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Yang Z, Chen W, Jia T, Shi H, Sun D. Integrated Transcriptomic and Metabolomic Analyses Identify Critical Genes and Metabolites Associated with Seed Vigor of Common Wheat. Int J Mol Sci 2023; 25:526. [PMID: 38203695 PMCID: PMC10779259 DOI: 10.3390/ijms25010526] [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: 11/30/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Seed aging is a common physiological phenomenon during storage which has a great impact on seed quality. An in-depth analysis of the physiological and molecular mechanisms of wheat seed aging is of great significance for cultivating high-vigor wheat varieties. This study reveals the physiological mechanisms of wheat seed aging in two cultivars differing in seed vigor, combining metabolome and transcriptome analyses. Differences between cultivars were examined based on metabolomic differential analysis. Artificial aging had a significant impact on the metabolism of wheat seeds. A total of 7470 (3641 upregulated and 3829 downregulated) DEGs were detected between non-aging HT and LT seeds; however, 10,648 (4506 up and 6142 down) were detected between the two cultivars after aging treatment. Eleven, eight, and four key metabolic-related gene families were identified in the glycolysis/gluconeogenesis and TCA cycle pathways, starch and sucrose metabolism pathways, and galactose metabolism pathways, respectively. In addition, 111 up-regulated transcription factor genes and 85 down-regulated transcription factor genes were identified in the LT 48h group. A total of 548 metabolites were detected across all samples. Cultivar comparisons between the non-aged groups and aged groups revealed 46 (30 upregulated and 16 downregulated) and 62 (38 upregulated and 24 downregulated) DIMs, respectively. Network analysis of the metabolites indicated that glucarate O-phosphoric acid, L-methionine sulfoxide, isocitric acid, and Gln-Gly might be the most crucial DIMs between HT and LT. The main related metabolites were enriched in pathways such as glyoxylate and dicarboxylate metabolism, biosynthesis of secondary metabolites, fatty acid degradation, etc. However, metabolites that exhibited differences between cultivars were mainly enriched in carbon metabolism, the TCA cycle, etc. Through combined metabolome and transcriptome analyses, it was found that artificial aging significantly affected glycolysis/gluconeogenesis, pyruvate metabolism, and glyoxylate and dicarboxylate metabolism, which involved key genes such as ACS, F16P2, and PPDK1. We thus speculate that these genes may be crucial in regulating physiological changes in seeds during artificial aging. In addition, an analysis of cultivar differences identified pathways related to amino acid and polypeptide metabolism, such as cysteine and methionine metabolism, glutathione metabolism, and amino sugar and nucleotide sugar metabolism, involving key genes such as BCAT3, CHI1, GAUT1, and GAUT4, which may play pivotal roles in vigor differences between cultivars.
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Affiliation(s)
- Zhenrong Yang
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Z.Y.); (T.J.); (H.S.)
| | - Weiguo Chen
- College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Tianxiang Jia
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Z.Y.); (T.J.); (H.S.)
| | - Huawei Shi
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Z.Y.); (T.J.); (H.S.)
| | - Daizhen Sun
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Z.Y.); (T.J.); (H.S.)
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2
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Malhotra B, Kumar P, Bisht NC. Defense versus growth trade-offs: Insights from glucosinolates and their catabolites. PLANT, CELL & ENVIRONMENT 2023; 46:2964-2984. [PMID: 36207995 DOI: 10.1111/pce.14462] [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: 06/22/2022] [Revised: 09/14/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Specialized metabolites are a structurally diverse group of naturally occurring compounds that facilitate plant-environment interactions. Their synthesis and maintenance in plants is overall a resource-demanding process that occurs at the expense of growth and reproduction and typically incurs several costs. Evidence emerging on different specialized compounds suggests that they serve multiple auxiliary functions to influence and moderate primary metabolism in plants. These new functionalities enable them to mediate trade-offs from defenses to growth and also to offset their production and maintenance costs in plants. Recent research on glucosinolates (GSLs), which are specialized metabolites of Brassicales, demonstrates their emerging multifunctionalities to fine-tune plant growth and development under variable environments. Herein, we present findings from the septennium on individual GSLs and their catabolites (GHPs) per se, that work as mobile signals within plants to mediate precise regulations of their primary physiological functions. Both GSLs and GHPs calibrate growth-defense trade-off interactions either synergistically or directly when they function as storage compounds, abiotic stress alleviators, and one-to-one regulators of growth pathways in plants. We finally summarize the overall lessons learned from GSLs and GHPs as a model and raise the most pressing questions to address the molecular-genetic intricacies of specialized metabolite-based trade-offs in plants.
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Affiliation(s)
- Bhanu Malhotra
- National Institute of Plant Genome Research, New Delhi, India
| | - Pawan Kumar
- National Institute of Plant Genome Research, New Delhi, India
| | - Naveen C Bisht
- National Institute of Plant Genome Research, New Delhi, India
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3
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Andrade-Marcial M, Ruíz-May E, Elizalde-Contreras JM, Pacheco N, Herrera-Pool E, De-la-Peña C. Proteome of Agave angustifolia Haw.: Uncovering metabolic alterations, over-accumulation of amino acids, and compensatory pathways in chloroplast-deficient albino plantlets. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107902. [PMID: 37506650 DOI: 10.1016/j.plaphy.2023.107902] [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: 03/23/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
Amino acids (AA) are essential molecules for plant physiology, acting as precursor molecules for proteins and other organic compounds. Chloroplasts play a vital role in AA metabolism, yet little is known about the impact on AA metabolism of albino plants' lack of chloroplasts. In this study, we conducted a quantitative proteome analysis on albino and variegated somaclonal variants of Agave angustifolia Haw. to investigate metabolic alterations in chloroplast-deficient plants, with a focus on AA metabolic pathways. We identified 82 enzymes involved in AA metabolism, with 32 showing differential accumulation between the somaclonal variants. AaCM, AaALS, AaBCAT, AaIPMS1, AaSHMT, AaAST, AaCGS, and AaMS enzymes were particularly relevant in chloroplast-deficient Agave plantlets. Both variegated and albino phenotypes exhibited excessive synthesis of AA typically associated with chloroplasts (aromatic AAs, BCAAs, Asp, Lys, Pro and Met). Consistent trends were observed for AaBCAT and AaCM at mRNA and protein levels in albino plantlets. These findings highlight the critical activation and reprogramming of AA metabolic pathways in plants lacking chloroplasts. This study contributes to unraveling the intricate relationship between AA metabolism and chloroplast absence, offering insights into survival mechanisms of albino plants.
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Affiliation(s)
- M Andrade-Marcial
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - E Ruíz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Congregación el Haya, 91070, Xalapa, Veracruz, México
| | - J M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Congregación el Haya, 91070, Xalapa, Veracruz, México
| | - N Pacheco
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Unidad Sureste, Tablaje Catastral 31264 Km 5.5 Carretera Sierra Papacal-Chuburná Puerto, Parque Científico Tecnológico de Yucatán, CP, 97302, Mérida, Yucatán, México
| | - E Herrera-Pool
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Unidad Sureste, Tablaje Catastral 31264 Km 5.5 Carretera Sierra Papacal-Chuburná Puerto, Parque Científico Tecnológico de Yucatán, CP, 97302, Mérida, Yucatán, México
| | - C De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México.
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4
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Lyu X, Li YH, Li Y, Li D, Han C, Hong H, Tian Y, Han L, Liu B, Qiu LJ. The domestication-associated L1 gene encodes a eucomic acid synthase pleiotropically modulating pod pigmentation and shattering in soybean. MOLECULAR PLANT 2023:S1674-2052(23)00169-7. [PMID: 37433301 DOI: 10.1016/j.molp.2023.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/23/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023]
Abstract
Pod coloration is a domestication-related trait in soybean, with modern cultivars typically displaying brown or tan pods, while their wild relative, Glycine soja, possesses black pods. However, the factors regulating this color variation remain unknown. In this study, we cloned and characterized L1, the classical locus responsible for black pods in soybean. By using map-based cloning and genetic analyses, we identified the causal gene of L1 and revealed that it encodes a hydroxymethylglutaryl-coenzyme A (CoA) lyase-like (HMGL-like) domain protein. Biochemical assays showed that L1 functions as a eucomic acid synthase and facilitates the synthesis of eucomic acid and piscidic acid, both of which contribute to coloration of pods and seed coats in soybean. Interestingly, we found that L1 plants are more prone to pod shattering under light exposure than l1 null mutants because dark pigmentation increases photothermal efficiency. Hence, pleiotropic effects of L1 on pod color and shattering, as well as seed pigmentation, likely contributed to the preference for l1 alleles during soybean domestication and improvement. Collectively, our study provides new insights into the mechanism of pod coloration and identifies a new target for future de novo domestication of legume crops.
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Affiliation(s)
- Xiangguang Lyu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Yanfei Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People''s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Delin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Chao Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Huilong Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Yu Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Lida Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
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5
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Qin H, King GJ, Borpatragohain P, Zou J. Developing multifunctional crops by engineering Brassicaceae glucosinolate pathways. PLANT COMMUNICATIONS 2023:100565. [PMID: 36823985 PMCID: PMC10363516 DOI: 10.1016/j.xplc.2023.100565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Glucosinolates (GSLs), found mainly in species of the Brassicaceae family, are one of the most well-studied classes of secondary metabolites. Produced by the action of myrosinase on GSLs, GSL-derived hydrolysis products (GHPs) primarily defend against biotic stress in planta. They also significantly affect the quality of crop products, with a subset of GHPs contributing unique food flavors and multiple therapeutic benefits or causing disagreeable food odors and health risks. Here, we explore the potential of these bioactive functions, which could be exploited for future sustainable agriculture. We first summarize our accumulated understanding of GSL diversity and distribution across representative Brassicaceae species. We then systematically discuss and evaluate the potential of exploited and unutilized genes involved in GSL biosynthesis, transport, and hydrolysis as candidate GSL engineering targets. Benefiting from available information on GSL and GHP functions, we explore options for multifunctional Brassicaceae crop ideotypes to meet future demand for food diversification and sustainable crop production. An integrated roadmap is subsequently proposed to guide ideotype development, in which maximization of beneficial effects and minimization of detrimental effects of GHPs could be combined and associated with various end uses. Based on several use-case examples, we discuss advantages and limitations of available biotechnological approaches that may contribute to effective deployment and could provide novel insights for optimization of future GSL engineering.
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Affiliation(s)
- Han Qin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | | | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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6
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Ghidoli M, Ponzoni E, Araniti F, Miglio D, Pilu R. Genetic Improvement of Camelina sativa (L.) Crantz: Opportunities and Challenges. PLANTS (BASEL, SWITZERLAND) 2023; 12:570. [PMID: 36771654 PMCID: PMC9920110 DOI: 10.3390/plants12030570] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
In recent years, a renewed interest in novel crops has been developing due to the environmental issues associated with the sustainability of agricultural practices. In particular, a cover crop, Camelina sativa (L.) Crantz, belonging to the Brassicaceae family, is attracting the scientific community's interest for several desirable features. It is related to the model species Arabidopsis thaliana, and its oil extracted from the seeds can be used either for food and feed, or for industrial uses such as biofuel production. From an agronomic point of view, it can grow in marginal lands with little or no inputs, and is practically resistant to the most important pathogens of Brassicaceae. Although cultivated in the past, particularly in northern Europe and Italy, in the last century, it was abandoned. For this reason, little breeding work has been conducted to improve this plant, also because of the low genetic variability present in this hexaploid species. In this review, we summarize the main works on this crop, focused on genetic improvement with three main objectives: yield, seed oil content and quality, and reduction in glucosinolates content in the seed, which are the main anti-nutritional substances present in camelina. We also report the latest advances in utilising classical plant breeding, transgenic approaches, and CRISPR-Cas9 genome-editing.
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Affiliation(s)
- Martina Ghidoli
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, Università degli Studi di Milano, Via G. Celoria 2, 20133 Milan, Italy
| | - Elena Ponzoni
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche, Via E. Bassini 15, 20133 Milan, Italy
| | - Fabrizio Araniti
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, Università degli Studi di Milano, Via G. Celoria 2, 20133 Milan, Italy
| | - Daniela Miglio
- Laboratory for Mother and Child Health, Department of Public Health, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20133 Milan, Italy
| | - Roberto Pilu
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, Università degli Studi di Milano, Via G. Celoria 2, 20133 Milan, Italy
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7
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Koper K, Han SW, Pastor DC, Yoshikuni Y, Maeda HA. Evolutionary Origin and Functional Diversification of Aminotransferases. J Biol Chem 2022; 298:102122. [PMID: 35697072 PMCID: PMC9309667 DOI: 10.1016/j.jbc.2022.102122] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Aminotransferases (ATs) are pyridoxal 5′-phosphate–dependent enzymes that catalyze the transamination reactions between amino acid donor and keto acid acceptor substrates. Modern AT enzymes constitute ∼2% of all classified enzymatic activities, play central roles in nitrogen metabolism, and generate multitude of primary and secondary metabolites. ATs likely diverged into four distinct AT classes before the appearance of the last universal common ancestor and further expanded to a large and diverse enzyme family. Although the AT family underwent an extensive functional specialization, many AT enzymes retained considerable substrate promiscuity and multifunctionality because of their inherent mechanistic, structural, and functional constraints. This review summarizes the evolutionary history, diverse metabolic roles, reaction mechanisms, and structure–function relationships of the AT family enzymes, with a special emphasis on their substrate promiscuity and multifunctionality. Comprehensive characterization of AT substrate specificity is still needed to reveal their true metabolic functions in interconnecting various branches of the nitrogen metabolic network in different organisms.
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Affiliation(s)
- Kaan Koper
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sang-Woo Han
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Yasuo Yoshikuni
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Global Center for Food, Land, and Water Resources, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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8
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Barnum CR, Endelman BJ, Ornelas IJ, Pignolet RM, Shih PM. Optimization of Heterologous Glucoraphanin Production In Planta. ACS Synth Biol 2022; 11:1865-1873. [PMID: 35438493 DOI: 10.1021/acssynbio.2c00030] [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] [Indexed: 11/29/2022]
Abstract
Glucoraphanin is a plant specialized metabolite found in cruciferous vegetables that has long been a target for production in a heterologous host because it can subsequently be hydrolyzed to form the chemopreventive compound sulforaphane before and during consumption. However, previous studies have only been able to produce small amounts of glucoraphanin in heterologous plant and microbial systems compared to the levels found in glucoraphanin-producing plants, suggesting that there may be missing auxiliary genes that play a role in improving production in planta. In an effort to identify auxiliary genes required for high glucoraphanin production, we leveraged transient expression in Nicotiana benthamiana to screen a combination of previously uncharacterized coexpressed genes and rationally selected genes alongside the glucoraphanin biosynthetic pathway. This strategy alleviated metabolic bottlenecks, which improved glucoraphanin production by 4.74-fold. Our optimized glucoraphanin biosynthetic pathway provides a pathway amenable for high glucoraphanin production.
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Affiliation(s)
- Collin R Barnum
- Department of Plant Biology, University of California, Davis, California 95616, United States
| | - Benjamin J Endelman
- Department of Plant Biology, University of California, Davis, California 95616, United States
| | - Izaiah J Ornelas
- Department of Plant Biology, University of California, Davis, California 95616, United States
| | - Roxanna M Pignolet
- Department of Plant Biology, University of California, Davis, California 95616, United States
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, California 95616, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute, University of California, Berkeley, California 94720, United States
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9
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Shang G, Zhao H, Tong L, Yin N, Hu R, Jiang H, Kamal F, Zhao Z, Xu L, Lu K, Li J, Qu C, Du D. Genome-Wide Association Study of Phenylalanine Derived Glucosinolates in Brassica rapa. PLANTS (BASEL, SWITZERLAND) 2022; 11:1274. [PMID: 35567275 PMCID: PMC9104335 DOI: 10.3390/plants11091274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022]
Abstract
Glucosinolates (GSLs) are sulfur-containing bioactive compounds usually present in Brassicaceae plants and are usually responsible for a pungent flavor and reduction of the nutritional values of seeds. Therefore, breeding rapeseed varieties with low GSL levels is an important breeding objective. Most GSLs in Brassica rapa are derived from methionine or tryptophan, but two are derived from phenylalanine, one directly (benzylGSL) and one after a round of chain elongation (phenethylGSL). In the present study, two phenylalanine (Phe)-derived GSLs (benzylGSL and phenethylGSL) were identified and quantified in seeds by liquid chromatography and mass spectrometry (LC-MS) analysis. Levels of benzylGSL were low but differed among investigated low and high GSL genotypes. Levels of phenethylGSL (also known as 2-phenylethylGSL) were high but did not differ among GSL genotypes. Subsequently, a genome-wide association study (GWAS) was conducted using 159 B. rapa accessions to demarcate candidate regions underlying 43 and 59 QTNs associated with benzylGSL and phenethylGSL that were distributed on 10 chromosomes and 9 scaffolds, explaining 0.56% to 70.86% of phenotypic variations, respectively. Furthermore, we find that 15 and 18 known or novel candidate genes were identified for the biosynthesis of benzylGSL and phenethylGSL, including known regulators of GSL biosynthesis, such as BrMYB34, BrMYB51, BrMYB28, BrMYB29 and BrMYB122, and novel regulators or structural genes, such as BrMYB44/BrMYB77 and BrMYB60 for benzylGSL and BrCYP79B2 for phenethylGSL. Finally, we investigate the expression profiles of the biosynthetic genes for two Phe-derived GSLs by transcriptomic analysis. Our findings provide new insight into the complex machinery of Phe-derived GSLs in seeds of B. rapa and help to improve the quality of Brassicaceae plant breeding.
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Affiliation(s)
- Guoxia Shang
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key Laboratory of Spring Rape Genetic Improvement, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (G.S.); (Z.Z.); (L.X.)
| | - Huiyan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Linhui Tong
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Nengwen Yin
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Ran Hu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Haiyan Jiang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Farah Kamal
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Zhi Zhao
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key Laboratory of Spring Rape Genetic Improvement, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (G.S.); (Z.Z.); (L.X.)
| | - Liang Xu
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key Laboratory of Spring Rape Genetic Improvement, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (G.S.); (Z.Z.); (L.X.)
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Dezhi Du
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key Laboratory of Spring Rape Genetic Improvement, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (G.S.); (Z.Z.); (L.X.)
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10
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Angelovici R, Kliebenstein D. A plant balancing act: Meshing new and existing metabolic pathways towards an optimized system. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102173. [PMID: 35144143 DOI: 10.1016/j.pbi.2022.102173] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/17/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Specialized metabolic pathways evolve from existing pathways, creating new functionality potentially boosting fitness. However, how these pathways are integrated into a pre-existing working and well-balanced metabolic system is unclear. They could be integrated to the system as a functional appendage, or they could be fully embedded into primary metabolism by establishing new biochemical and regulatory connections. A full integration into the primary metabolic system requires substantial system re-wiring and because of this complexity, the latter is often not experimentally pursued. New studies provide evidence that some specialized metabolic pathways are fully embedded in primary metabolism with extensive new regulatory and biochemical connections. This suggests, that we should consider whether other specialized metabolic pathways could be fully integrated rather than being simple appendages. In this mini review, we survey compelling evidence supporting that some specialized metabolic pathways are fully integrated and ask if these metabolites now act as de-facto primary metabolites?
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Affiliation(s)
- Ruthie Angelovici
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Dan Kliebenstein
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA; DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark.
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11
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A Comparative Transcriptome and Metabolome Combined Analysis Reveals the Key Genes and Their Regulatory Model Responsible for Glucoraphasatin Accumulation in Radish Fleshy Taproots. Int J Mol Sci 2022; 23:ijms23062953. [PMID: 35328374 PMCID: PMC8949420 DOI: 10.3390/ijms23062953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 02/01/2023] Open
Abstract
Radish (Raphanus sativus L.) is rich in specific glucosinolates (GSLs), which benefit human health and special flavor formation. Although the basic GSLs metabolic pathway in Brassicaceae plants is clear, the regulating mechanism for specific glucosinolates content in radish fleshy taproots is not well understood. In this study, we discovered that there was a significant difference in the GSLs profiles and the content of various GSLs components. Glucoraphasatin (GRH) is the most predominant GSL in radish taproots of different genotypes as assessed by HPLC analysis. Further, we compared the taproot transcriptomes of three radish genotypes with high and low GSLs content by employing RNA-seq. Totally, we identified forty-one differentially expressed genes related to GSLs metabolism. Among them, thirteen genes (RsBCAT4, RsIPMDH1, RsMAM1a, RsMAM1b, RsCYP79F1, RsGSTF9, RsGGP1, RsSUR1, RsUGT74C1, RsST5b, RsAPK1, RsGSL-OH, and RsMYB28) were significantly higher co-expressed in the high content genotypes than in low content genotype. Notably, correlation analysis indicated that the expression level of RsMYB28, as an R2R3 transcription factor directly regulating aliphatic glucosinolate biosynthesis, was positively correlated with the GRH content. Co-expression network showed that RsMYB28 probably positively regulated the expression of the above genes, particularly RsSUR1, and consequently the synthesis of GRH. Moreover, the molecular mechanism of the accumulation of this 4-carbon (4C) GSL in radish taproots was explored. This study provides new perspectives on the GSLs accumulation mechanism and genetic improvements in radish taproots.
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12
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Identification of Potential Genes Encoding Protein Transporters in Arabidopsis thaliana Glucosinolate (GSL) Metabolism. Life (Basel) 2022; 12:life12030326. [PMID: 35330077 PMCID: PMC8953324 DOI: 10.3390/life12030326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 12/24/2022] Open
Abstract
Several species in Brassicaceae produce glucosinolates (GSLs) to protect themselves against pests. As demonstrated in A. thaliana, the reallocation of defence compounds, of which GSLs are a major part, is highly dependent on transport processes and serves to protect high-value tissues such as reproductive tissues. This study aimed to identify potential GSL-transporter proteins (TPs) using a network-biology approach. The known A. thaliana GSL genes were retrieved from the literature and pathway databases and searched against several co-expression databases to generate a gene network consisting of 1267 nodes and 14,308 edges. In addition, 1151 co-expressed genes were annotated, integrated, and visualised using relevant bioinformatic tools. Based on three criteria, 21 potential GSL genes encoding TPs were selected. The AST68 and ABCG40 potential GSL TPs were chosen for further investigation because their subcellular localisation is similar to that of known GSL TPs (SULTR1;1 and SULTR1;2) and ABCG36, respectively. However, AST68 was selected for a molecular-docking analysis using AutoDOCK Vina and AutoDOCK 4.2 with the generated 3D model, showing that both domains were well superimposed on the homologs. Both molecular-docking tools calculated good binding-energy values between the sulphate ion and Ser419 and Val172, with the formation of hydrogen bonds and van der Waals interactions, respectively, suggesting that AST68 was one of the sulphate transporters involved in GSL biosynthesis. This finding illustrates the ability to use computational analysis on gene co-expression data to screen and characterise plant TPs on a large scale to comprehensively elucidate GSL metabolism in A. thaliana. Most importantly, newly identified potential GSL transporters can serve as molecular tools in improving the nutritional value of crops.
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13
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Regulation of the Leucine Metabolism in Mortierella alpina. J Fungi (Basel) 2022; 8:jof8020196. [PMID: 35205950 PMCID: PMC8880518 DOI: 10.3390/jof8020196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
The oleaginous fungus Mortierella alpina is a safe source of polyunsaturated fatty acids (PUFA) in industrial food and feed production. Besides PUFA production, pharmaceutically relevant surface-active and antimicrobial oligopeptides were isolated from this basal fungus. Both production of fatty acids and oligopeptides rely on the biosynthesis and high turnover of branched-chain-amino acids (BCAA), especially l-leucine. However, the regulation of BCAA biosynthesis in basal fungi is largely unknown. Here, we report on the regulation of the leucine, isoleucine, and valine metabolism in M. alpina. In contrast to higher fungi, the biosynthetic genes for BCAA are hardly transcriptionally regulated, as shown by qRT-PCR analysis, which suggests a constant production of BCAAs. However, the enzymes of the leucine metabolism are tightly metabolically regulated. Three enzymes of the leucine metabolism were heterologously produced in Escherichia coli, one of which is inhibited by allosteric feedback loops: The key regulator is the α-isopropylmalate synthase LeuA1, which is strongly disabled by l-leucine, α-ketoisocaproate, and propionyl-CoA, the precursor of the odd-chain fatty acid catabolism. Its gene is not related to homologs from higher fungi, but it has been inherited from a phototrophic ancestor by horizontal gene transfer.
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14
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Feng X, Ma J, Liu Z, Li X, Wu Y, Hou L, Li M. Analysis of Glucosinolate Content and Metabolism Related Genes in Different Parts of Chinese Flowering Cabbage. FRONTIERS IN PLANT SCIENCE 2022; 12:767898. [PMID: 35111173 PMCID: PMC8801782 DOI: 10.3389/fpls.2021.767898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Glucosinolates (GSLs) are important secondary metabolites that play important defensive roles in cruciferous plants. Chinese flowering cabbage, one of the most common vegetable crops, is rich in GSLs and thus has the potential to reduce the risk of cancer in humans. Many genes that are involved in GSL biosynthesis and metabolism have been identified in the model plant Arabidopsis thaliana; however, few studies investigated the genes related to GSL biosynthesis and metabolism in Chinese flowering cabbage. In the present study, the GSL composition and content in three different organs of Chinese flowering cabbage (leaf, stalk, and flower bud) were determined. Our results showed that the total GSL content in flower buds was significantly higher than in stalks and leaves, and aliphatic GSLs were the most abundant GSL type. To understand the molecular mechanisms underlying the variations of GSL content, we analyzed the expression of genes encoding enzymes involved in GSL biosynthesis and transport in different tissues of Chinese flowering cabbage using RNA sequencing; the expression levels of most genes were found to be consistent with the pattern of total GSL content. Correlation and consistency analysis of differentially expressed genes from different organs with the GSL content revealed that seven genes (Bra029966, Bra012640, Bra016787, Bra011761, Bra006830, Bra011759, and Bra029248) were positively correlated with GSL content. These findings provide a molecular basis for further elucidating GSL biosynthesis and transport in Chinese flowering cabbage.
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Affiliation(s)
- Xianjun Feng
- College of Horticulture, Shanxi Agricultural University, Taigu, China
- Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi, Taigu, China
| | - Jiajun Ma
- College of Horticulture, Shanxi Agricultural University, Taigu, China
- Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi, Taigu, China
| | - Zhiqian Liu
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, VIC, Australia
| | - Xuan Li
- College of Horticulture, Shanxi Agricultural University, Taigu, China
- Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi, Taigu, China
| | - Yinghua Wu
- College of Horticulture, Shanxi Agricultural University, Taigu, China
- Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi, Taigu, China
| | - Leiping Hou
- College of Horticulture, Shanxi Agricultural University, Taigu, China
- Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi, Taigu, China
| | - Meilan Li
- College of Horticulture, Shanxi Agricultural University, Taigu, China
- Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi, Taigu, China
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15
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Song C, Cao Y, Dai J, Li G, Manzoor MA, Chen C, Deng H. The Multifaceted Roles of MYC2 in Plants: Toward Transcriptional Reprogramming and Stress Tolerance by Jasmonate Signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:868874. [PMID: 35548315 PMCID: PMC9082941 DOI: 10.3389/fpls.2022.868874] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/17/2022] [Indexed: 05/12/2023]
Abstract
Environmental stress is one of the major restrictions on plant development and foodstuff production. The adaptive response in plants largely occurs through an intricate signaling system, which is crucial for regulating the stress-responsive genes. Myelocytomatosis (MYC) transcription factors are the fundamental regulators of the jasmonate (JA) signaling branch that participates in plant development and multiple stresses. By binding to the cis-acting elements of a large number of stress-responsive genes, JA-responsive transcription factors activate the stress-resistant defense genes. The mechanism of stress responses concerns myriad regulatory processes at the physiological and molecular levels. Discovering stress-related regulatory factors is of great value in disclosing the response mechanisms of plants to biotic or abiotic stress, which could guide the genetic improvement of plant resistance. This review summarizes recent researches in various aspects of MYC2-mediated JA signaling and emphasizes MYC2 involvement in plant growth and stress response.
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Affiliation(s)
- Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Yunpeng Cao
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Jun Dai
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Guohui Li
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | | | - Cunwu Chen
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Hui Deng
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- *Correspondence: Hui Deng,
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16
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AIP1, Encoding the Small Subunit of Acetolactate Synthase, Is Partially Responsible for Resistance to Hypoxic Stress in Arabidopsis thaliana. PLANTS 2021; 10:plants10112251. [PMID: 34834615 PMCID: PMC8621687 DOI: 10.3390/plants10112251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022]
Abstract
Flooding is a significant stress to land plants, depriving them of essential oxygen. Plants have evolved diverse strategies with variable success to survive flooding. Similar strategies have been described in organisms from other kingdoms. Several fungal species can successfully survive a low-oxygen environment by increasing their branched-chain amino acid (BCAA) contents. BCAAs may act as alternative electron acceptors in the respiratory chain under an oxygen-limited environment. The key and first enzyme for BCAA biosynthesis is acetolactate synthase (ALS). We identified two homologous genes encoding the small subunit of ALS in Arabidopsis (Arabidopsis thaliana). We determined that ALS INTERACTING PROTEIN1 (AIP1), which encodes the small subunit of ALS, is strongly expressed in all organs and highly expressed under submergence and low-oxygen stresses. We also showed that the overexpression of AIP1 confers tolerance to low-oxygen stress. These results indicate that ALS may play an essential role under prolonged flooding or oxygen deficiency in Arabidopsis.
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Li L, Zhang H, Chai X, Wei S, Luo S, Wang H, Lv J, Yu J, Liu Z. Transcriptome and Proteome Conjoint Analysis Revealed That Exogenous Sulfur Regulates Glucosinolate Synthesis in Cabbage. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10102104. [PMID: 34685913 PMCID: PMC8539766 DOI: 10.3390/plants10102104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Glucosinolates (GLS) are important anionic secondary metabolites that are rich in thiocyanin in cabbage, Brassica oleracea L. var. capitata. GLS are important in food flavor, plant antimicrobial activity, insect resistance, disease resistance, and human anti-cancer effects. Sulfur is an important raw material of GLS, directly affecting their synthesis. However, the mechanism of sulfur regulation of GLS biosynthesis in cabbage is unclear. In the present study, cabbage was treated with sulfur-free Hoagland nutrient solution (control; -S), and normal Hoagland nutrient solution (treatment; +S). Through joint transcriptomic and proteomic analyses, the effect of exogenous S on GLS synthesis was explored. S application induced GLS accumulation; especially, indole glycosides. Transcriptome analysis showed that +S treatment correlated positively with differentially expressed genes and proteins involved in amino acid biosynthesis, carbon metabolism, and plant hormone signal transduction. Compared with -S treatment, the mRNA expression of GLS synthesis genes (CYP, GSTU, UGT, and FMO) and those encoding transcription factors (RLK, MYB, AP2, bHLH, AUX/IAA, and WRKY) were upregulated significantly in the +S group. Combined transcriptome and proteome analysis suggested that the main pathway influenced by S during GLS synthesis in cabbage is amino acid biosynthesis. Moreover, S treatment activated GLS synthesis and accumulation.
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Affiliation(s)
- Lushan Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (L.L.); (H.Z.); (S.W.); (S.L.); (H.W.); (J.L.)
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua 617000, China
| | - Hui Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (L.L.); (H.Z.); (S.W.); (S.L.); (H.W.); (J.L.)
| | - Xiaohong Chai
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China;
| | - Shouhui Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (L.L.); (H.Z.); (S.W.); (S.L.); (H.W.); (J.L.)
| | - Shilei Luo
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (L.L.); (H.Z.); (S.W.); (S.L.); (H.W.); (J.L.)
| | - Huiping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (L.L.); (H.Z.); (S.W.); (S.L.); (H.W.); (J.L.)
| | - Jian Lv
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (L.L.); (H.Z.); (S.W.); (S.L.); (H.W.); (J.L.)
| | - Jihua Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (L.L.); (H.Z.); (S.W.); (S.L.); (H.W.); (J.L.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Zeci Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (L.L.); (H.Z.); (S.W.); (S.L.); (H.W.); (J.L.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
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18
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Kitainda V, Jez JM. Structural Studies of Aliphatic Glucosinolate Chain-Elongation Enzymes. Antioxidants (Basel) 2021; 10:antiox10091500. [PMID: 34573132 PMCID: PMC8468904 DOI: 10.3390/antiox10091500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Plants evolved specialized metabolic pathways through gene duplication and functional divergence of enzymes involved in primary metabolism. The results of this process are varied pathways that produce an array of natural products useful to both plants and humans. In plants, glucosinolates are a diverse class of natural products. Glucosinolate function stems from their hydrolysis products, which are responsible for the strong flavors of Brassicales plants, such as mustard, and serve as plant defense molecules by repelling insects, fighting fungal infections, and discouraging herbivory. Additionally, certain hydrolysis products such as isothiocyanates can potentially serve as cancer prevention agents in humans. The breadth of glucosinolate function is a result of its great structural diversity, which comes from the use of aliphatic, aromatic and indole amino acids as precursors and elongation of some side chains by up to nine carbons, which, after the formation of the core glucosinolate structure, can undergo further chemical modifications. Aliphatic methionine-derived glucosinolates are the most abundant form of these compounds. Although both elongation and chemical modification of amino acid side chains are important for aliphatic glucosinolate diversity, its elongation process has not been well described at the molecular level. Here, we summarize new insights on the iterative chain-elongation enzymes methylthioalkylmalate synthase (MAMS) and isopropylmalate dehydrogenase (IPMDH).
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Harun S, Afiqah-Aleng N, Karim MB, Altaf Ul Amin M, Kanaya S, Mohamed-Hussein ZA. Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach. PeerJ 2021; 9:e11876. [PMID: 34430080 PMCID: PMC8349163 DOI: 10.7717/peerj.11876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/06/2021] [Indexed: 01/10/2023] Open
Abstract
Background Glucosinolates (GSLs) are plant secondary metabolites that contain nitrogen-containing compounds. They are important in the plant defense system and known to provide protection against cancer in humans. Currently, increasing the amount of data generated from various omics technologies serves as a hotspot for new gene discovery. However, sometimes sequence similarity searching approach is not sufficiently effective to find these genes; hence, we adapted a network clustering approach to search for potential GSLs genes from the Arabidopsis thaliana co-expression dataset. Methods We used known GSL genes to construct a comprehensive GSL co-expression network. This network was analyzed with the DPClusOST algorithm using a density of 0.5. 0.6. 0.7, 0.8, and 0.9. Generating clusters were evaluated using Fisher’s exact test to identify GSL gene co-expression clusters. A significance score (SScore) was calculated for each gene based on the generated p-value of Fisher’s exact test. SScore was used to perform a receiver operating characteristic (ROC) study to classify possible GSL genes using the ROCR package. ROCR was used in determining the AUC that measured the suitable density value of the cluster for further analysis. Finally, pathway enrichment analysis was conducted using ClueGO to identify significant pathways associated with the GSL clusters. Results The density value of 0.8 showed the highest area under the curve (AUC) leading to the selection of thirteen potential GSL genes from the top six significant clusters that include IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1, and At3g14220. A total of Four potential genes (MTO1, SIR, SAL1, and IMDH3) were identified from the pathway enrichment analysis on the significant clusters. These genes are directly related to GSL-associated pathways such as sulfur metabolism and valine, leucine, and isoleucine biosynthesis. This approach demonstrates the ability of the network clustering approach in identifying potential GSL genes which cannot be found from the standard similarity search.
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Affiliation(s)
- Sarahani Harun
- Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Nor Afiqah-Aleng
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Mohammad Bozlul Karim
- Graduate School of Science and Technology & NAIST Data Science Center, Nara Institute of Science and Technology, Nara, Japan
| | - Md Altaf Ul Amin
- Graduate School of Science and Technology & NAIST Data Science Center, Nara Institute of Science and Technology, Nara, Japan
| | - Shigehiko Kanaya
- Graduate School of Science and Technology & NAIST Data Science Center, Nara Institute of Science and Technology, Nara, Japan
| | - Zeti-Azura Mohamed-Hussein
- Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia.,Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
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20
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Lazcano-Ramírez HG, Gamboa-Becerra R, García-López IJ, Montes RAC, Díaz-Ramírez D, de la Vega OM, Ordaz-Ortíz JJ, de Folter S, Tiessen-Favier A, Winkler R, Marsch-Martínez N. Effects of the Developmental Regulator BOLITA on the Plant Metabolome. Genes (Basel) 2021; 12:genes12070995. [PMID: 34209960 PMCID: PMC8305173 DOI: 10.3390/genes12070995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription factors are important regulators of gene expression. They can orchestrate the activation or repression of hundreds or thousands of genes and control diverse processes in a coordinated way. This work explores the effect of a master regulator of plant development, BOLITA (BOL), in plant metabolism, with a special focus on specialized metabolism. For this, we used an Arabidopsis thaliana line in which the transcription factor activity can be induced. Fingerprinting metabolomic analyses of whole plantlets were performed at different times after induction. After 96 h, all induced replicas clustered as a single group, in contrast with all controls which did not cluster. Metabolomic analyses of shoot and root tissues enabled the putative identification of differentially accumulated metabolites in each tissue. Finally, the analysis of global gene expression in induced vs. non-induced root samples, together with enrichment analyses, allowed the identification of enriched metabolic pathways among the differentially expressed genes and accumulated metabolites after the induction. We concluded that the induction of BOL activity can modify the Arabidopsis metabolome. Future work should investigate whether its action is direct or indirect, and the implications of the metabolic changes for development regulation and bioprospection.
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Affiliation(s)
- Hugo Gerardo Lazcano-Ramírez
- Cell Identity Laboratory, Biotechnology and Biochemistry Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico; (H.G.L.-R.); (D.D.-R.)
| | - Roberto Gamboa-Becerra
- Laboratory of Biochemical and Instrumental Analysis, Biotechnology and Biochemistry Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico;
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - Irving J. García-López
- Genetic Engineering Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico; (I.J.G.-L.); (A.T.-F.)
| | - Ricardo A. Chávez Montes
- Advanced Genomics Unit (UGA-Langebio), CINVESTAV-IPN, Irapuato 36824, Mexico; (R.A.C.M.); (O.M.d.l.V.); (J.J.O.-O.); (S.d.F.)
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA
| | - David Díaz-Ramírez
- Cell Identity Laboratory, Biotechnology and Biochemistry Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico; (H.G.L.-R.); (D.D.-R.)
| | - Octavio Martínez de la Vega
- Advanced Genomics Unit (UGA-Langebio), CINVESTAV-IPN, Irapuato 36824, Mexico; (R.A.C.M.); (O.M.d.l.V.); (J.J.O.-O.); (S.d.F.)
| | - José Juan Ordaz-Ortíz
- Advanced Genomics Unit (UGA-Langebio), CINVESTAV-IPN, Irapuato 36824, Mexico; (R.A.C.M.); (O.M.d.l.V.); (J.J.O.-O.); (S.d.F.)
| | - Stefan de Folter
- Advanced Genomics Unit (UGA-Langebio), CINVESTAV-IPN, Irapuato 36824, Mexico; (R.A.C.M.); (O.M.d.l.V.); (J.J.O.-O.); (S.d.F.)
| | - Axel Tiessen-Favier
- Genetic Engineering Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico; (I.J.G.-L.); (A.T.-F.)
| | - Robert Winkler
- Laboratory of Biochemical and Instrumental Analysis, Biotechnology and Biochemistry Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico;
- Correspondence: (R.W.); (N.M.-M.); Tel.: +52-(462)-623-9635 (R.W.); +52-462-623-9671 (N.M.-M.)
| | - Nayelli Marsch-Martínez
- Cell Identity Laboratory, Biotechnology and Biochemistry Department, CINVESTAV-IPN Irapuato Unit, Irapuato 36824, Mexico; (H.G.L.-R.); (D.D.-R.)
- Correspondence: (R.W.); (N.M.-M.); Tel.: +52-(462)-623-9635 (R.W.); +52-462-623-9671 (N.M.-M.)
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21
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Agerbirk N, Hansen CC, Olsen CE, Kiefer C, Hauser TP, Christensen S, Jensen KR, Ørgaard M, Pattison DI, Lange CBA, Cipollini D, Koch MA. Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates. PHYTOCHEMISTRY 2021; 185:112658. [PMID: 33744557 DOI: 10.1016/j.phytochem.2021.112658] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
A library of ion trap MS2 spectra and HPLC retention times reported here allowed distinction in plants of at least 70 known glucosinolates (GSLs) and some additional proposed GSLs. We determined GSL profiles of selected members of the tribe Cardamineae (Brassicaceae) as well as Reseda (Resedaceae) used as outgroup in evolutionary studies. We included several accessions of each species and a range of organs, and paid attention to minor peaks and GSLs not detected. In this way, we obtained GSL profiles of Barbarea australis, Barbarea grayi, Planodes virginica selected for its apparent intermediacy between Barbarea and the remaining tribe and family, and Rorippa sylvestris and Nasturtium officinale, for which the presence of acyl derivatives of GSLs was previously untested. We also screened Armoracia rusticana, with a remarkably diverse GSL profile, the emerging model species Cardamine hirsuta, for which we discovered a GSL polymorphism, and Reseda luteola and Reseda odorata. The potential for aliphatic GSL biosynthesis in Barbarea vulgaris was of interest, and we subjected P-type and G-type B. vulgaris to several induction regimes in an attempt to induce aliphatic GSL. However, aliphatic GSLs were not detected in any of the B. vulgaris types. We characterized the investigated chemotypes phylogenetically, based on nuclear rDNA internal transcribed spacer (ITS) sequences, in order to understand their relation to the species B. vulgaris in general, and found them to be representative of the species as it occurs in Europe, as far as documented in available ITS-sequence repositories. In short, we provide GSL profiles of a wide variety of tribe Cardamineae plants and conclude aliphatic GSLs to be absent or below our limit of detection in two major evolutionary lines of B. vulgaris. Concerning analytical chemistry, we conclude that availability of authentic reference compounds or reference materials is critical for reliable GSL analysis and characterize two publicly available reference materials: seeds of P. virginica and N. officinale.
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Affiliation(s)
- Niels Agerbirk
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| | - Cecilie Cetti Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Carl Erik Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Christiane Kiefer
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Thure P Hauser
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Stina Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Karen R Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Marian Ørgaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - David I Pattison
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Conny Bruun Asmussen Lange
- 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
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
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22
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Harun S, Rohani ER, Ohme-Takagi M, Goh HH, Mohamed-Hussein ZA. ADAP is a possible negative regulator of glucosinolate biosynthesis in Arabidopsis thaliana based on clustering and gene expression analyses. JOURNAL OF PLANT RESEARCH 2021; 134:327-339. [PMID: 33558947 DOI: 10.1007/s10265-021-01257-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Glucosinolates (GSLs) are plant secondary metabolites consisting of sulfur and nitrogen, commonly found in Brassicaceae crops, such as Arabidopsis thaliana. These compounds are known for their roles in plant defense mechanisms against pests and pathogens. 'Guilt-by-association' (GBA) approach predicts genes encoding proteins with similar function tend to share gene expression pattern generated from high throughput sequencing data. Recent studies have successfully identified GSL genes using GBA approach, followed by targeted verification of gene expression and metabolite data. Therefore, a GSL co-expression network was constructed using known GSL genes obtained from our in-house database, SuCComBase. DPClusO was used to identify subnetworks of the GSL co-expression network followed by Fisher's exact test leading to the discovery of a potential gene that encodes the ARIA-interacting double AP2-domain protein (ADAP) transcription factor (TF). Further functional analysis was performed using an effective gene silencing system known as CRES-T. By applying CRES-T, ADAP TF gene was fused to a plant-specific EAR-motif repressor domain (SRDX), which suppresses the expression of ADAP target genes. In this study, ADAP was proposed as a negative regulator in aliphatic GSL biosynthesis due to the over-expression of downstream aliphatic GSL genes (UGT74C1 and IPMI1) in ADAP-SRDX line. The significant over-expression of ADAP gene in the ADAP-SRDX line also suggests the behavior of the TF that negatively affects the expression of UGT74C1 and IPMI1 via a feedback mechanism in A. thaliana.
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Affiliation(s)
- S Harun
- Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - E R Rohani
- Centre for Plant Biotechnology, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - M Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - H-H Goh
- Centre for Plant Biotechnology, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Z-A Mohamed-Hussein
- Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
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23
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Ganugi P, Miras-Moreno B, Garcia-Perez P, Lucini L, Trevisan M. Concealed metabolic reprogramming induced by different herbicides in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110727. [PMID: 33487335 DOI: 10.1016/j.plantsci.2020.110727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 10/17/2020] [Indexed: 06/12/2023]
Abstract
Herbicide application is a common procedure in agriculture, whose potentially adverse effects are assessed mainly with respect to weeds or in terms of residues and environmental impact. However, recent evidence has highlighted possible effects of pesticide treatments on plant metabolism, with potential implications for fruit quality. Therefore, the goal of this study was to investigate the impact of four different herbicides on the metabolic processes in industrial tomato plants. To this aim, plants were treated either with the selective herbicides metribuzin and rimsulfuron or with the non-selective herbicides glyphosate and pelargonic acid. Thereafter, leaves were analyzed using a metabolomics approach, and 247 differential compounds were selected by multivariate statistics and used to examine the changes at the molecular level. Data interpretation via the PlantCyc Pathway Tool revealed that the tested herbicides induced distinctive responses to the treatments, with the phytohormone profile (gibberellins and jasmonates) and secondary metabolism (including stress-related compounds, such as phenylpropanoids and glucosinolates) showing the largest modulation. Surprisingly, such metabolic reprogramming also affected several aspects of the fruits even though the herbicides were applied several weeks before, thus opening the possibility of effects on food quality. To date, these hidden effects have been largely underestimated even though they deserve to be carefully considered since they may affect the qualitative and quantitative traits of the yield.
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Affiliation(s)
- Paola Ganugi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari Ambientali e Forestali, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144 Firenze, Italy
| | - Begoña Miras-Moreno
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Pascual Garcia-Perez
- Plant Biology and Soil Science Department, Biology Faculty, University of Vigo, 36310 Vigo, Spain
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy.
| | - Marco Trevisan
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
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24
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Mao S, Wang J, Wu Q, Liang M, Yuan Y, Wu T, Liu M, Wu Q, Huang K. Effect of selenium-sulfur interaction on the anabolism of sulforaphane in broccoli. PHYTOCHEMISTRY 2020; 179:112499. [PMID: 32980712 DOI: 10.1016/j.phytochem.2020.112499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
The effects of S (as sulphate) and Se (as selenite) treatment (S mM/Se μM: 1/0, 1/50, 1/100, 1/150, 4/0, 4/50, 4/100, and 4/150) on the production of sulforaphane (an anticancer compound), the accumulation of its precursor substance, and the expression of genes related to glucoraphanin biosynthesis in broccoli were examined. Sulforaphane yield and myrosinase activity increased significantly with the combined application of 4 mM S and 100 μM Se on broccoli. Furthermore, the concentrations of glucoraphanin (a sulforaphane precursor) and methionine (a glucoraphanin substrate) slightly changed after Se application. And the strong anticancer activity of compound Se-SMC was further improved. Analysis of related gene expression showed that MY, which encodes myrosinase, was strongly induced by Se treatment. Thus, the myrosinase activity induced by Se treatment is the dominant factor affecting sulforaphane yield from glucoraphanin hydrolyzation. Selenium-sulfur biofortification provides a technical support for the cultivation of broccoli with high sulforaphane and high anti-cancer selenium compounds.
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Affiliation(s)
- Shuxiang Mao
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China; Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, 410128, China; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, 410128, China
| | - Junwei Wang
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China; Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, 410128, China; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, 410128, China
| | - Qi Wu
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China; Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, 410128, China; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, 410128, China
| | - Mantian Liang
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China; Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, 410128, China; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, 410128, China
| | - Yiming Yuan
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China; Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, 410128, China; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, 410128, China
| | - Tao Wu
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China; Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, 410128, China; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, 410128, China
| | - Mingyue Liu
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China; Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, 410128, China; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, 410128, China
| | - Qiuyun Wu
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China; Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, 410128, China; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, 410128, China.
| | - Ke Huang
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China; Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, 410128, China; Key Laboratory for Vegetable Biology of Hunan Province, Changsha, 410128, China.
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25
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Induction of Glucoraphasatin Biosynthesis Genes by MYB29 in Radish ( Raphanus sativus L.) Roots. Int J Mol Sci 2020; 21:ijms21165721. [PMID: 32785002 PMCID: PMC7461053 DOI: 10.3390/ijms21165721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
Glucoraphasatin (GRH) is a specific aliphatic glucosinolate (GSL) that is only abundant in radish (Raphanus sativus L.). The gene expression regulating GRH biosynthesis in radish is still poorly understood. We employed a total of 59 radish accessions to analyze GSL profiles and showed that GRH was specific and predominant among the aliphatic GSLs in radish roots. We selected five accessions roots with high, moderate and low GSL biosynthesis, respectively, to conduct a comparative transcriptome analysis and the qRT-PCR of the biosynthesis genes for aliphatic GSLs. In this study, among all the accessions tested, roots with the accession RA157-74 had a high GRH content and showed a significant expression of the aliphatic GSL biosynthesis genes. We defined the genes involved in the GRH biosynthesis process and found that they were regulated by a transcription factor (RSG00789) at the MYB29 locus in radish roots. We found 13 aliphatic GSL biosynthesis genes regulated by the RSG00789 gene in the GRH biosynthesis pathway.
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26
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Harun S, Abdullah-Zawawi MR, Goh HH, Mohamed-Hussein ZA. A Comprehensive Gene Inventory for Glucosinolate Biosynthetic Pathway in Arabidopsis thaliana. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7281-7297. [PMID: 32551569 DOI: 10.1021/acs.jafc.0c01916] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Glucosinolates (GSLs) are plant secondary metabolites comprising sulfur and nitrogen mainly found in plants from the order of Brassicales, such as broccoli, cabbage, and Arabidopsis thaliana. The activated forms of GSL play important roles in fighting against pathogens and have health benefits to humans. The increasing amount of data on A. thaliana generated from various omics technologies can be investigated more deeply in search of new genes or compounds involved in GSL biosynthesis and metabolism. This review describes a comprehensive inventory of A. thaliana GSLs identified from published literature and databases such as KNApSAcK, KEGG, and AraCyc. A total of 113 GSL genes encoding for 23 transcription components, 85 enzymes, and five protein transporters were experimentally characterized in the past two decades. Continuous efforts are still on going to identify all molecules related to the production of GSLs. A manually curated database known as SuCCombase (http://plant-scc.org) was developed to serve as a comprehensive GSL inventory. Realizing lack of information on the regulation of GSL biosynthesis and degradation mechanisms, this review also includes relevant information and their connections with crosstalk among various factors, such as light, sulfur metabolism, and nitrogen metabolism, not only in A. thaliana but also in other crucifers.
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Affiliation(s)
- Sarahani Harun
- Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Muhammad-Redha Abdullah-Zawawi
- Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Centre for Plant Biotechnology, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
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27
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Ogden AJ, Bhatt JJ, Brewer HM, Kintigh J, Kariuki SM, Rudrabhatla S, Adkins JN, Curtis WR. Phloem Exudate Protein Profiles during Drought and Recovery Reveal Abiotic Stress Responses in Tomato Vasculature. Int J Mol Sci 2020; 21:E4461. [PMID: 32586033 PMCID: PMC7352395 DOI: 10.3390/ijms21124461] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 11/17/2022] Open
Abstract
Drought is the leading cause of agricultural yield loss among all abiotic stresses, and the link between water deficit and phloem protein contents is relatively unexplored. Here we collected phloem exudates from Solanum lycopersicum leaves during periods of drought stress and recovery. Our analysis identified 2558 proteins, the most abundant of which were previously localized to the phloem. Independent of drought, enrichment analysis of the total phloem exudate protein profiles from all samples suggests that the protein content of phloem sap is complex, and includes proteins that function in chaperone systems, branched-chain amino acid synthesis, trehalose metabolism, and RNA silencing. We observed 169 proteins whose abundance changed significantly within the phloem sap, either during drought or recovery. Proteins that became significantly more abundant during drought include members of lipid metabolism, chaperone-mediated protein folding, carboxylic acid metabolism, abscisic acid signaling, cytokinin biosynthesis, and amino acid metabolism. Conversely, proteins involved in lipid signaling, sphingolipid metabolism, cell wall organization, carbohydrate metabolism, and a mitogen-activated protein kinase are decreased during drought. Our experiment has achieved an in-depth profiling of phloem sap protein contents during drought stress and recovery that supports previous findings and provides new evidence that multiple biological processes are involved in drought adaptation.
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Affiliation(s)
- Aaron J. Ogden
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, 902 Battelle Blvd, Richland, WA 99301, USA; (A.J.O.); (H.M.B.); (J.N.A.)
| | - Jishnu J. Bhatt
- Plant Biology Graduate Program, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Heather M. Brewer
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, 902 Battelle Blvd, Richland, WA 99301, USA; (A.J.O.); (H.M.B.); (J.N.A.)
| | - Jack Kintigh
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (J.K.); (S.M.K.)
| | - Samwel M. Kariuki
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (J.K.); (S.M.K.)
| | - Sairam Rudrabhatla
- School of Science, Engineering, and Technology, The Pennsylvania State University, Harrisburg Campus, 777 W Harrisburg Pike, Middletown, PA 17057, USA;
| | - Joshua N. Adkins
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, 902 Battelle Blvd, Richland, WA 99301, USA; (A.J.O.); (H.M.B.); (J.N.A.)
| | - Wayne R. Curtis
- Plant Biology Graduate Program, The Pennsylvania State University, University Park, PA 16802, USA;
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (J.K.); (S.M.K.)
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28
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Züst T, Strickler SR, Powell AF, Mabry ME, An H, Mirzaei M, York T, Holland CK, Kumar P, Erb M, Petschenka G, Gómez JM, Perfectti F, Müller C, Pires JC, Mueller LA, Jander G. Independent evolution of ancestral and novel defenses in a genus of toxic plants ( Erysimum, Brassicaceae). eLife 2020; 9:e51712. [PMID: 32252891 PMCID: PMC7180059 DOI: 10.7554/elife.51712] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 03/24/2020] [Indexed: 11/13/2022] Open
Abstract
Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on co-expression, co-regulation, and diversification of these potentially redundant defenses across this genus. We sequenced and assembled the genome of E. cheiranthoides and foliar transcriptomes of 47 additional Erysimum species to construct a phylogeny from 9868 orthologous genes, revealing several geographic clades but also high levels of gene discordance. Concentrations, inducibility, and diversity of the two defenses varied independently among species, with no evidence for trade-offs. Closely related, geographically co-occurring species shared similar cardenolide traits, but not glucosinolate traits, likely as a result of specific selective pressures acting on each defense. Ancestral and novel chemical defenses in Erysimum thus appear to provide complementary rather than redundant functions.
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Affiliation(s)
- Tobias Züst
- Institute of Plant Sciences, University of BernBernSwitzerland
| | | | | | - Makenzie E Mabry
- Division of Biological Sciences, University of MissouriColumbiaUnited States
| | - Hong An
- Division of Biological Sciences, University of MissouriColumbiaUnited States
| | | | | | | | | | - Matthias Erb
- Institute of Plant Sciences, University of BernBernSwitzerland
| | - Georg Petschenka
- Institut für Insektenbiotechnologie, Justus-Liebig-Universität GiessenGiessenGermany
| | - José-María Gómez
- Department of Functional and Evolutionary Ecology, Estación Experimental de Zonas Áridas (EEZA-CSIC)AlmeríaSpain
| | - Francisco Perfectti
- Research Unit Modeling Nature, Department of Genetics, University of GranadaGranadaSpain
| | - Caroline Müller
- Department of Chemical Ecology, Bielefeld UniversityBielefeldGermany
| | - J Chris Pires
- Division of Biological Sciences, University of MissouriColumbiaUnited States
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29
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Neugart S, Hideg É, Czégény G, Schreiner M, Strid Å. Ultraviolet-B radiation exposure lowers the antioxidant capacity in the Arabidopsis thaliana pdx1.3-1 mutant and leads to glucosinolate biosynthesis alteration in both wild type and mutant. Photochem Photobiol Sci 2020; 19:217-228. [PMID: 31961357 DOI: 10.1039/c9pp00342h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Pyridoxine (vitamin B6) and its vitamers are used by living organisms both as enzymatic cofactors and as antioxidants. We used Arabidopsis pyridoxine biosynthesis mutant pdx1.3-1 to study the involvement of the PLP-synthase main polypeptide PDX1 in plant responses to ultraviolet radiation of two different qualities, one containing primarily UV-A (315-400 nm) and the other containing both UV-A and UV-B (280-315 nm). The antioxidant capacity and the flavonoid and glucosinolate (GS) profiles were examined. As an indicator of stress, Fv/Fm of photosystem II reaction centers was used. In pdx1.3-1, UV-A + B exposure led to a significant 5% decrease in Fv/Fm on the last day (day 15), indicating mild stress at this time point. The antioxidant capacity of Col-0 wildtype increased significantly (50-73%) after 1 and 3 days of UV-A + B. Instead, in pdx1.3-1, the antioxidant capacity significantly decreased by 44-52% over the same time period, proving the importance of a full complement of functional PDX1 genes for the detoxification of reactive oxygen species. There were no significant changes in the flavonoid glycoside profile under any light condition. However, the GS profile was significantly altered, both with respect to Arabidopsis accession and exposure to UV. The difference in flavonoid and GS profiles reflects that the GS biosynthesis pathway contains at least one pyridoxine-dependent enzyme, whereas no such enzyme is used in flavonoid biosynthesis. Also, there was strong correlation between the antioxidant capacity and the content of some GS compounds. Our results show that vitamin B6 vitamers, functioning both as antioxidants and co-factors, are of importance for the physiological fitness of plants.
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Affiliation(s)
- Susanne Neugart
- Division of Quality and Sensory of Plant Products, University of Göttingen, Göttingen, Germany
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30
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Jin C, Sun Y, Shi Y, Zhang Y, Chen K, Li Y, Liu G, Yao F, Cheng D, Li J, Zhou J, Qu L, Liu X, Luo J. Branched-chain amino acids regulate plant growth by affecting the homeostasis of mineral elements in rice. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1107-1110. [PMID: 31165351 DOI: 10.1007/s11427-019-9552-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/24/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Cheng Jin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yangyang Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuheng Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanyuan Zhang
- Institute of Tropical Agriculture and Forestry of Hainan University, Haikou, 570288, China
| | - Kai Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Guige Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Yao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Deng Cheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Li
- Department of Metabolic Biology John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Junjie Zhou
- Institute of Tropical Agriculture and Forestry of Hainan University, Haikou, 570288, China
| | - Lianghuan Qu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianqing Liu
- Institute of Tropical Agriculture and Forestry of Hainan University, Haikou, 570288, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China. .,Institute of Tropical Agriculture and Forestry of Hainan University, Haikou, 570288, China.
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Lee JH, Kim YC, Jung Y, Han JH, Zhang C, Yun CW, Lee S. The overexpression of cucumber (Cucumis sativus L.) genes that encode the branched-chain amino acid transferase modulate flowering time in Arabidopsis thaliana. PLANT CELL REPORTS 2019; 38:25-35. [PMID: 30298307 DOI: 10.1007/s00299-018-2346-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/28/2018] [Indexed: 06/08/2023]
Abstract
The overexpression of CsBCATs promotes flowering in Arabidopsis by regulating the expression of flowering time genes. The branched-chain amino acid transferases (BCATs) play an important role in the metabolism of branched-chain amino acids (BCAAs), such as isoleucine, leucine, and valine. They function in both the synthesis and the degradation of this class of amino acids. We identified and characterized the three BCAT genes in cucumber (Cucumis sativus L.). The tissue-specific expression profiling in cucumber plants revealed that CsBCAT2 and CsBCAT7 were highly expressed in the reproductive tissues, whereas CsBCAT3 expression was highly detected in the vegetative tissues. The subcellular localization patterns of three CsBCATs were observed in the mitochondria. The functional analyses of CsBCATs showed that CsBCAT2 and CsBCAT3 restored the growth of bat1Δ/bat2Δ double knockout yeast (Saccharomyces cerevisiae), and CsBCAT3 and CsBCAT7 with different substrate preferences acted in a reverse reaction. The transgenic approach demonstrated that the overexpression of the three CsBCATs resulted in early flowering phenotypes, which were associated with the upregulation of FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) in a manner in which they were dependent on GIGANTEA (GI)/CONSTANS (CO) and SHORT VEGETATIVE PHASE (SVP)/FLOWERING LOCUS C (FLC) modules. Our results, which are observed in conjunction, suggest that there is an interconnection between BCAT genes that function in BCAA metabolism and the flowering time in plants.
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Affiliation(s)
- Jeong Hwan Lee
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
- Division of Life Sciences, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, Jeollabuk-do, 54896, Republic of Korea
| | - Young-Cheon Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Youjin Jung
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Ji Hoon Han
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Chunying Zhang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Cheol-Won Yun
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sanghyeob Lee
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea.
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Prieto MA, López CJ, Simal-Gandara J. Glucosinolates: Molecular structure, breakdown, genetic, bioavailability, properties and healthy and adverse effects. ADVANCES IN FOOD AND NUTRITION RESEARCH 2019; 90:305-350. [PMID: 31445598 DOI: 10.1016/bs.afnr.2019.02.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Glucosinolates are a large group of plant secondary metabolites with nutritional effects and biologically active compounds. Glucosinolates are mainly found in cruciferous plants such as Brassicaceae family, including common edible plants such as broccoli (Brassica oleracea var. italica), cabbage (B. oleracea var. capitata f. alba), cauliflower (B. oleracea var. botrytis), rapeseed (Brassica napus), mustard (Brassica nigra), and horseradish (Armoracia rusticana). If cruciferous plants are consumed without processing, myrosinase enzyme will hydrolyze the glucosinolates to various metabolites, such as isothiocyanates, nitriles, oxazolidine-2-thiones, and indole-3-carbinols. On the other hand, when cruciferous are cooked before consumption, myrosinase is inactivated and glucosinolates could be partially absorbed in their intact form through the gastrointestinal mucosa. This review paper summarizes the glucosinolate molecular breakdown, their genetic aspects from biosynthesis to precursors, their bioavailability (assimilation, absorption, and elimination of these molecules), their sensory properties, identified healthy and adverse effects, as well as the impact of processing on their bioavailability.
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Affiliation(s)
- M A Prieto
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo-Ourense Campus, Ourense, Spain; Nutrition and Food Science Group, Department of Analytical and Food Chemistry, CITACA, CACTI, University of Vigo-Vigo Campus, Vigo, Spain
| | - Cecilia Jiménez López
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo-Ourense Campus, Ourense, Spain; Nutrition and Food Science Group, Department of Analytical and Food Chemistry, CITACA, CACTI, University of Vigo-Vigo Campus, Vigo, Spain
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo-Ourense Campus, Ourense, Spain.
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Cavalcanti JHF, Kirma M, Barros JAS, Quinhones CGS, Pereira-Lima ÍA, Obata T, Nunes-Nesi A, Galili G, Fernie AR, Avin-Wittenberg T, Araújo WL. An L,L-diaminopimelate aminotransferase mutation leads to metabolic shifts and growth inhibition in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5489-5506. [PMID: 30215754 PMCID: PMC6255705 DOI: 10.1093/jxb/ery325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
Lysine (Lys) connects the mitochondrial electron transport chain to amino acid catabolism and the tricarboxylic acid cycle. However, our understanding of how a deficiency in Lys biosynthesis impacts plant metabolism and growth remains limited. Here, we used a previously characterized Arabidopsis mutant (dapat) with reduced activity of the Lys biosynthesis enzyme L,L-diaminopimelate aminotransferase to investigate the physiological and metabolic impacts of impaired Lys biosynthesis. Despite displaying similar stomatal conductance and internal CO2 concentration, we observed reduced photosynthesis and growth in the dapat mutant. Surprisingly, whilst we did not find differences in dark respiration between genotypes, a lower storage and consumption of starch and sugars was observed in dapat plants. We found higher protein turnover but no differences in total amino acids during a diurnal cycle in dapat plants. Transcriptional and two-dimensional (isoelectric focalization/SDS-PAGE) proteome analyses revealed alterations in the abundance of several transcripts and proteins associated with photosynthesis and photorespiration coupled with a high glycine/serine ratio and increased levels of stress-responsive amino acids. Taken together, our findings demonstrate that biochemical alterations rather than stomatal limitations are responsible for the decreased photosynthesis and growth of the dapat mutant, which we hypothesize mimics stress conditions associated with impairments in the Lys biosynthesis pathway.
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Affiliation(s)
- João Henrique F Cavalcanti
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Menny Kirma
- Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel
| | - Jessica A S Barros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Carla G S Quinhones
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Ítalo A Pereira-Lima
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Toshihiro Obata
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Gad Galili
- Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Tamar Avin-Wittenberg
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem Israel
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Lee JH, Lee J, Kim H, Chae WB, Kim SJ, Lim YP, Oh MH. Brassinosteroids regulate glucosinolate biosynthesis in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2018; 163:450-458. [PMID: 29315590 DOI: 10.1111/ppl.12691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 06/07/2023]
Abstract
Plants must constantly adjust their growth and defense responses to deal with the wide variety of stresses they encounter in their environment. Among phytohormones, brassinosteroids (BRs) are an important group of plant steroid hormones involved in numerous aspects of the plant lifecycle including growth, development and responses to various stresses including insect attacks. Here, we show that BRs regulate glucosinolate (GS) biosynthesis and function in insect herbivory. Preference tests and larval feeding experiments using the generalist herbivore, diamondback moth (Plutella xylostella), revealed that the larvae prefer to feed on Arabidopsis thaliana brassinosteroid insensitive 1 (bri1-5) plants over wild-type Ws-2 or BRI1-Flag (bri1-5 background) transgenic plants, which results in an increase in larval weight. Analysis of GS contents showed that 3-(methylsulfinyl) propyl GS (C3) levels were higher in bri1-5 than in Ws2 and BRI1-Flag transgenic plants, whereas sinigrin (2-propenylglucosinolate), glucoerucin (4-methylthiobutylglucosinolate) and glucobrassicin (indol-3-ylmethylglucosinolate) levels were lower in this mutant. We investigated the effect of brassinolide (BL) on GS biosynthesis in Arabidopsis and radish (Raphanus sativus L.) by monitoring the expression levels of GS biosynthetic genes, including MAM1, MAM3, BCAT4 and AOP2, which increased in a BL-dependent manner. These results suggest that BRs regulate GS profiles in higher plants, which function in defense responses against insects.
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Affiliation(s)
- Ji H Lee
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jeongyeo Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - HyeRan Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Won B Chae
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju, Republic of Korea
| | - Sun-Ju Kim
- Department of Bio-Environmental Chemistry, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Yong P Lim
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, Republic of Korea
| | - Man-Ho Oh
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
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35
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Zhang T, Meng L, Kong W, Yin Z, Wang Y, Schneider JD, Chen S. Quantitative proteomics reveals a role of JAZ7 in plant defense response to Pseudomonas syringae DC3000. J Proteomics 2018; 175:114-126. [DOI: 10.1016/j.jprot.2018.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/15/2017] [Accepted: 01/02/2018] [Indexed: 12/11/2022]
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Yang H, Liu F, Li Y, Yu B. Reconstructing Biosynthetic Pathway of the Plant-Derived Cancer Chemopreventive-Precursor Glucoraphanin in Escherichia coli. ACS Synth Biol 2018; 7:121-131. [PMID: 29149798 DOI: 10.1021/acssynbio.7b00256] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Epidemiological data confirmed a strong correlation between regular consumption of cruciferous vegetables and lower cancer risk. This cancer preventive property is mainly attributed to the glucosinolate products, such as glucoraphanin found in broccoli that is derived from methionine. Here we report the first successful reconstruction of the complete biosynthetic pathway of glucoraphanin from methionine in Escherichia coli via gene selection, pathway design, and protein engineering. We used branched-chain amino transferase 3 to catalyze two transamination steps to ensure the purity of precursor molecules and used cysteine as a sulfur donor to simplify the synthesis pathway. Two chimeric cytochrome P450 enzymes were engineered and expressed in E. coli functionally. The original plant C-S lyase was replaced by the Neurospora crassa hercynylcysteine sulfoxide lyase. Other pathway enzymes were successfully mined from Arabidopsis thaliana, Brassica rapa, and Brassica oleracea. Biosynthesis of glucoraphanin upon coexpression of the optimized enzymes in vivo was confirmed by liquid chromatography-tandem mass spectrometry analysis. No other glucosinolate analogues (except for glucoiberin) were identified that could facilitate the downstream purification processes. Production of glucoraphanin in this study laid the foundation for microbial production of such health-beneficial glucosinolates in a large-scale.
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Affiliation(s)
- Han Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feixia Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Kaewchangwat N, Dueansawang S, Tumcharern G, Suttisintong K. Synthesis of Copper-Chelates Derived from Amino Acids and Evaluation of Their Efficacy as Copper Source and Growth Stimulator for Lactuca sativa in Nutrient Solution Culture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:9828-9837. [PMID: 29072914 DOI: 10.1021/acs.jafc.7b03809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Five tetradentate ligands were synthesized from l-amino acids and utilized for the synthesis of Cu(II)-chelates 1-5. The efficacy of Cu(II)-chelates as copper (Cu) source and growth stimulator in hydroponic cultivation was evaluated with Lactuca sativa. Their stability test was performed at pH 4-10. The results suggested that Cu(II)-chelate 3 is the most pH tolerant complex. Levels of Cu, Zn, and Fe accumulated in plants supplied with Cu(II)-chelates were compared with those supplied with CuSO4 at the same Cu concentration of 8.0 μM. The results showed that Cu(II)-chelate 3 significantly enhanced Cu, Zn, and Fe content in shoot by 35, 15, and 48%, respectively. Application of Cu(II)-chelate 3 also improved plant dry matter yield by 54%. According to the results, Cu(II)-chelate 3 demonstrated the highest stimulating effect on plant growth and plant mineral accumulation so that it can be used as an alternative to CuSO4 for supplying Cu in nutrient solutions and enhancing the plant growth.
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Affiliation(s)
- Narongpol Kaewchangwat
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA) , 111 Thailand Science Park, Thanon Phahonyothin, Tumbon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Sattawat Dueansawang
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA) , 111 Thailand Science Park, Thanon Phahonyothin, Tumbon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Gamolwan Tumcharern
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA) , 111 Thailand Science Park, Thanon Phahonyothin, Tumbon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Khomson Suttisintong
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA) , 111 Thailand Science Park, Thanon Phahonyothin, Tumbon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
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Sofer L, Cabanillas DG, Gayral M, Téplier R, Pouzoulet J, Ducousso M, Dufin L, Bréhélin C, Ziegler-Graff V, Brault V, Revers F. Identification of host factors potentially involved in RTM-mediated resistance during potyvirus long distance movement. Arch Virol 2017; 162:1855-1865. [PMID: 28251380 DOI: 10.1007/s00705-017-3292-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/29/2017] [Indexed: 12/28/2022]
Abstract
The long distance movement of potyviruses is a poorly understood step of the viral cycle. Only factors inhibiting this process, referred to as "Restricted TEV Movement" (RTM), have been identified in Arabidopsis thaliana. On the virus side, the potyvirus coat protein (CP) displays determinants required for long-distance movement and for RTM-based resistance breaking. However, the potyvirus CP was previously shown not to interact with the RTM proteins. We undertook the identification of Arabidopsis factors which directly interact with either the RTM proteins or the CP of lettuce mosaic virus (LMV). An Arabidopsis cDNA library generated from companion cells was screened with LMV CP and RTM proteins using the yeast two-hybrid system. Fourteen interacting proteins were identified. Two of them were shown to interact with CP and the RTM proteins suggesting that a multiprotein complex could be formed between the RTM proteins and virions or viral ribonucleoprotein complexes. Co-localization experiments in Nicotiana benthamiana showed that most of the viral and cellular protein pairs co-localized at the periphery of chloroplasts which suggests a putative role for plastids in this process.
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Affiliation(s)
- Luc Sofer
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Daniel Garcia Cabanillas
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval, QC, H7V 1B7, Canada
| | - Mathieu Gayral
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Rachèle Téplier
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Jérôme Pouzoulet
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Marie Ducousso
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
- UMR 0385 BGPI, Virus Insecte Plante, INRA, Campus international de Bailllarguet, Montpellier, France
| | - Laurène Dufin
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Claire Bréhélin
- UMR 5200, Laboratory of Membrane Biogenesis, CNRS, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Véronique Ziegler-Graff
- Institut de Biologie Moléculaire des Plantes, Laboratoire propre du CNRS conventionné avec l'Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
| | | | - Frédéric Revers
- BFP, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France.
- BIOGECO, INRA, University of Bordeaux, 33615, Pessac, France.
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Mohammadin S, Nguyen TP, van Weij MS, Reichelt M, Schranz ME. Flowering Locus C (FLC) Is a Potential Major Regulator of Glucosinolate Content across Developmental Stages of Aethionema arabicum (Brassicaceae). FRONTIERS IN PLANT SCIENCE 2017; 8:876. [PMID: 28603537 PMCID: PMC5445170 DOI: 10.3389/fpls.2017.00876] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/10/2017] [Indexed: 05/08/2023]
Abstract
The biochemical defense of plants can change during their life-cycle and impact herbivore feeding and plant fitness. The annual species Aethionema arabicum is part of the sister clade to all other Brassicaceae. Hence, it holds a phylogenetically important position for studying crucifer trait evolution. Glucosinolates (GS) are essentially Brassicales-specific metabolites involved in plant defense. Using two Ae. arabicum accessions (TUR and CYP) we identify substantial differences in glucosinolate profiles and quantities between lines, tissues and developmental stages. We find tissue specific side-chain modifications in aliphatic GS: methylthioalkyl in leaves, methylsulfinylalkyl in fruits, and methylsulfonylalkyl in seeds. We also find large differences in absolute glucosinolate content between the two accessions (up to 10-fold in fruits) that suggest a regulatory factor is involved that is not part of the quintessential glucosinolate biosynthetic pathway. Consistent with this hypothesis, we identified a single major multi-trait quantitative trait locus controlling total GS concentration across tissues in a recombinant inbred line population derived from TUR and CYP. With fine-mapping, we narrowed the interval to a 58 kb region containing 15 genes, but lacking any known GS biosynthetic genes. The interval contains homologs of both the sulfate transporter SULTR2;1 and FLOWERING LOCUS C. Both loci have diverse functions controlling plant physiological and developmental processes and thus are potential candidates regulating glucosinolate variation across the life-cycle of Aethionema. Future work will investigate changes in gene expression of the candidates genes, the effects of GS variation on insect herbivores and the trade-offs between defense and reproduction.
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Affiliation(s)
- Setareh Mohammadin
- Biosystematics, Plant Sciences Group, Wageningen University and ResearchWageningen, Netherlands
| | - Thu-Phuong Nguyen
- Biosystematics, Plant Sciences Group, Wageningen University and ResearchWageningen, Netherlands
| | - Marco S. van Weij
- Biosystematics, Plant Sciences Group, Wageningen University and ResearchWageningen, Netherlands
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical EcologyJena, Germany
| | - Michael E. Schranz
- Biosystematics, Plant Sciences Group, Wageningen University and ResearchWageningen, Netherlands
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Transcriptome Analysis of Genes Involved in Dendrobine Biosynthesis in Dendrobium nobile Lindl. Infected with Mycorrhizal Fungus MF23 (Mycena sp.). Sci Rep 2017; 7:316. [PMID: 28331229 PMCID: PMC5428410 DOI: 10.1038/s41598-017-00445-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 02/27/2017] [Indexed: 11/09/2022] Open
Abstract
Content determination and microscopic observation proved that dendrobine accumulation in the stem of Dendrobium nobile Lindl. increased after infection with mycorrhizal fungus MF23 (Mycena sp.). Large-scale transcriptome sequencing of symbiotic and asymbiotic D. nobile revealed that 30 unigenes encoding proteins were possibly related to the biosynthesis of dendrobine sesquiterpene backbone. A qRT-PCR experiment of 16 unigenes, selected randomly, proved that there were significant changes in the expression levels of AACT, MVD, PMK and TPS21 at 9 weeks after inoculation. These results implied that MF23 might stimulate dendrobine biosynthesis by regulating the expressions of genes involved in the mevalonate (MVA) pathway. The biogenetic pathway of dendrobine was suggested systematically according to the structural features of dendrobine alkaloids and their sesquiterpene precursors, which implied that post-modification enzymes might play a major role in dendrobine biosynthesis. Thus, genes encoding post-modification enzymes, including cytochrome P450, aminotransferase and methyltransferase, were screened for their possible involvement in dendrobine biosynthesis. This study provides a good example of endophytes promoting the formation of bioactive compounds in their host and paves the way for further investigation of the dendrobine biosynthetic pathway.
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Li Q, Ding G, Li B, Guo SX. Transcriptome Analysis of Genes Involved in Dendrobine Biosynthesis in Dendrobium nobile Lindl. Infected with Mycorrhizal Fungus MF23 (Mycena sp.). Sci Rep 2017. [PMID: 28331229 DOI: 10.1038/s41598-017-00445-9/2045-2322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Content determination and microscopic observation proved that dendrobine accumulation in the stem of Dendrobium nobile Lindl. increased after infection with mycorrhizal fungus MF23 (Mycena sp.). Large-scale transcriptome sequencing of symbiotic and asymbiotic D. nobile revealed that 30 unigenes encoding proteins were possibly related to the biosynthesis of dendrobine sesquiterpene backbone. A qRT-PCR experiment of 16 unigenes, selected randomly, proved that there were significant changes in the expression levels of AACT, MVD, PMK and TPS21 at 9 weeks after inoculation. These results implied that MF23 might stimulate dendrobine biosynthesis by regulating the expressions of genes involved in the mevalonate (MVA) pathway. The biogenetic pathway of dendrobine was suggested systematically according to the structural features of dendrobine alkaloids and their sesquiterpene precursors, which implied that post-modification enzymes might play a major role in dendrobine biosynthesis. Thus, genes encoding post-modification enzymes, including cytochrome P450, aminotransferase and methyltransferase, were screened for their possible involvement in dendrobine biosynthesis. This study provides a good example of endophytes promoting the formation of bioactive compounds in their host and paves the way for further investigation of the dendrobine biosynthetic pathway.
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Affiliation(s)
- Qing Li
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100193, People's Republic of China
| | - Gang Ding
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100193, People's Republic of China
| | - Biao Li
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100193, People's Republic of China.
| | - Shun-Xing Guo
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100193, People's Republic of China.
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42
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Knoch D, Riewe D, Meyer RC, Boudichevskaia A, Schmidt R, Altmann T. Genetic dissection of metabolite variation in Arabidopsis seeds: evidence for mQTL hotspots and a master regulatory locus of seed metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1655-1667. [PMID: 28338798 PMCID: PMC5444479 DOI: 10.1093/jxb/erx049] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
To gain insight into genetic factors controlling seed metabolic composition and its relationship to major seed properties, an Arabidopsis recombinant inbred line (RIL) population, derived from accessions Col-0 and C24, was studied using an MS-based metabolic profiling approach. Relative intensities of 311 polar primary metabolites were used to identify associated genomic loci and to elucidate their interactions by quantitative trait locus (QTL) mapping. A total of 786 metabolic QTLs (mQTLs) were unequally distributed across the genome, forming several hotspots. For the branched-chain amino acid leucine, mQTLs and candidate genes were elucidated in detail. Correlation studies displayed links between metabolite levels, seed protein content, and seed weight. Principal component analysis revealed a clustering of samples, with PC1 mapping to a region on the short arm of chromosome IV. The overlap of this region with mQTL hotspots indicates the presence of a potential master regulatory locus of seed metabolism. As a result of database queries, a series of candidate regulatory genes, including bZIP10, were identified within this region. Depending on the search conditions, metabolic pathway-derived candidate genes for 40-61% of tested mQTLs could be determined, providing an extensive basis for further identification and characterization of hitherto unknown genes causal for natural variation of Arabidopsis seed metabolism.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - David Riewe
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Rhonda Christiane Meyer
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Anastassia Boudichevskaia
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Renate Schmidt
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
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43
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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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44
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Scarpeci TE, Frea VS, Zanor MI, Valle EM. Overexpression of AtERF019 delays plant growth and senescence, and improves drought tolerance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:673-685. [PMID: 28204526 DOI: 10.1093/jxb/erw429] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The transcription factor superfamily, APETALA2/ethylene response factor, is involved in plant growth and development, as well as in environmental stress responses. Here, an uncharacterized gene of this family, AtERF019, was studied in Arabidopsis thaliana under abiotic stress situations. Arabidopsis plants overexpressing AtERF019 showed a delay in flowering time of 7 days and a delay in senescence of 2 weeks when comparison with wild type plants. These plants also showed increased tolerance to water deficiency that could be explained by a lower transpiration rate, owing to their smaller stomata aperture and lower cuticle and cell wall permeability. Furthermore, using a bottom-up proteomic approach, proteins produced in response to stress, namely branched-chain-amino-acid aminotransferase 3 (BCAT3) and the zinc finger transcription factor oxidative stress 2, were only identified in plants overexpressing AtERF019. Additionally, a BCAT3 mutant was more sensitive to water-deficit stress than wild type plants. Predicted gene targets of AtERF019 were oxidative stress 2 and genes related to cell wall metabolism. These data suggest that AtERF019 could play a primary role in plant growth and development that causes an increased tolerance to water deprivation, so strengthening their chances of reproductive success.
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Affiliation(s)
- Telma E Scarpeci
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Ocampo y Esmeralda, Predio CCT, Rosario, Argentina
| | - Vanesa S Frea
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Ocampo y Esmeralda, Predio CCT, Rosario, Argentina
| | - María I Zanor
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Ocampo y Esmeralda, Predio CCT, Rosario, Argentina
| | - Estela M Valle
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Ocampo y Esmeralda, Predio CCT, Rosario, Argentina
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45
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Borpatragohain P, Rose TJ, King GJ. Fire and Brimstone: Molecular Interactions between Sulfur and Glucosinolate Biosynthesis in Model and Crop Brassicaceae. FRONTIERS IN PLANT SCIENCE 2016; 7:1735. [PMID: 27917185 PMCID: PMC5116641 DOI: 10.3389/fpls.2016.01735] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/03/2016] [Indexed: 05/20/2023]
Abstract
Glucosinolates (GSLs) represent one of the most widely studied classes of plant secondary metabolite, and have a wide range of biological activities. Their unique properties also affect livestock and human health, and have been harnessed for food and other end-uses. Since GSLs are sulfur (S)-rich there are many lines of evidence suggesting that plant S status plays a key role in determining plant GSL content. However, there is still a need to establish a detailed knowledge of the distribution and remobilization of S and GSLs throughout the development of Brassica crops, and to represent this in terms of primary and secondary sources and sinks. The increased genome complexity, gene duplication and divergence within brassicas, together with their ontogenetic plasticity during crop development, appear to have a marked effect on the regulation of S and GSLs. Here, we review the current understanding of inorganic S (sulfate) assimilation into organic S forms, including GSLs and their precursors, the intracellular and inter-organ transport of inorganic and organic S forms, and the accumulation of GSLs in specific tissues. We present this in the context of overlapping sources and sinks, transport processes, signaling molecules and their associated molecular interactions. Our analysis builds on recent insights into the molecular regulation of sulfate uptake and transport by different transporters, transcription factors and miRNAs, and the role that these may play in GSL biosynthesis. We develop a provisional model describing the key processes that could be targeted in crop breeding programs focused on modifying GSL content.
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Affiliation(s)
| | - Terry J. Rose
- Southern Cross Plant Science, Southern Cross University, LismoreNSW, Australia
- Southern Cross GeoScience, Southern Cross University, LismoreNSW, Australia
| | - Graham J. King
- Southern Cross Plant Science, Southern Cross University, LismoreNSW, Australia
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46
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Pretali L, Bernardo L, Butterfield TS, Trevisan M, Lucini L. Botanical and biological pesticides elicit a similar Induced Systemic Response in tomato (Solanum lycopersicum) secondary metabolism. PHYTOCHEMISTRY 2016; 130:56-63. [PMID: 27251587 DOI: 10.1016/j.phytochem.2016.04.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 03/07/2016] [Accepted: 04/11/2016] [Indexed: 05/18/2023]
Abstract
Natural pesticides have attracted substantial interest due to the increase in organic agriculture and enhanced attention to environmental pollution. Plant Growth Promoting Bacteria (PGPB) are applied for both disease control and growth enhancement; PGPBs are known to elicit Induced Systemic Response (ISR) in plants. However, less is known about the effect of botanical pesticides, such as the azadirachtin-containing neem extracts, on plant metabolism. This study aimed to investigate the effects of foliar application of the above-mentioned natural pesticides on the metabolic profiling of tomato. Leaf application of Bacillus subtilis fostered Induced Systemic Resistance (ISR) in treated plants via the Jasmonic acid pathway, and enhanced production of secondary metabolites such as flavonoids, phytoalexins and auxins. Changes in sterols and terpenes, as well as an increase in glucosinolates were also observed. Interestingly, azadirachtin-treated tomatoes also showed an increase in ISR and our results revealed that most of the enriched metabolites are shared with a B. subtilis treatment, suggesting conserved biochemical responses. These (un)expected findings indicate that plants are not insensitive to application of natural pesticide and while Azadirachtin is applied as a direct pesticide, it also stimulates a defense response in tomatoes very similar to B. subtilis induced ISR.
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Affiliation(s)
- Luca Pretali
- Institute of Environmental and Agricultural Chemistry, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy.
| | - Letizia Bernardo
- Institute of Environmental and Agricultural Chemistry, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy.
| | | | - Marco Trevisan
- Institute of Environmental and Agricultural Chemistry, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy.
| | - Luigi Lucini
- Institute of Environmental and Agricultural Chemistry, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy.
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47
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van den Bergh E, Hofberger JA, Schranz ME. Flower power and the mustard bomb: Comparative analysis of gene and genome duplications in glucosinolate biosynthetic pathway evolution in Cleomaceae and Brassicaceae. AMERICAN JOURNAL OF BOTANY 2016; 103:1212-22. [PMID: 27313198 DOI: 10.3732/ajb.1500445] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/04/2016] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Glucosinolates (GS) are a class of plant secondary metabolites that provide defense against herbivores and may play an important role in pollinator attraction. Through coevolution with plant-interacting organisms, glucosinolates have diversified into a variety of chemotypes through gene sub- and neofunctionalization. Polyploidy has been of major importance in the evolutionary history of these gene families and the development of chemically separate GS types. Here we study the effects of polyploidy in Tarenaya hassleriana (Cleomaceae) on the genes underlying GS biosynthesis. METHODS We established putative orthologs of all gene families involved in GS biosynthesis through sequence comparison and their duplication method through calculation of synonymous substitution ratios, phylogenetic gene trees, and synteny comparison. We drew expression data from previously published work of the identified genes and compared expression in several tissues. KEY RESULTS We show that the majority of gene family expansion in T. hassleriana has taken place through the retention of polyploid duplicates, together with tandem and transpositional duplicates. We also show that the large majority (>75%) is actively expressed either globally or in specific tissues. We show that MAM and CYP83 gene families, which are crucial to GS diversification in Brassicaceae, are also recruited into specific tissue expression pathways in Cleomaceae. CONCLUSIONS Many GS genes have expanded through polyploidy, gene transposition duplication, and tandem duplication in Cleomaceae. Duplicate retention through these mechanisms is similar to A. thaliana, but based on the expression of GS genes, Cleomaceae-specific diversification of GS genes has taken place.
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Affiliation(s)
- Erik van den Bergh
- Biosystematics Group, Wageningen University & Research Center, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Johannes A Hofberger
- Biosystematics Group, Wageningen University & Research Center, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands Big Data Analytics, Detecon Co., Ltd., 100600 Beijing, PR China
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research Center, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
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48
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Lee SG, Nwumeh R, Jez JM. Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS. J Biol Chem 2016; 291:13421-30. [PMID: 27137927 DOI: 10.1074/jbc.m116.730358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 11/06/2022] Open
Abstract
Isopropylmalate dehydrogenase (IPMDH) and 3-(2'-methylthio)ethylmalate dehydrogenase catalyze the oxidative decarboxylation of different β-hydroxyacids in the leucine- and methionine-derived glucosinolate biosynthesis pathways, respectively, in plants. Evolution of the glucosinolate biosynthetic enzyme from IPMDH results from a single amino acid substitution that alters substrate specificity. Here, we present the x-ray crystal structures of Arabidopsis thaliana IPMDH2 (AtIPMDH2) in complex with either isopropylmalate and Mg(2+) or NAD(+) These structures reveal conformational changes that occur upon ligand binding and provide insight on the active site of the enzyme. The x-ray structures and kinetic analysis of site-directed mutants are consistent with a chemical mechanism in which Lys-232 activates a water molecule for catalysis. Structural analysis of the AtIPMDH2 K232M mutant and isothermal titration calorimetry supports a key role of Lys-232 in the reaction mechanism. This study suggests that IPMDH-like enzymes in both leucine and glucosinolate biosynthesis pathways use a common mechanism and that members of the β-hydroxyacid reductive decarboxylase family employ different active site features for similar reactions.
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Affiliation(s)
- Soon Goo Lee
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Ronald Nwumeh
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Joseph M Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
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49
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Galili G, Amir R, Fernie AR. The Regulation of Essential Amino Acid Synthesis and Accumulation in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:153-78. [PMID: 26735064 DOI: 10.1146/annurev-arplant-043015-112213] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although amino acids are critical for all forms of life, only proteogenic amino acids that humans and animals cannot synthesize de novo and therefore must acquire in their diets are classified as essential. Nine amino acids-lysine, methionine, threonine, phenylalanine, tryptophan, valine, isoleucine, leucine, and histidine-fit this definition. Despite their nutritional importance, several of these amino acids are present in limiting quantities in many of the world's major crops. In recent years, a combination of reverse genetic and biochemical approaches has been used to define the genes encoding the enzymes responsible for synthesizing, degrading, and regulating these amino acids. In this review, we describe recent advances in our understanding of the metabolism of the essential amino acids, discuss approaches for enhancing their levels in plants, and appraise efforts toward their biofortification in crop plants.
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Affiliation(s)
- Gad Galili
- Department of Plant Science, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Rachel Amir
- Laboratory of Plant Science, MIGAL-Galilee Research Institute, Kiryat Shmona 11016, Israel;
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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50
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Yin L, Chen C, Chen G, Cao B, Lei J. Molecular Cloning, Expression Pattern and Genotypic Effects on Glucoraphanin Biosynthetic Related Genes in Chinese Kale (Brassica oleracea var. alboglabra Bailey). Molecules 2015; 20:20254-67. [PMID: 26569208 PMCID: PMC6332273 DOI: 10.3390/molecules201119688] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 10/29/2015] [Accepted: 11/03/2015] [Indexed: 01/18/2023] Open
Abstract
Glucoraphanin is a plant secondary metabolite that is involved in plant defense and imparts health-promoting properties to cruciferous vegetables. In this study, three genes involved in glucoraphanin metabolism, branched-chain aminotransferase 4 (BCAT4), methylthioalkylmalate synthase 1 (MAM1) and dihomomethionine N-hydroxylase (CYP79F1), were cloned from Chinese kale (Brassica oleracea var. alboglabra Bailey). Sequence homology and phylogenetic analysis identified these genes and confirmed the evolutionary status of Chinese kale. The transcript levels of BCAT4, MAM1 and CYP79F1 were higher in cotyledon, leaf and stem compared with flower and silique. BCAT4, MAM1 and CYP79F1 were expressed throughout leaf development with lower transcript levels during the younger stages. Glucoraphanin content varied extensively among different varieties, which ranged from 0.25 to 2.73 µmol·g(-1) DW (dry weight). Expression levels of BCAT4 and MAM1 were high at vegetative-reproductive transition phase, while CYP79F1 was expressed high at reproductive phase. BCAT4, MAM1 and CYP79F1 were expressed significantly high in genotypes with high glucoraphanin content. All the results provided a better understanding of the roles of BCAT4, MAM1 and CYP79F1 in the glucoraphanin biosynthesis of Chinese kale.
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Affiliation(s)
- Ling Yin
- Department of Hortscience, South China Agricultural University, Guangzhou 510642, China.
| | - Changming Chen
- Department of Hortscience, South China Agricultural University, Guangzhou 510642, China.
| | - Guoju Chen
- Department of Hortscience, South China Agricultural University, Guangzhou 510642, China.
| | - Bihao Cao
- Department of Hortscience, South China Agricultural University, Guangzhou 510642, China.
| | - Jianjun Lei
- Department of Hortscience, South China Agricultural University, Guangzhou 510642, China.
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