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The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis. Int J Mol Sci 2022; 23:ijms232415932. [PMID: 36555572 PMCID: PMC9781956 DOI: 10.3390/ijms232415932] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.
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Chatterjee D, Wittmeyer K, Lee TF, Cui J, Yennawar NH, Yennawar HP, Meyers BC, Chopra S. Maize unstable factor for orange1 is essential for endosperm development and carbohydrate accumulation. PLANT PHYSIOLOGY 2021; 186:1932-1950. [PMID: 33905500 PMCID: PMC8331166 DOI: 10.1093/plphys/kiab183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Maize (Zea mays L.) Ufo1-1 is a spontaneous dominant mutation of the unstable factor for orange1 (ufo1). We recently cloned ufo1, which is a Poaceae-specific gene highly expressed during seed development in maize. Here, we have characterized Ufo1-1 and a loss-of-function Ds insertion allele (ufo1-Dsg) to decipher the role of ufo1 in maize. We found that both ufo1 mutant alleles impact sugars and hormones, and have defects in the basal endosperm transfer layer (BETL) and adjacent cell types. The Ufo1-1 BETL had reduced cell elongation and cell wall ingrowth, resulting in cuboidal shaped transfer cells. In contrast, the ufo1-Dsg BETL cells showed a reduced overall size with abnormal wall ingrowth. Expression analysis identified the impact of ufo1 on several genes essential for BETL development. The overexpression of Ufo1-1 in various tissues leads to ectopic phenotypes, including abnormal cell organization and stomata subsidiary cell defects. Interestingly, pericarp and leaf transcriptomes also showed that as compared with wild type, Ufo1-1 had ectopic expression of endosperm development-specific genes. This study shows that Ufo1-1 impacts the expression patterns of a wide range of genes involved in various developmental processes.
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Affiliation(s)
- Debamalya Chatterjee
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kameron Wittmeyer
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Tzuu-fen Lee
- The Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Jin Cui
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hemant P Yennawar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Blake C Meyers
- The Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65201, USA
| | - Surinder Chopra
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Jankowska U, Skupien-Rabian B, Swiderska B, Prus G, Dziedzicka-Wasylewska M, Kedracka-Krok S. Proteome Analysis of PC12 Cells Reveals Alterations in Translation Regulation and Actin Signaling Induced by Clozapine. Neurochem Res 2021; 46:2097-2111. [PMID: 34024016 PMCID: PMC8254727 DOI: 10.1007/s11064-021-03348-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/19/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022]
Abstract
Although antipsychotics are routinely used in the treatment of schizophrenia for the last decades, their precise mechanism of action is still unclear. In this study, we investigated changes in the PC12 cells’ proteome under the influence of clozapine, risperidone, and haloperidol to identify protein pathways regulated by antipsychotics. Analysis of the protein profiles in two time points: after 12 and 24 h of incubation with drugs revealed significant alterations in 510 proteins. Further canonical pathway analysis revealed an inhibition of ciliary trophic factor signaling after treatment with haloperidol and showed a decrease in acute phase response signaling in the risperidone group. Interestingly, all tested drugs have caused changes in PC12 proteome which correspond to inhibition of cytokines: tumor necrosis factor (TNF) and transforming growth factor beta 1 (TGF-β1). We also found that the 12-h incubation with clozapine caused up-regulation of protein kinase A signaling and translation machinery. After 24 h of treatment with clozapine, the inhibition of the actin cytoskeleton signaling and Rho proteins signaling was revealed. The obtained results suggest that the mammalian target of rapamycin complex 1 (mTORC1) and 2 (mTORC2) play a central role in the signal transduction of clozapine.
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Affiliation(s)
- Urszula Jankowska
- Proteomics and Mass Spectrometry Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a str, 30-387, Krakow, Poland.
| | - Bozena Skupien-Rabian
- Proteomics and Mass Spectrometry Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a str, 30-387, Krakow, Poland
| | - Bianka Swiderska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a, Warsaw, Poland
| | - Gabriela Prus
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, Poland
| | - Marta Dziedzicka-Wasylewska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, Poland
| | - Sylwia Kedracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, Poland
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Plant Volatile Organic Compounds Evolution: Transcriptional Regulation, Epigenetics and Polyploidy. Int J Mol Sci 2020; 21:ijms21238956. [PMID: 33255749 PMCID: PMC7728353 DOI: 10.3390/ijms21238956] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 12/15/2022] Open
Abstract
Volatile organic compounds (VOCs) are emitted by plants as a consequence of their interaction with biotic and abiotic factors, and have a very important role in plant evolution. Floral VOCs are often involved in defense and pollinator attraction. These interactions often change rapidly over time, so a quick response to those changes is required. Epigenetic factors, such as DNA methylation and histone modification, which regulate both genes and transcription factors, might trigger adaptive responses to these evolutionary pressures as well as regulating the rhythmic emission of VOCs through circadian clock regulation. In addition, transgenerational epigenetic effects and whole genome polyploidy could modify the generation of VOCs’ profiles of offspring, contributing to long-term evolutionary shifts. In this article, we review the available knowledge about the mechanisms that may act as epigenetic regulators of the main VOC biosynthetic pathways, and their importance in plant evolution.
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Xie Y, Zhang Y, Xie Y, Li X, Liu Y, Gao Z. Radio frequency treatment accelerates drying rates and improves vigor of corn seeds. Food Chem 2020; 319:126597. [PMID: 32187567 DOI: 10.1016/j.foodchem.2020.126597] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 11/30/2022]
Abstract
This research explored the application of combined radio frequency and hot air drying (RF-HAD) technology on corn seeds. Drying characteristics and seed vigor were investigated at different RF electrode gaps (140, 150 and 160 mm). To better demonstrate the feasibility of applying RF-HAD on corn seeds, tempering-intermittent hot air drying (HAD) was studied as a comparison. Reduced electrode gap corresponding to elevated average heating rate and power efficiency resulted in decreased seeds vigor and specific energy consumption. The assistance of RF significantly increased the drying rate of corn seeds and reduced drying duration by up to 70% compared with HAD. A higher dehydrogenase activity (DHA) but a lower germination percentage (GP) was observed in RF-HAD samples as compared with HAD ones. Corn seeds were promoted to be dormant by RF-HAD according to dormancy-breaking results and isobaric tags for relative and absolute quantification (iTRAQ) analysis.
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Affiliation(s)
- Yucen Xie
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yue Zhang
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yongkang Xie
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Xingyi Li
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yanhong Liu
- College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Zhenjiang Gao
- College of Engineering, China Agricultural University, Beijing 100083, China
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Xie G, Feng Y, Chen Y, Zhang M. Effects of 1-Methylcyclopropene (1-MCP) and Ethylene on Postharvest Lignification of Common Beans ( Phaseolus vulgaris L). ACS OMEGA 2020; 5:8659-8666. [PMID: 32337429 PMCID: PMC7178773 DOI: 10.1021/acsomega.0c00151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Postharvest 1-methylcyclopropene (1-MCP) treatment can inhibit the lignification of fruits and vegetables. The mode of action of 1-MCP is through inhibiting ethylene production, but the effect of 1-MCP and ethylene on lignification of common beans remains unknown. This work compared the effect of 0.5 μL L-1 1-MCP and 100 μL L-1 ethylene on the lignification of common beans during storage. Postharvest 1-MCP significantly inhibited the increase of the lignified cell group, sclerenchyma became thicker, vascular bundles thickened, and lignified cells grew during storage, while ethylene was the opposite. 1-MCP inhibited the increase in the respiration rate, sucrose phosphate synthase (SPS), sucrose synthase (SuSy), phenylalanine ammonialyase (PAL), cinnamyl alcohol dehydrogenase (CAD), and peroxidase (POD), whereas ethylene increased all of them. Ethylene treatment stimulated and 1-MCP inhibited the decline of reducing sugar and cellulose content. Expression of genes, including PvACO1, PvAOG1, PvSuSy2, PvPAL3, Pv4CL1, and PvCOMT1, with the lignin content being significantly increased in common beans during storage. 1-MCP treatment markedly inhibited the expression of PvACO1, PvSuSy2, PvPAL3, Pv4CL1, and PvCOMT1 genes, while strengthened the expression of PvETR1 and PvAOG1, while ethylene was the opposite. This work provides evidence that ethylene or abscisic acid (ABA) may play an important role in 1-MCP regulation of postharvest lignification in common beans and provides strategies for preserving the quality of fruits and vegetables during storage.
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Affiliation(s)
- Guofang Xie
- Key
Laboratory of Plant Resource Conservation and Germplasm Innovation
in Mountainous Region (Ministry of Education), Collaborative Innovation
Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College
of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
- Food
and Pharmaceutical Engineering Institute/Guizhou Engineering Research
Center for Fruit Processing, Guiyang University, Guiyang 550005, Guizhou, China
| | - Yingchun Feng
- Food
and Pharmaceutical Engineering Institute/Guizhou Engineering Research
Center for Fruit Processing, Guiyang University, Guiyang 550005, Guizhou, China
| | - Yao Chen
- Food
and Pharmaceutical Engineering Institute/Guizhou Engineering Research
Center for Fruit Processing, Guiyang University, Guiyang 550005, Guizhou, China
| | - Mingsheng Zhang
- Key
Laboratory of Plant Resource Conservation and Germplasm Innovation
in Mountainous Region (Ministry of Education), Collaborative Innovation
Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College
of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
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Sun Y, Liu N, Bai H, Li Y, Xue F, Ye J, Ma H, En H, Chen J. Differential proteomic analysis to identify proteins associated with beak deformity in chickens. Poult Sci 2019; 98:1833-1841. [PMID: 30452707 DOI: 10.3382/ps/pey519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/31/2018] [Indexed: 11/20/2022] Open
Abstract
The beak is the dominant avian facial feature, and beak deformity occurs in 0.5 to 2.5% of some indigenous chicken breeds, resulting in difficulties when eating, drinking, and performing natural behaviors. Previous studies on beak deformity focused largely on candidate molecules associated with skeletogenic development, providing insight into the molecular and genetic underpinnings of beak deformity. The present study was performed to identify candidate proteins related to this malformation in chickens. Three 12-day-old Beijing-You roosters with deformed beaks (D1, D2, and D3) and 3 with normal beaks (N1, N2, and N3) were used, and total beak proteins were isolated and subjected to standard iTRAQ labeling, strong cation-exchange chromatography, and liquid chromatography-tandem mass spectrometry. Mascot 2.3.02 was used to identify and quantitatively analyze proteins. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were used to identify functions and metabolic pathways of differentially expressed proteins, and key proteins were further validated using western blot. A total of 2,370, 2,401, and 2,378 proteins were reliably quantified in 3 biological replicates, among which, 2,345 were common to all, and 92 were differentially expressed between the 2 groups. These included 37 upregulated and 55 downregulated proteins in deformed beaks. Pentraxin-related protein 3, hemopexin, lipoprotein lipase, retinoid-binding protein 7, and biliverdin reductase A were downregulated in all 3 sets, while parvalbumin, peptidyl-prolyl cis-trans isomerase, and ubiquitin-fold modifier 1 were upregulated. Pathway analysis returned no enriched pathways, and western blot validated the iTRAQ results. Parvalbumin and lipoprotein lipase could be firstly selected as key proteins in view of their known functions in regulating the buffering of intracellular free Ca2+ in both cartilage and bone cells and bone mass, respectively. Their potential roles in beak deformity, however, deserve further studies. In summary, the onset of beak deformity could be very complex, and this study will be helpful for future investigation of mechanistic explanation for beak deformity.
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Affiliation(s)
- Yanyan Sun
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nian Liu
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hao Bai
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunlei Li
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fuguang Xue
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianhua Ye
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hui Ma
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - He En
- Chifeng Agriculture and Animal Husbandry Science Academy, Chifeng 024031, Inner Mongolia, China
| | - Jilan Chen
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Fan Y, Chen J, Wang Z, Tan T, Li S, Li J, Wang B, Zhang J, Cheng Y, Wu X, Yang W, Yang F. Soybean (Glycine max L. Merr.) seedlings response to shading: leaf structure, photosynthesis and proteomic analysis. BMC PLANT BIOLOGY 2019; 19:34. [PMID: 30665369 PMCID: PMC6341755 DOI: 10.1186/s12870-019-1633-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/07/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Intercropping and close planting are important cultivation methods that increase soybean yield in agricultural production. However, plant shading is a major abiotic stress factor that influences soybean growth and development. Although shade affects leaf morphological parameters and decreases leaf photosynthesis capacity, information on the responses of soybean leaf photosynthesis to shading at proteomic level is still lacking. RESULTS Compared with leaves under normal light (CK) treatment, leaves under shading treatment exhibited decreased palisade and spongy tissue thicknesses but significantly increased cell gap. Although shade increased the number of the chloroplast, the thickness of the grana lamella and the photosynthetic pigments per unit mass, but the size of the chloroplast and starch grains and the rate of net photosynthesis decreased compared with those of under CK treatment. A total of 248 differentially expressed proteins, among which 138 were upregulated, and 110 were downregulated, in soybean leaves under shading and CK treatments were detected via isobaric tags for relative and absolute quantification labeling in the three biological repeats. Differentially expressed proteins were classified into 3 large and 20 small groups. Most proteins involved in porphyrin and chlorophyll metabolism, photosynthesis-antenna proteins and carbon fixation in photosynthetic organisms were upregulated. By contrast, proteins involved in photosynthesis were downregulated. The gene family members corresponding to differentially expressed proteins, including protochlorophyllide reductase (Glyma06g247100), geranylgeranyl hydrogenase (Ggh), LHCB1 (Lhcb1) and ferredoxin (N/A) involved in the porphyrin and chlorophyll metabolism, photosynthesis-antenna proteins and photosynthesis pathway were verified with real-time qPCR. The results showed that the expression patterns of the genes were consistent with the expression patterns of the corresponding proteins. CONCLUSIONS This study combined the variation of the soybean leaf structure and differentially expressed proteins of soybean leaves under shading. These results demonstrated that shade condition increased the light capture efficiency of photosystem II (PSII) in soybean leaves but decreased the capacity from PSII transmitted to photosystem II (PSI). This maybe the major reason that the photosynthetic capacity was decreased in shading.
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Affiliation(s)
- Yuanfang Fan
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Junxu Chen
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Zhonglin Wang
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Tingting Tan
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
| | - Shenglan Li
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
| | - Jiafeng Li
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
| | - Beibei Wang
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Jiawei Zhang
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Yajiao Cheng
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Xiaoling Wu
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
| | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, 611130 People’s Republic of China
| | - Feng Yang
- College of Agronomy, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu, 611130 People’s Republic of China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130 People’s Republic of China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, 611130 People’s Republic of China
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Response mechanisms induced by exposure to high temperature in anthers from thermo-tolerant and thermo-sensitive tomato plants: A proteomic perspective. PLoS One 2018; 13:e0201027. [PMID: 30024987 PMCID: PMC6053223 DOI: 10.1371/journal.pone.0201027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/07/2018] [Indexed: 11/19/2022] Open
Abstract
Constant global warming is one of the most detrimental environmental factors for agriculture causing significant losses in productivity as heat stress (HS) conditions damage plant growth and reproduction. In flowering plants such as tomato, HS has drastic repercussions on development and functionality of male reproductive organs and pollen. Response mechanisms to HS in tomato anthers and pollen have been widely investigated by transcriptomics; on the contrary, exhaustive proteomic evidences are still lacking. In this context, a differential proteomic study was performed on tomato anthers collected from two genotypes (thermo-tolerant and thermo-sensitive) to explore stress response mechanisms and identify proteins possibly associated to thermo-tolerance. Results showed that HS mainly affected energy and amino acid metabolism and nitrogen assimilation and modulated the expression of proteins involved in assuring protein quality and ROS detoxification. Moreover, proteins potentially associated to thermo-tolerant features, such as glutamine synthetase, S-adenosylmethionine synthase and polyphenol oxidase, were identified.
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Eldakak M, Das A, Zhuang Y, Rohila JS, Glover K, Yen Y. A Quantitative Proteomics View on the Function of Qfhb1, a Major QTL for Fusarium Head Blight Resistance in Wheat. Pathogens 2018; 7:E58. [PMID: 29932155 PMCID: PMC6161305 DOI: 10.3390/pathogens7030058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 12/18/2022] Open
Abstract
Fusarium head blight (FHB) is a highly detrimental disease of wheat. A quantitative trait locus for FHB resistance, Qfhb1, is the most utilized source of resistance in wheat-breeding programs, but very little is known about its resistance mechanism. In this study, we elucidated a prospective FHB resistance mechanism by investigating the proteomic signatures of Qfhb1 in a pair of contrasting wheat near-isogenic lines (NIL) after 24 h of inoculation of wheat florets by Fusarium graminearum. Statistical comparisons of the abundances of protein spots on the 2D-DIGE gels of contrasting NILs (fhb1+ NIL = Qfhb1 present; fhb1- NIL = Qfhb1 absent) enabled us to select 80 high-ranking differentially accumulated protein (DAP) spots. An additional evaluation confirmed that the DAP spots were specific to the spikelet from fhb1- NIL (50 spots), and fhb1+ NIL (seven spots). The proteomic data also suggest that the absence of Qfhb1 makes the fhb1- NIL vulnerable to Fusarium attack by constitutively impairing several mechanisms including sucrose homeostasis by enhancing starch synthesis from sucrose. In the absence of Qfhb1, Fusarium inoculations severely damaged photosynthetic machinery; altered the metabolism of carbohydrates, nitrogen and phenylpropanoids; disrupted the balance of proton gradients across relevant membranes; disturbed the homeostasis of many important signaling molecules induced the mobility of cellular repair; and reduced translational activities. These changes in the fhb1- NIL led to strong defense responses centered on the hypersensitive response (HSR), resulting in infected cells suicide and the consequent initiation of FHB development. Therefore, the results of this study suggest that Qfhb1 largely functions to either alleviate HSR or to manipulate the host cells to not respond to Fusarium infection.
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Affiliation(s)
- Moustafa Eldakak
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA.
- Genetics Department, College of Agriculture, Alexandria University, Alexandria 21526, Egypt.
| | - Aayudh Das
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA.
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA.
| | - Yongbin Zhuang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA.
- College of Agronomy, Shandong Agricultural University, Taian 271018, China.
| | - Jai S Rohila
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA.
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
- Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA.
| | - Karl Glover
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
| | - Yang Yen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA.
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Yang C, Liang Y, Qiu D, Zeng H, Yuan J, Yang X. Lignin metabolism involves Botrytis cinerea BcGs1- induced defense response in tomato. BMC PLANT BIOLOGY 2018; 18:103. [PMID: 29866036 DOI: 10.1186/s12870-018-1319-1310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 05/24/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND BcGs1, a cell wall-degrading enzyme (CWDE), was originally derived from Botrytis cinerea. Our previous study revealed that BcGs1 could trigger defense responses and protect plants against various pathogens. We researched the defense response mechanism underlying this BcGs1 elicitation in tomato. RESULTS We revealed that the two domains were required for BcGs1's full necrosis activity. According to analysis and quantitative real-time PCR of the up-regulated proteins and genes filtered by iTRAQ-based quantitative proteome approach, oxidative metabolism and phenylpropanoid metabolism were speculated to be involved in BcGs1-triggered defense response in tomato. Furthermore, experimental evidence showed that BcGs1 triggered reactive oxygen species (ROS) burst and increased the level of phenylalanine-ammonia lyase (PAL) and peroxidase (POD) enzyme activity, as well as lignin accumulation. Moreover, histochemical analysis revealed that infiltration of BcGs1 in tomato leaves exhibited cell wall thickening compared with untreated plants. CONCLUSIONS The results suggested that BcGs1 activated the basal defense response included lignin metabolism contributed to BcGs1-induced resistance to Botrytis. cinerea infection in tomato.
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Affiliation(s)
- Chenyu Yang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081, China
| | - Yingbo Liang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081, China
| | - Dewen Qiu
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081, China
| | - Hongmei Zeng
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081, China
| | - Jingjing Yuan
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081, China
| | - Xiufen Yang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081, China.
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Yang C, Liang Y, Qiu D, Zeng H, Yuan J, Yang X. Lignin metabolism involves Botrytis cinerea BcGs1- induced defense response in tomato. BMC PLANT BIOLOGY 2018; 18:103. [PMID: 29866036 PMCID: PMC5987389 DOI: 10.1186/s12870-018-1319-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 05/24/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND BcGs1, a cell wall-degrading enzyme (CWDE), was originally derived from Botrytis cinerea. Our previous study revealed that BcGs1 could trigger defense responses and protect plants against various pathogens. We researched the defense response mechanism underlying this BcGs1 elicitation in tomato. RESULTS We revealed that the two domains were required for BcGs1's full necrosis activity. According to analysis and quantitative real-time PCR of the up-regulated proteins and genes filtered by iTRAQ-based quantitative proteome approach, oxidative metabolism and phenylpropanoid metabolism were speculated to be involved in BcGs1-triggered defense response in tomato. Furthermore, experimental evidence showed that BcGs1 triggered reactive oxygen species (ROS) burst and increased the level of phenylalanine-ammonia lyase (PAL) and peroxidase (POD) enzyme activity, as well as lignin accumulation. Moreover, histochemical analysis revealed that infiltration of BcGs1 in tomato leaves exhibited cell wall thickening compared with untreated plants. CONCLUSIONS The results suggested that BcGs1 activated the basal defense response included lignin metabolism contributed to BcGs1-induced resistance to Botrytis. cinerea infection in tomato.
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Affiliation(s)
- Chenyu Yang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081 China
| | - Yingbo Liang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081 China
| | - Dewen Qiu
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081 China
| | - Hongmei Zeng
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081 China
| | - Jingjing Yuan
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081 China
| | - Xiufen Yang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests/ Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture Institute of Plant protection, Chinese Academy of Agricultural science, No. 12 Zhong-guan-cun South Street, Beijing, 100081 China
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13
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iTRAQ-based quantitative proteomic analysis reveals pathways associated with re-establishing desiccation tolerance in germinating seeds of Caragana korshinskii Kom. J Proteomics 2018; 179:1-16. [DOI: 10.1016/j.jprot.2018.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/09/2018] [Accepted: 01/17/2018] [Indexed: 01/04/2023]
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You C, Chen L, He H, Wu L, Wang S, Ding Y, Ma C. iTRAQ-based proteome profile analysis of superior and inferior Spikelets at early grain filling stage in japonica Rice. BMC PLANT BIOLOGY 2017; 17:100. [PMID: 28592253 PMCID: PMC5463490 DOI: 10.1186/s12870-017-1050-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/29/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Large-panicle rice varieties often fail to achieve their yield potential due to poor grain filling of late-flowering inferior spikelets (IS). The physiological and molecular mechanisms of poor IS grain filling, and whether an increase in assimilate supply could regulate protein abundance and consequently improve IS grain filling for japonica rice with large panicles is still partially understood. RESULTS A field experiment was performed with two spikelet removal treatments at anthesis in the large-panicle japonica rice line W1844, including removal of the top 1/3 of spikelets (T1) and removal of the top 2/3 of spikelets (T2), with no spikelet removal as a control (T0). The size, weight, setting rate, and grain filling rate of IS were significantly increased after spikelet removing. The biological functions of the differentially expressed proteins (DEPs) between superior and inferior spikelets as well as the response of IS to the removal of superior spikelets (SS) were investigated by using iTRAQ at 10 days post anthesis. A total of 159, 87, and 28 DEPs were identified from group A (T0-SS/T0-IS), group B (T0-SS/T2-IS), and group C (T2-IS/T0-IS), respectively. Among these, 104, 63, and 22 proteins were up-regulated, and 55, 24, and 6 proteins were down-regulated, respectively. Approximately half of these DEPs were involved in carbohydrate metabolism (sucrose-to-starch metabolism and energy metabolism) and protein metabolism (protein synthesis, folding, degradation, and storage). CONCLUSIONS Reduced endosperm cell division and decreased activities of key enzymes associated with sucrose-starch metabolism and nitrogen metabolism are mainly attributed to the poor sink strength of IS. In addition, due to weakened photosynthesis and respiration, IS are unable to obtain a timely supply of materials and energy after fertilization, which might be resulted in the stagnation of IS development. Finally, an increased abundance of 14-3-3 protein in IS could be involved in the inhibition of starch synthesis. The removal of SS contributed to transfer of assimilates to IS and enhanced enzymatic activities of carbon metabolism (sucrose synthase, starch branching enzyme, soluble starch synthase, and pullulanase) and nitrogen metabolism (aspartate amino transferase and alanine amino transferase), promoting starch and protein synthesis in IS. In addition, improvements in energy metabolism (greater abundance of pyrophosphate-fructose 6-phosphate 1-phosphotransferase) might be played a vital role in inducing the initiation of grain filling. These results collectively demonstrate that carbohydrate supply is the main cause of poor IS grain filling.
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Affiliation(s)
- Cuicui You
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Lin Chen
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Haibing He
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Liquan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Shaohua Wang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
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15
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Characterization of factors underlying the metabolic shifts in developing kernels of colored maize. Sci Rep 2016; 6:35479. [PMID: 27739524 PMCID: PMC5064397 DOI: 10.1038/srep35479] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/30/2016] [Indexed: 12/25/2022] Open
Abstract
Elucidation of the metabolic pathways determining pigmentation and their underlying regulatory mechanisms in maize kernels is of high importance in attempts to improve the nutritional composition of our food. In this study, we compared dynamics in the transcriptome and metabolome between colored SW93 and white SW48 by integrating RNA-Seq and non-targeted metabolomics. Our data revealed that expression of enzyme coding genes and levels of primary metabolites decreased gradually from 11 to 21 DAP, corresponding well with the physiological change of developing maize kernels from differentiation through reserve accumulation to maturation, which was cultivar independent. A remarkable up-regulation of anthocyanin and phlobaphene pathway distinguished SW93 from SW48, in which anthocyanin regulating transcriptional factors (R1 and C1), enzyme encoding genes involved in both pathways and corresponding metabolic intermediates were up-regulated concurrently in SW93 but not in SW48. The shift from the shikimate pathway of primary metabolism to the flavonoid pathway of secondary metabolism, however, appears to be under posttranscriptional regulation. This study revealed the link between primary metabolism and kernel coloration, which facilitate further study to explore fundamental questions regarding the evolution of seed metabolic capabilities as well as their potential applications in maize improvement regarding both staple and functional foods.
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Huang Y, Ma HY, Huang W, Wang F, Xu ZS, Xiong AS. Comparative proteomic analysis provides novel insight into the interaction between resistant vs susceptible tomato cultivars and TYLCV infection. BMC PLANT BIOLOGY 2016; 16:162. [PMID: 27436092 PMCID: PMC4952150 DOI: 10.1186/s12870-016-0819-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/24/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Tomato yellow leaf curl virus (TYLCV) is a member of the family Geminiviridae, genus Begomovirus. The virus is a widespread plant virus that causes important economic losses in tomatoes. Genetic engineering strategies have increasingly been adopted to improve the resistance of tomatoes to TYLCV. RESULTS In this study, a proteomic approach was used to investigate the molecular mechanisms involved in tomato leaf defense against TYLCV infection. Proteins extracted from leaves of resistant tomato cultivar 'Zheza-301' and susceptible cultivar 'Jinpeng-1' after TYLCV infection were analyzed using two-dimensional gel electrophoresis. Eighty-six differentially expressed proteins were identified and classified into seven groups based on their functions. For several of the proteins, including CDC48, CHI and HSC70, expression patterns measured using quantitative real-time PCR differed from the results of the proteomic analysis. A putative interaction network between tomato leaves and TYLCV infection provides us with important information about the cellular activities that are involved in the response to TYLCV infection. CONCLUSIONS We conducted a comparative proteomic study of TYLCV infection in resistant and susceptible tomato cultivars. The proteins identified in our work show a variety of functions and expression patterns in the process of tomato-TYLCV interaction, and these results contribute to our understanding of the mechanism underlying TYLCV resistance in tomatoes at the protein level.
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Affiliation(s)
- Ying Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Hong-Yu Ma
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Wei Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, Jiangsu, China.
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17
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Balsamo GM, de Mello CS, Arisi ACM. Proteome Comparison of Grains from Two Maize Genotypes, with Colorless Kernel Pericarp (P1-ww) and Red Kernel Pericarp (P1-rr). FOOD BIOTECHNOL 2016. [DOI: 10.1080/08905436.2016.1166382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Cabezón V, Vialás V, Gil-Bona A, Reales-Calderón JA, Martínez-Gomariz M, Gutiérrez-Blázquez D, Monteoliva L, Molero G, Ramsdale M, Gil C. Apoptosis of Candida albicans during the Interaction with Murine Macrophages: Proteomics and Cell-Death Marker Monitoring. J Proteome Res 2016; 15:1418-34. [PMID: 27048922 DOI: 10.1021/acs.jproteome.5b00913] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Macrophages may induce fungal apoptosis to fight against C. albicans, as previously hypothesized by our group. To confirm this hypothesis, we analyzed proteins from C. albicans cells after 3 h of interaction with macrophages using two quantitative proteomic approaches. A total of 51 and 97 proteins were identified as differentially expressed by DIGE and iTRAQ, respectively. The proteins identified and quantified were different, with only seven in common, but classified in the same functional categories. The analyses of their functions indicated that an increase in the metabolism of amino acids and purine nucleotides were taking place, while the glycolysis and translation levels dropped after 3 h of interaction. Also, the response to oxidative stress and protein translation were reduced. In addition, seven substrates of metacaspase (Mca1) were identified (Cdc48, Fba1, Gpm1, Pmm1, Rct1, Ssb1, and Tal1) as decreased in abundance, plus 12 proteins previously described as related to apoptosis. Besides, the monitoring of apoptotic markers along 24 h of interaction (caspase-like activity, TUNEL assay, and the measurement of ROS and cell examination by transmission electron microscopy) revealed that apoptotic processes took place for 30% of the fungal cells, thus supporting the proteomic results and the hypothesis of macrophages killing C. albicans by apoptosis.
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Affiliation(s)
- Virginia Cabezón
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid , Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Vital Vialás
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid , Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain.,Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) , Ctra. de Colmenar Viejo, 28034 Madrid, Spain
| | - Ana Gil-Bona
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid , Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain.,Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) , Ctra. de Colmenar Viejo, 28034 Madrid, Spain
| | - Jose A Reales-Calderón
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid , Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain.,Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) , Ctra. de Colmenar Viejo, 28034 Madrid, Spain
| | - Montserrat Martínez-Gomariz
- Unidad de Proteómica, Universidad Complutense de Madrid-Parque Científico de Madrid (UCM-PCM) , 28040 Madrid, Spain
| | - Dolores Gutiérrez-Blázquez
- Unidad de Proteómica, Universidad Complutense de Madrid-Parque Científico de Madrid (UCM-PCM) , 28040 Madrid, Spain
| | - Lucía Monteoliva
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid , Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain.,Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) , Ctra. de Colmenar Viejo, 28034 Madrid, Spain
| | - Gloria Molero
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid , Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain.,Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) , Ctra. de Colmenar Viejo, 28034 Madrid, Spain
| | - Mark Ramsdale
- Biosciences, University of Exeter , Geoffrey Pope Building, Exeter, Devon, EX4 4QD, United Kingdom
| | - Concha Gil
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid , Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain.,Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) , Ctra. de Colmenar Viejo, 28034 Madrid, Spain
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19
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Paudel B, Das A, Tran M, Boe A, Palmer NA, Sarath G, Gonzalez-Hernandez JL, Rushton PJ, Rohila JS. Proteomic Responses of Switchgrass and Prairie Cordgrass to Senescence. FRONTIERS IN PLANT SCIENCE 2016; 7:293. [PMID: 27014316 PMCID: PMC4789367 DOI: 10.3389/fpls.2016.00293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/24/2016] [Indexed: 05/03/2023]
Abstract
Senescence in biofuel grasses is a critical issue because early senescence decreases potential biomass production by limiting aerial growth and development. 2-Dimensional, differential in-gel electrophoresis (2D-DIGE) followed by mass spectrometry of selected protein spots was used to evaluate differences between leaf proteomes of early (ES)- and late- senescing (LS) genotypes of Prairie cordgrass (ES/LS PCG) and switchgrass (ES/LS SG), just before and after senescence was initiated. Analysis of the manually filtered and statistically evaluated data indicated that 69 proteins were significantly differentially abundant across all comparisons, and a majority (41%) were associated with photosynthetic processes as determined by gene ontology analysis. Ten proteins were found in common between PCG and SG, and nine and 18 proteins were unique to PCG and SG respectively. Five of the 10 differentially abundant spots common to both species were increased in abundance, and five were decreased in abundance. Leaf proteomes of the LS genotypes of both grasses analyzed before senescence contained significantly higher abundances of a 14-3-3 like protein and a glutathione-S-transferase protein when compared to the ES genotypes, suggesting differential cellular metabolism in the LS vs. the ES genotypes. The higher abundance of 14-3-3 like proteins may be one factor that impacts the senescence process in both LS PCG and LS SG. Aconitase dehydratase was found in greater abundance in all four genotypes after the onset of senescence, consistent with literature reports from genetic and transcriptomic studies. A Rab protein of the Ras family of G proteins and an s-adenosylmethionine synthase were more abundant in ES PCG when compared with the LS PCG. In contrast, several proteins associated with photosynthesis and carbon assimilation were detected in greater abundance in LS PCG when compared to ES PCG, suggesting that a loss of these proteins potentially contributed to the ES phenotype in PCG. Overall, this study provides important data that can be utilized toward delaying senescence in both PCG and SG, and sets a foundational base for future improvement of perennial grass germplasm for greater aerial biomass productivity.
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Affiliation(s)
- Bimal Paudel
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, SD, USA
| | - Aayudh Das
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, SD, USA
| | - Michaellong Tran
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, SD, USA
| | - Arvid Boe
- Department of Plant Science, South Dakota State UniversityBrookings, SD, USA
| | - Nathan A. Palmer
- Grain, Forage and Bioenergy Research Unit, United States Department of Agriculture - Agricultural Research ServiceLincoln, NE, USA
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit, United States Department of Agriculture - Agricultural Research ServiceLincoln, NE, USA
| | | | | | - Jai S. Rohila
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, SD, USA
- Department of Plant Science, South Dakota State UniversityBrookings, SD, USA
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20
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Das A, Eldakak M, Paudel B, Kim DW, Hemmati H, Basu C, Rohila JS. Leaf Proteome Analysis Reveals Prospective Drought and Heat Stress Response Mechanisms in Soybean. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6021047. [PMID: 27034942 PMCID: PMC4808539 DOI: 10.1155/2016/6021047] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/01/2016] [Indexed: 12/26/2022]
Abstract
Drought and heat are among the major abiotic stresses that affect soybean crops worldwide. During the current investigation, the effect of drought, heat, and drought plus heat stresses was compared in the leaves of two soybean varieties, Surge and Davison, combining 2D-DIGE proteomic data with physiology and biochemical analyses. We demonstrated how 25 differentially expressed photosynthesis-related proteins affect RuBisCO regulation, electron transport, Calvin cycle, and carbon fixation during drought and heat stress. We also observed higher abundance of heat stress-induced EF-Tu protein in Surge. It is possible that EF-Tu might have activated heat tolerance mechanisms in the soybean. Higher level expressions of heat shock-related protein seem to be regulating the heat tolerance mechanisms. This study identifies the differential expression of various abiotic stress-responsive proteins that regulate various molecular processes and signaling cascades. One inevitable outcome from the biochemical and proteomics assays of this study is that increase of ROS levels during drought stress does not show significant changes at the phenotypic level in Davison and this seems to be due to a higher amount of carbonic anhydrase accumulation in the cell which aids the cell to become more resistant to cytotoxic concentrations of H2O2.
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Affiliation(s)
- Aayudh Das
- Department of Biology & Microbiology, South Dakota State University, Brookings, SD 57007, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840, USA
| | - Moustafa Eldakak
- Department of Biology & Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Bimal Paudel
- Department of Biology & Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Dea-Wook Kim
- National Institute of Crop Science, Rural Development Administration (RDA), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Homa Hemmati
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
| | - Chhandak Basu
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
| | - Jai S. Rohila
- Department of Biology & Microbiology, South Dakota State University, Brookings, SD 57007, USA
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21
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Mattei B, Spinelli F, Pontiggia D, De Lorenzo G. Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1107. [PMID: 27532006 PMCID: PMC4969306 DOI: 10.3389/fpls.2016.01107] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/12/2016] [Indexed: 05/03/2023]
Abstract
Early changes in the Arabidopsis thaliana membrane phosphoproteome in response to oligogalacturonides (OGs), a class of plant damage-associated molecular patterns (DAMPs), were analyzed by two complementary proteomic approaches. Differentially phosphorylated sites were determined through phosphopeptide enrichment followed by LC-MS/MS using label-free quantification; differentially phosphorylated proteins were identified by 2D-DIGE combined with phospho-specific fluorescent staining (phospho-DIGE). This large-scale phosphoproteome analysis of early OG-signaling enabled us to determine 100 regulated phosphosites using LC-MS/MS and 46 differential spots corresponding to 34 pdhosphoproteins using phospho-DIGE. Functional classification showed that the OG-responsive phosphoproteins include kinases, phosphatases and receptor-like kinases, heat shock proteins (HSPs), reactive oxygen species (ROS) scavenging enzymes, proteins related to cellular trafficking, transport, defense and signaling as well as novel candidates for a role in immunity, for which elicitor-induced phosphorylation changes have not been shown before. A comparison with previously identified elicitor-regulated phosphosites shows only a very limited overlap, uncovering the immune-related regulation of 70 phosphorylation sites and revealing novel potential players in the regulation of elicitor-dependent immunity.
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22
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Martínez-Esteso MJ, Martínez-Márquez A, Sellés-Marchart S, Morante-Carriel JA, Bru-Martínez R. The role of proteomics in progressing insights into plant secondary metabolism. FRONTIERS IN PLANT SCIENCE 2015; 6:504. [PMID: 26217358 PMCID: PMC4493368 DOI: 10.3389/fpls.2015.00504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 06/23/2015] [Indexed: 05/29/2023]
Abstract
The development of omics has enabled the genome-wide exploration of all kinds of biological processes at the molecular level. Almost every field of plant biology has been analyzed at the genomic, transcriptomic and proteomic level. Here we focus on the particular contribution that proteomic technologies have made in progressing knowledge and characterising plant secondary metabolism (SM) pathways since early expectations were created 15 years ago. We analyzed how three major issues in the proteomic analysis of plant SM have been implemented in various research studies. These issues are: (i) the selection of a suitable plant material rich in secondary metabolites of interest, such as specialized tissues and organs, and in vitro cell cultures; (ii) the proteomic strategy to access target proteins, either a comprehensive or a differential analysis; (iii) the proteomic approach, represented by the hypothesis-free discovery proteomics and the hypothesis-driven targeted proteomics. We also examine to what extent the most-advanced technologies have been incorporated into proteomic research in plant SM and highlight some cutting edge techniques that would strongly benefit the progress made in this field.
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Affiliation(s)
- María J. Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies “Ramon Margalef”, University of Alicante, Alicante, Spain
| | - Ascensión Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies “Ramon Margalef”, University of Alicante, Alicante, Spain
| | - Susana Sellés-Marchart
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies “Ramon Margalef”, University of Alicante, Alicante, Spain
- Biotechnology and Molecular Biology Group, Quevedo State Technical University, Quevedo, Ecuador
| | - Jaime A. Morante-Carriel
- Proteomics and Genomics Division, Research Technical Facility, University of Alicante, Alicante, Spain
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Multidisciplinary Institute for Environmental Studies “Ramon Margalef”, University of Alicante, Alicante, Spain
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A sorghum MYB transcription factor induces 3-deoxyanthocyanidins and enhances resistance against leaf blights in maize. Molecules 2015; 20:2388-404. [PMID: 25647576 PMCID: PMC6272393 DOI: 10.3390/molecules20022388] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/22/2015] [Indexed: 11/23/2022] Open
Abstract
Sorghum responds to the ingress of the fungal pathogen Colletotrichum sublineolum through the biosynthesis of 3-deoxyanthocyanidin phytoalexins at the site of primary infection. Biosynthesis of 3-deoxyanthocyanidins in sorghum requires a MYB transcription factor encoded by yellow seed1 (y1), an orthologue of the maize gene pericarp color1 (p1). Maize lines with a functional p1 and flavonoid structural genes do not produce foliar 3-deoxyanthocyanidins in response to fungal ingress. To perform a comparative metabolic analysis of sorghum and maize 3-deoxyanthocyanidin biosynthetic pathways, we developed transgenic maize lines expressing the sorghum y1 gene. In maize, the y1 transgene phenocopied p1-regulated pigment accumulation in the pericarp and cob glumes. LC-MS profiling of fungus-challenged Y1-maize leaves showed induction of 3-deoxyanthocyanidins, specifically luteolinidin. Y1-maize plants also induced constitutive and higher levels of flavonoids in leaves. In response to Colletotrichum graminicola, Y1-maize showed a resistance response.
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Hayashi G, Moro CF, Rohila JS, Shibato J, Kubo A, Imanaka T, Kimura S, Ozawa S, Fukutani S, Endo S, Ichikawa K, Agrawal GK, Shioda S, Hori M, Fukumoto M, Rakwal R. 2D-DIGE-based proteome expression changes in leaves of rice seedlings exposed to low-level gamma radiation at Iitate village, Fukushima. PLANT SIGNALING & BEHAVIOR 2015; 10:e1103406. [PMID: 26451896 PMCID: PMC4854340 DOI: 10.1080/15592324.2015.1103406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The present study continues our previous research on investigating the biological effects of low-level gamma radiation in rice at the heavily contaminated Iitate village in Fukushima, by extending the experiments to unraveling the leaf proteome. 14-days-old plants of Japonica rice (Oryza sativa L. cv. Nipponbare) were subjected to gamma radiation level of upto 4 µSv/h, for 72 h. Following exposure, leaf samples were taken from the around 190 µSv/3 d exposed seedling and total proteins were extracted. The gamma irradiated leaf and control leaf (harvested at the start of the experiment) protein lysates were used in a 2-D differential gel electrophoresis (2D-DIGE) experiment using CyDye labeling in order to asses which spots were differentially represented, a novelty of the study. 2D-DIGE analysis revealed 91 spots with significantly different expression between samples (60 positive, 31 negative). MALDI-TOF and TOF/TOF mass spectrometry analyses revealed those as comprising of 59 different proteins (50 up-accumulated, 9 down-accumulated). The identified proteins were subdivided into 10 categories, according to their biological function, which indicated that the majority of the differentially expressed proteins consisted of the general (non-energy) metabolism and stress response categories. Proteome-wide data point to some effects of low-level gamma radiation exposure on the metabolism of rice leaves.
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Affiliation(s)
- Gohei Hayashi
- Research Reactor Institute; Kyoto University; Osaka, Japan
- Institute of Development; Aging and Cancer; Tohoku University; Sendai, Japan
| | - Carlo F Moro
- Department of Anatomy; School of Medicine; Showa University; Tokyo, Japan
| | - Jai Singh Rohila
- Department of Biology and Microbiology; South Dakota State University; SD USA
| | - Junko Shibato
- Department of Anatomy; School of Medicine; Showa University; Tokyo, Japan
- Global Research Center for Innovative Life Science; School of Pharmacy and Pharmaceutical Sciences; Hoshi University; Tokyo, Japan
| | - Akihiro Kubo
- Environmental Stress Mechanisms Section; Center for Environmental Biology and Ecosystem Studies; National Institute for Environmental Studies; Tsukuba, Ibaraki, Japan
| | | | - Shinzo Kimura
- Laboratory of International Epidemiology; Center for International Cooperation; Dokkyo Medical University; Tochigi, Japan
| | | | | | - Satoru Endo
- Department of Quantam Energy Applications; Graduate School of Engineering; Hiroshima University; Higashi-Hiroshima, Japan
| | | | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu, Nepal
- GRADE (Global Research Arch for Developing Education) Academy Pvt. Ltd; Birgunj, Nepal
| | - Seiji Shioda
- Department of Anatomy; School of Medicine; Showa University; Tokyo, Japan
- Global Research Center for Innovative Life Science; School of Pharmacy and Pharmaceutical Sciences; Hoshi University; Tokyo, Japan
| | | | - Manabu Fukumoto
- Institute of Development; Aging and Cancer; Tohoku University; Sendai, Japan
| | - Randeep Rakwal
- Department of Anatomy; School of Medicine; Showa University; Tokyo, Japan
- Global Research Center for Innovative Life Science; School of Pharmacy and Pharmaceutical Sciences; Hoshi University; Tokyo, Japan
- Faculty of Health and Sport Sciences & Tsukuba International Academy for Sport Studies (TIAS); University of Tsukuba; Tsukuba, Ibaraki, Japan
- Correspondence to: Randeep Rakwal;
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Dong M, Gu J, Zhang L, Chen P, Liu T, Deng J, Lu H, Han L, Zhao B. Comparative proteomics analysis of superior and inferior spikelets in hybrid rice during grain filling and response of inferior spikelets to drought stress using isobaric tags for relative and absolute quantification. J Proteomics 2014; 109:382-99. [DOI: 10.1016/j.jprot.2014.07.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/27/2014] [Accepted: 07/04/2014] [Indexed: 01/30/2023]
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Gupta D, Eldakak M, Rohila JS, Basu C. Biochemical analysis of 'kerosene tree' Hymenaea courbaril L. under heat stress. PLANT SIGNALING & BEHAVIOR 2014; 9:e972851. [PMID: 25482765 PMCID: PMC4623024 DOI: 10.4161/15592316.2014.972851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 05/20/2023]
Abstract
Hymenaea courbaril or jatoba is a tropical tree known for its medically important secondary metabolites production. Considering climate change, the goal of this study was to investigate differential expression of proteins and lipids produced by this tree under heat stress conditions. Total lipid was extracted from heat stressed plant leaves and various sesquiterpenes produced by the tree under heat stress were identified. Gas chromatographic and mass spectrometric analysis were used to study lipid and volatile compounds produced by the plant. Several volatiles, isoprene, 2-methyl butanenitrile, β ocimene and a numbers of sesquiterpenes differentially produced by the plant under heat stress were identified. We propose these compounds were produced by the tree to cope up with heat stress. A protein gel electrophoresis (2-D DIGE) was performed to study differential expression of proteins in heat stressed plants. Several proteins were found to be expressed many folds different in heat stressed plants compared to the control. These proteins included heat shock proteins, histone proteins, oxygen evolving complex, and photosynthetic proteins, which, we believe, played key roles in imparting thermotolerance in Hymenaea tree. To the best of our knowledge, this is the first report of extensive molecular physiological study of Hymenaea trees under heat stress. This work will open avenues of further research on effects of heat stress in Hymenaea and the findings can be applied to understand how global warming can affect physiology of other plants.
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Affiliation(s)
- Dinesh Gupta
- Department of Biology; California State University Northridge; Northridge, CA USA
| | - Moustafa Eldakak
- Department of Biology and Microbiology; South Dakota State University; Brookings, SD USA
- Department of Genetics; Faculty of Agriculture, El Shatby; Alexandria University; Alexandria, Egypt
| | - Jai S Rohila
- Department of Biology and Microbiology; South Dakota State University; Brookings, SD USA
- Department of Plant Science; South Dakota State University; Brookings, SD USA
- Correspondence to: Jai S Rohila; , Chhandak Basu;
| | - Chhandak Basu
- Department of Biology; California State University Northridge; Northridge, CA USA
- Correspondence to: Jai S Rohila; , Chhandak Basu;
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