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Billah M, Renju L, Wei H, Qanmber G, Da Y, Lan Y, Qing-di Y, Fuguang L, Zhaoen Y. A cotton mitochondrial alternative electron transporter, GhD2HGDH, induces early flowering by modulating GA and photoperiodic pathways. PHYSIOLOGIA PLANTARUM 2024; 176:e14378. [PMID: 38887925 DOI: 10.1111/ppl.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 06/20/2024]
Abstract
D-2-hydroxyglutarate dehydrogenase (D2HGDH) is a mitochondrial enzyme containing flavin adenine dinucleotide FAD, existing as a dimer, and it facilitates the specific oxidation of D-2HG to 2-oxoglutarate (2-OG), which is a key intermediate in the tricarboxylic acid (TCA) cycle. A Genome-wide expression analysis (GWEA) has indicated an association between GhD2HGDH and flowering time. To further explore the role of GhD2HGDH, we performed a comprehensive investigation encompassing phenotyping, physiology, metabolomics, and transcriptomics in Arabidopsis thaliana plants overexpressing GhD2HGDH. Transcriptomic and qRT-PCR data exhibited heightened expression of GhD2HGDH in upland cotton flowers. Additionally, early-maturing cotton exhibited higher expression of GhD2HGDH across all tissues than delayed-maturing cotton. Subcellular localization confirmed its presence in the mitochondria. Overexpression of GhD2HGDH in Arabidopsis resulted in early flowering. Using virus-induced gene silencing (VIGS), we investigated the impact of GhD2HGDH on flowering in both early- and delayed-maturing cotton plants. Manipulation of GhD2HGDH expression levels led to changes in photosynthetic pigment and gas exchange attributes. GhD2HGDH responded to gibberellin (GA3) hormone treatment, influencing the expression of GA biosynthesis genes and repressing DELLA genes. Protein interaction studies, including yeast two-hybrid, luciferase complementation (LUC), and GST pull-down assays, confirmed the interaction between GhD2HGDH and GhSOX (Sulfite oxidase). The metabolomics analysis demonstrated GhD2HGDH's modulation of the TCA cycle through alterations in various metabolite levels. Transcriptome data revealed that GhD2HGDH overexpression triggers early flowering by modulating the GA3 and photoperiodic pathways of the flowering core factor genes. Taken together, GhD2HGDH positively regulates the network of genes associated with early flowering pathways.
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Affiliation(s)
- Masum Billah
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Liu Renju
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Hu Wei
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ghulam Qanmber
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Da
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Lan
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Yan Qing-di
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Li Fuguang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Zhaoen
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Li C, Wu Y, Li L, Zhao C, Li B, Wu Y, Wang H, Yan Z. Different techniques reveal the difference of community structure and function of fungi from root and rhizosphere of Salvia miltiorrhiza Bunge. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:848-859. [PMID: 37394812 DOI: 10.1111/plb.13556] [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: 10/29/2021] [Accepted: 06/23/2023] [Indexed: 07/04/2023]
Abstract
Fungi have essential functions in plant health and performance. However, the plant-associated functions of many cultured fungi have not been established in detail. Here, the fungal species diversity in Salvia miltiorrhiza roots and rhizosphere was assessed for the first time using culturomics and high-throughput sequencing. We present a comprehensive functional metagenomic analysis of these fungi and verified activity of cellulase and chitinase predicted in the metagenomic analysis. We first collected and cultured fungi from the root and rhizosphere of S. miltiorrhiza. We found 92 species across 37 families and five phyla, with Ascomycota being dominant. Many rDNA internal transcribed spacer sequences could not be assigned to lower taxonomic levels. There were 19 genera of endophytic fungi and 37 genera of rhizosphere fungi. The culturomics approach had lower taxonomic diversity than high-throughput sequencing, but some fungi were only found in cultures. Structural analyses indicated that the dominant species differed in cultured and non-cultured samples at other levels, apart from the phylum level. Functional analysis mapped 223 carbohydrate enzyme families and 393 pathways in the CAZy and KEGG databases, respectively. The most abundant families were glycoside hydrolases and those involved in carbohydrate metabolism. As predicted by metagenomics, we experimentally verified cellulase and chitinase activity for 29 and 74 fungi, respectively. We provide the first evidence of biomass recycling by fungi that are associated with plants. Culturing is essential to reveal the hidden microbial community and critical functions in plant-microbe interactions.
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Affiliation(s)
- C Li
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Y Wu
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - L Li
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - C Zhao
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - B Li
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Y Wu
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - H Wang
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Z Yan
- State Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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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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Zhang T, Peng JT, Klair A, Dickinson AJ. Non-canonical and developmental roles of the TCA cycle in plants. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102382. [PMID: 37210789 PMCID: PMC10524895 DOI: 10.1016/j.pbi.2023.102382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/23/2023]
Abstract
Over recent years, our understanding of the tricarboxylic acid cycle (TCAC) in living organisms has expanded beyond its canonical role in cellular energy production. In plants, TCAC metabolites and related enzymes have important roles in physiology, including vacuolar function, chelation of metals and nutrients, photorespiration, and redox regulation. Research in other organisms, including animals, has demonstrated unexpected functions of the TCAC metabolites in a number of biological processes, including signaling, epigenetic regulation, and cell differentiation. Here, we review the recent progress in discovery of non-canonical roles of the TCAC. We then discuss research on these metabolites in the context of plant development, with a focus on research related to tissue-specific functions of the TCAC. Additionally, we review research describing connections between TCAC metabolites and phytohormone signaling pathways. Overall, we discuss the opportunities and challenges in discovering new functions of TCAC metabolites in plants.
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Affiliation(s)
- Tao Zhang
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Jesus T Peng
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Amman Klair
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Alexandra J Dickinson
- Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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Igamberdiev AU, Bykova NV. Mitochondria in photosynthetic cells: Coordinating redox control and energy balance. PLANT PHYSIOLOGY 2023; 191:2104-2119. [PMID: 36440979 PMCID: PMC10069911 DOI: 10.1093/plphys/kiac541] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 05/21/2023]
Abstract
In photosynthetic tissues in the light, the function of energy production is associated primarily with chloroplasts, while mitochondrial metabolism adjusts to balance ATP supply, regulate the reduction level of pyridine nucleotides, and optimize major metabolic fluxes. The tricarboxylic acid cycle in the light transforms into a noncyclic open structure (hemicycle) maintained primarily by the influx of malate and the export of citrate to the cytosol. The exchange of malate and citrate forms the basis of feeding redox energy from the chloroplast into the cytosolic pathways. This supports the level of NADPH in different compartments, contributes to the biosynthesis of amino acids, and drives secondary metabolism via a supply of substrates for 2-oxoglutarate-dependent dioxygenase and for cytochrome P450-catalyzed monooxygenase reactions. This results in the maintenance of redox and energy balance in photosynthetic plant cells and in the formation of numerous bioactive compounds specific to any particular plant species. The noncoupled mitochondrial respiration operates in coordination with the malate and citrate valves and supports intensive fluxes of respiration and photorespiration. The metabolic system of plants has features associated with the remarkable metabolic plasticity of mitochondria that permit the use of energy accumulated during photosynthesis in a way that all anabolic and catabolic pathways become optimized and coordinated.
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Ramos M, Daranas N, Llugany M, Tolrà R, Montesinos E, Badosa E. Grapevine response to a Dittrichia viscosa extract and a Bacillus velezensis strain. FRONTIERS IN PLANT SCIENCE 2022; 13:1075231. [PMID: 36589113 PMCID: PMC9803176 DOI: 10.3389/fpls.2022.1075231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The present study aims to evaluate the response of the three Mediterranean local grapevines 'Garnacha Blanca', 'Garnacha Tinta', and 'Macabeo' to treatments with biocontrol products, namely a botanical extract (Akivi, Dittrichia viscosa extract) and a beneficial microorganism (Bacillus UdG, Bacillus velezensis). A combination of transcriptomics and metabolomics approaches were chosen in order to study grapevine gene expression and to identify gene marker candidates, as well as, to determine differentially concentrated grapevine metabolites in response to biocontrol product treatments. Grapevine plants were cultivated in greenhouse under controlled conditions and submitted to the treatments. Thereafter, leaves were sampled 24h after treatment to carry out the gene expression study by RT-qPCR for the three cultivars and by RNA-sequencing for 'Garnacha Blanca'. Differentially expressed genes (DEGs) were investigated for both treatments and highly influenced DEGs were selected to be tested in the three cultivars as treatment gene markers. In addition, the extraction of leaf components was performed to quantify metabolites, such as phytohormones, organic acids, and phenols. Considering the upregulated and downregulated genes and the enhanced metabolites concentrations, the treatments had an effect on jasmonic acid, ethylene, and phenylpropanoids defense pathways. In addition, several DEG markers were identified presenting a stable overexpression after the treatments in the three grapevine cultivars. These gene markers could be used to monitor the activity of the products in field treatments. Further research will be necessary to confirm these primary results under field conditions.
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Affiliation(s)
- Mélina Ramos
- Institute of Food and Agricultural Technology-CIDSAV-XaRTA, University of Girona, Girona, Spain
- Plant Physiology (BABVE), Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Núria Daranas
- Institute of Food and Agricultural Technology-CIDSAV-XaRTA, University of Girona, Girona, Spain
| | - Mercè Llugany
- Plant Physiology (BABVE), Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Roser Tolrà
- Plant Physiology (BABVE), Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Emilio Montesinos
- Institute of Food and Agricultural Technology-CIDSAV-XaRTA, University of Girona, Girona, Spain
| | - Esther Badosa
- Institute of Food and Agricultural Technology-CIDSAV-XaRTA, University of Girona, Girona, Spain
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Secgin Z, Uluisik S, Yıldırım K, Abdulla MF, Mostafa K, Kavas M. Genome-Wide Identification of the Aconitase Gene Family in Tomato ( Solanum lycopersicum) and CRISPR-Based Functional Characterization of SlACO2 on Male-Sterility. Int J Mol Sci 2022; 23:ijms232213963. [PMID: 36430441 PMCID: PMC9699144 DOI: 10.3390/ijms232213963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Tomato (Solanum lycopersicum) is one of the most cultivated vegetables in the world due to its consumption in a large variety of raw, cooked, or processed foods. Tomato breeding and productivity highly depend on the use of hybrid seeds and their higher yield, environmental adaption, and disease tolerance. However, the emasculation procedure during hybridization raises tomato seed production costs and labor expenses. Using male sterility is an effective way to reduce the cost of hybrid seeds and ensure cultivar purity. Recent developments in CRISPR genome editing technology enabled tomato breeders to investigate the male sterility genes and to develop male-sterile tomato lines. In the current study, the tomato Acotinase (SlACO) gene family was investigated via in silico tools and functionally characterized with CRISPR/Cas9-mediated gene disruption. Genome-wide blast and HMM search represented two SlACO genes located on different tomato chromosomes. Both genes were estimated to have a segmental duplication in the tomato genome due to their identical motif and domain structure. One of these genes, SlACO2, showed a high expression profile in all generative cells of tomato. Therefore, the SlACO2 gene was targeted with two different gRNA/Cas9 constructs to identify their functional role in tomatoes. The gene was mutated in a total of six genome-edited tomato lines, two of which were homozygous. Surprisingly, pollen viability was found to be extremely low in mutant plants compared to their wild-type (WT) counterparts. Likewise, the number of seeds per fruit also sharply decreased more than fivefold in mutant lines (10-12 seeds) compared to that in WT (67 seeds). The pollen shape, anther structures, and flower colors/shapes were not significantly varied between the mutant and WT tomatoes. The mutated lines were also subjected to salt and mannitol-mediated drought stress to test the effect of SlACO2 on abiotic stress tolerance. The results of the study indicated that mutant tomatoes have higher tolerance with significantly lower MDA content under stress conditions. This is the first CRISPR-mediated characterization of ACO genes on pollen viability, seed formation, and abiotic stress tolerance in tomatoes.
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Affiliation(s)
- Zafer Secgin
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55270 Samsun, Turkey
| | - Selman Uluisik
- Burdur Food Agriculture and Livestock Vocational School, Burdur Mehmet Akif Ersoy University, 15030 Burdur, Turkey
| | - Kubilay Yıldırım
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayıs University, 55270 Samsun, Turkey
| | - Mohamed Farah Abdulla
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55270 Samsun, Turkey
| | - Karam Mostafa
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55270 Samsun, Turkey
- The Central Laboratory for Date Palm Research and Development, Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Musa Kavas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55270 Samsun, Turkey
- Correspondence: ; Tel.: +90-3623121919; Fax: +90-3624576034
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Yang W, Li X, Jiang G, Long Y, Li H, Yu S, Zhao H, Liu J. Crotonylation versus acetylation in petunia corollas with reduced acetyl-CoA due to PaACL silencing. PHYSIOLOGIA PLANTARUM 2022; 174:e13794. [PMID: 36193016 DOI: 10.1111/ppl.13794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/08/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Protein acetylation and crotonylation are important posttranslational modifications of lysine. In animal cells, the correlation of acetylation and crotonylation has been well characterized and the lysines of some proteins are acetylated or crotonylated depending on the relative concentrations of acetyl-CoA and crotonyl-CoA. However, in plants, the correlation of acetylation and crotonylation and the effects of the relative intracellular concentrations of crotonyl-CoA and acetyl-CoA on protein crotonylation and acetylation are not well known. In our previous study, PaACL silencing changed the content of acetyl-CoA in petunia (Petunia hybrida) corollas, and the effect of PaACL silencing on the global acetylation proteome in petunia was analyzed. In the present study, we found that PaACL silencing did not significantly alter the content of crotonyl-CoA. We performed a global crotonylation proteome analysis of the corollas of PaACL-silenced and control petunia plants; we found that protein crotonylation was closely related to protein acetylation and that proteins with more crotonylation sites often had more acetylation sites. Crotonylated proteins and acetylated proteins were enriched in many common Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. However, PaACL silencing resulted in different KEGG pathway enrichments of proteins with different levels of crotonylation sites and acetylation sites. PaACLB1-B2 silencing did not led to changes in the opposite direction in crotonylation and acetylation levels at the same lysine site in cytoplasmic proteins, which indicated that cytoplasmic lysine acetylation and crotonylation might not depend on the relative concentrations of acetyl-CoA and crotonyl-CoA. Moreover, the global crotonylome and acetylome were weakly positively correlated in the corollas of PaACL-silenced and control plants.
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Affiliation(s)
- Weiyuan Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xin Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guiyun Jiang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yu Long
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Hui Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Shujun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Huina Zhao
- College of Horticulture, South China Agricultural University, Guangzhou, China
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- College of Horticulture, South China Agricultural University, Guangzhou, China
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Gerlin L, Cottret L, Escourrou A, Genin S, Baroukh C. A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations. PLANT PHYSIOLOGY 2022; 188:1709-1723. [PMID: 34907432 PMCID: PMC8896645 DOI: 10.1093/plphys/kiab548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
Predicting and understanding plant responses to perturbations require integrating the interactions between nutritional sources, genes, cell metabolism, and physiology in the same model. This can be achieved using metabolic modeling calibrated by experimental data. In this study, we developed a multi-organ metabolic model of a tomato (Solanum lycopersicum) plant during vegetative growth, named Virtual Young TOmato Plant (VYTOP) that combines genome-scale metabolic models of leaf, stem and root and integrates experimental data acquired from metabolomics and high-throughput phenotyping of tomato plants. It is composed of 6,689 reactions and 6,326 metabolites. We validated VYTOP predictions on five independent use cases. The model correctly predicted that glutamine is the main organic nutrient of xylem sap. The model estimated quantitatively how stem photosynthetic contribution impacts exchanges between the different organs. The model was also able to predict how nitrogen limitation affects vegetative growth and the metabolic behavior of transgenic tomato lines with altered expression of core metabolic enzymes. The integration of different components, such as a metabolic model, physiological constraints, and experimental data, generates a powerful predictive tool to study plant behavior, which will be useful for several other applications, such as plant metabolic engineering or plant nutrition.
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Affiliation(s)
- Léo Gerlin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Ludovic Cottret
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Antoine Escourrou
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Caroline Baroukh
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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10
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Fàbregas N, Fernie AR. The reliance of phytohormone biosynthesis on primary metabolite precursors. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153589. [PMID: 34896926 DOI: 10.1016/j.jplph.2021.153589] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 05/07/2023]
Abstract
There is some debate as to whether phytohormone metabolites should be classified as primary or secondary metabolites. Phytohormones have profound effects on growth - a typical trait of primary metabolites - yet several of them are formed from secondary metabolite precursors. This is further exacerbated by the blurred distinction between primary and secondary metabolism. What is clearer, however, is that phytohormones display distinctive regulatory mechanisms from other metabolites. Moreover, by contrast to microbial and mammalian systems, the majority of plant metabolite receptors characterized to date are hormone receptors. Here, we provide an overview of the metabolic links between primary metabolism and phytohormone biosynthesis in an attempt to complement recent reviews covering the signaling crosstalk between elements of core metabolism and the phytohormones. In doing so, we cover the biosynthesis of both the classical metabolic phytohormones namely auxins, salicylic acid, jasmonate, ethylene, cytokinins, brassinosteroids, gibberellins and abscisic acid as well as recently described plant growth regulators which have been proposed as novel phytohormones namely strigolactones blumenols, zaxinone and β-cyclocitral as well as melatonin. For each hormone, we describe the primary metabolite precursors which fuel its synthesis, act as conjugates or in the case of 2-oxoglutarate act more directly as a co-substrate in the biosynthesis of gibberellin, auxin and salicylic acid. Furthermore, several amino acids operate as hormone conjugates, such as jasmonate-conjugates. In reviewing the biosynthesis of all the phytohormones simultaneously, the exceptional intricacy of the biochemical interplay that underpins their interaction emerges.
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Affiliation(s)
- Norma Fàbregas
- 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.
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11
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Fàbregas N, Fernie AR. The interface of central metabolism with hormone signaling in plants. Curr Biol 2021; 31:R1535-R1548. [PMID: 34875246 DOI: 10.1016/j.cub.2021.09.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Amongst the myriad of metabolites produced by plants, primary metabolites and hormones play crucial housekeeping roles in the cell and are essential for proper plant growth and development. While the biosynthetic pathways of primary metabolism are well characterized, those of hormones are yet to be completely defined. Central metabolism provides precursors for hormone biosynthesis and the regulation and function of primary metabolites and hormones are tightly entwined. The combination of reverse genetics and technological advances in our ability to evaluate the levels of the molecular entities of the cell (transcripts, proteins and metabolites) has led to considerable improvements in our understanding of both the regulatory interaction between primary metabolites and hormones and its coordination in response to different conditions. Here, we provide an overview of the interaction of primary and hormone metabolism at the metabolic and signaling levels, as well as a perspective regarding the tools that can be used to tackle our current knowledge gaps at the signaling level.
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Affiliation(s)
- Norma Fàbregas
- 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.
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12
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Liu Y, Qu J, Shi Z, Zhang P, Ren M. Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum. BMC Genomics 2021; 22:821. [PMID: 34773990 PMCID: PMC8590752 DOI: 10.1186/s12864-021-08109-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/20/2021] [Indexed: 11/26/2022] Open
Abstract
Background The tricarboxylic acid (TCA) cycle is crucial for energy supply in animal, plant, and microbial cells. It is not only the main pathway of carbohydrate catabolism but also the final pathway of lipid and protein catabolism. Some TCA genes have been found to play important roles in the growth and development of tomato and potato, but no comprehensive study of TCA cycle genes in Solanaceae crops has been reported. Results In this study, we analyzed TCA cycle genes in four important Solanaceae vegetable crops (potato (Solanum tuberosum), tomato (Solanum lycopersicum), eggplant (Solanum melongena), and pepper (Capsicum annuum)) based on comparative genomics. The four Solanaceae crops had a total of 180 TCA cycle genes: 43 in potato, 44 in tomato, 40 in eggplant, and 53 in pepper. Phylogenetic analysis, collinearity analysis, and tissue expression patterns revealed the conservation of and differences in TCA cycle genes between the four Solanaceae crops and found that there were unique subgroup members in Solanaceae crops that were independent of Arabidopsis genes. The expression analysis of potato TCA cycle genes showed that (1) they were widely expressed in various tissues, and some transcripts like Soltu.DM.01G003320.1(SCoAL) and Soltu.DM.04G021520.1 (SDH) mainly accumulate in vegetative organs, and some transcripts such as Soltu.DM.12G005620.3 (SDH) and Soltu.DM.02G007400.4 (MDH) are preferentially expressed in reproductive organs; (2) several transcripts can be significantly induced by hormones, such as Soltu.DM.08G023870.2 (IDH) and Soltu.DM.06G029290.1 (SDH) under ABA treatment, and Soltu.DM.07G021850.2 (CSY) and Soltu.DM.09G026740.1 (MDH) under BAP treatment, and Soltu.DM.02G000940.1 (IDH) and Soltu.DM.01G031350.4 (MDH) under GA treatment; (3) Soltu.DM.11G024650.1 (SDH) can be upregulated by the three disease resistance inducers including Phytophthora infestans, acibenzolar-S-methyl (BTH), and DL-β-amino-n-butyric acid (BABA); and (4) the levels of Soltu.DM.01G045790.1 (MDH), Soltu.DM.01G028520.3 (CSY), and Soltu.DM.12G028700.1 (CSY) can be activated by both NaCl and mannitol. The subcellular localization results of three potato citrate synthases showed that Soltu.DM.01G028520.3 was localized in mitochondria, while Soltu.DM.12G028700.1 and Soltu.DM.07G021850.1 were localized in the cytoplasm. Conclusions This study provides a scientific foundation for the comprehensive understanding and functional studies of TCA cycle genes in Solanaceae crops and reveals their potential roles in potato growth, development, and stress response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08109-9.
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Affiliation(s)
- Yongming Liu
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, 610213, Chengdu, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural, Sciences of Zhengzhou University, 450000, Zhengzhou, China.,Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, China
| | - Jingtao Qu
- Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Ziwen Shi
- Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Peng Zhang
- Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, 610213, Chengdu, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural, Sciences of Zhengzhou University, 450000, Zhengzhou, China. .,Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, China.
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13
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Medeiros DB, Aarabi F, Martinez Rivas FJ, Fernie AR. The knowns and unknowns of intracellular partitioning of carbon and nitrogen, with focus on the organic acid-mediated interplay between mitochondrion and chloroplast. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153521. [PMID: 34537467 DOI: 10.1016/j.jplph.2021.153521] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/20/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
The presence of specialized cellular compartments in higher plants express an extraordinary degree of intracellular organization, which provides efficient mechanisms to avoid misbalancing of the metabolism. This offers the flexibility by which plants can quickly acclimate to fluctuating environmental conditions. For that, a fine temporal and spatial regulation of metabolic pathways is required and involves several players e.g. organic acids. In this review we discuss different facets of the organic acid metabolism within plant cells with special focus to those related to the interactions between organic acids compartmentalization and the partitioning of carbon and nitrogen. The connections between organic acids and CO2 assimilation, tricarboxylic acid (TCA) cycle, amino acids metabolism, and redox status are highlighted. Moreover, the key enzymes and transporters as well as their function on the coordination of interorganellar metabolic exchanges are discussed.
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Affiliation(s)
- David B Medeiros
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany.
| | - Fayezeh Aarabi
- 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.
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14
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Condori-Apfata JA, Batista-Silva W, Medeiros DB, Vargas JR, Valente LML, Pérez-Díaz JL, Fernie AR, Araújo WL, Nunes-Nesi A. Downregulation of the E2 Subunit of 2-Oxoglutarate Dehydrogenase Modulates Plant Growth by Impacting Carbon-Nitrogen Metabolism in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2021; 62:798-814. [PMID: 33693904 PMCID: PMC8484937 DOI: 10.1093/pcp/pcab036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 02/28/2021] [Accepted: 04/16/2021] [Indexed: 05/04/2023]
Abstract
In Arabidopsis thaliana, two genes encode the E2 subunit of the 2-oxoglutarate dehydrogenase (2-OGDH), a multimeric complex composed of three subunits. To functionally characterize the isoforms of E2 subunit, we isolated Arabidopsis mutant lines for each gene encoding the E2 subunit and performed a detailed molecular and physiological characterization of the plants under controlled growth conditions. The functional lack of expression of E2 subunit isoforms of 2-OGDH increased plant growth, reduced dark respiration and altered carbohydrate metabolism without changes in the photosynthetic rate. Interestingly, plants from e2-ogdh lines also exhibited reduced seed weight without alterations in total seed number. We additionally observed that downregulation of 2-OGDH activity led to minor changes in the levels of tricarboxylic acid cycle intermediates without clear correlation with the reduced expression of specific E2-OGDH isoforms. Furthermore, the e2-ogdh mutant lines exhibited a reduction by up to 25% in the leaf total amino acids without consistent changes in the amino acid profile. Taken together, our results indicate that the two isoforms of E2 subunit play a similar role in carbon-nitrogen metabolism, in plant growth and in seed weight.
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Affiliation(s)
- Jorge A Condori-Apfata
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Willian Batista-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - David Barbosa Medeiros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam Golm 14476, Germany
| | - Jonas Rafael Vargas
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Luiz M Lopes Valente
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Jorge Luis Pérez-Díaz
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Alisdair R Fernie
- * Corresponding authors: Alisdair R. Fernie, E-mail, ; Adriano Nunes-Nesi, E-mail,
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Adriano Nunes-Nesi
- * Corresponding authors: Alisdair R. Fernie, E-mail, ; Adriano Nunes-Nesi, E-mail,
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15
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Nascimento VL, Pereira AM, Pereira AS, Silva VF, Costa LC, Bastos CEA, Ribeiro DM, Caldana C, Sulpice R, Nunes-Nesi A, Zsögön A, Araújo WL. Physiological and metabolic bases of increased growth in the tomato ethylene-insensitive mutant Never ripe: extending ethylene signaling functions. PLANT CELL REPORTS 2021; 40:1377-1393. [PMID: 33074436 DOI: 10.1007/s00299-020-02623-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
The tomato mutant Never ripe (Nr), a loss-of-function for the ethylene receptor SlETR3, shows enhanced growth, associated with increased carbon assimilation and a rewiring of the central metabolism. Compelling evidence has demonstrated the importance of ethylene during tomato fruit development, yet its role on leaf central metabolism and plant growth remains elusive. Here, we performed a detailed characterization of Never ripe (Nr) tomato, a loss-of-function mutant for the ethylene receptor SlETR3, known for its fruits which never ripe. However, besides fruits, the Nr gene is also constitutively expressed in vegetative tissues. Nr mutant showed a growth enhancement during both the vegetative and reproductive stage, without an earlier onset of leaf senescence, with Nr plants exhibiting a higher number of leaves and an increased dry weight of leaves, stems, roots, and fruits. At metabolic level, Nr also plays a significant role with the mutant showing changes in carbon assimilation, carbohydrates turnover, and an exquisite reprogramming of a large number of metabolite levels. Notably, the expression of genes related to ethylene signaling and biosynthesis are not altered in Nr. We assess our results in the context of those previously published for tomato fruits and of current models of ethylene signal transduction, and conclude that ethylene insensitivity mediated by Nr impacts the whole central metabolism at vegetative stage, leading to increased growth rates.
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Affiliation(s)
- Vitor L Nascimento
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Auderlan M Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Aurelio S Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Victor F Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Lucas C Costa
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Carla E A Bastos
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Dimas M Ribeiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ronan Sulpice
- Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre and Ryan Institute, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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16
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Lihavainen J, Edlund E, Björkén L, Bag P, Robinson KM, Jansson S. Stem girdling affects the onset of autumn senescence in aspen in interaction with metabolic signals. PHYSIOLOGIA PLANTARUM 2021; 172:201-217. [PMID: 33368469 PMCID: PMC8248097 DOI: 10.1111/ppl.13319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/29/2020] [Accepted: 12/12/2020] [Indexed: 05/06/2023]
Abstract
Autumn senescence in aspen (Populus tremula) is precisely timed every year to relocate nutrients from leaves to storage organs before winter. Here we demonstrate how stem girdling, which leads to the accumulation of photosynthates in the crown, influences senescence. Girdling resulted in an early onset of senescence, but the chlorophyll degradation was slower and nitrogen more efficiently resorbed than during normal autumn senescence. Girdled stems accumulated or retained anthocyanins potentially providing photoprotection in senescing leaves. Girdling of one stem in a clonal stand sharing the same root stock did not affect senescence in the others, showing that the stems were autonomous in this respect. One girdled stem with unusually high chlorophyll and nitrogen contents maintained low carbon-to-nitrogen (C/N) ratio and did not show early senescence or depleted chlorophyll level unlike the other girdled stems suggesting that the responses depended on the genotype or its carbon and nitrogen status. Metabolite analysis highlighted that the tricarboxylic acid (TCA) cycle, salicylic acid pathway, and redox homeostasis are involved in the regulation of girdling-induced senescence. We propose that disrupted sink-source relation and C/N status can provide cues through the TCA cycle and phytohormone signaling to override the phenological control of autumn senescence in the girdled stems.
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Affiliation(s)
- Jenna Lihavainen
- Umeå Plant Science Centre, Department of Plant PhysiologyUmeå UniversityUmeåSweden
| | - Erik Edlund
- Umeå Plant Science Centre, Department of Plant PhysiologyUmeå UniversityUmeåSweden
| | - Lars Björkén
- Umeå Plant Science Centre, Department of Plant PhysiologyUmeå UniversityUmeåSweden
| | - Pushan Bag
- Umeå Plant Science Centre, Department of Plant PhysiologyUmeå UniversityUmeåSweden
| | - Kathryn M. Robinson
- Umeå Plant Science Centre, Department of Plant PhysiologyUmeå UniversityUmeåSweden
| | - Stefan Jansson
- Umeå Plant Science Centre, Department of Plant PhysiologyUmeå UniversityUmeåSweden
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17
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Zhu W, Han H, Liu A, Guan Q, Kang J, David L, Dufresne C, Chen S, Tian J. Combined ultraviolet and darkness regulation of medicinal metabolites in Mahonia bealei revealed by proteomics and metabolomics. J Proteomics 2020; 233:104081. [PMID: 33352312 DOI: 10.1016/j.jprot.2020.104081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022]
Abstract
Roots of Mahonia bealei have been used as traditional Chinese medicine with antibacterial, antioxidant and anti-inflammatory properties due to its high alkaloid content. Previously, we reported that alkaloid and flavonoid contents in the M. bealei leaves could be increased by the combined ultraviolet B and dark treatment (UV+D). To explore the underlying metabolic pathways and networks, proteomic and metabolomic analyses of the M. bealei leaves were conducted. Proteins related to tricarboxylic acid cycle, transport and signaling varied greatly under the UV + D. Among them, calmodulin involved in calcium signaling and ATP-binding cassette transporter involved in transport of berberine were increased. Significantly changed metabolites were overrepresented in phenylalanine metabolism, nitrogen metabolism, phenylpropanoid, flavonoid and alkaloid biosynthesis. In addition, the levels of salicylic acid and gibberellin decreased in the UV group and increased in the UV + D group. These results indicate that multi-hormone crosstalk may regulate the biosynthesis of flavonoids and alkaloids to alleviate oxidative stress caused by the UV + D treatment. Furthermore, protoberberine alkaloids may be induced through calcium signaling crosstalk with reaction oxygen species and transported to leaves. SIGNIFICANCE: Mahonia bealei root and stem, not leaf, were used as traditional medicine for a long history because of the high contents of active components. In the present study, UV-B combined with dark treatments induced the production of alkaloids and flavonoids in the M. bealei leaf, especially protoberberine alkaloids such as berberine. Multi-omics analyses indicated that multi-hormone crosstalk, enhanced tricarboxylic acid cycle and active calcium signaling were involved. The study informs a strategy for utilization of the leaves, and improves understanding of the functions of secondary metabolites in M. bealei.
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Affiliation(s)
- Wei Zhu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China; Department of Biology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida Genetics Institute, Gainesville, FL 32610, USA; Changsu Qiushi Technology Co., Ltd, Suzhou 215500, PR China
| | - Haote Han
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China
| | - Amin Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China
| | - Qijie Guan
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China; Department of Biology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida Genetics Institute, Gainesville, FL 32610, USA
| | - Jianing Kang
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida Genetics Institute, Gainesville, FL 32610, USA; College of Life Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Lisa David
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida Genetics Institute, Gainesville, FL 32610, USA
| | - Craig Dufresne
- Thermo Fisher Scientific, West Palm Beach, FL 33407, USA
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida Genetics Institute, Gainesville, FL 32610, USA; Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA.
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China.
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18
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Ma Q, Liu Y, Fang H, Wang P, Ahammed GJ, Zai W, Shi K. An Essential Role of Mitochondrial α-Ketoglutarate Dehydrogenase E2 in the Basal Immune Response Against Bacterial Pathogens in Tomato. FRONTIERS IN PLANT SCIENCE 2020; 11:579772. [PMID: 33193523 PMCID: PMC7661389 DOI: 10.3389/fpls.2020.579772] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/18/2020] [Indexed: 06/01/2023]
Abstract
Plants intensely modulate respiration when pathogens attack, but the function of mitochondrial respiration-related genes in plant-bacteria interaction is largely unclear. Here, the functions of α-ketoglutarate dehydrogenase (α-kGDH) E2 subunit and alternative oxidase (AOX) were investigated in the interaction between tomato and the virulent bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst). Pst inoculation suppressed the transcript abundance of α-kGDH E2, but enhanced AOX expression and salicylic acid (SA) accumulation. Gene silencing and transient overexpression approaches revealed that plant susceptibility to Pst was significantly reduced by silencing α-kGDH E2 in tomato, but increased by overexpressing α-kGDH E2 in Nicotiana benthamiana, whereas silencing or overexpressing of AOX1a did not affect plant defense. Moreover, silencing octanoyltransferase (LIP2), engaged in the lipoylation of α-kGDH E2, significantly reduced disease susceptibility and hydrogen peroxide accumulation. Use of transgenic NahG tomato plants that cannot accumulate SA as well as the exogenous SA application experiment evidenced that α-kGDH E2 acts downstream of SA defense pathway. These results demonstrate tomato α-kGDH E2 plays a negative role in plant basal defense against Pst in an AOX-independent pathway but was associated with lipoylation and SA defense pathways. The findings help to elucidate the mechanisms of mitochondria-involved plant basal immunity.
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Affiliation(s)
- Qiaomei Ma
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yaru Liu
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Hanmo Fang
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Ping Wang
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Golam Jalal Ahammed
- College of Forestry, Henan University of Science and Technology, Luoyang, China
| | - Wenshan Zai
- Wenzhou Vocational College of Science & Technology, Wenzhou, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, Hangzhou, China
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19
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Zhang Y, Ji TT, Li TT, Tian YY, Wang LF, Liu WC. Jasmonic acid promotes leaf senescence through MYC2-mediated repression of CATALASE2 expression in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110604. [PMID: 32900442 DOI: 10.1016/j.plantsci.2020.110604] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 05/25/2023]
Abstract
Plants relocate nutrients and energy from aging leaves to developing tissues during leaf senescence, which is important for plant growth, development, and responses to various environmental stimuli. Both jasmonic acid (JA) and H2O2 are two crucial signalling molecules positively regulating leaf senescence, whereas whether and how they are coordinated in leaf senescence remains elusive. Here, we report that H2O2 accumulates in JA-treated leaves, while scavenging the increased H2O2 can significantly suppresses JA-induced leaf senescence and the expression of senescence-associated genes (SAGs). The mutant myc2 with a mutation of MYC2, a master transcription factor in JA signalling pathway, exhibits delayed leaf senescence with increased catalase activity and decreased H2O2 accumulation compared with the wild type upon JA treatment. Further study showed that MYC2 downregulates CATALASE 2 (CAT2) expression by binding to its promoter, thus promoting JA-induced H2O2 accumulation and leaf senescence. Moreover, the delayed leaf senescence with reduced H2O2 accumulation and SAGs expression of the myc2 mutant is significantly reverted by the cat2-1 mutation in myc2 cat2-1 double mutant. Thus, our study reveals that JA represses CAT2 expression to increase H2O2 accumulation, thus promoting leaf senescence in a MYC2 dependent manner in Arabidopsis.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Tong-Tong Ji
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ting-Ting Li
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yang-Yang Tian
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Lin-Feng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wen-Cheng Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China.
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20
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Ji J, Shi Z, Xie T, Zhang X, Chen W, Du C, Sun J, Yue J, Zhao X, Jiang Z, Shi S. Responses of GABA shunt coupled with carbon and nitrogen metabolism in poplar under NaCl and CdCl 2 stresses. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 193:110322. [PMID: 32109582 DOI: 10.1016/j.ecoenv.2020.110322] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 02/05/2020] [Accepted: 02/08/2020] [Indexed: 05/20/2023]
Abstract
The γ-aminobutyric acid (GABA) shunt is closely associated with plant tolerance; however, little is known about its mechanism. This study aimed to decipher the responses of the GABA shunt and related carbon-nitrogen metabolism in poplar seedlings (Populus alba × Populus glandulosa) treated with different NaCl and CdCl2 concentrations for 30 h. The results showed that the activities of glutamate decarboxylase (GAD) and GABA-transaminase (GABA-T) were activated, as well as α-ketoglutarate dehydrogenase (α-KGDH) and succinate dehydrogenase (SDH) activities were enhanced by NaCl and CdCl2 stresses, except for SDH under CdCl2 stress. Meanwhile, the expression levels of GADs, GABA-Ts SDHs, succinyl-CoA ligases (SCSs), and succinic acid aldehyde dehydrogenases (SSADHs) were also increased. Notably, significant increases in the key components of GABA shunt, Glu and GABA, were observed under both stresses. Soluble sugars and free amino acids were enhanced, whereas citrate, malate and succinate were almost inhibited by both NaCl and CdCl2 stresses except that citrate was not changed or just increased by 50-mM NaCl stress. Thus, these results suggested that the carbon-nitrogen balance could be altered by activating the GABA shunt when main TCA-cycle intermediates were inhibited under NaCl and CdCl2 stresses. This study can enhance the understanding about the functions of the GABA shunt in woody plants under abiotic stresses and may be applied to the genetic improvement of trees for phytoremediation.
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Affiliation(s)
- Jing Ji
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 1958 Box, Beijing, 100091, China
| | - Zheng Shi
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Ecology and Environment of State Forestry and Grassland Administration, Chinese Academy of Forestry, 1958 Box, Beijing, 100091, China
| | - Tiantian Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 1958 Box, Beijing, 100091, China
| | - Xiaoman Zhang
- College of Landscape Architecture and Tourism, Hebei Agricultural University, No. 289 Lingyusi Street, Baoding, 071001, Hebei, China
| | - Wei Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 1958 Box, Beijing, 100091, China
| | - Changjian Du
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 1958 Box, Beijing, 100091, China
| | - Jiacheng Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 1958 Box, Beijing, 100091, China
| | - Jianyun Yue
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 1958 Box, Beijing, 100091, China
| | - Xiulian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 1958 Box, Beijing, 100091, China
| | - Zeping Jiang
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Ecology and Environment of State Forestry and Grassland Administration, Chinese Academy of Forestry, 1958 Box, Beijing, 100091, China
| | - Shengqing Shi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, 1958 Box, Beijing, 100091, China.
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Sink/Source Balance of Leaves Influences Amino Acid Pools and Their Associated Metabolic Fluxes in Winter Oilseed Rape ( Brassica napus L.). Metabolites 2020; 10:metabo10040150. [PMID: 32295054 PMCID: PMC7240945 DOI: 10.3390/metabo10040150] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/26/2020] [Accepted: 04/09/2020] [Indexed: 11/18/2022] Open
Abstract
Nitrogen remobilization processes from source to sink tissues in plants are determinant for seed yield and their implementation results in a complete reorganization of the primary metabolism during sink/source transition. Here, we decided to characterize the impact of the sink/source balance on amino acid metabolism in the leaves of winter oilseed rape grown at the vegetative stage. We combined a quantitative metabolomics approach with an instationary 15N-labeling experiment by using [15N]L-glycine as a metabolic probe on leaf ranks with a gradual increase in their source status. We showed that the acquisition of the source status by leaves was specifically accompanied by a decrease in asparagine, glutamine, proline and S-methyl-l-cysteine sulphoxide contents and an increase in valine and threonine contents. Dynamic analysis of 15N enrichment and concentration of amino acids revealed gradual changes in the dynamics of amino acid metabolism with respect to the sink/source status of leaf ranks. Notably, nitrogen assimilation into valine, threonine and proline were all decreased in source leaves compared to sink leaves. Overall, our results suggested a reduction in de novo amino acid biosynthesis during sink/source transition at the vegetative stage.
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22
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Dellero Y, Heuillet M, Marnet N, Bellvert F, Millard P, Bouchereau A. Sink/Source Balance of Leaves Influences Amino Acid Pools and Their Associated Metabolic Fluxes in Winter Oilseed Rape ( Brassica napus L.). Metabolites 2020; 10:metabo10040150. [PMID: 32295054 DOI: 10.15454/1i9pet] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/26/2020] [Accepted: 04/09/2020] [Indexed: 05/27/2023] Open
Abstract
Nitrogen remobilization processes from source to sink tissues in plants are determinant for seed yield and their implementation results in a complete reorganization of the primary metabolism during sink/source transition. Here, we decided to characterize the impact of the sink/source balance on amino acid metabolism in the leaves of winter oilseed rape grown at the vegetative stage. We combined a quantitative metabolomics approach with an instationary 15N-labeling experiment by using [15N]L-glycine as a metabolic probe on leaf ranks with a gradual increase in their source status. We showed that the acquisition of the source status by leaves was specifically accompanied by a decrease in asparagine, glutamine, proline and S-methyl-l-cysteine sulphoxide contents and an increase in valine and threonine contents. Dynamic analysis of 15N enrichment and concentration of amino acids revealed gradual changes in the dynamics of amino acid metabolism with respect to the sink/source status of leaf ranks. Notably, nitrogen assimilation into valine, threonine and proline were all decreased in source leaves compared to sink leaves. Overall, our results suggested a reduction in de novo amino acid biosynthesis during sink/source transition at the vegetative stage.
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Affiliation(s)
- Younès Dellero
- Department Plant Biology and Breeding, Agrocampus Ouest, Institute for Genetics, Environment and Plant Protection, French National Research Institute for Agriculture, Food and Environment, University of Rennes II, 35653 Le Rheu, France
| | - Maud Heuillet
- Department Plant Biology and Breeding, Department Microbiology and Food Chain, INSA, TBI, French National Center for Scientific Research, French National Research Institute for Agriculture, Food and Environment, University of Toulouse, 31400 Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 33140 Toulouse, France
| | - Nathalie Marnet
- Department Plant Biology and Breeding and Department Transform, Agrocampus Ouest, Plateau de Profilage Métabolique et Métabolique (P2M2), Biopolymers Interactions Assemblies, Institute for Genetics, Environment and Plant Protection, French National Research Institute for Agriculture, Food and Environment, University of Rennes II, 35653 Le Rheu, France
| | - Floriant Bellvert
- Department Plant Biology and Breeding, Department Microbiology and Food Chain, INSA, TBI, French National Center for Scientific Research, French National Research Institute for Agriculture, Food and Environment, University of Toulouse, 31400 Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 33140 Toulouse, France
| | - Pierre Millard
- Department Plant Biology and Breeding, Department Microbiology and Food Chain, INSA, TBI, French National Center for Scientific Research, French National Research Institute for Agriculture, Food and Environment, University of Toulouse, 31400 Toulouse, France
| | - Alain Bouchereau
- Department Plant Biology and Breeding, Agrocampus Ouest, Institute for Genetics, Environment and Plant Protection, French National Research Institute for Agriculture, Food and Environment, University of Rennes II, 35653 Le Rheu, France
- Department Plant Biology and Breeding and Department Transform, Agrocampus Ouest, Plateau de Profilage Métabolique et Métabolique (P2M2), Biopolymers Interactions Assemblies, Institute for Genetics, Environment and Plant Protection, French National Research Institute for Agriculture, Food and Environment, University of Rennes II, 35653 Le Rheu, France
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23
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Dellero Y, Clouet V, Marnet N, Pellizzaro A, Dechaumet S, Niogret MF, Bouchereau A. Leaf status and environmental signals jointly regulate proline metabolism in winter oilseed rape. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2098-2111. [PMID: 31807778 PMCID: PMC7242077 DOI: 10.1093/jxb/erz538] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/05/2019] [Indexed: 05/03/2023]
Abstract
Proline metabolism is an essential component of plant adaptation to multiple environmental stress conditions that is also known to participate in specific developmental phases, particularly in reproductive organs. Recent evidence suggested a possible role for proline catabolism in Brassica napus for nitrogen remobilization processes from source leaves at the vegetative stage. Here, we investigate transcript levels of Δ1-PYRROLINE-5-CARBOXYLATE SYNTHASE (P5CS) and PROLINE DEHYDROGENASE (ProDH) genes at the vegetative stage with respect to net proline biosynthesis and degradation fluxes in leaves having a different sink/source balance. We showed that the underexpression of three P5CS1 genes in source leaves was accompanied by a reduced commitment of de novo assimilated 15N towards proline biosynthesis and an overall depletion of free proline content. We found that the expression of ProDH genes was strongly induced by carbon starvation conditions (dark-induced senescence) compared with early senescing leaves. Our results suggested a role for proline catabolism in B. napus, but acting only at a late stage of senescence. In addition, we also identified some P5CS and ProDH genes that were differentially expressed during multiple processes (leaf status, dark to light transition, and stress response).
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Affiliation(s)
- Younes Dellero
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France
- Correspondence:
| | - Vanessa Clouet
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France
| | - Nathalie Marnet
- Plateau de Profilage Métabolique et Métabolique (P2M2), INRA-IGEPP and INRA-BIA, Le Rheu, France
| | - Anthoni Pellizzaro
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France
| | - Sylvain Dechaumet
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France
| | - Marie-Françoise Niogret
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France
| | - Alain Bouchereau
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France
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Xie T, Ji J, Chen W, Yue J, Du C, Sun J, Chen L, Jiang Z, Shi S. GABA negatively regulates adventitious root development in poplar. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1459-1474. [PMID: 31740934 DOI: 10.1093/jxb/erz520] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 11/18/2019] [Indexed: 05/25/2023]
Abstract
γ-Aminobutyric acid (GABA) influences plant growth, but little is known about how this metabolite regulates adventitious root (AR) development. Here, we investigate the effects of GABA on ARs using poplar lines overexpressing glutamate decarboxilase 2 (GAD2) and by treating poplar stem cuttings with exogenous GABA or vigabatrin (VGB; a specific GABA transaminase inhibitor). Endogenous GABA accumulation not only inhibited AR growth, but it also suppressed or delayed AR formation. Anatomical observations revealed that the GABA and VGB treatments resulted in a 1 d delay in the formation of AR primordia and the appearance of ARs. This delay coincided with changes in primary metabolism, including transient increases in hexose and amino acid levels. GABA-dependent changes in the expression of genes related to hormone synthesis and signalling, as well as analysis of hormone levels revealed that ethylene-dependent pathways were decreased at the earliest stage of AR formation. In contrast, auxin and abscisic acid were increased at 1-5 d as well as GA4 over a 5 d period of AR formation. These results demonstrate that GABA plays a crucial role in AR development. Evidence is presented demonstrating that GABA can interact with hormone-related pathways as well as carbon/nitrogen metabolism. These findings also elucidate the functions of GABA in plant development.
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Affiliation(s)
- Tiantian Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry Research, Chinese Academy of Forestry, Beijing, China
| | - Jing Ji
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry Research, Chinese Academy of Forestry, Beijing, China
| | - Wei Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry Research, Chinese Academy of Forestry, Beijing, China
| | - Jianyun Yue
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry Research, Chinese Academy of Forestry, Beijing, China
| | - Changjian Du
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry Research, Chinese Academy of Forestry, Beijing, China
| | - Jiacheng Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry Research, Chinese Academy of Forestry, Beijing, China
| | - Lanzhen Chen
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Risk Assessment Laboratory for Bee Products, Quality and Safety of Ministry of Agriculture, Beijing, China
| | - Zeping Jiang
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Ecology and Environment of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
| | - Shengqing Shi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry Research, Chinese Academy of Forestry, Beijing, China
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Aslam A, Zhao S, Azam M, Lu X, He N, Li B, Dou J, Zhu H, Liu W. Comparative analysis of primary metabolites and transcriptome changes between ungrafted and pumpkin-grafted watermelon during fruit development. PeerJ 2020; 8:e8259. [PMID: 31934503 PMCID: PMC6951286 DOI: 10.7717/peerj.8259] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/20/2019] [Indexed: 02/05/2023] Open
Abstract
Grafting has been reported as a factor that influences fruit quality. However, a comprehensive study of the metabolic profile related to fruit quality and the underlying molecular mechanism in grafted watermelon has not been carried out. Metabolomics and transcriptome analysis were performed on both pumpkin-grafted watermelon and ungrafted watermelon at different developmental stages. In total, 56 primary metabolites were identified with either high or low abundance between ungrafted and pumpkin-grafted watermelon. The results indicated that ornithine, arginine, lysine (amino acids), glucose, sucrose, glucosamine (sugars), malic acid, fumaric acid and succinic acid (organic acids) were among the dominant metabolites influencing fruit quality. Additionally, comparative RNA sequence analysis on grafted and ungrafted watermelon yielded 729, 174, 128 and 356 differentially expressed genes at 10, 18, 26 and 34 days after pollination (DAP), respectively. Functional annotations of these genes indicated that grafting significantly altered the biological and metabolic processes related to fruit quality. Our comparative metabolomics and transcriptome analysis revealed that FBA2, FK, SuSy, SPS, IAI, AI and sugar transporter gene (SWT3b) might play a central role in the accumulation of glucose and sucrose, whereas higher malic acid content was attributed to high down regulation of ALMT13 and ALMT8 in pumpkin-grafted watermelon. Changes in the ornithine, glutamine, alanine, tyrosine, valine, asparagine, phenylalanine, arginine and tryptophan contents were consistent with the transcript level of their metabolic genes such as NAOD, GS, AGT, TaT, aDH1, OGDH, aDC, 4CL 1, PaL, CaT and two nitrate transporter genes (NRT1) in pumpkin-grafted watermelon. This study provides the basis for understanding the graft-responsive changes in the metabolic profile and regulatory mechanism related to fruit quality.
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Affiliation(s)
- Ali Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Muhammad Azam
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Bingbing Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
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26
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Bai Q, Huang Y, Shen Y. The Physiological and Molecular Mechanism of Abscisic Acid in Regulation of Fleshy Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2020; 11:619953. [PMID: 33505417 PMCID: PMC7829184 DOI: 10.3389/fpls.2020.619953] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/09/2020] [Indexed: 05/18/2023]
Abstract
The ripening of fleshy fruits is coupled with the degradation of both chlorophyll and cell walls, as well as changes in the metabolism of phenylpropanoids, flavonoids, starch/sucrose, and carotenoids. These processes are controlled by phytohormones and other factors, including abscisic acid (ABA), ethylene, auxin, polyamines, sugar, and reactive oxygen species. The ripening of climacteric fruits is controlled by ethylene and non-climacteric fruit ripening is regulated mainly by ABA. Also, ABA and ethylene may interact in both types of fruit ripening. ABA concentrations in fleshy fruits are regulated in response to developmental and environmental cues and are controlled by the relative rates of ABA biosynthesis and catabolism, the former mainly via 9-cis-epoxycarotenoid dioxygenases (NCEDs) and β-glucosidases and the latter via ABA 8'-hydroxylases (CYP707As) and β-glycosyltransferases. In strawberry fruit ripening, ABA is perceived via at least two receptors, Pyrabactin resistance (PYR)/PYR-like (PYL) and putative abscisic acid receptor (ABAR), which are linked separately to the conserved signaling pathway ABA-FaPYR1-FaABIl-FaSnRK2 and the novel signaling pathway ABA-FaABAR-FaRIPK1-FaABI4. Downstream signaling components include important transcription factors, such as AREB (ABA responsive element binding protein)/ABF (ABRE binding factors ABA responsive factor), ethylene response factor (ERF), and V-myb Myeloblastosis viral oncogene homolog (MYB), as well as ripening-related genes. Finally, a comprehensive model of ABA linked to ethylene, sugar, polyamines, auxin and reactive oxygen species in the regulation of strawberry fruit ripening is proposed. Next, new integrated mechanisms, including two ABA signaling pathways, ABA and ethylene signaling pathways, and ABA/ethylene to other phytohormones are interesting and important research topics in ripening, especially in non-climacteric fruits.
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Affiliation(s)
- Qian Bai
- College of Horticulture, China Agricultural University, Beijing, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yun Huang
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
- Yun Huang,
| | - Yuanyue Shen
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
- *Correspondence: Yuanyue Shen,
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27
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Sultan S, Snider J, Conn A, Li M, Topp CN, Navlakha S. A Statistical Growth Property of Plant Root Architectures. PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:2073723. [PMID: 33313546 PMCID: PMC7706341 DOI: 10.34133/2020/2073723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/03/2020] [Indexed: 05/14/2023]
Abstract
Numerous types of biological branching networks, with varying shapes and sizes, are used to acquire and distribute resources. Here, we show that plant root and shoot architectures share a fundamental design property. We studied the spatial density function of plant architectures, which specifies the probability of finding a branch at each location in the 3-dimensional volume occupied by the plant. We analyzed 1645 root architectures from four species and discovered that the spatial density functions of all architectures are population-similar. This means that despite their apparent visual diversity, all of the roots studied share the same basic shape, aside from stretching and compression along orthogonal directions. Moreover, the spatial density of all architectures can be described as variations on a single underlying function: a Gaussian density truncated at a boundary of roughly three standard deviations. Thus, the root density of any architecture requires only four parameters to specify: the total mass of the architecture and the standard deviations of the Gaussian in the three (x, y, z) growth directions. Plant shoot architectures also follow this design form, suggesting that two basic plant transport systems may use similar growth strategies.
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Affiliation(s)
- Sam Sultan
- Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY, USA
| | - Joseph Snider
- University of California San Diego, Institute for Neural Computation, La Jolla, CA, USA
| | - Adam Conn
- Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY, USA
| | - Mao Li
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Saket Navlakha
- Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY, USA
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28
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Clemente-Moreno MJ, Omranian N, Sáez P, Figueroa CM, Del-Saz N, Elso M, Poblete L, Orf I, Cuadros-Inostroza A, Cavieres L, Bravo L, Fernie A, Ribas-Carbó M, Flexas J, Nikoloski Z, Brotman Y, Gago J. Cytochrome respiration pathway and sulphur metabolism sustain stress tolerance to low temperature in the Antarctic species Colobanthus quitensis. THE NEW PHYTOLOGIST 2020; 225:754-768. [PMID: 31489634 DOI: 10.1111/nph.16167] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/22/2019] [Indexed: 05/28/2023]
Abstract
Understanding the strategies employed by plant species that live in extreme environments offers the possibility to discover stress tolerance mechanisms. We studied the physiological, antioxidant and metabolic responses to three temperature conditions (4, 15, and 23°C) of Colobanthus quitensis (CQ), one of the only two native vascular species in Antarctica. We also employed Dianthus chinensis (DC), to assess the effects of the treatments in a non-Antarctic species from the same family. Using fused LASSO modelling, we associated physiological and biochemical antioxidant responses with primary metabolism. This approach allowed us to highlight the metabolic pathways driving the response specific to CQ. Low temperature imposed dramatic reductions in photosynthesis (up to 88%) but not in respiration (sustaining rates of 3.0-4.2 μmol CO2 m-2 s-1 ) in CQ, and no change in the physiological stress parameters was found. Its notable antioxidant capacity and mitochondrial cytochrome respiratory activity (20 and two times higher than DC, respectively), which ensure ATP production even at low temperature, was significantly associated with sulphur-containing metabolites and polyamines. Our findings potentially open new biotechnological opportunities regarding the role of antioxidant compounds and respiratory mechanisms associated with sulphur metabolism in stress tolerance strategies to low temperature.
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Affiliation(s)
- María José Clemente-Moreno
- Research Group on Plant Biology under Mediterranean Conditions, Instituto de Agroecología y Economía del Agua (INAGEA), Universitat de les Illes Balears (UIB), cta. Valldemossa km 7,5, 07122, Palma de Mallorca, Spain
| | - Nooshin Omranian
- Systems Biology and Mathematical Modeling Group, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Patricia Sáez
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, 4030000, Concepción, Chile
| | - Carlos María Figueroa
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, 3000, Santa Fe, Argentina
| | - Néstor Del-Saz
- Laboratorio de Fisiología Vegetal, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 4030000, Concepción, Chile
| | - Mhartyn Elso
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, 4030000, Concepción, Chile
| | - Leticia Poblete
- Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, 4030000, Concepción, Chile
| | - Isabel Orf
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501, Beer Sheva, Israel
| | | | - Lohengrin Cavieres
- ECOBIOSIS, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 4030000, Concepción, Chile
| | - León Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Cs. Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Instituto de Agroindustria, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Alisdair Fernie
- Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Golm, Germany
| | - Miquel Ribas-Carbó
- Research Group on Plant Biology under Mediterranean Conditions, Instituto de Agroecología y Economía del Agua (INAGEA), Universitat de les Illes Balears (UIB), cta. Valldemossa km 7,5, 07122, Palma de Mallorca, Spain
| | - Jaume Flexas
- Research Group on Plant Biology under Mediterranean Conditions, Instituto de Agroecología y Economía del Agua (INAGEA), Universitat de les Illes Balears (UIB), cta. Valldemossa km 7,5, 07122, Palma de Mallorca, Spain
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
- Center of Plant System Biology and Biotechnology (CPSBB), 4000, Plovdiv, Bulgaria
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501, Beer Sheva, Israel
| | - Jorge Gago
- Research Group on Plant Biology under Mediterranean Conditions, Instituto de Agroecología y Economía del Agua (INAGEA), Universitat de les Illes Balears (UIB), cta. Valldemossa km 7,5, 07122, Palma de Mallorca, Spain
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29
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Liu Y, Qu J, Zhang L, Xu X, Wei G, Zhao Z, Ren M, Cao M. Identification and characterization of the TCA cycle genes in maize. BMC PLANT BIOLOGY 2019; 19:592. [PMID: 31881988 PMCID: PMC6935159 DOI: 10.1186/s12870-019-2213-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/19/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND The tricarboxylic acid (TCA) cycle is crucial for cellular energy metabolism and carbon skeleton supply. However, the detailed functions of the maize TCA cycle genes remain unclear. RESULTS In this study, 91 TCA genes were identified in maize by a homology search, and they were distributed on 10 chromosomes and 1 contig. Phylogenetic results showed that almost all maize TCA genes could be classified into eight major clades according to their enzyme families. Sequence alignment revealed that several genes in the same subunit shared high protein sequence similarity. The results of cis-acting element analysis suggested that several TCA genes might be involved in signal transduction and plant growth. Expression profile analysis showed that many maize TCA cycle genes were expressed in specific tissues, and replicate genes always shared similar expression patterns. Moreover, qPCR analysis revealed that some TCA genes were highly expressed in the anthers at the microspore meiosis phase. In addition, we predicted the potential interaction networks among the maize TCA genes. Next, we cloned five TCA genes located on different TCA enzyme complexes, Zm00001d008244 (isocitrate dehydrogenase, IDH), Zm00001d017258 (succinyl-CoA synthetase, SCoAL), Zm00001d025258 (α-ketoglutarate dehydrogenase, αKGDH), Zm00001d027558 (aconitase, ACO) and Zm00001d044042 (malate dehydrogenase, MDH). Confocal observation showed that their protein products were mainly localized to the mitochondria; however, Zm00001d025258 and Zm00001d027558 were also distributed in the nucleus, and Zm00001d017258 and Zm00001d044042 were also located in other unknown positions in the cytoplasm. Through the bimolecular fluorescent complimentary (BiFC) method, it was determined that Zm00001d027558 and Zm00001d044042 could form homologous dimers, and both homologous dimers were mainly distributed in the mitochondria. However, no heterodimers were detected between these five genes. Finally, Arabidopsis lines overexpressing the above five genes were constructed, and those transgenic lines exhibited altered primary root length, salt tolerance, and fertility. CONCLUSION Sequence compositions, duplication patterns, phylogenetic relationships, cis-elements, expression patterns, and interaction networks were investigated for all maize TCA cycle genes. Five maize TCA genes were overexpressed in Arabidopsis, and they could alter primary root length, salt tolerance, and fertility. In conclusion, our findings may help to reveal the molecular function of the TCA genes in maize.
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Affiliation(s)
- Yongming Liu
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610213 China
- Chengdu National Agricultural Science and Technology Center, Chengdu, 610213 China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jingtao Qu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Ling Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Gui Wei
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130 China
| | - Zhuofan Zhao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610213 China
- Chengdu National Agricultural Science and Technology Center, Chengdu, 610213 China
| | - Moju Cao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
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Condori-Apfata JA, Batista-Silva W, Medeiros DB, Vargas JR, Valente LML, Heyneke E, Pérez-Diaz JL, Fernie AR, Araújo WL, Nunes-Nesi A. The Arabidopsis E 1 subunit of the 2-oxoglutarate dehydrogenase complex modulates plant growth and seed production. PLANT MOLECULAR BIOLOGY 2019; 101:183-202. [PMID: 31286324 DOI: 10.1007/s11103-019-00900-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 06/29/2019] [Indexed: 05/25/2023]
Abstract
Isoforms of 2-OGDH E1 subunit are not functionally redundant in plant growth and development of A. thaliana. The tricarboxylic acid cycle enzyme 2-oxoglutarate dehydrogenase (2-OGDH) converts 2-oxoglutarate (2-OG) to succinyl-CoA concomitant with the reduction of NAD+. 2-OGDH has an essential role in plant metabolism, being both a limiting step during mitochondrial respiration as well as a key player in carbon-nitrogen interactions. In Arabidopsis thaliana two genes encode for E1 subunit of 2-OGDH but the physiological roles of each isoform remain unknown. Thus, in the present study we isolated Arabidopsis T-DNA insertion knockout mutant lines for each of the genes encoding the E1 subunit of 2-OGDH enzyme. All mutant plants exhibited substantial reduction in both respiration and CO2 assimilation rates. Furthermore, mutant lines exhibited reduced levels of chlorophylls and nitrate, increased levels of sucrose, malate and fumarate and minor changes in total protein and starch levels in leaves. Despite the similar metabolic phenotypes for the two E1 isoforms the reduction in the expression of each gene culminated in different responses in terms of plant growth and seed production indicating distinct roles for each isoform. Collectively, our results demonstrated the importance of the E1 subunit of 2-OGDH in both autotrophic and heterotrophic tissues and suggest that the two E1 isoforms are not functionally redundant in terms of plant growth in A. thaliana.
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Affiliation(s)
- Jorge A Condori-Apfata
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Willian Batista-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - David Barbosa Medeiros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Jonas Rafael Vargas
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Luiz Mário Lopes Valente
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Elmien Heyneke
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam Golm, Germany
| | - Jorge Luis Pérez-Diaz
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam Golm, Germany
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil.
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Zuo J, Wang Y, Zhu B, Luo Y, Wang Q, Gao L. Network analysis of noncoding RNAs in pepper provides insights into fruit ripening control. Sci Rep 2019; 9:8734. [PMID: 31217463 PMCID: PMC6584694 DOI: 10.1038/s41598-019-45427-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/06/2019] [Indexed: 01/21/2023] Open
Abstract
Pepper is an important vegetable worldwide and is a model plant for nonclimacteric fleshy fruit ripening. Drastic visual changes and internal biochemical alterations are involved in fruit coloration, flavor, texture, aroma, and palatability to animals during the pepper fruit ripening process. To explore the regulation of bell pepper fruit ripening by noncoding RNAs (ncRNAs), we examined their expression profiles; 43 microRNAs (miRNAs), 125 circular RNAs (circRNAs), 366 long noncoding RNAs (lncRNAs), and 3266 messenger RNAs (mRNAs) were differentially expressed (DE) in mature green and red ripe fruit. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the targets of the DE ncRNAs and DE mRNAs included several kinds of transcription factors (TFs) (ERF, bHLH, WRKY, MYB, NAC, bZIP, and ARF), enzymes involved in cell wall metabolism (beta-galactosidase, beta-glucosidase, beta-amylase, chitinase, pectate lyase (PL), pectinesterase (PE) and polygalacturonase (PG)), enzymes involved in fruit color accumulation (bifunctional 15-cis-phytoene synthase, 9-cis-epoxycarotenoid dioxygenase, beta-carotene hydroxylase and carotene epsilon-monooxygenase), enzymes associated with fruit flavor and aroma (glutamate-1-semialdehyde 2,1-aminomutase, anthocyanin 5-aromatic acyltransferase, and eugenol synthase 1) and enzymes involved in the production of ethylene (ET) (ACO1/ACO4) as well as other plant hormones such as abscisic acid (ABA), auxin (IAA), and gibberellic acid (GA). Based on accumulation profiles, a network of ncRNAs and mRNAs associated with bell pepper fruit ripening was developed that provides a foundation for further developing a more refined understanding of the molecular biology of fruit ripening.
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Affiliation(s)
- Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing, Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. .,Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, 14853, USA.
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing, Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing, Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Yin Y, Tian L, Li X, Huang M, Liu L, Wu P, Li M, Jiang H, Wu G, Chen Y. The role of endogenous thiamine produced via THIC in root nodule symbiosis in Lotus japonicus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:311-320. [PMID: 31128701 DOI: 10.1016/j.plantsci.2019.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Thiamine is a pivotal primary metabolite which is indispensable to all organisms. Although its biosynthetic pathway has been well documented, the mechanism by which thiamine influences the legume-rhizobium symbiosis remains uncertain. Here, we used overexpressing transgenic plants, mutants and grafting experiments to investigate the roles played by thiamine in Lotus japonicus nodulation. ljthic mutants displayed lethal phenotypes and the defect could be overcome by supplementation of thiamine or by overexpression of LjTHIC. Reciprocal grafting between L. japonicus wild-type Gifu B-129 and ljthic showed that the photosynthetic products of the aerial part made a major contribution to overcoming the nodulation defect in ljthic. Overexpression of LjTHIC in Lotus japonicus (OE-LjTHIC) decreased shoot growth and increased the activity of the enzymes 2-oxoglutarate dehydrogenase and pyruvate dehydrogenase. OE-LjTHIC plants exhibited an increase in the number of infection threads and also developed more nodules, which were of smaller size but unchanged nitrogenase activity compared to the wildtype. Taken together, our results suggest that endogenous thiamine produced via LjTHIC acts as an essential nutrient provided by the host plant for rhizobial infection and nodule growth in the Lotus japonicus - rhizobium interaction.
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Affiliation(s)
- Yehu Yin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lu Tian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xueliu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Mingchao Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Leru Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Pingzhi Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Meiru Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Huawu Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Guojiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Yaping Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.
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Decros G, Baldet P, Beauvoit B, Stevens R, Flandin A, Colombié S, Gibon Y, Pétriacq P. Get the Balance Right: ROS Homeostasis and Redox Signalling in Fruit. FRONTIERS IN PLANT SCIENCE 2019; 10:1091. [PMID: 31620143 PMCID: PMC6760520 DOI: 10.3389/fpls.2019.01091] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/09/2019] [Indexed: 05/02/2023]
Abstract
Plant central metabolism generates reactive oxygen species (ROS), which are key regulators that mediate signalling pathways involved in developmental processes and plant responses to environmental fluctuations. These highly reactive metabolites can lead to cellular damage when the reduction-oxidation (redox) homeostasis becomes unbalanced. Whilst decades of research have studied redox homeostasis in leaves, fundamental knowledge in fruit biology is still fragmentary. This is even more surprising when considering the natural profusion of fruit antioxidants that can process ROS and benefit human health. In this review, we explore redox biology in fruit and provide an overview of fruit antioxidants with recent examples. We further examine the central role of the redox hub in signalling during development and stress, with particular emphasis on ascorbate, also referred to as vitamin C. Progress in understanding the molecular mechanisms involved in the redox regulations that are linked to central metabolism and stress pathways will help to define novel strategies for optimising fruit nutritional quality, fruit production and storage.
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Affiliation(s)
- Guillaume Decros
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- *Correspondence: Guillaume Decros, ; Pierre Pétriacq,
| | - Pierre Baldet
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | | | - Amélie Flandin
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
| | - Sophie Colombié
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Yves Gibon
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
| | - Pierre Pétriacq
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
- *Correspondence: Guillaume Decros, ; Pierre Pétriacq,
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Zhang Y, Fernie AR. On the role of the tricarboxylic acid cycle in plant productivity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1199-1216. [PMID: 29917310 DOI: 10.1111/jipb.12690] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 06/18/2018] [Indexed: 05/10/2023]
Abstract
The tricarboxylic acid (TCA) cycle is one of the canonical energy pathways of living systems, as well as being an example of a pathway in which dynamic enzyme assemblies, or metabolons, are well characterized. The role of the enzymes have been the subject of saturated transgenesis approaches, whereby the expression of the constituent enzymes were reduced or knocked out in order to ascertain their in vivo function. Some of the resultant plants exhibited improved photosynthesis and plant growth, under controlled greenhouse conditions. In addition, overexpression of the endogenous genes, or heterologous forms of a number of the enzymes, has been carried out in tomato fruit and the roots of a range of species, and in some instances improvement in fruit yield and postharvest properties and plant performance, under nutrient limitation, have been reported, respectively. Given a number of variants, in nature, we discuss possible synthetic approaches involving introducing these variants, or at least a subset of them, into plants. We additionally discuss the likely consequences of introducing synthetic metabolons, wherein certain pairs of reactions are artificially permanently assembled into plants, and speculate as to future strategies to further improve plant productivity by manipulation of the core metabolic pathway.
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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, 4000 Plovdiv, 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, 4000 Plovdiv, Bulgaria
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Batista-Silva W, Nascimento VL, Medeiros DB, Nunes-Nesi A, Ribeiro DM, Zsögön A, Araújo WL. Modifications in Organic Acid Profiles During Fruit Development and Ripening: Correlation or Causation? FRONTIERS IN PLANT SCIENCE 2018; 9:1689. [PMID: 30524461 PMCID: PMC6256983 DOI: 10.3389/fpls.2018.01689] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/31/2018] [Indexed: 05/21/2023]
Abstract
The pivotal role of phytohormones during fruit development and ripening is considered established knowledge in plant biology. Perhaps less well-known is the growing body of evidence suggesting that organic acids play a key function in plant development and, in particular, in fruit development, maturation and ripening. Here, we critically review the connection between organic acids and the development of both climacteric and non-climacteric fruits. By analyzing the metabolic content of different fruits during their ontogenetic trajectory, we noticed that the content of organic acids in the early stages of fruit development is directly related to the supply of substrates for respiratory processes. Although different organic acid species can be found during fruit development in general, it appears that citrate and malate play major roles in this process, as they accumulate on a broad range of climacteric and non-climacteric fruits. We further highlight the functional significance of changes in organic acid profile in fruits due to either the manipulation of fruit-specific genes or the use of fruit-specific promoters. Despite the complexity behind the fluctuation in organic acid content during fruit development and ripening, we extend our understanding on the importance of organic acids on fruit metabolism and the need to further boost future research. We suggest that engineering organic acid metabolism could improve both qualitative and quantitative traits of crop fruits.
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Affiliation(s)
- Willian Batista-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Vitor L. Nascimento
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - David B. Medeiros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Dimas M. Ribeiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Agustín Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Wagner L. Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
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Fukushima A, Hikosaka S, Kobayashi M, Nishizawa T, Saito K, Goto E, Kusano M. A Systems Analysis With "Simplified Source-Sink Model" Reveals Metabolic Reprogramming in a Pair of Source-to-Sink Organs During Early Fruit Development in Tomato by LED Light Treatments. FRONTIERS IN PLANT SCIENCE 2018; 9:1439. [PMID: 30364178 PMCID: PMC6191670 DOI: 10.3389/fpls.2018.01439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/10/2018] [Indexed: 05/29/2023]
Abstract
Tomato (Solanum lycopersicum) is a model crop for studying development regulation and ripening in flesh fruits and vegetables. Supplementary light to maintain the optimal light environment can lead to the stable growth of tomatoes in greenhouses and areas without sufficient daily light integral. Technological advances in genome-wide molecular phenotyping have dramatically enhanced our understanding of metabolic shifts in the plant metabolism across tomato fruit development. However, comprehensive metabolic and transcriptional behaviors along the developmental process under supplementary light provided by light-emitting diodes (LEDs) remain to be fully elucidated. We present integrative omic approaches to identify the impact on the metabolism of a single tomato plant leaf exposed to monochromatic red LEDs of different intensities during the fruit development stage. Our special light delivery system, the "simplified source-sink model," involves the exposure of a single leaf below the second truss to red LED light of different intensities. We evaluated fruit-size- and fruit-shape variations elicited by different light intensities. Our findings suggest that more than high-light treatment (500 μmol m-2 s-1) with the red LED light is required to accelerate fruit growth for 2 weeks after anthesis. To investigate transcriptomic and metabolomic changes in leaf- and fruit samples we used microarray-, RNA sequencing-, and gas chromatography-mass spectrometry techniques. We found that metabolic shifts in the carbohydrate metabolism and in several key pathways contributed to fruit development, including ripening and cell-wall modification. Our findings suggest that the proposed workflow aids in the identification of key metabolites in the central metabolism that respond to monochromatic red-LED treatment and contribute to increase the fruit size of tomato plants. This study expands our understanding of systems-level responses mediated by low-, appropriate-, and high levels of red light irradiation in the fruit growth of tomato plants.
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Affiliation(s)
| | - Shoko Hikosaka
- Graduate School of Horticulture, Chiba University, Chiba, Japan
| | | | | | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Eiji Goto
- Graduate School of Horticulture, Chiba University, Chiba, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Yue J, Du C, Ji J, Xie T, Chen W, Chang E, Chen L, Jiang Z, Shi S. Inhibition of α-ketoglutarate dehydrogenase activity affects adventitious root growth in poplar via changes in GABA shunt. PLANTA 2018; 248:963-979. [PMID: 29982922 DOI: 10.1007/s00425-018-2929-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/30/2018] [Indexed: 05/24/2023]
Abstract
Blocking α-ketoglutarate dehydrogenase results in up-regulation of γ-aminobutyric acid (GABA) shunt activity, and inhibits the growth of poplar adventitious roots (ARs), indicating that AR growth is closely associated with GABA shunt. γ-Aminobutyric acid (GABA) shunt starts from α-ketoglutarate in the tricarboxylic acid cycle, which is thought to represent the cross road between carbon and nitrogen metabolism. Previous studies (Araújo et al. 2012b, Plant Cell 24: 2328-2351) have shown that blocking α-ketoglutarate dehydrogenase (α-KGDH) affects the GABA shunt activity, and inhibits growth. However, its effects on the growth of adventitious roots (ARs) are unclear. In this study, the growth of ARs in tissue-cultured 84K poplar (Populus alba × Populus glandulosa cv. '84K') was significantly inhibited when succinyl phosphate (SP), a specific inhibitor of α-KGDH, was supplied. The inhibition of ARs was associated with significant changes in the levels of soluble sugars, organic acids, and amino acids, and was coupled with the up-regulation of the GABA shunt activity at the transcriptional and translational levels. Exogenous GABA also inhibited AR growth following the increase of the endogenous GABA level. Transcriptomic analyses further showed that genes related to cell wall carbon metabolism and phytohormone (indoleacetic acid, ABA, and ethylene) signaling were affected by the changes of GABA shunt activity, resulting from the α-KGDH inhibition. Thus, our study indicates that the inhibition of poplar AR growth by blocking α-KGDH is closely associated with GABA shunt, which would benefit a better understanding of GABA's roles in plant development and stress response.
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Affiliation(s)
- Jianyun Yue
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian, Beijing, 100091, China
| | - Changjian Du
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian, Beijing, 100091, China
| | - Jing Ji
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian, Beijing, 100091, China
| | - Tiantian Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian, Beijing, 100091, China
| | - Wei Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian, Beijing, 100091, China
| | - Ermei Chang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian, Beijing, 100091, China
| | - Lanzhen Chen
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Risk Assessment Laboratory for Bee Products, Quality and Safety of Ministry of Agriculture, Beijing, China
| | - Zeping Jiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian, Beijing, 100091, China.
- Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China.
| | - Shengqing Shi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian, Beijing, 100091, China.
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Kong F, Burlacot A, Liang Y, Légeret B, Alseekh S, Brotman Y, Fernie AR, Krieger-Liszkay A, Beisson F, Peltier G, Li-Beisson Y. Interorganelle Communication: Peroxisomal MALATE DEHYDROGENASE2 Connects Lipid Catabolism to Photosynthesis through Redox Coupling in Chlamydomonas. THE PLANT CELL 2018; 30:1824-1847. [PMID: 29997239 PMCID: PMC6139685 DOI: 10.1105/tpc.18.00361] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/12/2018] [Accepted: 07/10/2018] [Indexed: 05/17/2023]
Abstract
Plants and algae must tightly coordinate photosynthetic electron transport and metabolic activities given that they often face fluctuating light and nutrient conditions. The exchange of metabolites and signaling molecules between organelles is thought to be central to this regulation but evidence for this is still fragmentary. Here, we show that knocking out the peroxisome-located MALATE DEHYDROGENASE2 (MDH2) of Chlamydomonas reinhardtii results in dramatic alterations not only in peroxisomal fatty acid breakdown but also in chloroplast starch metabolism and photosynthesis. mdh2 mutants accumulated 50% more storage lipid and 2-fold more starch than the wild type during nitrogen deprivation. In parallel, mdh2 showed increased photosystem II yield and photosynthetic CO2 fixation. Metabolite analyses revealed a >60% reduction in malate, together with increased levels of NADPH and H2O2 in mdh2 Similar phenotypes were found upon high light exposure. Furthermore, based on the lack of starch accumulation in a knockout mutant of the H2O2-producing peroxisomal ACYL-COA OXIDASE2 and on the effects of H2O2 supplementation, we propose that peroxisome-derived H2O2 acts as a regulator of chloroplast metabolism. We conclude that peroxisomal MDH2 helps photoautotrophs cope with nitrogen scarcity and high light by transmitting the redox state of the peroxisome to the chloroplast by means of malate shuttle- and H2O2-based redox signaling.
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Affiliation(s)
- Fantao Kong
- Aix Marseille University, CEA, CNRS, BIAM, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, F-13108 Saint Paul-Lez-Durance, France
| | - Adrien Burlacot
- Aix Marseille University, CEA, CNRS, BIAM, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, F-13108 Saint Paul-Lez-Durance, France
| | - Yuanxue Liang
- Aix Marseille University, CEA, CNRS, BIAM, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, F-13108 Saint Paul-Lez-Durance, France
| | - Bertrand Légeret
- Aix Marseille University, CEA, CNRS, BIAM, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, F-13108 Saint Paul-Lez-Durance, France
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Yariv Brotman
- 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
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Anja Krieger-Liszkay
- Institute for Integrative Biology of the Cell, CEA Saclay, CNRS, University Paris-Sud, University Paris-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Fred Beisson
- Aix Marseille University, CEA, CNRS, BIAM, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, F-13108 Saint Paul-Lez-Durance, France
| | - Gilles Peltier
- Aix Marseille University, CEA, CNRS, BIAM, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, F-13108 Saint Paul-Lez-Durance, France
| | - Yonghua Li-Beisson
- Aix Marseille University, CEA, CNRS, BIAM, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, F-13108 Saint Paul-Lez-Durance, France
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Hanson AD, Amthor JS, Sun J, Niehaus TD, Gregory JF, Bruner SD, Ding Y. Redesigning thiamin synthesis: Prospects and potential payoffs. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:92-99. [PMID: 29907313 DOI: 10.1016/j.plantsci.2018.01.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/24/2018] [Accepted: 01/31/2018] [Indexed: 05/20/2023]
Abstract
Thiamin is essential for plant growth but is short-lived in vivo and energetically very costly to produce - a combination that makes thiamin biosynthesis a prime target for improvement by redesign. Thiamin consists of thiazole and pyrimidine moieties. Its high biosynthetic cost stems from use of the suicide enzyme THI4 to form the thiazole and the near-suicide enzyme THIC to form the pyrimidine. These energetic costs lower biomass yield potential and are likely compounded by environmental stresses that destroy thiamin and hence increase the rate at which it must be made. The energy costs could be slashed by refactoring the thiamin biosynthesis pathway to eliminate the suicidal THI4 and THIC reactions. To substantiate this design concept, we first document the energetic costs of the THI4 and THIC steps in the pathway and explain how cutting these costs could substantially increase crop biomass and grain yields. We then show that a refactored pathway must produce thiamin itself rather than a stripped-down analog because the thiamin molecule cannot be simplified without losing biological activity. Lastly, we consider possible energy-efficient alternatives to the inefficient natural THI4- and THIC-mediated steps.
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Affiliation(s)
- Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
| | | | - Jiayi Sun
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Jesse F Gregory
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL, USA
| | - Steven D Bruner
- Chemistry Department, University of Florida, Gainesville, FL, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA
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Ma X, Zhang Y, Turečková V, Xue GP, Fernie AR, Mueller-Roeber B, Balazadeh S. The NAC Transcription Factor SlNAP2 Regulates Leaf Senescence and Fruit Yield in Tomato. PLANT PHYSIOLOGY 2018; 177:1286-1302. [PMID: 29760199 PMCID: PMC6052983 DOI: 10.1104/pp.18.00292] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/02/2018] [Indexed: 05/18/2023]
Abstract
Leaf senescence is an essential physiological process in plants that supports the recycling of nitrogen and other nutrients to support the growth of developing organs, including young leaves, seeds, and fruits. Thus, the regulation of senescence is crucial for evolutionary success in wild populations and for increasing yield in crops. Here, we describe the influence of a NAC transcription factor, SlNAP2 (Solanum lycopersicum NAC-like, activated by Apetala3/Pistillata), that controls both leaf senescence and fruit yield in tomato (S. lycopersicum). SlNAP2 expression increases during age-dependent and dark-induced leaf senescence. We demonstrate that SlNAP2 activates SlSAG113 (S. lycopersicum SENESCENCE-ASSOCIATED GENE113), a homolog of Arabidopsis (Arabidopsis thaliana) SAG113, chlorophyll degradation genes such as SlSGR1 (S. lycopersicum senescence-inducible chloroplast stay-green protein 1) and SlPAO (S. lycopersicum pheide a oxygenase), and other downstream targets by directly binding to their promoters, thereby promoting leaf senescence. Furthermore, SlNAP2 directly controls the expression of genes important for abscisic acid (ABA) biosynthesis, S. lycopersicum 9-cis-epoxycarotenoid dioxygenase 1 (SlNCED1); transport, S. lycopersicum ABC transporter G family member 40 (SlABCG40); and degradation, S. lycopersicum ABA 8'-hydroxylase (SlCYP707A2), indicating that SlNAP2 has a complex role in establishing ABA homeostasis during leaf senescence. Inhibiting SlNAP2 expression in transgenic tomato plants impedes leaf senescence but enhances fruit yield and sugar content likely due to prolonged leaf photosynthesis in aging tomato plants. Our data indicate that SlNAP2 has a central role in controlling leaf senescence and fruit yield in tomato.
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Affiliation(s)
- Xuemin Ma
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- University of Potsdam, Institute of Biochemistry and Biology, 14476 Potsdam-Golm, Germany
| | - Youjun Zhang
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Veronika Turečková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, 78371 Olomouc, Czech Republic
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Bernd Mueller-Roeber
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- University of Potsdam, Institute of Biochemistry and Biology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Salma Balazadeh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Song H, Lei Y, Zhang S. Differences in resistance to nitrogen and phosphorus deficiencies explain male-biased populations of poplar in nutrient-deficient habitats. J Proteomics 2018; 178:123-127. [DOI: 10.1016/j.jprot.2017.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/06/2017] [Accepted: 11/17/2017] [Indexed: 12/30/2022]
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Obata T, Rosado-Souza L, Fernie AR. Coupling Radiotracer Experiments with Chemical Fractionation for the Estimation of Respiratory Fluxes. Methods Mol Biol 2017; 1670:17-30. [PMID: 28871530 DOI: 10.1007/978-1-4939-7292-0_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Carbohydrates catabolized via respiratory processes are not only used for energy production but also for biosynthesis of cellular components including soluble molecules (sugars, amino acids, organic acids, and their derivatives) and insoluble macromolecules (proteins, starch, and cell wall). Radiotracer experiments using 14C-labeled glucose provide a global picture of the fate of respired carbon in the metabolic network. This method is based on a chemical fractionation of biomolecules in 14C-glucose fed plant materials and the subsequent determination of radioactivity in each fraction. Metabolic flux into each fraction can be estimated from the specific activity of the hexose phosphate pool. Here, we describe the procedure for glucose metabolism in potato tuber but similar protocols can be adopted for various plant organs and substrates.
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Affiliation(s)
- Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.,Department of Biochemistry, University of Nebraska Lincoln, 1901 Vine St, 68588, Lincoln, NE, USA
| | - Laise Rosado-Souza
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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43
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Artiukhov AV, Graf AV, Bunik VI. Directed regulation of multienzyme complexes of 2-oxo acid dehydrogenases using phosphonate and phosphinate analogs of 2-oxo acids. BIOCHEMISTRY (MOSCOW) 2016; 81:1498-1521. [DOI: 10.1134/s0006297916120129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Florez-Sarasa I, Ribas-Carbo M, Del-Saz NF, Schwahn K, Nikoloski Z, Fernie AR, Flexas J. Unravelling the in vivo regulation and metabolic role of the alternative oxidase pathway in C3 species under photoinhibitory conditions. THE NEW PHYTOLOGIST 2016; 212:66-79. [PMID: 27321208 DOI: 10.1111/nph.14030] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/23/2016] [Indexed: 06/06/2023]
Abstract
The mitochondrial alternative oxidase pathway (AOP) has been suggested to act as a sink for excess reducing power generated in the chloroplast under high-light (HL) stress and thus may reduce photoinhibition. The aim of this study was to compare different species to investigate the in vivo regulation and role of AOP under HL stress. The in vivo activities of AOP (νalt ) and the cytochrome oxidase pathway, chlorophyll fluorescence, metabolite profiles, alternative oxidase (AOX) capacity and protein amount were determined in leaves of five C3 species under growth light and after HL treatment. Differences in respiration and metabolite levels were observed among species under growth light conditions. The HL response of νalt was highly species dependent, correlated with the AOP capacity and independent of AOX protein content. Nevertheless, significant correlations were observed between νalt , levels of key metabolites and photosynthetic parameters. The results show that the species-specific response of νalt is caused by the differential post-translational regulation of AOX. Significant correlations between respiration, metabolites and photosynthetic performance across species suggest that AOP may permit stress-related amino acid synthesis, whilst maintaining photosynthetic activity under HL stress.
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Affiliation(s)
- Igor Florez-Sarasa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Miquel Ribas-Carbo
- Grup de Recerca en Biologia de les Plantes en Condicions Mediterranies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Spain
| | - Néstor Fernández Del-Saz
- Grup de Recerca en Biologia de les Plantes en Condicions Mediterranies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Spain
| | - Kevin Schwahn
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jaume Flexas
- Grup de Recerca en Biologia de les Plantes en Condicions Mediterranies, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Spain
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Flexas J, Díaz-Espejo A, Conesa MA, Coopman RE, Douthe C, Gago J, Gallé A, Galmés J, Medrano H, Ribas-Carbo M, Tomàs M, Niinemets Ü. Mesophyll conductance to CO2 and Rubisco as targets for improving intrinsic water use efficiency in C3 plants. PLANT, CELL & ENVIRONMENT 2016; 39:965-82. [PMID: 26297108 DOI: 10.1111/pce.12622] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 07/09/2015] [Accepted: 07/26/2015] [Indexed: 05/20/2023]
Abstract
Water limitation is a major global constraint for plant productivity that is likely to be exacerbated by climate change. Hence, improving plant water use efficiency (WUE) has become a major goal for the near future. At the leaf level, WUE is the ratio between photosynthesis and transpiration. Maintaining high photosynthesis under water stress, while improving WUE requires either increasing mesophyll conductance (gm ) and/or improving the biochemical capacity for CO2 assimilation-in which Rubisco properties play a key role, especially in C3 plants at current atmospheric CO2 . The goals of the present analysis are: (1) to summarize the evidence that improving gm and/or Rubisco can result in increased WUE; (2) to review the degree of success of early attempts to genetically manipulate gm or Rubisco; (3) to analyse how gm , gsw and the Rubisco's maximum velocity (Vcmax ) co-vary across different plant species in well-watered and drought-stressed conditions; (4) to examine how these variations cause differences in WUE and what is the overall extent of variation in individual determinants of WUE; and finally, (5) to use simulation analysis to provide a theoretical framework for the possible control of WUE by gm and Rubisco catalytic constants vis-à-vis gsw under water limitations.
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Affiliation(s)
- J Flexas
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Illes Balears, Spain
| | - A Díaz-Espejo
- Irrigation and Crop Ecophysiology Group, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS, CSIC), Avenida Reina Mercedes 10, 41012, Sevilla, Spain
| | - M A Conesa
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Illes Balears, Spain
| | - R E Coopman
- Ecophysiology Laboratory for Forest Conservation, Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Casilla 567, 5110566, Valdivia, Chile
| | - C Douthe
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Illes Balears, Spain
| | - J Gago
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Illes Balears, Spain
- Applied Plant and Soil Biology, Faculty of Biology, University of Vigo, 36310, Vigo, Spain
| | - A Gallé
- Bayer CropScience NV, Innovation Center, Technologiepark 38, 9052, Zwijnaarde, Belgium
| | - J Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Illes Balears, Spain
| | - H Medrano
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Illes Balears, Spain
| | - M Ribas-Carbo
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Illes Balears, Spain
| | - M Tomàs
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, Carretera de Valldemossa Km 7.5, 07122, Palma de Mallorca, Illes Balears, Spain
| | - Ü Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu, 51014, Estonia
- Estonian Academy of Sciences, Kohtu 6, 10130, Tallinn, Estonia
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Obata T, Florian A, Timm S, Bauwe H, Fernie AR. On the metabolic interactions of (photo)respiration. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3003-14. [PMID: 27029352 DOI: 10.1093/jxb/erw128] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Given that photorespiration is inextricably linked to the process of photosynthesis by virtue of sharing the common first enzyme Rubisco, the photorespiratory pathway has been less subject to study in isolation than many other metabolic pathways. That said, despite often being described to be linked to reactions of ammonia assimilation, C1 metabolism and respiratory metabolism, the precise molecular mechanisms governing these linkages in land plants remain partially obscure. The application of broad metabolite profiling on mutants with altered levels of metabolic enzymes has facilitated the identification of common and distinct metabolic responses among them. Here we provide an update of the recent findings from such studies, focusing particularly on the interplay between photorespiration and the metabolic reactions of mitochondrial respiration. In order to do so we evaluated (i) changes in organic acids following environmental perturbation of metabolism, (ii) changes in organic acid levels in a wide range of photorespiratory mutants, (iii) changes in levels of photorespiratory metabolites in transgenic tomato lines deficient in the expression of enzymes of the tricarboxylic acid cycle. In addition, we estimated the rates of photorespiration in a complete set of tricarboxylic acid cycle transgenic tomato lines. Finally, we discuss insight concerning the interaction between photorespiration and other pathways that has been attained following the development of (13)CO2-based flux profiling methods.
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Affiliation(s)
- Toshihiro Obata
- Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alexandra Florian
- Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stefan Timm
- Plant Physiology Department, University of Rostock, D-18051 Rostock, Germany
| | - Hermann Bauwe
- Plant Physiology Department, University of Rostock, D-18051 Rostock, Germany
| | - Alisdair R Fernie
- Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Comparative shotgun proteomic analysis of wild and domesticated Opuntia spp. species shows a metabolic adaptation through domestication. J Proteomics 2016; 143:353-364. [PMID: 27072113 DOI: 10.1016/j.jprot.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 01/01/2023]
Abstract
UNLABELLED The Opuntia genus is widely distributed in America, but the highest richness of wild species are found in Mexico, as well as the most domesticated Opuntia ficus-indica, which is the most domesticated species and an important crop in agricultural economies of arid and semiarid areas worldwide. During domestication process, the Opuntia morphological characteristics were favored, such as less and smaller spines in cladodes and less seeds in fruits, but changes at molecular level are almost unknown. To obtain more insights about the Opuntia molecular changes through domestication, a shotgun proteomic analysis and database-dependent searches by homology was carried out. >1000 protein species were identified and by using a label-free quantitation method, the Opuntia proteomes were compared in order to identify differentially accumulated proteins among wild and domesticated species. Most of the changes were observed in glucose, secondary, and 1C metabolism, which correlate with the observed protein, fiber and phenolic compounds accumulation in Opuntia cladodes. Regulatory proteins, ribosomal proteins, and proteins related with response to stress were also observed in differential accumulation. These results provide new valuable data that will help to the understanding of the molecular changes of Opuntia species through domestication. BIOLOGICAL SIGNIFICANCE Opuntia species are well adapted to dry and warm conditions in arid and semiarid regions worldwide, and they are highly productive plants showing considerable promises as an alternative food source. However, there is a gap regarding Opuntia molecular mechanisms that enable them to grow in extreme environmental conditions and how the domestication processes has changed them. In the present study, a shotgun analysis was carried out to characterize the proteomes of five Opuntia species selected by its domestication degree. Our results will help to a better understanding of proteomic features underlying the selection and specialization under evolution and domestication of Opuntia and will provide a platform for basic biology research and gene discovery.
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48
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Naconsie M, Lertpanyasampatha M, Viboonjun U, Netrphan S, Kuwano M, Ogasawara N, Narangajavana J. Cassava root membrane proteome reveals activities during storage root maturation. JOURNAL OF PLANT RESEARCH 2016; 129:51-65. [PMID: 26547558 DOI: 10.1007/s10265-015-0761-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/13/2015] [Indexed: 06/05/2023]
Abstract
Cassava (Manihot esculenta Crantz) is one of the most important crops of Thailand. Its storage roots are used as food, feed, starch production, and be the important source for biofuel and biodegradable plastic production. Despite the importance of cassava storage roots, little is known about the mechanisms involved in their formation. This present study has focused on comparison of the expression profiles of cassava root proteome at various developmental stages using two-dimensional gel electrophoresis and LC-MS/MS. Based on an anatomical study using Toluidine Blue, the secondary growth was confirmed to be essential during the development of cassava storage root. To investigate biochemical processes occurring during storage root maturation, soluble and membrane proteins were isolated from storage roots harvested from 3-, 6-, 9-, and 12-month-old cassava plants. The proteins with differential expression pattern were analysed and identified to be associated with 8 functional groups: protein folding and degradation, energy, metabolism, secondary metabolism, stress response, transport facilitation, cytoskeleton, and unclassified function. The expression profiling of membrane proteins revealed the proteins involved in protein folding and degradation, energy, and cell structure were highly expressed during early stages of development. Integration of these data along with the information available in genome and transcriptome databases is critical to expand knowledge obtained solely from the field of proteomics. Possible role of identified proteins were discussed in relation with the activities during storage root maturation in cassava.
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Affiliation(s)
- Maliwan Naconsie
- Deparment of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Rd.,Rajthewee, Phayathai, Bangkok, 10400, Thailand
| | - Manassawe Lertpanyasampatha
- Deparment of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Rd.,Rajthewee, Phayathai, Bangkok, 10400, Thailand
| | - Unchera Viboonjun
- Deparment of Plant Science, Faculty of Science, Mahidol University, Phayathai, Bangkok, 10400, Thailand
| | - Supatcharee Netrphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Rangsit, Pathumthani, 10210, Thailand
| | - Masayoshi Kuwano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Jarunya Narangajavana
- Deparment of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Rd.,Rajthewee, Phayathai, Bangkok, 10400, Thailand.
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Yuan H, Cheung CYM, Poolman MG, Hilbers PAJ, van Riel NAW. A genome-scale metabolic network reconstruction of tomato (Solanum lycopersicum L.) and its application to photorespiratory metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:289-304. [PMID: 26576489 DOI: 10.1111/tpj.13075] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/01/2015] [Accepted: 11/03/2015] [Indexed: 05/09/2023]
Abstract
Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health-promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the growth, yield and fruit quality of tomatoes can be affected by drought stress, a common abiotic stress for tomato. To investigate the potential metabolic response of tomato plants to drought, we reconstructed iHY3410, a genome-scale metabolic model of tomato leaf, and used this metabolic network to simulate tomato leaf metabolism. The resulting model includes 3410 genes and 2143 biochemical and transport reactions distributed across five intracellular organelles including cytosol, plastid, mitochondrion, peroxisome and vacuole. The model successfully described the known metabolic behaviour of tomato leaf under heterotrophic and phototrophic conditions. The in silico investigation of the metabolic characteristics for photorespiration and other relevant metabolic processes under drought stress suggested that: (i) the flux distributions through the mevalonate (MVA) pathway under drought were distinct from that under normal conditions; and (ii) the changes in fluxes through core metabolic pathways with varying flux ratio of RubisCO carboxylase to oxygenase may contribute to the adaptive stress response of plants. In addition, we improved on previous studies of reaction essentiality analysis for leaf metabolism by including potential alternative routes for compensating reaction knockouts. Altogether, the genome-scale model provides a sound framework for investigating tomato metabolism and gives valuable insights into the functional consequences of abiotic stresses.
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Affiliation(s)
- Huili Yuan
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | | | - Mark G Poolman
- Cell Systems Modelling Group, Department of Biomedical and Medical Science, Oxford Brookes University, Oxford, UK
| | - Peter A J Hilbers
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Natal A W van Riel
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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50
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Tohge T, Fernie AR. Metabolomics-Inspired Insight into Developmental, Environmental and Genetic Aspects of Tomato Fruit Chemical Composition and Quality. PLANT & CELL PHYSIOLOGY 2015; 56:1681-96. [PMID: 26228272 DOI: 10.1093/pcp/pcv093] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/12/2015] [Indexed: 05/20/2023]
Abstract
Tomato was one of the first plant species to be evaluated using metabolomics and remains one of the best characterized, with tomato fruit being both an important source of nutrition in the human diet and a valuable model system for the development of fleshy fruits. Additionally, given the broad habitat range of members of the tomato clade and the extensive use of exotic germplasm in tomato genetic research, it represents an excellent genetic model system for understanding both metabolism per se and the importance of various metabolites in conferring stress tolerance. This review summarizes technical approaches used to characterize the tomato metabolome to date and details insights into metabolic pathway structure and regulation that have been obtained via analysis of tissue samples taken under different developmental or environmental circumstance as well as following genetic perturbation. Particular attention is paid to compounds of importance for nutrition or the shelf-life of tomatoes. We propose furthermore how metabolomics information can be coupled to the burgeoning wealth of genome sequence data from the tomato clade to enhance further our understanding of (i) the shifts in metabolic regulation occurring during development and (ii) specialization of metabolism within the tomato clade as a consequence of either adaptive evolution or domestication.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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