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Li Y, Liu S, Shawky E, Tao M, Liu A, Sulaiman K, Tian J, Zhu W. SWATH-based quantitative proteomic analysis of Morus alba L. leaves after exposure to ultraviolet-B radiation and incubation in the dark. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 230:112443. [PMID: 35429828 DOI: 10.1016/j.jphotobiol.2022.112443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 02/23/2022] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
Morus alba is a woody shrub of the family Moraceae and used as traditional Chinese medicine for a long history. Ultraviolet-B (UV-B) radiation, as a kind of abiotic stress factor, affected the growth and secondary metabolism in M. alba. Previous studies indicated that the contents of several secondary metabolites such as moracin N, chalcomaricin were significantly increased under high level UV-B radiation and dark incubation in M. alba leaves. To reveal the response mechanism under UV-B radiation and dark incubation in M. alba leaves, SWATH-based quantitative proteomic analysis was performed. Totally, 716 proteins were identified and quantified in the control, UVB, and UVD groups. Among them, 123 proteins and 96 proteins were identified as differentially abundant proteins in UVB group and UVD groups, respectively. Proteins related to photosynthesis, amino acid biosynthesis, and tocopherol biosynthesis were significantly altered in UVB group, while proteins related to the biosynthesis of phenolic compounds were significantly altered in UVD group. In addition, the abundances of proteins involved in the ubiquitin-proteasome system (UPS) were significantly increased in both UVB and UVD groups, indicating that UPS combined with secondary mechanism participated in the resistance to UV-B radiation and dark incubation. The obtained results provide novel insight into the effects of high level UV-B radiation on M. alba leaves and on the strategies used for maximizing the chemical constituents and the medicinal value of the M. alba leaves.
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Affiliation(s)
- Yaohan Li
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China; The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China
| | - Shengzhi Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Eman Shawky
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Minglei Tao
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Amin Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Kaisa Sulaiman
- The Xinjiang Uygur Autonomous Region National Institute of Traditional Chinese Medicine, Urumchi 830092, China
| | - Jingkui Tian
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China.
| | - Wei Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China.
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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Coelho AC, Pires R, Schütz G, Santa C, Manadas B, Pinto P. Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots: A long-term proteomics approach. PLoS One 2021; 16:e0245148. [PMID: 33481834 PMCID: PMC7822296 DOI: 10.1371/journal.pone.0245148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
The pathological interaction between oak trees and Phytophthora cinnamomi has implications in the cork oak decline observed over the last decades in the Iberian Peninsula. During host colonization, the phytopathogen secretes effector molecules like elicitins to increase disease effectiveness. The objective of this study was to unravel the proteome changes associated with the cork oak immune response triggered by P. cinnamomi inoculation in a long-term assay, through SWATH-MS quantitative proteomics performed in the oak leaves. Using the Arabidopis proteome database as a reference, 424 proteins were confidently quantified in cork oak leaves, of which 80 proteins showed a p-value below 0.05 or a fold-change greater than 2 or less than 0.5 in their levels between inoculated and control samples being considered as altered. The inoculation of cork oak roots with P. cinnamomi increased the levels of proteins associated with protein-DNA complex assembly, lipid oxidation, response to endoplasmic reticulum stress, and pyridine-containing compound metabolic process in the leaves. In opposition, several proteins associated with cellular metabolic compound salvage and monosaccharide catabolic process had significantly decreased abundances. The most significant abundance variations were observed for the Ribulose 1,5-Bisphosphate Carboxylase small subunit (RBCS1A), Heat Shock protein 90–1 (Hsp90-1), Lipoxygenase 2 (LOX2) and Histone superfamily protein H3.3 (A8MRLO/At4G40030) revealing a pertinent role for these proteins in the host-pathogen interaction mechanism. This work represents the first SWATH-MS analysis performed in cork oak plants inoculated with P. cinnamomi and highlights host proteins that have a relevant action in the homeostatic states that emerge from the interaction between the oomycete and the host in the long term and in a distal organ.
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Affiliation(s)
- Ana Cristina Coelho
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
- Escola Superior de Educação e Comunicação (ESEC), University of Algarve, Faro, Portugal
- * E-mail:
| | - Rosa Pires
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
| | - Gabriela Schütz
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
- Instituto Superior de Engenharia, University of Algarve, Faro, Portugal
| | - Cátia Santa
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Patrícia Pinto
- Center for Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
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Qiu X, Xu Y, Xiong B, Dai L, Huang S, Dong T, Sun G, Liao L, Deng Q, Wang X, Zhu J, Wang Z. Effects of exogenous methyl jasmonate on the synthesis of endogenous jasmonates and the regulation of photosynthesis in citrus. PHYSIOLOGIA PLANTARUM 2020; 170:398-414. [PMID: 32691420 DOI: 10.1111/ppl.13170] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/28/2020] [Accepted: 07/15/2020] [Indexed: 05/21/2023]
Abstract
Methyl jasmonate (MeJA) is an airborne signaling phytohormone that can induce changes in endogenous jasmonates (JAs) and cause photosynthetic responses. However, the response of these two aspects of citrus plants at different MeJA concentrations is still unclear. Four MeJA concentrations were used in two citrus varieties, Huangguogan (C. reticulata × C. sinensis) and Shiranuhi [C. reticulata × (C. reticulata × C. sinensis)], to investigate the effects of MeJA dose on the endogenous JAs pathway and photosynthetic capacity. We observed that MeJA acted in a dose-dependent manner, and its stimulation in citrus leaves showed a bidirectional character at different concentrations. This work demonstrates that MeJA at only a concentration of 2.2 mM or less contributed to the activation of magnesium protoporphyrin IX methyltransferase (ChlM, EC 2.1.1.11) and protochlorophyllide oxidoreductase (POR, EC 1.3.1.11) and the simultaneous accumulation of Chl a and Chl b, which in turn contributed to an improved photosynthetic capacity and PSII photochemistry efficiency of citrus. Meanwhile, the inhibition of endogenous JAs synthesis by exogenous MeJA was observed. This was achieved by reducing the ratio of monogalactosyl diacylglycerol (MGDG) to diagalactosyl diacylglycerol (DGDG) and inhibiting the activities of key enzymes in JAs synthesis, especially 12-oxo-phytodienoic acid reductase (OPR, EC 1.3.1.42). Another noteworthy finding is that there may exist a JA-independent pathway that could regulate 12-oxo-phytodienoic acid (OPDA) synthesis. This study jointly analyzed the internal hormone regulation mechanism and the external physiological response, as well as revealed the effects of exogenous MeJA on promoting the photosynthesis and inhibiting the endogenous JAs synthesis.
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Affiliation(s)
- Xia Qiu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yinghuan Xu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
- Neusoft Institute Guangdong, Guangdong, 528225, China
| | - Bo Xiong
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lin Dai
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shengjia Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tiantian Dong
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guochao Sun
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ling Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qunxian Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xun Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jin Zhu
- Sichuan Horticultural Crop Extension Station, Sichuan, 610041, China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
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Jamil IN, Remali J, Azizan KA, Nor Muhammad NA, Arita M, Goh HH, Aizat WM. Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology. FRONTIERS IN PLANT SCIENCE 2020; 11:944. [PMID: 32754171 PMCID: PMC7371031 DOI: 10.3389/fpls.2020.00944] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/10/2020] [Indexed: 05/03/2023]
Abstract
Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics data can answer targeted biological questions regarding the expression of transcripts, proteins, and metabolites, independently, but a systematic multi-omics integration (MOI) can comprehensively assimilate, annotate, and model these large data sets. Previous MOI studies and reviews have detailed its usage and practicality on various organisms including human, animals, microbes, and plants. Plants are especially challenging due to large poorly annotated genomes, multi-organelles, and diverse secondary metabolites. Hence, constructive and methodological guidelines on how to perform MOI for plants are needed, particularly for researchers newly embarking on this topic. In this review, we thoroughly classify multi-omics studies on plants and verify workflows to ensure successful omics integration with accurate data representation. We also propose three levels of MOI, namely element-based (level 1), pathway-based (level 2), and mathematical-based integration (level 3). These MOI levels are described in relation to recent publications and tools, to highlight their practicality and function. The drawbacks and limitations of these MOI are also discussed for future improvement toward more amenable strategies in plant systems biology.
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Affiliation(s)
- Ili Nadhirah Jamil
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Juwairiah Remali
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Kamalrul Azlan Azizan
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Masanori Arita
- Bioinformation & DDBJ Center, National Institute of Genetics (NIG), Mishima, Japan
- Metabolome Informatics Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hoe-Han Goh
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
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Rahnamaie-Tajadod R, Goh HH, Mohd Noor N. Methyl jasmonate-induced compositional changes of volatile organic compounds in Polygonum minus leaves. JOURNAL OF PLANT PHYSIOLOGY 2019; 240:152994. [PMID: 31226543 DOI: 10.1016/j.jplph.2019.152994] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/10/2019] [Accepted: 06/10/2019] [Indexed: 05/19/2023]
Abstract
Polygonum minus Huds. is a medicinal aromatic plant rich in terpenes, aldehydes, and phenolic compounds. Methyl jasmonate (MeJA) is a plant signaling molecule commonly applied to elicit stress responses to produce plant secondary metabolites. In this study, the effects of exogenous MeJA treatment on the composition of volatile organic compounds (VOCs) in P. minus leaves were investigated by using a metabolomic approach. Time-course changes in the leaf composition of VOCs on days 1, 3, and 5 after MeJA treatment were analyzed through solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS). The VOCs found in MeJA-elicited leaves were similar to those found in mock-treated leaves but varied in quantity at different time points. We focused our analysis on the content and composition of monoterpenes, sesquiterpenes, and green leaf volatiles (GLVs) within the leaf samples. Our results suggest that MeJA enhances the activity of biosynthetic pathways for aldehydes and terpenes in P. minus. Hence, the production of aromatic compounds in this medicinal herb can be increased by MeJA elicitation. Furthermore, the relationship between MeJA elicitation and terpene biosynthesis in P. minus was shown through SPME-GC-MS analysis of VOCs combined with transcriptomic analysis of MeJA-elicited P. minus leaves from our previous study.
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Affiliation(s)
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia.
| | - Normah Mohd Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
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Wan Zakaria WNA, Aizat WM, Goh HH, Mohd Noor N. Protein replenishment in pitcher fluids of Nepenthes × ventrata revealed by quantitative proteomics (SWATH-MS) informed by transcriptomics. JOURNAL OF PLANT RESEARCH 2019; 132:681-694. [PMID: 31422552 DOI: 10.1007/s10265-019-01130-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/07/2019] [Indexed: 05/19/2023]
Abstract
Carnivorous plants capture and digest insects for nutrients, allowing them to survive in soil deprived of nitrogenous nutrients. Plants from the genus Nepenthes produce unique pitchers containing secretory glands, which secrete enzymes into the digestive fluid. We performed RNA-seq analysis on the pitcher tissues and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis on the pitcher fluids of Nepenthes × ventrata to study protein expression in this carnivory organ during early days of pitcher opening. This transcriptome provides a sequence database for pitcher fluid protein identification. A total of 32 proteins of diverse functions were successfully identified in which 19 proteins can be quantified based on label-free quantitative proteomics (SWATH-MS) analysis while 16 proteins were not reported previously. Our findings show that certain proteins in the pitcher fluid were continuously secreted or replenished after pitcher opening, even without any prey or chitin induction. We also discovered a new aspartic proteinase, Nep6, secreted into pitcher fluid. This is the first SWATH-MS analysis of protein expression in Nepenthes pitcher fluid using a species-specific reference transcriptome. Taken together, our study using a gel-free shotgun proteomics informed by transcriptomics (PIT) approach showed the dynamics of endogenous protein secretion in the digestive organ of N. × ventrata and provides insights on protein regulation during early pitcher opening prior to prey capture.
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Affiliation(s)
- Wan Nor Adibah Wan Zakaria
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor Darul Ehsan, Malaysia
| | - Wan Mohd Aizat
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor Darul Ehsan, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor Darul Ehsan, Malaysia.
| | - Normah Mohd Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor Darul Ehsan, Malaysia
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