PMID: 37373359 DOI: 10.3390/ijms241210211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The expression and methylation of promoters of the genes encoding succinate dehydrogenase, fumarase, and NAD-malate dehydrogenase in maize (Zea mays L.) leaves depending on the light regime were studied. The genes encoding the catalytic subunits of succinate dehydrogenase showed suppression of expression upon irradiation by red light, which was abolished by far-red light. This was accompanied by an increase in promoter methylation of the gene Sdh1-2 encoding the flavoprotein subunit A, while methylation was low for Sdh2-3 encoding the iron-sulfur subunit B under all conditions. The expression of Sdh3-1 and Sdh4 encoding the anchoring subunits C and D was not affected by red light. The expression of Fum1 encoding the mitochondrial form of fumarase was regulated by red and far-red light via methylation of its promoter. Only one gene encoding the mitochondrial NAD-malate dehydrogenase gene (mMdh1) was regulated by red and far-red light, while the second gene (mMdh2) did not respond to irradiation, and neither gene was controlled by promoter methylation. It is concluded that the dicarboxylic branch of the tricarboxylic acid cycle is regulated by light via the phytochrome mechanism, and promoter methylation is involved with the flavoprotein subunit of succinate dehydrogenase and the mitochondrial fumarase.
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Affiliation(s)
- Alexander T Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia
| | - Dmitry N Fedorin
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
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49
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Le QTN, Sugi N, Yamaguchi M, Hirayama T, Kobayashi M, Suzuki Y, Kusano M, Shiba H. Morphological and metabolomics profiling of intraspecific Arabidopsis hybrids in relation to biomass heterosis. Sci Rep 2023; 13:9529. [PMID: 37308530 DOI: 10.1038/s41598-023-36618-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
Heterosis contributes greatly to the worldwide agricultural yield. However, the molecular mechanism underlying heterosis remains unclear. This study took advantage of Arabidopsis intraspecific hybrids to identify heterosis-related metabolites. Forty-six intraspecific hybrids were used to examine parental effects on seed area and germination time. The degree of heterosis was evaluated based on biomass: combinations showing high heterosis of F1 hybrids exhibited a biomass increase from 6.1 to 44% over the better parent value (BPV), whereas that of the low- and no-heterosis hybrids ranged from - 19.8 to 9.8% over the BPV. Metabolomics analyses of F1 hybrids with high heterosis and those with low one suggested that changes in TCA cycle intermediates are key factors that control growth. Notably, higher fumarate/malate ratios were observed in the high heterosis F1 hybrids, suggesting they provide metabolic support associated with the increased biomass. These hybrids may produce more energy-intensive biomass by speeding up the efficiency of TCA fluxes. However, the expression levels of TCA-process-related genes in F1 hybrids were not associated with the intensity of heterosis, suggesting that the post-transcriptional or post-translational regulation of these genes may affect the productivity of the intermediates in the TCA cycle.
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Affiliation(s)
- Quynh Thi Ngoc Le
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- Thuyloi University, 175 Tay Son, Dong Da, Hanoi, Viet Nam
| | - Naoya Sugi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Masaaki Yamaguchi
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
| | - Touko Hirayama
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Suehiro 1-7-22, Tsurumi, Yokohama, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Japan
| | - Miyako Kusano
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- RIKEN Center for Sustainable Resource Science, Suehiro 1-7-22, Tsurumi, Yokohama, Japan
| | - Hiroshi Shiba
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan.
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ten-Nodai 1-1-1, Tsukuba, Ibaraki, Japan.
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50
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Yao M, Mu L, Gao Z, Hu X. Persistence of algal toxicity induced by polystyrene nanoplastics at environmentally relevant concentrations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162853. [PMID: 36924955 DOI: 10.1016/j.scitotenv.2023.162853] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/23/2023] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
Polystyrene (PS) often found in the ocean is one of the most commonly used plastic polymers in the world and can exist in different particle sizes. In particular, PS degrades relatively faster and widely accumulates at the nanoscale. Therefore, the penetration is strong and it is easy to enter the body and cause adverse effects. However, the persistence or recovery of their toxicity remains largely unclear. Here, we designed two subexperiments (exposure and recovery experiments) and investigated the persistence of the toxicity of polystyrene (PS) NPs at a wide concentration range (0.01-10 mg/L) to diatoms (Phaeodactylum tricornutum). PS-NPs significantly inhibited algal growth and clearly wrinkled the surfaces of cells, membrane permeability was significantly increased, and the steady-state state of cell redox and mitochondrial membrane potential was disturbed. However, in the recovery experiment, the increased membrane permeability was observed to persist, but the induced oxidative damage was reversible, and the absorbed NPs could be excreted. Integrated omics techniques (metabolomics and transcriptomics) revealed that PS-NPs significantly disrupts cell metabolism, including disturbances in fatty acid biosynthesis and enhanced biosynthesis of phenylalanine, tyrosine, and tryptophan. Inhibition of fatty acid, amino acid, energy and carbohydrate metabolism and disturbance of the antioxidant system contribute to the persistence of toxicity. These findings highlight the phenomena and mechanisms of the persistence of phytotoxicity and are critical to the accurate assessment of NPs.
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Affiliation(s)
- Mingqi Yao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, 300350 Tianjin, China; Tianjin Key Laboratory of Agro-Environment and Safe-Product, Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, 300191 Tianjin, China; Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, 300350 Tianjin, China
| | - Li Mu
- Tianjin Key Laboratory of Agro-Environment and Safe-Product, Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, 300191 Tianjin, China.
| | - Ziwei Gao
- Tianjin Key Laboratory of Agro-Environment and Safe-Product, Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, 300191 Tianjin, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, 300350 Tianjin, China; Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, 300350 Tianjin, China
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