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Shaheen N, Hossen MS, Akhter KT, Halima O, Hasan MK, Wahab A, Gamagedara S, Bhargava K, Holmes T, Najar FZ, Khandaker M, Peng Z, Yang Z, Ahsan N. Comparative Seed Proteome Profile Reveals No Alternation of Major Allergens in High-Yielding Mung Bean Cultivars. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38836763 DOI: 10.1021/acs.jafc.4c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Mung bean contains up to 32.6% protein and is one of the great sources of plant-based protein. Because many allergens also function as defense-related proteins, it is important to determine their abundance levels in the high-yielding, disease-resistant cultivars. In this study, for the first time, we compared the seed proteome of high-yielding mung bean cultivars developed by a conventional breeding approach. Using a label-free quantitative proteomic platform, we successfully identified and quantified a total of 1373 proteins. Comparative analysis between the high-yielding disease-resistant cultivar (MC5) and the other three cultivars showed that a total of 69 common proteins were significantly altered in their abundances across all cultivars. Bioinformatic analysis of these altered proteins demonstrated that PDF1 (a defensin-like protein) exhibited high sequence similarity and epitope matching with the established peanut allergens, indicating a potential mung bean allergen that showed a cultivar-specific response. Conversely, known mung bean allergen proteins such as PR-2/PR-10 (Vig r 1), Vig r 2, Vig r 4, LTP1, β-conglycinin, and glycinin G4 showed no alternation in the MC5 compared to other cultivars. Taken together, our findings suggest that the known allergen profiles may not be impacted by the conventional plant breeding method to develop improved mung bean cultivars.
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Affiliation(s)
- Nazma Shaheen
- Institute of Nutrition and Food Science, University of Dhaka, Dhaka 1000, Bangladesh
| | - Md Sujan Hossen
- Bangladesh Council of Scientific and Industrial Research, Dhaka 1205, Bangladesh
| | - Kazi Turjaun Akhter
- Institute of Nutrition and Food Science, University of Dhaka, Dhaka 1000, Bangladesh
| | - Oumma Halima
- Institute of Nutrition and Food Science, University of Dhaka, Dhaka 1000, Bangladesh
| | - Md Kamrul Hasan
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Asfia Wahab
- Department of Biology, University of York, York YO10, U.K
| | - Sanjeewa Gamagedara
- Department of Chemistry, University of Central Oklahoma, Edmond, Oklahoma 73034, United States
| | - Kanika Bhargava
- Department of Human Environmental Sciences, University of Central Oklahoma, Edmond, Oklahoma 73034, United States
| | - Tawni Holmes
- Department of Human Environmental Sciences, University of Central Oklahoma, Edmond, Oklahoma 73034, United States
| | - Fares Z Najar
- High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Morshed Khandaker
- Nanobiology Laboratory, School of Engineering, University of Central Oklahoma, Edmond, Oklahoma 73034, United States
| | - Zongkai Peng
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Nagib Ahsan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma 73019, United States
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Hong H, Li M, Chen Y, Wang H, Wang J, Guo B, Gao H, Ren H, Yuan M, Han Y, Qiu L. Genome-wide association studies for soybean epicotyl length in two environments using 3VmrMLM. FRONTIERS IN PLANT SCIENCE 2022; 13:1033120. [PMID: 36452100 PMCID: PMC9704727 DOI: 10.3389/fpls.2022.1033120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/04/2022] [Indexed: 06/17/2023]
Abstract
Germination of soybean seed is the imminent vital process after sowing. The status of plumular axis and radicle determine whether soybean seed can emerge normally. Epicotyl, an organ between cotyledons and first functional leaves, is essential for soybean seed germination, seedling growth and early morphogenesis. Epicotyl length (EL) is a quantitative trait controlled by multiple genes/QTLs. Here, the present study analyzes the phenotypic diversity and genetic basis of EL using 951 soybean improved cultivars and landraces from Asia, America, Europe and Africa. 3VmrMLM was used to analyze the associations between EL in 2016 and 2020 and 1,639,846 SNPs for the identification of QTNs and QTN-by-environment interactions (QEIs)".A total of 180 QTNs and QEIs associated with EL were detected. Among them, 74 QTNs (ELS_Q) and 16 QEIs (ELS_QE) were identified to be associated with ELS (epicotyl length of single plant emergence), and 60 QTNs (ELT_Q) and 30 QEIs (ELT_QE) were identified to be associated with ELT (epicotyl length of three seedlings). Based on transcript abundance analysis, GO (Gene Ontology) enrichment and haplotype analysis, ten candidate genes were predicted within nine genic SNPs located in introns, upstream or downstream, which were supposed to be directly or indirectly involved in the process of seed germination and seedling development., Of 10 candidate genes, two of them (Glyma.04G122400 and Glyma.18G183600) could possibly affect epicotyl length elongation. These results indicate the genetic basis of EL and provides a valuable basis for specific functional studies of epicotyl traits.
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Affiliation(s)
- Huilong Hong
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mei Li
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yijie Chen
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Haorang Wang
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, China
| | - Jun Wang
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Bingfu Guo
- Nanchang Branch of National Center of Oil crops Improvement, Jiangxi Province Key Laboratory of Oil crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Huawei Gao
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglei Ren
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ming Yuan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, China
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Bhat KA, Mahajan R, Pakhtoon MM, Urwat U, Bashir Z, Shah AA, Agrawal A, Bhat B, Sofi PA, Masi A, Zargar SM. Low Temperature Stress Tolerance: An Insight Into the Omics Approaches for Legume Crops. FRONTIERS IN PLANT SCIENCE 2022; 13:888710. [PMID: 35720588 PMCID: PMC9204169 DOI: 10.3389/fpls.2022.888710] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/27/2022] [Indexed: 05/27/2023]
Abstract
The change in climatic conditions is the major cause for decline in crop production worldwide. Decreasing crop productivity will further lead to increase in global hunger rate. Climate change results in environmental stress which has negative impact on plant-like deficiencies in growth, crop yield, permanent damage, or death if the plant remains in the stress conditions for prolonged period. Cold stress is one of the main abiotic stresses which have already affected the global crop production. Cold stress adversely affects the plants leading to necrosis, chlorosis, and growth retardation. Various physiological, biochemical, and molecular responses under cold stress have revealed that the cold resistance is more complex than perceived which involves multiple pathways. Like other crops, legumes are also affected by cold stress and therefore, an effective technique to mitigate cold-mediated damage is critical for long-term legume production. Earlier, crop improvement for any stress was challenging for scientific community as conventional breeding approaches like inter-specific or inter-generic hybridization had limited success in crop improvement. The availability of genome sequence, transcriptome, and proteome data provides in-depth sight into different complex mechanisms under cold stress. Identification of QTLs, genes, and proteins responsible for cold stress tolerance will help in improving or developing stress-tolerant legume crop. Cold stress can alter gene expression which further leads to increases in stress protecting metabolites to cope up the plant against the temperature fluctuations. Moreover, genetic engineering can help in development of new cold stress-tolerant varieties of legume crop. This paper provides a general insight into the "omics" approaches for cold stress in legume crops.
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Affiliation(s)
- Kaisar Ahmad Bhat
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Reetika Mahajan
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
| | - Mohammad Maqbool Pakhtoon
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
- Department of Life Sciences, Rabindranath Tagore University, Bhopal, India
| | - Uneeb Urwat
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
| | - Zaffar Bashir
- Deparment of Microbiology, University of Kashmir, Srinagar, India
| | - Ali Asghar Shah
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ankit Agrawal
- Department of Life Sciences, Rabindranath Tagore University, Bhopal, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Parvaze A. Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
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Significance of brassinosteroids and their derivatives in the development and protection of plants under abiotic stress. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00853-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Modifications of morphological and anatomical characteristics of plants by application of brassinosteroids under various abiotic stress conditions - A review. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.06.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants. Proc Natl Acad Sci U S A 2016; 113:E5982-E5991. [PMID: 27655893 DOI: 10.1073/pnas.1611477113] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Brassinosteroids (BRs) are growth-promoting plant hormones that play a role in abiotic stress responses, but molecular modes that enable this activity remain largely unknown. Here we show that BRs participate in the regulation of freezing tolerance. BR signaling-defective mutants of Arabidopsis thaliana were hypersensitive to freezing before and after cold acclimation. The constitutive activation of BR signaling, in contrast, enhanced freezing resistance. Evidence is provided that the BR-controlled basic helix-loop-helix transcription factor CESTA (CES) can contribute to the constitutive expression of the C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR (CBF) transcriptional regulators that control cold responsive (COR) gene expression. In addition, CBF-independent classes of BR-regulated COR genes are identified that are regulated in a BR- and CES-dependent manner during cold acclimation. A model is presented in which BRs govern different cold-responsive transcriptional cascades through the posttranslational modification of CES and redundantly acting factors. This contributes to the basal resistance against freezing stress, but also to the further improvement of this resistance through cold acclimation.
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Černý M, Novák J, Habánová H, Cerna H, Brzobohatý B. Role of the proteome in phytohormonal signaling. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:1003-15. [PMID: 26721743 DOI: 10.1016/j.bbapap.2015.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/30/2015] [Accepted: 12/16/2015] [Indexed: 02/07/2023]
Abstract
Phytohormones are orchestrators of plant growth and development. A lot of time and effort has been invested in attempting to comprehend their complex signaling pathways but despite success in elucidating some key components, molecular mechanisms in the transduction pathways are far from being resolved. The last decade has seen a boom in the analysis of phytohormone-responsive proteins. Abscisic acid, auxin, brassinosteroids, cytokinin, ethylene, gibberellins, nitric oxide, oxylipins, strigolactones, salicylic acid--all have been analyzed to various degrees. For this review, we collected data from proteome-wide analyses resulting in a list of over 2000 annotated proteins from Arabidopsis proteomics and nearly 500 manually filtered protein families merged from all the data available from different species. We present the currently accepted model of phytohormone signaling, highlight the contributions made by proteomic-based research and describe the key nodes in phytohormone signaling networks, as revealed by proteome analysis. These include ubiquitination and proteasome mediated degradation, calcium ion signaling, redox homeostasis, and phosphoproteome dynamics. Finally, we discuss potential pitfalls and future perspectives in the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Martin Černý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Jan Novák
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Hana Habánová
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Hana Cerna
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | - Břetislav Brzobohatý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
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Robison FM, Heuberger AL, Brick MA, Prenni JE. Proteome Characterization of Leaves in Common Bean. Proteomes 2015; 3:236-248. [PMID: 28248269 PMCID: PMC5217379 DOI: 10.3390/proteomes3030236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/30/2015] [Accepted: 08/07/2015] [Indexed: 01/12/2023] Open
Abstract
Dry edible bean (Phaseolus vulgaris L.) is a globally relevant food crop. The bean genome was recently sequenced and annotated allowing for proteomics investigations aimed at characterization of leaf phenotypes important to agriculture. The objective of this study was to utilize a shotgun proteomics approach to characterize the leaf proteome and to identify protein abundance differences between two bean lines with known variation in their physiological resistance to biotic stresses. Overall, 640 proteins were confidently identified. Among these are proteins known to be involved in a variety of molecular functions including oxidoreductase activity, binding peroxidase activity, and hydrolase activity. Twenty nine proteins were found to significantly vary in abundance (p-value < 0.05) between the two bean lines, including proteins associated with biotic stress. To our knowledge, this work represents the first large scale shotgun proteomic analysis of beans and our results lay the groundwork for future studies designed to investigate the molecular mechanisms involved in pathogen resistance.
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Affiliation(s)
- Faith M Robison
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO 80523, USA.
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Adam L Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523, USA.
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Jessica E Prenni
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO 80523, USA.
- Department of Biochemistry, Colorado State University, Fort Collins, CO 80523, USA.
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Lin LL, Hsu CL, Hu CW, Ko SY, Hsieh HL, Huang HC, Juan HF. Integrating Phosphoproteomics and Bioinformatics to Study Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis. BMC Genomics 2015; 16:533. [PMID: 26187819 PMCID: PMC4506601 DOI: 10.1186/s12864-015-1753-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 07/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein phosphorylation regulated by plant hormone is involved in the coordination of fundamental plant development. Brassinosteroids (BRs), a group of phytohormones, regulated phosphorylation dynamics remains to be delineated in plants. In this study, we performed a mass spectrometry (MS)-based phosphoproteomics to conduct a global and dynamic phosphoproteome profiling across five time points of BR treatment in the period between 5 min and 12 h. MS coupling with phosphopeptide enrichment techniques has become the powerful tool for profiling protein phosphorylation. However, MS-based methods tend to have data consistency and coverage issues. To address these issues, bioinformatics approaches were used to complement the non-detected proteins and recover the dynamics of phosphorylation events. RESULTS A total of 1104 unique phosphorylated peptides from 739 unique phosphoproteins were identified. The time-dependent gene ontology (GO) analysis shows the transition of biological processes from signaling transduction to morphogenesis and stress response. The protein-protein interaction analysis found that most of identified phosphoproteins have strongly connections with known BR signaling components. The analysis by using Motif-X was performed to identify 15 enriched motifs, 11 of which correspond to 6 known kinase families. To uncover the dynamic activities of kinases, the enriched motifs were combined with phosphorylation profiles and revealed that the substrates of casein kinase 2 and mitogen-activated protein kinase were significantly phosphorylated and dephosphorylated at initial time of BR treatment, respectively. The time-dependent kinase-substrate interaction networks were constructed and showed many substrates are the downstream of other signals, such as auxin and ABA signaling. While comparing BR responsive phosphoproteome and gene expression data, we found most of phosphorylation changes were not led by gene expression changes. Our results suggested many downstream proteins of BR signaling are induced by phosphorylation via various kinases, not through transcriptional regulation. CONCLUSIONS Through a large-scale dynamic profile of phosphoproteome coupled with bioinformatics, a complicated kinase-centered network related to BR-regulated growth was deciphered. The phosphoproteins and phosphosites identified in our study provide a useful dataset for revealing signaling networks of BR regulation, and also expanded our knowledge of protein phosphorylation modification in plants as well as further deal to solve the plant growth problems.
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Affiliation(s)
- Li-Ling Lin
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Chia-Lang Hsu
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Chia-Wei Hu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Shiao-Yun Ko
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Hsu-Liang Hsieh
- Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan.
| | - Hsueh-Fen Juan
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. .,Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. .,Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
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Asgher M, Khan MIR, Anjum NA, Khan NA. Minimising toxicity of cadmium in plants--role of plant growth regulators. PROTOPLASMA 2015; 252:399-413. [PMID: 25303855 DOI: 10.1007/s00709-014-0710-4] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 05/20/2023]
Abstract
A range of man-made activities promote the enrichment of world-wide agricultural soils with a myriad of chemical pollutants including cadmium (Cd). Owing to its significant toxic consequences in plants, Cd has been one of extensively studied metals. However, sustainable strategies for minimising Cd impacts in plants have been little explored. Plant growth regulators (PGRs) are known for their role in the regulation of numerous developmental processes. Among major PGRs, plant hormones (such as auxins, gibberellins, cytokinins, abscisic acid, jasmonic acid, ethylene and salicylic acid), nitric oxide (a gaseous signalling molecule), brassinosteroids (steroidal phytohormones) and polyamines (group of phytohormone-like aliphatic amine natural compounds with aliphatic nitrogen structure) have gained attention by agronomist and physiologist as a sustainable media to induce tolerance in abiotic-stressed plants. Considering recent literature, this paper: (a) overviews Cd status in soil and its toxicity in plants, (b) introduces major PGRs and overviews their signalling in Cd-exposed plants, (c) appraises mechanisms potentially involved in PGR-mediated enhanced plant tolerance to Cd and (d) highlights key aspects so far unexplored in the subject area.
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Affiliation(s)
- Mohd Asgher
- Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
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Jin SH, Li XQ, Wang GG, Zhu XT. Brassinosteroids alleviate high-temperature injury in Ficus concinna seedlings via maintaining higher antioxidant defence and glyoxalase systems. AOB PLANTS 2015; 7:plv009. [PMID: 25609563 PMCID: PMC4344480 DOI: 10.1093/aobpla/plv009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Although brassinosteroids (BRs) play crucial roles in plant development and stress tolerance, the mechanisms by which they have these effects are poorly understood. Here, we investigated the possible mechanism of exogenously applied BRs on reactive oxygen species (ROS), antioxidant defence and methylglyoxal (MG) detoxification systems in Ficus concinna seedlings grown under high-temperature (HT) stress for 48 h. Our results showed that the activities of ascorbate peroxidase (APX), superoxide dismutase (SOD), glutathione S-transferase (GST), glutathione peroxidase (GPX) and glyoxalase II (Gly II) were increased under two levels of HT stress. Compared with control the activities of catalase (CAT) and dehydroascorbate reductase (DHAR) were not changed due to HT stress. The activities of glutathione reductase (GR), monodehydroascorbate reductase (MDHAR) and glyoxalase I (Gly I) were increased only at moderate HT stress. Despite these protective mechanisms, HT stress induced oxidative stress in F. concinna seedlings, as indicated by the increased levels of ROS, malondialdehyde (MDA) and MG, and the reductions in chlorophyll levels and relative water content. The contents of reduced glutathione (GSH) and ascorbate (AsA) were not changed under moderate HT stress. Spraying with 24-epibrassinolide (EBR) alone had little influence on the non-enzymatic antioxidants and the activities of antioxidant enzymes. However, EBR pretreatment under HT stress resulted in an increase in GSH and AsA content, maintenance of high redox state of GSH and AsA, and enhanced ROS and MG detoxification by further elevating the activities of SOD, GST, GPX, APX, MDHAR, GR, DHAR, Gly I and Gly II, as evident by lower level of ROS, MDA and MG. It may be concluded that EBR could alleviate the HT-induced oxidative stress by increasing the enzymatic and non-enzymatic antioxidant defence, and glyoxalase systems in F. concinna seedlings.
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Affiliation(s)
- Song Heng Jin
- Jiyang College, Zhejiang A & F University, Zhuji, Zhejiang Province 311800, China School of Forestry and Biotechnology, Zhejiang A & F University, Lin'an, Zhejiang Province 311300, China
| | - Xue Qin Li
- Jiyang College, Zhejiang A & F University, Zhuji, Zhejiang Province 311800, China
| | - G Geoff Wang
- Department of Forestry and Natural Resources, Clemson University, 226 Lehotsky Hall, Clemson, SC 29634-0317, USA
| | - Xiang Tao Zhu
- Jiyang College, Zhejiang A & F University, Zhuji, Zhejiang Province 311800, China
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Komatsu S, Kamal AHM, Hossain Z. Wheat proteomics: proteome modulation and abiotic stress acclimation. FRONTIERS IN PLANT SCIENCE 2014; 5:684. [PMID: 25538718 PMCID: PMC4259124 DOI: 10.3389/fpls.2014.00684] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 11/18/2014] [Indexed: 05/21/2023]
Abstract
Cellular mechanisms of stress sensing and signaling represent the initial plant responses to adverse conditions. The development of high-throughput "Omics" techniques has initiated a new era of the study of plant molecular strategies for adapting to environmental changes. However, the elucidation of stress adaptation mechanisms in plants requires the accurate isolation and characterization of stress-responsive proteins. Because the functional part of the genome, namely the proteins and their post-translational modifications, are critical for plant stress responses, proteomic studies provide comprehensive information about the fine-tuning of cellular pathways that primarily involved in stress mitigation. This review summarizes the major proteomic findings related to alterations in the wheat proteomic profile in response to abiotic stresses. Moreover, the strengths and weaknesses of different sample preparation techniques, including subcellular protein extraction protocols, are discussed in detail. The continued development of proteomic approaches in combination with rapidly evolving bioinformatics tools and interactive databases will facilitate understanding of the plant mechanisms underlying stress tolerance.
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Affiliation(s)
- Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Abu H. M. Kamal
- National Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Zahed Hossain
- Plant Stress Biology Lab, Department of Botany, West Bengal State UniversityKolkata, India
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Jiang YP, Huang LF, Cheng F, Zhou YH, Xia XJ, Mao WH, Shi K, Yu JQ. Brassinosteroids accelerate recovery of photosynthetic apparatus from cold stress by balancing the electron partitioning, carboxylation and redox homeostasis in cucumber. PHYSIOLOGIA PLANTARUM 2013; 148:133-45. [PMID: 22998725 DOI: 10.1111/j.1399-3054.2012.01696.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/03/2012] [Accepted: 08/10/2012] [Indexed: 05/20/2023]
Abstract
The aim of this study was to examine the role of brassinosteroids (BRs) in protecting the photosynthetic apparatus from cold-induced damage in cucumber (Cucumis sativus) plants. Recovery at both high light (HL) and low light (LL) after a cooling at 10/7°C induced irreversible inhibition of CO2 assimilation, photoinhibition at photosystem I (PSI) and inhibition of enzyme activities of Calvin cycle and ascorbate (AsA)-reduced glutathione (GSH) cycle, followed by accumulation of H2 O2 and malondialdehyde. However, cold-induced photoinhibition at PSII was fully recovered at LL but not at HL. Meanwhile, recovery at HL increased electron flux to O2 -dependent alternative pathway [Ja(O2 -dependent)]. Foliar application of 24-epibrassinolide (EBR) accelerated recovery from photoinhibition of PSII but not of PSI. EBR also significantly increased CO2 assimilation, activity of Calvin cycle enzymes and electron flux to carbon reduction [Je(PCR)], with a concomitant decrease in Ja(O2 -dependent); meanwhile EBR increased the activity of enzymes in AsA-GSH cycle and cellular redox states. However, the positive effect of EBR on plant recovery was observed only at HL, but not LL. These results indicate that BR accelerates the recovery of photosynthetic apparatus at HL by activation of enzymes in Calvin cycle and increasing the antioxidant capacity, which in turn mitigate the photooxidative stress and the inhibition of plant growth during the recovery.
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Affiliation(s)
- Yu-Ping Jiang
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang, 310058, PR China
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14
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Lucau-Danila A, Toitot C, Goulas E, Blervacq AS, Hot D, Bahrman N, Sellier H, Lejeune-Hénaut I, Delbreil B. Transcriptome analysis in pea allows to distinguish chilling and acclimation mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 58:236-44. [PMID: 22858528 DOI: 10.1016/j.plaphy.2012.07.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/12/2012] [Indexed: 05/04/2023]
Abstract
In order to distinguish chilling and freezing tolerance mechanisms in pea, responses to cold exposure were compared between the freezing tolerant line Champagne and the sensitive line Terese. Global gene expression was considered in the two lines and associated with morphological, histological and biochemical approaches. The chilling tolerance in both lines was related to responses of the CBF, COR and LEA genes belonging to the CBF regulon, with greater earliness of expression in the Champagne genotype. The freezing tolerance, only observed in Champagne, was associated with acclimation processes such as cellular osmotic stabilization, photosynthesis modifications, antioxidants production, modifications in hormone metabolism, cell wall composition and dynamics.
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Affiliation(s)
- A Lucau-Danila
- UMR 1281, Université Lille1-INRA, USTL, Stress Abiotiques et Différenciation des Végétaux cultivés, Bâtiment SN2, F-59650 Villeneuve d'Ascq, France.
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15
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Qu T, Liu R, Wang W, An L, Chen T, Liu G, Zhao Z. Brassinosteroids regulate pectin methylesterase activity and AtPME41 expression in Arabidopsis under chilling stress. Cryobiology 2011; 63:111-7. [PMID: 21819976 DOI: 10.1016/j.cryobiol.2011.07.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 06/28/2011] [Accepted: 07/19/2011] [Indexed: 01/13/2023]
Abstract
Pectin methylesterases (PMEs) are important cell wall enzymes that may play important roles in plant chilling/freezing tolerance. We investigated the possible roles of brassinosteroids (BRs) in regulation of PMEs under chilling stress. Chilling stress or 24-epibrassinolide (eBL) treatments induced significant increases in PME activity in wild type (Col-0) seedlings of Arabidopsis. The chilling-stress-induced increases in PME activity were also found in bzr1-D mutant, a BZR1 stabilized mutant with a constitutively active BR signaling pathway, but not in bri1-116, a BR insensitive null allele of the BR receptor BRI1. The results suggest that the regulation of PME activity in Arabidopsis under chilling stress depends on the BR signaling pathway. Furthermore, we showed that the effect of chilling stress on PME activity was impaired in pme41, a knockout mutant of AtPME41. Semi-quantitative RT-PCR results showed that expression of AtPME41 was induced by chilling stress in wild type plants but not in the bri1-116 mutant. The expression of AtPME41 increased in bzr1-D and eBL treated wild type seedlings, but decreased in bri1-116 seedlings. Furthermore, ion leakage induced by low temperature were dramatically increased in both bri1-116 and pme41, while lipid peroxidation was increased in bri1-116 only. The results suggest that BRs may modulate total PME activity in Arabidopsis under chilling stress by regulating AtPME41 expression. Regulation of PME activity may serve as one of the mechanisms that BR participates in chilling tolerance of plants.
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Affiliation(s)
- Tao Qu
- School of Life Sciences, Key Lab of Arid and Grassland Agroecology of MOE, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, China
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16
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Sengupta D, Kannan M, Reddy AR. A root proteomics-based insight reveals dynamic regulation of root proteins under progressive drought stress and recovery in Vigna radiata (L.) Wilczek. PLANTA 2011; 233:1111-1127. [PMID: 21298284 DOI: 10.1007/s00425-011-1365-1364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 01/14/2011] [Indexed: 05/18/2023]
Abstract
To understand the complex drought response mechanism in crop plants, a systematic root proteomics approach was adopted to identify and analyze the expression patterns of differentially expressed major root proteins of Vigna radiata during short-term (3 days) and consecutive long-term water-deficit (6 days) as well as during recovery (6 days after re-watering). Photosynthetic gas exchange parameters of the plant were measured simultaneously during the stress treatment and recovery period. A total of 26 major protein spots were successfully identified by mass spectrometry, which were grouped according to their expression pattern during short-term stress as significantly up-regulated (9), down-regulated (10), highly down-regulated, beyond detection level of the software (2) and unchanged (5). The subsequent changes in the expression patterns of these proteins during long-term stress treatment and recovery period was analyzed to focus on the dynamic regulation of these functionally important proteins during progressive drought and recovery period. Cytoskeleton-related proteins were down-regulated initially (3d) but regained their expression levels during subsequent water-deficit (6d) while glycoprotein like lectins, which were primarily known to be involved in legume-rhizobia symbiosis, maintained their enhanced expression levels during both short and long-term drought treatment indicating their possible role in drought stress response of legumes. Oxidative stress-related proteins including Cu/Zn superoxide dismutase, oxidoreductase and aldehyde reductase were also up-regulated. The analyses of the dynamic regulation of these root proteins during short- and long-term water-deficit as well as recovery period may prove crucial for further understanding of drought response mechanisms in food legumes.
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Affiliation(s)
- Debashree Sengupta
- Photosynthesis and Plant Stress Biology Laboratory, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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17
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Sengupta D, Kannan M, Reddy AR. A root proteomics-based insight reveals dynamic regulation of root proteins under progressive drought stress and recovery in Vigna radiata (L.) Wilczek. PLANTA 2011; 233:1111-27. [PMID: 21298284 DOI: 10.1007/s00425-011-1365-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 01/14/2011] [Indexed: 05/20/2023]
Abstract
To understand the complex drought response mechanism in crop plants, a systematic root proteomics approach was adopted to identify and analyze the expression patterns of differentially expressed major root proteins of Vigna radiata during short-term (3 days) and consecutive long-term water-deficit (6 days) as well as during recovery (6 days after re-watering). Photosynthetic gas exchange parameters of the plant were measured simultaneously during the stress treatment and recovery period. A total of 26 major protein spots were successfully identified by mass spectrometry, which were grouped according to their expression pattern during short-term stress as significantly up-regulated (9), down-regulated (10), highly down-regulated, beyond detection level of the software (2) and unchanged (5). The subsequent changes in the expression patterns of these proteins during long-term stress treatment and recovery period was analyzed to focus on the dynamic regulation of these functionally important proteins during progressive drought and recovery period. Cytoskeleton-related proteins were down-regulated initially (3d) but regained their expression levels during subsequent water-deficit (6d) while glycoprotein like lectins, which were primarily known to be involved in legume-rhizobia symbiosis, maintained their enhanced expression levels during both short and long-term drought treatment indicating their possible role in drought stress response of legumes. Oxidative stress-related proteins including Cu/Zn superoxide dismutase, oxidoreductase and aldehyde reductase were also up-regulated. The analyses of the dynamic regulation of these root proteins during short- and long-term water-deficit as well as recovery period may prove crucial for further understanding of drought response mechanisms in food legumes.
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Affiliation(s)
- Debashree Sengupta
- Photosynthesis and Plant Stress Biology Laboratory, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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18
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Dumont E, Bahrman N, Goulas E, Valot B, Sellier H, Hilbert JL, Vuylsteker C, Lejeune-Hénaut I, Delbreil B. A proteomic approach to decipher chilling response from cold acclimation in pea (Pisum sativum L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:86-98. [PMID: 21421351 DOI: 10.1016/j.plantsci.2010.09.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 09/16/2010] [Accepted: 09/20/2010] [Indexed: 05/05/2023]
Abstract
Two pea lines (Pisum sativum L.) with contrasted behaviours towards chilling and subsequent frost were studied by a proteomic approach to better understand cold acclimation. Following a chilling period, the Champagne line becomes tolerant to frost whereas Terese remains sensitive. Variance analysis allowed to select 260 statistically variable spots with 68 identified proteins (35 in leaves, 18 in stems, and 15 in roots). These proteins were shared out in proteins related to chilling response or cold acclimation. The better adaptation of Champagne to chilling might be related to a higher content in proteins involved in photosynthesis and in defence mechanisms. Moreover Champagne might prevent freezing damage particularly thanks to a higher constitutive expression of housekeeping proteins related to Terese. After three days of subsequent frost, proteomes of previously chilled plants also showed significant differences compared to unchilled plants. Out of 112 statistically variable spots (44 in leaves, 38 in stems, and 30 in roots), 32 proteins were identified. These proteins were related to frost response or frost resistance. It seems that Champagne could resist to frost with the reorientation of the energy metabolism.
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Affiliation(s)
- Estelle Dumont
- USTL INRA UMR 1281, Laboratoire des Stress Abiotiques et Différenciation des Végétaux Cultivés bât SN2, 3ème étage, Université des Sciences et Technologies de Lille 1, F-59655 Villeneuve d'Ascq, France
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19
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Neilson KA, Gammulla CG, Mirzaei M, Imin N, Haynes PA. Proteomic analysis of temperature stress in plants. Proteomics 2010; 10:828-45. [PMID: 19953552 DOI: 10.1002/pmic.200900538] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this review we examine current approaches used for proteomic analysis of temperature stress in plants. Rapid advances in this field in recent years are discussed, including metabolic, chemical and isotopic labeling, and label-free quantitative techniques. These are compared and contrasted with well-established methods such as 2-DE approaches. Examples of applications of various methods are presented, and technical difficulties and limitations of each are also considered. Results of previous studies are examined in detail, and commonly occurring temperature stress response proteins are collated. We conclude that technical advances, and improvements in genome sequence availability, will have an ever increasing impact on our understanding of molecular mechanisms of stress response in plants.
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Affiliation(s)
- Karlie A Neilson
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW, Australia
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20
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Gaur V, Qureshi IA, Singh A, Chanana V, Salunke DM. Crystal structure and functional insights of hemopexin fold protein from grass pea. PLANT PHYSIOLOGY 2010; 152:1842-50. [PMID: 20147493 PMCID: PMC2850029 DOI: 10.1104/pp.109.150680] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2009] [Accepted: 02/08/2010] [Indexed: 05/15/2023]
Abstract
A regulatory protein from grass pea (Lathyrus sativus), LS-24, a close homolog of albumin 2 from garden pea (Pisum sativum) that is associated with polyamine biosynthesis, was characterized and the structure of a hemopexin-type fold among plant proteins illustrated. Crystal structure of LS-24 determined at 2.2 A resolution by multiple isomorphous replacement phasing showed four-bladed beta-propeller structure having a pseudo 4-fold molecular symmetry along a metal ion-binding central channel. The structure represents typical mammalian hemopexin fold with discernible features correlated with the possible functional variations. The protein was found to exist in the dimeric state. While LS-24 dimer binds to spermine in the crystal structure as well as in solution, binding of heme in solution resulted in the dissociation of the dimer into monomers with concomitant release of bound spermine. Interactions of heme and spermine with LS-24 bear physiological implications. While binding of spermine to LS-24 can be linked with polyamine biosynthesis that of heme correlates with oxidative stress. Mutually exclusive binding of heme and spermine in different oligomeric states suggest a role for LS-24 in sensing oxidative stress through a ligand-regulated monomer-dimer transition switch.
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Affiliation(s)
| | | | | | | | - Dinakar M. Salunke
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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21
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Gao X, Zhang X, Zheng J, He F. Proteomics in China: Ready for prime time. SCIENCE CHINA-LIFE SCIENCES 2010; 53:22-33. [DOI: 10.1007/s11427-010-0027-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Accepted: 12/28/2009] [Indexed: 12/27/2022]
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22
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Bai S, Willard B, Chapin LJ, Kinter MT, Francis DM, Stead AD, Jones ML. Proteomic analysis of pollination-induced corolla senescence in petunia. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:1089-109. [PMID: 20110265 PMCID: PMC2826652 DOI: 10.1093/jxb/erp373] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Senescence represents the last phase of petal development during which macromolecules and organelles are degraded and nutrients are recycled to developing tissues. To understand better the post-transcriptional changes regulating petal senescence, a proteomic approach was used to profile protein changes during the senescence of Petuniaxhybrida 'Mitchell Diploid' corollas. Total soluble proteins were extracted from unpollinated petunia corollas at 0, 24, 48, and 72 h after flower opening and at 24, 48, and 72 h after pollination. Two-dimensional gel electrophoresis (2-DE) was used to identify proteins that were differentially expressed in non-senescing (unpollinated) and senescing (pollinated) corollas, and image analysis was used to determine which proteins were up- or down-regulated by the experimentally determined cut-off of 2.1-fold for P <0.05. One hundred and thirty-three differentially expressed protein spots were selected for sequencing. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to determine the identity of these proteins. Searching translated EST databases and the NCBI non-redundant protein database, it was possible to assign a putative identification to greater than 90% of these proteins. Many of the senescence up-regulated proteins were putatively involved in defence and stress responses or macromolecule catabolism. Some proteins, not previously characterized during flower senescence, were identified, including an orthologue of the tomato abscisic acid stress ripening protein 4 (ASR4). Gene expression patterns did not always correlate with protein expression, confirming that both proteomic and genomic approaches will be required to obtain a detailed understanding of the regulation of petal senescence.
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Affiliation(s)
- Shuangyi Bai
- Department of Horticulture and Crop Science, The Ohio State University, OARDC, 1680 Madison Ave, Wooster, Ohio 44691, USA
| | - Belinda Willard
- Proteomics Laboratory, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
| | - Laura J. Chapin
- Department of Horticulture and Crop Science, The Ohio State University, OARDC, 1680 Madison Ave, Wooster, Ohio 44691, USA
| | - Michael T. Kinter
- Proteomics Laboratory, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
| | - David M. Francis
- Department of Horticulture and Crop Science, The Ohio State University, OARDC, 1680 Madison Ave, Wooster, Ohio 44691, USA
| | - Anthony D. Stead
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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23
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Cell wall proteome of wheat roots under flooding stress using gel-based and LC MS/MS-based proteomics approaches. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:124-36. [PMID: 19786127 DOI: 10.1016/j.bbapap.2009.09.023] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 09/18/2009] [Accepted: 09/21/2009] [Indexed: 11/21/2022]
Abstract
Cell wall proteins (CWPs) are important both for maintenance of cell structure and for responses to abiotic and biotic stresses. In this study, a destructive CWP purification procedure was adopted using wheat seedling roots and the purity of the CWP extract was confirmed by minimizing the activity of glucose-6-phosphate dehydrogenase, a cytoplasmic marker enzyme. To determine differentially expressed CWPs under flooding stress, gel-based proteomic and LC-MS/MS-based proteomic techniques were applied. Eighteen proteins were found to be significantly regulated in response to flood by gel-based proteomics and 15 proteins by LC MS/MS-based proteomics. Among the flooding down-regulated proteins, most were related to the glycolysis pathway and cell wall structure and modification. However, the most highly up-regulated proteins in response to flooding belong to the category of defense and disease response proteins. Among these differentially expressed proteins, only methionine synthase, beta-1,3-glucanases, and beta-glucosidase were consistently identified by both techniques. The down-regulation of these three proteins suggested that wheat seedlings respond to flooding stress by restricting cell growth to avoid energy consumption; by coordinating methionine assimilation and cell wall hydrolysis, CWPs played critical roles in flooding responsiveness.
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24
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Bajguz A, Hayat S. Effects of brassinosteroids on the plant responses to environmental stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2009; 47:1-8. [PMID: 19010688 DOI: 10.1016/j.plaphy.2008.10.002] [Citation(s) in RCA: 333] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 10/01/2008] [Indexed: 05/18/2023]
Abstract
Brassinosteroids are found in a wide range of organisms from lower to higher plants. They are steroidal plant hormones implicated in the promotion of plant growth and development. Brassinosteroid metabolism has long been known to be altered in plants responding to abiotic stresses and to undergo profound changes in plants interacting with bacterial, fungal and viral pathogens. This review describes the role of brassinosteroids in response to various kinds of stresses via activation of different mechanisms.
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Affiliation(s)
- Andrzej Bajguz
- Department of Plant Biochemistry, University of Bialystok, Swierkowa 20B, 15-950 Bialystok, Poland.
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25
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The interactome: predicting the protein-protein interactions in cells. Cell Mol Biol Lett 2008; 14:1-22. [PMID: 18839074 PMCID: PMC6275871 DOI: 10.2478/s11658-008-0024-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 04/03/2008] [Indexed: 12/03/2022] Open
Abstract
The term Interactome describes the set of all molecular interactions in cells, especially in the context of protein-protein interactions. These interactions are crucial for most cellular processes, so the full representation of the interaction repertoire is needed to understand the cell molecular machinery at the system biology level. In this short review, we compare various methods for predicting protein-protein interactions using sequence and structure information. The ultimate goal of those approaches is to present the complete methodology for the automatic selection of interaction partners using their amino acid sequences and/or three dimensional structures, if known. Apart from a description of each method, details of the software or web interface needed for high throughput prediction on the whole genome scale are also provided. The proposed validation of the theoretical methods using experimental data would be a better assessment of their accuracy.
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26
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Tang W, Deng Z, Oses-Prieto JA, Suzuki N, Zhu S, Zhang X, Burlingame AL, Wang ZY. Proteomics studies of brassinosteroid signal transduction using prefractionation and two-dimensional DIGE. Mol Cell Proteomics 2008; 7:728-38. [PMID: 18182375 DOI: 10.1074/mcp.m700358-mcp200] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Signal transduction involves posttranslational modifications and protein-protein interactions, which can be studied by proteomics. In Arabidopsis, the steroid hormone (brassinosteroid (BR)) binds to the extracellular domain of a receptor kinase (BRI1) to initiate a phosphorylation/dephosphorylation cascade that controls gene expression and plant growth. Here we detected early BR signaling events and identified early response proteins using prefractionation and two-dimensional (2-D) DIGE. Proteomic changes induced rapidly by BR treatments were detected in phosphoprotein and plasma membrane (PM) fractions by 2-D DIGE but not in total protein extracts. LC-MS/MS analysis of gel spots identified 19 BR-regulated PM proteins and six proteins from phosphoprotein fractions. These include the BAK1 receptor kinase and BZR1 transcription factor of the BR signaling pathway. Both proteins showed spot shifts consistent with BR-regulated phosphorylation. In addition, in vivo phosphorylation sites were identified for BZR1, two tetratricopeptide repeat proteins, and a phosphoenolpyruvate carboxykinase (PCK1). Overexpression of a novel BR-induced PM protein (DREPP) partially suppressed the phenotypes of a BR-deficient mutant, demonstrating its important function in BR responses. Our study demonstrates that prefractionation coupled with 2-D DIGE is a powerful approach for studying signal transduction.
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Affiliation(s)
- Wenqiang Tang
- Department of Plant Biology, Carnegie Institution of Washington, Stanford, California 94305, USA
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27
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Deng Z, Zhang X, Tang W, Oses-Prieto JA, Suzuki N, Gendron JM, Chen H, Guan S, Chalkley RJ, Peterman TK, Burlingame AL, Wang ZY. A proteomics study of brassinosteroid response in Arabidopsis. Mol Cell Proteomics 2007; 6:2058-71. [PMID: 17848588 PMCID: PMC2966871 DOI: 10.1074/mcp.m700123-mcp200] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The plant steroid hormones brassinosteroids (BRs) play an important role in a wide range of developmental and physiological processes. How BR signaling regulates diverse processes remains unclear. To understand the molecular details of BR responses, we performed a proteomics study of BR-regulated proteins in Arabidopsis using two-dimensional DIGE coupled with LC-MS/MS. We identified 42 BR-regulated proteins, which are predicted to play potential roles in BR regulation of specific cellular processes, such as signaling, cytoskeleton rearrangement, vesicle trafficking, and biosynthesis of hormones and vitamins. Analyses of the BR-insensitive mutant bri1-116 and BR-hypersensitive mutant bzr1-1D identified five proteins (PATL1, PATL2, THI1, AtMDAR3, and NADP-ME2) affected both by BR treatment and in the mutants, suggesting their importance in BR action. Selected proteins were further studied using insertion knock-out mutants or immunoblotting. Interestingly about 80% of the BR-responsive proteins were not identified in previous microarray studies, and direct comparison between protein and RNA changes in BR mutants revealed a very weak correlation. RT-PCR analysis of selected genes revealed gene-specific kinetic relationships between RNA and protein responses. Furthermore BR-regulated posttranslational modification of BiP2 protein was detected as spot shifts in two-dimensional DIGE. This study provides novel insights into the molecular networks that link BR signaling to specific cellular and physiological responses.
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Affiliation(s)
- Zhiping Deng
- Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA 94305
| | - Xin Zhang
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco CA 94143
| | - Wenqiang Tang
- Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA 94305
| | - Juan A Oses-Prieto
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco CA 94143
| | - Nagi Suzuki
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco CA 94143
| | - Joshua M Gendron
- Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA 94305
- Department of Biological Sciences, Stanford University, Stanford, CA 94305
| | - Huanjing Chen
- Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA 94305
| | - Shenheng Guan
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco CA 94143
| | - Robert J. Chalkley
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco CA 94143
| | - T. Kaye Peterman
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481
| | - Alma L. Burlingame
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco CA 94143
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA 94305
- To whom correspondence should be addressed: Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305. Phone: 650-325-1521 ext 205. Fax: 650-325-6857
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28
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Abstract
Low temperature is one of the important environmental changes that affect plant growth and agricultural production. To investigate the responses of rice to cold stress, changes in protein expression were analyzed using a proteomic approach. Two-week-old rice seedlings were exposed to 5 degrees C for 48 h, then total crude proteins were extracted from leaf blades, leaf sheaths and roots, separated by 2-DE and stained with CBB. Of the 250-400 protein spots from each organ, 39 proteins changed in abundance after cold stress, with 19 proteins increasing, and 20 proteins decreasing. In leaf blades, it was difficult to detect the changes in stress-responsive proteins due to the presence of an abundant protein, ribulose bisphosphate carboxylase/oxygenase large subunit (RuBisCO LSU), which accounted for about 50% of the total proteins. To overcome this problem, an antibody-affinity column was prepared to trap RuBisCO LSU, and the remaining proteins in the flow through from the column were subsequently separated using 2-DE. As a result, slight changes in stress responsive proteins were clearly displayed, and four proteins were newly detected after cold stress. From identified proteins, it was concluded that proteins related to energy metabolism were up-regulated, and defense-related proteins were down-regulated in leaf blades, by cold stress. These results suggest that energy production is activated in the chilling environment; furthermore, stress-related proteins are rapidly up-regulated, while defense-related proteins disappear, under long-term cold stress.
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