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Bian J, Chen R, Gu S, Wang W, Yang X. Quantitative proteomics analysis identified new interacting proteins of JAL30 in Arabidopsis. J Proteomics 2024; 297:105127. [PMID: 38367771 DOI: 10.1016/j.jprot.2024.105127] [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: 10/29/2023] [Revised: 01/26/2024] [Accepted: 02/14/2024] [Indexed: 02/19/2024]
Abstract
Jacalin-related lectins (JALs) are a unique group of plant lectins derived from the jacalin protein family, which play important roles in plant defense responses. JAL30/PBP1 (PYK10 binding protein 1) interacts with inactive PYK10, exerting negative regulatory control over the size of the PYK10 complex, which is formed and activated upon insect or pathogen invasion. However, the precise interplay between JAL30 and other components remains elusive. In this study, we found JAL30 as a nucleocytoplasmic protein, but no obvious phenotype was observed in jal30-1 single mutant. Through immunoprecipitation (IP) enrichment combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), dozens of new JAL30 interacting proteins were found in addition to several reported ones. Gene Ontology (GO) analysis revealed that these interacting proteins were highly related to the wounding and bacterial stimuli, suggesting their potential involvement in the jasmonate (JA) response. Importantly, the expression of JAL30 was induced by MeJA treatment, further highlighting its relevance in plant defense mechanisms. A novel JAL30 interacting protein, ESM1, was identified and its interaction with JAL30 was confirmed by Co-immunoprecipitation. Moreover, ESM1 was found as an O-GlcNAcylated protein, suggesting that JAL30 may possess glycosylated protein binding ability, particularly in O-GlcNAcylated protein and peptide recognition. Overall, our study provides valuable insights into the interacting protein network and biological function of JAL30, demonstrates the interaction between JAL30 and ESM1, and uncovers the potential significance of JAL30 in plant defense system, potentially through its association with PYK10 complex or JA response. SIGNIFICANCE: The biological functions of lectin proteins, including defense responses, immunity responses, signal transduction, have been well studied. Lectin proteins were also utilized to enrich glycosylated proteins for their specific carbohydrates binding capability. Jacalin-related lectins (JALs) were found to involve in plant defense mechanism. However, it is not yet clear whether JALs could use for enrichment of glycosylated proteins. In this study, we used label-free quantification method to identify interacting proteins of JAL30. A novel interacting protein, ESM1, as an O-GlcNAcylated protein was found. ESM1 has been reported to take part in defense against insect herbivory. Therefore, our findings provided experimental evidence to confirm that JALs have potential to be developed as the bio-tools to enrich glycosylated proteins. Finally, our data not only illustrated the vital biological role of JALs in plants, but also verified unique function of JAL30 in recognizing O-GlcNAcylated proteins.
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Affiliation(s)
- Jianghu Bian
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rongqing Chen
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shiting Gu
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenfei Wang
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou, China
| | - Xuelian Yang
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China.
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Ye Q, Zhang L, Li Q, Ji Y, Zhou Y, Wu Z, Hu Y, Ma Y, Wang J, Zhang C. Genome and GWAS analysis identified genes significantly related to phenotypic state of Rhododendron bark. HORTICULTURE RESEARCH 2024; 11:uhae008. [PMID: 38487544 PMCID: PMC10939351 DOI: 10.1093/hr/uhae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/01/2024] [Indexed: 03/17/2024]
Abstract
As an important horticultural plant, Rhododendron is often used in urban greening and landscape design. However, factors such as the high rate of genetic recombination, frequent outcrossing in the wild, weak linkage disequilibrium, and the susceptibility of gene expression to environmental factors limit further exploration of functional genes related to important horticultural traits, and make the breeding of new varieties require a longer time. Therefore, we choose bark as the target trait which is not easily affected by environmental factors, but also has ornamental properties. Genome-wide association study (GWAS) of Rhododendron delavayi (30 samples), R. irroratum (30 samples) and their F1 generation R. agastum (200 samples) was conducted on the roughness of bark phenotypes. Finally, we obtained 2416.31 Gbp of clean data and identified 5 328 800 high-quality SNPs. According to the P-value and the degree of linkage disequilibrium of SNPs, we further identified 4 out of 11 candidate genes that affect bark roughness. The results of gene differential expression analysis further indicated that the expression levels of Rhdel02G0243600 and Rhdel08G0220700 in different bark phenotypes were significantly different. Our study identified functional genes that influence important horticultural traits of Rhododendron, and illustrated the powerful utility and great potential of GWAS in understanding and exploiting wild germplasm genetic resources of Rhododendron.
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Affiliation(s)
- Qiannan Ye
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Yunnan Academy of Agricultural Sciences Kunming 650000, China
| | - Qing Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaliang Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Yanli Zhou
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
| | - Zhenzhen Wu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanting Hu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Yunnan Academy of Agricultural Sciences Kunming 650000, China
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- Haiyan Engineering & Technology Center, Zhejiang Institute of Advanced Technology, Jiaxing 314022, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
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Kliebenstein DJ. Specificity and breadth of plant specialized metabolite-microbe interactions. CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102459. [PMID: 37743122 DOI: 10.1016/j.pbi.2023.102459] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/10/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023]
Abstract
Plant specialized metabolites shape plant interactions with the environment including plant-microbe interactions. While we often group compounds into generic classes, it is the precise structure of a compound that creates a specific role in plant-microbe or-pathogen interactions. Critically, the structure guides definitive targets in individual interactions, yet single compounds are not limited to singular mechanistic targets allowing them to influence interactions across broad ranges of attackers, from bacteria to fungi to animals. Further, the direction of the effect can be altered by counter evolution within the interacting organism leading to single compounds being both beneficial and detrimental. Thus, the benefit of a single compound to a host needs to be assessed by measuring the net benefit across all interactions while in each specific interaction. Factoring this complexity for single compounds in plant-microbe interactions with the massive expansion in our identification of specialized metabolite pathways means that we need systematic studies to classify the full breadth of activities. Only with this full biological knowledge we can develop mechanistic, ecological, and evolutionary models to understand how plant specialized metabolites fully influence plant-microbe and plant-biotic interactions more broadly.
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Barker EI, Rabbi F, Brisbourne WA, Aparato VPM, Escarrega Valenzuela V, Renzaglia KS, Suh DY. Genome-wide analysis of the GDSL esterase/lipase family genes in Physcomitrium patens and the involvement of GELP31 in spore germination. Mol Genet Genomics 2023; 298:1155-1172. [PMID: 37338594 DOI: 10.1007/s00438-023-02041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/28/2023] [Indexed: 06/21/2023]
Abstract
In plants, the ability to produce hydrophobic substances that would provide protection from dehydration was required for the transition to land. This genome-wide investigation outlines the evolution of GDSL-type esterase/lipase (GELP) proteins in the moss Physcomitrium patens and suggests possible functions of some genes. GELP proteins play roles in the formation of hydrophobic polymers such as cutin and suberin that protect against dehydration and pathogen attack. GELP proteins are also implicated in processes such as pollen development and seed metabolism and germination. The P. patens GELP gene family comprises 48 genes and 14 pseudogenes. Phylogenetic analysis of all P. patens GELP sequences along with vascular plant GELP proteins with reported functions revealed that the P. patens genes clustered within previously identified A, B and C clades. A duplication model predicting the expansion of the GELP gene family within the P. patens lineage was constructed. Expression analysis combined with phylogenetic analysis suggested candidate genes for functions such as defence against pathogens, cutin metabolism, spore development and spore germination. The presence of relatively fewer GELP genes in P. patens may reduce the occurrence of functional redundancy that complicates the characterization of vascular plant GELP genes. Knockout lines of GELP31, which is highly expressed in sporophytes, were constructed. Gelp31 spores contained amorphous oil bodies and germinated late, suggesting (a) role(s) of GELP31 in lipid metabolism in spore development or germination. Future knockout studies of other candidate GELP genes will further elucidate the relationship between expansion of the family and the ability to withstand the harsh land environment.
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Affiliation(s)
- Elizabeth I Barker
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada.
| | - Fazle Rabbi
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | - Wyllie A Brisbourne
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | - Vincent P M Aparato
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Karen S Renzaglia
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, USA
| | - Dae-Yeon Suh
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada.
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Ji Z, Wang M, Zhang S, Du Y, Cong J, Yan H, Guo H, Xu B, Zhou Z. GDSL Esterase/Lipase GELP1 Involved in the Defense of Apple Leaves against Colletotrichum gloeosporioides Infection. Int J Mol Sci 2023; 24:10343. [PMID: 37373491 DOI: 10.3390/ijms241210343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
GDSL esterases/lipases are a subclass of lipolytic enzymes that play critical roles in plant growth and development, stress response, and pathogen defense. However, the GDSL esterase/lipase genes involved in the pathogen response of apple remain to be identified and characterized. Thus, in this study, we aimed to analyze the phenotypic difference between the resistant variety, Fuji, and susceptible variety, Gala, during infection with C. gloeosporioides, screen for anti-disease-associated proteins in Fuji leaves, and elucidate the underlying mechanisms. The results showed that GDSL esterase/lipase protein GELP1 contributed to C. gloeosporioides infection defense in apple. During C. gloeosporioides infection, GELP1 expression was significantly upregulated in Fuji. Fuji leaves exhibited a highly resistant phenotype compared with Gala leaves. The formation of infection hyphae of C. gloeosporioides was inhibited in Fuji. Moreover, recombinant His:GELP1 protein suppressed hyphal formation during infection in vitro. Transient expression in Nicotiana benthamiana showed that GELP1-eGFP localized to the endoplasmic reticulum and chloroplasts. GELP1 overexpression in GL-3 plants increased resistance to C. gloeosporioides. MdWRKY15 expression was upregulated in the transgenic lines. Notably, GELP1 transcript levels were elevated in GL-3 after salicylic acid treatment. These results suggest that GELP1 increases apple resistance to C. gloeosporioides by indirectly regulating salicylic acid biosynthesis.
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Affiliation(s)
- Zhirui Ji
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
| | - Meiyu Wang
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
| | - Shuwu Zhang
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Yinan Du
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
| | - Jialin Cong
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
| | - Haifeng Yan
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
| | - Haimeng Guo
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
| | - Bingliang Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Zongshan Zhou
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
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Jiao Y, Long Y, Xu K, Zhao F, Zhao J, Li S, Geng S, Gao W, Sun P, Deng X, Chen Q, Li C, Qu Y. Weighted Gene Co-Expression Network Analysis Reveals Hub Genes for Fuzz Development in Gossypium hirsutum. Genes (Basel) 2023; 14:208. [PMID: 36672949 PMCID: PMC9858766 DOI: 10.3390/genes14010208] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
Fuzzless Gossypium hirsutum mutants are ideal materials for investigating cotton fiber initiation and development. In this study, we used the fuzzless G. hirsutum mutant Xinluzao 50 FLM as the research material and combined it with other fuzzless materials for verification by RNA sequencing to explore the gene expression patterns and differences between genes in upland cotton during the fuzz period. A gene ontology (GO) enrichment analysis showed that differentially expressed genes (DEGs) were mainly enriched in the metabolic process, microtubule binding, and other pathways. A weighted gene co-expression network analysis (WGCNA) showed that two modules of Xinluzao 50 and Xinluzao 50 FLM and four modules of CSS386 and Sicala V-2 were highly correlated with fuzz. We selected the hub gene with the highest KME value among the six modules and constructed an interaction network. In addition, we selected some genes with high KME values from the six modules that were highly associated with fuzz in the four materials and found 19 common differential genes produced by the four materials. These 19 genes are likely involved in the formation of fuzz in upland cotton. Several hub genes belong to the arabinogalactan protein and GDSL lipase, which play important roles in fiber development. According to the differences in expression level, 4 genes were selected from the 19 genes and tested for their expression level in some fuzzless materials. The modules, hub genes, and common genes identified in this study can provide new insights into the formation of fiber and fuzz, and provide a reference for molecular design breeding for the genetic improvement of cotton fiber.
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Affiliation(s)
- Yang Jiao
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yilei Long
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Kaixiang Xu
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Fuxiang Zhao
- Xinjiang Academy of Agricultural Reclamation, Shihezi 832000, China
| | - Jieyin Zhao
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Shengmei Li
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Shiwei Geng
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wenju Gao
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Peng Sun
- Xinjiang Kuitun Agricultural and Rural Bureau, KuiTun 833200, China
| | - Xiaojuan Deng
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Chunpin Li
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Yanying Qu
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
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Zhou Z, Chen M, Wu Q, Zeng W, Chen Z, Sun W. Combined analysis of lipidomics and transcriptomics revealed the key pathways and genes of lipids in light-sensitive albino tea plant ( Camellia sinensis cv. Baijiguan). FRONTIERS IN PLANT SCIENCE 2022; 13:1035119. [PMID: 36330254 PMCID: PMC9623167 DOI: 10.3389/fpls.2022.1035119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Currently, the mechanism by which light-sensitive albino tea plants respond to light to regulate pigment synthesis has been only partially elucidated. However, few studies have focused on the role of lipid metabolism in the whitening of tea leaves. Therefore, in our study, the leaves of the Baijiguan (BJG) tea tree under shade and light restoration conditions were analyzed by a combination of lipidomics and transcriptomics. The leaf color of BJG was regulated by light intensity and responded to light changes in light by altering the contents and proportions of lipids. According to the correlation analysis, we found three key lipid components that were significantly associated with the chlorophyll SPAD value, namely, MGDG (36:6), DGDG (36:6) and DGDG (34:3). Further weighted gene coexpression network analysis (WGCNA) showed that HY5 TF and GLIP genes may be hub genes involved lipid regulation in albino tea leaves. Our results lay a foundation for further exploration of the color changes in albino tea leaves.
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Affiliation(s)
- Zhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingjie Chen
- College of Life Science, Xinyang Normal University, Xinyang, China
| | - Quanjin Wu
- Department of Finance and Management, The Open University of Fujian, Fuzhou, China
| | - Wen Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhidan Chen
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Anxi College of Tea Science, Fujian Agriculture and Forestry University, Quanzhou, China
| | - Weijiang Sun
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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Plaszkó T, Szűcs Z, Vasas G, Gonda S. Interactions of fungi with non-isothiocyanate products of the plant glucosinolate pathway: A review on product formation, antifungal activity, mode of action and biotransformation. PHYTOCHEMISTRY 2022; 200:113245. [PMID: 35623473 DOI: 10.1016/j.phytochem.2022.113245] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 05/05/2023]
Abstract
The glucosinolate pathway, which is present in the order Brassicales, is one of the most researched defensive natural product biosynthesis pathways. Its core molecules, the glucosinolates are broken down upon pathogen challenge or tissue damage to yield an array of natural products that may help plants defend against the stressor. Though the most widely known glucosinolate decomposition products are the antimicrobial isothiocyanates, there is a wide range of other volatile and non-volatile natural products that arise from this biosynthetic pathway. This review summarizes our current knowledge on the interaction of these much less examined, non-isothiocyanate products with fungi. It deals with compounds including (1) glucosinolates and their biosynthesis precursors; (2) glucosinolate-derived nitriles (e.g. derivatives of 1H-indole-3-acetonitrile), thiocyanates, epithionitriles and oxazolidine-2-thiones; (3) putative isothiocyanate downstream products such as raphanusamic acid, 1H-indole-3-methanol (= indole-3-carbinol) and its oligomers, 1H-indol-3-ylmethanamine and ascorbigen; (4) 1H-indole-3-acetonitrile downstream products such as 1H-indole-3-carbaldehyde (indole-3-carboxaldehyde), 1H-indole-3-carboxylic acid and their derivatives; and (5) indole phytoalexins including brassinin, cyclobrassinin and brassilexin. Herein, a literature review on the following aspects is provided: their direct antifungal activity and the proposed mechanisms of antifungal action, increased biosynthesis after fungal challenge, as well as data on their biotransformation/detoxification by fungi, including but not limited to fungal myrosinase activity.
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Affiliation(s)
- Tamás Plaszkó
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary; Doctoral School of Pharmaceutical Sciences, University of Debrecen, 4032, Debrecen, Hungary.
| | - Zsolt Szűcs
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary; Healthcare Industry Institute, University of Debrecen, 4032, Debrecen, Hungary.
| | - Gábor Vasas
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| | - Sándor Gonda
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
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Underwood W. Arabidopsis GOLD36/MVP1/ERMO3 Is Required for Powdery Mildew Penetration Resistance and Proper Targeting of the PEN3 Transporter. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:393-400. [PMID: 35147444 DOI: 10.1094/mpmi-09-21-0240-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The Arabidopsis PENETRATION 3 (PEN3) ATP binding cassette (ABC) transporter contributes to penetration resistance against nonadapted powdery mildew fungi and is targeted to papillae deposited at sites of interaction with the fungus. Timely recruitment of PEN3 and other components of penetration resistance to the host-pathogen interface is important for successful defense against this biotrophic pathogen. A forward genetic screen was previously carried out to identify Arabidopsis mutants that mistarget the PEN3 transporter or fail to accumulate PEN3 at sites of attempted powdery mildew penetration. This study focuses on PEN3 mistargeting in the aberrant localization of PEN3 4 (alp4) mutant and identification of the causal gene. In the alp4 mutant, PEN3 accumulates within the endomembrane system in an apparently abnormal endoplasmic reticulum and is not exported into papillae at powdery mildew penetration sites. This targeting defect compromises defenses at the host-pathogen interface, resulting in increased penetration success by a nonadapted powdery mildew. Genetic mapping identified alp4 as an allele of GOLGI DEFECTS 36 (GOLD36), a gene encoding a GDSL-lipase/esterase family protein that is involved in maintaining normal morphology and organization of multiple endomembrane compartments. Genetic complementation confirmed that mutation in GOLD36 is responsible for the PEN3 targeting and powdery mildew penetration resistance defects in alp4. These results reinforce the importance of endomembrane trafficking in resistance to haustorium-forming phytopathogens such as powdery mildew fungi.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- William Underwood
- United States Department of Agriculture-Agricultural Research Service Sunflower & Plant Biology Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, U.S.A
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Plaszkó T, Szűcs Z, Cziáky Z, Ács-Szabó L, Csoma H, Géczi L, Vasas G, Gonda S. Correlations Between the Metabolome and the Endophytic Fungal Metagenome Suggests Importance of Various Metabolite Classes in Community Assembly in Horseradish ( Armoracia rusticana, Brassicaceae) Roots. FRONTIERS IN PLANT SCIENCE 2022; 13:921008. [PMID: 35783967 PMCID: PMC9247618 DOI: 10.3389/fpls.2022.921008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/27/2022] [Indexed: 05/07/2023]
Abstract
The plant microbiome is an increasingly intensive research area, with significance in agriculture, general plant health, and production of bioactive natural products. Correlations between the fungal endophytic communities and plant chemistry can provide insight into these interactions, and suggest key contributors on both the chemical and fungal side. In this study, roots of various horseradish (Armoracia rusticana) accessions grown under the same conditions were sampled in two consecutive years and chemically characterized using a quality controlled, untargeted metabolomics approach by LC-ESI-MS/MS. Sinigrin, gluconasturtiin, glucoiberin, and glucobrassicin were also quantified. Thereafter, a subset of roots from eight accessions (n = 64) with considerable chemical variability was assessed for their endophytic fungal community, using an ITS2 amplicon-based metagenomic approach using a custom primer with high coverage on fungi, but no amplification of host internal transcribed spacer (ITS). A set of 335 chemical features, including putatively identified flavonoids, phospholipids, peptides, amino acid derivatives, indolic phytoalexins, a glucosinolate, and a glucosinolate downstream product was detected. Major taxa in horseradish roots belonged to Cantharellales, Glomerellales, Hypocreales, Pleosporales, Saccharomycetales, and Sordariales. Most abundant genera included typical endophytes such as Plectosphaerella, Thanatephorus, Podospora, Monosporascus, Exophiala, and Setophoma. A surprising dominance of single taxa was observed for many samples. In summary, 35.23% of reads of the plant endophytic fungal microbiome correlated with changes in the plant metabolome. While the concentration of flavonoid kaempferol glycosides positively correlated with the abundance of many fungal strains, many compounds showed negative correlations with fungi including indolic phytoalexins, a putative glucosinolate but not major glucosinolates and a glutathione isothiocyanate adduct. The latter is likely an in vivo glucosinolate decomposition product important in fungal arrest. Our results show the potency of the untargeted metabolomics approach in deciphering plant-microbe interactions and depicts a complex array of various metabolite classes in shaping the endophytic fungal community.
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Affiliation(s)
- Tamás Plaszkó
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Zsolt Szűcs
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Zoltán Cziáky
- Agricultural and Molecular Research and Service Institute, University of Nyíregyháza, Nyíregyháza, Hungary
| | - Lajos Ács-Szabó
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Hajnalka Csoma
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - László Géczi
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Gábor Vasas
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Sándor Gonda
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- *Correspondence: Sándor Gonda, ,
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11
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Sandor A, Fricker MD, Kriechbaumer V, Sweetlove LJ. IntEResting structures: formation and applications of organized smooth endoplasmic reticulum in plant cells. PLANT PHYSIOLOGY 2021; 185:550-561. [PMID: 33822222 PMCID: PMC8892044 DOI: 10.1104/pp.20.00719] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 07/21/2020] [Indexed: 06/12/2023]
Abstract
The endoplasmic reticulum (ER) is an organelle with remarkable plasticity, capable of rapidly changing its structure to accommodate different functions based on intra- and extracellular cues. One of the ER structures observed in plants is known as "organized smooth endoplasmic reticulum" (OSER), consisting of symmetrically stacked ER membrane arrays. In plants, these structures were first described in certain specialized tissues, e.g. the sieve elements of the phloem, and more recently in transgenic plants overexpressing ER membrane resident proteins. To date, much of the investigation of OSER focused on yeast and animal cells but research into plant OSER has started to grow. In this update, we give a succinct overview of research into the OSER phenomenon in plant cells with case studies highlighting both native and synthetic occurrences of OSER. We also assess the primary driving forces that trigger the formation of OSER, collating evidence from the literature to compare two competing theories for the origin of OSER: that OSER formation is initiated by oligomerizing protein accumulation in the ER membrane or that OSER is the result of ER membrane proliferation. This has long been a source of controversy in the field and here we suggest a way to integrate arguments from both sides into a single unifying theory. Finally, we discuss the potential biotechnological uses of OSER as a tool for the nascent plant synthetic biology field with possible applications as a synthetic microdomain for metabolic engineering and as an extensive membrane surface for synthetic chemistry or protein accumulation.
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Affiliation(s)
- Andras Sandor
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Mark D Fricker
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Verena Kriechbaumer
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
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12
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Guo DL, Wang ZG, Pei MS, Guo LL, Yu YH. Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment. BMC Genomics 2020; 21:784. [PMID: 33176674 PMCID: PMC7657363 DOI: 10.1186/s12864-020-07180-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Background In a previous study, the early ripening of Kyoho grape following H2O2 treatment was explored at the physiological level, but the mechanism by which H2O2 promotes ripening at the molecular level is unclear. To reveal the molecular mechanism, RNA-sequencing analysis was conducted on the different developmental stages of Kyoho berry treated with H2O2. Results In the comparison of treatment and control groups, 406 genes were up-regulated and 683 were down-regulated. Time course sequencing (TCseq) analysis showed that the expression patterns of most of the genes were similar between the treatment and control, except for some genes related to chlorophyll binding and photosynthesis. Differential expression analysis and the weighted gene co-expression network were used to screen significantly differentially expressed genes and hub genes associated with oxidative stress (heat shock protein, HSP), cell wall deacetylation (GDSL esterase/lipase, GDSL), cell wall degradation (xyloglucan endotransglucosylase/ hydrolase, XTH), and photosynthesis (chlorophyll a-b binding protein, CAB1). Gene expression was verified with RT-qPCR, and the results were largely consistent with those of RNA sequencing. Conclusions The RNA-sequencing analysis indicated that H2O2 treatment promoted the early ripening of Kyoho berry by affecting the expression levels of HSP, GDSL, XTH, and CAB1 and- photosynthesis- pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07180-y.
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Affiliation(s)
- Da-Long Guo
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China. .,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China.
| | - Zhen-Guang Wang
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
| | - Mao-Song Pei
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
| | - Li-Li Guo
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
| | - Yi-He Yu
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
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13
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Zhu Y, Ji C, Cao W, Shen J, Zhao Q, Jiang L. Identification and characterization of unconventional membrane protein trafficking regulators in Arabidopsis: A genetic approach. JOURNAL OF PLANT PHYSIOLOGY 2020; 252:153229. [PMID: 32750645 DOI: 10.1016/j.jplph.2020.153229] [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: 02/10/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
Proper trafficking and subcellular localization of membrane proteins are essential for plant growth and development. The plant endomembrane system contains several membrane-bound organelles with distinct functions including the endoplasmic reticulum (ER), Golgi apparatus, trans-Golgi network (TGN) or early endosome, prevacuolar compartment (PVC) or multivesicular body (MVB) and vacuole. Multiple approaches have been successfully used to identify and study the regulators and components important for signal transduction, growth and development, as well as membrane trafficking in the endomembrane system in plants. These include the homologous characterization of the counterparts in mammals or yeast employing both reverse genetic as well as the forward genetic screen approaches. However, the deletion or mutation of membrane trafficking related proteins usually leads to seedling lethality due to their essential roles in plant development and organelle biogenesis. To overcome the limitation of lethal phenotype of the target proteins, we used DEX-inducible RNAi knock-down lines to study their function in plants. More recently, we developed and used both RNAi knock-down and T-DNA insertional lines as starting materials to screen for mutations that could suppress and rescue the lethal phenotype, or a suppressor screening. Further characterization of the newly identified suppressor mutants has resulted in the identification of novel negative regulators in mediating membrane trafficking and organelle biogenesis in plants. In this review, we summarize the current approaches in studying protein trafficking in the endomembrane system. We then describe three examples of suppressor screening with distinct starting materials (i.e. FREE1, MON1, and SH3P2 that are regulators of MVB, vacuole, and autophagosomes, respectively) to discuss the rationale, procedures, advantages and disadvantages, and possible outcomes of such a suppressor screening. We finally propose that these novel screening approaches will lead to the identification of new unconventional players in regulating protein trafficking and organelle biogenesis in plants and discuss their impact on plant cell biology research.
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Affiliation(s)
- Ying Zhu
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Changyang Ji
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Wenhan Cao
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Qiong Zhao
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- Center for Cell and Developmental Biology, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; CUHK Shenzhen Research Institute, Shenzhen, China.
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14
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Lou L, Su X, Liu X, Liu Z. Transcriptome analysis of Luffa cylindrica (L.) Roem response to infection with Cucumber mosaic virus (CMV). Gene 2020; 737:144451. [PMID: 32035243 DOI: 10.1016/j.gene.2020.144451] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/02/2020] [Accepted: 02/04/2020] [Indexed: 10/25/2022]
Abstract
Cucumber mosaic virus (CMV) can cause serious losses in Luffa cylindrica (L.) Roem. Chemical application to control CMV is ineffective and environmentally unfriendly. The development of resistant hybrids is the best way to control CMV disease. Elucidating the virus-host interaction of CMV and molecular basis underlying Luffa spp. resistance against CMV would undoubtedly facilitate breeding for resistance against CMV disease. Transcriptome sequencing was used to analyze differentially expressed genes (DEGs) caused by CMV infection. A total of 138,336 unigenes were assembled, and 74,525 unigenes were annotated. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the three major enrichment pathways (according to the p-values) were flavonoid biosynthesis, sulfur metabolism, and photosynthesis. Genes involved in basal defenses, probably R genes, were determined to be related to CMV resistance. Using quantitative real-time PCR, we validated the differential expression of 8 genes. A number of genes associated with CMV resistance were found in this study. This study provides transcriptomic information regarding CMV-Luffa spp. interactions and will shed light on our understanding of host-virus interactions.
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Affiliation(s)
- Lina Lou
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province 210014, China.
| | - Xiaojun Su
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province 210014, China
| | - Xiaohong Liu
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province 210014, China
| | - Zhe Liu
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu Province 210014, China
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15
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Wang ZG, Guo LL, Ji XR, Yu YH, Zhang GH, Guo DL. Transcriptional Analysis of the Early Ripening of 'Kyoho' Grape in Response to the Treatment of Riboflavin. Genes (Basel) 2019; 10:genes10070514. [PMID: 31284601 PMCID: PMC6678464 DOI: 10.3390/genes10070514] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 12/16/2022] Open
Abstract
Previous study has demonstrated that the riboflavin treatment promoted the early ripening of the ‘Kyoho’ grape berry. However, the molecular mechanism causing this was unclear. In order to reveal the regulation mechanism of riboflavin treatment on grape berry development and ripening, the different berry developmental stages of the ‘Kyoho’ berry treated with 0.5 mmol/L of riboflavin was sampled for transcriptome profiling. RNA-seq revealed that 1526 and 430 genes were up-regulated and down-regulated, respectively, for the comparisons of the treatment to the control. TCseq analysis showed that the expression patterns of most of the genes were similar between the treatment and the control, except for some genes that were related to the chlorophyll metabolism, photosynthesis–antenna proteins, and photosynthesis, which were revealed by the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The differentially expressed genes and weighted gene co-expression network analysis (WGCNA) analysis identified some significantly differentially expressed genes and some hub genes, including up-regulation of the photosynthesis-related ELIP1 and growth and development-related GDSL; and down-regulation of the oxidative stress-related ATHSP22 and berry softening-related XTH32 and GH9B15. The results suggested that the riboflavin treatment resulted in the variations of the expression levels of these genes, and then led to the early ripening of the ‘Kyoho’ berry.
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Affiliation(s)
- Zhen-Guang Wang
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China
| | - Li-Li Guo
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China
- College of Agriculture, Henan University of Science and Technology, Luoyang 471023, Henan Province, China
| | - Xiao-Ru Ji
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China
| | - Yi-He Yu
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China
| | - Guo-Hai Zhang
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, Henan Province, China.
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China.
| | - Da-Long Guo
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, Henan Province, China.
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China.
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16
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Bhat R, Vyas D. Myrosinase: insights on structural, catalytic, regulatory, and environmental interactions. Crit Rev Biotechnol 2019; 39:508-523. [PMID: 30939944 DOI: 10.1080/07388551.2019.1576024] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Glucosinolate-myrosinase is a substrate-enzyme defense mechanism present in Brassica crops. This binary system provides the plant with an efficient system against herbivores and pathogens. For humans, it is well known for its anti-carcinogenic, anti-inflammatory, immunomodulatory, anti-bacterial, cardio-protective, and central nervous system protective activities. Glucosinolate and myrosinase are spatially present in different cells that upon tissue disruption come together and result in the formation of a variety of hydrolysis products with diverse physicochemical and biological properties. The myrosinase-catalyzed reaction starts with cleavage of the thioglucosidic linkage resulting in release of a D-glucose and an unstable thiohydroximate-O-sulfate. The outcome of this thiohydroximate-O-sulfate has been shown to depend on the structure of the glucosinolate side chain, the presence of supplementary proteins known as specifier proteins and/or on the physiochemical condition. Myrosinase was first reported in mustard seed during 1939 as a protein responsible for release of essential oil. Until this date, myrosinases have been characterized from more than 20 species of Brassica, cabbage aphid, and many bacteria residing in the human intestine. All the plant myrosinases are reported to be activated by ascorbic acid while aphid and bacterial myrosinases are found to be either neutral or inhibited. Myrosinase catalyzes hydrolysis of the S-glycosyl bond, O-β glycosyl bond, and O-glycosyl bond. This review summarizes information on myrosinase, an essential component of this binary system, including its structural and molecular properties, mechanism of action, and its regulation and will be beneficial for the research going on the understanding and betterment of the glucosinolate-myrosinase system from an ecological and nutraceutical perspective.
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Affiliation(s)
- Rohini Bhat
- a Biodiversity and Applied Botany Division , Indian Institute of Integrative Medicine (CSIR) , Jammu , India.,b Academy of Scientific and Innovative Research , Indian Institute of Integrative Medicine (CSIR) , Jammu , India
| | - Dhiraj Vyas
- a Biodiversity and Applied Botany Division , Indian Institute of Integrative Medicine (CSIR) , Jammu , India.,b Academy of Scientific and Innovative Research , Indian Institute of Integrative Medicine (CSIR) , Jammu , India
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17
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Chhajed S, Misra BB, Tello N, Chen S. Chemodiversity of the Glucosinolate-Myrosinase System at the Single Cell Type Resolution. FRONTIERS IN PLANT SCIENCE 2019; 10:618. [PMID: 31164896 PMCID: PMC6536577 DOI: 10.3389/fpls.2019.00618] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/25/2019] [Indexed: 05/08/2023]
Abstract
Glucosinolates (GLSs) are a well-defined group of specialized metabolites, and like any other plant specialized metabolites, their presence does not directly affect the plant survival in terms of growth and development. However, specialized metabolites are essential to combat environmental stresses, such as pathogens and herbivores. GLSs naturally occur in many pungent plants in the order of Brassicales. To date, more than 200 different GLS structures have been characterized and their distribution differs from species to species. GLSs co-exist with classical and atypical myrosinases, which can hydrolyze GLS into an unstable aglycone thiohydroximate-O-sulfonate, which rearranges to produce different degradation products. GLSs, myrosinases, myrosinase interacting proteins, and GLS degradation products constitute the GLS-myrosinase (GM) system ("mustard oil bomb"). This review discusses the cellular and subcellular organization of the GM system, its chemodiversity, and functions in different cell types. Although there are many studies on the functions of GLSs and/or myrosinases at the tissue and whole plant levels, very few studies have focused on different single cell types. Single cell type studies will help to reveal specific functions that are missed at the tissue and organismal level. This review aims to highlight (1) recent progress in cellular and subcellular compartmentation of GLSs, myrosinases, and myrosinase interacting proteins; (2) molecular and biochemical diversity of GLSs and myrosinases; and (3) myrosinase interaction with its interacting proteins, and how it regulates the degradation of GLSs and thus the biological functions (e.g., plant defense against pathogens). Future prospects may include targeted approaches for engineering/breeding of plants and crops in the cell type-specific manner toward enhanced plant defense and nutrition.
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Affiliation(s)
- Shweta Chhajed
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Biswapriya B. Misra
- Department of Biology, University of Florida, Gainesville, FL, United States
- Section on Molecular Medicine, Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Nathalia Tello
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
- *Correspondence: Sixue Chen,
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18
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Associations of canopy leaf traits with SNP markers in durum wheat (Triticum turgidum L. durum (Desf.)). PLoS One 2018; 13:e0206226. [PMID: 30352102 PMCID: PMC6198983 DOI: 10.1371/journal.pone.0206226] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/09/2018] [Indexed: 11/23/2022] Open
Abstract
The canopy leaves including the top three, i.e., the flag, the 2nd and 3rd from the top, are important for photosynthesis and grain yield of wheat. Molecular markers associated with traits of these leaves should be helpful for the high-yielding breeding. In this study, 1366 single nucleotide polymorphisms (SNP) markers covering the whole genome of durum wheat were used to genotype 150 cultivars collected from 46 countries and regions in the world. Leaf length, leaf width and chlorophyll content of the top three leaves were measured, respectively, in three consecutive years. Association analyses were performed on the leaf traits and SNP markers. A total of 120 SNP marker associations were detected on 13 of the 14 chromosomes. Among these markers, 83 were associated with the canopy leaf traits, 10 with 1000-grain weight, and 29 with kernel number per spike. This study is helpful for better understanding the potential and genetic basis of functional leaves, and facilitates pyramiding of the favorable alleles using marker assisted selection for ideal plant-type and high photosynthesis efficiency in durum wheat breeding.
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19
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Ma R, Yuan H, An J, Hao X, Li H. A Gossypium hirsutum GDSL lipase/hydrolase gene (GhGLIP) appears to be involved in promoting seed growth in Arabidopsis. PLoS One 2018; 13:e0195556. [PMID: 29621331 PMCID: PMC5886685 DOI: 10.1371/journal.pone.0195556] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/23/2018] [Indexed: 01/20/2023] Open
Abstract
GDSL lipase (GLIP) plays a pivotal role in plant cell growth as a multifunctional hydrolytic enzyme. Herein, a cotton (Gossypium hirsutum L. cv Xuzhou 142) GDSL lipase gene (GhGLIP) was obtained from developing ovules and fibers. The GhGLIP cDNA contained an open reading frame (ORF) of 1,143 base pairs (bp) and encodes a putative polypeptide of 380 amino acid residues. Sequence alignment indicated that GhGLIP includes four enzyme catalytic amino acid residue sites of Ser (S), Gly (G), Asn (N) and His (H), located in four conserved blocks. Phylogenetic tree analysis showed that GhGLIP belongs to the typical class IV lipase family with potential functions in plant secondary metabolism. Subcellular distribution analysis demonstrated that GhGLIP localized to the nucleus, cytoplasm and plasma membrane. GhGLIP was expressed predominantly at 5-15 day post anthesis (dpa) in developing ovules and elongating fibers, measured as mRNA levels and enzyme activity. Ectopic overexpression of GhGLIP in Arabidopsis plants resulted in enhanced seed development, including length and fresh weight. Meanwhile, there was increased soluble sugar and protein storage in transgenic Arabidopsis plants, coupled with the promotion of lipase activity. Moreover, the expression of cotton GhGLIP is induced by ethylene (ETH) treatment in vitro. A 1,954-bp GhGLIP promoter was isolated and expressed high activity in driving green fluorescence protein (GFP) expression in tobacco leaves. Cis-acting element analysis of the GhGLIP promoter (pGhGLIP) indicated the presence of an ethylene-responsive element (ERE), and transgenic tobacco leaves with ectopic expression of pGhGLIP::GFP-GUS showed increased GUS activity after ETH treatment. In summary, these results suggest that GhGLIP is a functional enzyme involved in ovule and fiber development and performs significant roles in seed development.
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Affiliation(s)
- Rendi Ma
- College of Life Sciences, Key Laboratory of Agrobiotechnolog, Shihezi University, Shihezi, Xinjiang, China
| | - Hali Yuan
- College of Life Sciences, Key Laboratory of Agrobiotechnolog, Shihezi University, Shihezi, Xinjiang, China
| | - Jing An
- College of Life Sciences, Key Laboratory of Agrobiotechnolog, Shihezi University, Shihezi, Xinjiang, China
| | - Xiaoyun Hao
- College of Life Sciences, Key Laboratory of Agrobiotechnolog, Shihezi University, Shihezi, Xinjiang, China
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Agrobiotechnolog, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Shihezi, Xinjiang, China
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20
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Wang JZ, Li B, Xiao Y, Ni Y, Ke H, Yang P, de Souza A, Bjornson M, He X, Shen Z, Balcke GU, Briggs SP, Tissier A, Kliebenstein DJ, Dehesh K. Initiation of ER Body Formation and Indole Glucosinolate Metabolism by the Plastidial Retrograde Signaling Metabolite, MEcPP. MOLECULAR PLANT 2017; 10:1400-1416. [PMID: 28965830 PMCID: PMC6368977 DOI: 10.1016/j.molp.2017.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 05/09/2023]
Abstract
Plants have evolved tightly regulated signaling networks to respond and adapt to environmental perturbations, but the nature of the signaling hub(s) involved have remained an enigma. We have previously established that methylerythritol cyclodiphosphate (MEcPP), a precursor of plastidial isoprenoids and a stress-specific retrograde signaling metabolite, enables cellular readjustments for high-order adaptive functions. Here, we specifically show that MEcPP promotes two Brassicaceae-specific traits, namely endoplasmic reticulum (ER) body formation and induction of indole glucosinolate (IGs) metabolism selectively, via transcriptional regulation of key regulators NAI1 for ER body formation and MYB51/122 for IGs biosynthesis). The specificity of MEcPP is further confirmed by the lack of induction of wound-inducible ER body genes as well as IGs by other altered methylerythritol phosphate pathway enzymes. Genetic analyses revealed MEcPP-mediated COI1-dependent induction of these traits. Moreover, MEcPP signaling integrates the biosynthesis and hydrolysis of IGs through induction of nitrile-specifier protein1 and reduction of the suppressor, ESM1, and production of simple nitriles as the bioactive end product. The findings position the plastidial metabolite, MEcPP, as the initiation hub, transducing signals to adjust the activity of hard-wired gene circuitry to expand phytochemical diversity and alter the associated subcellular structure required for functionality of the secondary metabolites, thereby tailoring plant stress responses.
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Affiliation(s)
- Jin-Zheng Wang
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Yanmei Xiao
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Yu Ni
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Haiyan Ke
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Panyu Yang
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Amancio de Souza
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Marta Bjornson
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Xiang He
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Zhouxin Shen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gerd Ulrich Balcke
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant Biochemistry, Halle, Germany
| | - Steve P Briggs
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant Biochemistry, Halle, Germany
| | | | - Katayoon Dehesh
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; Department of Plant Biology, University of California, Davis, CA 95616, USA.
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D'Ippólito S, Arias LA, Casalongué CA, Pagnussat GC, Fiol DF. The DC1-domain protein VACUOLELESS GAMETOPHYTES is essential for development of female and male gametophytes in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:261-275. [PMID: 28107777 DOI: 10.1111/tpj.13486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/06/2017] [Accepted: 01/11/2017] [Indexed: 06/06/2023]
Abstract
In this work we identified VACUOLELESS GAMETOPHYTES (VLG) as a DC1 domain-containing protein present in the endomembrane system and essential for development of both female and male gametophytes. VLG was originally annotated as a gene coding for a protein of unknown function containing DC1 domains. DC1 domains are cysteine- and histidine-rich zinc finger domains found exclusively in the plant kingdom that have been named on the basis of similarity with the C1 domain present in protein kinase C (PKC). In Arabidopsis, both male and female gametophytes are characterized by the formation of a large vacuole early in development; this is absent in vlg mutant plants. As a consequence, development is arrested in embryo sacs and pollen grains at the first mitotic division. VLG is specifically located in multivesicular bodies or pre-vacuolar compartments, and our results suggest that vesicular fusion is affected in the mutants, disrupting vacuole formation. Supporting this idea, AtPVA12 - a member of the SNARE vesicle-associated protein family and previously related to a sterol-binding protein, was identified as a VLG interactor. A role for VLG is proposed mediating vesicular fusion in plants as part of the sterol trafficking machinery required for vacuole biogenesis in plants.
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Affiliation(s)
- Sebastián D'Ippólito
- Instituto de Investigaciones Biológicas, IIB-CONICET-Universidad Nacional de Mar del Plata, Funes 3250 Cuarto Nivel, 7600, Mar del Plata, Argentina
| | - Leonardo Agustín Arias
- Instituto de Investigaciones Biológicas, IIB-CONICET-Universidad Nacional de Mar del Plata, Funes 3250 Cuarto Nivel, 7600, Mar del Plata, Argentina
| | - Claudia Anahí Casalongué
- Instituto de Investigaciones Biológicas, IIB-CONICET-Universidad Nacional de Mar del Plata, Funes 3250 Cuarto Nivel, 7600, Mar del Plata, Argentina
| | - Gabriela Carolina Pagnussat
- Instituto de Investigaciones Biológicas, IIB-CONICET-Universidad Nacional de Mar del Plata, Funes 3250 Cuarto Nivel, 7600, Mar del Plata, Argentina
| | - Diego Fernando Fiol
- Instituto de Investigaciones Biológicas, IIB-CONICET-Universidad Nacional de Mar del Plata, Funes 3250 Cuarto Nivel, 7600, Mar del Plata, Argentina
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Li S, Le B, Ma X, Li S, You C, Yu Y, Zhang B, Liu L, Gao L, Shi T, Zhao Y, Mo B, Cao X, Chen X. Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis. eLife 2016; 5:e22750. [PMID: 27938667 PMCID: PMC5207768 DOI: 10.7554/elife.22750] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/11/2016] [Indexed: 12/17/2022] Open
Abstract
Small RNAs are central players in RNA silencing, yet their cytoplasmic compartmentalization and the effects it may have on their activities have not been studied at the genomic scale. Here we report that Arabidopsis microRNAs (miRNAs) and small interfering RNAs (siRNAs) are distinctly partitioned between the endoplasmic reticulum (ER) and cytosol. All miRNAs are associated with membrane-bound polysomes (MBPs) as opposed to polysomes in general. The MBP association is functionally linked to a deeply conserved and tightly regulated activity of miRNAs - production of phased siRNAs (phasiRNAs) from select target RNAs. The phasiRNA precursor RNAs, thought to be noncoding, are on MBPs and are occupied by ribosomes in a manner that supports miRNA-triggered phasiRNA production, suggesting that ribosomes on the rough ER impact siRNA biogenesis. This study reveals global patterns of cytoplasmic partitioning of small RNAs and expands the known functions of ribosomes and ER.
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Affiliation(s)
- Shengben Li
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Brandon Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Xuan Ma
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Beijing, China
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yu Yu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Bailong Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Lin Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Ting Shi
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yonghui Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Beijing, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Howard Hughes Medical Institute, University of California, Riverside, Riverside, United States
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Pastor-Cantizano N, Montesinos JC, Bernat-Silvestre C, Marcote MJ, Aniento F. p24 family proteins: key players in the regulation of trafficking along the secretory pathway. PROTOPLASMA 2016; 253:967-985. [PMID: 26224213 DOI: 10.1007/s00709-015-0858-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 07/13/2015] [Indexed: 05/20/2023]
Abstract
p24 family proteins have been known for a long time, but their functions have remained elusive. However, they are emerging as essential regulators of protein trafficking along the secretory pathway, influencing the composition, structure, and function of different organelles in the pathway, especially the ER and the Golgi apparatus. In addition, they appear to modulate the transport of specific cargos, including GPI-anchored proteins, G-protein-coupled receptors, or K/HDEL ligands. As a consequence, they have been shown to play specific roles in signaling, development, insulin secretion, and the pathogenesis of Alzheimer's disease. The search of new putative ligands may open the way to discover new functions for this fascinating family of proteins.
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Affiliation(s)
- Noelia Pastor-Cantizano
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de València, Avenida Vicente Andrés Estellés, s/n, E-46100, Burjassot, Valencia, Spain
| | - Juan Carlos Montesinos
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de València, Avenida Vicente Andrés Estellés, s/n, E-46100, Burjassot, Valencia, Spain
| | - César Bernat-Silvestre
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de València, Avenida Vicente Andrés Estellés, s/n, E-46100, Burjassot, Valencia, Spain
| | - María Jesús Marcote
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de València, Avenida Vicente Andrés Estellés, s/n, E-46100, Burjassot, Valencia, Spain
| | - Fernando Aniento
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de València, Avenida Vicente Andrés Estellés, s/n, E-46100, Burjassot, Valencia, Spain.
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24
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Vujaklija I, Bielen A, Paradžik T, Biđin S, Goldstein P, Vujaklija D. An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom. BMC Bioinformatics 2016; 17:91. [PMID: 26892257 PMCID: PMC4757993 DOI: 10.1186/s12859-016-0919-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/29/2016] [Indexed: 01/29/2023] Open
Abstract
Background The massive accumulation of protein sequences arising from the rapid development of high-throughput sequencing, coupled with automatic annotation, results in high levels of incorrect annotations. In this study, we describe an approach to decrease annotation errors of protein families characterized by low overall sequence similarity. The GDSL lipolytic family comprises proteins with multifunctional properties and high potential for pharmaceutical and industrial applications. The number of proteins assigned to this family has increased rapidly over the last few years. In particular, the natural abundance of GDSL enzymes reported recently in plants indicates that they could be a good source of novel GDSL enzymes. We noticed that a significant proportion of annotated sequences lack specific GDSL motif(s) or catalytic residue(s). Here, we applied motif-based sequence analyses to identify enzymes possessing conserved GDSL motifs in selected proteomes across the plant kingdom. Results Motif-based HMM scanning (Viterbi decoding-VD and posterior decoding-PD) and the here described PD/VD protocol were successfully applied on 12 selected plant proteomes to identify sequences with GDSL motifs. A significant number of identified GDSL sequences were novel. Moreover, our scanning approach successfully detected protein sequences lacking at least one of the essential motifs (171/820) annotated by Pfam profile search (PfamA) as GDSL. Based on these analyses we provide a curated list of GDSL enzymes from the selected plants. CLANS clustering and phylogenetic analysis helped us to gain a better insight into the evolutionary relationship of all identified GDSL sequences. Three novel GDSL subfamilies as well as unreported variations in GDSL motifs were discovered in this study. In addition, analyses of selected proteomes showed a remarkable expansion of GDSL enzymes in the lycophyte, Selaginella moellendorffii. Finally, we provide a general motif-HMM scanner which is easily accessible through the graphical user interface (http://compbio.math.hr/). Conclusions Our results show that scanning with a carefully parameterized motif-HMM is an effective approach for annotation of protein families with low sequence similarity and conserved motifs. The results of this study expand current knowledge and provide new insights into the evolution of the large GDSL-lipase family in land plants. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0919-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ivan Vujaklija
- Faculty of Electrical Engineering and Computing, Unska 3, Zagreb, 10000, Croatia.
| | - Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, Zagreb, 10000, Croatia. .,Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, 10000, Croatia.
| | - Tina Paradžik
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, 10000, Croatia.
| | - Siniša Biđin
- Faculty of Electrical Engineering and Computing, Unska 3, Zagreb, 10000, Croatia.
| | - Pavle Goldstein
- Department of Mathematics, Faculty of Science, University of Zagreb, Bijenička 30, Zagreb, 10000, Croatia.
| | - Dušica Vujaklija
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, 10000, Croatia.
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25
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Miernyk JA, Jett AA, Johnston ML. Analysis of soybean tissue culture protein dynamics using difference gel electrophoresis. J Proteomics 2016; 130:56-64. [PMID: 26344131 DOI: 10.1016/j.jprot.2015.08.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/10/2015] [Accepted: 08/26/2015] [Indexed: 01/05/2023]
Abstract
UNLABELLED Excised hypocotyls from developing soybean (Glycine max (L.) merr. cv. Jack) were cultivated on agar-solidified medium until callus formed. The calli were then propagated in liquid medium until stable, relatively uniform, finely-divided suspension cultures were obtained. Cells were typically transferred to fresh medium at 7-day intervals. Cultures were harvested by filtration five days (early log phase) or eight days (late log phase) after transfer. In order to evaluate dynamic changes, both intracellular and extracellular proteins were analyzed by 2-dimensional difference gel electrophoresis. Selected spots were subjected to in-gel tryptic-digestion and the resultant peptides were analyzed by nLC-MS/MS. In follow-up studies gel-free shot-gun analyses led to identification of 367 intracellular proteins and 188 extracellular proteins. SIGNIFICANCE The significance of the described research is two-fold. First a gel-based proteomics method was applied to the study of the dynamics of the secretome (extracellular proteins). Second, results of a shot-gun non-gel based proteomic survey of both cellular and extracellular proteins are presented.
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Affiliation(s)
- Ján A Miernyk
- Plant Genetics Research Unit, USDA, Agricultural Research Service, 102 Curtis Hall, University of Missouri, Columbia, MO 65211 USA; Division of Biochemistry, University of Missouri, Columbia, MO 65211 USA.
| | - Alissa A Jett
- School of Social Work, University of Missouri, Columbia, MO 65211 USA
| | - Mark L Johnston
- Plant Genetics Research Unit, USDA, Agricultural Research Service, 102 Curtis Hall, University of Missouri, Columbia, MO 65211 USA
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26
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Colombo M, Tadini L, Peracchio C, Ferrari R, Pesaresi P. GUN1, a Jack-Of-All-Trades in Chloroplast Protein Homeostasis and Signaling. FRONTIERS IN PLANT SCIENCE 2016; 7:1427. [PMID: 27713755 PMCID: PMC5032792 DOI: 10.3389/fpls.2016.01427] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/07/2016] [Indexed: 05/04/2023]
Abstract
The GENOMES UNCOUPLED 1 (GUN1) gene has been reported to encode a chloroplast-localized pentatricopeptide-repeat protein, which acts to integrate multiple indicators of plastid developmental stage and altered plastid function, as part of chloroplast-to-nucleus retrograde communication. However, the molecular mechanisms underlying signal integration by GUN1 have remained elusive, up until the recent identification of a set of GUN1-interacting proteins, by co-immunoprecipitation and mass-spectrometric analyses, as well as protein-protein interaction assays. Here, we review the molecular functions of the different GUN1 partners and propose a major role for GUN1 as coordinator of chloroplast translation, protein import, and protein degradation. This regulatory role is implemented through proteins that, in most cases, are part of multimeric protein complexes and whose precise functions vary depending on their association states. Within this framework, GUN1 may act as a platform to promote specific functions by bringing the interacting enzymes into close proximity with their substrates, or may inhibit processes by sequestering particular pools of specific interactors. Furthermore, the interactions of GUN1 with enzymes of the tetrapyrrole biosynthesis (TPB) pathway support the involvement of tetrapyrroles as signaling molecules in retrograde communication.
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Affiliation(s)
- Monica Colombo
- Centro Ricerca e Innovazione, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Luca Tadini
- Dipartimento di Bioscienze, Università degli Studi di MilanoMilan, Italy
| | - Carlotta Peracchio
- Dipartimento di Bioscienze, Università degli Studi di MilanoMilan, Italy
| | - Roberto Ferrari
- Dipartimento di Bioscienze, Università degli Studi di MilanoMilan, Italy
| | - Paolo Pesaresi
- Dipartimento di Bioscienze, Università degli Studi di MilanoMilan, Italy
- *Correspondence: Paolo Pesaresi
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27
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Dong X, Yi H, Han CT, Nou IS, Hur Y. GDSL esterase/lipase genes in Brassica rapa L.: genome-wide identification and expression analysis. Mol Genet Genomics 2015; 291:531-42. [DOI: 10.1007/s00438-015-1123-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/18/2015] [Indexed: 11/29/2022]
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Dorn KM, Fankhauser JD, Wyse DL, Marks MD. A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop. DNA Res 2015; 22:121-31. [PMID: 25632110 PMCID: PMC4401323 DOI: 10.1093/dnares/dsu045] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/21/2014] [Indexed: 12/30/2022] Open
Abstract
Field pennycress (Thlaspi arvense L.) is being domesticated as a new winter cover crop and biofuel species for the Midwestern United States that can be double-cropped between corn and soybeans. A genome sequence will enable the use of new technologies to make improvements in pennycress. To generate a draft genome, a hybrid sequencing approach was used to generate 47 Gb of DNA sequencing reads from both the Illumina and PacBio platforms. These reads were used to assemble 6,768 genomic scaffolds. The draft genome was annotated using the MAKER pipeline, which identified 27,390 predicted protein-coding genes, with almost all of these predicted peptides having significant sequence similarity to Arabidopsis proteins. A comprehensive analysis of pennycress gene homologues involved in glucosinolate biosynthesis, metabolism, and transport pathways revealed high sequence conservation compared with other Brassicaceae species, and helps validate the assembly of the pennycress gene space in this draft genome. Additional comparative genomic analyses indicate that the knowledge gained from years of basic Brassicaceae research will serve as a powerful tool for identifying gene targets whose manipulation can be predicted to result in improvements for pennycress.
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Affiliation(s)
- Kevin M Dorn
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | | | - Donald L Wyse
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - M David Marks
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA
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29
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Zhang C, Hicks GR, Raikhel NV. Plant vacuole morphology and vacuolar trafficking. FRONTIERS IN PLANT SCIENCE 2014; 5:476. [PMID: 25309565 PMCID: PMC4173805 DOI: 10.3389/fpls.2014.00476] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 08/29/2014] [Indexed: 05/23/2023]
Abstract
Plant vacuoles are essential organelles for plant growth and development, and have multiple functions. Vacuoles are highly dynamic and pleiomorphic, and their size varies depending on the cell type and growth conditions. Vacuoles compartmentalize different cellular components such as proteins, sugars, ions and other secondary metabolites and play critical roles in plants response to different biotic/abiotic signaling pathways. In this review, we will summarize the patterns of changes in vacuole morphology in certain cell types, our understanding of the mechanisms of plant vacuole biogenesis, and the role of SNAREs and Rab GTPases in vacuolar trafficking.
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Affiliation(s)
- Chunhua Zhang
- *Correspondence: Chunhua Zhang, Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA e-mail:
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30
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Lai YS, Stefano G, Brandizzi F. ER stress signaling requires RHD3, a functionally conserved ER-shaping GTPase. J Cell Sci 2014; 127:3227-32. [PMID: 24876222 DOI: 10.1242/jcs.147447] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Whether structure and function are correlated features of organelles is a fundamental question in cell biology. Here, we have assessed the ability of Arabidopsis mutants with a defective endoplasmic reticulum (ER) structure to invoke the unfolded protein response (UPR), an essential ER signaling pathway. Through molecular and genetic approaches, we show that loss of the ER-shaping GTPase Root Hair Defective 3 (RHD3) specifically disrupts the UPR by interfering with the mRNA splicing function of the master regulator IRE1. These findings establish a new role for RHD3 in the ER and support specificity of the effects of ER-shaping mutations on ER function.
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Affiliation(s)
- Ya-Shiuan Lai
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Giovanni Stefano
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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Jancowski S, Catching A, Pighin J, Kudo T, Foissner I, Wasteneys GO. Trafficking of the myrosinase-associated protein GLL23 requires NUC/MVP1/GOLD36/ERMO3 and the p24 protein CYB. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:497-510. [PMID: 24330158 DOI: 10.1111/tpj.12408] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/22/2013] [Accepted: 11/28/2013] [Indexed: 05/08/2023]
Abstract
Proteins detrimental to endoplasmic reticulum (ER) morphology need to be efficiently exported. Here, we identify two mechanisms that control trafficking of Arabidopsis thalianaGLL23, a 43 kDa GDSL-like lipase implicated in glucosinolate metabolism through its association with the β-glucosidase myrosinase. Using immunofluorescence, we identified two mutants that showed aberrant accumulation of GLL23: large perinuclear ER aggregates in the nuclear cage (nuc) mutant; and small compartments contiguous with the peripheral ER in the cytoplasmic bodies (cyb) mutant. Live imaging of fluorescently tagged GLL23 confirmed its presence in the nuc and cyb compartments, but lack of fluorescent signals in the wild-type plants suggested that GLL23 is normally post-translationally modified for ER export. NUC encodes the MVP1/GOLD36/ERMO3 myrosinase-associated protein, previously shown to have vacuolar distribution. CYB is an ER and Golgi-localized p24 type I membrane protein component of coat protein complex (COP) vesicles, animal and yeast homologues of which are known to be involved in selective cargo sorting for ER-Golgi export. Without NUC, GLL23 accumulates in the ER this situation suggests that NUC is in fact active in the ER. Without CYB, both GLL23 and NUC were found to accumulate in cyb compartments, consistent with a role for NUC in GLL23 processing and indicated that GLL23 is the likely sorting target of the CYB p24 protein.
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Affiliation(s)
- Sylwia Jancowski
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Nakano RT, Yamada K, Bednarek P, Nishimura M, Hara-Nishimura I. ER bodies in plants of the Brassicales order: biogenesis and association with innate immunity. FRONTIERS IN PLANT SCIENCE 2014; 5:73. [PMID: 24653729 PMCID: PMC3947992 DOI: 10.3389/fpls.2014.00073] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/12/2014] [Indexed: 05/20/2023]
Abstract
The endoplasmic reticulum (ER) forms highly organized network structures composed of tubules and cisternae. Many plant species develop additional ER-derived structures, most of which are specific for certain groups of species. In particular, a rod-shaped structure designated as the ER body is produced by plants of the Brassicales order, which includes Arabidopsis thaliana. Genetic analyses and characterization of A. thaliana mutants possessing a disorganized ER morphology or lacking ER bodies have provided insights into the highly organized mechanisms responsible for the formation of these unique ER structures. The accumulation of proteins specific for the ER body within the ER plays an important role in the formation of ER bodies. However, a mutant that exhibits morphological defects of both the ER and ER bodies has not been identified. This suggests that plants in the Brassicales order have evolved novel mechanisms for the development of this unique organelle, which are distinct from those used to maintain generic ER structures. In A. thaliana, ER bodies are ubiquitous in seedlings and roots, but rare in rosette leaves. Wounding of rosette leaves induces de novo formation of ER bodies, suggesting that these structures are associated with resistance against pathogens and/or herbivores. ER bodies accumulate a large amount of β-glucosidases, which can produce substances that potentially protect against invading pests. Biochemical studies have determined that the enzymatic activities of these β-glucosidases are enhanced during cell collapse. These results suggest that ER bodies are involved in plant immunity, although there is no direct evidence of this. In this review, we provide recent perspectives of ER and ER body formation in A. thaliana, and discuss clues for the functions of ER bodies. We highlight defense strategies against biotic stress that are unique for the Brassicales order, and discuss how ER structures could contribute to these strategies.
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Affiliation(s)
- Ryohei T. Nakano
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Kenji Yamada
- Department of Cell Biology, National Institute for Basic BiologyOkazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (Sokendai)Okazaki, Japan
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznañ, Poland
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic BiologyOkazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (Sokendai)Okazaki, Japan
| | - Ikuko Hara-Nishimura
- Department of Botany, Graduate School of Science, Kyoto UniversityKyoto, Japan
- *Correspondence: Ikuko Hara-Nishimura, Laboratory of Plant Molecular and Cell Biology, Department of Botany, Graduate School of Science, Kyoto University, Kita-Shirakawa Oiwake-cho, Sakyo-ku, 606-8502 Kyoto, Japan e-mail:
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Zhou LZ, Li S, Feng QN, Zhang YL, Zhao X, Zeng YL, Wang H, Jiang L, Zhang Y. Protein S-ACYL Transferase10 is critical for development and salt tolerance in Arabidopsis. THE PLANT CELL 2013; 25:1093-107. [PMID: 23482856 PMCID: PMC3634679 DOI: 10.1105/tpc.112.108829] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/11/2013] [Accepted: 02/17/2013] [Indexed: 05/18/2023]
Abstract
Protein S-acylation, commonly known as palmitoylation, is a reversible posttranslational modification that catalyzes the addition of a saturated lipid group, often palmitate, to the sulfhydryl group of a Cys. Palmitoylation regulates enzyme activity, protein stability, subcellular localization, and intracellular sorting. Many plant proteins are palmitoylated. However, little is known about protein S-acyl transferases (PATs), which catalyze palmitoylation. Here, we report that the tonoplast-localized PAT10 is critical for development and salt tolerance in Arabidopsis thaliana. PAT10 loss of function resulted in pleiotropic growth defects, including smaller leaves, dwarfism, and sterility. In addition, pat10 mutants are hypersensitive to salt stresses. We further show that PAT10 regulates the tonoplast localization of several calcineurin B-like proteins (CBLs), including CBL2, CBL3, and CBL6, whose membrane association also depends on palmitoylation. Introducing a C192S mutation within the highly conserved catalytic motif of PAT10 failed to complement pat10 mutants, indicating that PAT10 functions through protein palmitoylation. We propose that PAT10-mediated palmitoylation is critical for vacuolar function by regulating membrane association or the activities of tonoplast proteins.
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Affiliation(s)
- Liang-Zi Zhou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Sha Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Qiang-Nan Feng
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yu-Ling Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xinying Zhao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Yong-lun Zeng
- School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Hao Wang
- School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yan Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, Shandong, China
- Address correspondence to
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Liebminger E, Grass J, Jez J, Neumann L, Altmann F, Strasser R. Myrosinases TGG1 and TGG2 from Arabidopsis thaliana contain exclusively oligomannosidic N-glycans. PHYTOCHEMISTRY 2012; 84:24-30. [PMID: 23009876 PMCID: PMC3494833 DOI: 10.1016/j.phytochem.2012.08.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/27/2012] [Accepted: 08/29/2012] [Indexed: 05/08/2023]
Abstract
In all eukaryotes N-glycosylation is the most prevalent protein modification of secretory and membrane proteins. Although the N-glycosylation capacity and the individual steps of the N-glycan processing pathway have been well studied in the model plant Arabidopsis thaliana, little attention has been paid to the characterization of the glycosylation status of individual proteins. We report here the structural analysis of all N-glycans present on the endogenous thioglucoside glucohydrolases (myrosinases) TGG1 and TGG2 from A. thaliana. All nine glycosylation sites of TGG1 and all four glycosylation sites of TGG2 are occupied by oligomannosidic structures with Man₅GlcNAc₂ as the major glycoform. Analysis of the oligomannosidic isomers from wild-type plants and mannose trimming deficient mutants by liquid chromatography with porous graphitic carbon and mass spectrometry revealed that the N-glycans from both myrosinases are processed by Golgi-located α-mannosidases.
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Affiliation(s)
- Eva Liebminger
- Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Josephine Grass
- Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Jakub Jez
- Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Laura Neumann
- Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- Corresponding author. Tel.: +43 1 47654 6705; fax: +43 1 47654 6392.
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ERMO3/MVP1/GOLD36 is involved in a cell type-specific mechanism for maintaining ER morphology in Arabidopsis thaliana. PLoS One 2012; 7:e49103. [PMID: 23155454 PMCID: PMC3498303 DOI: 10.1371/journal.pone.0049103] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/04/2012] [Indexed: 11/19/2022] Open
Abstract
The endoplasmic reticulum (ER) has a unique, network-like morphology. The ER structures are composed of tubules, cisternae, and three-way junctions. This morphology is highly conserved among eukaryotes, but the molecular mechanism that maintains ER morphology has not yet been elucidated. In addition, certain Brassicaceae plants develop a unique ER-derived organelle called the ER body. This organelle accumulates large amounts of PYK10, a β-glucosidase, but its physiological functions are still obscure. We aimed to identify a novel factor required for maintaining the morphology of the ER, including ER bodies, and employed a forward-genetic approach using transgenic Arabidopsis thaliana (GFP-h) with fluorescently-labeled ER. We isolated and investigated a mutant (designated endoplasmic reticulum morphology3, ermo3) with huge aggregates and abnormal punctate structures of ER. ERMO3 encodes a GDSL-lipase/esterase family protein, also known as MVP1. Here, we showed that, although ERMO3/MVP1/GOLD36 was expressed ubiquitously, the morphological defects of ermo3 were specifically seen in a certain type of cells where ER bodies developed. Coimmunoprecipitation analysis combined with mass spectrometry revealed that ERMO3/MVP1/GOLD36 interacts with the PYK10 complex, a huge protein complex that is thought to be important for ER body-related defense systems. We also found that the depletion of transcription factor NAI1, a master regulator for ER body formation, suppressed the formation of ER-aggregates in ermo3 cells, suggesting that NAI1 expression plays an important role in the abnormal aggregation of ER. Our results suggest that ERMO3/MVP1/GOLD36 is required for preventing ER and other organelles from abnormal aggregation and for maintaining proper ER morphology in a coordinated manner with NAI1.
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Gu Y, Innes RW. The KEEP ON GOING protein of Arabidopsis regulates intracellular protein trafficking and is degraded during fungal infection. THE PLANT CELL 2012; 24:4717-30. [PMID: 23192225 PMCID: PMC3531862 DOI: 10.1105/tpc.112.105254] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 10/12/2012] [Accepted: 11/04/2012] [Indexed: 05/18/2023]
Abstract
In plants, the trans-Golgi network and early endosomes (TGN/EE) function as the central junction for major endomembrane trafficking events, including endocytosis and secretion. Here, we demonstrate that the KEEP ON GOING (KEG) protein of Arabidopsis thaliana localizes to the TGN/EE and plays an essential role in multiple intracellular trafficking processes. Loss-of-function keg mutants exhibited severe defects in cell expansion, which correlated with defects in vacuole morphology. Confocal microscopy revealed that KEG is required for targeting of plasma membrane proteins to the vacuole. This targeting process appeared to be blocked at the step of multivesicular body (MVB) fusion with the vacuolar membrane as the MVB-associated small GTPase ARA6 was also blocked in vacuolar delivery. In addition, loss of KEG function blocked secretion of apoplastic defense proteins, indicating that KEG plays a role in plant immunity. Significantly, KEG was degraded specifically in cells infected by the fungus Golovinomyces cichoracearum, suggesting that this pathogen may target KEG to manipulate the host secretory system as a virulence strategy. Taking these results together, we conclude that KEG is a key component of TGN/EE that regulates multiple post-Golgi trafficking events in plants, including vacuole biogenesis, targeting of membrane-associated proteins to the vacuole, and secretion of apoplastic proteins.
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Affiliation(s)
- Yangnan Gu
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Roger W. Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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Engineering glucosinolates in plants: current knowledge and potential uses. Appl Biochem Biotechnol 2012; 168:1694-717. [PMID: 22983743 DOI: 10.1007/s12010-012-9890-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/31/2012] [Indexed: 01/19/2023]
Abstract
Glucosinolates (GSL) and their derivatives are well known for the characteristic roles they play in plant defense as signaling molecules and as bioactive compounds for human health. More than 130 GSLs have been reported so far, and most of them belong to the Brassicaceae family. Several enzymes and transcription factors involved in the GSL biosynthesis have been studied in the model plant, Arabidopsis, and in a few other Brassica crop species. Recent studies in GSL research have defined the regulation, distribution, and degradation of GSL biosynthetic pathways; however, the underlying mechanism behind transportation of GSLs in plants is still largely unknown. This review highlights the recent advances in the metabolic engineering of GSLs in plants and discusses their potential applications.
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Au KKC, Pérez-Gómez J, Neto H, Müller C, Meyer AJ, Fricker MD, Moore I. A perturbation in glutathione biosynthesis disrupts endoplasmic reticulum morphology and secretory membrane traffic in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:881-94. [PMID: 22507191 DOI: 10.1111/j.1365-313x.2012.05022.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
To identify potentially novel and essential components of plant membrane trafficking mechanisms we performed a GFP-based forward genetic screen for seedling-lethal biosynthetic membrane trafficking mutants in Arabidopsis thaliana. Amongst these mutants, four recessive alleles of GSH2, which encodes glutathione synthase (GSH2), were recovered. Each allele was characterized by loss of the typical polygonal endoplasmic reticulum (ER) network and the accumulation of swollen ER-derived bodies which accumulated a soluble secretory marker. Since GSH2 is responsible for converting γ-glutamylcysteine (γ-EC) to glutathione (GSH) in the glutathione biosynthesis pathway, gsh2 mutants exhibited γ-EC hyperaccumulation and GSH deficiency. Redox-sensitive GFP revealed that gsh2 seedlings maintained redox poise in the cytoplasm but were more sensitive to oxidative challenge. Genetic and pharmacological evidence indicated that γ-EC accumulation rather than GSH deficiency was responsible for the perturbation of ER morphology. Use of soluble and membrane-bound ER markers suggested that the swollen ER bodies were derived from ER fusiform bodies. Despite the gross perturbation of ER morphology, gsh2 seedlings did not suffer from constitutive oxidative ER stress or lack of an unfolded protein response, and homozygotes for the weakest allele could be propagated. The link between glutathione biosynthesis and ER morphology and function is discussed.
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Affiliation(s)
- Kenneth K C Au
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
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Voelckel C, Gruenheit N, Biggs P, Deusch O, Lockhart P. Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species. BMC Genomics 2012; 13:322. [PMID: 22812500 PMCID: PMC3460751 DOI: 10.1186/1471-2164-13-322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 07/19/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Expression profiling has been proposed as a means for screening non-model organisms in their natural environments to identify genes potentially important in adaptive diversification. Tag profiling using high throughput sequencing is a relatively low cost means of expression profiling with deep coverage. However the extent to which very short cDNA sequences can be effectively used in screening for candidate genes is unclear. Here we investigate this question using an evolutionarily distant as well as a closely related transcriptome for referencing tags. We do this by comparing differentially expressed genes and processes between two closely related allopolyploid species of Pachycladon which have distinct altitudinal preferences in the New Zealand Southern Alps. We validate biological inferences against earlier microarray analyses. RESULTS Statistical and gene annotation enrichment analyses of tag profiles identified more differentially expressed genes of potential adaptive significance than previous analyses of array-based expression profiles. These include genes involved in glucosinolate metabolism, flowering time, and response to cold, desiccation, fungi and oxidation. In addition, despite the short length of 20mer tags, we were able to infer patterns of homeologous gene expression for 700 genes in our reference library of 7,128 full-length Pachycladon ESTs. We also demonstrate that there is significant information loss when mapping tags to the non-conspecific reference transcriptome of A. thaliana as opposed to P. fastigiatum ESTs but also describe mapping strategies by which the larger collection of A. thaliana ESTs can be used as a reference. CONCLUSION When coupled with a reference transcriptome generated using RNA-seq, tag sequencing offers a promising approach for screening natural populations and identifying candidate genes of potential adaptive significance. We identify computational issues important for the successful application of tag profiling in a non-model allopolyploid plant species.
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Affiliation(s)
- Claudia Voelckel
- Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand.
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Chepyshko H, Lai CP, Huang LM, Liu JH, Shaw JF. Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis. BMC Genomics 2012; 13:309. [PMID: 22793791 PMCID: PMC3412167 DOI: 10.1186/1471-2164-13-309] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 07/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND GDSL esterases/lipases are a newly discovered subclass of lipolytic enzymes that are very important and attractive research subjects because of their multifunctional properties, such as broad substrate specificity and regiospecificity. Compared with the current knowledge regarding these enzymes in bacteria, our understanding of the plant GDSL enzymes is very limited, although the GDSL gene family in plant species include numerous members in many fully sequenced plant genomes. Only two genes from a large rice GDSL esterase/lipase gene family were previously characterised, and the majority of the members remain unknown. In the present study, we describe the rice OsGELP (Oryza sativa GDSL esterase/lipase protein) gene family at the genomic and proteomic levels, and use this knowledge to provide insights into the multifunctionality of the rice OsGELP enzymes. RESULTS In this study, an extensive bioinformatics analysis identified 114 genes in the rice OsGELP gene family. A complete overview of this family in rice is presented, including the chromosome locations, gene structures, phylogeny, and protein motifs. Among the OsGELPs and the plant GDSL esterase/lipase proteins of known functions, 41 motifs were found that represent the core secondary structure elements or appear specifically in different phylogenetic subclades. The specification and distribution of identified putative conserved clade-common and -specific peptide motifs, and their location on the predicted protein three dimensional structure may possibly signify their functional roles. Potentially important regions for substrate specificity are highlighted, in accordance with protein three-dimensional model and location of the phylogenetic specific conserved motifs. The differential expression of some representative genes were confirmed by quantitative real-time PCR. The phylogenetic analysis, together with protein motif architectures, and the expression profiling were analysed to predict the possible biological functions of the rice OsGELP genes. CONCLUSIONS Our current genomic analysis, for the first time, presents fundamental information on the organization of the rice OsGELP gene family. With combination of the genomic, phylogenetic, microarray expression, protein motif distribution, and protein structure analyses, we were able to create supported basis for the functional prediction of many members in the rice GDSL esterase/lipase family. The present study provides a platform for the selection of candidate genes for further detailed functional study.
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Affiliation(s)
- Hanna Chepyshko
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, Taiwan, 402, ROC
| | - Chia-Ping Lai
- Department of Food and Beverage Management, Far East University, Tainan, Taiwan, 74448, ROC
| | - Li-Ming Huang
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan, 701, ROC
| | - Jyung-Hurng Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan, 40227, ROC
| | - Jei-Fu Shaw
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, Taiwan, 402, ROC
- Department of Biological Science and Technology, I-Shou University, Kaohsiung, Taiwan, 84001, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, 40227, ROC
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taiwan, 115, ROC
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Zwiewka M, Friml J. Fluorescence imaging-based forward genetic screens to identify trafficking regulators in plants. FRONTIERS IN PLANT SCIENCE 2012; 3:97. [PMID: 22654887 PMCID: PMC3359526 DOI: 10.3389/fpls.2012.00097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 04/25/2012] [Indexed: 05/25/2023]
Abstract
Coordinated, subcellular trafficking of proteins is one of the fundamental properties of the multicellular eukaryotic organisms. Trafficking involves a large diversity of compartments, pathways, cargo molecules, and vesicle-sorting events. It is also crucial in regulating the localization and, thus, the activity of various proteins, but the process is still poorly genetically defined in plants. In the past, forward genetics screens had been used to determine the function of genes by searching for a specific morphological phenotype in the organism population in which mutations had been induced chemically or by irradiation. Unfortunately, these straightforward genetic screens turned out to be limited in identifying new regulators of intracellular protein transport, because mutations affecting essential trafficking pathways often lead to lethality. In addition, the use of these approaches has been restricted by functional redundancy among trafficking regulators. Screens for mutants that rely on the observation of changes in the cellular localization or dynamics of fluorescent subcellular markers enable, at least partially, to circumvent these issues. Hence, such image-based screens provide the possibility to identify either alleles with weak effects or components of the subcellular trafficking machinery that have no strong impact on the plant growth.
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Affiliation(s)
- Marta Zwiewka
- Department of Plant Systems Biology, VIB Life Sciences Research InstituteGent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent UniversityGent, Belgium
| | - Jiří Friml
- Department of Plant Systems Biology, VIB Life Sciences Research InstituteGent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent UniversityGent, Belgium
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Sparkes I, Brandizzi F. Fluorescent protein-based technologies: shedding new light on the plant endomembrane system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:96-107. [PMID: 22449045 DOI: 10.1111/j.1365-313x.2011.04884.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Without doubt, GFP and spectral derivatives have revolutionized the way biologists approach their journey toward the discovery of how plant cells function. It is fascinating that in its early days GFP was used merely for localization studies, but as time progressed researchers successfully explored new avenues to push the power of GFP technology to reach new and exciting research frontiers. This has had a profound impact on the way we can now study complex and dynamic systems such as plant endomembranes. Here we briefly describe some of the approaches where GFP has revolutionized in vivo studies of protein distribution and dynamics and focus on two emerging approaches for the application of GFP technology in plant endomembranes, namely optical tweezers and forward genetics approaches, which are based either on the light or on genetic manipulation of secretory organelles to gain insights on the factors that control their activities and integrity.
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Affiliation(s)
- Imogen Sparkes
- Biosciences,College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, UK
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43
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Gruenheit N, Deusch O, Esser C, Becker M, Voelckel C, Lockhart P. Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. BMC Genomics 2012; 13:92. [PMID: 22417298 PMCID: PMC3378427 DOI: 10.1186/1471-2164-13-92] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 03/14/2012] [Indexed: 01/08/2023] Open
Abstract
Background Transcriptome analysis is increasingly being used to study the evolutionary origins and ecology of non-model plants. One issue for both transcriptome assembly and differential gene expression analyses is the common occurrence in plants of hybridisation and whole genome duplication (WGD) and hybridization resulting in allopolyploidy. The divergence of duplicated genes following WGD creates near identical homeologues that can be problematic for de novo assembly and also reference based assembly protocols that use short reads (35 - 100 bp). Results Here we report a successful strategy for the assembly of two transcriptomes made using 75 bp Illumina reads from Pachycladon fastigiatum and Pachycladon cheesemanii. Both are allopolyploid plant species (2n = 20) that originated in the New Zealand Alps about 0.8 million years ago. In a systematic analysis of 19 different coverage cutoffs and 20 different k-mer sizes we showed that i) none of the genes could be assembled across all of the parameter space ii) assembly of each gene required an optimal set of parameter values and iii) these parameter values could be explained in part by different gene expression levels and different degrees of similarity between genes. Conclusions To obtain optimal transcriptome assemblies for allopolyploid plants, k-mer size and k-mer coverage need to be considered simultaneously across a broad parameter space. This is important for assembling a maximum number of full length ESTs and for avoiding chimeric assemblies of homeologous and paralogous gene copies.
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Affiliation(s)
- Nicole Gruenheit
- Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand.
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Frerigmann H, Böttcher C, Baatout D, Gigolashvili T. Glucosinolates are produced in trichomes of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2012; 3:242. [PMID: 23115560 PMCID: PMC3483630 DOI: 10.3389/fpls.2012.00242] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/10/2012] [Indexed: 05/03/2023]
Abstract
Glucosinolates (GS) are important plant secondary metabolites in plant resistance to herbivores, bacteria, and fungi, which have been shown to be accumulating in different organs and tissue types at varying concentrations. There are more than 200 GS species found in order Brassicales and presence of these compounds is well documented on organ-specific but not on cell-specific level. We used UPLC/ESI-QTOF-MS to measure the presence of GS and qRT-PCR to analyse the expression of GS biosynthetic and regulatory genes in isolated Arabidopsis thaliana trichomes. Trichomes of Arabidopsis are shown to synthesize chemoprotective aliphatic glucosinolates (AGS) and indolic glucosinolates (IGS), which are known for their biological activities against fungi, bacterial pathogens, or herbivores. UPLC/ESI-QTOF-MS analysis of various IGS mutants reveal increased or decreased levels of IGS in trichomes of gain- and loss-of-function mutants correspondingly. Using pMYB51/HIG1-uidA and pMYB28/PMG1/HAG1-uidA reporter plants we demonstrate that production of these important compounds is activated in trichomes of leaves or inflorescences in response to wounding. Since trichomes represent the first interface in plant-environment interactions, the possible role of GS containing trichomes in plant defense or signaling is discussed.
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Affiliation(s)
| | - Christoph Böttcher
- Department of Stress and Developmental Biology, Leibniz Institute of Plant BiochemistryHalle/Saale, Germany
| | - Dunja Baatout
- Universität zu Köln, Biozentrum Köln, Botanisches InstitutKöln, Germany
| | - Tamara Gigolashvili
- Universität zu Köln, Biozentrum Köln, Botanisches InstitutKöln, Germany
- *Correspondence: Tamara Gigolashvili, Universität zu Köln, Biozentrum Köln, Botanisches Institut, Zülpicher Street 47 B, 50674 Köln, Germany. e-mail:
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45
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Marti L, Stefano G, Tamura K, Hawes C, Renna L, Held MA, Brandizzi F. A missense mutation in the vacuolar protein GOLD36 causes organizational defects in the ER and aberrant protein trafficking in the plant secretory pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:901-913. [PMID: 20626647 DOI: 10.1111/j.1365-313x.2010.04296.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A central question in cell biology is how the identity of organelles is established and maintained. Here, we report on GOLD36, an EMS mutant identified through a screen for partial displacement of the Golgi marker, ST-GFP, to other organelles. GOLD36 showed partial distribution of ST-GFP into a modified endoplasmic reticulum (ER) network, which formed bulges and large skein-like structures entangling Golgi stacks. GOLD36 showed defects in ER protein export as evidenced by our observations that, besides the partial retention of Golgi markers in the ER, the trafficking of a soluble bulk-flow marker to the cell surface was also compromised. Using a combination of classical mapping and next-generation DNA sequencing approaches, we linked the mutant phenotype to a missense mutation of a proline residue in position 80 to a leucine residue in a small endomembrane protein encoded by the gold36 locus (At1g54030). Subcellular localization analyses indicated that GOLD36 is a vacuolar protein and that its mutated form is retained in the ER. Interestingly also, a gold36 knock-out mutant mirrored the GOLD36 subcellular phenotype. These data indicate that GOLD36 is a protein destined to post-ER compartments and suggest that its export from the ER is a requirement to ensure steady-state maintenance of the organelle's organization and functional activity in relation to other secretory compartments. We speculate that GOLD36 may be a factor that is necessary for ER integrity because of its ability to limit deleterious effects of other secretory proteins on the ER.
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Affiliation(s)
- Lucia Marti
- Michigan State University-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
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46
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Volokita M, Rosilio-Brami T, Rivkin N, Zik M. Combining Comparative Sequence and Genomic Data to Ascertain Phylogenetic Relationships and Explore the Evolution of the Large GDSL-Lipase Family in Land Plants. Mol Biol Evol 2010; 28:551-65. [DOI: 10.1093/molbev/msq226] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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47
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Wittstock U, Burow M. Glucosinolate breakdown in Arabidopsis: mechanism, regulation and biological significance. THE ARABIDOPSIS BOOK 2010. [PMID: 22303260 DOI: 10.1199/tab0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Glucosinolates are a group of thioglucosides in plants of the Brassicales order. Together with their hydrolytic enzymes, the myrosinases, they constitute the 'mustard oil bomb' involved in plant defense. Here we summarize recent studies in Arabidopsis that have provided molecular evidence that the glucosinolate-myrosinase system is much more than a 'two-component defense system,' and started to unravel the roles of different glucosinolate breakdown pathways in the context of plant responses to biotic and abiotic stresses.
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Wittstock U, Burow M. Glucosinolate breakdown in Arabidopsis: mechanism, regulation and biological significance. THE ARABIDOPSIS BOOK 2010; 8:e0134. [PMID: 22303260 PMCID: PMC3244901 DOI: 10.1199/tab.0134] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Glucosinolates are a group of thioglucosides in plants of the Brassicales order. Together with their hydrolytic enzymes, the myrosinases, they constitute the 'mustard oil bomb' involved in plant defense. Here we summarize recent studies in Arabidopsis that have provided molecular evidence that the glucosinolate-myrosinase system is much more than a 'two-component defense system,' and started to unravel the roles of different glucosinolate breakdown pathways in the context of plant responses to biotic and abiotic stresses.
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Affiliation(s)
- Ute Wittstock
- Institut für Pharmazeutische Biologie, Technische Universität Braunschweig
- Address for correspondence:
| | - Meike Burow
- Department of Plant Biology and Biotechnology, VKR Research Centre Pro-Active Plants
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