1
|
Auler PA, Lemos MDS, Porto NP, Mendes KDR, Bret RSC, Daloso DM. Abscisic acid-mediated guard cell metabolism regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108889. [PMID: 38954945 DOI: 10.1016/j.plaphy.2024.108889] [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: 12/11/2023] [Revised: 06/10/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024]
Abstract
Abscisic acid (ABA) is crucial for plant water deficit (WD) acclimation, but how the interplay between ABA and guard cell (GC) metabolism aids plant WD acclimation remains unclear. Here, we investigated how ABA regulates GC metabolism and how this contributes to plant WD acclimation using tomato wild type (WT) and the ABA-deficient sitiens mutant. These genotypes were characterized at physiological, metabolic, and transcriptional levels under recurring WD periods and were used to perform a13C-glucose labelling experiment using isolated guard cells following exogenously applied ABA. ABA deficiency altered the level of sugars and organic acids in GCs in both irrigated and WD plants and the dynamic of accumulation/degradation of these compounds in GCs during the dark-to-light transition. WD-induced metabolic changes were more pronounced in sitiens than WT GCs. Results from the 13C-labelling experiment indicate that ABA is required for the glycolytic fluxes toward malate and acts as a negative regulator of a putative sucrose substrate cycle. The expression of key ABA-biosynthetic genes was higher in WT than in sitiens GCs after two cycles of WD. Additionally, the intrinsic leaf water use efficiency increased only in WT after the second WD cycle, compared to sitiens. Our results highlight that ABA deficiency disrupts the homeostasis of GC primary metabolism and the WD memory, negatively affecting plant WD acclimation. Our study demonstrates which metabolic pathways are activated by WD and/or regulated by ABA in GCs, which improves our understanding of plant WD acclimation, with clear consequences for plant metabolic engineering in the future.
Collapse
Affiliation(s)
- Priscila A Auler
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Moaciria de S Lemos
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Nicole P Porto
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Kellyane da R Mendes
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Raissa S C Bret
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Danilo M Daloso
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil.
| |
Collapse
|
2
|
Kong Y, Chen H, Huang X, Chang L, Yang B, Chen W. Precise metabolic modeling in post-omics era: accomplishments and perspectives. Crit Rev Biotechnol 2024:1-19. [PMID: 39198033 DOI: 10.1080/07388551.2024.2390089] [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: 03/31/2023] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 09/01/2024]
Abstract
Microbes have been extensively utilized for their sustainable and scalable properties in synthesizing desired bio-products. However, insufficient knowledge about intracellular metabolism has impeded further microbial applications. The genome-scale metabolic models (GEMs) play a pivotal role in facilitating a global understanding of cellular metabolic mechanisms. These models enable rational modification by exploring metabolic pathways and predicting potential targets in microorganisms, enabling precise cell regulation without experimental costs. Nonetheless, simplified GEM only considers genome information and network stoichiometry while neglecting other important bio-information, such as enzyme functions, thermodynamic properties, and kinetic parameters. Consequently, uncertainties persist particularly when predicting microbial behaviors in complex and fluctuant systems. The advent of the omics era with its massive quantification of genes, proteins, and metabolites under various conditions has led to the flourishing of multi-constrained models and updated algorithms with improved predicting power and broadened dimension. Meanwhile, machine learning (ML) has demonstrated exceptional analytical and predictive capacities when applied to training sets of biological big data. Incorporating the discriminant strength of ML with GEM facilitates mechanistic modeling efficiency and improves predictive accuracy. This paper provides an overview of research innovations in the GEM, including multi-constrained modeling, analytical approaches, and the latest applications of ML, which may contribute comprehensive knowledge toward genetic refinement, strain development, and yield enhancement for a broad range of biomolecules.
Collapse
Affiliation(s)
- Yawen Kong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Xinlei Huang
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| | - Lulu Chang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Bo Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, P. R. China
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Hogg M, Wolfschmitt EM, Wachter U, Zink F, Radermacher P, Vogt JA. Bayesian 13C-Metabolic Flux Analysis of Parallel Tracer Experiments in Granulocytes: A Directional Shift within the Non-Oxidative Pentose Phosphate Pathway Supports Phagocytosis. Metabolites 2023; 14:24. [PMID: 38248827 PMCID: PMC10820746 DOI: 10.3390/metabo14010024] [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: 11/09/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
The pentose phosphate pathway (PPP) plays a key role in the cellular regulation of immune function; however, little is known about the interplay of metabolic adjustments in granulocytes, especially regarding the non-oxidative PPP. For the determination of metabolic mechanisms within glucose metabolism, we propose a novel set of measures for 13C-metabolic flux analysis based on ex vivo parallel tracer experiments ([1,2-13C]glucose, [U-13C]glucose, [4,5,6-13C]glucose) and gas chromatography-mass spectrometry labeling measurements of intracellular metabolites, such as sugar phosphates and their fragments. A detailed constraint analysis showed that the permission range for net and irreversible fluxes was limited to a three-dimensional space. The overall workflow, including its Bayesian flux estimation, resulted in precise flux distributions and pairwise confidence intervals, some of which could be represented as a line due to the strength of their correlation. The principal component analysis that was enabled by these behaviors comprised three components that explained 99.6% of the data variance. It showed that phagocytic stimulation reversed the direction of non-oxidative PPP net fluxes from ribose-5-phosphate biosynthesis toward glycolytic pathways. This process was closely associated with the up-regulation of the oxidative PPP to promote the oxidative burst.
Collapse
Affiliation(s)
- Melanie Hogg
- Institute for Anesthesiological Pathophysiology and Process Engineering, Ulm University Medical Center, 89081 Ulm, Germany; (E.-M.W.); (U.W.); (F.Z.); (P.R.); (J.A.V.)
| | | | | | | | | | | |
Collapse
|
6
|
He S, Sun L, Chen J, Ouyang Y. Recent Advances and Perspectives in Relation to the Metabolomics-Based Study of Diabetic Retinopathy. Metabolites 2023; 13:1007. [PMID: 37755287 PMCID: PMC10536395 DOI: 10.3390/metabo13091007] [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: 08/13/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023] Open
Abstract
Diabetic retinopathy (DR), a prevalent microvascular complication of diabetes, is a major cause of acquired blindness in adults. Currently, a clinical diagnosis of DR primarily relies on fundus fluorescein angiography, with a limited availability of effective biomarkers. Metabolomics, a discipline dedicated to scrutinizing the response of various metabolites within living organisms, has shown noteworthy advancements in uncovering metabolic disorders and identifying key metabolites associated with DR in recent years. Consequently, this review aims to present the latest advancements in metabolomics techniques and comprehensively discuss the principal metabolic outcomes derived from analyzing blood, vitreous humor, aqueous humor, urine, and fecal samples.
Collapse
Affiliation(s)
| | | | | | - Yang Ouyang
- Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (S.H.)
| |
Collapse
|
7
|
Souza PVL, Hou LY, Sun H, Poeker L, Lehman M, Bahadar H, Domingues-Junior AP, Dard A, Bariat L, Reichheld JP, Silveira JAG, Fernie AR, Timm S, Geigenberger P, Daloso DM. Plant NADPH-dependent thioredoxin reductases are crucial for the metabolism of sink leaves and plant acclimation to elevated CO 2. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37267089 DOI: 10.1111/pce.14631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 05/05/2023] [Accepted: 05/13/2023] [Indexed: 06/04/2023]
Abstract
Plants contain three NADPH-thioredoxin reductases (NTR) located in the cytosol/mitochondria (NTRA/B) and the plastid (NTRC) with important metabolic functions. However, mutants deficient in all NTRs remained to be investigated. Here, we generated and characterised the triple Arabidopsis ntrabc mutant alongside with ntrc single and ntrab double mutants under different environmental conditions. Both ntrc and ntrabc mutants showed reduced growth and substantial metabolic alterations, especially in sink leaves and under high CO2 (HC), as compared to the wild type. However, ntrabc showed higher effective quantum yield of PSII under both constant and fluctuating light conditions, altered redox states of NADH/NAD+ and glutathione (GSH/GSSG) and lower potential quantum yield of PSII in sink leaves in ambient but not high CO2 concentrations, as compared to ntrc, suggesting a functional interaction between chloroplastic and extra-chloroplastic NTRs in photosynthesis regulation depending on leaf development and environmental conditions. Our results unveil a previously unknown role of the NTR system in regulating sink leaf metabolism and plant acclimation to HC, while it is not affecting full plant development, indicating that the lack of the NTR system can be compensated, at least to some extent, by other redox mechanisms.
Collapse
Affiliation(s)
- Paulo V L Souza
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Liang-Yu Hou
- Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Hu Sun
- University of Rostock, Rostock, Germany
| | - Louis Poeker
- Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Martin Lehman
- Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Humaira Bahadar
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | | | - Avilien Dard
- Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Centre National de la Recherche Scientifique, Université de Perpignan Via Domitia, Perpignan, France
| | - Laetitia Bariat
- Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Centre National de la Recherche Scientifique, Université de Perpignan Via Domitia, Perpignan, France
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Centre National de la Recherche Scientifique, Université de Perpignan Via Domitia, Perpignan, France
| | | | | | | | | | - Danilo M Daloso
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| |
Collapse
|
8
|
Daloso DDM, Morais EG, Oliveira E Silva KF, Williams TCR. Cell-type-specific metabolism in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1093-1114. [PMID: 36987968 DOI: 10.1111/tpj.16214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/20/2023] [Accepted: 03/25/2023] [Indexed: 05/31/2023]
Abstract
Every plant organ contains tens of different cell types, each with a specialized function. These functions are intrinsically associated with specific metabolic flux distributions that permit the synthesis of the ATP, reducing equivalents and biosynthetic precursors demanded by the cell. Investigating such cell-type-specific metabolism is complicated by the mosaic of different cells within each tissue combined with the relative scarcity of certain types. However, techniques for the isolation of specific cells, their analysis in situ by microscopy, or modeling of their function in silico have permitted insight into cell-type-specific metabolism. In this review we present some of the methods used in the analysis of cell-type-specific metabolism before describing what we know about metabolism in several cell types that have been studied in depth; (i) leaf source and sink cells; (ii) glandular trichomes that are capable of rapid synthesis of specialized metabolites; (iii) guard cells that must accumulate large quantities of the osmolytes needed for stomatal opening; (iv) cells of seeds involved in storage of reserves; and (v) the mesophyll and bundle sheath cells of C4 plants that participate in a CO2 concentrating cycle. Metabolism is discussed in terms of its principal features, connection to cell function and what factors affect the flux distribution. Demand for precursors and energy, availability of substrates and suppression of deleterious processes are identified as key factors in shaping cell-type-specific metabolism.
Collapse
Affiliation(s)
- Danilo de Menezes Daloso
- Lab Plant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CA, 60451-970, Brazil
| | - Eva Gomes Morais
- Lab Plant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CA, 60451-970, Brazil
| | - Karen Fernanda Oliveira E Silva
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília-DF, 70910-900, Brazil
| | | |
Collapse
|
9
|
Dellero Y, Filangi O, Bouchereau A. Evaluation of GC/MS-Based 13C-Positional Approaches for TMS Derivatives of Organic and Amino Acids and Application to Plant 13C-Labeled Experiments. Metabolites 2023; 13:metabo13040466. [PMID: 37110124 PMCID: PMC10142191 DOI: 10.3390/metabo13040466] [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: 02/28/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
Analysis of plant metabolite 13C-enrichments with gas-chromatography mass spectrometry (GC/MS) has gained interest recently. By combining multiple fragments of a trimethylsilyl (TMS) derivative, 13C-positional enrichments can be calculated. However, this new approach may suffer from analytical biases depending on the fragments selected for calculation leading to significant errors in the final results. The goal of this study was to provide a framework for the validation of 13C-positional approaches and their application to plants based on some key metabolites (glycine, serine, glutamate, proline, α-alanine and malate). For this purpose, we used tailor-made 13C-PT standards, harboring known carbon isotopologue distributions and 13C-positional enrichments, to evaluate the reliability of GC-MS measurements and positional calculations. Overall, we showed that some mass fragments of proline_2TMS, glutamate_3TMS, malate_3TMS and α-alanine_2TMS had important biases for 13C measurements resulting in significant errors in the computational estimation of 13C-positional enrichments. Nevertheless, we validated a GC/MS-based 13C-positional approach for the following atomic positions: (i) C1 and C2 of glycine_3TMS, (ii) C1, C2 and C3 of serine_3TMS, and (iii) C1 of malate_3TMS and glutamate_3TMS. We successfully applied this approach to plant 13C-labeled experiments for investigating key metabolic fluxes of plant primary metabolism (photorespiration, tricarboxylic acid cycle and phosphoenolpyruvate carboxylase activity).
Collapse
Affiliation(s)
- Younès Dellero
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Institut Agro, Université Rennes, 35650 Le Rheu, France
- Metabolic Profiling and Metabolomic Platform (P2M2), Biopolymers Interactions Assemblies, Institute for Genetics, Environment and Plant Protection, 35650 Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 35650 Le Rheu, France
| | - Olivier Filangi
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Institut Agro, Université Rennes, 35650 Le Rheu, France
- Metabolic Profiling and Metabolomic Platform (P2M2), Biopolymers Interactions Assemblies, Institute for Genetics, Environment and Plant Protection, 35650 Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 35650 Le Rheu, France
| | - Alain Bouchereau
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Institut Agro, Université Rennes, 35650 Le Rheu, France
- Metabolic Profiling and Metabolomic Platform (P2M2), Biopolymers Interactions Assemblies, Institute for Genetics, Environment and Plant Protection, 35650 Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 35650 Le Rheu, France
| |
Collapse
|
10
|
Porto NP, Bret RSC, Souza PVL, Cândido-Sobrinho SA, Medeiros DB, Fernie AR, Daloso DM. Thioredoxins regulate the metabolic fluxes throughout the tricarboxylic acid cycle and associated pathways in a light-independent manner. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 193:36-49. [PMID: 36323196 DOI: 10.1016/j.plaphy.2022.10.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
The metabolic fluxes throughout the tricarboxylic acid cycle (TCAC) are inhibited in the light by the mitochondrial thioredoxin (TRX) system. However, it is unclear how this system orchestrates the fluxes throughout the TCAC and associated pathways in the dark. Here we carried out a13C-HCO3 labelling experiment in Arabidopsis leaves from wild type (WT) and mutants lacking TRX o1 (trxo1), TRX h2 (trxh2), or both NADPH-dependent TRX reductase A and B (ntra ntrb) exposed to 0, 30 and 60 min of dark or light conditions. No 13C-enrichment in TCAC metabolites in illuminated WT leaves was observed. However, increased succinate content was found in parallel to reductions in Ala in the light, suggesting the latter operates as an alternative carbon source for succinate synthesis. By contrast to WT, all mutants showed substantial changes in the content and 13C-enrichment in TCAC metabolites under both dark and light conditions. Increased 13C-enrichment in glutamine in illuminated trxo1 leaves was also observed, strengthening the idea that TRX o1 restricts in vivo carbon fluxes from glycolysis and the TCAC to glutamine. We further demonstrated that both photosynthetic and gluconeogenic fluxes toward glucose are increased in trxo1 and that the phosphoenolpyruvate carboxylase (PEPc)-mediated 13C-incorporation into malate is higher in trxh2 mutants, as compared to WT. Our results collectively provide evidence that TRX h2 and the mitochondrial NTR/TRX system regulate the metabolic fluxes throughout the TCAC and associated pathways, including glycolysis, gluconeogenesis and the synthesis of glutamine in a light-independent manner.
Collapse
Affiliation(s)
- Nicole P Porto
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Raissa S C Bret
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Paulo V L Souza
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - Silvio A Cândido-Sobrinho
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil
| | - David B Medeiros
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Danilo M Daloso
- LabPlant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, 60451-970, Fortaleza, Ceará, Brazil.
| |
Collapse
|
11
|
Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology. Int J Mol Sci 2022; 23:ijms23136985. [PMID: 35805979 PMCID: PMC9266571 DOI: 10.3390/ijms23136985] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.
Collapse
|
12
|
Nießer J, Müller MF, Kappelmann J, Wiechert W, Noack S. Hot isopropanol quenching procedure for automated microtiter plate scale 13C-labeling experiments. Microb Cell Fact 2022; 21:78. [PMID: 35527247 PMCID: PMC9082905 DOI: 10.1186/s12934-022-01806-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/26/2022] [Indexed: 11/12/2022] Open
Abstract
Background Currently, the generation of genetic diversity for microbial cell factories outpaces the screening of strain variants with omics-based phenotyping methods. Especially isotopic labeling experiments, which constitute techniques aimed at elucidating cellular phenotypes and supporting rational strain design by growing microorganisms on substrates enriched with heavy isotopes, suffer from comparably low throughput and the high cost of labeled substrates. Results We present a miniaturized, parallelized, and automated approach to 13C-isotopic labeling experiments by establishing and validating a hot isopropanol quenching method on a robotic platform coupled with a microbioreactor cultivation system. This allows for the first time to conduct automated labeling experiments at a microtiter plate scale in up to 48 parallel batches. A further innovation enabled by the automated quenching method is the analysis of free amino acids instead of proteinogenic ones on said microliter scale. Capitalizing on the latter point and as a proof of concept, we present an isotopically instationary labeling experiment in Corynebacterium glutamicum ATCC 13032, generating dynamic labeling data of free amino acids in the process. Conclusions Our results show that a robotic liquid handler is sufficiently fast to generate informative isotopically transient labeling data. Furthermore, the amount of biomass obtained from a sub-milliliter cultivation in a microbioreactor is adequate for the detection of labeling patterns of free amino acids. Combining the innovations presented in this study, isotopically stationary and instationary automated labeling experiments can be conducted, thus fulfilling the prerequisites for 13C-metabolic flux analyses in high-throughput. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01806-4.
Collapse
|
13
|
Lim SL, Flütsch S, Liu J, Distefano L, Santelia D, Lim BL. Arabidopsis guard cell chloroplasts import cytosolic ATP for starch turnover and stomatal opening. Nat Commun 2022; 13:652. [PMID: 35115512 PMCID: PMC8814037 DOI: 10.1038/s41467-022-28263-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 01/12/2022] [Indexed: 01/28/2023] Open
Abstract
Stomatal opening requires the provision of energy in the form of ATP for proton pumping across the guard cell (GC) plasma membrane and for associated metabolic rearrangements. The source of ATP for GCs is a matter of ongoing debate that is mainly fuelled by controversies around the ability of GC chloroplasts (GCCs) to perform photosynthesis. By imaging compartment-specific fluorescent ATP and NADPH sensor proteins in Arabidopsis, we show that GC photosynthesis is limited and mitochondria are the main source of ATP. Unlike mature mesophyll cell (MC) chloroplasts, which are impermeable to cytosolic ATP, GCCs import cytosolic ATP through NUCLEOTIDE TRANSPORTER (NTT) proteins. GCs from ntt mutants exhibit impaired abilities for starch biosynthesis and stomatal opening. Our work shows that GCs obtain ATP and carbohydrates via different routes from MCs, likely to compensate for the lower chlorophyll contents and limited photosynthesis of GCCs. Stomatal guard cells require ATP in order to fuel stomatal movements. Here the authors show that guard cell photosynthesis is limited, mitochondria are the main source of ATP and that guard cell chloroplasts import ATP via nucleotide transporters.
Collapse
Affiliation(s)
- Shey-Li Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Sabrina Flütsch
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Jinhong Liu
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Luca Distefano
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Diana Santelia
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China. .,HKU Shenzhen Institute of Research and Innovation, Shenzhen, China. .,State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
14
|
Dellero Y, Berardocco S, Berges C, Filangi O, Bouchereau A. Validation of carbon isotopologue distribution measurements by GC-MS and application to 13C-metabolic flux analysis of the tricarboxylic acid cycle in Brassica napus leaves. FRONTIERS IN PLANT SCIENCE 2022; 13:885051. [PMID: 36704152 PMCID: PMC9871494 DOI: 10.3389/fpls.2022.885051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 11/28/2022] [Indexed: 05/14/2023]
Abstract
The estimation of metabolic fluxes in photosynthetic organisms represents an important challenge that has gained interest over the last decade with the development of 13C-Metabolic Flux Analysis at isotopically non-stationary steady-state. This approach requires a high level of accuracy for the measurement of Carbon Isotopologue Distribution in plant metabolites. But this accuracy has still not been evaluated at the isotopologue level for GC-MS, leading to uncertainties for the metabolic fluxes calculated based on these fragments. Here, we developed a workflow to validate the measurements of CIDs from plant metabolites with GC-MS by producing tailor-made E. coli standard extracts harboring a predictable binomial CID for some organic and amino acids. Overall, most of our TMS-derivatives mass fragments were validated with these standards and at natural isotope abundance in plant matrices. Then, we applied this validated MS method to investigate the light/dark regulation of plant TCA cycle by incorporating U-13C-pyruvate to Brassica napus leaf discs. We took advantage of pathway-specific isotopologues/isotopomers observed between two and six hours of labeling to show that the TCA cycle can operate in a cyclic manner under both light and dark conditions. Interestingly, this forward cyclic flux mode has a nearly four-fold higher contribution for pyruvate-to-citrate and pyruvate-to-malate fluxes than the phosphoenolpyruvate carboxylase (PEPc) flux reassimilating carbon derived from some mitochondrial enzymes. The contribution of stored citrate to the mitochondrial TCA cycle activity was also questioned based on dynamics of 13C-enrichment in citrate, glutamate and succinate and variations of citrate total amounts under light and dark conditions. Interestingly, there was a light-dependent 13C-incorporation into glycine and serine showing that decarboxylations from pyruvate dehydrogenase complex and TCA cycle enzymes were actively reassimilated and could represent up to 5% to net photosynthesis.
Collapse
Affiliation(s)
- Younès Dellero
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Université Rennes, Institut Agro, Le Rheu, France
- Metabolic Profiling and Metabolomics platform (P2M2), Institute for Genetics, Environment and Plant Protection (IGEPP), Biopolymers Interactions Assemblies (BIA), Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
- *Correspondence: Younès Dellero,
| | - Solenne Berardocco
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Université Rennes, Institut Agro, Le Rheu, France
- Metabolic Profiling and Metabolomics platform (P2M2), Institute for Genetics, Environment and Plant Protection (IGEPP), Biopolymers Interactions Assemblies (BIA), Le Rheu, France
| | - Cécilia Berges
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
- Toulouse Biotechnology Institute, Université de Toulouse, National center for Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), National Institute of Applied Sciences (INSA), Toulouse, France
| | - Olivier Filangi
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Université Rennes, Institut Agro, Le Rheu, France
- Metabolic Profiling and Metabolomics platform (P2M2), Institute for Genetics, Environment and Plant Protection (IGEPP), Biopolymers Interactions Assemblies (BIA), Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Alain Bouchereau
- Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Université Rennes, Institut Agro, Le Rheu, France
- Metabolic Profiling and Metabolomics platform (P2M2), Institute for Genetics, Environment and Plant Protection (IGEPP), Biopolymers Interactions Assemblies (BIA), Le Rheu, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| |
Collapse
|