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Sun T, Wang M, Li X, Chen Y, Zhang W. Different Phenotypic, Photosynthetic, and Physiological Responses to Flooding between Q. nuttallii and Q. palustris. PLANTS (BASEL, SWITZERLAND) 2024; 13:1658. [PMID: 38931092 PMCID: PMC11207582 DOI: 10.3390/plants13121658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Flooding stress is an increasingly serious problem in wetlands, often affecting large areas of crops and timber production areas. The current study aimed to explore the species differences in responses to flooding stress between Q. nuttallii and Q. palustris in an outdoor environment. All the tested plants survived after a 60-day flooding treatment that left 5 cm of water above the soil surface. This suggests that the two species are flood-tolerant, so they can be applied in the construction of riparian protection forests and wetland restoration. Compared with control conditions, flooding treatment significantly decreased seedling height and diameter and the Pn, Gs, Tr, Fv/Fm, ABS/CSm, TR0/CSm, ET0/CSm, RE0/CSm, IAA, and GA3 content and significantly increased the content of MDA, H2O2, soluble sugars, SOD, POD, ADH, ABA, and JA. Under control conditions, Q. nuttallii showed significantly greater growth and photosynthetic capability than Q. palustris. In contrast, Q. palustris exhibited less inhibition of growth and photosynthesis, oxidative stress levels, and antioxidant enzyme activities than Q. nuttallii under flooding conditions. The findings indicate that Q. palustris has better defense mechanisms against the damage caused by flooding stress than Q. nuttallii. Q. nuttallii was more sensitive and responsive to flooding than Q. palustris.
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Affiliation(s)
- Tiantian Sun
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (M.W.); (X.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Mengzhu Wang
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (M.W.); (X.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xin Li
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (M.W.); (X.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yongxia Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Civil Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Wangxiang Zhang
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (M.W.); (X.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Komatsu S, Zhou T, Kono Y. Biochemical Analysis to Understand the Flooding Tolerance of Mutant Soybean Irradiated with Gamma Rays. Int J Mol Sci 2023; 25:517. [PMID: 38203688 PMCID: PMC10779331 DOI: 10.3390/ijms25010517] [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: 12/10/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Flooding stress, which reduces plant growth and seed yield, is a serious problem for soybean. To improve the productivity of flooded soybean, flooding-tolerant soybean was produced by gamma-ray irradiation. Three-day-old wild-type and mutant-line plants were flooded for 2 days. Protein, RNA, and genomic DNA were then analyzed based on oppositely changed proteins between the wild type and the mutant line under flooding stress. They were associated with cell organization, RNA metabolism, and protein degradation according to proteomic analysis. Immunoblot analysis confirmed that the accumulation of beta-tubulin/beta-actin increased in the wild type under flooding stress and recovered to the control level in the mutant line; however, alpha-tubulin increased in both the wild type and the mutant line under stress. Ubiquitin was accumulated and genomic DNA was degraded by flooding stress in the wild type; however, they were almost the same as control levels in the mutant line. On the other hand, the gene expression level of RNase H and 60S ribosomal protein did not change in either the wild type or the mutant line under flooding stress. Furthermore, chlorophyll a/b decreased and increased in the wild type and the mutant line, respectively, under flooding stress. These results suggest that the regulation of cell organization and protein degradation might be an important factor in the acquisition of flooding tolerance in soybean.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan;
| | - Tiantian Zhou
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan;
| | - Yuhi Kono
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Joetsu 943-0193, Japan;
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3
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Abbey L, Ofoe R, Wang Z, Chada S. How Central Carbon Metabolites of Mexican Mint ( Plectranthus amboinicus) Plants Are Impacted under Different Watering Regimes. Metabolites 2023; 13:metabo13040539. [PMID: 37110197 PMCID: PMC10141017 DOI: 10.3390/metabo13040539] [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: 02/08/2023] [Revised: 04/02/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Plants are sessile, and their ability to reprogram their metabolism to adapt to fluctuations in soil water level is crucial but not clearly understood. A study was performed to determine alterations in intermediate metabolites involved in central carbon metabolism (CCM) following exposure of Mexican mint (Plectranthus amboinicus) to varying watering regimes. The water treatments were regular watering (RW), drought (DR), flooding (FL), and resumption of regular watering after flooding (DHFL) or after drought (RH). Leaf cluster formation and leaf greening were swift following the resumption of regular watering. A total of 68 key metabolites from the CCM routes were found to be significantly (p < 0.01) impacted by water stress. Calvin cycle metabolites in FL plants, glycolytic metabolites in DR plants, total tricarboxylic acid (TCA) cycle metabolites in DR and DHFL plants, and nucleotide biosynthetic molecules in FL and RH plants were significantly (p < 0.05) increased. Pentose phosphate pathway (PPP) metabolites were equally high in all the plants except DR plants. Total Calvin cycle metabolites had a significantly (p < 0.001) strong positive association with TCA cycle (r = 0.81) and PPP (r = 0.75) metabolites. Total PPP metabolites had a moderately positive association with total TCA cycle metabolites (r = 0.68; p < 0.01) and a negative correlation with total glycolytic metabolites (r = -0.70; p < 0.005). In conclusion, the metabolic alterations of Mexican mint plants under different watering regimes were revealed. Future studies will use transcriptomic and proteomic approaches to identify genes and proteins that regulate the CCM route.
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Affiliation(s)
- Lord Abbey
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Raphael Ofoe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Zijing Wang
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Sparsha Chada
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
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Lin J, Monsalvo I, Ly M, Jahan MA, Wi D, Martirosyan I, Kovinich N. RNA-Seq Dissects Incomplete Activation of Phytoalexin Biosynthesis by the Soybean Transcription Factors GmMYB29A2 and GmNAC42-1. PLANTS (BASEL, SWITZERLAND) 2023; 12:545. [PMID: 36771629 PMCID: PMC9921300 DOI: 10.3390/plants12030545] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Glyceollins, isoflavonoid-derived antimicrobial metabolites, are the major phytoalexins in soybean (Glycine max). They play essential roles in providing resistance to the soil-borne pathogen Phytophthora sojae and have unconventional anticancer and neuroprotective activities that render them desirable for pharmaceutical development. Our previous studies revealed that the transcription factors GmMYB29A2 and GmNAC42-1 have essential roles in activating glyceollin biosynthesis, yet each cannot activate the transcription of all biosynthesis genes in the absence of a pathogen elicitor treatment. Here, we report that co-overexpressing both transcription factors is also insufficient to activate glyceollin biosynthesis. To understand this insufficiency, we compared the transcriptome profiles of hairy roots overexpressing each transcription factor with glyceollin-synthesizing roots treated with wall glucan elicitor (WGE) from P. sojae. GmMYB29A2 upregulated most of the WGE-regulated genes that encode enzymatic steps spanning from primary metabolism to the last step of glyceollin biosynthesis. By contrast, GmNAC42-1 upregulated glyceollin biosynthesis genes only when overexpressed in the presence of WGE treatment. This is consistent with our recent discovery that, in the absence of WGE, GmNAC42-1 is bound by GmJAZ1 proteins that inhibit its transactivation activity. WGE, and not GmMYB29A2 or GmNAC42-1, upregulated the heat shock family gene GmHSF6-1, the homolog of Arabidopsis HSFB2a that directly activated the transcription of several glyceollin biosynthesis genes. Our results provide important insights into what biosynthesis genes will need to be upregulated to activate the entire glyceollin biosynthetic pathway.
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Affiliation(s)
- Jie Lin
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Ivan Monsalvo
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Melissa Ly
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Md Asraful Jahan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Dasol Wi
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Izabella Martirosyan
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Nik Kovinich
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
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5
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Zhong Z, Wang X, Yin X, Tian J, Komatsu S. Morphophysiological and Proteomic Responses on Plants of Irradiation with Electromagnetic Waves. Int J Mol Sci 2021; 22:12239. [PMID: 34830127 PMCID: PMC8618018 DOI: 10.3390/ijms222212239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 01/25/2023] Open
Abstract
Electromagnetic energy is the backbone of wireless communication systems, and its progressive use has resulted in impacts on a wide range of biological systems. The consequences of electromagnetic energy absorption on plants are insufficiently addressed. In the agricultural area, electromagnetic-wave irradiation has been used to develop crop varieties, manage insect pests, monitor fertilizer efficiency, and preserve agricultural produce. According to different frequencies and wavelengths, electromagnetic waves are typically divided into eight spectral bands, including audio waves, radio waves, microwaves, infrared, visible light, ultraviolet, X-rays, and gamma rays. In this review, among these electromagnetic waves, effects of millimeter waves, ultraviolet, and gamma rays on plants are outlined, and their response mechanisms in plants through proteomic approaches are summarized. Furthermore, remarkable advancements of irradiating plants with electromagnetic waves, especially ultraviolet, are addressed, which shed light on future research in the electromagnetic field.
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Affiliation(s)
- Zhuoheng Zhong
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China; (Z.Z.); (J.T.)
| | - Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Xiaojian Yin
- Department of Pharmacognosy, China Pharmaceutical University, Nanjing 211198, China;
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China; (Z.Z.); (J.T.)
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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Liang LL, Song YK, Qian WJ, Ruan JY, Ding ZT, Zhang QF, Hu JH. Metabolomics analysis reveals the responses of tea plants to excessive calcium. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:5678-5687. [PMID: 33792039 DOI: 10.1002/jsfa.11222] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/10/2021] [Accepted: 03/31/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND The proper growth and development of tea plants requires moderately acidic soils and relatively low calcium levels, and excessive calcium at high pH can damage tea plant roots. To reveal the effects of calcium on the responses of tea plant to three pH levels (3.5, 5.0 and 6.5), a repeated test of two factors was designed. RESULTS Root growth and elemental analysis indicated that excessive calcium improved the growth of tea roots at low pH conditions, whereas it did not harm the growth of tea roots under normal and high pH conditions, especially at pH 6.5. Excessive calcium antagonized the absorption and utilization of magnesium by tea plants. Gas chromatography-mass spectrometry results showed that the addition of Ca2+ resulted in the primary metabolism in roots being more active at a low pH level. By contrast, it had obvious adverse effects on the accumulation of root metabolites with high calcium treatment at normal or high pH. Differential metabolites identified using ultra-performance liquid chromatography quadrupole time of flight mass spectrometry indicated that flavonoids demonstrated the largest number of changes, and their biosynthesis was partially enriched with excessive calcium at low and high pH conditions, whereas it was down-regulated under normal pH conditions. Kaempferol 3-(2'-rhamnosyl-6'-acetylgalactoside) 7-rhamnoside, quercetin 3-(6'-sinapoylsophorotrioside) and delphinidin 3-(3'-p-coumaroylglucoside) showed the greatest increase. The results of gene expression related to root growth and calcium regulation were consistent with root growth and root metabolism. CONCLUSION The overall results demonstrated that high Ca concentrations further aggravate the detrimental effects of high pH to tea roots. However, it is interesting that excessive calcium reduced the harm of a low pH on tea root growth to some extent. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Li-Li Liang
- College of Horticulture/College of Foreign Languages, Qingdao Agricultural University, Qingdao, China
| | - Ya-Kang Song
- College of Horticulture/College of Foreign Languages, Qingdao Agricultural University, Qingdao, China
| | - Wen-Jun Qian
- College of Horticulture/College of Foreign Languages, Qingdao Agricultural University, Qingdao, China
| | - Jian-Yun Ruan
- Key Laboratory of Tea Plant Biology and Resources Utilization, Tea Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Hangzhou, China
| | - Zhao-Tang Ding
- College of Horticulture/College of Foreign Languages, Qingdao Agricultural University, Qingdao, China
| | - Qun-Feng Zhang
- Key Laboratory of Tea Plant Biology and Resources Utilization, Tea Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Hangzhou, China
| | - Jian-Hui Hu
- College of Horticulture/College of Foreign Languages, Qingdao Agricultural University, Qingdao, China
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7
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Komatsu S, Yamaguchi H, Hitachi K, Tsuchida K, Kono Y, Nishimura M. Proteomic and Biochemical Analyses of the Mechanism of Tolerance in Mutant Soybean Responding to Flooding Stress. Int J Mol Sci 2021; 22:9046. [PMID: 34445752 PMCID: PMC8396653 DOI: 10.3390/ijms22169046] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
To investigate the mechanism of flooding tolerance of soybean, flooding-tolerant mutants derived from gamma-ray irradiated soybean were crossed with parent cultivar Enrei for removal of other factors besides the genes related to flooding tolerance in primary generated mutant soybean. Although the growth of the wild type was significantly suppressed by flooding compared with the non-flooding condition, that of the mutant lines was better than that of the wild type even if it was treated with flooding. A two-day-old mutant line was subjected to flooding for 2 days and proteins were analyzed using a gel-free/label-free proteomic technique. Oppositely changed proteins in abundance between the wild type and mutant line under flooding stress were associated in endoplasmic reticulum according to gene-ontology categorization. Immunoblot analysis confirmed that calnexin accumulation increased in both the wild type and mutant line; however, calreticulin accumulated in only the mutant line under flooding stress. Furthermore, although glycoproteins in the wild type decreased by flooding compared with the non-flooding condition, those in the mutant line increased even if it was under flooding stress. Alcohol dehydrogenase accumulated in the wild type and mutant line; however, this enzyme activity significantly increased and mildly increased in the wild type and mutant line, respectively, under flooding stress compared with the non-flooding condition. Cell death increased and decreased in the wild type and mutant line, respectively, by flooding stress. These results suggest that the regulation of cell death through the fermentation system and glycoprotein folding might be an important factor for the acquisition of flooding tolerance in mutant soybean.
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Hisateru Yamaguchi
- Department of Medical Technology, Yokkaichi Nursing and Medical Care University, Yokkaichi 512-8045, Japan;
| | - Keisuke Hitachi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (K.T.)
| | - Kunihiro Tsuchida
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (K.T.)
| | - Yuhi Kono
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Joetsu 943-0193, Japan;
| | - Minoru Nishimura
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
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De Ollas C, González-Guzmán M, Pitarch Z, Matus JT, Candela H, Rambla JL, Granell A, Gómez-Cadenas A, Arbona V. Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato ( Solanum lycopersicum L. Mill). FRONTIERS IN PLANT SCIENCE 2021; 12:613059. [PMID: 33746996 PMCID: PMC7973378 DOI: 10.3389/fpls.2021.613059] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/19/2021] [Indexed: 05/25/2023]
Abstract
Soil flooding is a compound abiotic stress that alters soil properties and limits atmospheric gas diffusion (O2 and CO2) to the roots. The involvement of abscisic acid (ABA) in the regulation of soil flooding-specific genetic and metabolic responses has been scarcely studied despite its key importance as regulator in other abiotic stress conditions. To attain this objective, wild type and ABA-deficient tomatoes were subjected to short-term (24 h) soil waterlogging. After this period, gas exchange parameters were reduced in the wild type but not in ABA-deficient plants that always had higher E and g s . Transcript and metabolite alterations were more intense in waterlogged tissues, with genotype-specific variations. Waterlogging reduced the ABA levels in the roots while inducing PYR/PYL/RCAR ABA receptors and ABA-dependent transcription factor transcripts, of which induction was less pronounced in the ABA-deficient genotype. Ethylene/O2-dependent genetic responses (ERFVIIs, plant anoxia survival responses, and genes involved in the N-degron pathway) were induced in hypoxic tissues independently of the genotype. Interestingly, genes encoding a nitrate reductase and a phytoglobin involved in NO biosynthesis and scavenging and ERFVII stability were induced in waterlogged tissues, but to a lower extent in ABA-deficient tomato. At the metabolic level, flooding-induced accumulation of Ala was enhanced in ABA-deficient lines following a differential accumulation of Glu and Asp in both hypoxic and aerated tissues, supporting their involvement as sources of oxalacetate to feed the tricarboxylic acid cycle in waterlogged tissues and constituting a potential advantage upon long periods of soil waterlogging. The promoter analysis of upregulated genes indicated that the production of oxalacetate from Asp via Asp oxidase, energy processes such as acetyl-CoA, ATP, and starch biosynthesis, and the lignification process were likely subjected to ABA regulation. Taken together, these data indicate that ABA depletion in waterlogged tissues acts as a positive signal, inducing several specific genetic and metabolic responses to soil flooding.
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Affiliation(s)
- Carlos De Ollas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
| | - Miguel González-Guzmán
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
| | - Zara Pitarch
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology, Universitat de València – Consejo Superior de Investigaciones Científicas, Paterna, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - José Luis Rambla
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València – Consejo Superior de Investigaciones Científicas, València, Spain
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
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Wang X, Li F, Chen Z, Yang B, Komatsu S, Zhou S. Proteomic analysis reveals the effects of melatonin on soybean root tips under flooding stress. J Proteomics 2021; 232:104064. [PMID: 33276190 DOI: 10.1016/j.jprot.2020.104064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/14/2020] [Accepted: 11/22/2020] [Indexed: 11/30/2022]
Abstract
Flooding constrains soybean growth, while melatonin enhances the ability of plants to tolerate abiotic stresses. To interpret the melatonin-mediated flooding response in soybeans, proteomic analysis was performed in root tips. Retarded growth and severe cell death were observed in flooded soybeans, but these phenotypes were ameliorated by melatonin treatment. A total of 634, 1401, and 1205 proteins were identified under control, flood, and flood plus melatonin conditions, respectively; and these proteins were predominantly associated with metabolism of protein, RNA, and the cell wall. Among these melatonin-induced proteins, eukaryotic aspartyl protease family protein was increased after flood compared with melatonin treatment group, in accordance with its upregulated transcript levels during stress. Eukaryotic translation initiation factor 5A was decreased after flood compared with melatonin. When stress was prolonged, its transcript levels were upregulated by flood, while they were not changed by melatonin. Furthermore, 13-hydroxylupanine O-tigloyltransferase was decreased by flood compared with melatonin; however, its transcription was upregulated by melatonin. In addition, reduced lignification in root tips of flooded soybeans was restored by melatonin. These results suggest that factors related to protein degradation and functional states of RNA play critical roles in promoting the effects of melatonin on soybean plants under flooding. SIGNIFICANCE: Flooding stress threatens soybean growth, while melatonin treatment enhances plant tolerance to stress stimuli. To examine the effects of melatonin on flooded soybeans, morphological analysis was performed. Melatonin promoted soybean growth as judged from greater fresh weight of plant, longer seedling length, and less evident cell death in flooding-stressed soybeans treated with melatonin than those plants exposed to flood alone. Proteomic analysis was conducted to explore the promoting effects of melatonin on soybeans under flooding stress. As a result, metabolism of protein metabolism, RNA regulation, and cell wall was enriched by proteins identified under control, flood, and flood plus melatonin conditions. Among these melatonin-induced proteins, abundance of eukaryotic aspartyl protease family protein, eukaryotic translation initiation factor 5A, and 13-hydroxylupanine O-tigloyltransferase displayed similar change patterns between the control and melatonin compared with flood; and transcript levels of genes encoding these proteins responded to flooding stress and melatonin treatment. In addition, activated cell degradation, expanded intercellular spaces, and reduced lignification in root tips of flooded soybeans were ameliorated by melatonin treatment.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Fang Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhenyuan Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Bingxian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Shunli Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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10
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Li C, Hou D, Zhang L, Li X, Fan J, Dong Y, Zhu J, Huang Z, Xu Z, Li L. Molecular characterization and function analysis of the rice OsDUF617 family. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1934541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Chunliu Li
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Dejia Hou
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Lin Zhang
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Xiaohong Li
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Jiangbo Fan
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Yilun Dong
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Jianqing Zhu
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Zhengjian Huang
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Zhengjun Xu
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, PR China
| | - Lihua Li
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, PR China
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11
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Wang X, Komatsu S. Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean. Int J Mol Sci 2020; 21:E7497. [PMID: 33053653 PMCID: PMC7589014 DOI: 10.3390/ijms21207497] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/04/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Soybean, which is rich in protein and oil as well as phytochemicals, is cultivated in several climatic zones. However, its growth is markedly decreased by flooding stress, which is caused by climate change. Proteomic techniques were used for understanding the flood-response and -tolerant mechanisms in soybean. Subcellular proteomics has potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and under stress stimuli. Furthermore, post-translational modifications play important roles in stress response and tolerance to flooding stress. Although many flood-response mechanisms have been reported, flood-tolerant mechanisms have not been fully clarified for soybean because of limitations in germplasm with flooding tolerance. This review provides an update on current biochemical and molecular networks involved in soybean tolerance against flooding stress, as well as recent developments in the area of functional genomics in terms of developing flood-tolerant soybeans. This work will expedite marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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12
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Zhong Z, Kobayashi T, Zhu W, Imai H, Zhao R, Ohno T, Rehman SU, Uemura M, Tian J, Komatsu S. Plant-derived smoke enhances plant growth through ornithine-synthesis pathway and ubiquitin-proteasome pathway in soybean. J Proteomics 2020; 221:103781. [PMID: 32294531 DOI: 10.1016/j.jprot.2020.103781] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/31/2020] [Accepted: 04/11/2020] [Indexed: 11/20/2022]
Abstract
To investigate the mechanism of promotive effect of plant-derived smoke on the soybean growth, a gel-free/label-free proteomics was performed. Smoke solutions were irrigated on soybean or supplied simultaneously with flooding stress. Morphological and physiological analyses were performed for the confirmation of proteomic result. Metabolomic change was investigated to correlate proteomic change with metabolism regulation. Under normal condition, the length of root including hypocotyl increased in soybean treated with 2000 ppm plant-derived smoke within 4 days, as well as nitric oxide content. Proteins related to protein synthesis especially arginine metabolism were altered; metabolites related to amino acid, carboxylic acids, and sugars were mostly altered. Integrated analysis of omics data indicated that plant-derived smoke regulated nitrogen‑carbon transformation through ornithine synthesis pathway and promoted soybean normal growth. Under flooding, the number of lateral roots increased with root tip degradation in soybean treated with smoke solutions. Proteins related to ubiquitin-proteasome pathway were altered and led to sacrifice-for-survival-mechanism-driven degradation of root tip in soybean, which enabled accumulation of metabolites and guaranteed lateral root development during soybean recovery after flooding. These findings suggest that plant-derived smoke improves early stage of growth in soybean with regulation of ornithine-synthesis pathway and ubiquitin-proteasome pathway. BIOLOGICAL SIGNIFICANCE: Plant-derived smoke plays a key role in crop growth, however, the understanding of soybean in response to smoke treatment remains premature. Therefore, gel-free/label-free proteomic analysis was used for comprehensive study on the dual effect of smoke to soybean under normal and flooding conditions. Under normal condition, plant-derived smoke regulated nitrogen‑carbon transformation through ornithine synthesis pathway and resulted in the increase of the length of root including hypocotyl in soybean within 4 days. Under flooding condition, plant-derived smoke induced inhibition of ubiquitin-proteasome pathway and led to sacrifice-for-survival-mechanism-driven degradation of root tip in soybean, which enabled accumulation of metabolites and promoted lateral root development during soybean recovery after flooding.
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Affiliation(s)
- Zhuoheng Zhong
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Tomoki Kobayashi
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Wei Zhu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Hiroyuki Imai
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
| | - Rongyi Zhao
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Toshihisa Ohno
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Shafiq Ur Rehman
- Department of Botany, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China.
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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13
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Feng Z, Ding C, Li W, Wang D, Cui D. Applications of metabolomics in the research of soybean plant under abiotic stress. Food Chem 2020; 310:125914. [PMID: 31835223 DOI: 10.1016/j.foodchem.2019.125914] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 09/19/2019] [Accepted: 11/14/2019] [Indexed: 12/25/2022]
Abstract
Qualitative and quantitative metabolomics analysis of all small-molecule metabolites in organisms is an emerging omics technology alongside genomics and proteomics. Plant metabolites are extremely diverse both within species and in terms of their physiological function. Plant metabolomics studies use mainly liquid/gas chromatography-mass spectrometry (LC/GC-MS) and nuclear magnetic resonance (NMR) techniques combined with chemometrics and multivariate statistical analysis to analyze plant metabolites, and metabolomics plays a key role in agricultural and food science research. In this review, we discuss the status of metabolomics in soybean in response to abiotic stresses such as drought, heat, salinity, flooding, chilling and heavy metal stresses and analyze the challenges and opportunities. Furthermore, the notable metabolites detected in response to different stresses are summarized to provide a reference for applications of metabolomics in soybean research.
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Affiliation(s)
- Zhe Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Chengqiao Ding
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Weihao Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Dachen Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Di Cui
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China.
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14
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Fukushima A, Kuroha T, Nagai K, Hattori Y, Kobayashi M, Nishizawa T, Kojima M, Utsumi Y, Oikawa A, Seki M, Sakakibara H, Saito K, Ashikari M, Kusano M. Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress. Metabolites 2020; 10:metabo10020068. [PMID: 32075002 PMCID: PMC7074043 DOI: 10.3390/metabo10020068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 02/02/2023] Open
Abstract
Rice varieties that can survive under submergence conditions respond to flooding either by enhancing internode elongation or by quiescence of shoot elongation. Despite extensive efforts to identify key metabolites triggered by complete submergence of rice possessing SUBMERGENCE 1 (SUB1) locus, metabolic responses of internode elongation of deepwater rice governed by the SNORKEL 1 and 2 genes remain elusive. This study investigated specific metabolomic responses under partial submergence (PS) to deepwater- (C9285) and non-deepwater rice cultivars (Taichung 65 (T65)). In addition, we examined the response in a near-isogenic line (NIL-12) that has a C9285 genomic fragment on chromosome 12 introgressed into the genetic background of T65. Under short-term submergence (0-24 h), metabolite profiles of C9285, NIL-12, and T65 were compared to extract significantly changed metabolites in deepwater rice under PS conditions. Comprehensive metabolite and phytohormone profiling revealed increases in metabolite levels in the glycolysis pathway in NIL-12 plants. Under long-term submergence (0-288 h), we found decreased amino acid levels. These metabolomic changes were opposite when compared to those in flood-tolerant rice with SUB1 locus. Auxin conjugate levels related to stress response decreased in NIL-12 lines relative to T65. Our analysis helped clarify the complex metabolic reprogramming in deepwater rice as an escape strategy.
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Affiliation(s)
- Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Yoko Hattori
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Tomoko Nishizawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Yoshinori Utsumi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata 997-8555, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 263-8522, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Correspondence:
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15
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Lin Y, Li W, Zhang Y, Xia C, Liu Y, Wang C, Xu R, Zhang L. Identification of Genes/Proteins Related to Submergence Tolerance by Transcriptome and Proteome Analyses in Soybean. Sci Rep 2019; 9:14688. [PMID: 31604973 PMCID: PMC6789146 DOI: 10.1038/s41598-019-50757-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 09/16/2019] [Indexed: 11/19/2022] Open
Abstract
Flooding can lead to yield reduction of soybean. Therefore, identification of flooding tolerance genes has great significance in production practice. In this study, Qihuang 34, a highly-resistant variety to flooding stress, was selected for submergence treatments. Transcriptome and proteome analyses were conducted, by which twenty-two up-regulated differentially expressed genes (DEGs)/differentially expressed proteins (DEPs) associated with five KEGG pathways were isolated. The number of the DEGs/DEPs enriched in glycolysis/gluconeogenesis was the highest. Four of these genes were confirmed by RT-qPCR, suggesting that glycolysis/gluconeogenesis may be activated to generate energy for plant survival under anaerobic conditions. Thirty-eight down-regulated DEGs/DEPs associated with six KEGG pathways were identified under submergence stress. Eight DEGs/DEPs enriched in phenylpropanoid biosynthesis were assigned to peroxidase, which catalyzes the conversion of coumaryl alcohol to hydroxy-phenyl lignin in the final step of lignin biosynthesis. Three of these genes were confirmed by RT-qPCR. The decreased expression of these genes led to the inhibition of lignin biosynthesis, which may be the cause of plant softening under submergence stress for a long period of time. This study revealed a number of up-/down-regulated pathways and the corresponding DEGs/DEPs, by which, a better understanding of the mechanisms of submergence tolerance in soybean may be achieved.
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Affiliation(s)
- Yanhui Lin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Institute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Wei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yanwei Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Changjian Xia
- Haikou Cigar Research Institute, Hainan Provincial Branch of China National Tobacco Corporation, Haikou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun Liu
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Caijie Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lifeng Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China.
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16
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Alseekh S, Bermudez L, de Haro LA, Fernie AR, Carrari F. Crop metabolomics: from diagnostics to assisted breeding. Metabolomics 2018; 14:148. [PMID: 30830402 DOI: 10.1007/s11306-018-1446-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding. AIM OF REVIEW We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality. KEY SCIENTIFIC CONCEPTS OF REVIEW Translational metabolomics applied to crop breeding programs.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Luisa Bermudez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luis Alejandro de Haro
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina.
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, 05508-090, Brazil.
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina.
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17
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Proteomic Analysis of Rapeseed Root Response to Waterlogging Stress. PLANTS 2018; 7:plants7030071. [PMID: 30205432 PMCID: PMC6160990 DOI: 10.3390/plants7030071] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 01/03/2023]
Abstract
The overall health of a plant is constantly affected by the changing and hostile environment. Due to climate change and the farming pattern of rice (Oryza sativa) and rapeseed (Brassica napus L.), stress from waterlogging poses a serious threat to productivity assurance and the yield of rapeseed in China's Yangtze River basin. In order to improve our understanding of the complex mechanisms behind waterlogging stress and identify waterlogging-responsive proteins, we firstly conducted iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomic analysis of rapeseed roots under waterlogging treatments, for both a tolerant cultivar ZS9 and sensitive cultivar GH01. A total of 7736 proteins were identified by iTRAQ, of which several hundred showed different expression levels, including 233, 365, and 326 after waterlogging stress for 4H, 8H, and 12H in ZS9, respectively, and 143, 175, and 374 after waterlogging stress for 4H, 8H, and 12H in GH01, respectively. For proteins repeatedly identified at different time points, gene ontology (GO) cluster analysis suggested that the responsive proteins of the two cultivars were both enriched in the biological process of DNA-dependent transcription and the oxidation⁻reduction process, and response to various stress and hormone stimulus, while different distribution frequencies in the two cultivars was investigated. Moreover, overlap proteins with similar or opposite tendencies of fold change between ZS9 and GH01 were observed and clustered based on the different expression ratios, suggesting the two genotype cultivars exhibited diversiform molecular mechanisms or regulation pathways in their waterlogging stress response. The following qRT-PCR (quantitative real-time polymerase chain reaction) results verified the candidate proteins at transcription levels, which were prepared for further research. In conclusion, proteins detected in this study might perform different functions in waterlogging responses and would provide information conducive to better understanding adaptive mechanisms under environmental stresses.
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18
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Li X, Rehman SU, Yamaguchi H, Hitachi K, Tsuchida K, Yamaguchi T, Sunohara Y, Matsumoto H, Komatsu S. Proteomic analysis of the effect of plant-derived smoke on soybean during recovery from flooding stress. J Proteomics 2018; 181:238-248. [PMID: 29704570 DOI: 10.1016/j.jprot.2018.04.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/13/2018] [Accepted: 04/20/2018] [Indexed: 11/26/2022]
Abstract
Flooding negatively affects the growth of soybean, whereas the plant-derived smoke enhances seedling growth of crops. To clarify the mechanism underlying the recovery from flooding stress, proteomic analysis was performed based on morphological results. Growth of soybean seedlings was inhibited under flooding stress, but it recovered after water removal following treatment with plant-derived smoke. Sucrose/starch metabolism and glycolysis were suppressed in smoke-treated flooded soybean compared to flooded soybean. The protein abundance and gene expression of O-fucosyltransferase family proteins related to the cell wall were higher in smoke-treated flooded soybean than in flooded soybean. Protein abundance and gene expression of peptidyl-prolyl cis-trans isomerase and Bowman-Birk proteinase isoinhibitor D-II were lower in smoke-treated flooded soybean than in flooded soybean. Taken together, these results suggest that plant-derived smoke enhances soybean growth during recovery from flooding stress through the balance of sucrose/starch metabolism and glycolysis. Furthermore, the accumulation of cell-wall related protein might be an important factor contributing to recovery of soybean from flooding stress. BIOLOGICAL SIGNIFICANCE Flooding negatively affects the growth of soybean, whereas the plant-derived smoke enhances the seedling growth of crops. To clarify the mechanism underlying the recovery from flooding stress, proteomic analysis of soybean with different treatments including normal conditions, flooding stress, and flooding stress in the presence of plant-derived smoke was performed in this study. Growth of soybean seedlings was inhibited under flooding stress, however, it recovered with plant-derived smoke treatment during recovery from flooding stress. Sucrose/starch metabolism and glycolysis were suppressed in smoke-treated flooded soybean compared to flooded soybean, which suggests altered sucrose/starch metabolism and glycolysis contribute to soybean growth recovery from flood stress. Furthermore, the protein abundance and gene expression of O-fucosyltransferase family proteins related to the cell wall was higher in smoke-treated flooded soybean than in flooded soybean, which might be an important factor contributing to the recovery of soybean from flooding stress.
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Affiliation(s)
- Xinyue Li
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Shafiq Ur Rehman
- Department of Botany, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Hisateru Yamaguchi
- Division of Biomedical Polymer Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Keisuke Hitachi
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Kunihiro Tsuchida
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Takuya Yamaguchi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Yukari Sunohara
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Hiroshi Matsumoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Setsuko Komatsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
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19
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Wang X, Sakata K, Komatsu S. An Integrated Approach of Proteomics and Computational Genetic Modification Effectiveness Analysis to Uncover the Mechanisms of Flood Tolerance in Soybeans. Int J Mol Sci 2018; 19:E1301. [PMID: 29701710 PMCID: PMC5983631 DOI: 10.3390/ijms19051301] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 12/21/2022] Open
Abstract
Flooding negatively affects the growth of soybeans. Recently, omic approaches have been used to study abiotic stress responses in plants. To explore flood-tolerant genes in soybeans, an integrated approach of proteomics and computational genetic modification effectiveness analysis was applied to the soybean (Glycine max L. (Merrill)). Flood-tolerant mutant and abscisic acid (ABA)-treated soybean plants were used as the flood-tolerant materials. Among the primary metabolism, glycolysis, fermentation, and tricarboxylic acid cycle were markedly affected under flooding. Fifteen proteins, which were related to the affected processes, displayed similar protein profiles in the mutant and ABA-treated soybean plants. Protein levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), aconitase 1, and 2-oxoglutarate dehydrogenase were higher in flood-tolerant materials than in wild-type soybean plants under flood conditions. These three proteins were positioned in each of the three enzyme groups revealed by our computational genetic modification effectiveness analysis, and the three proteins configured a candidate set of genes to promote flood tolerance. Additionally, transcript levels of GAPDH were similar in flood-tolerant materials and in unstressed plants. These results suggest that proteins related to energy metabolism might play an essential role to confer flood tolerance in soybeans.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
| | - Katsumi Sakata
- Department of Life Science and Informatics, Maebashi Institute of Technology, Maebashi 371-0816, Japan.
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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