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Monterisi S, Zhang L, Garcia-Perez P, Alzate Zuluaga MY, Ciriello M, El-Nakhel C, Buffagni V, Cardarelli M, Colla G, Rouphael Y, Cesco S, Lucini L, Pii Y. Integrated multi-omic approach reveals the effect of a Graminaceae-derived biostimulant and its lighter fraction on salt-stressed lettuce plants. Sci Rep 2024; 14:10710. [PMID: 38729985 PMCID: PMC11087557 DOI: 10.1038/s41598-024-61576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/07/2024] [Indexed: 05/12/2024] Open
Abstract
Plant biostimulants are widely applied in agriculture for their ability to improve plant fitness. In the present work, the impact of Graminaceae-derived protein hydrolysate (P) and its lighter molecular fraction F3 (< 1 kDa) on lettuce plants, subjected to either no salt or high salt conditions, was investigated through the combination of metabolomics and transcriptomics. The results showed that both treatments significantly modulated the transcriptome and metabolome of plants under salinity stress, highlighting an induction of the hormonal response. Nevertheless, P and F3 also displayed several peculiarities. F3 specifically modulated the response to ethylene and MAPK signaling pathway, whereas P treatment induced a down-accumulation of secondary metabolites, albeit genes controlling the biosynthesis of osmoprotectants and antioxidants were up-regulated. Moreover, according with the auxin response modulation, P promoted cell wall biogenesis and plasticity in salt-stressed plants. Notably, our data also outlined an epigenetic control of gene expression induced by P treatment. Contrarily, experimental data are just partially in agreement when not stressed plants, treated with P or F3, were considered. Indeed, the reduced accumulation of secondary metabolites and the analyses of hormone pathways modulation would suggest a preferential allocation of resources towards growth, that is not coherent with the down-regulation of the photosynthetic machinery, the CO2 assimilation rate and leaves biomass. In conclusion, our data demonstrate that, although they might activate different mechanisms, both the P and F3 can result in similar benefits, as far as the accumulation of protective osmolytes and the enhanced tolerance to oxidative stress are concerned. Notably, the F3 fraction exhibits slightly greater growth promotion effects under high salt conditions. Most importantly, this research further corroborates that biostimulants' mode of action is dependent on plants' physiological status and their composition, underscoring the importance of investigating the bioactivity of the different molecular components to design tailored applications for the agricultural practice.
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Affiliation(s)
- Sonia Monterisi
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen/Bolzano, 39100, Bolzano, Italy
| | - Leilei Zhang
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Pascual Garcia-Perez
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | - Michele Ciriello
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Christophe El-Nakhel
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Valentina Buffagni
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100, Viterbo, Italy
| | - Mariateresa Cardarelli
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100, Viterbo, Italy
| | - Giuseppe Colla
- Department of Agriculture and Forest Sciences, University of Tuscia, 01100, Viterbo, Italy
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Stefano Cesco
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen/Bolzano, 39100, Bolzano, Italy
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Youry Pii
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen/Bolzano, 39100, Bolzano, Italy.
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Lu H, Zheng S, Ma C, Gao X, Ji J, Luo J, Hua H, Cui J. Integrated Omics Analysis Reveals Key Pathways in Cotton Defense against Mirid Bug ( Adelphocoris suturalis Jakovlev) Feeding. INSECTS 2024; 15:254. [PMID: 38667384 PMCID: PMC11049813 DOI: 10.3390/insects15040254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/05/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024]
Abstract
The recent dominance of Adelphocoris suturalis Jakovlev as the primary cotton field pest in Bt-cotton-cultivated areas has generated significant interest in cotton pest control research. This study addresses the limited understanding of cotton defense mechanisms triggered by A. suturalis feeding. Utilizing LC-QTOF-MS, we analyzed cotton metabolomic changes induced by A. suturalis, and identified 496 differential positive ions (374 upregulated, 122 downregulated) across 11 categories, such as terpenoids, alkaloids, phenylpropanoids, flavonoids, isoflavones, etc. Subsequent iTRAQ-LC-MS/MS analysis of the cotton proteome revealed 1569 differential proteins enriched in 35 metabolic pathways. Integrated metabolome and proteome analysis highlighted significant upregulation of 17 (89%) proteases in the α-linolenic acid (ALA) metabolism pathway, concomitant with a significant increase in 14 (88%) associated metabolites. Conversely, 19 (73%) proteases in the fructose and mannose biosynthesis pathway were downregulated, with 7 (27%) upregulated proteases corresponding to the downregulation of 8 pathway-associated metabolites. Expression analysis of key regulators in the ALA pathway, including allene oxidase synthase (AOS), phospholipase A (PLA), allene oxidative cyclase (AOC), and 12-oxophytodienoate reductase3 (OPR3), demonstrated significant responses to A. suturalis feeding. Finally, this study pioneers the exploration of molecular mechanisms in the plant-insect relationship, thereby offering insights into potential novel control strategies against this cotton pest.
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Affiliation(s)
- Hui Lu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Green Agricultural Products Safety and Warning Laboratory, Research Center of Soil Resource Comprehensive Utilization and Ecological Environment in Western Inner Mongolia, Hetao College, Bayannur 015000, China
| | - Shuaichao Zheng
- Henan Institute of Science and Technology, College of Life Science, Hualan St. 90, Xinxiang 453003, China;
| | - Chao Ma
- Anhui Provincial Center for Disease Control and Prevention, Hefei 230601, China;
| | - Xueke Gao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Jichao Ji
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Junyu Luo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Hongxia Hua
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jinjie Cui
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
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3
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Fatima S, Khan MO, Iqbal N, Iqbal MM, Qamar H, Imtiaz M, Hundleby P, Wei Z, Ahmad N. Studying Salt-Induced Shifts in Gene Expression Patterns of Glucosinolate Transporters and Glucosinolate Accumulation in Two Contrasting Brassica Species. Metabolites 2024; 14:179. [PMID: 38668307 PMCID: PMC11052333 DOI: 10.3390/metabo14040179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024] Open
Abstract
Brassica crops are well known for the accumulation of glucosinolates-secondary metabolites crucial for plants' adaptation to various stresses. Glucosinolates also functioning as defence compounds pose challenges to food quality due to their goitrogenic properties. Their disruption leaves plants susceptible to insect pests and diseases. Hence, a targeted reduction in seed glucosinolate content is of paramount importance to increase food acceptance. GLUCOSINOLATE TRANSPORTERS (GTRs) present a promising avenue for selectively reducing glucosinolate concentrations in seeds while preserving biosynthesis elsewhere. In this study, 54 putative GTR protein sequences found in Brassica were retrieved, employing Arabidopsis GTR1 and GTR2 templates. Comprehensive bioinformatics analyses, encompassing gene structure organization, domain analysis, motif assessments, promoter analysis, and cis-regulatory elements, affirmed the existence of transporter domains and stress-related regulatory elements. Phylogenetic analysis revealed patterns of conservation and divergence across species. Glucosinolates have been shown to increase under stress conditions, indicating a potential role in stress response. To elucidate the role of GTRs in glucosinolate transportation under NaCl stress in two distinct Brassica species, B. juncea and B. napus, plants were subjected to 0, 100, or 200 mM NaCl. Based on the literature, key GTR genes were chosen and their expression across various plant parts was assessed. Both species displayed divergent trends in their biochemical profiles as well as glucosinolate contents under elevated salt stress conditions. Statistical modelling identified significant contributors to glucosinolate variations, guiding the development of targeted breeding strategies for low-glucosinolate varieties. Notably, GTR2A2 exhibited pronounced expressions in stems, contributing approximately 52% to glucosinolate content variance, while GTR2B1/C2 displayed significant expression in flowers. Additionally, GTR2A1 and GTR1A2/B1 demonstrated noteworthy expression in roots. This study enhances our understanding of glucosinolate regulation under stress conditions, offering avenues to improve Brassica crop quality and resilience.
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Affiliation(s)
- Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
| | - Muhammad Omar Khan
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
| | - Nadia Iqbal
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
| | - Muhammad Mudassar Iqbal
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
| | - Huma Qamar
- Oilseeds Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan;
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Muhammad Imtiaz
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
| | - Penny Hundleby
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK;
| | - Zhengyi Wei
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
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4
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Shin D, Perez VC, Dickinson GK, Zhao H, Dai R, Tomiczek B, Cho KH, Zhu N, Koh J, Grenning A, Kim J. Altered methionine metabolism impacts phenylpropanoid production and plant development in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:187-200. [PMID: 37366635 PMCID: PMC11392427 DOI: 10.1111/tpj.16370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Phenylpropanoids are specialized metabolites derived from phenylalanine. Glucosinolates are defense compounds derived mainly from methionine and tryptophan in Arabidopsis. It was previously shown that the phenylpropanoid pathway and glucosinolate production are metabolically linked. The accumulation of indole-3-acetaldoxime (IAOx), the precursor of tryptophan-derived glucosinolates, represses phenylpropanoid biosynthesis through accelerated degradation of phenylalanine ammonia lyase (PAL). As PAL functions at the entry point of the phenylpropanoid pathway, which produces indispensable specialized metabolites such as lignin, aldoxime-mediated phenylpropanoid repression is detrimental to plant survival. Although methionine-derived glucosinolates in Arabidopsis are abundant, any impact of aliphatic aldoximes (AAOx) derived from aliphatic amino acids such as methionine on phenylpropanoid production remains unclear. Here, we investigate the impact of AAOx accumulation on phenylpropanoid production using Arabidopsis aldoxime mutants, ref2 and ref5. REF2 and REF5 metabolize aldoximes to respective nitrile oxides redundantly, but with different substrate specificities. ref2 and ref5 mutants have decreased phenylpropanoid contents due to the accumulation of aldoximes. As REF2 and REF5 have high substrate specificity toward AAOx and IAOx, respectively, it was assumed that ref2 accumulates AAOx, not IAOx. Our study indicates that ref2 accumulates both AAOx and IAOx. Removing IAOx partially restored phenylpropanoid content in ref2, but not to the wild-type level. However, when AAOx biosynthesis was silenced, phenylpropanoid production and PAL activity in ref2 were completely restored, suggesting an inhibitory effect of AAOx on phenylpropanoid production. Further feeding studies revealed that the abnormal growth phenotype commonly observed in Arabidopsis mutants lacking AAOx production is a consequence of methionine accumulation.
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Affiliation(s)
- Doosan Shin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Veronica C Perez
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA
| | - Gabriella K Dickinson
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA
| | - Haohao Zhao
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ru Dai
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Breanna Tomiczek
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Keun Ho Cho
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ning Zhu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32611, USA
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32611, USA
| | - Alexander Grenning
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Jeongim Kim
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA
- Genetic Institute, University of Florida, Gainesville, FL, USA
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5
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Shin D, Perez VC, Dickinson GK, Zhao H, Dai R, Tomiczek B, Cho KH, Zhu N, Koh J, Grenning A, Kim J. Altered methionine metabolism impacts phenylpropanoid production and plant development in Arabidopsis thaliana. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542770. [PMID: 37398371 PMCID: PMC10312446 DOI: 10.1101/2023.05.29.542770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Phenylpropanoids are specialized metabolites derived from phenylalanine. Glucosinolates are defense compounds derived mainly from methionine and tryptophan in Arabidopsis. It was previously shown that the phenylpropanoid pathway and glucosinolate production are metabolically linked. The accumulation of indole-3-acetaldoxime (IAOx), the precursor of tryptophan-derived glucosinolates, represses phenylpropanoid biosynthesis through accelerated degradation of phenylalanine-ammonia lyase (PAL). As PAL functions at the entry point of the phenylpropanoid pathway which produces indispensable specialized metabolites such as lignin, aldoxime-mediated phenylpropanoid repression is detrimental to plant survival. Although methionine-derived glucosinolates in Arabidopsis are abundant, any impact of aliphatic aldoximes (AAOx) derived from aliphatic amino acids such as methionine on phenylpropanoid production remains unclear. Here, we investigate the impact of AAOx accumulation on phenylpropanoid production using Arabidopsis aldoxime mutants, ref2 and ref5 . REF2 and REF5 metabolize aldoximes to respective nitrile oxides redundantly, but with different substrate specificities. ref2 and ref5 mutants have decreased phenylpropanoid contents due to the accumulation of aldoximes. As REF2 and REF5 have high substrate specificity toward AAOx and IAOx respectively, it was assumed that ref2 accumulates AAOx, not IAOx. Our study indicates that ref2 accumulates both AAOx and IAOx. Removing IAOx partially restored phenylpropanoid production in ref2 , but not to the wild-type level. However, when AAOx biosynthesis was silenced, phenylpropanoid production and PAL activity in ref2 were completely restored, suggesting an inhibitory effect of AAOx on phenylpropanoid production. Further feeding studies revealed that the abnormal growth phenotype commonly observed in Arabidopsis mutants lacking AAOx production is a consequence of methionine accumulation. Significance Statement Aliphatic aldoximes are precursors of various specialized metabolites including defense compounds. This study reveals that aliphatic aldoximes repress phenylpropanoid production and that altered methionine metabolism affects plant growth and development. As phenylpropanoids include vital metabolites such as lignin, a major sink of fixed carbon, this metabolic link may contribute to available resource allocation during defense.
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AbdElgawad H, Zinta G, Hornbacher J, Papenbrock J, Markakis MN, Asard H, Beemster GTS. Elevated CO 2 mitigates the impact of drought stress by upregulating glucosinolate metabolism in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2023; 46:812-830. [PMID: 36541032 DOI: 10.1111/pce.14521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Elevated CO2 (eCO2 ) reduces the impact of drought, but the mechanisms underlying this effect remain unclear. Therefore, we used a multidisciplinary approach to investigate the interaction of drought and eCO2 in Arabidopsis thaliana leaves. Transcriptome and subsequent metabolite analyses identified a strong induction of the aliphatic glucosinolate (GL) biosynthesis as a main effect of eCO2 in drought-stressed leaves. Transcriptome results highlighted the upregulation of ABI5 and downregulation of WRKY63 transcription factors (TF), known to enhance and inhibit the expression of genes regulating aliphatic GL biosynthesis (e.g., MYB28 and 29 TFs), respectively. In addition, eCO2 positively regulated aliphatic GL biosynthesis by MYB28/29 and increasing the accumulation of GL precursors. To test the role of GLs in the stress-mitigating effect of eCO2 , we investigated the effect of genetic perturbations of the GL biosynthesis. Overexpression of MYB28, 29 and 76 improved drought tolerance by inducing stomatal closure and maintaining plant turgor, whereas loss of cyp79f genes reduced the stress-mitigating effect of eCO2 and decreased drought tolerance. Overall, the crucial role of GL metabolism in drought stress mitigation by eCO2 could be a beneficial trait to overcome future climate challenges.
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Affiliation(s)
- Hamada AbdElgawad
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Botany and Microbiology, Science Faculty, Beni-Suef University, Beni-Suef, Egypt
| | - Gaurav Zinta
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Uttar Pradesh, Ghaziabad, India
| | | | - Jutta Papenbrock
- Institute of Botany, Leibniz University Hannove, Hannover, Germany
| | - Marios N Markakis
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Han Asard
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Gerrit T S Beemster
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
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Yan S, Bhawal R, Yin Z, Thannhauser TW, Zhang S. Recent advances in proteomics and metabolomics in plants. MOLECULAR HORTICULTURE 2022; 2:17. [PMID: 37789425 PMCID: PMC10514990 DOI: 10.1186/s43897-022-00038-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 10/05/2023]
Abstract
Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.
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Affiliation(s)
- Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | | | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA.
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Differential response of physiology and metabolic response to drought stress in different sweetpotato cultivars. PLoS One 2022; 17:e0264847. [PMID: 35271628 PMCID: PMC8912141 DOI: 10.1371/journal.pone.0264847] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/17/2022] [Indexed: 11/19/2022] Open
Abstract
Sweetpotato (Ipomoea batatas [L.] Lam) is a widely cultivated food crop with generally good adaptability. However, drought stress can cause a significant decline in yield. To reveal the response mechanism of sweetpotato to drought stress, an integrated physiological, proteomic and metabolomic investigation was conducted in leaves of two sweetpotato varieties with differing responses to drought stress, drought-resistant Wanzishu56 (WZ56) and a more sensitive variety, Ningzishu2(NZ2). Physiological analysis showed that the variety with better drought tolerance had superior performance in water retention capacity and photosynthetic efficiency under drought stress. A total of 1140 proteins were identified within the two varieties. Among them, 192 differentially expressed proteins were detected under drought conditions, including 97 that were up-regulated. Functional analysis showed that these up-regulated proteins were primarily involved in photosynthesis, reactive oxygen species metabolism, organonitrogen compound metabolism, and precursor metabolite catabolism and energy generation. All differentially expressed proteins in WZ56 that were involved in photosynthetic and glutathione metabolic processes were up-regulated. Enzyme activity assays were carried out to validate the proteomics data. Moreover, 75 metabolites were found to have a higher expression level in WZ56 than NZ2 under drought stress. The higher concentration of carbohydrates, amino acids, flavonoids and organic acids found in drought-stressed leaves of WZ56 suggested that these metabolites may improve the drought resistance of sweetpotato. This study uncovered specific-proteins and metabolites associated with drought resistance, providing new insights into the molecular mechanisms of drought tolerance in sweetpotato.
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Akram W, Yasin NA, Shah AA, Khan WU, Li G, Ahmad A, Ahmed S, Hussaan M, Rizwan M, Ali S. Exogenous application of liquiritin alleviated salt stress and improved growth of Chinese kale plants. SCIENTIA HORTICULTURAE 2022; 294:110762. [DOI: 10.1016/j.scienta.2021.110762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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10
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Zhang L, Miras-Moreno B, Yildiztugay E, Ozfidan-Konakci C, Arikan B, Elbasan F, Ak G, Rouphael Y, Zengin G, Lucini L. Metabolomics and Physiological Insights into the Ability of Exogenously Applied Chlorogenic Acid and Hesperidin to Modulate Salt Stress in Lettuce Distinctively. Molecules 2021; 26:6291. [PMID: 34684872 PMCID: PMC8537907 DOI: 10.3390/molecules26206291] [Citation(s) in RCA: 9] [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: 09/29/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/18/2022] Open
Abstract
Recent studies in the agronomic field indicate that the exogenous application of polyphenols can provide tolerance against various stresses in plants. However, the molecular processes underlying stress mitigation remain unclear, and little is known about the impact of exogenously applied phenolics, especially in combination with salinity. In this work, the impacts of exogenously applied chlorogenic acid (CA), hesperidin (HES), and their combination (HES + CA) have been investigated in lettuce (Lactuca sativa L.) through untargeted metabolomics to evaluate mitigation effects against salinity. Growth parameters, physiological measurements, leaf relative water content, and osmotic potential as well as gas exchange parameters were also measured. As expected, salinity produced a significant decline in the physiological and biochemical parameters of lettuce. However, the treatments with exogenous phenolics, particularly HES and HES + CA, allowed lettuce to cope with salt stress condition. Interestingly, the treatments triggered a broad metabolic reprogramming that involved secondary metabolism and small molecules such as electron carriers, enzyme cofactors, and vitamins. Under salinity conditions, CA and HES + CA distinctively elicited secondary metabolism, nitrogen-containing compounds, osmoprotectants, and polyamines.
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Affiliation(s)
- Leilei Zhang
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (L.Z.); (L.L.)
| | - Begoña Miras-Moreno
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (L.Z.); (L.L.)
| | - Evren Yildiztugay
- Department of Biotechnology, Faculty of Science, Selcuk University, Selcuklu, Konya 42130, Turkey; (E.Y.); (B.A.); (F.E.)
| | - Ceyda Ozfidan-Konakci
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Meram, Konya 42090, Turkey;
| | - Busra Arikan
- Department of Biotechnology, Faculty of Science, Selcuk University, Selcuklu, Konya 42130, Turkey; (E.Y.); (B.A.); (F.E.)
| | - Fevzi Elbasan
- Department of Biotechnology, Faculty of Science, Selcuk University, Selcuklu, Konya 42130, Turkey; (E.Y.); (B.A.); (F.E.)
| | - Gunes Ak
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, Selcuklu, Konya 42130, Turkey; (G.A.); (G.Z.)
| | - Youssef Rouphael
- Department of Agriculture, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Gokhan Zengin
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, Selcuklu, Konya 42130, Turkey; (G.A.); (G.Z.)
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (L.Z.); (L.L.)
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11
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Genomic Prediction Informed by Biological Processes Expands Our Understanding of the Genetic Architecture Underlying Free Amino Acid Traits in Dry Arabidopsis Seeds. G3-GENES GENOMES GENETICS 2020; 10:4227-4239. [PMID: 32978264 PMCID: PMC7642941 DOI: 10.1534/g3.120.401240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Plant growth, development, and nutritional quality depends upon amino acid homeostasis, especially in seeds. However, our understanding of the underlying genetics influencing amino acid content and composition remains limited, with only a few candidate genes and quantitative trait loci identified to date. Improved knowledge of the genetics and biological processes that determine amino acid levels will enable researchers to use this information for plant breeding and biological discovery. Toward this goal, we used genomic prediction to identify biological processes that are associated with, and therefore potentially influence, free amino acid (FAA) composition in seeds of the model plant Arabidopsis thaliana. Markers were split into categories based on metabolic pathway annotations and fit using a genomic partitioning model to evaluate the influence of each pathway on heritability explained, model fit, and predictive ability. Selected pathways included processes known to influence FAA composition, albeit to an unknown degree, and spanned four categories: amino acid, core, specialized, and protein metabolism. Using this approach, we identified associations for pathways containing known variants for FAA traits, in addition to finding new trait-pathway associations. Markers related to amino acid metabolism, which are directly involved in FAA regulation, improved predictive ability for branched chain amino acids and histidine. The use of genomic partitioning also revealed patterns across biochemical families, in which serine-derived FAAs were associated with protein related annotations and aromatic FAAs were associated with specialized metabolic pathways. Taken together, these findings provide evidence that genomic partitioning is a viable strategy to uncover the relative contributions of biological processes to FAA traits in seeds, offering a promising framework to guide hypothesis testing and narrow the search space for candidate genes.
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12
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Panthapulakkal Narayanan S, Liao P, Taylor PWJ, Lo C, Chye ML. Overexpression of a Monocot Acyl-CoA-Binding Protein Confers Broad-Spectrum Pathogen Protection in a Dicot. Proteomics 2020; 19:e1800368. [PMID: 31054181 DOI: 10.1002/pmic.201800368] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/14/2019] [Indexed: 01/17/2023]
Abstract
Plants are continuously infected by various pathogens throughout their lifecycle. Previous studies have reported that the expression of Class III acyl-CoA-binding proteins (ACBPs) such as the Arabidopsis ACBP3 and rice ACBP5 were induced by pathogen infection. Transgenic Arabidopsis AtACBP3-overexpressors (AtACBP3-OEs) displayed enhanced protection against the bacterial biotroph, Pseudomonas syringae, although they became susceptible to the fungal necrotroph Botrytis cinerea. A Class III ACBP from a monocot, rice (Oryza sativa) OsACBP5 was overexpressed in the dicot Arabidopsis. The resultant transgenic Arabidopsis lines conferred resistance not only to the bacterial biotroph P. syringae but to fungal necrotrophs (Rhizoctonia solani, B. cinerea, Alternaria brassicicola) and a hemibiotroph (Colletotrichum siamense). Changes in protein expression in R. solani-infected Arabidopsis OsACBP5-overexpressors (OsACBP5-OEs) were demonstrated using proteomic analysis. Biotic stress-related proteins including cell wall-related proteins such as FASCILIN-LIKE ARABINOGALACTAN-PROTEIN10, LEUCINE-RICH REPEAT EXTENSIN-LIKE PROTEINS, XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE PROTEIN4, and PECTINESTERASE INHIBITOR18; proteins associated with glucosinolate degradation including GDSL-LIKE LIPASE23, EPITHIOSPECIFIER MODIFIER1, MYROSINASE1, MYROSINASE2, and NITRILASE1; as well as a protein involved in jasmonate biosynthesis, ALLENE OXIDE CYCLASE2, were induced in OsACBP5-OEs upon R. solani infection. These results indicated that upregulation of these proteins in OsACBP5-OEs conferred protection against various plant pathogens.
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Affiliation(s)
| | - Pan Liao
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Paul W J Taylor
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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13
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Jiang D, Lei J, Cao B, Wu S, Chen G, Chen C. Molecular Cloning and Characterization of Three Glucosinolate Transporter (GTR) Genes from Chinese Kale. Genes (Basel) 2019; 10:genes10030202. [PMID: 30857170 PMCID: PMC6471314 DOI: 10.3390/genes10030202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 02/17/2019] [Accepted: 02/28/2019] [Indexed: 11/25/2022] Open
Abstract
Chinese kale is a native vegetable in Southern China and the flowering stalk is the most commonly used edible part due to its high glucosinolate content and other nutritional qualities. The GTR protein played important roles in the glucosinolate transport process. In this study, three BocGTR1 genes were cloned from Chinese kale for the first time. Their gene structure, physicochemical properties, signal peptides, transmembrane structures, functional domains, second and third-order protein structures, and phylogenetic relationships were predicted. The expression levels of BocGTR1a and BocGTR1c were much higher than those of BocGTR1b in various tissues, especially in leaves and buds. In addition, the expression patterns of three genes were examined under various abiotic stresses or hormone treatment, including those induced by wounding, heat stress, methyl jasmonate, salicylic acid, salt, and MgCl2 treatment. BocGTR1a and BocGTR1c were strongly induced by wounding and heat stress. The expression of BocGTR1a and BocGTR1c was significantly silenced in plants transformed by RNAi technology. Total glucosinolate content was significantly decreased in mature leaves and increased in roots of RNAi-transformed plants compared to wild-type plants. In addition, we found that BocGTR1a and BocGTR1c may participate in glucosinolate accumulation in different tissues with a selection for specific glucosinolates. These results indicated that BocGTR1a and BocGTR1c may be the key genes involved in the glucosinolate accumulation in different tissues of Chinese kale.
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Affiliation(s)
- Ding Jiang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
| | - Jianjun Lei
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
| | - Bihao Cao
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
| | - Siyuan Wu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
| | - Guoju Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
| | - Changming Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Vegetable Engineering and Technology Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
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14
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Zhu FY, Chen MX, Chan WL, Yang F, Tian Y, Song T, Xie LJ, Zhou Y, Xiao S, Zhang J, Lo C. SWATH-MS quantitative proteomic investigation of nitrogen starvation in Arabidopsis reveals new aspects of plant nitrogen stress responses. J Proteomics 2018; 187:161-170. [DOI: 10.1016/j.jprot.2018.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/04/2018] [Accepted: 07/19/2018] [Indexed: 01/10/2023]
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15
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Silva AT, Ligterink W, Hilhorst HWM. Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed-to-seedling transition in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2017; 95:481-496. [PMID: 29046998 PMCID: PMC5688192 DOI: 10.1007/s11103-017-0665-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 10/04/2017] [Indexed: 05/02/2023]
Abstract
Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes. The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant's life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational. The transition involves several developmental stages from seed germination to seedling establishment, i.e. between imbibition of the mature dry seed and opening of the cotyledons, the final stage of seedling establishment. We hypothesized that the advancement of growth is associated with certain signature metabolite profiles. Metabolite-metabolite correlation analysis underlined two specific profiles which appear to be involved in the metabolic preparation for seed germination and efficient seedling establishment, respectively. Metabolite profiles were also compared to transcript profiles and although transcriptional changes did not always equate to a proportional metabolic response, in depth correlation analysis identified several transcripts that may directly influence the flux through metabolic pathways during the seed-to-seedling transition. This correlation analysis also pinpointed metabolic pathways which are significant for the seed-to-seedling transition, and metabolite contents that appeared to be controlled directly by transcript abundance. This global view of the transcriptional and metabolic changes during the seed-to-seedling transition in Arabidopsis opens up new perspectives for understanding the complex regulatory mechanism underlying this transition.
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Affiliation(s)
- Anderson Tadeu Silva
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA.
| | - Wilco Ligterink
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Henk W M Hilhorst
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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16
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Ngwene B, Neugart S, Baldermann S, Ravi B, Schreiner M. Intercropping Induces Changes in Specific Secondary Metabolite Concentration in Ethiopian Kale ( Brassica carinata) and African Nightshade ( Solanum scabrum) under Controlled Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:1700. [PMID: 29033969 PMCID: PMC5626848 DOI: 10.3389/fpls.2017.01700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/15/2017] [Indexed: 05/03/2023]
Abstract
Intercropping is widespread in small-holder farming systems in tropical regions and is also practiced in the cultivation of indigenous vegetables, to alleviate the multiple burdens of malnutrition. Due to interspecific competition and/or complementation between intercrops, intercropping may lead to changes in plants accumulation of minerals and secondary metabolites and hence, alter nutritional quality for consumers. Intercropping aims to intensify land productivity, while ensuring that nutritional quality is not compromised. This study aimed to investigate changes in minerals and secondary plant metabolites in intercropped Brassica carinata and Solanum scabrum, two important African indigenous vegetables, and evaluated the suitability of this combination for dryer areas. B. carinata and S. scabrum were grown for 6 weeks under controlled conditions in a greenhouse trial. Large rootboxes (8000 cm3 volume) were specifically designed for this experiment. Each rootbox was planted with two plants, either of the same plant species (mono) or one of each plant species (mixed). A quartz sand/soil substrate was used and fertilized adequately for optimal plant growth. During the last 4 weeks of the experiment, the plants were either supplied with optimal (65% WHC) or low (30% WHC) irrigation, to test the effect of a late-season drought. Intercropping increased total glucosinolate content in B. carinata, while maintaining biomass production and the contents of other health related minerals in both B. carinata and S. scabrum. Moreover, low irrigation led to an increase in carotene accumulation in both mono and intercropped S. scabrum, but not in B. carinata, while the majority of kaempferol glycosides and hydroxycinnamic acid derivatives of both species were decreased by intercropping and drought treatment. This study indicates that some health-related phytochemicals can be modified by intercropping or late-season drought, but field validation of these results is necessary before definite recommendation can be made to stakeholders.
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Affiliation(s)
- Benard Ngwene
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Susanne Neugart
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Susanne Baldermann
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Beena Ravi
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
- Department of Crop and Animal Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Monika Schreiner
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
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17
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Coleto I, de la Peña M, Rodríguez-Escalante J, Bejarano I, Glauser G, Aparicio-Tejo PM, González-Moro MB, Marino D. Leaves play a central role in the adaptation of nitrogen and sulfur metabolism to ammonium nutrition in oilseed rape (Brassica napus). BMC PLANT BIOLOGY 2017; 17:157. [PMID: 28931380 PMCID: PMC5607504 DOI: 10.1186/s12870-017-1100-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/05/2017] [Indexed: 05/14/2023]
Abstract
BACKGROUND The coordination between nitrogen (N) and sulfur (S) assimilation is required to suitably provide plants with organic compounds essential for their development and growth. The N source induces the adaptation of many metabolic processes in plants; however, there is scarce information about the influence that it may exert on the functioning of S metabolism. The aim of this work was to provide an overview of N and S metabolism in oilseed rape (Brassica napus) when exposed to different N sources. To do so, plants were grown in hydroponic conditions with nitrate or ammonium as N source at two concentrations (0.5 and 1 mM). RESULTS Metabolic changes mainly occurred in leaves, where ammonium caused the up-regulation of enzymes involved in the primary assimilation of N and a general increase in the concentration of N-compounds (NH4+, amino acids and proteins). Similarly, the activity of key enzymes of primary S assimilation and the content of S-compounds (glutathione and glucosinolates) were also higher in leaves of ammonium-fed plants. Interestingly, sulfate level was lower in leaves of ammonium-fed plants, which was accompanied by the down-regulation of SULTR1 transporters gene expression. CONCLUSIONS The results highlight the impact of the N source on different steps of N and S metabolism in oilseed rape, notably inducing N and S assimilation in leaves, and put forward the potential of N source management to modulate the synthesis of compounds with biotechnological interest, such as glucosinolates.
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Affiliation(s)
- Inmaculada Coleto
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
| | - Marlon de la Peña
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
| | - Jon Rodríguez-Escalante
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
| | - Iraide Bejarano
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
| | - Gaëtan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Avenue de Bellevaux 51, 2000 Neuchâtel, Switzerland
| | - Pedro M. Aparicio-Tejo
- Departamento de Ciencias del Medio Natural, Universidad Pública de Navarra, Pamplona, Navarre Spain
| | - M. Begoña González-Moro
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
| | - Daniel Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
- Ikerbasque, Basque Foundation for Science, E-48011 Bilbao, Spain
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18
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Greenham K, Guadagno CR, Gehan MA, Mockler TC, Weinig C, Ewers BE, McClung CR. Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa. eLife 2017; 6:e29655. [PMID: 28826479 PMCID: PMC5628015 DOI: 10.7554/elife.29655] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/11/2017] [Indexed: 11/13/2022] Open
Abstract
The dynamics of local climates make development of agricultural strategies challenging. Yield improvement has progressed slowly, especially in drought-prone regions where annual crop production suffers from episodic aridity. Underlying drought responses are circadian and diel control of gene expression that regulate daily variations in metabolic and physiological pathways. To identify transcriptomic changes that occur in the crop Brassica rapa during initial perception of drought, we applied a co-expression network approach to associate rhythmic gene expression changes with physiological responses. Coupled analysis of transcriptome and physiological parameters over a two-day time course in control and drought-stressed plants provided temporal resolution necessary for correlation of network modules with dynamic changes in stomatal conductance, photosynthetic rate, and photosystem II efficiency. This approach enabled the identification of drought-responsive genes based on their differential rhythmic expression profiles in well-watered versus droughted networks and provided new insights into the dynamic physiological changes that occur during drought.
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Affiliation(s)
- Kathleen Greenham
- Department of Biological SciencesDartmouth CollegeHanoverUnited States
| | | | - Malia A Gehan
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Todd C Mockler
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Cynthia Weinig
- Department of BotanyUniversity of WyomingLaramieUnited States
- Department of Molecular BiologyUniversity of WyomingLaramieUnited States
- Program in EcologyUniversity of WyomingLaramieUnited States
| | - Brent E Ewers
- Department of BotanyUniversity of WyomingLaramieUnited States
- Program in EcologyUniversity of WyomingLaramieUnited States
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19
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Mostafa I, Yoo MJ, Zhu N, Geng S, Dufresne C, Abou-Hashem M, El-Domiaty M, Chen S. Membrane Proteomics of Arabidopsis Glucosinolate Mutants cyp79B2/B3 and myb28/29. FRONTIERS IN PLANT SCIENCE 2017; 8:534. [PMID: 28443122 PMCID: PMC5387099 DOI: 10.3389/fpls.2017.00534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/24/2017] [Indexed: 05/09/2023]
Abstract
Glucosinolates (Gls) constitute a major group of natural metabolites represented by three major classes (aliphatic, indolic and aromatic) of more than 120 chemical structures. In our previous work, soluble proteins and metabolites in Arabidopsis mutants deficient of aliphatic (myb28/29) and indolic Gls (cyp79B2B3) were analyzed. Here we focus on investigating the changes at the level of membrane proteins in these mutants. Our LC/MS-MS analyses of tandem mass tag (TMT) labeled peptides derived from the cyp79B2/B3 and myb28/29 relative to wild type resulted in the identification of 4,673 proteins, from which 2,171 are membrane proteins. Fold changes and statistical analysis showed 64 increased and 74 decreased in cyp79B2/B3, while 28 increased and 17 decreased in myb28/29. As to the shared protein changes between the mutants, one protein was increased and eight were decreased. Bioinformatics analysis of the changed proteins led to the discovery of three cytochromes in glucosinolate molecular network (GMN): cytochrome P450 86A7 (At1g63710), cytochrome P450 71B26 (At3g26290), and probable cytochrome c (At1g22840). CYP86A7 and CYP71B26 may play a role in hydroxyl-indolic Gls production. In addition, flavone 3'-O-methyltransferase 1 represents an interesting finding as it is likely to participate in the methylation process of the hydroxyl-indolic Gls to form methoxy-indolic Gls. The analysis also revealed additional new nodes in the GMN related to stress and defense activity, transport, photosynthesis, and translation processes. Gene expression and protein levels were found to be correlated in the cyp79B2/B3, but not in the myb28/29.
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Affiliation(s)
- Islam Mostafa
- Department of Biology, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig UniversityZagazig, Egypt
| | - Mi-Jeong Yoo
- Department of Biology, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
| | - Ning Zhu
- Department of Biology, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
| | - Sisi Geng
- Department of Biology, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
| | | | - Maged Abou-Hashem
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig UniversityZagazig, Egypt
| | - Maher El-Domiaty
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig UniversityZagazig, Egypt
| | - Sixue Chen
- Department of Biology, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
- Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
- *Correspondence: Sixue Chen
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20
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Zhu FY, Chan WL, Chen MX, Kong RPW, Cai C, Wang Q, Zhang JH, Lo C. SWATH-MS Quantitative Proteomic Investigation Reveals a Role of Jasmonic Acid during Lead Response in Arabidopsis. J Proteome Res 2016; 15:3528-3539. [DOI: 10.1021/acs.jproteome.6b00258] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fu-Yuan Zhu
- School
of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- School
of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Shenzhen
Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Wai-Lung Chan
- School
of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Mo-Xian Chen
- School
of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | | | - Congxi Cai
- Department
of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Qiaomei Wang
- Department
of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Jian-Hua Zhang
- School
of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Clive Lo
- School
of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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21
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Ku KM, Becker TM, Juvik JA. Transcriptome and Metabolome Analyses of Glucosinolates in Two Broccoli Cultivars Following Jasmonate Treatment for the Induction of Glucosinolate Defense to Trichoplusia ni (Hübner). Int J Mol Sci 2016; 17:ijms17071135. [PMID: 27428958 PMCID: PMC4964508 DOI: 10.3390/ijms17071135] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 01/16/2023] Open
Abstract
Lepidopteran larvae growth is influenced by host plant glucosinolate (GS) concentrations, which are, in turn, influenced by the phytohormone jasmonate (JA). In order to elucidate insect resistance biomarkers to lepidopteran pests, transcriptome and metabolome analyses following JA treatments were conducted with two broccoli cultivars, Green Magic and VI-158, which have differentially induced indole GSs, neoglucobrassicin and glucobrassicin, respectively. To test these two inducible GSs on growth of cabbage looper (Trichoplusia ni), eight neonate cabbage looper larvae were placed onto each of three plants per JA treatments (0, 100, 200, 400 µM) three days after treatment. After five days of feeding, weight of larvae and their survival rate was found to decrease with increasing JA concentrations in both broccoli cultivars. JA-inducible GSs were measured by high performance liquid chromatography. Neoglucobrassicin in Green Magic and glucobrassicin in VI-158 leaves were increased in a dose-dependent manner. One or both of these glucosinolates and/or their hydrolysis products showed significant inverse correlations with larval weight and survival (five days after treatment) while being positively correlated with the number of days to pupation. This implies that these two JA-inducible glucosinolates can influence the growth and survival of cabbage looper larvae. Transcriptome profiling supported the observed changes in glucosinolate and their hydrolysis product concentrations following JA treatments. Several genes related to GS metabolism differentiate the two broccoli cultivars in their pattern of transcriptional response to JA treatments. Indicative of the corresponding change in indole GS concentrations, transcripts of the transcription factor MYB122, core structure biosynthesis genes (CYP79B2, UGT74B1, SUR1, SOT16, SOT17, and SOT18), an indole glucosinolate side chain modification gene (IGMT1), and several glucosinolate hydrolysis genes (TGG1, TGG2, and ESM1) were significantly increased in Green Magic (statistically significant in most cases at 400 µM) while UGT74B1 and MYB122 were significantly increased in VI-158. Therefore, these metabolite and transcript biomarker results indicate that transcriptome profiling can identify genes associated with the formation of two different indole GS and their hydrolysis products. Therefore, these metabolite and transcript biomarkers could be useful in an effective marker-assisted breeding strategy for resistance to generalist lepidopteran pests in broccoli and potentially other Brassica vegetables.
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Affiliation(s)
- Kang-Mo Ku
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26505, USA.
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Talon M Becker
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - John A Juvik
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Qian L, Qian W, Snowdon RJ. Haplotype hitchhiking promotes trait coselection in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1578-88. [PMID: 26800855 PMCID: PMC5066645 DOI: 10.1111/pbi.12521] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/16/2015] [Accepted: 11/25/2015] [Indexed: 05/18/2023]
Abstract
Local haplotype patterns surrounding densely spaced DNA markers with significant trait associations can reveal information on selective sweeps and genome diversity associated with important crop traits. Relationships between haplotype and phenotype diversity, coupled with analysis of gene content in conserved haplotype blocks, can provide insight into coselection for nonrelated traits. We performed genome-wide analysis of haplotypes associated with the important physiological and agronomic traits leaf chlorophyll and seed glucosinolate content, respectively, in the major oilseed crop species Brassica napus. A locus on chromosome A01 showed opposite effects on leaf chlorophyll content and seed glucosinolate content, attributed to strong linkage disequilibrium (LD) between orthologues of the chlorophyll biosynthesis genes EARLY LIGHT-INDUCED PROTEIN and CHLOROPHYLL SYNTHASE, and the glucosinolate synthesis gene ATP SULFURYLASE 1. Another conserved haplotype block, on chromosome A02, contained a number of chlorophyll-related genes in LD with orthologues of the key glucosinolate biosynthesis genes METHYLTHIOALKYMALATE SYNTHASE-LIKE 1 and 3. Multigene haplogroups were found to have a significantly greater contribution to variation for chlorophyll content than haplotypes for any single gene, suggesting positive effects of additive locus accumulation. Detailed reanalysis of population substructure revealed a clade of ten related accessions exhibiting high leaf chlorophyll and low seed glucosinolate content. These accessions each carried one of the above-mentioned haplotypes from A01 or A02, generally in combination with further chlorophyll-associated haplotypes from chromosomes A05 and/or C05. The phenotypic rather than pleiotropic correlations between leaf chlorophyll content index and seed GSL suggest that LD may have led to inadvertent coselection for these two traits.
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Affiliation(s)
- Lunwen Qian
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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Baek SA, Jung YH, Lim SH, Park SU, Kim JK. Metabolic Profiling in Chinese Cabbage (Brassica rapa L. subsp. pekinensis) Cultivars Reveals that Glucosinolate Content Is Correlated with Carotenoid Content. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:4426-4434. [PMID: 27172980 DOI: 10.1021/acs.jafc.6b01323] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A total of 38 bioactive compounds, including glucosinolates, carotenoids, tocopherols, sterols, and policosanols, were characterized from nine varieties of Chinese cabbage (Brassica rapa L. subsp. pekinensis) to determine their phytochemical diversity and analyze their abundance relationships. The metabolite profiles were evaluated with principal component analysis (PCA), Pearson correlation analysis, and hierarchical clustering analysis (HCA). PCA and HCA identified two distinct varieties of Chinese cabbage (Cheonsangcheonha and Waldongcheonha) with higher levels of glucosinolates and carotenoids. Pairwise comparisons of the 38 metabolites were calculated using Pearson correlation coefficients. The HCA, which used the correlation coefficients, clustered metabolites that are derived from closely related biochemical pathways. Significant correlations were discovered between chlorophyll and carotenoids. Additionally, aliphatic glucosinolate and carotenoid levels were positively correlated. The Cheonsangcheonha and Waldongcheonha varieties appear to be good candidates for breeding because they have high glucosinolate and carotenoid levels.
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Affiliation(s)
- Seung-A Baek
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University , Incheon 22012, Republic of Korea
| | - Young-Ho Jung
- Biotechnology Institute, Nongwoo Bio Company, Limited , Yeoju, Gyeonggi 12655, Republic of Korea
| | - Sun-Hyung Lim
- National Academy of Agricultural Science, Rural Development Administration , Jeonju 54874, Republic of Korea
| | - Sang Un Park
- Department of Crop Science, Chungnam National University , 99 Daehak-Ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Jae Kwang Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University , Incheon 22012, Republic of Korea
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Mostafa I, Zhu N, Yoo MJ, Balmant KM, Misra BB, Dufresne C, Abou-Hashem M, Chen S, El-Domiaty M. New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants. J Proteomics 2016; 138:1-19. [PMID: 26915584 DOI: 10.1016/j.jprot.2016.02.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/07/2016] [Accepted: 02/17/2016] [Indexed: 12/24/2022]
Abstract
UNLABELLED Glucosinolates present in Brassicales are important for human health and plant defense against insects and pathogens. Here we investigate the proteomes and metabolomes of Arabidopsis myb28/29 and cyp79B2/B3 mutants deficient in aliphatic glucosinolates and indolic glucosinolates, respectively. Quantitative proteomics of the myb28/29 and cyp79B2/B3 mutants led to the identification of 2785 proteins, of which 142 proteins showed significant changes in the two mutants compared to wild type (WT). By mapping the differential proteins using STRING, we detected 59 new edges in the glucosinolate metabolic network. These connections can be classified as primary with direct roles in glucosinolate metabolism, secondary related to plant stress responses, and tertiary involved in other biological processes. Gene Ontology analysis of the differential proteins showed high level of enrichment in the nodes belonging to metabolic process including glucosinolate biosynthesis and response to stimulus. Using metabolomics, we quantified 292 metabolites covering a broad spectrum of metabolic pathways, and 89 exhibited differential accumulation patterns between the mutants and WT. The changing metabolites (e.g., γ-glutamyl amino acids, auxins and glucosinolate hydrolysis products) complement our proteomics findings. This study contributes toward engineering and breeding of glucosinolate profiles in plants in efforts to improve human health, crop quality and productivity. BIOLOGICAL SIGNIFICANCE Glucosinolates in Brassicales constitute an important group of natural metabolites important for plant defense and human health. Its biosynthetic pathways and transcriptional regulation have been well-studied. Using Arabidopsis mutants of important genes in glucosinolate biosynthesis, quantitative proteomics and metabolomics led to identification of many proteins and metabolites that are potentially related to glucosinolate metabolism. This study provides a comprehensive insight into the molecular networks of glucosinolate metabolism, and will facilitate efforts toward engineering and breeding of glucosinolate profiles for enhanced crop defense, and nutritional value.
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Affiliation(s)
- Islam Mostafa
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Ning Zhu
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mi-Jeong Yoo
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Kelly M Balmant
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Biswapriya B Misra
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Craig Dufresne
- Thermo Fisher Scientific, West Palm Beach, FL 33407, USA
| | - Maged Abou-Hashem
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA.
| | - Maher El-Domiaty
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
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26
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Buffon G, Blasi ÉAR, Adamski JM, Ferla NJ, Berger M, Santi L, Lavallée-Adam M, Yates JR, Beys-da-Silva WO, Sperotto RA. Physiological and Molecular Alterations Promoted by Schizotetranychus oryzae Mite Infestation in Rice Leaves. J Proteome Res 2015; 15:431-46. [PMID: 26667653 DOI: 10.1021/acs.jproteome.5b00729] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Infestation of phytophagous mite Schizotetranychus oryzae in rice causes critical yield losses. To better understand this interaction, we employed Multidimensional Protein Identification Technology (MudPIT) approach to identify differentially expressed proteins. We detected 18 and 872 unique proteins in control and infested leaves, respectively, along with 32 proteins more abundant in control leaves. S. oryzae infestation caused decreased abundance of proteins related to photosynthesis (mostly photosystem II-related), carbon assimilation and energy production, chloroplast detoxification, defense, and fatty acid and gibberellin synthesis. On the contrary, infestation caused increased abundance of proteins involved in protein modification and degradation, gene expression at the translation level, protein partitioning to different organelles, lipid metabolism, actin cytoskeleton remodeling, and synthesis of jasmonate, amino acid, and molecular chaperones. Our results also suggest that S. oryzae infestation promotes cell-wall remodeling and interferes with ethylene biosynthesis in rice leaves. Proteomic data were positively correlated with enzymatic assays and RT-qPCR analysis. Our findings describe the protein expression patterns of infested rice leaves and suggest that the acceptor side of PSII is probably the major damaged target in the photosynthetic apparatus. These data will be useful in future biotechnological approaches aiming to induce phytophagous mite resistance in rice.
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Affiliation(s)
| | | | | | | | | | | | - Mathieu Lavallée-Adam
- Department of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States
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Li QF, Wang JH, Pulkkinen P, Kong LS. Changes in the Metabolome of Picea balfouriana Embryogenic Tissues That Were Linked to Different Levels of 6-BAP by Gas Chromatography-Mass Spectrometry Approach. PLoS One 2015; 10:e0141841. [PMID: 26517840 PMCID: PMC4627733 DOI: 10.1371/journal.pone.0141841] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/13/2015] [Indexed: 11/19/2022] Open
Abstract
Embryogenic cultures of Picea balfouriana, which is an important commercial species for reforestation in Southern China, easily lose their embryogenic ability during long-term culture. Embryogenic tissue that proliferated at lower concentrations (3.6 μM and 2.5 μM) of 6-benzylaminopurine (6-BAP) were more productive, and generated 113 ± 6 and 89 ± 3 mature embryos per 100 mg embryogenic tissue, respectively. A metabolomic approach was used to study the changes in metabolites linked to embryogenic competence related to three different 6-BAP concentrations (2.5 μM, 3.6 μM, and 5 μM). A total of 309 compounds were obtained, among which 123 metabolites mapped to Kyoto Encyclopedia of Genes and genomes (KEGG) pathways. The levels of 35 metabolites were significantly differentially regulated among the three 6-BAP treatments, and 32 metabolites differed between the 2.5 μM and 5 μM treatments. A total of 17 metabolites appeared only once among the three comparisons. The combination of a score plot and a loading plot showed that in the samples with higher embryogenic ability (3.6 μM and 2.5 μM), up-regulated metabolites were mostly amino acids and down-regulated metabolites were mostly primary carbohydrates (especially sugars). These results suggested that 6-BAP may influence embryogenic competence by nitrogen metabolism, which could cause an increase in amino acid levels and higher amounts of aspartate, isoleucine, and leucine in tissues with higher embryogenic ability. Furthermore, we speculated that 6-BAP may affect the amount of tryptophan in tissues, which would change the indole-3-acetic acid levels and influence the embryogenic ability.
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Affiliation(s)
- Q. F. Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation & Utilization, GuangXi Zhuang Autonomous Region Forestry Research Institute, Nanning, China
| | - J. H. Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- * E-mail:
| | - P. Pulkkinen
- Finnish Forest Research Institute, Haapastensyrjä, Finland
| | - L. S. Kong
- Unit Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, Canada
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Kage U, Kumar A, Dhokane D, Karre S, Kushalappa AC. Functional molecular markers for crop improvement. Crit Rev Biotechnol 2015; 36:917-30. [DOI: 10.3109/07388551.2015.1062743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Udaykumar Kage
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Arun Kumar
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Dhananjay Dhokane
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Shailesh Karre
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Ajjamada C. Kushalappa
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
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Martínez-Ballesta M, Moreno-Fernández DA, Castejón D, Ochando C, Morandini PA, Carvajal M. The impact of the absence of aliphatic glucosinolates on water transport under salt stress in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2015; 6:524. [PMID: 26236322 PMCID: PMC4502342 DOI: 10.3389/fpls.2015.00524] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 06/29/2015] [Indexed: 05/21/2023]
Abstract
Members of the Brassicaceae are known for their contents of nutrients and health-promoting phytochemicals, including glucosinolates. Exposure to salinity increases the levels of several of these compounds, but their role in abiotic stress response is unclear. The effect of aliphatic glucosinolates on plant water balance and growth under salt stress, involving aquaporins, was investigated by means of Arabidopsis thaliana mutants impaired in aliphatic glucosinolate biosynthesis, which is controlled by two transcription factors: Myb28 and Myb29. The double mutant myb28myb29, completely lacking aliphatic glucosinolates, was compared to wild type Col-0 (WT) and the single mutant myb28. A greater reduction in the hydraulic conductivity of myb28myb29 was observed under salt stress, when compared to the WT and myb28; this correlated with the abundance of both PIP1 and PIP2 aquaporin subfamilies. Also, changes in root architecture in response to salinity were genotype dependent. Treatment with NaCl altered glucosinolates biosynthesis in a similar way in WT and the single mutant and differently in the double mutant. The results indicate that short-chain aliphatic glucosinolates may contribute to water saving under salt stress.
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Affiliation(s)
- Mcarmen Martínez-Ballesta
- Plant Nutrition Department, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC)Murcia, Spain
- *Correspondence: Mcarmen Martínez-Ballesta, Plant Nutrition Department, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, 30100 Espinardo, Murcia, Spain
| | - Diego A. Moreno-Fernández
- Food Science and Technology Department, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC)Murcia, Spain
| | - Diego Castejón
- Plant Nutrition Department, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC)Murcia, Spain
| | - Cristina Ochando
- Plant Nutrition Department, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC)Murcia, Spain
| | - Piero A. Morandini
- Department of Biosciences, CNR Biophysics Institute, University of MilanMilano, Italy
| | - Micaela Carvajal
- Plant Nutrition Department, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC)Murcia, Spain
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Data for iTRAQ-based quantitative proteomics analysis of Brassica napus leaves in response to chlorophyll deficiency. Data Brief 2014. [PMID: 26217696 PMCID: PMC4459558 DOI: 10.1016/j.dib.2014.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The essential pigment chlorophyll (Chl) plays important roles in light harvesting and energy transfer during photosynthesis. Here we present the data from a comparative proteomic analysis of chlorophyll-deficient Brassica napus mutant cde1 and its corresponding wild-type using the iTRAQ approach (Pu Chu et al., 2014 [1]). The distribution of length and number of peptides, mass and sequence coverage of proteins identified was calculated, and the repeatability of the replicates was analyzed. A total of 443 differentially expressed proteins were identified in B. napus leaves, including 228 down-accumulated proteins mainly involved in photosynthesis, porphyrin and chlorophyll metabolism, biosynthesis of secondary metabolites, carbon fixation and 215 up-accumulated proteins that enriched in the spliceosome, mRNA surveillance and RNA degradation.
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Chu P, Yan GX, Yang Q, Zhai LN, Zhang C, Zhang FQ, Guan RZ. iTRAQ-based quantitative proteomics analysis of Brassica napus leaves reveals pathways associated with chlorophyll deficiency. J Proteomics 2014; 113:244-59. [PMID: 25317966 DOI: 10.1016/j.jprot.2014.10.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/10/2014] [Accepted: 10/02/2014] [Indexed: 11/15/2022]
Abstract
Photosynthesis, the primary source of plant biomass, is important for plant growth and crop yield. Chlorophyll is highly abundant in plant leaves and plays essential roles in photosynthesis. We recently isolated a chlorophyll-deficient mutant (cde1) from ethyl methanesulfonate (EMS) mutagenized Brassica napus. Herein, quantitative proteomics analysis using the iTRAQ approach was conducted to investigate cde1-induced changes in the proteome. We identified 5069 proteins from B. napus leaves, of which 443 showed differential accumulations between the cde1 mutant and its corresponding wild-type. The differentially accumulated proteins were found to be involved in photosynthesis, porphyrin and chlorophyll metabolism, biosynthesis of secondary metabolites, carbon fixation, spliceosome, mRNA surveillance and RNA degradation. Our results suggest that decreased abundance of chlorophyll biosynthetic enzymes and photosynthetic proteins, impaired carbon fixation efficiency and disturbed redox homeostasis might account for the reduced chlorophyll contents, impaired photosynthetic capacity and increased lipid peroxidation in this mutant. Epigenetics was implicated in the regulation of gene expression in cde1, as proteins involved in DNA/RNA/histone methylation and methylation-dependent chromatin silencing were up-accumulated in the mutant. Biological significance Photosynthesis produces more than 90% of plant biomass and is an important factor influencing potential crop yield. The pigment chlorophyll plays essential roles in light harvesting and energy transfer during photosynthesis. Mutants deficient in chlorophyll synthesis have been used extensively to investigate the chlorophyll metabolism, development and photosynthesis. However, limited information is available with regard to the changes of protein profiles upon chlorophyll deficiency. Here, a combined physiological, histological, proteomics and molecular analysis revealed several important pathways associated with chlorophyll deficiency. This work provides new insights into the regulation of chlorophyll biosynthesis and photosynthesis in higher plants and these findings may be applied to genetic engineering for high photosynthetic efficiency in crops.
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Affiliation(s)
- Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Gui Xia Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Na Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Cheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Qi Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Rong Zhan Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; Nanjing Agricultural University, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China.
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32
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Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts. J Biosci 2014; 39:631-42. [DOI: 10.1007/s12038-014-9453-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Li Y, Nie Y, Zhang Z, Ye Z, Zou X, Zhang L, Wang Z. Comparative proteomic analysis of methyl jasmonate-induced defense responses in different rice cultivars. Proteomics 2014; 14:1088-101. [DOI: 10.1002/pmic.201300104] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 01/20/2014] [Accepted: 01/24/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Yunfeng Li
- Laboratory of Physiological Plant Pathology; South China Agricultural University; Guangzhou P. R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
| | - Yanfang Nie
- College of Natural Resources and Environment; South China Agricultural University; Guangzhou P. R. China
| | - Zhihui Zhang
- Laboratory of Physiological Plant Pathology; South China Agricultural University; Guangzhou P. R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
| | - Zhijian Ye
- Laboratory of Physiological Plant Pathology; South China Agricultural University; Guangzhou P. R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
| | - Xiaotao Zou
- Laboratory of Physiological Plant Pathology; South China Agricultural University; Guangzhou P. R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
| | - Lianhui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
| | - Zhenzhong Wang
- Laboratory of Physiological Plant Pathology; South China Agricultural University; Guangzhou P. R. China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control; South China Agricultural University; Guangzhou P. R. China
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Tong Y, Gabriel-Neumann E, Ngwene B, Krumbein A, George E, Platz S, Rohn S, Schreiner M. Topsoil drying combined with increased sulfur supply leads to enhanced aliphatic glucosinolates in Brassica juncea leaves and roots. Food Chem 2013; 152:190-6. [PMID: 24444925 DOI: 10.1016/j.foodchem.2013.11.099] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 10/01/2013] [Accepted: 11/19/2013] [Indexed: 10/26/2022]
Abstract
The decrease of water availability is leading to an urgent demand to reduce the plants' water supply. This study evaluates the effect of topsoil drying, combined with varying sulfur (S) supply on glucosinolates in Brassica juncea in order to reveal whether a partial root drying may already lead to a drought-induced glucosinolate increase promoted by an enhanced S supply. Without decreasing biomass, topsoil drying initiated an increase in aliphatic glucosinolates in leaves and in topsoil dried roots supported by increased S supply. Simultaneously, abscisic acid was determined, particularly in dehydrated roots, associated with an increased abscisic acid concentration in leaves under topsoil drying. This indicates that the dehydrated roots were the direct interface for the plants' stress response and that the drought-induced accumulation of aliphatic glucosinolates is related to abscisic acid formation. Indole and aromatic glucosinolates decreased, suggesting that these glucosinolates are less involved in the plants' response to drought.
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Affiliation(s)
- Yu Tong
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren and Erfurt e.V., Theodor-Echtermeyer-Weg 1, 14979 Grossbeeren, Germany; Department of Crop Sciences, Humboldt University, Unter den Linden 6, 10099 Berlin, Germany.
| | - Elke Gabriel-Neumann
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren and Erfurt e.V., Theodor-Echtermeyer-Weg 1, 14979 Grossbeeren, Germany; Department of Aridland Agriculture, Faculty of Food and Agriculture, UAE University, P.O. Box 17555, Al Ain, United Arab Emirates
| | - Benard Ngwene
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren and Erfurt e.V., Theodor-Echtermeyer-Weg 1, 14979 Grossbeeren, Germany
| | - Angelika Krumbein
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren and Erfurt e.V., Theodor-Echtermeyer-Weg 1, 14979 Grossbeeren, Germany
| | - Eckhard George
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren and Erfurt e.V., Theodor-Echtermeyer-Weg 1, 14979 Grossbeeren, Germany; Department of Crop Sciences, Humboldt University, Unter den Linden 6, 10099 Berlin, Germany
| | - Stefanie Platz
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Sascha Rohn
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Monika Schreiner
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren and Erfurt e.V., Theodor-Echtermeyer-Weg 1, 14979 Grossbeeren, Germany
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del Carmen Martínez-Ballesta M, Moreno DA, Carvajal M. The physiological importance of glucosinolates on plant response to abiotic stress in Brassica. Int J Mol Sci 2013; 14:11607-25. [PMID: 23722664 PMCID: PMC3709749 DOI: 10.3390/ijms140611607] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 05/14/2013] [Accepted: 05/20/2013] [Indexed: 11/30/2022] Open
Abstract
Glucosinolates, a class of secondary metabolites, mainly found in Brassicaceae, are affected by the changing environment. This review is focusing on the physiological significance of glucosinolates and their hydrolysis products in the plant response to different abiotic stresses. Special attention is paid to the crosstalk between some of the physiological processes involved in stress response and glucosinolate metabolism, with the resulting connection between both pathways in which signaling mechanisms glucosinolate may act as signals themselves. The function of glucosinolates, further than in defense switching, is discussed in terms of alleviating pathogen attack under abiotic stress. The fact that the exogenous addition of glucosinolate hydrolysis products may alleviate certain stress conditions through its effect on specific proteins is described in light of the recent reports, but the molecular mechanisms involved in this response merit further research. Finally, the transient allocation and re-distribution of glucosinolates as a response to environmental changes is summarized.
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Affiliation(s)
- María del Carmen Martínez-Ballesta
- Plant Nutrition Department, Centre of Edaphology and Applied Biology of Segura (CEBAS-CSIC), Campus of Espinardo, Building 25, Murcia E-30100, Spain; E-Mail:
| | - Diego A. Moreno
- Phytochemistry Lab, Food Science and Technology Department, Centre of Edaphology and Applied Biology of Segura (CEBAS-CSIC), Campus of Espinardo, Building 25, Murcia E-30100, Spain; E-Mail:
| | - Micaela Carvajal
- Plant Nutrition Department, Centre of Edaphology and Applied Biology of Segura (CEBAS-CSIC), Campus of Espinardo, Building 25, Murcia E-30100, Spain; E-Mail:
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He Y, Dai S, Dufresne CP, Zhu N, Pang Q, Chen S. Integrated proteomics and metabolomics of Arabidopsis acclimation to gene-dosage dependent perturbation of isopropylmalate dehydrogenases. PLoS One 2013; 8:e57118. [PMID: 23533573 PMCID: PMC3606340 DOI: 10.1371/journal.pone.0057118] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/10/2013] [Indexed: 12/02/2022] Open
Abstract
Maintaining metabolic homeostasis is critical for plant growth and development. Here we report proteome and metabolome changes when the metabolic homeostasis is perturbed due to gene-dosage dependent mutation of Arabidopsis isopropylmalate dehydrogenases (IPMDHs). By integrating complementary quantitative proteomics and metabolomics approaches, we discovered that gradual ablation of the oxidative decarboxylation step in leucine biosynthesis caused imbalance of amino acid homeostasis, redox changes and oxidative stress, increased protein synthesis, as well as a decline in photosynthesis, which led to rearrangement of central metabolism and growth retardation. Disruption of IPMDHs involved in aliphatic glucosinolate biosynthesis led to synchronized increase of both upstream and downstream biosynthetic enzymes, and concomitant repression of the degradation pathway, indicating metabolic regulatory mechanisms in controlling glucosinolate biosynthesis.
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Affiliation(s)
- Yan He
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
| | - Shaojun Dai
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
| | - Craig P. Dufresne
- Unity Lab Services, Thermo Fisher Scientific Inc., West Palm Beach, Florida, United States of America
| | - Ning Zhu
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
| | - Qiuying Pang
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, Florida, United States of America
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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