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Li Q, Dai Y, Huang XC, Sun L, Wang K, Guo X, Xu D, Wan D, An L, Wang Z, Tang H, Qi Q, Zeng H, Qin M, Xue JY, Zhao Y. The chromosome-scale assembly of the Notopterygium incisum genome provides insight into the structural diversity of coumarins. Acta Pharm Sin B 2024; 14:3760-3773. [PMID: 39220882 PMCID: PMC11365381 DOI: 10.1016/j.apsb.2024.04.005] [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: 12/07/2023] [Revised: 03/17/2024] [Accepted: 04/03/2024] [Indexed: 09/04/2024] Open
Abstract
Coumarins, derived from the phenylpropanoid pathway, represent one of the primary metabolites found in angiosperms. The alignment of the tetrahydropyran (THP) and tetrahydrofuran (THF) rings with the lactone structure results in the formation of at least four types of complex coumarins. However, the mechanisms underlying the structural diversity of coumarin remain poorly understood. Here, we report the chromosome-level genome assembly of Notopterygium incisum, spanning 1.64 Gb, with a contig N50 value of 22.7 Mb and 60,021 annotated protein-coding genes. Additionally, we identified the key enzymes responsible for shaping the structural diversity of coumarins, including two p-coumaroyl CoA 2'-hydroxylases crucial for simple coumarins basic skeleton architecture, two UbiA prenyltransferases responsible for angular or linear coumarins biosynthesis, and five CYP736 cyclases involved in THP and THF ring formation. Notably, two bifunctional enzymes capable of catalyzing both demethylsuberosin and osthenol were identified for the first time. Evolutionary analysis implies that tandem and ectopic duplications of the CYP736 subfamily, specifically arising in the Apiaceae, contributed to the structural diversity of coumarins in N. incisum. Conclusively, this study proposes a parallel evolution scenario for the complex coumarin biosynthetic pathway among different angiosperms and provides essential synthetic biology elements for the heterologous industrial production of coumarins.
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Affiliation(s)
- Qien Li
- Tibetan Medicine Research Center of Qinghai University, Tibetan Medical College, Qinghai University, Xining 810016, China
| | - Yiqun Dai
- School of Pharmacy, Bengbu Medical University, Bengbu 233030, China
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xin-Cheng Huang
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Lanlan Sun
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Kaixuan Wang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao Guo
- Tibetan Medicine Research Center of Qinghai University, Tibetan Medical College, Qinghai University, Xining 810016, China
| | - Dingqiao Xu
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xi'an 712046, China
| | - Digao Wan
- Tibetan Medicine Research Center of Qinghai University, Tibetan Medical College, Qinghai University, Xining 810016, China
| | - Latai An
- Tibetan Medicine Research Center of Qinghai University, Tibetan Medical College, Qinghai University, Xining 810016, China
| | - Zixuan Wang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Huanying Tang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qi Qi
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Huihui Zeng
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Minjian Qin
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jia-Yu Xue
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yucheng Zhao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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Deng S, Pan L, Ke T, Liang J, Zhang R, Chen H, Tang M, Hu W. Rhizophagus Irregularis regulates flavonoids metabolism in paper mulberry roots under cadmium stress. MYCORRHIZA 2024; 34:317-339. [PMID: 38836935 DOI: 10.1007/s00572-024-01155-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/26/2024] [Indexed: 06/06/2024]
Abstract
Broussonetia papyrifera is widely found in cadmium (Cd) contaminated areas, with an inherent enhanced flavonoids metabolism and inhibited lignin biosynthesis, colonized by lots of symbiotic fungi, such as arbuscular mycorrhizal fungi (AMF). However, the physiological and molecular mechanisms by which Rhizophagus irregularis, an AM fungus, regulates flavonoids and lignin in B. papyrifera under Cd stress remain unclear. Here, a pot experiment of B. papyrifera inoculated and non-inoculated with R. irregularis under Cd stress was carried out. We determined flavonoids and lignin concentrations in B. papyrifera roots by LC-MS and GC-MS, respectively, and measured the transcriptional levels of flavonoids- or lignin-related genes in B. papyrifera roots, aiming to ascertain the key components of flavonoids or lignin, and key genes regulated by R. irregularis in response to Cd stress. Without R. irregularis, the concentrations of eriodictyol, quercetin and myricetin were significantly increased under Cd stress. The concentrations of eriodictyol and genistein were significantly increased by R. irregularis, while the concentration of rutin was significantly decreased. Total lignin and lignin monomer had no alteration under Cd stress or with R. irregularis inoculation. As for flavonoids- or lignin-related genes, 26 genes were co-regulated by Cd stress and R. irregularis. Among these genes, BpC4H2, BpCHS8 and BpCHI5 were strongly positively associated with eriodictyol, indicating that these three genes participate in eriodictyol biosynthesis and were involved in R. irregularis assisting B. papyrifera to cope with Cd stress. This lays a foundation for further research revealing molecular mechanisms by which R. irregularis regulates flavonoids synthesis to enhance tolerance of B. papyrifera to Cd stress.
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Affiliation(s)
- Shuiqing Deng
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Lan Pan
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Tong Ke
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Jingwei Liang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Rongjing Zhang
- College of Life Science, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Tang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Wentao Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
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Liu H, Wang Y, Chang Q, Li Q, Fang J, Cao N, Tong X, Jiang X, Yu X, Cheng Y. Combined metabolome and transcriptome reveal HmF6'H1 regulating simple coumarin accumulation against powdery mildew infection in Heracleum moellendorffii Hance. BMC PLANT BIOLOGY 2024; 24:507. [PMID: 38844853 PMCID: PMC11155083 DOI: 10.1186/s12870-024-05185-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/22/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Powdery mildew, caused by Eeysiphe heraclei, seriously threatens Heracleum moellendorffii Hance. Plant secondary metabolites are essential to many activities and are necessary for defense against biotic stress. In order to clarify the functions of these metabolites in response to the pathogen, our work concentrated on the variations in the accumulation of secondary metabolites in H. moellendorffii during E. heraclei infection. RESULTS Following E. heraclei infection, a significant upregulation of coumarin metabolites-particularly simple coumarins and associated genes was detected by RNA-seq and UPLC-MS/MS association analysis. Identifying HmF6'H1, a Feruloyl CoA 6'-hydroxylase pivotal in the biosynthesis of the coumarin basic skeleton through ortho-hydroxylation, was a significant outcome. The cytoplasmic HmF6'H1 protein was shown to be able to catalyze the ortho-hydroxylation of p-coumaroyl-CoA and caffeoyl-CoA, resulting in the formation of umbelliferone and esculetin, respectively. Over-expression of the HmF6'H1 gene resulted in increased levels of simple coumarins, inhibiting the biosynthesis of furanocoumarins and pyranocoumarins by suppressing PT gene expression, enhancing H. moellendorffii resistance to powdery mildew. CONCLUSIONS These results established HmF6'H1 as a resistance gene aiding H. moellendorffii in combatting E. heraclei infection, offering additional evidence of feruloyl-CoA 6'-hydroxylase role in catalyzing various types of simple coumarins. Therefore, this work contributes to our understanding of the function of simple coumarins in plants' defense against powdery mildew infection.
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Affiliation(s)
- Hanbing Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Yiran Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - QinZheng Chang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Qiubi Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Jiahui Fang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Ning Cao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Xuejiao Tong
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Xinmei Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Xihong Yu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China
| | - Yao Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China.
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Yan C, Li C, Jiang M, Xu Y, Zhang S, Hu X, Chen Y, Lu S. Systematic characterization of gene families and functional analysis of PvRAS3 and PvRAS4 involved in rosmarinic acid biosynthesis in Prunella vulgaris. FRONTIERS IN PLANT SCIENCE 2024; 15:1374912. [PMID: 38751843 PMCID: PMC11094360 DOI: 10.3389/fpls.2024.1374912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/15/2024] [Indexed: 05/18/2024]
Abstract
Prunella vulgaris is an important material for Chinese medicines with rosmarinic acid (RA) as its index component. Based on the chromosome-level genome assembly we obtained recently, 51 RA biosynthesis-related genes were identified. Sequence feature, gene expression pattern and phylogenetic relationship analyses showed that 17 of them could be involved in RA biosynthesis. In vitro enzymatic assay showed that PvRAS3 catalyzed the condensation of p-coumaroyl-CoA and caffeoyl-CoA with pHPL and DHPL. Its affinity toward p-coumaroyl-CoA was higher than caffeoyl-CoA. PvRAS4 catalyzed the condensation of p-coumaroyl-CoA with pHPL and DHPL. Its affinity toward p-coumaroyl-CoA was lower than PvRAS3. UPLC and LC-MS/MS analyses showed the existence of RA, 4-coumaroyl-3',4'-dihydroxyphenyllactic acid, 4-coumaroyl-4'-hydroxyphenyllactic acid and caffeoyl-4'-hydroxyphenyllactic acid in P. vulgaris. Generation and analysis of pvras3 homozygous mutants showed significant decrease of RA, 4-coumaroyl-3',4'-dihydroxyphenyllactic acid, 4-coumaroyl-4'-hydroxyphenyllactic acid and caffeoyl-4'-hydroxyphenyllactic acid and significant increase of DHPL and pHPL. It suggests that PvRAS3 is the main enzyme catalyzing the condensation of acyl donors and acceptors during RA biosynthesis. The role of PvRAS4 appears minor. The results provide significant information for quality control of P. vulgaris medicinal materials.
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Affiliation(s)
- Chao Yan
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- College of Pharmaceutical Sciences, Chengdu Medical College, Chengdu, China
| | - Caili Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Maochang Jiang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yayun Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Sixuan Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiangling Hu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- College of Pharmaceutical Sciences, Chengdu Medical College, Chengdu, China
| | - Yuhang Chen
- College of Pharmaceutical Sciences, Chengdu Medical College, Chengdu, China
| | - Shanfa Lu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Song C, Zhang Y, Zhang Y, Yi S, Pan H, Liao R, Wang Y, Han B. Genome sequencing-based transcriptomic analysis reveals novel genes in Peucedanum praeruptorum. BMC Genom Data 2023; 24:53. [PMID: 37723451 PMCID: PMC10506206 DOI: 10.1186/s12863-023-01157-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/13/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Peucedanum praeruptorum Dunn, a traditional Chinese herbal medicine, contains coumarin and volatile oil components that have clinical application value. However, early bolting often occurs in the medicinal materials of Apiaceae plants. The rhizomes of the medicinal parts are gradually lignified after bolting, resulting in a sharp decrease in the content of coumarins. At present, the link between coumarin biosynthesis and early bolting in P. praeruptorum has not been elucidated. RESULTS Combining the genome sequencing and the previous transcriptome sequencing results, we reanalyzed the differential transcripts of P. praeruptorum before and after bolting. A total of 62,088 new transcripts were identified, of which 31,500 were unknown transcripts. Functional classification and annotation showed that many genes were involved in the regulation of transcription, defense response, and carbohydrate metabolic processes. The main domains are the pentatricopeptide repeat, protein kinase, RNA recognition motif, leucine-rich repeat, and ankyrin repeat domains, indicating their pivotal roles in protein modification and signal transduction. Gene structure analysis showed that skipped exon (SE) was the most dominant alternative splicing, followed by the alternative 3' splice site (A3SS) and the alternative 5' splice site (A5SS). Functional enrichment of differentially expressed genes showed that these differentially expressed genes mainly include transmembrane transporters, channel proteins, DNA-binding proteins, polysaccharide-binding proteins, etc. In addition, genes involved in peroxisome, hexose phosphate pathway, phosphatidylinositol signaling system, and inositol phosphate metabolism pathway were greatly enriched. A protein-protein interaction network analysis discoverd 1,457 pairs of proteins that interact with each other. The expression levels of six UbiA genes, three UGT genes, and four OMT genes were higher during the bolting stage. This observation suggests their potential involvement in the catalytic processes of prenylation, glycosylation, and methylation of coumarins, respectively. A total of 100 peroxidase (PRX) genes were identified being involved in lignin polymerization, but only nine PRX genes were highly expressed at the bolting stage. It is worth noting that 73 autophagy-related genes (ATGs) were first identified from the KEGG pathway-enriched genes. Some ATGs, such as BHQH00009837, BHQH00013830, and novel8944, had higher expression levels after bolting. CONCLUSIONS Comparative transcriptome analysis and large-scale genome screening provide guidance and new opinions for the identification of bolting-related genes in P. praeruptorum.
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Affiliation(s)
- Cheng Song
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China.
| | - Yingyu Zhang
- Henan Key Laboratory of Rare Diseases, The First Affiliated Hospital, College of Clinical Medicine of Henan, University of Science and Technology, Luoyang, 471003, China
| | - Yunpeng Zhang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Science, East China Normal University, Shanghai, 200241, China
| | - Shanyong Yi
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Haoyu Pan
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Ranran Liao
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Yuanyuan Wang
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Bangxing Han
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China.
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Pinch M, Bendzus-Mendoza H, Hansen IA. Transcriptomics analysis of ethanol treatment of male Aedes aegypti reveals a small set of putative radioprotective genes. Front Physiol 2023; 14:1120408. [PMID: 36793417 PMCID: PMC9922702 DOI: 10.3389/fphys.2023.1120408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023] Open
Abstract
Introduction: Sterile Insect Technique (SIT) is based on releasing sterilized male insects into wild insect populations to compete for mating with wild females. Wild females mated with sterile males will produce inviable eggs, leading to a decline in population of that insect species. Sterilization with ionizing radiation (x-rays) is a commonly used mechanism for sterilization of males. Since irradiation can cause damage to both, somatic and germ cells, and can severely reduce the competitiveness of sterilized males relative to wild males, means to minimize the detrimental effects of radiation are required to produce sterile, competitive males for release. In an earlier study, we identified ethanol as a functional radioprotector in mosquitoes. Methods: Here, we used Illumina RNA-seq to profile changes in gene expression of male Aedes aegypti mosquitoes fed on 5% ethanol for 48 hours prior to receiving a sterilizing x-ray dose, compared to males fed on water prior to sterilization. Results: RNA-seq revealed a robust activation of DNA repair genes in both ethanol-fed and water-fed males after irradiation, but surprisingly few differences in gene expression between ethanol-fed and water-fed males regardless of radiation treatment. Discussion: While differences in gene expression due to ethanol exposure were minimal, we identified a small group of genes that may prime ethanol-fed mosquitoes for improved survivability in response to sterilizing radiation.
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Affiliation(s)
- Matthew Pinch
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
| | - Harley Bendzus-Mendoza
- Department of Computer Science, New Mexico State University, Las Cruces, NM, United States
| | - Immo A. Hansen
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
- Institute of Applied Biosciences, New Mexico State University, Las Cruces, NM, United States
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Li M, Guo L, Wang Y, Li Y, Jiang X, Liu Y, Xie DY, Gao L, Xia T. Molecular and biochemical characterization of two 4-coumarate: CoA ligase genes in tea plant (Camellia sinensis). PLANT MOLECULAR BIOLOGY 2022; 109:579-593. [PMID: 35553312 DOI: 10.1007/s11103-022-01269-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Two 4-coumarate: CoA ligase genes in tea plant involved in phenylpropanoids biosynthesis and response to environmental stresses. Tea plant is rich in flavonoids benefiting human health. Lignin is essential for tea plant growth. Both flavonoids and lignin defend plants from stresses. The biosynthesis of lignin and flavonoids shares a key intermediate, 4-coumaroyl-CoA, which is formed from 4-coumaric acid catalyzed by 4-coumaric acid: CoA ligase (4CL). Herein, we report two 4CL paralogs from tea plant, Cs4CL1 and Cs4CL2, which are a member of class I and II of this gene family, respectively. Cs4CL1 was mainly expressed in roots and stems, while Cs4CL2 was mainly expressed in leaves. The promoter of Cs4CL1 had AC, nine types of light sensitive (LSE), four types of stress-inducible (SIE), and two types of meristem-specific elements (MSE). The promoter of Cs4CL2 also had AC and nine types of LSEs, but only had two types of SIEs and did not have MSEs. In addition, the LSEs varied in the two promoters. Based on the different features of regulatory elements, three stress treatments were tested to understand their expression responses to different conditions. The resulting data indicated that the expression of Cs4CL1 was sensitive to mechanical wounding, while the expression of Cs4CL2 was UV-B-inducible. Enzymatic assays showed that both recombinant Cs4CL1 and Cs4CL2 transformed 4-coumaric acid (CM), ferulic acid (FR), and caffeic acid (CF) to their corresponding CoA ethers. Kinetic analysis indicated that the recombinant Cs4CL1 preferred to catalyze CF, while the recombinant Cs4CL2 favored to catalyze CM. The overexpression of both Cs4CL1 and Cs4CL2 increased the levels of chlorogenic acid and total lignin in transgenic tobacco seedlings. In addition, the overexpression of Cs4CL2 consistently increased the levels of three flavonoid compounds. These findings indicate the differences of Cs4CL1 and Cs4CL2 in the phenylpropanoid metabolism.
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Affiliation(s)
- Mingzhuo Li
- State Key Laboratory of Tea Plant Biochemistry and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Lili Guo
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Yeru Wang
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Yanzhi Li
- State Key Laboratory of Tea Plant Biochemistry and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaolan Jiang
- State Key Laboratory of Tea Plant Biochemistry and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yajun Liu
- State Key Laboratory of Tea Plant Biochemistry and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - De-Yu Xie
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China.
| | - Tao Xia
- State Key Laboratory of Tea Plant Biochemistry and Utilization, Anhui Agricultural University, Hefei, 230036, China.
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Song C, Li X, Jia B, Liu L, Wei P, Manzoor MA, Wang F, Li BY, Wang G, Chen C, Han B. Comparative Transcriptomics Unveil the Crucial Genes Involved in Coumarin Biosynthesis in Peucedanum praeruptorum Dunn. FRONTIERS IN PLANT SCIENCE 2022; 13:899819. [PMID: 35656010 PMCID: PMC9152428 DOI: 10.3389/fpls.2022.899819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Peucedanum praeruptorum Dunn is a commonly used traditional Chinese medicine that is abundant in furano- and dihydropyrano coumarins. When P. praeruptorum reaches the bolting stage, the roots gradually lignified, and the content of coumarins declines rapidly. Non-bolting has always been a decisive factor for harvesting the P. praeruptorum materials. To evaluate the amount of coumarin components in unbolted and bolted P. praeruptorum, the variations of praeruptorin A, praeruptorin B, praeruptorin E, peucedanocoumarin I, and peucedanocoumarin II were determined. Additionally, 336,505 transcripts were obtained from the comparative transcriptome data. Among them, a total of 1,573 differentially expressed genes were screened out. To identify the critical genes involved in coumarin biosynthesis, comparative transcriptomics coupled with co-expression associated analysis was conducted. Finally, coumarin biosynthesis-related eighteen candidate genes were selected for the validation of qPCR. Additionally, a phylogenetic tree and the expression profile of ATP-binding cassette (ABC) transporters were constructed. To clarify the main genes in the regulation of coumarin biosynthesis, the interaction network of the co-expression genes from thirteen modules was constructed. Current results exhibited the significant increment of praeruptorin A, praeruptorin B and praeruptorin E in the bolted P. praeruptorum. Although, peucedanocoumarin I and peucedanocoumarin II were slightly increased. Besides the content of coumarins, the essential genes involved in the coumarin biosynthesis also exhibited an overall downward trend after bolting. Three peroxidases (PRXs) involved in the production of lignin monomers had been demonstrated to be downregulated. PAL, C4H, HCT, COMT, CCoAOMT, and some ABC transporters were dramatically downregulated at the bolting stage. These results indicated that the downregulation of coumarin biosynthetic genes in the bolted P. praeruptorum ultimately reduced the formation of coumarins. However, the mechanism through which bolting indirectly affects the formation of coumarin still needs extra functional verification.
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Affiliation(s)
- Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Xiaoli Li
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Bin Jia
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Li Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Peipei Wei
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | | | - Fang Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Biqi Yao Li
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Guanglin Wang
- Analytical and Testing Center, West Anhui University, Lu’an, China
| | - Cunwu Chen
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
| | - Bangxing Han
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an, China
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9
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Dong H, Li M, Jin L, Xie X, Li M, Wei J. Cool Temperature Enhances Growth, Ferulic Acid and Flavonoid Biosynthesis While Inhibiting Polysaccharide Biosynthesis in Angelica sinensis. Molecules 2022; 27:320. [PMID: 35011549 PMCID: PMC8746531 DOI: 10.3390/molecules27010320] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 12/15/2022] Open
Abstract
Angelica sinensis, a perennial herb that produces ferulic acid and phthalides for the treatment of cardio-cerebrovascular diseases, prefers growing at an altitude of 1800-3000 m. Geographical models have predicted that high altitude, cool temperature and sunshade play determining roles in geo-authentic formation. Although the roles of altitude and light in yield and quality have been investigated, the role of temperature in regulating growth, metabolites biosynthesis and gene expression is still unclear. In this study, growth characteristics, metabolites contents and related genes expression were investigated by exposing A. sinensis to cooler (15 °C) and normal temperatures (22 °C). The results showed that plant biomass, the contents of ferulic acid and flavonoids and the expression levels of genes related to the biosynthesis of ferulic acid (PAL1, 4CLL4, 4CLL9, C3H, HCT, CCOAMT and CCR) and flavonoids (CHS and CHI) were enhanced at 15 °C compared to 22 °C. The contents of ligustilide and volatile oils exhibited slight increases, while polysaccharide contents decreased in response to cooler temperature. Based on gene expression levels, ferulic acid biosynthesis probably depends on the CCOAMT pathway and not the COMT pathway. It can be concluded that cool temperature enhances plant growth, ferulic acid and flavonoid accumulation but inhibits polysaccharide biosynthesis in A. sinensis. These findings authenticate that cool temperature plays a determining role in the formation of geo-authentic and also provide a strong foundation for regulating metabolites production of A. sinensis.
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Affiliation(s)
- Han Dong
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730030, China; (H.D.); (L.J.)
| | - Meiling Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China;
| | - Ling Jin
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730030, China; (H.D.); (L.J.)
| | - Xiaorong Xie
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730030, China; (H.D.); (L.J.)
| | - Mengfei Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China;
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China;
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10
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González-Gordo S, Palma JM, Corpas FJ. Peroxisomal Proteome Mining of Sweet Pepper ( Capsicum annuum L.) Fruit Ripening Through Whole Isobaric Tags for Relative and Absolute Quantitation Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:893376. [PMID: 35615143 PMCID: PMC9125320 DOI: 10.3389/fpls.2022.893376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/21/2022] [Indexed: 05/05/2023]
Abstract
Peroxisomes are ubiquitous organelles from eukaryotic cells characterized by an active nitro-oxidative metabolism. They have a relevant metabolic plasticity depending on the organism, tissue, developmental stage, or physiological/stress/environmental conditions. Our knowledge of peroxisomal metabolism from fruits is very limited but its proteome is even less known. Using sweet pepper (Capsicum annuum L.) fruits at two ripening stages (immature green and ripe red), it was analyzed the proteomic peroxisomal composition by quantitative isobaric tags for relative and absolute quantitation (iTRAQ)-based protein profiling. For this aim, it was accomplished a comparative analysis of the pepper fruit whole proteome obtained by iTRAQ versus the identified peroxisomal protein profile from Arabidopsis thaliana. This allowed identifying 57 peroxisomal proteins. Among these proteins, 49 were located in the peroxisomal matrix, 36 proteins had a peroxisomal targeting signal type 1 (PTS1), 8 had a PTS type 2, 5 lacked this type of peptide signal, and 8 proteins were associated with the membrane of this organelle. Furthermore, 34 proteins showed significant differences during the ripening of the fruits, 19 being overexpressed and 15 repressed. Based on previous biochemical studies using purified peroxisomes from pepper fruits, it could be said that some of the identified peroxisomal proteins were corroborated as part of the pepper fruit antioxidant metabolism (catalase, superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductaseglutathione reductase, 6-phosphogluconate dehydrogenase and NADP-isocitrate dehydrogenase), the β-oxidation pathway (acyl-coenzyme A oxidase, 3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase), while other identified proteins could be considered "new" or "unexpected" in fruit peroxisomes like urate oxidase (UO), sulfite oxidase (SO), 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (METE1), 12-oxophytodienoate reductase 3 (OPR3) or 4-coumarate-CoA ligase (4CL), which participate in different metabolic pathways such as purine, sulfur, L-methionine, jasmonic acid (JA) or phenylpropanoid metabolisms. In summary, the present data provide new insights into the complex metabolic machinery of peroxisomes in fruit and open new windows of research into the peroxisomal functions during fruit ripening.
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11
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Xu Z, Kang A, Shan J, Song M, Xie T. An LC-MS/MS Method for the Pharmacokinetic and in Vitro Metabolism Studies of Praeruptorin A in Rat. CURR PHARM ANAL 2021. [DOI: 10.2174/1573412917666210827103645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Objective:
The study aims to investigate the pharmacokinetic profile of Praeruptorin A and khellactone and in vitro hydrolysis of praeruptorin A to khellactone in different biological samples.
Methods:
A LC-MS/MS method was established. Analytes and internal standard (IS) were isolated using the protein precipitation method and then separated on a Thermo BDS Hypersil C18 (2.1 mm×50 mm, 2.4μm) column using a mobile phase consisting of 0.05% formic acid solution and acetonitrile. Samples were analyzed in positive electrospray-ionization (ESI) mode using multiple reaction monitoring (MRM).
Results:
The calibration plots gave desirable linearity (r2>0.99) in the concentration range from 0.99-990.0 and 2.0-2000.0 ng/mL for Praeruptorin A and khellactone, respectively. In addition, the LOQs of these analytes were sufficient for vivo pharmacokinetic study and vitro hydrolysis study of Praeruptorin A. The intra-batch and inter-batch precision were all within 14.05%, and the accuracy was between 89.39% and 109.50%. The extraction efficiency of PA and khellactone ranged from 76.35 ~ 89.58%. The matrix effects of analytes and the IS were between 89.67% ~ 105.26%.
Conclusion:
The liver CYPs mediated by the metabolism of PA may contribute to the systemic exposure of its active metabolite, khellactone, in rats.
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Affiliation(s)
- Zhuicheng Xu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - An Kang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Mengmeng Song
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Tong Xie
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
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12
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Grigoreva E, Tkachenko A, Arkhimandritova S, Beatovic A, Ulianich P, Volkov V, Karzhaev D, Ben C, Gentzbittel L, Potokina E. Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar ( Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis. Genes (Basel) 2021; 12:genes12070952. [PMID: 34206279 PMCID: PMC8303896 DOI: 10.3390/genes12070952] [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: 04/08/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 01/08/2023] Open
Abstract
Guar (Cyamopsis tetragonoloba (L.) Taub.) is an annual legume crop native to India and Pakistan. Seeds of the plant serve as a source of galactomannan polysaccharide (guar gum) used in the food industry as a stabilizer (E412) and as a gelling agent in oil and gas fracturing fluids. There were several attempts to introduce this crop to countries of more northern latitudes. However, guar is a plant of a short photoperiod, therefore, its introduction, for example, to Russia is complicated by a long day length during the growing season. Breeding of new guar varieties insensitive to photoperiod slowed down due to the lack of information on functional molecular markers, which, in turn, requires information on guar genome. Modern breeding strategies, e.g., genomic predictions, benefit from integration of multi-omics approaches such as transcriptome, proteome and metabolome assays. Here we present an attempt to use transcriptome-metabolome integration to understand the genetic determination of flowering time variation among guar plants that differ in their photoperiod sensitivity. This study was performed on nine early- and six delayed-flowering guar varieties with the goal to find a connection between 63 metabolites and 1,067 differentially expressed transcripts using Shiny GAM approach. For the key biomarker of flowering in guar myo-inositol we also evaluated the KEGG biochemical pathway maps available for Arabidopsis thaliana. We found that the phosphatidylinositol signaling pathway is initiated in guar plants that are ready for flowering through the activation of the phospholipase C (PLC) gene, resulting in an exponential increase in the amount of myo-inositol in its free form observed on GC-MS chromatograms. The signaling pathway is performed by suppression of myo-inositol phosphate kinases (phosphorylation) and alternative overexpression of phosphatases (dephosphorylation). Our study suggests that metabolome and transcriptome information taken together, provide valuable information about biomarkers that can be used as a tool for marker-assisted breeding, metabolomics and functional genomics of this important legume crop.
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Affiliation(s)
- Elizaveta Grigoreva
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia; (E.G.); (A.B.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia; (V.V.); (E.P.)
- Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Alexander Tkachenko
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia; (E.G.); (A.B.)
- Correspondence: ; Tel.: +7-9217634039
| | | | - Aleksandar Beatovic
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia; (E.G.); (A.B.)
| | - Pavel Ulianich
- All-Russian Research Institute of Agricultural Microbiology, 196608 St. Petersburg, Russia;
| | - Vladimir Volkov
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia; (V.V.); (E.P.)
- Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Dmitry Karzhaev
- Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Cécile Ben
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (C.B.); (L.G.)
| | - Laurent Gentzbittel
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (C.B.); (L.G.)
| | - Elena Potokina
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia; (V.V.); (E.P.)
- Sirius University of Science and Technology, 354340 Sochi, Russia;
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13
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Song C, Li X, Jia B, Liu L, Ou J, Han B. De novo Transcriptome Sequencing Coupled With Co-expression Analysis Reveal the Transcriptional Regulation of Key Genes Involved in the Formation of Active Ingredients in Peucedanum praeruptorum Dunn Under Bolting Period. Front Genet 2021; 12:683037. [PMID: 34194480 PMCID: PMC8236723 DOI: 10.3389/fgene.2021.683037] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Peucedanum praeruptorum Dunn is a perennial and one-off flowering plant of the Peucedanum genus in Umbelliferae. The cultivated P. praeruptorum Dunn usually grows nutritionally in the first year and then moves into the reproductive growth in the second year. The lignification of the roots caused by bolting leads to the quality decline of crude materials. Since most of the previous studies have dealt with coumarin biosynthesis and identification of functional genes in P. praeruptorum, the scientific connotation of the inability that the bolted P. praeruptorum cannot be used medically is still unclear. Here, we employed a transcriptome sequencing combined with coexpression analysis to unearth the regulation mechanism of key genes related to coumarin synthesis in pre- and postbolting period, and to explore the mechanisms underlying the effects of bolting on the formation and transport of coumarins between the annual and biennial plants. Six cDNA libraries were constructed, and the transcripts were sequenced and assembled by Illumina Hiseq platform. A total of 336,505 unigenes were obtained from 824,129 non-redundant spliced transcripts. Unigenes (114,488) were annotated to the NCBI nr database, 119,017 and 10,475 unigenes were aligned to Gene Ontology (GO) functional groups and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. Differential expression analysis screened out a series of upregulated and downregulated genes related to the phenylpropanoid pathway. The heatmap clustering showed that the similar expression patterns were both observed in groups C vs. D and groups C vs. F. The WGCNA-based coexpression was performed to elucidate the module and trait relationship to unearth important genes related to the bolting process. Seven pivotal modules on the KEGG functional annotations suggested these genes were mainly enriched in the process of plant–pathogen interaction, plant hormone signal transduction, MAPK signaling pathway, α-linolenic acid metabolism, circadian rhythm, and phenylpropanoid pathway. Further analysis provided clues that the key genes of the phenylpropanoid pathway, the ABC transporters, the apoptosis-related and circadian rhythm regulatory genes may play pivotal roles in regulating bolting signaling, biosynthesis, and transportation of coumarins.
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Affiliation(s)
- Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, China
| | - Xiaoli Li
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, China.,College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Bin Jia
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, China.,College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Li Liu
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, China.,College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Jinmei Ou
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Bangxing Han
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, China.,College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
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14
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Jian X, Zhao Y, Wang Z, Li S, Li L, Luo J, Kong L. Two CYP71AJ enzymes function as psoralen synthase and angelicin synthase in the biosynthesis of furanocoumarins in Peucedanum praeruptorum Dunn. PLANT MOLECULAR BIOLOGY 2020; 104:327-337. [PMID: 32761540 DOI: 10.1007/s11103-020-01045-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Psoralen synthase and angelicin synthase responsible for the formation of psoralen and angelicin in Peucedanum praeruptorum Dunn were identified and functionally characterized, respectively. Furanocoumarins were reported to possess several activities such as anticancer, anti-inflammatory and neuroprotective, and function as phytotoxin and allelochemical in plants. Furanocoumarins are the main bioactive ingredient in P. praeruptorum which is a commonly used traditional Chinese medicine. Phenylalanine ammonia lyase (PAL), 4-coumarate: CoA ligase (4CL), p-coumaroyl CoA 2'-hyfroxylase (C2'H) were cloned previously to elucidate the biosynthetic mechanism of coumarin lactone ring. However, the genes involved in complex coumarins in P. praeruptorum have not been explored. Herein, putative psoralen synthase CYP71AJ49 and angelicin synthase CYP71AJ51 were cloned from P. praeruptorum. In vivo and in vitro yeast assays were conducted to confirm their activities. Furthermore, the results of High Performance Liquid Chromatography-Electrospray Ionization Mass Spectrometry (HPLC-ESI-MS) verified that CYP71AJ49 catalyzed the conversion of marmesin to psoralen, and CYP71AJ51 catalyzed columbianetin to angelicin. Subsequently, the expression profile showed that CYP71AJ49 and CYP71AJ51 were easily affected by environmental conditions, especially UV and temperature. The genes tissue-specific expression and compounds tissue-specific distribution pattern indicated the existence of substance transport in P. praeruptorum. Phylogenetic analysis was conducted with 27 CYP71AJs, CYP71AJ49 and CYP71AJ51 were classified in I-4 and I-2, respectively. These results provide further insight to understand the biosynthetic mechanism of complex coumarins.
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Affiliation(s)
- Xiangyun Jian
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Ziwen Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Shan Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Li Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China.
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15
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Srividya N, Lange I, Hartmann M, Li Q, Mirzaei M, Lange BM. Biochemical characterization of acyl activating enzymes for side chain moieties of Taxol and its analogs. J Biol Chem 2020; 295:4963-4973. [PMID: 32086380 DOI: 10.1074/jbc.ra120.012663] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/14/2020] [Indexed: 12/24/2022] Open
Abstract
Taxol (paclitaxel) is a very widely used anticancer drug, but its commercial sources mainly consist of stripped bark or suspension cultures of members of the plant genus Taxus. Taxol accumulates as part of a complex mixture of chemical analogs, termed taxoids, which complicates its production in pure form, highlighting the need for metabolic engineering approaches for high-level Taxol production in cell cultures or microbial hosts. Here, we report on the characterization of acyl-activating enzymes (AAEs) that catalyze the formation of CoA esters of different organic acids relevant for the N-substitution of the 3-phenylisoserine side chain of taxoids. On the basis of similarities to AAE genes of known function from other organisms, we identified candidate genes in publicly available transcriptome data sets obtained with Taxus × media. We cloned 17 AAE genes, expressed them heterologously in Escherichia coli, purified the corresponding recombinant enzymes, and performed in vitro assays with 27 organic acids as potential substrates. We identified TmAAE1 and TmAAE5 as the most efficient enzymes for the activation of butyric acid (Taxol D side chain), TmAAE13 as the best candidate for generating a CoA ester of tiglic acid (Taxol B side chain), TmAAE3 and TmAAE13 as suitable for the activation of 4-methylbutyric acid (N-debenzoyl-N-(2-methylbutyryl)taxol side chain), TmAAE15 as a highly efficient candidate for hexanoic acid activation (Taxol C side chain), and TmAAE4 as suitable candidate for esterification of benzoic acid with CoA (Taxol side chain). This study lays important groundwork for metabolic engineering efforts aimed at improving Taxol production in cell cultures.
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Affiliation(s)
- Narayanan Srividya
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Iris Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Michael Hartmann
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Qunrui Li
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Maryam Mirzaei
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Bernd Markus Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
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16
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4-Coumarate:coenzyme A ligase isoform 3 from Piper nigrum (Pn4CL3) catalyzes the CoA thioester formation of 3,4-methylenedioxycinnamic and piperic acids. Biochem J 2020; 477:61-74. [DOI: 10.1042/bcj20190527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 12/11/2022]
Abstract
Black pepper, dried green fruit of Piper nigrum L., is a household spice most popular in the world. Piperine, the pungency compound of black pepper, is proposed to partially arise from phenylpropanoid pathway. In the biosynthesis of piperine, 4-coumarate:CoA ligase (4CLs) must play a pivotal role in activating intermediate acids to corresponding CoA thioesters to serve as substrates. Based on transcriptome data, we isolated three P. nigrum 4CL isoforms (Pn4CL1, -2, and -3) from unripe peppercorn. These Pn4CLs were expressed in E. coli for in vitro enzyme assay with putative substrates, namely cinnamic, coumaric, ferulic, piperonylic, 3,4-methylenedioxycinnamic (3,4-MDCA), and piperic acids. Phylogenetic analysis and substrate usage study indicated that Pn4CL1, active towards coumaric and ferulic acids, belongs to class I 4CL for lignin synthesis. Pn4CL2 was a typical cinnamate-specific coumarate:CoA ligase-like (CLL) protein. The Pn4CL3, as class II enzyme, exhibited general 4CL activity towards coumaric and ferulic acids. However, Pn4CL3 was also active towards piperonylic acid, 3,4-MDCA, and piperic acid. Pn4CL3 possessed ∼2.6 times higher catalytic efficiency (kcat/KM) towards 3,4-MDCA and piperic acid than towards coumaric and ferulic acids, suggesting its specific role in piperine biosynthesis. Different substrate preference among the Pn4CL isoforms can be explained by 3-dimensional protein structure modeling, which demonstrated natural variants in amino acid residues of binding pocket to accommodate different substrates. Quantitative PCR analysis of these isoforms indicated that Pn4CL1 transcript level was highest in the roots whereas Pn4CL2 in the fruits and Pn4CL3 in the leaves.
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17
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Zhao Y, Jian X, Wu J, Huang W, Huang C, Luo J, Kong L. Elucidation of the biosynthesis pathway and heterologous construction of a sustainable route for producing umbelliferone. J Biol Eng 2019; 13:44. [PMID: 31139252 PMCID: PMC6530170 DOI: 10.1186/s13036-019-0174-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/30/2019] [Indexed: 11/10/2022] Open
Abstract
Background Coumarins play roles in many biological processes. Angelica decursiva is one of the major sources of coumarins in China. Due to increasing demand for coumarins in the marketplace, traditional extraction from plants is now considered economically insufficient and unsustainable. Microbial synthesis is a promising strategy for scalable production of coumarins. However, the biosynthetic pathway of coumarin remains poorly understood, and even more, the genes associated with this process have not been characterized in A. decursiva. Results RNA-seq was employed to elucidate the umbelliferone biosynthetic pathway. The results indicated that three enzymes, phenylalanine ammonia-lyase (PAL), 4-Coumarate: Coenzyme A Ligase (4CL), and p-coumaroyl CoA 2'-hydroxylase (C2'H) were involved in umbelliferone biosynthesis. Using the cloned genes, we generated a synthetic biology based microbial cell factory that produces coumarins from tyrosine utilizing Rhodotorula glutinis tyrosine ammonia lyase (RgTAL) to bypass cinnamic acid 4-hydroxylase (C4H). With metabolic engineering strategies, we deleted prephenate dehydratase (pheA), anthranilate synthase (trpE) and transcriptional regulatory protein (tyrR) and overexpressed six related genes involved in tyrosine biosynthesis, to drive the carbon flux from tyrosine. To overcome the limitation of 4CL, a virtual screening and site-specific mutagenesis-based protein engineering approach was applied. In addition, induction/culture conditions and different ions were employed to further improve the yield of umbelliferone. Finally, a yield of 356.59 mg/L umbelliferone was obtained. Conclusions The current study elucidated the umbelliferone biosynthesis pathway in A. decursiva. The results also demonstrated the feasibility of integrating gene mining with synthetic biology techniques to produce natural compounds.
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Affiliation(s)
- Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009 People's Republic of China
| | - Xiangyun Jian
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009 People's Republic of China
| | - Jialin Wu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009 People's Republic of China
| | - Wanchun Huang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009 People's Republic of China
| | - Chuanlong Huang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009 People's Republic of China
| | - Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009 People's Republic of China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009 People's Republic of China
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Xiong W, Wu Z, Liu Y, Li Y, Su K, Bai Z, Guo S, Hu Z, Zhang Z, Bao Y, Sun J, Yang G, Fu C. Mutation of 4-coumarate: coenzyme A ligase 1 gene affects lignin biosynthesis and increases the cell wall digestibility in maize brown midrib5 mutants. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:82. [PMID: 31007716 PMCID: PMC6456989 DOI: 10.1186/s13068-019-1421-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/29/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Maize brown midrib (bm) mutants associated with impaired lignin biosynthesis are a potential source for the breed of novel germplasms with improved cell wall digestibility. The spontaneous bm5 mutants had been identified since 2008. However, the gene responsible for the bm5 locus, and the comprehensive effects of bm5 mutation on lignin biosynthesis, soluble phenolics accumulation, and cell wall degradation have yet to be elucidated. RESULTS The bm5 locus was identified to encode a major 4-coumarate: coenzyme A ligase (Zm4CL1) through analyzing MutMap-assisted gene mapping data. Two alleles of Zm4CL1 isolated from bm5 mutants contained two transposons inserted in the first exon and the second intron, respectively, and consequently, the activities of 4CLs in the crude enzyme extracts from bm5 midribs were reduced by 51-62% compared with the wild type. Furthermore, five 4CLs were retrieved from maize genome, and Zm4CL1 was the most highly expressed one in the lignified tissues. Mutation of Zm4CL1 mainly impeded the biosynthesis of guaiacyl (G) lignins and increased the level of soluble feruloyl derivatives without impacting maize growth and development. Moreover, both neutral detergent fiber digestibility and saccharification efficiency of cell walls were significantly elevated in the bm5 mutant. CONCLUSIONS Zm4CL1 was identified as the Bm5 gene, since two independent alleles of Zm4CL1 were associated with the same mutant phenotype. Mutation of Zm4CL1 mainly affected G lignin biosynthesis and soluble feruloyl derivatives accumulation in maize lignified tissues. The reduced recalcitrance of the bm5 mutant suggests that Zm4CL1 is an elite target for cell wall engineering, and genetic manipulation of this gene will facilitate the utilization of crop straw and stover that have to be dealt with for environmental protection.
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Affiliation(s)
- Wangdan Xiong
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Zhenying Wu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Yuchen Liu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Yu Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Kunlong Su
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Zetao Bai
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Siyi Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, 475001 China
| | - Zhubing Hu
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, 475001 China
| | - Zhiming Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yan Bao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Juan Sun
- School of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- School of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
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Liu XY, Wang PP, Wu YF, Cheng AX, Lou HX. Cloning and Functional Characterization of Two 4-Coumarate: CoA Ligase Genes from Selaginella moellendorffii. Molecules 2018; 23:E595. [PMID: 29518887 PMCID: PMC6017068 DOI: 10.3390/molecules23030595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/15/2023] Open
Abstract
Selaginella is an extant lycopodiophyte genus, which is representative of an ancient lineage of tracheophytes. The important evolutionary status makes it a valuable resource for the study of metabolic evolution in vascular plants. 4-coumarate: CoA ligase (4CL) is the pivotal enzyme that controls the flow of carbon through the phenylpropanoid metabolic pathway into the specific lignin, flavonoid, and wall-bound phenolics biosynthesis pathways. Although 4CLs have been extensively characterized in other vascular plants, little is known of their functions in Selaginella. Here, we isolated two 4CL genes (Sm4CL1 and Sm4CL2) from Selaginella moellendorffii. Based on the enzymatic activities of the recombinant proteins, both of these genes encoded bona fide 4CLs. The 4CL isoforms in S. moellendorffii have different activities: Sm4CL2 was more active than Sm4CL1. The enzymatic properties and gene expression patterns indicated that the 4CL genes have been conserved in the evolution of vascular plants.
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Affiliation(s)
- Xin-Yan Liu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
| | - Ping-Ping Wang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
| | - Yi-Feng Wu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
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20
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Yao R, Zhao Y, Liu T, Huang C, Xu S, Sui Z, Luo J, Kong L. Identification and functional characterization of a p-coumaroyl CoA 2'-hydroxylase involved in the biosynthesis of coumarin skeleton from Peucedanum praeruptorum Dunn. PLANT MOLECULAR BIOLOGY 2017; 95:199-213. [PMID: 28822035 DOI: 10.1007/s11103-017-0650-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
A p-coumaroyl CoA 2'-hydroxylase responsible for the formation of coumarin lactone ring was identified from Peucedanum praeruptorum Dunn and functionally characterized in vitro. Coumarins are important plant secondary metabolites with a variety of biological activities. Ortho-hydroxylation of cinnamates leads to the formation of coumarin lactone ring and is generally thought to be a key step in coumarin biosynthesis. However, ortho-hydroxylases, especially p-coumaroyl CoA 2'-hydroxylase (C2'H) responsible for the biosynthesis of the most common coumarin skeleton, have received insufficient attention. Here, a putative ortho-hydroxylase PpC2'H was isolated from P. praeruptorum Dunn, a traditional Chinese medicinal herb rich in coumarins. Expression profile indicated that PpC2'H exhibited the highest transcript level in roots and could be up-regulated by MeJA elicitation. Subcellular localization of PpC2'H was demonstrated to be cytosol in planta. In order to functionally characterize PpC2'H, the purified recombinant protein was incubated with various potential substrates. HPLC-ESI-MS analysis indicated that PpC2'H catalyzed the conversion of p-coumaroyl CoA into hydroxylated intermediate, which then underwent spontaneous lactonization to generate umbelliferone. Our data also showed that light would promote the spontaneous process. In addition, based on homology modeling and site-directed mutagenesis, amino acid residues Phe-130, Lys-141, Asn-207, His-224, Asp-226, His-282 and Phe-298 were verified essential for enzymatic activity. These findings provide insight into structure-function relationship of this pivotal ortho-hydroxylase and also contribute to elucidating the biosynthetic mechanism of coumarin skeleton.
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MESH Headings
- Amino Acid Sequence
- Apiaceae/enzymology
- Biosynthetic Pathways/genetics
- Chromatography, High Pressure Liquid
- Coumarins/chemistry
- Coumarins/metabolism
- DNA, Complementary/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Plant/drug effects
- Gene Expression Regulation, Plant/radiation effects
- Kinetics
- Light
- Mixed Function Oxygenases/chemistry
- Mixed Function Oxygenases/metabolism
- Models, Molecular
- Mutagenesis, Site-Directed
- Organ Specificity/genetics
- Organ Specificity/radiation effects
- Phylogeny
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Protoplasts/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Alignment
- Spectrometry, Mass, Electrospray Ionization
- Structural Homology, Protein
- Subcellular Fractions/enzymology
- Transcriptome/genetics
- Transcriptome/radiation effects
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Affiliation(s)
- Ruolan Yao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| | - Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| | - Tingting Liu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| | - Chuanlong Huang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| | - Sheng Xu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, People's Republic of China
| | - Ziwei Sui
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| | - Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China.
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China.
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21
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Luo K, Wu F, Zhang D, Dong R, Fan Z, Zhang R, Yan Z, Wang Y, Zhang J. Transcriptomic profiling of Melilotus albus near-isogenic lines contrasting for coumarin content. Sci Rep 2017; 7:4577. [PMID: 28676637 PMCID: PMC5496894 DOI: 10.1038/s41598-017-04111-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/09/2017] [Indexed: 12/30/2022] Open
Abstract
Coumarin and its derivatives are widely used as fragrances in industrial products and have medical value. The goal of the present study was to discover genes and pathways related to coumarin biosynthesis in Melilotus albus using transcriptome analysis. The genes of five M. albus near-isogenic lines (NILs) that had different coumarin content and β-glucosidase activity according to the investigation of pedigree were quantified and then analysed by RNA-Seq. Using transcriptome analysis, differentially expressed genes (DEGs) were identified in two pairwise comparisons that differed in coumarin content as well as in two pairwise comparisons that differed in β-glucosidase activity. Gene expression pattern analysis suggested similar transcriptional trends in the genotypes with the same coumarin levels. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database of DEGs was used to identify functional pathways associated with coumarin biosynthesis. We identified 111 unigenes, with several DEGs among them possibly being related to coumarin synthesis pathways. Unigenes encoding a hexokinase, an abscisic acid receptor, a phenylalanine ammonia-lyase (PAL) and two peroxidases particularly showed correspondence with the coumarin content of different genotypes. These results will contribute to a better understanding of the coumarin biosynthesis in M. albus.
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Affiliation(s)
- Kai Luo
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Fan Wu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Daiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Rui Dong
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhichao Fan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Rui Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhuanzhuan Yan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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