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Yang J, Wang Y, Sun J, Li Y, Zhu R, Yin Y, Wang C, Yin X, Qin L. Metabolome and Transcriptome Association Analysis Reveals Mechanism of Synthesis of Nutrient Composition in Quinoa ( Chenopodium quinoa Willd.) Seeds. Foods 2024; 13:1325. [PMID: 38731698 PMCID: PMC11082971 DOI: 10.3390/foods13091325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Quinoa (Chenopodium quinoa Willd.) seeds are rich in nutrition, superior to other grains, and have a high market value. However, the biosynthesis mechanisms of protein, starch, and lipid in quinoa grain are still unclear. The objective of this study was to ascertain the nutritional constituents of white, yellow, red, and black quinoa seeds and to employ a multi-omics approach to analyze the synthesis mechanisms of these nutrients. The findings are intended to furnish a theoretical foundation and technical support for the biological breeding of quinoa in China. In this study, the nutritional analysis of white, yellow, red, and black quinoa seeds from the same area showed that the nutritional contents of the quinoa seeds were significantly different, and the protein content increased with the deepening of color. The protein content of black quinoa was the highest (16.1 g/100 g) and the lipid content was the lowest (2.7 g/100 g), among which, linoleic acid was the main fatty acid. A combined transcriptome and metabolome analysis exhibited that differentially expressed genes were enriched in "linoleic acid metabolism", "unsaturated fatty acid biosynthesis", and "amino acid biosynthesis". We mainly identified seven genes involved in starch synthesis (LOC110716805, LOC110722789, LOC110738785, LOC110720405, LOC110730081, LOC110692055, and LOC110732328); five genes involved in lipid synthesis (LOC110701563, LOC110699636, LOC110709273, LOC110715590, and LOC110728838); and nine genes involved in protein synthesis (LOC110710842, LOC110720003, LOC110687170, LOC110716004, LOC110702086, LOC110724454 LOC110724577, LOC110704171, and LOC110686607). The data presented in this study based on nutrient, transcriptome, and metabolome analyses contribute to an enhanced understanding of the genetic regulation of seed quality traits in quinoa, and provide candidate genes for further genetic improvements to improve the nutritional value of quinoa seeds.
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Affiliation(s)
- Jindan Yang
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Yiyun Wang
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Jiayi Sun
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Yuzhe Li
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Renbin Zhu
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230036, China;
| | - Yongjie Yin
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Chuangyun Wang
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Xuebin Yin
- Suzhou Selenium Valley Technology Co., Ltd., Suzhou 215100, China;
- Anhui Province Key Laboratory of Functional Agriculture and Functional Food, Anhui Science and Technology University, Chuzhou 239000, China
| | - Lixia Qin
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230036, China;
- Suzhou Selenium Valley Technology Co., Ltd., Suzhou 215100, China;
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Sánchez-López ÁM, Bahaji A, Gámez-Arcas S, De Diego N, Vrobel O, Tarkowski P, Baroja-Fernández E, Muñoz FJ, Almagro G, Seguí-Simarro JM, Tabernero-Mendoza M, López-Serrano L, Morcillo RJL, Pozueta-Romero J. PGI1-mediated vascular oxidative pentose phosphate pathway modulates photosynthesis via long-distance cytokinin signaling. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 209:108520. [PMID: 38522131 DOI: 10.1016/j.plaphy.2024.108520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/01/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024]
Abstract
In Arabidopsis, the plastidial isoform of phosphoglucose isomerase, PGI1, mediates growth and photosynthesis, likely due to its involvement in the vascular production of cytokinins (CK). To examine this hypothesis, we characterized pgi1-2 knockout plants impaired in PGI1 and pgi1-2 plants specifically expressing PGI1 in root tips and vascular tissues. Moreover, to investigate whether the phenotype of pgi1-2 plants is due to impairments in the plastidial oxidative pentose phosphate pathway (OPPP) or the glycolytic pathway, we characterized pgl3-1 plants with reduced OPPP and pfk4pfk5 knockout plants impaired in plastidial glycolysis. Compared with wild-type (WT) leaves, pgi1-2 leaves exhibited weaker expression of photosynthesis- and 2-C-methyl-D-erythritol 4-P (MEP) pathway-related proteins, and stronger expression of oxidative stress protection-related enzymes. Consistently, pgi1-2 leaves accumulated lower levels of chlorophyll, and higher levels of tocopherols, flavonols and anthocyanins than the WT. Vascular- and root tip-specific PGI1 expression countered the reduced photosynthesis, low MEP pathway-derived CK content, dwarf phenotype and the metabolic characteristics of pgi1-2 plants, reverting them to WT-like levels. Moreover, pgl3-1, but not pfk4pfk5 plants phenocopied pgi1-2. Histochemical analyses of plants expressing GUS under the control of promoter regions of genes encoding plastidial OPPP enzymes exhibited strong GUS activity in root tips and vascular tissues. Overall, our findings show that root tip and vascular PGI1-mediated plastidial OPPP activity affects photosynthesis and growth through mechanisms involving long-distance modulation of the leaf proteome by MEP pathway-derived CKs.
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Affiliation(s)
- Ángela María Sánchez-López
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Iruñako etorbidea 123, 31192, Mutiloabeti, Nafarroa, Spain
| | - Abdellatif Bahaji
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Iruñako etorbidea 123, 31192, Mutiloabeti, Nafarroa, Spain.
| | - Samuel Gámez-Arcas
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Iruñako etorbidea 123, 31192, Mutiloabeti, Nafarroa, Spain; Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, 41092, Sevilla, Spain
| | - Nuria De Diego
- Czech Advanced Technology and Research Institute, Palacky University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Ondřej Vrobel
- Czech Advanced Technology and Research Institute, Palacky University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Petr Tarkowski
- Czech Advanced Technology and Research Institute, Palacky University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Edurne Baroja-Fernández
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Iruñako etorbidea 123, 31192, Mutiloabeti, Nafarroa, Spain
| | - Francisco José Muñoz
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Iruñako etorbidea 123, 31192, Mutiloabeti, Nafarroa, Spain
| | - Goizeder Almagro
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Iruñako etorbidea 123, 31192, Mutiloabeti, Nafarroa, Spain
| | | | | | - Lidia López-Serrano
- Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM), CSIC-UMA, Campus de Teatinos, Avda. Louis Pasteur, 49, 29010, Málaga, Spain
| | - Rafael J L Morcillo
- Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM), CSIC-UMA, Campus de Teatinos, Avda. Louis Pasteur, 49, 29010, Málaga, Spain
| | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Iruñako etorbidea 123, 31192, Mutiloabeti, Nafarroa, Spain; Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM), CSIC-UMA, Campus de Teatinos, Avda. Louis Pasteur, 49, 29010, Málaga, Spain.
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Laihonen L, Rantala M, Ranasinghe U, Tyystjärvi E, Mulo P. Transcriptomic and proteomic analyses of distinct Arabidopsis organs reveal high PSI-NDH complex accumulation in stems. PHYSIOLOGIA PLANTARUM 2024; 176:e14227. [PMID: 38410876 DOI: 10.1111/ppl.14227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/09/2024] [Indexed: 02/28/2024]
Abstract
In addition to leaves, the main site of photosynthetic reactions, active photosynthesis also takes place in stems, siliques and tree trunks. Although non-foliar photosynthesis has a marked effect on plant growth and yield, only limited information on the expression patterns of photosynthesis-related genes and the structure of photosynthetic machinery in different plant organs has been available. Here, we report the results of transcriptomic analysis of various organs of Arabidopsis thaliana and compare the gene expression profiles of young and mature leaves with a special focus on photosynthetic genes. Further, we analyzed the composition and organization of the photosynthetic electron transfer machinery in leaves, stems and green siliques at the protein level using BN-PAGE. RNA-Seq analysis revealed unique gene expression profiles in different plant organs and showed major differences in the expression of photosynthesis-related genes in young as compared to mature rosettes. Gel-based proteomic analysis of the thylakoid protein complex organization further showed that all studied plant organs contain the necessary components of the photosynthetic electron transfer chain. Intriguingly, stems accumulate high amounts of PSI-NDH complex, which has previously been implicated in cyclic electron transfer.
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Affiliation(s)
- Laura Laihonen
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Marjaana Rantala
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Umanga Ranasinghe
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Esa Tyystjärvi
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Paula Mulo
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
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Zhou Y, Zhang H, Ren Y, Wang X, Wang B, Yuan F. The transmembrane protein LbRSG from the recretohalophyte Limonium bicolor enhances salt gland development and salt tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:498-515. [PMID: 37856574 DOI: 10.1111/tpj.16505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
Salt glands are the unique epidermal structures present in recretohalophytes, plants that actively excrete excess Na+ by salt secretory structures to avoid salt damage. Here, we describe a transmembrane protein that localizes to the plasma membrane of the recretohalophyte Limonium bicolor. As virus-induced gene silencing of the corresponding gene LbRSG in L. bicolor decreased the number of salt glands, we named the gene Reduced Salt Gland. We detected LbRSG transcripts in salt glands by in situ hybridization and transient transformation. Overexpression and silencing of LbRSG in L. bicolor pointed to a positive role in salt gland development and salt secretion by interacting with Lb3G16832. Heterologous LbRSG expression in Arabidopsis enhanced salt tolerance during germination and the seedling stage by alleviating NaCl-induced ion stress and osmotic stress after replacing or deleting the (highly) negatively charged region of extramembranous loop. After screened by immunoprecipitation-mass spectrometry and verified using yeast two-hybrid, PGK1 and BGLU18 were proposed to interact with LbRSG to strengthen salt tolerance. Therefore, we identified (highly) negatively charged regions in the extramembrane loop that may play an essential role in salt tolerance, offering hints about LbRSG function and its potential to confer salt resistance.
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Affiliation(s)
- Yingli Zhou
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, P.R. China
| | - Haonan Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, P.R. China
| | - Yanpeng Ren
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China
| | - Xi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, P.R. China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, P.R. China
- Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, No. 2 Kangyang Road, Dongying, 257000, China
| | - Fang Yuan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, P.R. China
- Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, No. 2 Kangyang Road, Dongying, 257000, China
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Yu A, Zhou Z, Chen Y, Sun J, Li P, Gu X, Liu A. Functional Genome Analyses Reveal the Molecular Basis of Oil Accumulation in Developing Seeds of Castor Beans. Int J Mol Sci 2023; 25:92. [PMID: 38203263 PMCID: PMC10778879 DOI: 10.3390/ijms25010092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Castor (Ricinus communis L.) seeds produce abundant ricinoleic acid during seed maturation, which is important for plant development and human demands. Ricinoleic acid, as a unique hydroxy fatty acid (HFA), possesses a distinct bond structure that could be used as a substitute for fossil fuels. Here, we identified all homologous genes related to glycolysis, hydroxy fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in castor seeds. Furthermore, we investigated their expression patterns globally during five seed development stages. We characterized a total of 66 genes involved in the glycolysis pathway, with the majority exhibiting higher expression levels during the early stage of castor bean seed development. This metabolic process provided abundant acetyl-CoA for fatty acid (FA) biosynthesis. Subsequently, we identified 82 genes involved in the processes of de novo FA biosynthesis and TAG assembly, with the majority exhibiting high expression levels during the middle or late stages. In addition, we examined the expression patterns of the transcription factors involved in carbohydrate and oil metabolism. For instance, RcMYB73 and RcERF72 exhibited high expression levels during the early stage, whereas RcWRI1, RcABI3, and RcbZIP67 showed relatively higher expression levels during the middle and late stages, indicating their crucial roles in seed development and oil accumulation. Our study suggests that the high HFA production in castor seeds is attributed to the interaction of multiple genes from sugar transportation to lipid droplet packaging. Therefore, this research comprehensively characterizes all the genes related to glycolysis, fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in the castor and provides novel insight into exploring the genetic mechanisms underlying seed oil accumulation in the endosperm of castor beans.
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Affiliation(s)
| | | | | | | | | | | | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (A.Y.); (Z.Z.); (Y.C.); (J.S.); (P.L.); (X.G.)
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Lee DH, Choi I, Park SJ, Kim S, Choi MS, Lee HS, Pai HS. Three consecutive cytosolic glycolysis enzymes modulate autophagic flux. PLANT PHYSIOLOGY 2023; 193:1797-1815. [PMID: 37539947 PMCID: PMC10602606 DOI: 10.1093/plphys/kiad439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 08/05/2023]
Abstract
Autophagy serves as an important recycling route for the growth and survival of eukaryotic organisms in nutrient-deficient conditions. Since starvation induces massive changes in the metabolic flux that are coordinated by key metabolic enzymes, specific processing steps of autophagy may be linked with metabolic flux-monitoring enzymes. We attempted to identify carbon metabolic genes that modulate autophagy using VIGS screening of 45 glycolysis- and Calvin-Benson cycle-related genes in Arabidopsis (Arabidopsis thaliana). Here, we report that three consecutive triose-phosphate-processing enzymes involved in cytosolic glycolysis, triose-phosphate-isomerase (TPI), glyceraldehyde-3-phosphate dehydrogenase (GAPC), and phosphoglycerate kinase (PGK), designated TGP, negatively regulate autophagy. Depletion of TGP enzymes causes spontaneous autophagy induction and increases AUTOPHAGY-RELATED 1 (ATG1) kinase activity. TGP enzymes interact with ATG101, a regulatory component of the ATG1 kinase complex. Spontaneous autophagy induction and abnormal growth under insufficient sugar in TGP mutants are suppressed by crossing with the atg101 mutant. Considering that triose-phosphates are photosynthates transported to the cytosol from active chloroplasts, the TGP enzymes would be strategically positioned to monitor the flow of photosynthetic sugars and modulate autophagy accordingly. Collectively, these results suggest that TGP enzymes negatively control autophagy acting upstream of the ATG1 complex, which is critical for seedling development.
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Affiliation(s)
- Du-Hwa Lee
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| | - Ilyeong Choi
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| | - Seung Jun Park
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| | - Sumin Kim
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| | - Min-Soo Choi
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ho-Seok Lee
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
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Vranić M, Perochon A, Doohan FM. Transcriptional Profiling Reveals the Wheat Defences against Fusarium Head Blight Disease Regulated by a NAC Transcription Factor. PLANTS (BASEL, SWITZERLAND) 2023; 12:2708. [PMID: 37514322 PMCID: PMC10383764 DOI: 10.3390/plants12142708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
The wheat NAC transcription factor TaNACL-D1 enhances resistance to the economically devastating Fusarium head blight (FHB) disease. The objective of this study was to decipher the alterations in gene expression, pathways and biological processes that led to enhanced resistance as a result of the constitutive expression of TaNACL-D1 in wheat. Transcriptomic analysis was used to determine the genes and processes enhanced in wheat due to TaNACL-D1 overexpression, both in the presence and absence of the causal agent of FHB, Fusarium graminearum (0- and 1-day post-treatment). The overexpression of TaNACL-D1 resulted in more pronounced transcriptional reprogramming as a response to fungal infection, leading to the enhanced expression of genes involved in detoxification, immune responses, secondary metabolism, hormone biosynthesis, and signalling. The regulation and response to JA and ABA were differentially regulated between the OE and the WT. Furthermore, the results suggest that the OE may more efficiently: (i) regulate the oxidative burst; (ii) modulate cell death; and (iii) induce both the phenylpropanoid pathway and lignin synthesis. Thus, this study provides insights into the mode of action and downstream target pathways for this novel NAC transcription factor, further validating its potential as a gene to enhance FHB resistance in wheat.
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Affiliation(s)
- Monika Vranić
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Alexandre Perochon
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Fiona M Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, D04 V1W8 Dublin, Ireland
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Félix JW, Granados-Alegría MI, Gómez-Tah R, Tzec-Simá M, Ruíz-May E, Canto-Canché B, Zamora-Briseño JA, Bojórquez-Velázquez E, Oropeza-Salín C, Islas-Flores I. Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation. Int J Mol Sci 2023; 24:10431. [PMID: 37445609 DOI: 10.3390/ijms241310431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms.
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Affiliation(s)
- Jean Wildort Félix
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - María Inés Granados-Alegría
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Rufino Gómez-Tah
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Miguel Tzec-Simá
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Eliel Ruíz-May
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Jesús Alejandro Zamora-Briseño
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Esaú Bojórquez-Velázquez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Carlos Oropeza-Salín
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
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Wang H, Liu J, Huang J, Xiao Q, Hayward A, Li F, Gong Y, Liu Q, Ma M, Fu D, Xiao M. Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in Brassica napus Revealed by Combined BSA-Seq and RNA-Seq Analysis. Int J Mol Sci 2023; 24:10163. [PMID: 37373312 DOI: 10.3390/ijms241210163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Rapeseed has the ability to absorb cadmium in the roots and transfer it to aboveground organs, making it a potential species for remediating soil cadmium (Cd) pollution. However, the genetic and molecular mechanisms underlying this phenomenon in rapeseed are still unclear. In this study, a 'cadmium-enriched' parent, 'P1', with high cadmium transport and accumulation in the shoot (cadmium root: shoot transfer ratio of 153.75%), and a low-cadmium-accumulation parent, 'P2', (with a cadmium transfer ratio of 48.72%) were assessed for Cd concentration using inductively coupled plasma mass spectrometry (ICP-MS). An F2 genetic population was constructed by crossing 'P1' with 'P2' to map QTL intervals and underlying genes associated with cadmium enrichment. Fifty extremely cadmium-enriched F2 individuals and fifty extremely low-accumulation F2 individuals were selected based on cadmium content and cadmium transfer ratio and used for bulk segregant analysis (BSA) in combination with whole genome resequencing. This generated a total of 3,660,999 SNPs and 787,034 InDels between these two segregated phenotypic groups. Based on the delta SNP index (the difference in SNP frequency between the two bulked pools), nine candidate Quantitative trait loci (QTLs) from five chromosomes were identified, and four intervals were validated. RNA sequencing of 'P1' and 'P2' in response to cadmium was also performed and identified 3502 differentially expressed genes (DEGs) between 'P1' and 'P2' under Cd treatment. Finally, 32 candidate DEGs were identified within 9 significant mapping intervals, including genes encoding a glutathione S-transferase (GST), a molecular chaperone (DnaJ), and a phosphoglycerate kinase (PGK), among others. These genes are strong candidates for playing an active role in helping rapeseed cope with cadmium stress. Therefore, this study not only sheds new light on the molecular mechanisms of Cd accumulation in rapeseed but could also be useful for rapeseed breeding programs targeting this trait.
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Affiliation(s)
- Huadong Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jiajia Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Juan Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qing Xiao
- Graduate School of Jiangxi Normal University, Jiangxi Normal University, Nanchang 330045, China
| | - Alice Hayward
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072, Australia
| | - Fuyan Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yingying Gong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qian Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Miao Ma
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
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10
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Zhang N, Wang S, Zhao S, Chen D, Tian H, Li J, Zhang L, Li S, Liu L, Shi C, Yu X, Ren Y, Chen F. Global crotonylatome and GWAS revealed a TaSRT1- TaPGK model regulating wheat cold tolerance through mediating pyruvate. SCIENCE ADVANCES 2023; 9:eadg1012. [PMID: 37163591 PMCID: PMC10171821 DOI: 10.1126/sciadv.adg1012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here, we reported the complete profiling of the crotonylation proteome in common wheat. Through a combination of crotonylation and multi-omics analysis, we identified a TaPGK associated with wheat cold stress. Then, we confirmed the positive role of TaPGK-modulating wheat cold tolerance. Meanwhile, we found that cold stress induced lysine crotonylation of TaPGK. Moreover, we screened a lysine decrotonylase TaSRT1 interacting with TaPGK and found that TaSRT1 negatively regulated wheat cold tolerance. We subsequently demonstrated TaSRT1 inhibiting the accumulation of TaPGK protein, and this inhibition was possibly resulted from decrotonylation of TaPGK by TaSRT1. Transcriptome sequencing indicated that overexpression of TaPGK activated glycolytic key genes and thereby increased pyruvate content. Moreover, we found that exogenous application of pyruvate sharply enhanced wheat cold tolerance. These findings suggest that the TaSRT1-TaPGK model regulating wheat cold tolerance is possibly through mediating pyruvate. This study provided two valuable cold tolerance genes and dissected diverse mechanism of glycolytic pathway involving in wheat cold stress.
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Affiliation(s)
- Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Sisheng Wang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Simin Zhao
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Daiying Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Hongyan Tian
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Jia Li
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Lingran Zhang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Songgang Li
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Lu Liu
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Chaonan Shi
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Xiaodong Yu
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Yan Ren
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, China
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11
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Zhou J, Liu Y, Li Y, Ling W, Fan X, Feng Q, Ming R, Yang F. Combined analyses of transcriptome and metabolome reveal the mechanism of exogenous strigolactone regulating the response of elephant grass to drought stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1186718. [PMID: 37223793 PMCID: PMC10200884 DOI: 10.3389/fpls.2023.1186718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Elephant grass is widely used in feed production and ecological restoration because of its huge biomass and low occurrence of diseases and insect pets. However, drought seriously affects growth and development of this grass. Strigolactone (SL), a small molecular phytohormone, reportedly participates in improving resilience to cope with arid environment. But the mechanism of SL regulating elephant grass to response to drought stress remains unknown and needs further investigation. We conducted RNA-seq experiments and identified 84,296 genes including 765 and 2325 upregulated differential expression genes (DEGs) and 622 and 1826 downregulated DEGs, compared drought rehydration with spraying SL in roots and leaves, respectively. Combined with targeted phytohormones metabolite analysis, five hormones including 6-BA, ABA, MeSA, NAA, and JA had significant changes under re-watering and spraying SL stages. Moreover, a total of 17 co-expression modules were identified, of which eight modules had the most significant correlation with all physiological indicators with weighted gene co-expression network analysis. The venn analysis revealed the common genes between Kyoto Encyclopedia of Genes and Genomes enriched functional DEGs and the top 30 hub genes of higher weights in eight modules, respectively. Finally, 44 DEGs had been identified as key genes which played a major role in SL response to drought stress. After verification of its expression level by qPCR, six key genes in elephant grass including PpPEPCK, PpRuBPC, PpPGK, PpGAPDH, PpFBA, and PpSBPase genes regulated photosynthetic capacity under the SL treatment to respond to drought stress. Meanwhile, PpACAT, PpMFP2, PpAGT2, PpIVD, PpMCCA, and PpMCCB regulated root development and phytohormone crosstalk to respond to water deficit conditions. Our research led to a more comprehensive understanding about exogenous SL that plays a role in elephant grass response to drought stress and revealed insights into the SL regulating molecular mechanism in plants to adapt to the arid environment.
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Affiliation(s)
- Jing Zhou
- National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yijia Liu
- National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Li
- National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenqing Ling
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoyu Fan
- National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qixian Feng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fulin Yang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
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12
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Guan B, Jiang YT, Lin DL, Lin WH, Xue HW. Phosphatidic acid suppresses autophagy through competitive inhibition by binding GAPC (glyceraldehyde-3-phosphate dehydrogenase) and PGK (phosphoglycerate kinase) proteins. Autophagy 2022; 18:2656-2670. [PMID: 35289711 PMCID: PMC9629070 DOI: 10.1080/15548627.2022.2046449] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Macroautophagy/autophagy is a finely-regulated process in which cytoplasm encapsulated within transient organelles termed autophagosomes is delivered to lysosomes or vacuoles for degradation. Phospholipids, particularly phosphatidic acid (PA) that functions as a second messenger, play crucial and differential roles in autophagosome formation; however, the underlying mechanism remains largely unknown. Here we demonstrated that PA inhibits autophagy through competitive inhibition of the formation of ATG3 (autophagy-related)-ATG8e and ATG6-VPS34 (vacuolar protein sorting 34) complexes. PA bound to GAPC (glyceraldehyde-3-phosphate dehydrogenase) or PGK (phosphoglycerate kinase) and promoted their interaction with ATG3 or ATG6, which further attenuated the interactions of ATG3-ATG8e or ATG6-VPS34, respectively. Structural and mutational analyses revealed the mechanism of PA binding with GAPCs and PGK3, and that GAPCs or ATG8e competitively interacted with ATG3, and PGK3 or VPS34 competitively interacted with ATG6, at the same binding interface. These results elucidate the molecular mechanism of how PA inhibits autophagy through binding GAPC or PGK3 proteins and expand the understanding of the functional mode of PA, demonstrating the importance of phospholipids in plant autophagy and providing a new perspective for autophagy regulation by phospholipids.Abbreviation: ATG: autophagy-related; BiFC: bimolecular fluorescence complementation; co-IP: co-immunoprecipitation; Con A: concanamycin A; ER: endoplasmic reticulum; EZ: elongation zone; FRET-FLIM: fluorescence resonance energy transfer with fluorescence lifetime imaging microscopy; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GST: glutathione S-transferase; MDC: monodansylcadaverine; MZ: meristem zone; PA: phosphatidic acid; PAS: phagophore assembly site; PC: phosphatidylcholine; PE: phosphatidylethanolamine; PGK3: phosphoglycerate kinase; PtdIns3K: phosphatidylinositol 3-kinase; PLD: phospholipase D; TEM: transmission electron microscopy; TOR: target of rapamycin; VPS34: vacuolar protein sorting 34; WT: wild type; Y2H: yeast two-hybrid.
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Affiliation(s)
- Bin Guan
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, Minhang, China,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, Xuhui, China
| | - Yu-Tong Jiang
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, Minhang, China
| | - De-Li Lin
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, Minhang, China
| | - Wen-Hui Lin
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, Minhang, China,CONTACT Hong-Wei Xue Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, ofAgriculture, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hong-Wei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, Minhang, China,Wen-Hui Lin School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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13
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Zhang Y, Fernie AR. Metabolite profiling of Arabidopsis mutants of lower glycolysis. Sci Data 2022; 9:614. [PMID: 36220829 PMCID: PMC9553893 DOI: 10.1038/s41597-022-01673-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/04/2022] [Indexed: 11/09/2022] Open
Abstract
We have previously shown that in Arabidopsis the three enzymes of lower glycolysis namely phosphoglycerate mutase (PGAM), enolase and pyruvate kinase form a complex which plays an important role in tethering the mitochondria to the chloroplast. Given that the metabolism of these mutants, the complemented of pgam mutant and overexpression lines of PGAM were unclear, here, we present gas chromatography mass spectrometry-based metabolomics data of them alongside their plant growth phenotypes. Compared with wild type, both sugar and amino acid concentration are significantly altered in phosphoglycerate mutase, enolase and pyruvate kinase. Conversely, overexpression of PGAM could decrease the content of 3PGA, sugar and several amino acids and increase the content of alanine and pyruvate. In addition, the pgam mutant could not be fully complemented by either a nuclear target pgam, a side-directed-mutate of pgam or a the E.coli PGAM in term of plant phenotype or metabolite profiles, suggesting the low glycolysis complete formation is required to support normal metabolism and growth.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria. .,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria. .,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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14
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Han M, Xu M, Su T, Wang S, Wu L, Feng J, Ding C. Transcriptome Analysis Reveals Critical Genes and Pathways in Carbon Metabolism and Ribosome Biogenesis in Poplar Fertilized with Glutamine. Int J Mol Sci 2022; 23:ijms23179998. [PMID: 36077396 PMCID: PMC9456319 DOI: 10.3390/ijms23179998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Exogenous Gln as a single N source has been shown to exert similar roles to the inorganic N in poplar 'Nanlin895' in terms of growth performance, yet the underlying molecular mechanism remains unclear. Herein, transcriptome analyses of both shoots (L) and roots (R) of poplar 'Nanlin895' fertilized with Gln (G) or the inorganic N (control, C) were performed. Compared with the control, 3109 differentially expressed genes (DEGs) and 5071 DEGs were detected in the GL and GR libraries, respectively. In the shoots, Gln treatment resulted in downregulation of a large number of ribosomal genes but significant induction of many starch and sucrose metabolism genes, demonstrating that poplars tend to distribute more energy to sugar metabolism rather than ribosome biosynthesis when fertilized with Gln-N. By contrast, in the roots, most of the DEGs were annotated to carbon metabolism, glycolysis/gluconeogenesis and phenylpropanoid biosynthesis, suggesting that apart from N metabolism, exogenous Gln has an important role in regulating the redistribution of carbon resources and secondary metabolites. Therefore, it can be proposed that the promotion impact of Gln on poplar growth and photosynthesis may result from the improvement of both carbon and N allocation, accompanied by an efficient energy switch for growth and stress responses.
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Affiliation(s)
- Mei Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Mingyue Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: (T.S.); (C.D.); Tel.: +86-1589-598-3381 (T.S.)
| | - Shizhen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Liangdan Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Junhu Feng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Changjun Ding
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Correspondence: (T.S.); (C.D.); Tel.: +86-1589-598-3381 (T.S.)
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15
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Suzuki Y, Konno Y, Takegahara-Tamakawa Y, Miyake C, Makino A. Effects of suppression of chloroplast phosphoglycerate kinase on photosynthesis in rice. PHOTOSYNTHESIS RESEARCH 2022; 153:83-91. [PMID: 35635654 DOI: 10.1007/s11120-022-00923-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
As chloroplast phosphoglycerate kinase (cpPGK) is one of the enzymes which has the highest capacity among the Calvin-Benson cycle enzymes, it has not been regarded as a determinant for photosynthetic capacity. However, it was reported that the rate of CO2 assimilation decreased under high irradiance and normal [CO2] levels in the Arabidopsis cpPGK-knockdown mutant, implying that cpPGK has a control over photosynthetic capacity at a normal [CO2] level. In the present study, the contribution of cpPGK to photosynthetic capacity was evaluated in transgenic rice plants with decreased amounts of cpPGK protein under high irradiance and various [CO2] levels. The gene encoding cpPGK was suppressed using RNA interference techniques. Two lines of transgenic plants, Pi3 and Pi5, in which the amount of cpPGK protein decreased to 21% and 76% of that in wild-type plants, respectively, were obtained. However, there was no substantial difference in the rates of CO2 assimilation between wild-type and transgenic plants. The rates of CO2 assimilation decreased only slightly at elevated [CO2] levels in the transgenic line Pi3 and did not differ between wild-type plants and the transgenic line Pi5, irrespective of [CO2] level. These results clearly indicate that cpPGK does not have a strong control over photosynthetic capacity at various [CO2] levels in rice.
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Affiliation(s)
- Yuji Suzuki
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan.
| | - Yume Konno
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
| | | | - Chikahiro Miyake
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
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16
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Zeng D, Cui J, Yin Y, Dai C, Zhao H, Song C, Guan S, Cheng D, Sun Y, Lu W. Combining Proteomics and Metabolomics to Analyze the Effects of Spaceflight on Rice Progeny. FRONTIERS IN PLANT SCIENCE 2022; 13:900143. [PMID: 35800606 PMCID: PMC9253829 DOI: 10.3389/fpls.2022.900143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Spaceflight is a special abiotic stress, the biological effect mechanism of which on contemporary rice has been clarified, However, its effect on offspring rice was still unclear. In order to understand the response mechanism of F2 generation plants to space flight, this study used SJ-10 recoverable satellite to carry DN423 rice seeds for 12.5 days in orbit flight. After returning to the ground, the plants were then planted to F2 generation to explore the biological effect mechanism. Our research showed that in the F2 generation of TLS, the rice plant height of the space flight group increased by 33.8%, the ear length and thousand-grain weight decreased by 9.7 and 4.6%, respectively, and the grain number per panicle increased by 6.5%. Moreover, related proteins that control changes in agronomic traits have been identified. The changes of MDA, H2O2, soluble sugar, electron leakage and antioxidant enzyme activity confirmed the stress response in F2 generation plants. ITRAQ and LC-MS technology were used to reveal the change pattern of protein levels and metabolite levels in F2 generation plants, 389 and 405 proteins were identified as differentially abundant proteins in TLS and TS, respectively. In addition, there were 124 and 125 metabolites that changed during these two periods. The proteome and metabolome result further confirmed that the F2 generation plants still retained the memory of space flight stress, and retained the memory of space flight stress through genome instability. Oxidative stress signals activated sugar signals to rebuild metabolic networks to adapt to space flight stress. The reconstruction of energy metabolism, amino acid metabolism, phenylalanine metabolism, and flavonoid metabolism played an important role in the process of adapting to space flight stress. The results of this study broaden the perspective of space biological effects and provide a basis for studying the effects of abiotic stress on plant progeny.
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Affiliation(s)
- Deyong Zeng
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
- The Intelligent Equipment Research Center for the Exploitation of Characteristic Food & Medicine Resources, Chongqing Research Institute, Harbin Institute of Technology, Chongqing, China
| | - Jie Cui
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Yishu Yin
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Cuihong Dai
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Haitian Zhao
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- The Intelligent Equipment Research Center for the Exploitation of Characteristic Food & Medicine Resources, Chongqing Research Institute, Harbin Institute of Technology, Chongqing, China
| | - Chen Song
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Shuanghong Guan
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Dayou Cheng
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Yeqing Sun
- Institute of Environmental Systems Biology, Dalian Maritime University, Dalian, China
| | - Weihong Lu
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
- The Intelligent Equipment Research Center for the Exploitation of Characteristic Food & Medicine Resources, Chongqing Research Institute, Harbin Institute of Technology, Chongqing, China
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17
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Exploring New Routes for Genetic Resistances to Potyviruses: The Case of the Arabidopsis thaliana Phosphoglycerates Kinases (PGK) Metabolic Enzymes. Viruses 2022; 14:v14061245. [PMID: 35746717 PMCID: PMC9228606 DOI: 10.3390/v14061245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 02/04/2023] Open
Abstract
The development of recessive resistance by loss of susceptibility is a consistent strategy to combat and limit damages caused by plant viruses. Susceptibility genes can be turned into resistances, a feat that can either be selected among the plant’s natural diversity or engineered by biotechnology. Here, we summarize the current knowledge on the phosphoglycerate kinases (PGK), which have emerged as a new class of susceptibility factors to single-stranded positive RNA viruses, including potyviruses. PGKs are metabolic enzymes involved in glycolysis and the carbon reduction cycle, encoded by small multigene families in plants. To fulfil their role in the chloroplast and in the cytosol, PGKs genes encode differentially addressed proteins. Here, we assess the diversity and homology of chloroplastic and cytosolic PGKs sequences in several crops and review the current knowledge on their redundancies during plant development, taking Arabidopsis as a model. We also show how PGKs have been shown to be involved in susceptibility—and resistance—to viruses. Based on this knowledge, and drawing from the experience with the well-characterized translation initiation factors eIF4E, we discuss how PGKs genes, in light of their subcellular localization, function in metabolism, and susceptibility to viruses, could be turned into efficient genetic resistances using genome editing techniques.
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Sun Y, Jiang L, Gong S, Diaz-Pulido G, Yuan X, Tong H, Huang L, Zhou G, Zhang Y, Huang H. Changes in physiological performance and protein expression in the larvae of the coral Pocillopora damicornis and their symbionts in response to elevated temperature and acidification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151251. [PMID: 34728194 DOI: 10.1016/j.scitotenv.2021.151251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Climate change causes ocean warming and acidification, which threaten coral reef ecosystems. Ocean warming and acidification cause bleaching and mortality, and decrease calcification in adult corals, leading to changes in the composition of coral communities; however, their interactive effects on coral larvae are not comprehensively understood. To examine the underlying molecular mechanisms of larval responses to elevated temperature and pCO2, we examined the physiological performance and protein expression profiles of Pocillopora damicornis at two temperatures (29 and 33 °C) and pCO2 levels (500 and 1000 μatm) for 5 d. Extensive physiological and proteomic changes were observed in coral larvae. The results indicated a significant decrease in net photosynthesis (PNET) and autotrophic capability (PNET/RD) of larvae exposed to elevated temperature but a marked increase in PNET and PNET/RD of larvae exposed to high pCO2 levels. Elevated temperature significantly reduced endosymbiont densities by 70% and photochemical efficiency, indicating that warming impaired host-symbiont symbiosis. Expression of photosynthesis-related proteins, the photosystem (PS) I reaction center subunits IV and XI as well as oxygen-evolving enhancer 1, was downregulated at higher temperatures in symbionts, whereas expression of the PS I iron‑sulfur center protein was increased under high pCO2 conditions. Furthermore, expression of phosphoribulokinase (involved in the Calvin cycle) and phosphoenolpyruvate carboxylase (related to the C4 pathway) was downregulated in symbionts under thermal stress; this finding suggests reduced carbon fixation at high temperatures. The abundance of carbonic anhydrase-associated proteins, which are predicted to exert biochemical roles in dissolved inorganic carbon transport in larvae, was reduced in coral host and symbionts at high temperatures. These results elucidate potential mechanisms underlying the responses of coral larvae exposed to elevated temperature and acidification and suggest an important role of symbionts in the response to warming and acidification.
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Affiliation(s)
- Youfang Sun
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong 999077, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong 999077, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China
| | - Sanqiang Gong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Guillermo Diaz-Pulido
- School of Environment and Science, and Australian Rivers Institute - Coast & Estuaries, Nathan Campus, Griffith University, Brisbane, Nathan Campus, Queensland 4111, Australia
| | - Xiangcheng Yuan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China
| | - Haoya Tong
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong 999077, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China
| | - Lintao Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guowei Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China
| | - Yuyang Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Sanya National Marine Ecosystem Research Station; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China.
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Lavell A, Smith M, Xu Y, Froehlich JE, De La Mora C, Benning C. Proteins associated with the Arabidopsis thaliana plastid rhomboid-like protein RBL10. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1332-1345. [PMID: 34582071 PMCID: PMC9219029 DOI: 10.1111/tpj.15514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/10/2021] [Accepted: 09/21/2021] [Indexed: 05/07/2023]
Abstract
Rhomboid-like proteins are intramembrane proteases with a variety of regulatory roles in cells. Though many rhomboid-like proteins are predicted in plants, their detailed molecular mechanisms or cellular functions are not yet known. Of the 13 predicted rhomboids in Arabidopsis thaliana, one, RBL10, affects lipid metabolism in the chloroplast, because in the respective rbl10 mutant the transfer of phosphatidic acid through the inner envelope membrane is disrupted. Here we show that RBL10 is part of a high-molecular-weight complex of 250 kDa or greater in size. Nine likely components of this complex are identified by two independent methods and include Acyl Carrier Protein 4 (ACP4) and Carboxyltransferase Interactor1 (CTI1), which have known roles in chloroplast lipid metabolism. The acp4 mutant has decreased C16:3 fatty acid content of monogalactosyldiacylglycerol, similar to the rbl10 mutant, prompting us to offer a mechanistic model of how an interaction between ACP4 and RBL10 might affect chloroplast lipid assembly. We also demonstrate the presence of a seventh transmembrane domain in RBL10, refining the currently accepted topology of this protein. Taken together, the identity of possible RBL10 complex components as well as insights into RBL10 topology and distribution in the membrane provide a stepping-stone towards a deeper understanding of RBL10 function in Arabidopsis lipid metabolism.
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Affiliation(s)
- Anastasiya Lavell
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
| | - Montgomery Smith
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
- Department of Chemical Engineering and Material Science, Michigan State University, East Lansing, MI 48824
| | - Yang Xu
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
| | - John E. Froehlich
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
| | - Cameron De La Mora
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
- Dept. of Molecular & Cellular Biology, Illinois State University, Normal, IL 61761
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
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Doron S, Lampl N, Savidor A, Katina C, Gabashvili A, Levin Y, Rosenwasser S. SPEAR: A proteomics approach for simultaneous protein expression and redox analysis. Free Radic Biol Med 2021; 176:366-377. [PMID: 34619326 DOI: 10.1016/j.freeradbiomed.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
Oxidation and reduction of protein cysteinyl thiols serve as molecular switches, which is considered the most central mechanism for redox regulation of biological processes, altering protein structure, biochemical activity, subcellular localization, and binding affinity. Redox proteomics allows global identification of redox-modified cysteine (Cys) sites and quantification of their reversible oxidation/reduction responses, serving as a hypothesis-generating platform to stimulate redox biology mechanistic research. Here, we developed Simultaneous Protein Expression and Redox (SPEAR) analysis, a new redox-proteomics approach based on differential labeling of reversibly oxidized and reduced cysteines with light and heavy isotopic forms of commercially available isotopically-labeled N-ethylmaleimide (NEM). The presented method does not require enrichment for labeled peptides, thus enabling simultaneous quantification of Cys reversible oxidation state and protein abundance. Using SPEAR, we were able to quantify the in-vivo reversible oxidation state of thousands of cysteines across the Arabidopsis proteome under steady-state and oxidative stress conditions. Functional assignment of the identified redox-sensitive proteins demonstrated the widespread effect of oxidative conditions on various cellular functions and highlighted the enrichment of chloroplastic proteins. SPEAR provides a simple, straightforward, and cost-effective means of studying redox proteome dynamics. The presented data provide a global quantitative view of the reversible oxidation of well-known redox-regulated active sites and many novel redox-sensitive sites whose role in plant acclimation to stress conditions remains to be further explored.
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Affiliation(s)
- Shani Doron
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Nardy Lampl
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Corine Katina
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alexandra Gabashvili
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel.
| | - Shilo Rosenwasser
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610000, Israel.
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Müller-Schüssele SJ, Bohle F, Rossi J, Trost P, Meyer AJ, Zaffagnini M. Plasticity in plastid redox networks: evolution of glutathione-dependent redox cascades and glutathionylation sites. BMC PLANT BIOLOGY 2021; 21:322. [PMID: 34225654 PMCID: PMC8256493 DOI: 10.1186/s12870-021-03087-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 06/08/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Flexibility of plant metabolism is supported by redox regulation of enzymes via posttranslational modification of cysteine residues, especially in plastids. Here, the redox states of cysteine residues are partly coupled to the thioredoxin system and partly to the glutathione pool for reduction. Moreover, several plastid enzymes involved in reactive oxygen species (ROS) scavenging and damage repair draw electrons from glutathione. In addition, cysteine residues can be post-translationally modified by forming a mixed disulfide with glutathione (S-glutathionylation), which protects thiol groups from further oxidation and can influence protein activity. However, the evolution of the plastid glutathione-dependent redox network in land plants and the conservation of cysteine residues undergoing S-glutathionylation is largely unclear. RESULTS We analysed the genomes of nine representative model species from streptophyte algae to angiosperms and found that the antioxidant enzymes and redox proteins belonging to the plastid glutathione-dependent redox network are largely conserved, except for lambda- and the closely related iota-glutathione S-transferases. Focussing on glutathione-dependent redox modifications, we screened the literature for target thiols of S-glutathionylation, and found that 151 plastid proteins have been identified as glutathionylation targets, while the exact cysteine residue is only known for 17% (26 proteins), with one or multiple sites per protein, resulting in 37 known S-glutathionylation sites for plastids. However, 38% (14) of the known sites were completely conserved in model species from green algae to flowering plants, with 22% (8) on non-catalytic cysteines. Variable conservation of the remaining sites indicates independent gains and losses of cysteines at the same position during land plant evolution. CONCLUSIONS We conclude that the glutathione-dependent redox network in plastids is highly conserved in streptophytes with some variability in scavenging and damage repair enzymes. Our analysis of cysteine conservation suggests that S-glutathionylation in plastids plays an important and yet under-investigated role in redox regulation and stress response.
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Affiliation(s)
- Stefanie J Müller-Schüssele
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany.
- Present Address: Department of Biology, Technische Universität Kaiserslautern, 67663, Kaiserslautern, Germany.
| | - Finja Bohle
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
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Maignan V, Bernay B, Géliot P, Avice JC. Biostimulant impacts of Glutacetine® and derived formulations (VNT1 and VNT4) on the bread wheat grain proteome. J Proteomics 2021; 244:104265. [PMID: 33992839 DOI: 10.1016/j.jprot.2021.104265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/20/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022]
Abstract
Nitrogen (N) fertilizer is essential to ensure grain yield and quality in bread wheat. Improving N use efficiency is therefore crucial for wheat grain protein quality. In the present work, we analysed the effects on the winter wheat grain proteome of biostimulants containing Glutacetine® or two derived formulations (VNT1 and 4) when mixed with urea-ammonium-nitrate fertilizer. A large-scale quantitative proteomics analysis of two wheat flour fractions produced a dataset of 4369 identified proteins. Quantitative analysis revealed 9, 39 and 96 proteins with a significant change in abundance after Glutacetine®, VNT1 and VNT4 treatments, respectively, with a common set of 11 proteins that were affected by two different biostimulants. The major effects impacted proteins involved in (i) protein synthesis regulation (mainly ribosomal and binding proteins), (ii) defence and responses to stresses (including chitin-binding protein, heat shock 70 kDa protein 1 and glutathione S-transferase proteins), (iii) storage functions related to gluten protein alpha-gliadins and starch synthase and (iv) seed development with proteins implicated in protease activity, energy machinery, and the C and N metabolism pathways. Altogether, our study showed that Glutacetine®, VNT1 and VNT4 biostimulants positively affected protein composition related to grain quality. Data are available via ProteomeXchange with identifier PXD021513. SIGNIFICANCE: We performed a large-scale quantitative proteomics study of the total protein extracts from flour samples to determine the effect of Glutacetine®-based biostimulants treatment on the protein composition of bread wheat grain. To our knowledge, only a few studies in the literature have applied proteomic approaches to study bread wheat grains and in particular to investigate the effect of biostimulants on the grain proteome of this cereal crop. In addition, most approaches used fractional extraction of proteins to target reserve proteins followed electrophoresis which leads to low identification rate of proteins. We identified and quantified a large protein dataset of 4369 proteins and determined ontological class of proteins affected by biostimulants treatments. Our proteomics investigation revealed the important role of these new biostimulants in achieving significant changes in protein synthesis regulation, storage functions, protease activity, energy machinery, C and N metabolism pathways and responses to biotic and abiotic stresses in grain.
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Affiliation(s)
- Victor Maignan
- Normandie Univ, UNICAEN, INRAE, UMR EVA, SFR Normandie Végétal FED4277, Esplanade de la Paix, F-14032 Caen, France; Via Végétale, 44430 Le Loroux-Bottereau, France.
| | - Benoit Bernay
- Plateforme Proteogen, SFR ICORE 4206, Université de Caen Basse-Normandie, Esplanade de la paix, 14032 Caen cedex, France
| | | | - Jean-Christophe Avice
- Normandie Univ, UNICAEN, INRAE, UMR EVA, SFR Normandie Végétal FED4277, Esplanade de la Paix, F-14032 Caen, France
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Suzuki Y, Ishiyama K, Sugawara M, Suzuki Y, Kondo E, Takegahara-Tamakawa Y, Yoon DK, Suganami M, Wada S, Miyake C, Makino A. Overproduction of Chloroplast Glyceraldehyde-3-Phosphate Dehydrogenase Improves Photosynthesis Slightly under Elevated [CO2] Conditions in Rice. PLANT & CELL PHYSIOLOGY 2021; 62:156-165. [PMID: 33289530 DOI: 10.1093/pcp/pcaa149] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) limits the regeneration of ribulose 1,5-bisphosphate (RuBP) in the Calvin-Benson cycle. However, it does not always limit the rate of CO2 assimilation. In the present study, the effects of overproduction of GAPDH on the rate of CO2 assimilation under elevated [CO2] conditions, where the capacity for RuBP regeneration limits photosynthesis, were examined in transgenic rice (Oryza sativa). GAPDH activity was increased to 3.2- and 4.5-fold of the wild-type levels by co-overexpression of the GAPDH genes, GAPA and GAPB, respectively. In the transgenic rice plants, the rate of CO2 assimilation under elevated [CO2] conditions increased by approximately 10%, whereas that under normal and low [CO2] conditions was not affected. These results indicate that overproduction of GAPDH is effective in improving photosynthesis under elevated [CO2] conditions, although its magnitude is relatively small. By contrast, biomass production of the transgenic rice plants was not greater than that of wild-type plants under elevated [CO2] conditions, although starch content tended to increase marginally.
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Affiliation(s)
- Yuji Suzuki
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550 Japan
| | - Keiki Ishiyama
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550 Japan
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572 Japan
| | - Misaki Sugawara
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550 Japan
| | - Yuka Suzuki
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550 Japan
| | - Eri Kondo
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572 Japan
| | | | - Dong-Kyung Yoon
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572 Japan
| | - Mao Suganami
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572 Japan
| | - Shinya Wada
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550 Japan
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Chikahiro Miyake
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572 Japan
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Changes in the Flower and Leaf Proteome of Common Buckwheat ( Fagopyrum esculentum Moench) under High Temperature. Int J Mol Sci 2021; 22:ijms22052678. [PMID: 33800930 PMCID: PMC7961373 DOI: 10.3390/ijms22052678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/03/2023] Open
Abstract
Common buckwheat (Fagopyrum esculentum Moench), a pseudocereal crop, produces a large number of flowers, but this does not guarantee high seed yields. This species demonstrates strong abortion of flowers and embryos. High temperatures during the generative growth phase result in an increase in the degeneration of embryo sacs. The aim of this study was to investigate proteomic changes in flowers and leaves of two common buckwheat accessions with different degrees of heat tolerance, Panda and PA15. Two-dimensional gel electrophoresis and mass spectrometry techniques were used to analyze the proteome profiles. Analyses were conducted for flower buds, open flowers capable of fertilization, and wilted flowers, as well as donor leaves, i.e., those growing closest to the inflorescences. High temperature up-regulated the expression of 182 proteins. The proteomic response to heat stress differed between the accessions and among their organs. In the Panda accession, we observed a change in abundance of 17, 13, 28, and 11 proteins, in buds, open and wilted flowers, and leaves, respectively. However, in the PA15 accession there were 34, 21, 63, and 21 such proteins, respectively. Fifteen heat-affected proteins were common to both accessions. The indole-3-glycerol phosphate synthase chloroplastic-like isoform X2 accumulated in the open flowers of the heat-sensitive cultivar Panda in response to high temperature, and may be a candidate protein as a marker of heat sensitivity in buckwheat plants.
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Li J, Wang Y, Wei H, Kang X. Comparative proteomic analysis provides insight into the molecular mechanism of vegetative growth advantage in allotriploid Populus. Genomics 2021; 113:1180-1192. [PMID: 33677055 DOI: 10.1016/j.ygeno.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/04/2021] [Accepted: 03/02/2021] [Indexed: 10/22/2022]
Abstract
Though allotriploid poplar shows a salient vegetative growth advantage that impacts biomass and lumber yield, the proteomic data of Populus allotriploids have not been scrutinized for identifying the underlying molecular mechanisms. We conducted a large-scale label-free proteomics profiling of the 5th, 10th, and 25th leaves of allotriploids and diploids, and identified 4587 protein groups. Among 932 differentially expressed proteins (DEPs), 22 are transcription factors (TFs) that could regulate vegetative growth advantage in allotriploids. The DEPs involved in light reaction, Calvin cycle, and photorespiration, protein synthesis, sucrose synthesis, starch synthesis, and starch decomposition displayed elevated expression in Populus allotriploids. However, the DEPs functioning in sucrose decomposition, tricarboxylic acid (TCA) cycle, and protein degradation exhibited significantly downregulated expression. The alternations of these DEPs augmented efficiency of photosynthesis, carbon fixation, sucrose and starch accumulation, and decreased capacity of carbohydrate consumption, leading to larger volume of biomass and vigorous growth in Populus allotriploids.
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Affiliation(s)
- Jiang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China
| | - Yi Wang
- Zhongkai University of Agriculture and Engineering, Guangzhou 510225, PR China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton 49931, USA
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China; National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, PR China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China.
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Zafari S, Vanlerberghe GC, Igamberdiev AU. Nitric Oxide Turnover Under Hypoxia Results in the Rapid Increased Expression of the Plastid-Localized Phosphorylated Pathway of Serine Biosynthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:780842. [PMID: 35173748 PMCID: PMC8841671 DOI: 10.3389/fpls.2021.780842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/28/2021] [Indexed: 05/03/2023]
Abstract
The plant mitochondrial electron transport chain influences carbon and nitrogen metabolism under near anoxic conditions through its involvement in the phytoglobin-nitric oxide cycle, where the respiratory chain reduces nitrite to nitric oxide (NO), followed by NO conversion to nitrate by class 1 phytoglobin. Wild type (WT) and transgenic tobacco (Nicotiana tabacum L.) with differing amounts of alternative oxidase (AOX) were used to manipulate NO generation under hypoxia, and to examine whether this in turn influenced the gene expression of two stress-related amino acid biosynthetic pathways, the plastid-localized phosphorylated pathway of serine biosynthesis (PPSB), and the γ-aminobutyric acid (GABA) shunt. Under hypoxia, leaf NO emission rate was highest in AOX overexpressors and lowest in AOX knockdowns, with WT showing an intermediate rate. In turn, the rate of NO emission correlated with the degree to which amino acids accumulated. This amino acid accumulation was associated with the increased expression of the enzymes of the stress-related amino acid biosynthetic pathways. However, induction of the PPSB occurred much earlier than the GABA shunt. This work shows that high rates of NO turnover associate with rapid gene induction of the PPSB, establishing a clear link between this pathway and the maintenance of carbon, nitrogen and energy metabolism under hypoxia.
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Affiliation(s)
- Somaieh Zafari
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Greg C. Vanlerberghe
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto Scarborough, Toronto, ON, Canada
| | - Abir U. Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
- *Correspondence: Abir U. Igamberdiev,
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Massange-Sánchez JA, Casados-Vázquez LE, Juarez-Colunga S, Sawers RJH, Tiessen A. The Phosphoglycerate Kinase (PGK) Gene Family of Maize ( Zea mays var. B73). PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9121639. [PMID: 33255472 PMCID: PMC7761438 DOI: 10.3390/plants9121639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/27/2020] [Accepted: 09/08/2020] [Indexed: 05/17/2023]
Abstract
Phosphoglycerate kinase (PGK, E.C. 2.7.2.3) interconverts ADP + 1,3-bisphospho-glycerate (1,3-bPGA) to ATP + 3-phosphoglycerate (3PGA). While most bacteria have a single pgk gene and mammals possess two copies, plant genomes contain three or more PGK genes. In this study, we identified five Pgk genes in the Zea mays var. B73 genome, predicted to encode proteins targeted to different subcellular compartments: ZmPgk1, ZmPgk2, and ZmPgk4 (chloroplast), ZmPgk3 (cytosol), and ZmPgk5 (nucleus). The expression of ZmPgk3 was highest in non-photosynthetic tissues (roots and cobs), where PGK activity was also greatest, consistent with a function in glycolysis. Green tissues (leaf blade and husk leaf) showed intermediate levels of PGK activity, and predominantly expressed ZmPgk1 and ZmPgk2, suggesting involvement in photosynthetic metabolism. ZmPgk5 was weakly expressed and ZmPgk4 was not detected in any tissue. Phylogenetic analysis showed that the photosynthetic and glycolytic isozymes of plants clustered together, but were distinct from PGKs of animals, fungi, protozoa, and bacteria, indicating that photosynthetic and glycolytic isozymes of plants diversified after the divergence of the plant lineage from other groups. These results show the distinct role of each PGK in maize and provide the basis for future studies into the regulation and function of this key enzyme.
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Affiliation(s)
- Julio A. Massange-Sánchez
- Departamento de Ingeniería Genética, CINVESTAV Unidad Irapuato, Irapuato 36821, Mexico; (L.E.C.-V.); (S.J.-C.); (A.T.)
- Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ) Subsede Zapopan, Guadalajara 44270, Mexico
- Correspondence: ; Tel.: +52-(33)-3345-5200 (ext. 1700)
| | - Luz E. Casados-Vázquez
- Departamento de Ingeniería Genética, CINVESTAV Unidad Irapuato, Irapuato 36821, Mexico; (L.E.C.-V.); (S.J.-C.); (A.T.)
- Life Science Division Food Department, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato 36500, Mexico
| | - Sheila Juarez-Colunga
- Departamento de Ingeniería Genética, CINVESTAV Unidad Irapuato, Irapuato 36821, Mexico; (L.E.C.-V.); (S.J.-C.); (A.T.)
| | - Ruairidh J. H. Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA 16801, USA;
| | - Axel Tiessen
- Departamento de Ingeniería Genética, CINVESTAV Unidad Irapuato, Irapuato 36821, Mexico; (L.E.C.-V.); (S.J.-C.); (A.T.)
- Laboratorio Nacional PlanTECC, Ciudad de México C.P. 06020, Mexico
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Abraham-Juárez MJ, Schrager-Lavelle A, Man J, Whipple C, Handakumbura P, Babbitt C, Bartlett M. Evolutionary Variation in MADS Box Dimerization Affects Floral Development and Protein Abundance in Maize. THE PLANT CELL 2020; 32:3408-3424. [PMID: 32873631 PMCID: PMC7610293 DOI: 10.1105/tpc.20.00300] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/19/2020] [Accepted: 09/01/2020] [Indexed: 05/19/2023]
Abstract
Interactions between MADS box transcription factors are critical in the regulation of floral development, and shifting MADS box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation in protein-protein interactions affects MADS box protein function remains unknown. To assess the impact of changing MADS box protein-protein interactions on transcription factor function, we turned to the grasses, where interactions between B-class MADS box proteins vary. We tested the functional consequences of this evolutionary variability using maize (Zea mays) as an experimental system. We found that differential B-class dimerization was associated with subtle, quantitative differences in stamen shape. In contrast, differential dimerization resulted in large-scale changes to downstream gene expression. Differential dimerization also affected B-class complex composition and abundance, independent of transcript levels. This indicates that differential B-class dimerization affects protein degradation, revealing an important consequence for evolutionary variability in MADS box interactions. Our results highlight complexity in the evolution of developmental gene networks: changing protein-protein interactions could affect not only the composition of transcription factor complexes but also their degradation and persistence in developing flowers. Our results also show how coding change in a pleiotropic master regulator could have small, quantitative effects on development.
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Affiliation(s)
- María Jazmín Abraham-Juárez
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
- CONACYT-Instituto Potosino de Investigación Científica y Tecnológica A.C., 78216 San Luis Potosi, Mexico
| | - Amanda Schrager-Lavelle
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
- Biology Department, Colorado Mesa University, Grand Junction, 81501 Colorado
| | - Jarrett Man
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
| | - Clinton Whipple
- Biology Department, Brigham Young University, Provo, 84602 Utah
| | - Pubudu Handakumbura
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
- Pacific Northwest National Laboratory, Richland, 99354 Washington
| | - Courtney Babbitt
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
| | - Madelaine Bartlett
- Biology Department, University of Massachusetts, Amherst, 01003 Massachusetts
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Alves RDFB, Menezes-Silva PE, Sousa LF, Loram-Lourenço L, Silva MLF, Almeida SES, Silva FG, Perez de Souza L, Fernie AR, Farnese FS. Evidence of drought memory in Dipteryx alata indicates differential acclimation of plants to savanna conditions. Sci Rep 2020; 10:16455. [PMID: 33020558 PMCID: PMC7536413 DOI: 10.1038/s41598-020-73423-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
The remarkable phytogeographic characteristics of the Brazilian savanna (Cerrado) resulted in a vegetation domain composed of plants with high structural and functional diversity to tolerate climate extremes. Here we used a key Cerrado species (Dipteryx alata) to evaluate if species of this domain present a mechanism of stress memory, responding more quickly and efficiently when exposed to recurrent drought episodes. The exposure of D. alata seedlings to drought resulted in several changes, mainly in physiological and biochemical traits, and these changes differed substantially when the water deficit was imposed as an isolated event or when the plants were subjected to drought cycles, suggesting the existence of a drought memory mechanism. Plants submitted to recurrent drought events were able to maintain essential processes for plant survival when compared to those submitted to drought for the first time. This differential acclimation to drought was the result of orchestrated changes in several metabolic pathways, involving differential carbon allocation for defense responses and the reprogramming and coordination of primary, secondary and antioxidant metabolism. The stress memory in D. alata is probably linked the evolutionary history of the species and reflects the environment in which it evolved.
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Affiliation(s)
| | | | - Leticia F Sousa
- Instituto Federal Goiano, Campus Rio Verde, Rio Verde, GO, 75.901-970, Brazil
| | | | - Maria L F Silva
- Instituto Federal Goiano, Campus Rio Verde, Rio Verde, GO, 75.901-970, Brazil
| | - Sabrina E S Almeida
- Instituto Federal Goiano, Campus Rio Verde, Rio Verde, GO, 75.901-970, Brazil
| | - Fabiano G Silva
- Instituto Federal Goiano, Campus Rio Verde, Rio Verde, GO, 75.901-970, Brazil
| | | | - Alisdair R Fernie
- Max-Planck-Institute for Molecular Plant Physiology, 14476, Potsdam-Gölm, Germany
| | - Fernanda S Farnese
- Instituto Federal Goiano, Campus Rio Verde, Rio Verde, GO, 75.901-970, Brazil.
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Bhattacharya O, Ortiz I, Walling LL. Methodology: an optimized, high-yield tomato leaf chloroplast isolation and stroma extraction protocol for proteomics analyses and identification of chloroplast co-localizing proteins. PLANT METHODS 2020; 16:131. [PMID: 32983250 PMCID: PMC7513546 DOI: 10.1186/s13007-020-00667-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/04/2020] [Indexed: 06/09/2023]
Abstract
BACKGROUND Chloroplasts are critical organelles that perceive and convey metabolic and stress signals to different cellular components, while remaining the seat of photosynthesis and a metabolic factory. The proteomes of intact leaves, chloroplasts, and suborganellar fractions of plastids have been evaluated in the model plant Arabidopsis, however fewer studies have characterized the proteomes of plastids in crops. Tomato (Solanum lycopersicum) is an important world-wide crop and a model system for the study of wounding, herbivory and fruit ripening. While significant advances have been made in understanding proteome and metabolome changes in fruit ripening, far less is known about the tomato chloroplast proteome or its subcompartments. RESULTS With the long-term goal of understanding chloroplast proteome dynamics in response to stress, we describe a high-yielding method to isolate intact tomato chloroplasts and stromal proteins for proteomic studies. The parameters that limit tomato chloroplast yields were identified and revised to increase yields. Compared to published data, our optimized method increased chloroplast yields by 6.7- and 4.3-fold relative to published spinach and Arabidopsis leaf protocols, respectively; furthermore, tomato stromal protein yields were up to 79-fold higher than Arabidopsis stromal proteins yields. We provide immunoblot evidence for the purity of the stromal proteome isolated using our enhanced methods. In addition, we leverage our nanoliquid chromatography tandem mass spectrometry (nanoLC-MS/MS) data to assess the quality of our stromal proteome. Using strict criteria, proteins detected by 1 peptide spectral match, by one peptide, or were sporadically detected were designated as low-level contaminating proteins. A set of 254 proteins that reproducibly co-isolated with the tomato chloroplast stroma were identified. The subcellular localization, frequency of detection, normalized spectral abundance, and functions of the co-isolating proteins are discussed. CONCLUSIONS Our optimized method for chloroplast isolation increased the yields of tomato chloroplasts eightfold enabling the proteomics analysis of the chloroplast stromal proteome. The set of 254 proteins that co-isolate with the chloroplast stroma provides opportunities for developing a better understanding of the extensive and dynamic interactions of chloroplasts with other organelles. These co-isolating proteins also have the potential for expanding our knowledge of proteins that are co-localized in multiple subcellular organelles.
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Affiliation(s)
- Oindrila Bhattacharya
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521 USA
| | - Irma Ortiz
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521 USA
| | - Linda L. Walling
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521 USA
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Proteomic analyses unraveling water stress response in two Eucalyptus species originating from contrasting environments for aridity. Mol Biol Rep 2020; 47:5191-5205. [PMID: 32564226 DOI: 10.1007/s11033-020-05594-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/17/2020] [Indexed: 12/24/2022]
Abstract
Eucalyptus are widely cultivated in several regions of the world due to their adaptability to different climatic conditions and amenable to tree breeding programs. With changes in environmental conditions pointing to an increase in aridity in many areas of the globe, the demand for genetic materials that adapt to this situation is required. Therefore, the aim of this work was to identify contrasting differences between two Eucalyptus species under water stress through the identification of differentially abundant proteins. For this, total protein extraction was proceeded from leaves of both species maintained at 40 and 80% of field capacity (FC). The 80% FC water regime was considered as the control and the 40% FC, severe water stress. The proteins were separated by 2-DE with subsequent identification of those differentially abundant by liquid nanocromatography coupled to high resolution MS (Q-Exactive). Comparative proteomics allowed to identify four proteins (ATP synthase gamma and alpha, glutamine synthetase and a vacuolar protein) that were more abundant in drought-tolerant species and simultaneously less abundant or unchanged in the drought- sensitive species, an uncharacterized protein found exclusively in plants under drought stress and also 10 proteins (plastid-lipid, ruBisCO activase, ruBisCO, protease ClpA, transketolase, isoflavone reductase, ferredoxin-NADP reductase, malate dehydrogenase, aminobutyrate transaminase and sedoheptulose-1-bisphosphatase) induced exclusively in the drought-tolerant species in response to water stress. These results suggest that such proteins may play a crucial role as potential markers of water stress tolerance through the identification of species-specific proteins, and future targets for genetic engineering.
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32
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Fang Y, Deng X, Lu X, Zheng J, Jiang H, Rao Y, Zeng D, Hu J, Zhang X, Xue D. Differential phosphoproteome study of the response to cadmium stress in rice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 180:780-788. [PMID: 31154203 DOI: 10.1016/j.ecoenv.2019.05.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
Cadmium (Cd) is one of the most toxic heavy metals, and its accumulation in plants will seriously affect growth and yield. In this study, Cd-sensitive line D69 and Cd-tolerant line D28 were selected, which the Cd content of D28 was higher than D69 in both above and underground parts after Cd treatment. Using a combination of two-dimensional gel electrophoresis (2-DE) and MALDI-TOF-TOF MS/MS, the differential expression changes of phosphorylated proteins between D69 and D28 in leaves were classified and analyzed after Cd treatment. A total of 53 differentially expressed phosphoproteins were identified, which mainly involved in metabolism, signal transduction, gene expression regulation, material transport, and membrane fusion. The phosphorylated proteins of Cd-tolerant and Cd-sensitive lines were all analyzed, and found that some proteins associated with carbon metabolism, proteolytic enzymes, F-box containing transcription factors, RNA helicases, DNA replication/transcription/repair enzymes and ankyrins were detected in Cd-tolerant line D28, which might alleviate the abiotic stress caused by Cd treatment. These results will clarify the phosphorylated pathways in response and resistance to Cd stress in rice.
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Affiliation(s)
- Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xiasha Road, 310036, Hangzhou, China
| | - Xiangxiong Deng
- College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xiasha Road, 310036, Hangzhou, China
| | - Xueli Lu
- College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xiasha Road, 310036, Hangzhou, China; State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyu Road, 310006, Hangzhou, China
| | - Junjun Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xiasha Road, 310036, Hangzhou, China
| | - Hua Jiang
- Zhejiang Academy of Agricultural Science, 298 Deshengzhong Road, 310021, Hangzhou, China
| | - Yuchun Rao
- College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, 321004, Jinhua, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyu Road, 310006, Hangzhou, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 359 Tiyu Road, 310006, Hangzhou, China.
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xiasha Road, 310036, Hangzhou, China.
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xiasha Road, 310036, Hangzhou, China.
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Xiong Q, Zhong L, Shen T, Cao C, He H, Chen X. iTRAQ-based quantitative proteomic and physiological analysis of the response to N deficiency and the compensation effect in rice. BMC Genomics 2019; 20:681. [PMID: 31462233 PMCID: PMC6714431 DOI: 10.1186/s12864-019-6031-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 08/13/2019] [Indexed: 01/21/2023] Open
Abstract
Background The crop growth compensation effect is a naturally biological phenomenon, and nitrogen (N) is essential for crop growth and development, especially for yield formation. Little is known about the molecular mechanism of N deficiency and N compensation in rice. Thus, the N-sensitive stage of rice was selected to study N deficiency at the tillering stage and N compensation at the young panicle differentiation stage. In this study, a proteome analysis was performed to analyze leaf differentially expressed proteins (DEPs), and to investigate the leaf physiological characteristics and yield under N deficiency and after N compensation. Results The yield per plant presented an equivalent compensatory effect. The net photosynthetic rate, optimal/maximal quantum yield of photosystem II (Fv/Fm), soil and plant analyzer development (SPAD) value, and glutamic pyruvic transaminase (GPT) activity of T1 (N deficiency at the tillering stage, and N compensation at the young panicle differentiation stage) were lower than those of CK (N at different stages of growth by constant distribution) under N deficiency. However, after N compensation, the net photosynthetic rate, Fv/Fm, SPAD value and GPT activity were increased. Using an iTRAQ-based quantitative approach, a total of 1665 credible proteins were identified in the three 4-plex iTRAQ experiments. Bioinformatics analysis indicated that DEPs were enriched in photosynthesis, photosynthesis-antenna proteins, carbon metabolism and carbon fixation in the photosynthetic organism pathways. Moreover, the photosynthesis-responsive proteins of chlorophyll a-b binding protein, ribulose bisphosphate carboxylase small chain and phosphoglycerate kinase were significantly downregulated under N deficiency. After N compensation, chlorophyll a-b binding protein, NADH dehydrogenase subunit 5, NADH dehydrogenase subunit 7, and peroxidase proteins were significantly upregulated in rice leaves. Conclusion Through physiological and quantitative proteomic analysis, we concluded that a variety of metabolic pathway changes was induced by N deficiency and N compensation. GO and KEGG enrichment analysis revealed that DEPs were significantly associated with photosynthesis pathway-, energy metabolism pathway- and stress resistance-related proteins. The DEPs play an important role in the regulation of N deficiency and the compensation effect in rice. Electronic supplementary material The online version of this article (10.1186/s12864-019-6031-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiangqiang Xiong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.,College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Lei Zhong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.,College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Tianhua Shen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.,College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Chaohao Cao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.,College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China. .,College of Agronomy, Jiangxi Agricultural University, Nanchang, China. .,Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China.
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China. .,College of Agronomy, Jiangxi Agricultural University, Nanchang, China. .,Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China.
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Shameer S, Ratcliffe RG, Sweetlove LJ. Leaf Energy Balance Requires Mitochondrial Respiration and Export of Chloroplast NADPH in the Light. PLANT PHYSIOLOGY 2019; 180:1947-1961. [PMID: 31213510 PMCID: PMC6670072 DOI: 10.1104/pp.19.00624] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
Key aspects of leaf mitochondrial metabolism in the light remain unresolved. For example, there is debate about the relative importance of exporting reducing equivalents from mitochondria for the peroxisomal steps of photorespiration versus oxidation of NADH to generate ATP by oxidative phosphorylation. Here, we address this and explore energetic coupling between organelles in the light using a diel flux balance analysis model. The model included more than 600 reactions of central metabolism with full stoichiometric accounting of energy production and consumption. Different scenarios of energy availability (light intensity) and demand (source leaf versus a growing leaf) were considered, and the model was constrained by the nonlinear relationship between light and CO2 assimilation rate. The analysis demonstrated that the chloroplast can theoretically generate sufficient ATP to satisfy the energy requirements of the rest of the cell in addition to its own. However, this requires unrealistic high light use efficiency and, in practice, the availability of chloroplast-derived ATP is limited by chloroplast energy dissipation systems, such as nonphotochemical quenching, and the capacity of the chloroplast ATP export shuttles. Given these limitations, substantial mitochondrial ATP synthesis is required to fulfill cytosolic ATP requirements, with only minimal, or zero, export of mitochondrial reducing equivalents. The analysis also revealed the importance of exporting reducing equivalents from chloroplasts to sustain photorespiration. Hence, the chloroplast malate valve and triose phosphate-3-phosphoglycerate shuttle are predicted to have important metabolic roles, in addition to their more commonly discussed contribution to the avoidance of photooxidative stress.
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Affiliation(s)
- Sanu Shameer
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
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35
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Quantitative proteomics analysis reveals proteins and pathways associated with anthocyanin accumulation in barley. Food Chem 2019; 298:124973. [PMID: 31261005 DOI: 10.1016/j.foodchem.2019.124973] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/24/2019] [Accepted: 06/09/2019] [Indexed: 11/23/2022]
Abstract
The aim of the present study was to explore the underlying mechanisms involved in anthocyanin biosynthesis in purple, blue, and white barley using quantitative proteomics analysis. We identified the differences in protein expression and related functions involved in anthocyanin biosynthesis in purple, blue, and white barley (named H, M, and L groups, respectively, based on their anthocyanin content) using TMT-liquid chromatography/mass spectroscopy-based proteomic methods. Totally, 297, 300, 254, and 1421 differentially expressed proteins (DEPs) were found in H vs. L, H vs. M, L vs. M, and H vs. L vs. M groups, respectively. Six clusters of proteins from the 1421 DEPs were mainly involved in carbon metabolism, amino acid and secondary metabolite biosynthesis, and metabolic pathways. Several proteins were validated using parallel reaction monitoring. The proteins involved in amino acid biosynthesis, carbon metabolism, metabolic pathways, and phenylpropanoid biosynthesis were responsible for the color differences in the three barley varieties.
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36
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Li R, Qiu Z, Wang X, Gong P, Xu Q, Yu QB, Guan Y. Pooled CRISPR/Cas9 reveals redundant roles of plastidial phosphoglycerate kinases in carbon fixation and metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:1078-1089. [PMID: 30834637 DOI: 10.1111/tpj.14303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 05/07/2023]
Abstract
Phosphoglycerate kinase (PGK) is a highly conserved reversible enzyme that participates in both glycolysis and photosynthesis. In Arabidopsis thaliana, one cytosolic PGK (PGKc) and two plastidial PGKs (PGKp) are known. It remains debatable whether the two PGKp isozymes are functionally redundant or specialized in plastidial carbon metabolism and fixation. Here, using a pooled clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) strategy, we found that plants with single mutations in pgkp1 or pgkp2 were not significantly affected, whereas a pgkp1pgkp2 double mutation was lethal due to retarded carbon fixation, suggesting that PGKp isozymes play redundant functional roles. Metabolomic analysis demonstrated that the sugar-deficient pgkp1pgkp2 double mutation was partially complemented by exogenous sugar, although respiration intermediates were not rescued. Chloroplast development was defective in pgkp1pgkp2, due to a deficiency in glycolysis-dependent galactoglycerolipid biosynthesis. Ectopic expression of a plastid targeting PGKc did not reverse the pgkp1pgkp2 double-mutant phenotypes. Therefore, PGKp1 and PGKp2 play redundant roles in carbon fixation and metabolism, whereas the molecular function of PGKc is more divergent. Our study demonstrated the functional conservation and divergence of glycolytic enzymes.
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Affiliation(s)
- Ruizi Li
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhimin Qiu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaoguo Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Pingping Gong
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qinzhen Xu
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Qing-Bo Yu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Yuefeng Guan
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Zhu X, Liao J, Xia X, Xiong F, Li Y, Shen J, Wen B, Ma Y, Wang Y, Fang W. Physiological and iTRAQ-based proteomic analyses reveal the function of exogenous γ-aminobutyric acid (GABA) in improving tea plant (Camellia sinensis L.) tolerance at cold temperature. BMC PLANT BIOLOGY 2019; 19:43. [PMID: 30700249 PMCID: PMC6354415 DOI: 10.1186/s12870-019-1646-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/11/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Internal γ-Aminobutyric Acid (GABA) interacting with stress response substances may be involved in the regulation of differentially abundant proteins (DAPs) associated with optimum temperature and cold stress in tea plants (Camellia sinensis (L.) O. Kuntze). RESULTS Tea plants supplied with or without 5.0 mM GABA were subjected to optimum or cold temperatures in this study. The increased GABA level induced by exogenous GABA altered levels of stress response substances - such as glutamate, polyamines and anthocyanins - in association with improved cold tolerance. Isobaric tags for relative and absolute quantification (iTRAQ) - based DAPs were found for protein metabolism and nucleotide metabolism, energy, amino acid transport and metabolism other biological processes, inorganic ion transport and metabolism, lipid metabolism, carbohydrate transport and metabolism, biosynthesis of secondary metabolites, antioxidant and stress defense. CONCLUSIONS The iTRAQ analysis could explain the GABA-induced physiological effects associated with cold tolerance in tea plants. Analysis of functional protein-protein networks further showed that alteration of endogenous GABA and stress response substances induced interactions among photosynthesis, amino acid biosynthesis, and carbon and nitrogen metabolism, and the corresponding differences could contribute to improved cold tolerance of tea plants.
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Affiliation(s)
- Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu Province 210095 People’s Republic of China
| | - Jieren Liao
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu Province 210095 People’s Republic of China
| | - Xingli Xia
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu Province 210095 People’s Republic of China
| | - Fei Xiong
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu Province 210095 People’s Republic of China
| | - Yue Li
- Wuxi NextCODE Genomics, 288 Fute Zhong Road, Shanghai, 200131 People’s Republic of China
| | - Jiazhi Shen
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu Province 210095 People’s Republic of China
| | - Bo Wen
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu Province 210095 People’s Republic of China
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu Province 210095 People’s Republic of China
| | - Yuhua Wang
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu Province 210095 People’s Republic of China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu Province 210095 People’s Republic of China
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Lu ZS, Chen QS, Zheng QX, Shen JJ, Luo ZP, Fan K, Xu SH, Shen Q, Liu PP. Proteomic and Phosphoproteomic Analysis in Tobacco Mosaic Virus-Infected Tobacco (Nicotiana tabacum). Biomolecules 2019; 9:E39. [PMID: 30678100 PMCID: PMC6406717 DOI: 10.3390/biom9020039] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 12/11/2022] Open
Abstract
Tobacco mosaic virus (TMV) is a common source of biological stress that significantly affects plant growth and development. It is also useful as a model in studies designed to clarify the mechanisms involved in plant viral disease. Plant responses to abiotic stress were recently reported to be regulated by complex mechanisms at the post-translational modification (PTM) level. Protein phosphorylation is one of the most widespread and major PTMs in organisms. Using immobilized metal ion affinity chromatography (IMAC) enrichment, high-pH C18 chromatography fraction, and high-accuracy mass spectrometry (MS), a set of proteins and phosphopeptides in both TMV-infected tobacco and control tobacco were identified. A total of 4905 proteins and 3998 phosphopeptides with 3063 phosphorylation sites were identified. These 3998 phosphopeptides were assigned to 1311 phosphoproteins, as some proteins carried multiple phosphorylation sites. Among them, 530 proteins and 337 phosphopeptides corresponding to 277 phosphoproteins differed between the two groups. There were 43 upregulated phosphoproteins, including phosphoglycerate kinase, pyruvate phosphate dikinase, protein phosphatase 2C, and serine/threonine protein kinase. To the best of our knowledge, this is the first phosphoproteomic analysis of leaves from a tobacco cultivar, K326. The results of this study advance our understanding of tobacco development and TMV action at the protein phosphorylation level.
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Affiliation(s)
- Zi-Shu Lu
- Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450000, China.
| | - Qian-Si Chen
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, China.
| | - Qing-Xia Zheng
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, China.
| | - Juan-Juan Shen
- Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450000, China.
| | - Zhao-Peng Luo
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, China.
| | - Kai Fan
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, China.
| | - Sheng-Hao Xu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Qi Shen
- Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450000, China.
| | - Ping-Ping Liu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, China.
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Yao L, Yu Q, Huang M, Hung W, Grosser J, Chen S, Wang Y, Gmitter FG. Proteomic and metabolomic analyses provide insight into the off-flavour of fruits from citrus trees infected with ' Candidatus Liberibacter asiaticus'. HORTICULTURE RESEARCH 2019; 6:31. [PMID: 30792870 PMCID: PMC6375920 DOI: 10.1038/s41438-018-0109-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/11/2018] [Accepted: 11/15/2018] [Indexed: 05/18/2023]
Abstract
Orange fruit from trees infected by 'Candidatus Liberibacter asiaticus' (CaLas) often do not look fully mature and exhibit off-flavours described as bitter, harsh, and metallic rather than juicy and fruity. Although previous studies have been carried out to understand the effect of CaLas on the flavour of orange juice using metabolomic methods, the mechanisms leading to the off-flavour that occurs in Huanglongbing (HLB)-symptomatic fruit are not well understood. In this study, fruits were collected from symptomatic and healthy Valencia sweet orange (Citrus sinensis) trees grafted on Swingle (C. paradisi X Poncirus trifoliata) rootstock. Isobaric tags for relative and absolute quantification (iTRAQ) and gas chromatography-mass spectrometry (GC-MS) were used to measure the proteins, sugars, organic acids, amino acids, and volatile terpenoids. The results showed that most of the differentially expressed proteins involved in glycolysis, the tricarboxylic acid (TCA) cycle and amino-acid biosynthesis were degraded, and terpenoid metabolism was significantly downregulated in the symptomatic fruit. Valencene, limonene, 3-carene, linalool, myrcene, and α-terpineol levels were significantly lower in fruit from CaLas-infected trees than from healthy trees. Similar phenomena were observed for sucrose and glucose. Our study indicated that off-flavour of symptomatic fruit was associated with a reduction in the levels of terpenoid products and the downregulation of proteins in glycolysis, the TCA cycle, and the terpenoid biosynthesis pathway.
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Affiliation(s)
- Lixiao Yao
- Citrus Research Institute, Southwest University, Chongqing, China
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850 USA
| | - Qibin Yu
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850 USA
| | - Ming Huang
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850 USA
| | - Weilun Hung
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850 USA
| | - Jude Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850 USA
| | - Shanchun Chen
- Citrus Research Institute, Southwest University, Chongqing, China
| | - Yu Wang
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850 USA
| | - Frederick G. Gmitter
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850 USA
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Chen X, Yang B, Huang W, Wang T, Li Y, Zhong Z, Yang L, Li S, Tian J. Comparative Proteomic Analysis Reveals Elevated Capacity for Photosynthesis in Polyphenol Oxidase Expression-Silenced Clematis terniflora DC. Leaves. Int J Mol Sci 2018; 19:E3897. [PMID: 30563128 PMCID: PMC6321541 DOI: 10.3390/ijms19123897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/01/2018] [Accepted: 12/02/2018] [Indexed: 12/15/2022] Open
Abstract
Polyphenol oxidase (PPO) catalyzes the o-hydroxylation of monophenols and oxidation of o-diphenols to quinones. Although the effects of PPO on plant physiology were recently proposed, little has been done to explore the inherent molecular mechanisms. To explore the in vivo physiological functions of PPO, a model with decreased PPO expression and enzymatic activity was constructed on Clematis terniflora DC. using virus-induced gene silencing (VIGS) technology. Proteomics was performed to identify the differentially expressed proteins (DEPs) in the model (VC) and empty vector-carrying plants (VV) untreated or exposed to high levels of UV-B and dark (HUV-B+D). Following integration, it was concluded that the DEPs mainly functioned in photosynthesis, glycolysis, and redox in the PPO silence plants. Mapman analysis showed that the DEPs were mainly involved in light reaction and Calvin cycle in photosynthesis. Further analysis illustrated that the expression level of adenosine triphosphate (ATP) synthase, the content of chlorophyll, and the photosynthesis rate were increased in VC plants compared to VV plants pre- and post HUV-B+D. These results indicate that the silence of PPO elevated the plant photosynthesis by activating the glycolysis process, regulating Calvin cycle and providing ATP for energy metabolism. This study provides a prospective approach for increasing crop yield in agricultural production.
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Affiliation(s)
- Xi Chen
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
| | - Bingxian Yang
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
| | - Wei Huang
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
| | - Tantan Wang
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
| | - Yaohan Li
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
| | - Zhuoheng Zhong
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
| | - Lin Yang
- Zhuhai Weilan Pharmaceutical Co., Ltd., Zhuhai 519030, China.
| | - Shouxin Li
- Changshu Qiushi Technology Co., Ltd., Suzhou 215500, China.
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
- Zhejiang-Malaysia Joint Research Center for Traditional Medicine, Zhejiang University, Hangzhou 310027, China.
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41
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Nováková S, Danchenko M, Skultety L, Fialová I, Lešková A, Beke G, Flores-Ramírez G, Glasa M. Photosynthetic and Stress Responsive Proteins Are Altered More Effectively in Nicotiana benthamiana Infected with Plum pox virus Aggressive PPV-CR versus Mild PPV-C Cherry-Adapted Isolates. J Proteome Res 2018; 17:3114-3127. [PMID: 30084641 DOI: 10.1021/acs.jproteome.8b00230] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plum pox virus (PPV, family Potyviridae) is one of the most important viral pathogens of Prunus spp. causing considerable damage to stone-fruit industry worldwide. Among the PPV strains identified so far, only PPV-C, PPV-CR, and PPV-CV are able to infect cherries under natural conditions. Herein, we evaluated the pathogenic potential of two viral isolates in herbaceous host Nicotiana benthamiana. Significantly higher accumulation of PPV capsid protein in tobacco leaves infected with PPV-CR (RU-30sc isolate) was detected in contrast to PPV-C (BY-101 isolate). This result correlated well with the symptoms observed in the infected plants. To further explore the host response upon viral infection at the molecular level, a comprehensive proteomic profiling was performed. Using reverse-phase ultra-high-performance liquid chromatography followed by label-free mass spectrometry quantification, we identified 38 unique plant proteins as significantly altered due to the infection. Notably, the abundances of photosynthesis-related proteins, mainly from the Calvin-Benson cycle, were found more aggressively affected in plants infected with PPV-CR isolate than those of PPV-C. This observation was accompanied by a significant reduction in the amount of photosynthetic pigments extracted from the leaves of PPV-CR infected plants. Shifts in the abundance of proteins that are involved in stimulation of photosynthetic capacity, modification of amino acid, and carbohydrate metabolism may affect plant growth and initiate energy formation via gluconeogenesis in PPV infected N. benthamiana. Furthermore, we suggest that the higher accumulation of H2O2 in PPV-CR infected leaves plays a crucial role in plant defense and development by activating the glutathione synthesis.
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Affiliation(s)
- Slavomíra Nováková
- Biomedical Research Center, Institute of Virology , Slovak Academy of Sciences , Dubravska cesta 9 , 845 05 Bratislava , Slovak Republic
| | - Maksym Danchenko
- Biomedical Research Center, Institute of Virology , Slovak Academy of Sciences , Dubravska cesta 9 , 845 05 Bratislava , Slovak Republic
| | - Ludovit Skultety
- Biomedical Research Center, Institute of Virology , Slovak Academy of Sciences , Dubravska cesta 9 , 845 05 Bratislava , Slovak Republic
- Institute of Microbiology , The Czech Academy of Sciences , Videnska 1083 , 142 20 Prague , Czech Republic
| | - Ivana Fialová
- Plant Science and Biodiversity Center, Institute of Botany , Slovak Academy of Sciences , Dubravska cesta 9 , 845 23 Bratislava , Slovak Republic
| | - Alexandra Lešková
- Plant Science and Biodiversity Center, Institute of Botany , Slovak Academy of Sciences , Dubravska cesta 9 , 845 23 Bratislava , Slovak Republic
| | - Gábor Beke
- Institute of Molecular Biology , Slovak Academy of Sciences , Dúbravská cesta 21 , 845 51 Bratislava , Slovak Republic
| | - Gabriela Flores-Ramírez
- Biomedical Research Center, Institute of Virology , Slovak Academy of Sciences , Dubravska cesta 9 , 845 05 Bratislava , Slovak Republic
| | - Miroslav Glasa
- Biomedical Research Center, Institute of Virology , Slovak Academy of Sciences , Dubravska cesta 9 , 845 05 Bratislava , Slovak Republic
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42
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Guan Z, Wang W, Yu X, Lin W, Miao Y. Comparative Proteomic Analysis of Coregulation of CIPK14 and WHIRLY1/3 Mediated Pale Yellowing of Leaves in Arabidopsis. Int J Mol Sci 2018; 19:E2231. [PMID: 30065159 PMCID: PMC6121582 DOI: 10.3390/ijms19082231] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/27/2018] [Accepted: 07/27/2018] [Indexed: 01/08/2023] Open
Abstract
Pale yellowing of leaf variegation is observed in the mutant Arabidopsis lines Calcineurin B-Like-Interacting Protein Kinase14 (CIPK14) overexpression (oeCIPK14) and double-knockout WHIRLY1/WHIRLY3 (why1/3). Further, the relative distribution of WHIRLY1 (WHY1) protein between plastids and the nucleus is affected by the phosphorylation of WHY1 by CIPK14. To elucidate the coregulation of CIPK14 and WHIRLY1/WHIRLY3-mediated pale yellowing of leaves, a differential proteomic analysis was conducted between the oeCIPK14 variegated (oeCIPK14-var) line, why1/3 variegated (why1/3-var) line, and wild type (WT). More than 800 protein spots were resolved on each gel, and 67 differentially abundant proteins (DAPs) were identified by matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF-MS). Of these 67 proteins, 34 DAPs were in the oeCIPK14-var line and 33 DAPs were in the why1/3-var line compared to the WT. Five overlapping proteins were differentially expressed in both the oeCIPK14-var and why1/3-var lines: ATP-dependent Clp protease proteolytic subunit-related protein 3 (ClpR3), Ribulose bisphosphate carboxylase large chain (RBCL), Beta-amylase 3 (BAM3), Ribosome-recycling factor (RRF), and Ribulose bisphosphate carboxylase small chain (RBCS). Bioinformatics analysis showed that most of the DAPs are involved in photosynthesis, defense and antioxidation pathways, protein metabolism, amino acid metabolism, energy metabolism, malate biosynthesis, lipid metabolism, and transcription. Thus, in the why1/3-var and oeCIPK14-var lines, there was a decrease in the photosystem parameters, including the content of chlorophyll, the photochemical efficiency of photosystem (PS II) (Fv/Fm), and electron transport rates (ETRs), but there was an increase in non-photochemical quenching (NPQ). Both mutants showed high sensitivity to intense light. Based on the annotation of the DAPs from both why1/3-var and oeCIPK14-var lines, we conclude that the CIPK14 phosphorylation-mediated WHY1 deficiency in plastids is related to the impairment of protein metabolism, leading to chloroplast dysfunction.
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Affiliation(s)
- Zhe Guan
- Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wanzhen Wang
- Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xingle Yu
- Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenfang Lin
- Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ying Miao
- Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Chen W, Gong P, Guo J, Li H, Li R, Xing W, Yang Z, Guan Y. Glycolysis regulates pollen tube polarity via Rho GTPase signaling. PLoS Genet 2018; 14:e1007373. [PMID: 29702701 PMCID: PMC5942846 DOI: 10.1371/journal.pgen.1007373] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/09/2018] [Accepted: 04/19/2018] [Indexed: 12/25/2022] Open
Abstract
As a universal energy generation pathway utilizing carbon metabolism, glycolysis plays an important housekeeping role in all organisms. Pollen tubes expand rapidly via a mechanism of polarized growth, known as tip growth, to deliver sperm for fertilization. Here, we report a novel and surprising role of glycolysis in the regulation of growth polarity in Arabidopsis pollen tubes via impingement of Rho GTPase-dependent signaling. We identified a cytosolic phosphoglycerate kinase (pgkc-1) mutant with accelerated pollen germination and compromised pollen tube growth polarity. pgkc-1 mutation greatly diminished apical exocytic vesicular distribution of REN1 RopGAP (Rop GTPase activating protein), leading to ROP1 hyper-activation at the apical plasma membrane. Consequently, pgkc-1 pollen tubes contained higher amounts of exocytic vesicles and actin microfilaments in the apical region, and showed reduced sensitivity to Brefeldin A and Latrunculin B, respectively. While inhibition of mitochondrial respiration could not explain the pgkc-1 phenotype, the glycolytic activity is indeed required for PGKc function in pollen tubes. Moreover, the pgkc-1 pollen tube phenotype was mimicked by the inhibition of another glycolytic enzyme. These findings highlight an unconventional regulatory function for a housekeeping metabolic pathway in the spatial control of a fundamental cellular process. Glycolysis, which breaks down glucose to produce energy, has long been considered a “housekeeping” pathway in living cells, i.e., it helps maintain basic cellular functions. Here, we found that the glycolysis pathway plays an unconventional regulatory role in cell polarity, i.e., the intrinsic asymmetry in the shape, structure, and organization of cellular components. Mutation in the gene encoding the glycolytic enzyme cytosolic phosphoglycerate kinase (PGKc) leads to swollen and shorter pollen tubes in Arabidopsis thaliana, which is associated with the over-activation of Rho GTPase—a master regulator of cell polarity. Our results suggest that this phenomenon is caused by a specific regulatory role of cytosolic glycolysis rather than the global energy supply or moonlighting functions of glycolytic enzymes that modulate pollen tube growth polarity. Our findings shed light on the diverse biological roles of glycolysis in plants beyond simple “housekeeping” functions.
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Affiliation(s)
- Wei Chen
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Pingping Gong
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jingzhe Guo
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Center for Plant Cell Biology, Institute of Integrated Genome Biology, and Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Hui Li
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- Center for Plant Cell Biology, Institute of Integrated Genome Biology, and Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Ruizi Li
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Weiman Xing
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Zhenbiao Yang
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Center for Plant Cell Biology, Institute of Integrated Genome Biology, and Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Yuefeng Guan
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- * E-mail:
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Bailey-Serres J, Pierik R, Ruban A, Wingler A. The Dynamic Plant: Capture, Transformation, and Management of Energy. PLANT PHYSIOLOGY 2018; 176:961-966. [PMID: 29438068 PMCID: PMC5813544 DOI: 10.1104/pp.18.00041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Julia Bailey-Serres
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521; Plant Ecophysiology, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Ronald Pierik
- Plant Ecophysiology, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Alexander Ruban
- Department of Cell and Molecular Biology, School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Astrid Wingler
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland
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45
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Fernie AR, Zhang Y, Sweetlove LJ. Passing the Baton: Substrate Channelling in Respiratory Metabolism. RESEARCH (WASHINGTON, D.C.) 2018; 2018:1539325. [PMID: 31549022 PMCID: PMC6750097 DOI: 10.1155/2018/1539325] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/01/2018] [Indexed: 11/18/2022]
Abstract
Despite species-specific differences in the pathways of respiratory metabolism are remarkably conserved across the kingdoms of life with glycolysis, the tricarboxylic acid cycle, and mitochondrial electron transport chain representing the major components of the process in the vast majority of organisms. In addition to being of critical importance in fueling life itself these pathways serve as interesting case studies for substrate channelling with research on this theme having been carried out for over 40 years. Here we provide a cross-kingdom review of the ample evidence for protein-protein interaction and enzyme assemblies within the three component pathways as well as describing the scarcer available evidence for substrate channelling itself.
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Affiliation(s)
- Alisdair R. Fernie
- 1Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- 2Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Youjun Zhang
- 1Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- 2Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Lee J. Sweetlove
- 3Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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