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Yang X, Jiang Z, He J, Shen L. iTRAQ-Based Quantitative Proteomics Unveils Protein Dynamics in the Root of Solanum melongena L. under Waterlogging Stress Conditions. Life (Basel) 2023; 13:1399. [PMID: 37374181 DOI: 10.3390/life13061399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Waterlogging poses significant abiotic stress that endangers the survival of plants, including crops. In response, plants dramatically change their physiology to enhance their tolerance to waterlogging, such as proteome reconfiguration. Here, we utilized isobaric tags for the relative and absolute quantitation (iTRAQ)-based protein labeling technique to examine the proteomic changes induced by waterlogging in the roots of Solanum melongena L., a solanaceous plant. The plants were subjected to 6, 12, and 24 h of waterlogging stress at the flowering stage. Of the 4074 identified proteins, compared to the control, the abundance of the proteins increased and decreased in 165 and 78 proteins, respectively, in 6 h of treatments; 219 and 89 proteins, respectively, in 12 h of treatments; and 126 and 127 proteins, respectively, in 24 h of treatments. The majority of these differentially regulated proteins participated in processes such as energy metabolism, amino acid biosynthesis, signal transduction, and nitrogen metabolism. Fructose-bisphosphate aldolase and three alcohol dehydrogenase genes, in particular, were up- or down-regulated in waterlogging-treated Solanum melongena roots, suggesting that some proteins related to anaerobic metabolism (glycolysis and fermentation) may play vital roles in protecting its roots from waterlogging stress to enable long-term survival. Overall, this research not only offers a comprehensive dataset of protein alterations in waterlogged Solanum melongena roots but also insights into the mechanisms by which solanaceous plants adapt to waterlogging stress.
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Affiliation(s)
- Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Zheng Jiang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jie He
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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2
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Chen X, Sun Y, Zhang T, Shu L, Roepstorff P, Yang F. Quantitative Proteomics Using Isobaric Labeling: A Practical Guide. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:689-706. [PMID: 35007772 PMCID: PMC9170757 DOI: 10.1016/j.gpb.2021.08.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 05/19/2021] [Accepted: 09/27/2021] [Indexed: 01/09/2023]
Abstract
In the past decade, relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological samples. Although its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions, its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification results. Here, we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling method. We also discuss which precautions should be taken at each step of the isobaric labeling workflow, to obtain reliable quantification results in large-scale quantitative proteomics experiments. In the last section, we discuss the broad applications of the isobaric labeling technology in biological and clinical studies, with an emphasis on thermal proteome profiling and proteogenomics.
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Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China.
| | - Yaping Sun
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Tingting Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Lian Shu
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China.
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3
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Ngumbi EN, Ugarte CM. Flooding and Herbivory Interact to Alter Volatile Organic Compound Emissions in Two Maize Hybrids. J Chem Ecol 2021; 47:707-718. [PMID: 34125370 DOI: 10.1007/s10886-021-01286-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/18/2021] [Accepted: 05/26/2021] [Indexed: 10/21/2022]
Abstract
Flooding is a major plant abiotic stress factor that is frequently experienced by plants simultaneously with other biotic stresses, including herbivory. How plant volatile emissions, which mediate interactions with a wide range of organisms, are influenced by flooding and by multiple co-occurring stress factors remains largely unexplored. Using Spodoptera frugiperda (Lepidoptera: Noctuidae) (fall armyworm) as the insect pest and two maize (Zea mays, L. Poaceae) hybrids differentially marketed for conventional and organic production, we assessed the effects of flooding, herbivory, and both stress factors on the composition of blends of emitted volatiles. Headspace volatiles were collected from all treatment combinations seven days after flooding. We documented metrics indicative of biomass allocation to determine the effects of individual and combined stressors on plant growth. We also evaluated relationships between volatile emissions and indicators of soil chemical characteristics as influenced by treatment factors. Flooding and herbivory induced the emission of volatile organic compounds (VOCs) in similar ways on both maize hybrids, but the interaction of both stress factors produced significantly larger quantities of emitted volatiles. Thirty-eight volatile compounds were identified, including green leaf volatiles, monoterpenes, an aldehyde, a benzoate ester, sesquiterpenes, a diterpene alcohol, and alkane hydrocarbons. The hybrid marketed for organic production was a stronger VOC emitter. As expected, plant biomass was detrimentally affected by flooding. Soil chemical properties were less responsive to the treatment factors. Taken together, the results suggest that flooding stress and the interactions of flooding and insect attack can shape the emission of plant volatiles and further influence insect-plant interactions.
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Affiliation(s)
- Esther N Ngumbi
- Department of Entomology, University of Illinois at Urbana-Champaign, IL, 61801, Urbana, USA.
| | - Carmen M Ugarte
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, IL, 61801, Urbana, USA
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4
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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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5
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Block AK, Hunter CT, Sattler SE, Rering C, McDonald S, Basset GJ, Christensen SA. Fighting on two fronts: Elevated insect resistance in flooded maize. PLANT, CELL & ENVIRONMENT 2020; 43:223-234. [PMID: 31411732 DOI: 10.1111/pce.13642] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/25/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
To grow and thrive plants must be able to adapt to both adverse environmental conditions and attack by a variety of pests. Elucidating the sophisticated mechanisms plants have developed to achieve this has been the focus of many studies. What is less well understood is how plants respond when faced with multiple stressors simultaneously. In this study, we assess the response of Zea mays (maize) to the combinatorial stress of flooding and infestation with the insect pest Spodoptera frugiperda (fall armyworm). This combined stress leads to elevated production of the defence hormone salicylic acid, which does not occur in the individual stresses, and the resultant salicylic acid-dependent increase in S. frugiperda resistance. Remodelling of phenylpropanoid pathways also occurs in response to this combinatorial stress leading to increased production of the anti-insect C-glycosyl flavones (maysins) and the herbivore-induced volatile phenolics, benzyl acetate, and phenethyl acetate. Furthermore, changes in cellular redox status also occur, as indicated by reductions in peroxidase and polyphenol oxidase activity. These data suggest that metabolite changes important for flooding tolerance and anti-insect defence may act both additively and synergistically to provide extra protection to the plant.
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Affiliation(s)
- Anna K Block
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, U.S. Department of Agriculture-Agricultural Research Service, Gainesville, FL, 32608, USA
| | - Charles T Hunter
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, U.S. Department of Agriculture-Agricultural Research Service, Gainesville, FL, 32608, USA
| | - Scott E Sattler
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE, 68583, USA
| | - Caitlin Rering
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, U.S. Department of Agriculture-Agricultural Research Service, Gainesville, FL, 32608, USA
| | - Samantha McDonald
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, U.S. Department of Agriculture-Agricultural Research Service, Gainesville, FL, 32608, USA
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Gilles J Basset
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Shawn A Christensen
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, U.S. Department of Agriculture-Agricultural Research Service, Gainesville, FL, 32608, USA
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6
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Yu F, Liang K, Fang T, Zhao H, Han X, Cai M, Qiu F. A group VII ethylene response factor gene, ZmEREB180, coordinates waterlogging tolerance in maize seedlings. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2286-2298. [PMID: 31033158 PMCID: PMC6835127 DOI: 10.1111/pbi.13140] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 04/01/2019] [Accepted: 04/25/2019] [Indexed: 05/24/2023]
Abstract
Group VII ethylene response factors (ERFVIIs) play important roles in ethylene signalling and plant responses to flooding. However, natural ERFVII variations in maize (ZmERFVIIs) that are directly associated with waterlogging tolerance have not been reported. Here, a candidate gene association analysis of the ZmERFVII gene family showed that a waterlogging-responsive gene, ZmEREB180, was tightly associated with waterlogging tolerance. ZmEREB180 expression specifically responded to waterlogging and was up-regulated by ethylene; in addition, its gene product localized to the nucleus. Variations in the 5'-untranslated region (5'-UTR) and mRNA abundance of this gene under waterlogging conditions were significantly associated with survival rate (SR). Ectopic expression of ZmEREB180 in Arabidopsis increased the SR after submergence stress, and overexpression of ZmEREB180 in maize also enhanced the SR after long-term waterlogging stress, apparently through enhanced formation of adventitious roots (ARs) and regulation of antioxidant levels. Transcriptomic assays of the transgenic maize line under normal and waterlogged conditions further provided evidence that ZmEREB180 regulated AR development and reactive oxygen species homeostasis. Our study provides direct evidence that a ZmERFVII gene is involved in waterlogging tolerance. These findings could be applied directly to breed waterlogging-tolerant maize cultivars and improve our understanding of waterlogging stress.
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Affiliation(s)
- Feng Yu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Kun Liang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Tian Fang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Hailiang Zhao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xuesong Han
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Manjun Cai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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Sharma JK, Sihmar M, Santal AR, Singh NP. Impact assessment of major abiotic stresses on the proteome profiling of some important crop plants: a current update. Biotechnol Genet Eng Rev 2019; 35:126-160. [PMID: 31478455 DOI: 10.1080/02648725.2019.1657682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abiotic stresses adversely affect the plant's growth and development leading to loss of crop plants and plant products in terms of both the quality and quantity. Two main strategies are adopted by plants to acclimatize to stresses; avoidance and tolerance. These adaptive strategies of plants at the cellular and metabolic level enable them to withstand such detrimental conditions. Acclimatization is associated with intensive changes in the proteome of plants and these changes are directly involved in plants response to stress. Proteome studies can be used to screen for these proteins and their involvement in plants response to various abiotic stresses evaluated. In this review, proteomic studies of different plants species under different abiotic stresses, particularly drought, salinity, heat, cold, and waterlogging, are discussed. From different proteomic studies, the stress response can be determined by an interaction between proteomic and physiological changes which occur in plants during such stress conditions. These identified proteins from different processes under different abiotic stress conditions definitely add to our understanding for exploiting them in various biotechnological applications in crop improvement.
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Affiliation(s)
| | - Monika Sihmar
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Anita Rani Santal
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - N P Singh
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
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Zeng N, Yang Z, Zhang Z, Hu L, Chen L. Comparative Transcriptome Combined with Proteome Analyses Revealed Key Factors Involved in Alfalfa ( Medicago sativa) Response to Waterlogging Stress. Int J Mol Sci 2019; 20:ijms20061359. [PMID: 30889856 PMCID: PMC6471898 DOI: 10.3390/ijms20061359] [Citation(s) in RCA: 15] [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: 01/30/2019] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/26/2022] Open
Abstract
Alfalfa (Medicago sativa) is the most widely grown and most important forage crop in the world. However, alfalfa is susceptible to waterlogging stress, which is the major constraint for its cultivation area and crop production. So far, the molecular mechanism of alfalfa response to the waterlogging is largely unknown. Here, comparative transcriptome combined with proteomic analyses of two cultivars (M12, tolerant; M25, sensitive) of alfalfa showing contrasting tolerance to waterlogging were performed to understand the mechanism of alfalfa in response to waterlogging stress. Totally, 748 (581 up- and 167 down-regulated) genes were differentially expressed in leaves of waterlogging-stressed alfalfa compared with the control (M12_W vs. M12_CK), whereas 1193 (740 up- and 453 down-regulated) differentially abundant transcripts (DATs) were detected in the leaves of waterlogging-stressed plants in comparison with the control plants (M25_W vs. M25_CK). Furthermore, a total of 187 (122 up- and 65 down-regulated) and 190 (105 up- and 85 down-regulated) differentially abundant proteins (DAPs) were identified via isobaric tags for relative and absolute quantification (iTRAQ) method in M12_W vs. M12_CK and M25_W vs. M25_CK comparison, respectively. Compared dataset analysis of proteomics and transcriptomics revealed that 27 and eight genes displayed jointly up-regulated or down-regulated expression profiles at both mRNA and protein levels in M12_W vs. M12_CK comparison, whereas 30 and 27 genes were found to be co-up-regulated or co-down-regulated in M25_W vs. M25_CK comparison, respectively. The strongly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for co-up-regulated genes at mRNA and protein levels in M12_W vs. M12_CK comparison were 'Amino sugar and nucleotide sugar metabolism', 'Arginine and proline metabolism' and 'Starch and sucrose metabolism', whereas co-up-regulated protein-related pathways including 'Arginine and proline metabolism' and 'Valine, leucine and isoleucine degradation' were largely enriched in M25_W vs. M25_CK comparison. Importantly, the identified genes related to beta-amylase, Ethylene response Factor (ERF), Calcineurin B-like (CBL) interacting protein kinases (CIPKs), Glutathione peroxidase (GPX), and Glutathione-S-transferase (GST) may play key roles in conferring alfalfa tolerance to waterlogging stress. The present study may contribute to our understanding the molecular mechanism underlying the responses of alfalfa to waterlogging stress, and also provide important clues for further study and in-depth characterization of waterlogging-resistance breeding candidate genes in alfalfa.
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Affiliation(s)
- Ningbo Zeng
- Department of Pratacultural Sciences, College of Agriculture, Hunan Agricultural University, Changsha 410128, China.
| | - Zhijian Yang
- Department of Pratacultural Sciences, College of Agriculture, Hunan Agricultural University, Changsha 410128, China.
| | - Zhifei Zhang
- Department of Pratacultural Sciences, College of Agriculture, Hunan Agricultural University, Changsha 410128, China.
| | - Longxing Hu
- Department of Pratacultural Sciences, College of Agriculture, Hunan Agricultural University, Changsha 410128, China.
| | - Liang Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Science, Wuhan 430074, China.
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Pan R, He D, Xu L, Zhou M, Li C, Wu C, Xu Y, Zhang W. Proteomic analysis reveals response of differential wheat (Triticum aestivum L.) genotypes to oxygen deficiency stress. BMC Genomics 2019; 20:60. [PMID: 30658567 PMCID: PMC6339445 DOI: 10.1186/s12864-018-5405-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/21/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Waterlogging is one of the main abiotic stresses that limit wheat production. Quantitative proteomics analysis has been applied in the study of crop abiotic stress as an effective way in recent years (e.g. salt stress, drought stress, heat stress and waterlogging stress). However, only a few proteins related to primary metabolism and signal transduction, such as UDP - glucose dehydrogenase, UGP, beta glucosidases, were reported to response to waterlogging stress in wheat. The differentially expressed proteins between genotypes of wheat in response to waterlogging are less-defined. In this study, two wheat genotypes, one is sensitive to waterlogging stress (Seri M82, named as S) and the other is tolerant to waterlogging (CIGM90.863, named as T), were compared in seedling roots under hypoxia conditions to evaluate the different responses at proteomic level. RESULTS A total of 4560 proteins were identified and the number of differentially expressed proteins (DEPs) were 361, 640, 788 in S and 33, 207, 279 in T in 1, 2, 3 days, respectively. These DEPs included 270 common proteins, 681 S-specific and 50 T-specific proteins, most of which were misc., protein processing, DNA and RNA processing, amino acid metabolism and stress related proteins induced by hypoxia. Some specific proteins related to waterlogging stress, including acid phosphatase, oxidant protective enzyme, S-adenosylmethionine synthetase 1, were significantly different between S and T. A total of 20 representative genes encoding DEPs, including 7 shared DEPs and 13 cultivar-specific DEPs, were selected for further RT-qPCR analysis. Fourteen genes showed consistent dynamic expression patterns at mRNA and protein levels. CONCLUSIONS Proteins involved in primary metabolisms and protein processing were inclined to be affected under hypoxia stress. The negative effects were more severe in the sensitive genotype. The expression patterns of some specific proteins, such as alcohol dehydrogenases and S-adenosylmethionine synthetase 1, could be applied as indexes for improving the waterlogging tolerance in wheat. Some specific proteins identified in this study will facilitate the subsequent protein function validation and biomarker development.
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Affiliation(s)
- Rui Pan
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
| | - Dongli He
- College of Life Sciences, Hubei University, Wuhan, 430074 China
| | - Le Xu
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
| | - Meixue Zhou
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, Hobart, Tasmania 7250 Australia
| | - Chengdao Li
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
- Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA Australia
| | - Chu Wu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 China
| | - Yanhao Xu
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry/ School of Agriculture, Yangtze University, Jingzhou, 434025 China
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10
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Yu F, Liang K, Zhang Z, Du D, Zhang X, Zhao H, Ui Haq B, Qiu F. Dissecting the genetic architecture of waterlogging stress-related traits uncovers a key waterlogging tolerance gene in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2299-2310. [PMID: 30062652 DOI: 10.1007/s00122-018-3152-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
A key candidate gene, GRMZM2G110141, which could be used in marker-assisted selection in maize breeding programs, was detected among the 16 genetic loci associated with waterlogging tolerance identified through genome-wide association study. Waterlogging stress seriously affects the growth and development of upland crops such as maize (Zea mays L.). However, the genetic basis of waterlogging tolerance in crop plants is largely unknown. Here, we identified genetic loci for waterlogging tolerance-related traits by conducting a genome-wide association study using maize phenotypes evaluated in the greenhouse under waterlogging stress and normal conditions. A total of 110 trait-single nucleotide polymorphism associations spanning 16 genomic regions were identified; single associations explained 2.88-10.67% of the phenotypic variance. Among the genomic regions identified, 14 co-localized with previously detected waterlogging tolerance-related quantitative trail loci. Furthermore, 33 candidate genes involved in a wide range of stress-response pathways were predicted. We resequenced a key candidate gene (GRMZM2G110141) in 138 randomly selected inbred lines and found that variations in the 5'-UTR and in the mRNA abundance of this gene under waterlogging conditions were significantly associated with leaf injury. Furthermore, we detected favorable alleles of this gene and validated the favorable alleles in two different recombinant inbred line populations. These alleles enhanced waterlogging tolerance in segregating populations, strongly suggesting that GRMZM2G110141 is a key waterlogging tolerance gene. The set of waterlogging tolerance-related genomic regions and associated markers identified here could be valuable for isolating waterlogging tolerance genes and improving this trait in maize.
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Affiliation(s)
- Feng Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kun Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dengxiang Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuehai Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Basir Ui Haq
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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11
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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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12
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Niu L, Xu X, Liu H, Wu X, Wang W. On the Promising Role of Enzyme Activity Assay in Interpreting Comparative Proteomic Data in Plants. Proteomics 2018; 18:e1800234. [PMID: 30179302 DOI: 10.1002/pmic.201800234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/18/2018] [Indexed: 11/09/2022]
Abstract
Comparative proteomics is widely used to detect protein changes, especially differential abundance proteins (DAPs) that are involved in plant responses to development, disease, or environment. Once DAPs are identified, it is essential to validate any change in their abundance, and their role in the biological process under study. In addition to common confirmation by quantitative RT-PCR, immunoblot, and multiple reaction monitoring analysis, it has been proposed that enzyme activity assay (EAA) can be complementary to the standard proteomics results, especially regarding the elucidation of protein (enzyme) function and the mechanism of enzyme-associated biochemical or metabolic pathways. The enzymes discussed here are the DAPs identified in comparative plant proteomics. Despite the small number of enzymes in a proteome, they often make up a substantial proportion of the DAPs identified in comparative studies. Currently, only a few studies have performed EAA to complement the interpretation of proteomic data, especially activity-based protein profiling. This viewpoint aims to arouse the attention of proteomic researchers on the promising role of EAA in plant proteomics and highlights the need for high-throughput assays of enzyme activities in comparative plant proteomics.
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Affiliation(s)
- Liangjie Niu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangru Xu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hui Liu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaolin Wu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wei Wang
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China.,College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
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13
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Cen W, Liu J, Lu S, Jia P, Yu K, Han Y, Li R, Luo J. Comparative proteomic analysis of QTL CTS-12 derived from wild rice (Oryza rufipogon Griff.), in the regulation of cold acclimation and de-acclimation of rice (Oryza sativa L.) in response to severe chilling stress. BMC PLANT BIOLOGY 2018; 18:163. [PMID: 30097068 PMCID: PMC6086036 DOI: 10.1186/s12870-018-1381-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/30/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is a thermophilic crop vulnerable to chilling stress. However, common wild rice (Oryza rufipogon Griff.) in Guangxi (China) has the ability to tolerate chilling stress. To better understand the molecular mechanisms underlying chilling tolerance in wild rice, iTRAQ-based proteomic analysis was performed to examine CTS-12, a major chilling tolerance QTL derived from common wild rice, mediated chilling and recovery-induced differentially expressed proteins (DEPs) between the chilling-tolerant rice line DC90 and the chilling-sensitive 9311. RESULTS Comparative analysis identified 206 and 155 DEPs in 9311 and DC90, respectively, in response to the whole period of chilling and recovery. These DEPs were clustered into 6 functional groups in 9311 and 4 in DC90. The majority were enriched in the 'structural constituent of ribosome', 'protein-chromophore linkage', and 'photosynthesis and light harvesting' categories. Short Time-series Expression Miner (STEM) analysis revealed distinct dynamic responses of both chloroplast photosynthetic and ribosomal proteins between 9311 and DC90. CONCLUSION CTS-12 might mediate the dynamic response of chloroplast photosynthetic and ribosomal proteins in DC90 under chilling (cold acclimation) and recovery (de-acclimation) and thereby enhancing the chilling stress tolerance of this rice line. The identified DEPs and the involvement of CTS-12 in mediating the dynamic response of DC90 at the proteomic level illuminate and deepen the understanding of the mechanisms that underlie chilling stress tolerance in wild rice.
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Affiliation(s)
- Weijian Cen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004 China
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Jianbin Liu
- College of Life Science and Technology, Guangxi University, Nanning, 530004 China
| | - Siyuan Lu
- College of Life Science and Technology, Guangxi University, Nanning, 530004 China
| | - Peilong Jia
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Kai Yu
- Shanghai MHelix BioTech Co., Ltd, Shanghai, 201900 People’s Republic of China
| | - Yue Han
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004 China
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Jijing Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004 China
- College of Life Science and Technology, Guangxi University, Nanning, 530004 China
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14
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Luan H, Shen H, Pan Y, Guo B, Lv C, Xu R. Elucidating the hypoxic stress response in barley (Hordeum vulgare L.) during waterlogging: A proteomics approach. Sci Rep 2018; 8:9655. [PMID: 29941955 PMCID: PMC6018542 DOI: 10.1038/s41598-018-27726-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 06/08/2018] [Indexed: 12/25/2022] Open
Abstract
Waterlogging is one of the major abiotic stresses that affects barley production and yield quality. Proteomics techniques have been widely utilized to explore the mechanisms involved in the responses to abiotic stress. In this study, two barley genotypes with contrasting responses to waterlogging stress were analyzed with proteomic technology. The waterlogging treatment caused a greater reduction in biomass and photosynthetic performance in the waterlogging-sensitive genotype TF57 than that in the waterlogging-tolerant genotype TF58. Under waterlogging stress, 30, 30, 20 and 20 differentially expressed proteins were identified through tandem mass spectrometry analysis in the leaves, adventitious roots, nodal roots and seminal roots, respectively. Among these proteins, photosynthesis-, metabolism- and energy-related proteins were differentially expressed in the leaves, with oxygen-evolving enhancer protein 1, ATP synthase subunit and heat shock protein 70 being up-regulated in TF58. Pyruvate decarboxylase (PDC), 1-amino cyclopropane 1-carboxylic acid oxidase (ACO), glutamine synthetase (GS), glutathione S-transferases (GST) and beta-1, 3-glucanase in adventitious, nodal and seminal roots were more abundant in TF58 than those in TF57 under waterlogging stress. Ten representative genes were selected for validation by qRT-PCR in different genotypes with known waterlogging tolerance, and the expression levels of three candidate genes (PDC, ACO and GST) increased in the roots of all genotypes in response to the waterlogging stress. These three genes might play a significant role in the adaptation process of barley under waterlogging stress. The current results partially determined the mechanisms of waterlogging tolerance and provided valuable information for the breeding of barley with enhanced tolerance to waterlogging.
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Affiliation(s)
- Haiye Luan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, 225009, China
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, 224002, China
| | - Huiquan Shen
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, 224002, China
| | - Yuhan Pan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, 225009, China
| | - Baojian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, 225009, China
| | - Chao Lv
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, 225009, China
| | - Rugen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, 225009, China.
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15
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Quantitative proteomic analysis using iTRAQ to identify salt-responsive proteins during the germination stage of two Medicago species. Sci Rep 2018; 8:9553. [PMID: 29934583 PMCID: PMC6015060 DOI: 10.1038/s41598-018-27935-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/12/2018] [Indexed: 01/01/2023] Open
Abstract
Salt stress is one of the primary abiotic stresses responsible for decreasing crop yields worldwide. Germinating seeds can be greatly influenced by saline conditions. In this study, the physiological and phenotypic changes induced by salt treatments (10–50 mM NaCl and Na2SO4 mixtures) were analysed for Zhongmu-3 (Medicago sativa) and R108 (Medicago truncatula) seedlings. Our observations indicated that Zhongmu-3 was more salt-tolerant than R108. To characterize the protein expression profiles of these two Medicago species in response to salt stress, an iTRAQ-based quantitative proteomic analysis was applied to examine salt-responsive proteins. We identified 254 differentially changed salt-responsive proteins. Compared with control levels, the abundance of 121 proteins increased and 44 proteins decreased in salt-treated Zhongmu-3 seedlings, while 119 proteins increased and 18 proteins decreased in R108 seedlings. Moreover, 48 differentially changed proteins were common to Zhongmu-3 and R108 seedlings. A subsequent functional annotation indicated these proteins influenced diverse processes, such as catalytic activity, binding, and antioxidant activity. Furthermore, the corresponding transcript levels of 15 differentially changed proteins were quantified by qRT-PCR. The data presented herein provide new insights into salt-responsive proteins, with potential implications for enhancing the salt tolerance of Medicago species.
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16
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Su H, Zhang H, Wei X, Pan D, Jing L, Zhao D, Zhao Y, Qi B. Comparative Proteomic Analysis of Rana chensinensis Oviduct. Molecules 2018; 23:1384. [PMID: 29890619 PMCID: PMC6099995 DOI: 10.3390/molecules23061384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/31/2018] [Accepted: 06/05/2018] [Indexed: 12/31/2022] Open
Abstract
As one of most important traditional Chinese medicine resources, the oviduct of female Rana chensinensis (Chinese brown frog) was widely used in the treatment of asthenia after sickness or delivery, deficiency in vigor, palpitation, and insomnia. Unlike other vertebrates, the oviduct of Rana chensinensis oviduct significantly expands during prehibernation, in contrast to the breeding period. To explain this phenomenon at the molecular level, the protein expression profiles of Rana chensinensis oviduct during the breeding period and prehibernation were observed using isobaric tags for relative and absolute quantitation (iTRAQ) technique. Then, all identified proteins were used to obtain gene ontology (GO) annotation. Ultimately, KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis was performed to predict the pathway on differentially expressed proteins (DEPs). A total of 4479 proteins were identified, and 312 of them presented different expression profiling between prehibernation and breeding period. Compared with prehibernation group, 86 proteins were upregulated, and 226 proteins were downregulated in breeding period. After KEGG enrichment analysis, 163 DEPs were involved in 6 pathways, which were lysosome, RNA transport, glycosaminoglycan degradation, extracellular matrix (ECM)⁻receptor interaction, metabolic pathways and focal adhesion. This is the first report on the protein profiling of Rana chensinensis oviduct during the breeding period and prehibernation. Results show that this distinctive physiological phenomenon of Rana chensinensis oviduct was mainly involved in ECM⁻receptor interaction, metabolic pathways, and focal adhesion.
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Affiliation(s)
- Hang Su
- Practice Innovations Center, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - He Zhang
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Xinghua Wei
- Jilin Science Service Center, Changchun 130021, China.
| | - Daian Pan
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Li Jing
- Practice Innovations Center, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Daqing Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Yu Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Bin Qi
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China.
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17
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do Nascimento SV, Magalhães MM, Cunha RL, Costa PHDO, Alves RCDO, de Oliveira GC, Valadares RBDS. Differential accumulation of proteins in oil palms affected by fatal yellowing disease. PLoS One 2018; 13:e0195538. [PMID: 29621343 PMCID: PMC5886584 DOI: 10.1371/journal.pone.0195538] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/23/2018] [Indexed: 11/20/2022] Open
Abstract
There is still no consensus on the true origin of fatal yellowing, one of the most important diseases affecting oil palm (Elaeis guineensis Jacq.) plantations. This study involved two-dimensional liquid chromatography coupled with tandem mass spectrometry (2D-UPLC-MSE) analyses to identify changes in protein profiles of oil palms affected by FY disease. Oil palm roots were sampled from two growing areas. Differential accumulation of proteins was assessed by comparing plants with and without symptoms and between plants at different stages of FY development. Most of the proteins identified with differential accumulation were those related to stress response and energy metabolism. The latter proteins include the enzymes alcohol dehydrogenase and aldehyde dehydrogenase, related to alcohol fermentation, which were identified in plants with and without symptoms. The presence of these enzymes suggests an anaerobic condition before or during FY. Transketolase, isoflavone reductase, cinnamyl alcohol dehydrogenase, caffeic acid 3-O-methyltransferase, S-adenosylmethionine synthase, aldehyde dehydrogenase and ferritin, among others, were identified as potential marker proteins and could be used to guide selection of FY-tolerant oil palm genotypes or to understand the source of this anomaly. When comparing different stages of FY, we observed high accumulation of alcohol dehydrogenase and other abiotic stress related-proteins at all disease stages. On the other hand, biological stress-related proteins were more accumulated at later stages of the disease. These results suggest that changes in abiotic factors can trigger FY development, creating conditions for the establishment of opportunistic pathogens.
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Affiliation(s)
- Sidney Vasconcelos do Nascimento
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Biotecnologia Aplicada à Agropecuária, Universidade Federal Rural da Amazônia, Belém, Pará, Brazil
| | | | - Roberto Lisboa Cunha
- Programa de Pós-Graduação em Biotecnologia Aplicada à Agropecuária, Universidade Federal Rural da Amazônia, Belém, Pará, Brazil
- Analysis of sustainable system laboratory, Embrapa Amazônia Oriental, Belém, Pará, Brazil
| | | | | | | | - Rafael Borges da Silva Valadares
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Biotecnologia Aplicada à Agropecuária, Universidade Federal Rural da Amazônia, Belém, Pará, Brazil
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18
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Luo M, Zhao Y, Wang Y, Shi Z, Zhang P, Zhang Y, Song W, Zhao J. Comparative Proteomics of Contrasting Maize Genotypes Provides Insights into Salt-Stress Tolerance Mechanisms. J Proteome Res 2017; 17:141-153. [DOI: 10.1021/acs.jproteome.7b00455] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Meijie Luo
- Beijing
Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding,
Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100097, China
| | - Yanxin Zhao
- Beijing
Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding,
Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100097, China
| | - Yuandong Wang
- Beijing
Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding,
Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100097, China
| | - Zi Shi
- Beijing
Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding,
Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100097, China
| | - Panpan Zhang
- Beijing
Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding,
Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100097, China
| | - Yunxia Zhang
- Beijing
Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding,
Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100097, China
| | - Wei Song
- Beijing
Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding,
Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100097, China
| | - Jiuran Zhao
- Beijing
Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding,
Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100097, China
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19
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Xiang J, Wu H, Zhang Y, Zhang Y, Wang Y, Li Z, Lin H, Chen H, Zhang J, Zhu D. Transcriptomic Analysis of Gibberellin- and Paclobutrazol-Treated Rice Seedlings under Submergence. Int J Mol Sci 2017; 18:E2225. [PMID: 29064391 PMCID: PMC5666904 DOI: 10.3390/ijms18102225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/16/2017] [Accepted: 10/19/2017] [Indexed: 01/08/2023] Open
Abstract
Submergence stress is a limiting factor for rice growing in rainfed lowland areas of the world. It is known that the phytohormone gibberellin (GA) has negative effects on submergence tolerance in rice, while its inhibitor paclobutrazol (PB) does the opposite. However, the physiological and molecular basis underlying the GA- and PB-regulated submergence response remains largely unknown. In this study, we reveal that PB could significantly enhance rice seedling survival by retaining a higher level of chlorophyll content and alcohol dehydrogenase activity, and decelerating the consumption of non-structure carbohydrate when compared with the control and GA-treated samples. Further transcriptomic analysis identified 3936 differentially expressed genes (DEGs) among the GA- and PB-treated samples and control, which are extensively involved in the submergence and other abiotic stress responses, phytohormone biosynthesis and signaling, photosynthesis, and nutrient metabolism. The results suggested that PB enhances rice survival under submergence through maintaining the photosynthesis capacity and reducing nutrient metabolism. Taken together, the current study provided new insight into the mechanism of phytohormone-regulated submergence response in rice.
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Affiliation(s)
- Jing Xiang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Hui Wu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Yuping Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Yikai Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Haiyan Lin
- Yuan LongPing High-TechAgriculture Co., Ltd., Changsha 410001, China.
| | - Huizhe Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Defeng Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
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20
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Zheng X, Zhou J, Tan DX, Wang N, Wang L, Shan D, Kong J. Melatonin Improves Waterlogging Tolerance of Malus baccata (Linn.) Borkh. Seedlings by Maintaining Aerobic Respiration, Photosynthesis and ROS Migration. FRONTIERS IN PLANT SCIENCE 2017; 8:483. [PMID: 28424730 PMCID: PMC5380759 DOI: 10.3389/fpls.2017.00483] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/20/2017] [Indexed: 05/18/2023]
Abstract
Waterlogging, one of the notorious abiotic stressors, retards the growth of apple plants and reduces their production. Thus, it is an urgent agenda for scientists to identify the suitable remedies for this problem. In the current study, we found that melatonin significantly improved the tolerance of apple seedlings against waterlogging stress. This was indicated by the reduced chlorosis and wilting of the seedlings after melatonin applications either by leaf spray or root irrigation. The mechanisms involve in that melatonin functions to maintain aerobic respiration, preserves photosynthesis and reduces oxidative damage of the plants which are under waterlogging stress. Melatonin application also enhances the gene expression of its synthetic enzymes (MbT5H1, MbAANAT3, MbASMT9) and increases melatonin production. This is the first report of a positive feedback that exogenous melatonin application promotes the melatonin synthesis in plants. A post-transcriptional regulation apparently participated in this regulation. When exogenous melatonin meets the requirement of the plants it is found that the protein synthesis of MbASMT9 was suppressed. Taken together, the results showed that melatonin was an effective molecule to protect plant, particularly apple plant, against waterlogging stress.
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Affiliation(s)
- Xiaodong Zheng
- College of Horticulture, China Agricultural UniversityBeijing, China
| | - Jingzhe Zhou
- Beijing Soil and Fertilizer Work StationBeijing, China
| | - Dun-Xian Tan
- Department of Cellular and Structural Biology, UT Health Science Center San Antonio, San AntonioTX, USA
| | - Na Wang
- College of Horticulture, China Agricultural UniversityBeijing, China
| | - Lin Wang
- College of Horticulture, China Agricultural UniversityBeijing, China
| | - Dongqian Shan
- College of Horticulture, China Agricultural UniversityBeijing, China
| | - Jin Kong
- College of Horticulture, China Agricultural UniversityBeijing, China
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21
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Zhang X, Shabala S, Koutoulis A, Shabala L, Zhou M. Meta-analysis of major QTL for abiotic stress tolerance in barley and implications for barley breeding. PLANTA 2017; 245:283-295. [PMID: 27730410 DOI: 10.1007/s00425-016-2605-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/04/2016] [Indexed: 05/24/2023]
Abstract
We projected meta-QTL (MQTL) for drought, salinity, and waterlogging tolerance to the physical map of barley through meta-analysis. The positions of these MQTL were refined and candidate genes were identified. Drought, salinity and waterlogging are three major abiotic stresses limiting barley yield worldwide. Breeding for abiotic stress-tolerant crops has drawn increased attention, and a large number of quantitative trait loci (QTL) for drought, salinity, and waterlogging tolerance in barley have been detected. However, very few QTL have been successfully used in marker-assisted selection (MAS) in breeding. In this study, we summarized 632 QTL for drought, salinity and waterlogging tolerance in barley. Among all these QTL, only 195 major QTL were used to conduct meta-analysis to refine QTL positions for MAS. Meta-analysis was used to map the summarized major QTL for drought, salinity, and waterlogging tolerance from different mapping populations on the barley physical map. The positions of identified meta-QTL (MQTL) were used to search for candidate genes for drought, salinity, and waterlogging tolerance in barley. Both MQTL3H.4 and MQTL6H.2 control drought tolerance in barley. Fine-mapped QTL for salinity tolerance, HvNax4 and HvNax3, were validated on MQTL1H.4 and MQTL7H.2, respectively. MQTL2H.1 and MQTL5H.3 were also the target regions for improving salinity tolerance in barley. MQTL4H.4 is the main region controlling waterlogging tolerance in barley with fine-mapped QTL for aerenchyma formation under waterlogging conditions. Detected and refined MQTL and candidate genes are crucial for future successful MAS in barley breeding.
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Affiliation(s)
- Xuechen Zhang
- School of Land and Food, University of Tasmania, P.O. Box 46, Kings Meadows, Tasmania, TAS 7249, Australia
| | - Sergey Shabala
- School of Land and Food, University of Tasmania, P.O. Box 46, Kings Meadows, Tasmania, TAS 7249, Australia
| | - Anthony Koutoulis
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Lana Shabala
- School of Land and Food, University of Tasmania, P.O. Box 46, Kings Meadows, Tasmania, TAS 7249, Australia
| | - Meixue Zhou
- School of Land and Food, University of Tasmania, P.O. Box 46, Kings Meadows, Tasmania, TAS 7249, Australia.
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22
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Wu J, Zhao HB, Yu D, Xu X. Transcriptome profiling of the floating-leaved aquatic plant Nymphoides peltata in response to flooding stress. BMC Genomics 2017; 18:119. [PMID: 28143394 PMCID: PMC5282827 DOI: 10.1186/s12864-017-3515-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 01/26/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Waterlogging or flooding is one of the most challenging abiotic stresses experienced by plants. Unlike many flooding-tolerant plants, floating-leaved aquatic plants respond actively to flooding stress by fast growth and elongation of its petioles to make leaves re-floating. However, the molecular mechanisms of this plant group responding to flood have not been investigated before. Here, we investigated the genetic basis of this adaptive response by characterizing the petiole transcriptomes of a floating-leaved species Nymphoides peltata under normal and flooding conditions. RESULTS Clean reads under normal and flooding conditions with pooled sampling strategy were assembled into 124,302 unigenes. A total of 8883 unigenes were revealed to be differentially expressed between normal and flooding conditions. Among them, top ranked differentially expressed genes were mainly involved in antioxidant process, photosynthesis process and carbohydrate metabolism, including the glycolysis and a modified tricarboxylic acid cycle - alanine metabolism. Eight selected unigenes with significantly differentiated expression changes between normal and flooding conditions were validated by qRT-PCR. CONCLUSIONS Among these processes, antioxidant process and glycolysis are commonly induced by waterlogging or flooding environment in plants, whereas photosynthesis and alanine metabolism are rarely occurred in other flooding-tolerant plants, suggesting the significant contributions of the two processes in the active response of N. peltata to flooding stress. Our results provide a valuable genomic resource for future studies on N. peltata and deepen our understanding of the genetic basis underlying the response to flooding stress in aquatic plants.
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Affiliation(s)
- Jinwei Wu
- Department of Ecology, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, 430072, China
| | - Hua-Bin Zhao
- Department of Ecology, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, 430072, China
| | - Dan Yu
- Department of Ecology, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, 430072, China
| | - Xinwei Xu
- Department of Ecology, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, 430072, China.
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23
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Yang X, Zhang Z, Gu T, Dong M, Peng Q, Bai L, Li Y. Quantitative proteomics reveals ecological fitness cost of multi-herbicide resistant barnyardgrass ( Echinochloa crus-galli L.). J Proteomics 2017; 150:160-169. [DOI: 10.1016/j.jprot.2016.09.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/18/2016] [Accepted: 09/21/2016] [Indexed: 01/10/2023]
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24
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Xu X, Ji J, Xu Q, Qi X, Chen X. Inheritance and quantitative trail loci mapping of adventitious root numbers in cucumber seedlings under waterlogging conditions. Mol Genet Genomics 2016; 292:353-364. [PMID: 27988808 DOI: 10.1007/s00438-016-1280-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/07/2016] [Indexed: 12/23/2022]
Abstract
The hypocotyl-derived adventitious root (AR) is an important morphological acclimation to waterlogging stress; however, its genetic basis has not been adequately understood. In the present study, a mixed major gene plus polygene inheritance model was used to analyze AR numbers (ARN) 7 days after waterlogging treatment in six generations (P1, P2, F1, B1, B2, and F2), using cucumber waterlogging tolerant line Zaoer-N and sensitive Pepino as parents. The results showed that the genetic model D-4, mixed one negative dominance major gene and additive-dominance polygenes, is the best-fitting genetic model for waterlogging-triggered ARN phenotype. A genetic linkage map spanning 550.8 cM and consisting of 149 simple sequence repeat (SSR) markers segregating into seven linkage groups was constructed. Three QTLs (ARN3.1, ARN5.1, and ARN6.1) distributed on chromosomes 3, 5, and 6 were identified by composite interval mapping. The major-effect QTL, ARN6.1, located between SSR12898 and SSR04751, was the only locus detected in three seasons, with least likelihood (LOD) scores of 8.8, 10.4, and 9.5 and account for 17.6, 24, and 19.8% of the phenotypic variance, respectively. Using five additional single nucleotide polymorphism (SNP) makers, the ARN6.1 was narrowed down to a 0.79 Mb interval franked by SSR12898 and SNP25558853. Illumina RNA-sequencing data generated on hypocotyls of two parents 48 h after waterlogging treatment revealed 15 genes in the 0.79 Mb interval were differentially expressed, including Csa6G503880 encoding a salicylic acid methyl transferase-like protein, Csa6G504590 encoding a cytochrome P450 monooxygenase, and Csa6G505230 encoding a heavy metal-associated protein. Our findings shed light on the genetic architecture underlying adventitious rooting during waterlogging stress in cucumber, and provide a list of potential gene targets for further elucidating waterlogging tolerance in plants.
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Affiliation(s)
- Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Jing Ji
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Qiang Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.
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25
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Qin N, Xu W, Hu L, Li Y, Wang H, Qi X, Fang Y, Hua X. Drought tolerance and proteomics studies of transgenic wheat containing the maize C 4 phosphoenolpyruvate carboxylase (PEPC) gene. PROTOPLASMA 2016; 253:1503-1512. [PMID: 26560113 DOI: 10.1007/s00709-015-0906-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/29/2015] [Indexed: 05/12/2023]
Abstract
Enhancing drought tolerance of crops has been a great challenge in crop improvement. Here, we report the maize phosphoenolpyruvate carboxylase (PEPC) gene was able to confer drought tolerance and increase grain yield in transgenic wheat (Triticum aestivum L.) plants. The improved of drought tolerance was associated with higher levels of proline, soluble sugar, soluble protein, and higher water use efficiency. The transgenic wheat plants had also a more extensive root system as well as increased photosynthetic capacity during stress treatments. The increased grain yield of the transgenic wheat was contributed by improved biomass, larger spike and grain numbers, and heavier 1000-grain weight under drought-stress conditions. Under non-stressed conditions, there were no significant increases in these of the measured traits except for photosynthetic rate when compared with parental wheat. Proteomic research showed that the expression levels of some proteins, including chlorophyll A-B binding protein and pyruvate, phosphate dikinase, which are related to photosynthesis, PAP fibrillin, which is involved in cytoskeleton synthesis, S-adenosylmethionine synthetase, which catalyzes methionine synthesis, were induced in the transgenic wheat under drought stress. Additionally, the expression of glutamine synthetase, which is involved in ammonia assimilation, was induced by drought stress in the wheat. Our study shows that PEPC can improve both stress tolerance and grain yield in wheat, demonstrating the efficacy of PEPC in crop improvement.
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Affiliation(s)
- Na Qin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China
| | - Weigang Xu
- Wheat Research Institute, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, Henan, China.
| | - Lin Hu
- Wheat Research Institute, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, Henan, China
| | - Yan Li
- Wheat Research Institute, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, Henan, China
| | - Huiwei Wang
- Wheat Research Institute, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, Henan, China
| | - Xueli Qi
- Wheat Research Institute, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, Henan, China
| | - Yuhui Fang
- Wheat Research Institute, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, Henan, China
| | - Xia Hua
- Wheat Research Institute, Henan Academy of Agricultural Sciences, 450002, Zhengzhou, Henan, China
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26
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Sanchez-Lucas R, Mehta A, Valledor L, Cabello-Hurtado F, Romero-Rodrıguez MC, Simova-Stoilova L, Demir S, Rodriguez-de-Francisco LE, Maldonado-Alconada AM, Jorrin-Prieto AL, Jorrín-Novo JV. A year (2014-2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists. Proteomics 2016; 16:866-76. [PMID: 26621614 DOI: 10.1002/pmic.201500351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 12/23/2022]
Abstract
The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.
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Affiliation(s)
- Rosa Sanchez-Lucas
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, Brazil
| | - Luis Valledor
- Department of Biology of Organisms and Systems (BOS), University of Oviedo, Oviedo, Spain
| | | | - M Cristina Romero-Rodrıguez
- Centro Multidisciplinario de Investigaciones Tecnológicas, and Departamento de Fitoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Sekvan Demir
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Luis E Rodriguez-de-Francisco
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain.,INTEC-Sto. Domingo, Santo Domingo, República Dominicana
| | - Ana M Maldonado-Alconada
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Ana L Jorrin-Prieto
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
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27
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Xu X, Ji J, Ma X, Xu Q, Qi X, Chen X. Comparative Proteomic Analysis Provides Insight into the Key Proteins Involved in Cucumber ( Cucumis sativus L.) Adventitious Root Emergence under Waterlogging Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:1515. [PMID: 27790230 PMCID: PMC5062059 DOI: 10.3389/fpls.2016.01515] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/26/2016] [Indexed: 05/20/2023]
Abstract
Waterlogging is a common abiotic stress in both natural and agricultural systems, and it primarily affects plant growth by the slow oxygen diffusion in water. To sustain root function in the hypoxic environment, a key adaptation for waterlogging tolerant plants is the formation of adventitious roots (ARs). We found that cucumber waterlogging tolerant line Zaoer-N seedlings adapt to waterlogging stress by developing a larger number of ARs in hypocotyls, while almost no AR is generated in sensitive line Pepino. To understand the molecular mechanisms underlying AR emergence, the iTRAQ-based quantitative proteomics approach was employed to map the proteomes of hypocotyls cells of the Zaoer-N and Pepino under control and waterlogging conditions. A total of 5508 proteins were identified and 146 were differentially regulated proteins (DRPs), of which 47 and 56 DRPs were specific to tolerant and sensitive line, respectively. In the waterlogged Zaoer-N hypocotyls, DRPs related to alcohol dehydrogenases (ADH), 1-aminocyclopropane-1-carboxylicacid oxidases, peroxidases, 60S ribosomal proteins, GSDL esterases/lipases, histone deacetylases, and histone H5 and were strongly overrepresented to manage the energy crisis, promote ethylene release, minimize oxidative damage, mobilize storage lipids, and stimulate cell division, differentiation and growth. The evaluations of ethylene production, ADH activity, pyruvate decarboxylase (PDC) activity and ethanol production were in good agreement with the proteomic results. qRT-PCR analysis of the corresponding 146 genes further confirmed the accuracy of the observed protein abundance. These findings shed light on the mechanisms underlying waterlogging triggered cucumber ARs emergence, and provided valuable information for the breeding of cucumber with enhanced tolerance to waterlogging.
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Kosová K, Vítámvás P, Urban MO, Klíma M, Roy A, Prášil IT. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops--A Proteomic Perspective. Int J Mol Sci 2015; 16:20913-42. [PMID: 26340626 PMCID: PMC4613235 DOI: 10.3390/ijms160920913] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/16/2015] [Accepted: 08/10/2015] [Indexed: 12/26/2022] Open
Abstract
Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.
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Affiliation(s)
- Klára Kosová
- Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 16106 Prague, Czech Republic.
| | - Pavel Vítámvás
- Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 16106 Prague, Czech Republic.
| | - Milan Oldřich Urban
- Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 16106 Prague, Czech Republic.
| | - Miroslav Klíma
- Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 16106 Prague, Czech Republic.
| | - Amitava Roy
- Research Institute of Agricultural Engineering, Drnovská 507, 16106 Prague, Czech Republic.
| | - Ilja Tom Prášil
- Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, Drnovská 507/73, 16106 Prague, Czech Republic.
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