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Wang L, Wang R, Lei W, Wu J, Li C, Shi H, Meng L, Yuan F, Zhou Q, Cui C. Transcriptome analysis reveals gene responses to herbicide, tribenuron methyl, in Brassica napus L. during seed germination. BMC Genomics 2021; 22:299. [PMID: 33892633 PMCID: PMC8067372 DOI: 10.1186/s12864-021-07614-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/14/2021] [Indexed: 11/25/2022] Open
Abstract
Background Tribenuron methyl (TBM) is an herbicide that inhibits sulfonylurea acetolactate synthase (ALS) and is one of the most widely used broad-leaved herbicides for crop production. However, soil residues or drifting of the herbicide spray might affect the germination and growth of rapeseed, Brassica napus, so it is imperative to understand the response mechanism of rape to TBM during germination. The aim of this study was to use transcriptome analysis to reveal the gene responses in herbicide-tolerant rapeseed to TBM stress during seed germination. Results 2414, 2286, and 1068 differentially expressed genes (DEGs) were identified in TBM-treated resistant vs sensitive lines, treated vs. control sensitive lines, treated vs. control resistant lines, respectively. GO analysis showed that most DEGs were annotated to the oxidation-reduction pathways and catalytic activity. KEGG enrichment was mainly involved in plant-pathogen interactions, α-linolenic acid metabolism, glucosinolate biosynthesis, and phenylpropanoid biosynthesis. Based on GO and KEGG enrichment, a total of 137 target genes were identified, including genes involved in biotransferase activity, response to antioxidant stress and lipid metabolism. Biotransferase genes, CYP450, ABC and GST, detoxify herbicide molecules through physical or biochemical processes. Antioxidant genes, RBOH, WRKY, CDPK, MAPK, CAT, and POD regulate plant tolerance by transmitting ROS signals and triggering antioxidant enzyme expression. Lipid-related genes and hormone-related genes were also found, such as LOX3, ADH1, JAZ6, BIN2 and ERF, and they also played an important role in herbicide resistance. Conclusions This study provides insights for selecting TBM-tolerant rapeseed germplasm and exploring the molecular mechanism of TBM tolerance during germination. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07614-1.
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Affiliation(s)
- Liuyan Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Ruili Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Wei Lei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jiayi Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Chenyang Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Hongsong Shi
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Lijiao Meng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Fang Yuan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Qingyuan Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
| | - Cui Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
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Schenck CA, Last RL. Location, location! cellular relocalization primes specialized metabolic diversification. FEBS J 2019; 287:1359-1368. [PMID: 31623016 DOI: 10.1111/febs.15097] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/12/2019] [Accepted: 10/14/2019] [Indexed: 12/31/2022]
Abstract
Specialized metabolites are structurally diverse and cell- or tissue-specific molecules produced in restricted plant lineages. In contrast, primary metabolic pathways are highly conserved in plants and produce metabolites essential for all of life, such as amino acids and nucleotides. Substrate promiscuity - the capacity to accept non-native substrates - is a common characteristic of enzymes, and its impact is especially apparent in generating specialized metabolite variation. However, promiscuity only leads to metabolic diversity when alternative substrates are available; thus, enzyme cellular and subcellular localization directly influence chemical phenotypes. We review a variety of mechanisms that modulate substrate availability for promiscuous plant enzymes. We focus on examples where evolution led to modification of the 'cellular context' through changes in cell-type expression, subcellular relocalization, pathway sequestration, and cellular mixing via tissue damage. These varied mechanisms contributed to the emergence of structurally diverse plant specialized metabolites and inform future metabolic engineering approaches.
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Affiliation(s)
- Craig A Schenck
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, USA
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Cuong DM, Kim JK, Bong SJ, Baek SA, Jeon J, Park JS, Park SU. Comparative analysis of glucosinolates and metabolite profiling of green and red mustard ( brassica juncea) hairy roots. 3 Biotech 2018; 8:382. [PMID: 30148032 PMCID: PMC6104223 DOI: 10.1007/s13205-018-1393-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 08/06/2018] [Indexed: 12/30/2022] Open
Abstract
Here, accumulation of glucosinolates and expression of glucosinolates biosynthesis genes in green and red mustard hairy roots were identified and quantified by HPLC and qRT-PCR analyses. The total glucosinolates content of green mustard hairy root (10.09 µg/g dry weight) was 3.88 times higher than that of red mustard hairy root. Indolic glucosinolates (glucobrassicin, 4-methoxyglucobrassicin, and neoglucobrassicin) in green mustard were found at 30.92, 6.95, and 5.29 times higher than in red mustard hairy root, respectively. Conversely, levels of glucotropaeolin (aromatic glucosinolate) was significantly higher in red mustard than in green mustard. Accumulation of glucoraphasatin, an aliphatic glucosinolate, was only observed only in red mustard hairy roots. Quantitative real-time PCR analysis showed that the expression level of genes related to aliphatic and aromatic glucosinolate biosynthesis were higher in red mustard, exception BjCYP83B. The expression of BjCYP79B2, which encodes a key enzyme involved in the indolic glucosinolate biosynthetic pathway, was higher in green mustard than in red mustard. Additionally, to further distinguish between green mustard and red mustard hairy roots, hydrophilic and lipophilic compounds were identified by gas chromatography-mass spectrometry and subjected to principal component analysis. The results indicated that core primary metabolites and glucosinolate levels were higher in the hairy roots of green mustard than in those of red mustard.
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Affiliation(s)
- Do Manh Cuong
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134 South Korea
| | - Jae Kwang Kim
- Division of Life Sciences and Convergence Research Center for Insect Vectors, Incheon National University, Incheon, 22012 South Korea
| | - Sun Ju Bong
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134 South Korea
| | - Seung A Baek
- Division of Life Sciences and Convergence Research Center for Insect Vectors, Incheon National University, Incheon, 22012 South Korea
| | - Jin Jeon
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134 South Korea
| | - Jong Seok Park
- Department of Horticultural Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134 South Korea
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134 South Korea
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Wu S, Lei J, Chen G, Chen H, Cao B, Chen C. De novo Transcriptome Assembly of Chinese Kale and Global Expression Analysis of Genes Involved in Glucosinolate Metabolism in Multiple Tissues. FRONTIERS IN PLANT SCIENCE 2017; 8:92. [PMID: 28228764 PMCID: PMC5296335 DOI: 10.3389/fpls.2017.00092] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 01/16/2017] [Indexed: 05/18/2023]
Abstract
Chinese kale, a vegetable of the cruciferous family, is a popular crop in southern China and Southeast Asia due to its high glucosinolate content and nutritional qualities. However, there is little research on the molecular genetics and genes involved in glucosinolate metabolism and its regulation in Chinese kale. In this study, we sequenced and characterized the transcriptomes and expression profiles of genes expressed in 11 tissues of Chinese kale. A total of 216 million 150-bp clean reads were generated using RNA-sequencing technology. From the sequences, 98,180 unigenes were assembled for the whole plant, and 49,582~98,423 unigenes were assembled for each tissue. Blast analysis indicated that a total of 80,688 (82.18%) unigenes exhibited similarity to known proteins. The functional annotation and classification tools used in this study suggested that genes principally expressed in Chinese kale, were mostly involved in fundamental processes, such as cellular and molecular functions, the signal transduction, and biosynthesis of secondary metabolites. The expression levels of all unigenes were analyzed in various tissues of Chinese kale. A large number of candidate genes involved in glucosinolate metabolism and its regulation were identified, and the expression patterns of these genes were analyzed. We found that most of the genes involved in glucosinolate biosynthesis were highly expressed in the root, petiole, and in senescent leaves. The expression patterns of ten glucosinolate biosynthetic genes from RNA-seq were validated by quantitative RT-PCR in different tissues. These results provided an initial and global overview of Chinese kale gene functions and expression activities in different tissues.
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Affiliation(s)
- Shuanghua Wu
- Department of Vegetable Science, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Jianjun Lei
- Department of Vegetable Science, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Guoju Chen
- Department of Vegetable Science, College of Horticulture, South China Agricultural UniversityGuangzhou, China
| | - Hancai Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Bihao Cao
- Department of Vegetable Science, College of Horticulture, South China Agricultural UniversityGuangzhou, China
- *Correspondence: Bihao Cao
| | - Changming Chen
- Department of Vegetable Science, College of Horticulture, South China Agricultural UniversityGuangzhou, China
- Changming Chen
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Augustine R, Bisht NC. Regulation of Glucosinolate Metabolism: From Model Plant Arabidopsis thaliana to Brassica Crops. REFERENCE SERIES IN PHYTOCHEMISTRY 2017. [DOI: 10.1007/978-3-319-25462-3_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Olsen CE, Huang XC, Hansen CIC, Cipollini D, Ørgaard M, Matthes A, Geu-Flores F, Koch MA, Agerbirk N. Glucosinolate diversity within a phylogenetic framework of the tribe Cardamineae (Brassicaceae) unraveled with HPLC-MS/MS and NMR-based analytical distinction of 70 desulfoglucosinolates. PHYTOCHEMISTRY 2016; 132:33-56. [PMID: 27743600 DOI: 10.1016/j.phytochem.2016.09.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/29/2016] [Accepted: 09/29/2016] [Indexed: 05/22/2023]
Abstract
As a basis for future investigations of evolutionary trajectories and biosynthetic mechanisms underlying variations in glucosinolate structures, we screened members of the crucifer tribe Cardamineae by HPLC-MS/MS, isolated and identified glucosinolates by NMR, searched the literature for previous data for the tribe, and collected HPLC-MS/MS data for nearly all glucosinolates known from the tribe as well as some related structures (70 in total). This is a considerable proportion of the approximately 142 currently documented natural glucosinolates. Calibration with authentic references allowed distinction (or elucidation) of isomers in many cases, such as distinction of β-hydroxyls, methylthios, methylsulfinyls and methylsulfonyls. A mechanism for fragmentation of secondary β-hydroxyls in MS was elucidated, and two novel glucosinolates were discovered: 2-hydroxy-3-methylpentylglucosinolate in roots of Cardamine pratensis and 2-hydroxy-8-(methylsulfinyl)octylglucosinolate in seeds of Rorippa amphibia. A large number of glucosinolates (ca. 54 with high structural certainty and a further 28 or more suggested from tandem MS), representing a wide structural variation, is documented from the tribe. This included glucosinolates apparently derived from Met, Phe, Trp, Val/Leu, Ile and higher homologues. Normal side chain elongation and side chain decoration by oxidation or methylation was observed, as well as rare abnormal side chain decoration (hydroxylation of aliphatics at the δ rather than β-position). Some species had diverse profiles, e.g. R. amphibia and C. pratensis (19 and 16 individual glucosinolates, respectively), comparable to total diversity in literature reports of Armoracia rusticana (17?), Barbarea vulgaris (20-24), and Rorippa indica (>20?). The ancestor or the tribe would appear to have used Trp, Met, and homoPhe as glucosinolate precursor amino acids, and to exhibit oxidation of thio to sulfinyl, formation of alkenyls, β-hydroxylation of aliphatic chains and hydroxylation and methylation of indole glucosinolates. Two hotspots of apparent biochemical innovation and loss were identified: C. pratensis and the genus Barbarea. Diversity in other species mainly included structures also known from other crucifers. In addition to a role of gene duplication, two contrasting genetic/biochemical mechanisms for evolution of such combined diversity and redundancy are discussed: (i) involvement of widespread genes with expression varying during evolution, and (ii) mutational changes in substrate specificities of CYP79F and GS-OH enzymes.
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Affiliation(s)
- Carl Erik Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Xiao-Chen Huang
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Cecilie I C Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Don Cipollini
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
| | - Marian Ørgaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Annemarie Matthes
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Fernando Geu-Flores
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Niels Agerbirk
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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Yi GE, Robin AHK, Yang K, Park JI, Hwang BH, Nou IS. Exogenous Methyl Jasmonate and Salicylic Acid Induce Subspecies-Specific Patterns of Glucosinolate Accumulation and Gene Expression in Brassica oleracea L. Molecules 2016; 21:molecules21101417. [PMID: 27783045 PMCID: PMC6273115 DOI: 10.3390/molecules21101417] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/18/2016] [Accepted: 10/19/2016] [Indexed: 01/18/2023] Open
Abstract
Glucosinolates have anti-carcinogenic properties. In the recent decades, the genetics of glucosinolate biosynthesis has been widely studied, however, the expression of specific genes involved in glucosinolate biosynthesis under exogenous phytohormone treatment has not been explored at the subspecies level in Brassica oleracea. Such data are vital for strategies aimed at selective exploitation of glucosinolate profiles. This study quantified the expression of 38 glucosinolate biosynthesis-related genes in three B. oleracea subspecies, namely cabbage, broccoli and kale, and catalogued associations between gene expression and increased contents of individual glucosinolates under methyl jasmonate (MeJA) and salicylic acid (SA) treatments. Glucosinolate accumulation and gene expression in response to phytohormone elicitation was subspecies specific. For instance, cabbage leaves showed enhanced accumulation of the aliphatic glucoiberin, progoitrin, sinigrin and indolic neoglucobrassicin under both MeJA and SA treatment. MeJA treatment induced strikingly higher accumulation of glucobrassicin (GBS) in cabbage and kale and of neoglucobrassicin (NGBS) in broccoli compared to controls. Notably higher expression of ST5a (Bol026200), CYP81F1 (Bol028913, Bol028914) and CYP81F4 genes was associated with significantly higher GBS accumulation under MeJA treatment compared to controls in all three subspecies. CYP81F4 genes, trans-activated by MYB34 genes, were expressed at remarkably high levels in all three subspecies under MeJA treatment, which also induced in higher indolic NGBS accumulation in all three subspecies. Remarkably higher expression of MYB28 (Bol036286), ST5b, ST5c, AOP2, FMOGS-OX5 (Bol031350) and GSL-OH (Bol033373) was associated with much higher contents of aliphatic glucosinolates in kale leaves compared to the other two subspecies. The genes expressed highly could be utilized in strategies to selectively increase glucosinolate compounds in B. oleracea subspecies. These results promote efforts to develop genotypes of B. oleracea and other species with enhanced levels of desired glucosinolates.
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Affiliation(s)
- Go-Eun Yi
- Department of Horticulture, Sunchon National University, Suncheon-si 540-950, Korea.
| | - Arif Hasan Khan Robin
- Department of Horticulture, Sunchon National University, Suncheon-si 540-950, Korea.
| | - Kiwoung Yang
- Department of Horticulture, Sunchon National University, Suncheon-si 540-950, Korea.
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon-si 540-950, Korea.
| | - Byung Ho Hwang
- R & D Center for Crop Breeding, Asia Seed Ltd., Icheon-si, Gyeonggi-do 467-906, Korea.
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon-si 540-950, Korea.
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Chandna R, Augustine R, Kanchupati P, Kumar R, Kumar P, Arya GC, Bisht NC. Class-Specific Evolution and Transcriptional Differentiation of 14-3-3 Family Members in Mesohexaploid Brassica rapa. FRONTIERS IN PLANT SCIENCE 2016; 7:12. [PMID: 26858736 PMCID: PMC4726770 DOI: 10.3389/fpls.2016.00012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 01/07/2016] [Indexed: 05/22/2023]
Abstract
14-3-3s are highly conserved, multigene family proteins that have been implicated in modulating various biological processes. The presence of inherent polyploidy and genome complexity has limited the identification and characterization of 14-3-3 proteins from globally important Brassica crops. Through data mining of Brassica rapa, the model Brassica genome, we identified 21 members encoding 14-3-3 proteins namely, BraA.GRF14.a to BraA.GRF14.u. Phylogenetic analysis indicated that B. rapa contains both ε (epsilon) and non-ε 14-3-3 isoforms, having distinct intron-exon structural organization patterns. The non-ε isoforms showed lower divergence rate (Ks < 0.45) compared to ε protein isoforms (Ks > 0.48), suggesting class-specific divergence pattern. Synteny analysis revealed that mesohexaploid B. rapa genome has retained 1-5 orthologs of each Arabidopsis 14-3-3 gene, interspersed across its three fragmented sub-genomes. qRT-PCR analysis showed that 14 of the 21 BraA.GRF14 were expressed, wherein a higher abundance of non-ε transcripts was observed compared to the ε genes, indicating class-specific transcriptional bias. The BraA.GRF14 genes showed distinct expression pattern during plant developmental stages and in response to abiotic stress, phytohormone treatments, and nutrient deprivation conditions. Together, the distinct expression pattern and differential regulation of BraA.GRF14 genes indicated the occurrence of functional divergence of B. rapa 14-3-3 proteins during plant development and stress responses.
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Augustine R, Bisht NC. Biofortification of oilseed Brassica juncea with the anti-cancer compound glucoraphanin by suppressing GSL-ALK gene family. Sci Rep 2015; 5:18005. [PMID: 26657321 PMCID: PMC4997087 DOI: 10.1038/srep18005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 11/10/2015] [Indexed: 12/25/2022] Open
Abstract
Glucosinolates are amino acids derived secondary metabolites, invariably present in Brassicales, which have huge health and agricultural benefits. Sulphoraphane, the breakdown product of glucosinolate glucoraphanin is known to posses anti-cancer properties. AOP (2-oxoglutarate-dependent dioxygenases) or GSL-ALK enzyme catalyzes the conversion of desirable glucoraphanin to deleterious gluconapin and progoitrin, which are present in very high amounts in most of the cultivable Brassica species including Brassica juncea. In this study we showed that B. juncea encodes four functional homologs of GSL-ALK gene and constitutive silencing of GSL-ALK homologs resulted in accumulation of glucoraphanin up to 43.11 μmoles g(-1) DW in the seeds with a concomitant reduction in the anti-nutritional glucosinolates. Glucoraphanin content was found remarkably high in leaves as well as sprouts of the transgenic lines. Transcript quantification of high glucoraphanin lines confirmed significant down-regulation of GSL-ALK homologs. Growth and other seed quality parameters of the transgenic lines did not show drastic difference, compared to the untransformed control. High glucoraphanin lines also showed higher resistance towards stem rot pathogen Sclerotinia sclerotiorum. Our results suggest that metabolic engineering of GSL-ALK has huge potential for enriching glucoraphanin content, and improve the oil quality and vegetable value of Brassica crops.
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Affiliation(s)
- Rehna Augustine
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, INDIA
| | - Naveen C. Bisht
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, INDIA
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