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Wang W, Guo Y, Xu J, Zhang H, Ma Z, Wu H. Isolation of anthraquinone derivatives from Rubia cordifolia (Rubiaceae) and their bioactivities against plant pathogenic microorganisms. PEST MANAGEMENT SCIENCE 2024; 80:4617-4627. [PMID: 38747671 DOI: 10.1002/ps.8177] [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: 02/23/2024] [Revised: 04/10/2024] [Accepted: 05/02/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND The discovery of antimicrobial ingredients from natural products could be an effective way to create novel fungicides. Rubia cordifolia L., a traditional Chinese herb, may have antimicrobial effects on plant pathogens according to our previous screening study. RESULTS Rubia cordifolia L. extracts had moderate inhibitory effects on apple Valsa canker (Valsa mali) and tomato grey mould (Botrytis cinerea) at a concentration of 10 mg mL-1. With the use of bioguided isolation methods, eight compounds (1-8) were obtained, including the new compound 2,2,6-trimethyl-6-(4-methylphenyl)-tetrahydropyrano- 3-ol (7), and seven quinone derivatives. Two compounds, mollugin (1) and 1,3,6-trihydroxy-2-methylanthraquinone (6), were found to exhibit outstanding antifungal activities against V. mali and Phytophthora capsici Leon. The half maximal effective concentration (EC50) of compound 1 and compound 6 against V. mali were 79.08 and 81.78 μg mL-1, respectively, and the EC50 of compound 6 against P. capsici was 4.86 μg mL-1. Compound 1 also showed excellent activity against tobacco mosaic virus (TMV). The inactive, inductive, protective and curative activities against TMV were 84.29%, 83.38%, 86.81%, and 60.02%, respectively, at a concentration of 500 μg mL-1, which were all close to or greater than that of the positive control (100 μg mL-1 chitosan oligosaccharide, COS). CONCLUSION Mollugin and 1,3,6-trihydroxy-2-methylanthraquinone are potentially valuable active compounds that lay a foundation for research on botanical fungicide products derived from R. cordifolia L. and provide lead structures for quinone derivative synthesis and structural modification. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Wenhao Wang
- College of Plant Protection, Northwest A&F University, Yangling, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Yangling, China
| | - Yifei Guo
- College of Plant Protection, Northwest A&F University, Yangling, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Yangling, China
| | - Jialu Xu
- College of Plant Protection, Northwest A&F University, Yangling, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Yangling, China
| | - Hao Zhang
- College of Plant Protection, Northwest A&F University, Yangling, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Yangling, China
| | - Zhiqing Ma
- College of Plant Protection, Northwest A&F University, Yangling, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Yangling, China
| | - Hua Wu
- College of Plant Protection, Northwest A&F University, Yangling, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Yangling, China
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Yang L, Sun J, Zhang T, Chu D, Zhou T, Wang X. Comparative transcriptome analysis and HPLC reveal candidate genes associated with synthesis of bioactive constituents in Rheum palmatum complex. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1239-1252. [PMID: 39184557 PMCID: PMC11341509 DOI: 10.1007/s12298-024-01492-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/06/2024] [Accepted: 07/15/2024] [Indexed: 08/27/2024]
Abstract
Content of bioactive constituents is one of the most important characteristics in Rheum palmatum complex. Increasing ingredient content through genetic breeding is an effective strategy to solve the contradiction between large market demand and resource depletion, but currently hampered by limited understanding of metabolite biosynthesis in rhubarb. In this study, deep transcriptome sequencing was performed to compare roots, stems, and leaves of two Rheum species (PL and ZK) that show different levels of anthraquinone contents. Approximately 0.52 billion clean reads were assembled into 58,782 unigenes, of which around 80% (46,550) were found to be functionally annotated in public databases. Expression patterns of differential unigenes between PL and ZK were thoroughly investigated in different tissues. This led to the identification of various differentially expressed genes (DEGs) involved in shikimate, MEP, MVA, and polyketide pathways, as well as those involved in catechin and gallic acid biosynthesis. Some structural enzyme genes were shown to be significantly up-regulated in roots of ZK with high anthraquinone content, implying potential central roles in anthraquinone synthesis. Taken together, our study provides insights for future functional studies to unravel the mechanisms underlying metabolite biosynthesis in rhubarb. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01492-z.
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Affiliation(s)
- Li Yang
- Department of Gastroenterology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 China
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Jiangyan Sun
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Tianyi Zhang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Dake Chu
- Department of Gastroenterology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 China
| | - Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
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Xiao F, Zhao Y, Wang X, Jian X, Zhou H. Analysis of differential mRNA and miRNA expression induced by heterogeneous grafting in Gleditsia sinensis. Int J Biol Macromol 2024; 270:132235. [PMID: 38734341 DOI: 10.1016/j.ijbiomac.2024.132235] [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: 04/01/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Gleditsia sinensis Lam. is a multifaceted plant with medicinal, edible, chemical, timber, and ornamental applications. However, the effect of rootstocks on scions after grafting is still unclear. This study examined the mRNA and miRNA transcriptome among homografts, heterografts, and seedlings. GO enrichment analysis between seedlings and homograft/heterograft combinations revealed that biosynthesis, degradation, and transport were enriched. The KEGG enrichment results showed that plant hormone signal transduction and the plant MAPK signaling pathway were enriched in both seedlings and heterograft combinations. Through weighted correlation network analysis (WGCNA), the hub genes related to the content of plant hormones were obtained. Taking G. sinensis as the scion, there were 4594, 2887, 3429, and 5959 mRNAs that were specifically expressed in the grafted plants of G. sinensis/G. fera, G. sinensis/G. delavayi, G. sinensis/G. microphylla, and G. sinensis/G. japonica, respectively. The specifically expressed mRNA genes may participate in such processes and pathways as the rhythmic process, circadian rhythm, gibberellic-acid-mediated signaling pathway, and peptide-based amino acid modification. Additionally, 3, 16, 2, and 15 specifically expressed miRNAs were identified. This study examines the impact of grafting on gene expression in Gleditsia plants and establishes a foundation for the development of new resources and rootstock breeding.
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Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China.
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China
| | - Xueyan Jian
- College of Continuing Education, Yanbian University, Yanji 133002, Jilin, China
| | - Heying Zhou
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China
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Chen R, Meng S, Wang A, Jiang F, Yuan L, Lei L, Wang H, Fan W. The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis. PLANT COMMUNICATIONS 2024:100944. [PMID: 38733080 DOI: 10.1016/j.xplc.2024.100944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
The Caesalpinioideae subfamily contains many well-known trees that are important for economic sustainability and human health, but a lack of genomic resources has hindered their breeding and utilization. Here, we present chromosome-level reference genomes for the two food and industrial trees Gleditsia sinensis (921 Mb) and Biancaea sappan (872 Mb), the three shade and ornamental trees Albizia julibrissin (705 Mb), Delonix regia (580 Mb), and Acacia confusa (566 Mb), and the two pioneer and hedgerow trees Leucaena leucocephala (1338 Mb) and Mimosa bimucronata (641 Mb). Phylogenetic inference shows that the mimosoid clade has a much higher evolutionary rate than the other clades of Caesalpinioideae. Macrosynteny comparison suggests that the fusion and breakage of an unstable chromosome are responsible for the difference in basic chromosome number (13 or 14) for Caesalpinioideae. After an ancient whole-genome duplication (WGD) shared by all Caesalpinioideae species (CWGD, ∼72.0 million years ago [MYA]), there were two recent successive WGD events, LWGD-1 (16.2-19.5 MYA) and LWGD-2 (7.1-9.5 MYA), in L. leucocephala. Thereafter, ∼40% gene loss and genome-size contraction have occurred during the diploidization process in L. leucocephala. To investigate secondary metabolites, we identified all gene copies involved in mimosine metabolism in these species and found that the abundance of mimosine biosynthesis genes in L. leucocephala largely explains its high mimosine production. We also identified the set of all potential genes involved in triterpenoid saponin biosynthesis in G. sinensis, which is more complete than that based on previous transcriptome-derived unigenes. Our results and genomic resources will facilitate biological studies of Caesalpinioideae and promote the utilization of valuable secondary metabolites.
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Affiliation(s)
- Rong Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Sihan Meng
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Lihua Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Lihong Lei
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
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Ushasree MV, Jia Q, Do SG, Lee EY. New opportunities and perspectives on biosynthesis and bioactivities of secondary metabolites from Aloe vera. Biotechnol Adv 2024; 72:108325. [PMID: 38395206 DOI: 10.1016/j.biotechadv.2024.108325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/10/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Historically, the genus Aloe has been an indispensable part of both traditional and modern medicine. Decades of intensive research have unveiled the major bioactive secondary metabolites of this plant. Recent pandemic outbreaks have revitalized curiosity in aloe metabolites, as they have proven pharmacokinetic profiles and repurposable chemical space. However, the structural complexity of these metabolites has hindered scientific advances in the chemical synthesis of these compounds. Multi-omics research interventions have transformed aloe research by providing insights into the biosynthesis of many of these compounds, for example, aloesone, aloenin, noreugenin, aloin, saponins, and carotenoids. Here, we summarize the biological activities of major aloe secondary metabolites with a focus on their mechanism of action. We also highlight the recent advances in decoding the aloe metabolite biosynthetic pathways and enzymatic machinery linked with these pathways. Proof-of-concept studies on in vitro, whole-cell, and microbial synthesis of aloe compounds have also been briefed. Research initiatives on the structural modification of various aloe metabolites to expand their chemical space and activity are detailed. Further, the technological limitations, patent status, and prospects of aloe secondary metabolites in biomedicine have been discussed.
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Affiliation(s)
- Mrudulakumari Vasudevan Ushasree
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Qi Jia
- Unigen, Inc., 2121 South street suite 400 Tacoma, Washington 98405, USA
| | - Seon Gil Do
- Naturetech, Inc., 29-8, Yongjeong-gil, Chopyeong-myeon, Jincheon-gun, Chungcheongbuk-do 27858, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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Zhang T, Zhou L, Pu Y, Tang Y, Liu J, Yang L, Zhou T, Feng L, Wang X. A chromosome-level genome reveals genome evolution and molecular basis of anthraquinone biosynthesis in Rheum palmatum. BMC PLANT BIOLOGY 2024; 24:261. [PMID: 38594606 PMCID: PMC11005207 DOI: 10.1186/s12870-024-04972-2] [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: 02/27/2024] [Accepted: 04/01/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Rhubarb is one of common traditional Chinese medicine with a diverse array of therapeutic efficacies. Despite its widespread use, molecular research into rhubarb remains limited, constraining our comprehension of the geoherbalism. RESULTS We assembled the genome of Rheum palmatum L., one of the source plants of rhubarb, to elucidate its genome evolution and unpack the biosynthetic pathways of its bioactive compounds using a combination of PacBio HiFi, Oxford Nanopore, Illumina, and Hi-C scaffolding approaches. Around 2.8 Gb genome was obtained after assembly with more than 99.9% sequences anchored to 11 pseudochromosomes (scaffold N50 = 259.19 Mb). Transposable elements (TE) with a continuous expansion of long terminal repeat retrotransposons (LTRs) is predominant in genome size, contributing to the genome expansion of R. palmatum. Totally 30,480 genes were predicted to be protein-coding genes with 473 significantly expanded gene families enriched in diverse pathways associated with high-altitude adaptation for this species. Two successive rounds of whole genome duplication event (WGD) shared by Fagopyrum tataricum and R. palmatum were confirmed. We also identified 54 genes involved in anthraquinone biosynthesis and other 97 genes entangled in flavonoid biosynthesis. Notably, RpALS emerged as a compelling candidate gene for the octaketide biosynthesis after the key residual screening. CONCLUSION Overall, our findings offer not only an enhanced understanding of this remarkable medicinal plant but also pave the way for future innovations in its genetic breeding, molecular design, and functional genomic studies.
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Affiliation(s)
- Tianyi Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lipan Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yang Pu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yadi Tang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jie Liu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Yang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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Lu Y, Chen X, Yu H, Zhang C, Xue Y, Zhang Q, Wang H. Haplotype-resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:488-505. [PMID: 38173092 DOI: 10.1111/tpj.16620] [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: 06/16/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Phanera championii is a medicinal liana plant that has successfully adapted to hostile karst habitats. Despite extensive research on its medicinal components and pharmacological effects, the molecular mechanisms underlying the biosynthesis of critical flavonoids and its adaptation to karst habitats remain elusive. In this study, we performed high-coverage PacBio and Hi-C sequencing of P. championii, which revealed its high heterozygosity and phased the genome into two haplotypes: Hap1 (384.60 Mb) and Hap2 (383.70 Mb), encompassing a total of 58 612 annotated genes. Comparative genomes analysis revealed that P. championii experienced two whole-genome duplications (WGDs), with approximately 59.59% of genes originating from WGD events, thereby providing a valuable genetic resource for P. championii. Moreover, we identified a total of 112 genes that were strongly positively selected. Additionally, about 81.60 Mb of structural variations between the two haplotypes. The allele-specific expression patterns suggested that the dominant effect of P. championii was the elimination of deleterious mutations and the promotion of beneficial mutations to enhance fitness. Moreover, our transcriptome and metabolome analysis revealed alleles in different tissues or different haplotypes collectively regulate the synthesis of flavonoid metabolites. In summary, our comprehensive study highlights the significance of genomic and morphological adaptation in the successful adaptation of P. championii to karst habitats. The high-quality phased genomes obtained in this study serve as invaluable genomic resources for various applications, including germplasm conservation, breeding, evolutionary studies, and elucidation of pathways governing key biological traits of P. championii.
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Affiliation(s)
- Yongbin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China
| | - Xiao Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Chao Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Yajie Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China
| | - Haifeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
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Wei ZF, Li LL, Sun DD, Liu XY, Zhou X, Ma FY, Zhao M, Chen XD, Zhang LJ. Biotransformation of Bioactive Metabolites in Cassiae Semen by Endogenous Enzymes and Probiotics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5293-5306. [PMID: 38441033 DOI: 10.1021/acs.jafc.3c06864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
The present study evaluated the potential of endogenous enzymes and probiotics in transforming bioactive metabolites to reduce the purgative effect and improve the functional activity of Cassiae Semen and verified and revealed the biotransformation effect of endogenous enzymes. Although probiotics, especially Lactobacillus rhamnosus, exerted the transformation effect, the endogenous enzymes proved to be more effective in transforming the components of Cassiae Semen. After biotransformation by endogenous enzymes for 12 h, the levels of six anthraquinones in Cassiae Semen increased by at least 2.98-fold, and free anthraquinones, total phenolics, and antioxidant activity also showed significant improvement, accompanied by an 82.2% reduction in combined anthraquinones responsible for the purgative effect of Cassiae Semen. Further metabolomic analysis revealed that the biotransformation effect of endogenous enzymes on the bioactive metabolites of Cassiae Semen was complex and diverse, and the biotransformation of quinones and flavonoids was particularly prominent and occurred by three primary mechanisms, hydrolyzation, methylation, and dimerization, might under the action of glycosyl hydrolases, SAM-dependent methyltransferases, and CYP450s. Accordingly, biotransformation by endogenous enzymes emerges as a mild, economical, food safety risk-free, and effective strategy to modify Cassiae Semen into an excellent functional food.
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Affiliation(s)
- Zuo-Fu Wei
- School of Life Science, Shanxi Normal University, Taiyuan 030006, China
| | - Ling-Ling Li
- School of Life Science, Shanxi Normal University, Taiyuan 030006, China
| | - Dan-Dan Sun
- School of Theater and Film and Television, Shanxi Normal University, Taiyuan 030006, China
| | - Xin-Yu Liu
- School of Life Science, Shanxi Normal University, Taiyuan 030006, China
| | - Xueyong Zhou
- School of Life Science, Shanxi Normal University, Taiyuan 030006, China
| | - Fei-Yue Ma
- National Oat Improvement Center, Baicheng Academy of Agricultural Sciences, Baicheng 137000, China
| | - Meng Zhao
- School of Life Science, Shanxi Normal University, Taiyuan 030006, China
| | - Xiao-Dan Chen
- School of Life Science, Shanxi Normal University, Taiyuan 030006, China
| | - Lin-Jing Zhang
- School of Life Science, Shanxi Normal University, Taiyuan 030006, China
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Zhou T, Tang Y, Zhou L, Liu J, Pu Y, Jiang F, Wang J, Wang X. Transcriptomic divergence of the Rheum palmatum complex derived from top-geoherb and non-geoherb areas provides the insights into geoherbalism properties of rhubarb. BMC Genomics 2024; 25:212. [PMID: 38408895 PMCID: PMC10898026 DOI: 10.1186/s12864-024-10142-3] [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: 09/25/2023] [Accepted: 02/19/2024] [Indexed: 02/28/2024] Open
Abstract
Geoherb usually represents high-quality medicinal herbs with better clinical therapeutic effects, and elucidating the geoherbalism is essential for the quality improvement of traditional Chinese Medicine. However, few researches were conducted to clarify the geoherbalism based on a large scale of transcriptomics. In the present study, we compared the transcriptomes of Rheum palmatum complex derived from top-geoherb and non-geoherb areas to show the geoherbalism properties of rhubarb. A total of 412.32 Gb clean reads were obtained with unigene numbers of 100,615 after assembly. Based on the obtained transcriptome datasets, key enzyme-encoding genes involved in the anthraquinones biosynthesis were also obtained. We also found that 21 anthraquinone-related unigenes were differentially expressed between two different groups, and some of these DEGs were correlated to the content accumulation of five free anthraquinones, indicating that the gene expression profiles may promote the geoherbalism formation of rhubarb. In addition, the selective pressure analyses indicated that most paired orthologous genes between these two groups were subject to negative selection, and only a low proportion of orthologs under positive selection were detected. Functional annotation analyses indicated that these positive-selected genes related to the functions such as gene expression, substance transport, stress response and metabolism, indicating that discrepant environment also enhanced the formation of geoherbalism. Our study not only provided insights for the genetic mechanism of geoherbalism of rhubarb, but also laid more genetic cues for the future rhubarb germplasms improvement and utilization.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Yadi Tang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lipan Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jie Liu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yang Pu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Fan Jiang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jian Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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Zhao X, Yan F, Li YM, Tang J, Hu XC, Feng Z, Gao J, Peng L, Zhang G. Comparative transcriptome analysis and identification of candidate R2R3-MYB genes involved in anthraquinone biosynthesis in Rheum palmatum L. Chin Med 2024; 19:23. [PMID: 38317158 PMCID: PMC10845799 DOI: 10.1186/s13020-024-00891-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/21/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Rheum palmatum L. has important medicinal value because it contains biologically active anthraquinones. However, the key genes and TFs involved in anthraquinone biosynthesis and regulation in R. palmatum remain unclear. METHODS Based on full length transcriptome data, in this study, we screened the differentially expressed genes in the anthraquinone biosynthesis pathway. The R2R3-MYB family genes of R. palmatum were systematically identified based on full-length transcriptome sequencing followed by bioinformatics analyses. The correlation analysis was carried out by using co-expression analysis, protein interaction analysis, and real-time fluorescence quantitative analysis after MeJA treatment. The RpMYB81 and RpMYB98 genes were amplified by RT-PCR, and their subcellular localization and self-activation characteristics were analyzed. RESULTS Comparative transcriptome analysis results revealed a total of 3525 upregulated and 6043 downregulated DEGs in the CK versus MeJA group; 28 DEGs were involved in the anthraquinone pathway. Eleven CHS genes that belonged to the PKS family were differentially expressed and involved in anthraquinone biosynthesis. Twelve differentially expressed MYBs genes were found to be co-expressed and interact with CHS genes. Furthermore, 52 MYB genes were identified as positive regulators of anthraquinone biosynthesis and were further characterized. Three MYB genes including RpMYB81, RpMYB98, and RpMYB100 responded to MeJA treatment in R. palmatum, and the levels of these genes were verified by qRT-PCR. RpMYB81 was related to anthraquinone biosynthesis. RpMYB98 had an interaction with genes in the anthraquinone biosynthesis pathway. RpMYB81 and RpMYB98 were mainly localized in the nucleus. RpMYB81 had self-activation activity, while RpMYB98 had no self-activation activity. CONCLUSION RpMYB81, RpMYB98, and RpMYB100 were significantly induced by MeJA treatment. RpMYB81 and RpMYB98 are located in the nucleus, and RpMYB81 has transcriptional activity, suggesting that it might be involved in the transcriptional regulation of anthraquinone biosynthesis in R. palmatum.
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Affiliation(s)
- Xia Zhao
- Key Laboratory for Research and Development of "Qin Medicine" of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
- College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
| | - Feng Yan
- Key Laboratory for Research and Development of "Qin Medicine" of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
- College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
| | - Yi-Min Li
- Key Laboratory for Research and Development of "Qin Medicine" of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China.
- College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China.
| | - Jing Tang
- Key Laboratory for Research and Development of "Qin Medicine" of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
- College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
| | - Xiao-Chen Hu
- Key Laboratory for Research and Development of "Qin Medicine" of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
- College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
| | - Zhao Feng
- Key Laboratory for Research and Development of "Qin Medicine" of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
| | - Jing Gao
- Key Laboratory for Research and Development of "Qin Medicine" of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
- College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
| | - Liang Peng
- Key Laboratory for Research and Development of "Qin Medicine" of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
- College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China
| | - Gang Zhang
- Key Laboratory for Research and Development of "Qin Medicine" of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China.
- College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xianyang, 712046, China.
- State Key Laboratory of Research and Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi University of Chinese Medicine, Xianyang, 712083, China.
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Zhang H, He Q, Xing L, Wang R, Wang Y, Liu Y, Zhou Q, Li X, Jia Z, Liu Z, Miao Y, Lin T, Li W, Du H. The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones. PLANT COMMUNICATIONS 2024; 5:100677. [PMID: 37634079 PMCID: PMC10811376 DOI: 10.1016/j.xplc.2023.100677] [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: 04/23/2023] [Revised: 06/05/2023] [Accepted: 08/24/2023] [Indexed: 08/28/2023]
Abstract
Rheum officinale, a member of the Polygonaceae family, is an important medicinal plant that is widely used in traditional Chinese medicine. Here, we report a 7.68-Gb chromosome-scale assembly of R. officinale with a contig N50 of 3.47 Mb, which was clustered into 44 chromosomes across four homologous groups. Comparative genomics analysis revealed that transposable elements have made a significant contribution to its genome evolution, gene copy number variation, and gene regulation and expression, particularly of genes involved in metabolite biosynthesis, stress resistance, and root development. We placed the recent autotetraploidization of R. officinale at ∼0.58 mya and analyzed the genomic features of its homologous chromosomes. Although no dominant monoploid genomes were observed at the overall expression level, numerous allele-differentially-expressed genes were identified, mainly with different transposable element insertions in their regulatory regions, suggesting that they functionally diverged after polyploidization. Combining genomics, transcriptomics, and metabolomics, we explored the contributions of gene family amplification and tetraploidization to the abundant anthraquinone production of R. officinale, as well as gene expression patterns and differences in anthraquinone content among tissues. Our report offers unprecedented genomic resources for fundamental research on the autopolyploid herb R. officinale and guidance for polyploid breeding of herbs.
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Affiliation(s)
- Hongyu Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Qiang He
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Longsheng Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Ruyu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yu Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Qinghong Zhou
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Xuanzhao Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Zheng Jia
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Ze Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yuqing Miao
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Tao Lin
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China.
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12
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Nguyen TH, Kang BY, Kim HH. Chromosomal dynamics in Senna: comparative PLOP-FISH analysis of tandem repeats and flow cytometric nuclear genome size estimations. FRONTIERS IN PLANT SCIENCE 2023; 14:1288220. [PMID: 38173930 PMCID: PMC10762312 DOI: 10.3389/fpls.2023.1288220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024]
Abstract
Introduction Tandem repeats (TRs) occur abundantly in plant genomes. They play essential roles that affect genome organization and evolution by inducing or generating chromosomal rearrangements such as duplications, deletions, inversions, and translocations. These impact gene expression and chromosome structure and even contribute to the emergence of new species. Method We investigated the effects of TRs on speciation in Senna genus by performing a comparative analysis using fluorescence in situ hybridization (FISH) with S. tora-specific TR probes. We examined the chromosomal distribution of these TRs and compared the genome sizes of seven Senna species (estimated using flow cytometry) to better understand their evolutionary relationships. Results Two (StoTR03_159 and StoTR04_55) of the nine studied TRs were not detected in any of the seven Senna species, whereas the remaining seven were found in all or some species with patterns that were similar to or contrasted with those of S. tora. Of these studies species, only S. angulata showed significant genome rearrangements and dysploid karyotypes resembling those of S. tora. The genome sizes varied among these species and did not positively correlate with chromosome number. Notably, S. angulata had the fewest chromosomes (2n = 22) but a relatively large genome size. Discussion These findings reveal the dynamics of TRs and provide a cytogenetic depiction of chromosomal rearrangements during speciation in Senna. To further elucidate the dynamics of repeat sequences in Senna, future studies must include related species and extensive repeatomic studies, including those on transposable elements.
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Affiliation(s)
| | | | - Hyun Hee Kim
- Chromosome Research Institute, Department of Chemistry & Life Science, Sahmyook University, Seoul, Republic of Korea
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13
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Xiao F, Zhao Y, Wang X, Jian X. Full-length transcriptome characterization and comparative analysis of Gleditsia sinensis. BMC Genomics 2023; 24:757. [PMID: 38066414 PMCID: PMC10709882 DOI: 10.1186/s12864-023-09843-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
As an economically important tree, Gleditsia sinensis Lam. is widely planted. A lack of background genetic information on G. sinensis hinders molecular breeding. Based on PacBio single-molecule real-time (SMRT) sequencing and analysis of G. sinensis, a total of 95,183 non-redundant transcript sequences were obtained, of which 93,668 contained complete open reading frames (ORFs), 2,858 were long non-coding RNAs (LncRNAs) and 18,855 alternative splicing (AS) events were identified. Genes orthologous to different Gleditsia species pairs were identified, stress-related genes had been positively selected during the evolution. AGA, AGG, and CCA were identified as the universal optimal codon in the genus of Gleditsia. EIF5A was selected as a suitable fluorescent quantitative reference gene. 315 Cytochrome P450 monooxygenases (CYP450s) and 147 uridine diphosphate (UDP)-glycosyltransferases (UGTs) were recognized through the PacBio SMRT transcriptome. Randomized selection of GsIAA14 for cloning verified the reliability of the PacBio SMRT transcriptome assembly sequence. In conclusion, the research data lay the foundation for further analysis of the evolutionary mechanism and molecular breeding of Gleditsia.
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Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xueyan Jian
- School of Continuing Education, Yanbian University, Yanji, 133002, Jilin, China
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14
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Krishna TA, Maharajan T, Krishna TA, Ceasar SA. Insights into Metabolic Engineering of Bioactive Molecules in Tetrastigma hemsleyanum Diels & Gilg: A Traditional Medicinal Herb. Curr Genomics 2023; 24:72-83. [PMID: 37994327 PMCID: PMC10662378 DOI: 10.2174/0113892029251472230921053135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/17/2023] [Accepted: 08/20/2023] [Indexed: 11/24/2023] Open
Abstract
Plants are a vital source of bioactive molecules for various drug development processes. Tetrastigma hemsleyanum is one of the endangered medicinal plant species well known to the world due to its wide range of therapeutic effects. Many bioactive molecules have been identified from this plant, including many classes of secondary metabolites such as flavonoids, phenols, terpenoids, steroids, alkaloids, etc. Due to its slow growth, it usually takes 3-5 years to meet commercial medicinal materials for this plant. Also, T. hemsleyanum contains low amounts of specific bioactive compounds, which are challenging to isolate easily. Currently, scientists are attempting to increase bioactive molecules' production from medicinal plants in different ways or to synthesize them chemically. The genomic tools helped to understand medicinal plants' genome organization and led to manipulating genes responsible for various biosynthesis pathways. Metabolic engineering has made it possible to enhance the production of secondary metabolites by introducing manipulated biosynthetic pathways to attain high levels of desirable bioactive molecules. Metabolic engineering is a promising approach for improving the production of secondary metabolites over a short time period. In this review, we have highlighted the scope of various biotechnological approaches for metabolic engineering to enhance the production of secondary metabolites for pharmaceutical applications in T. hemsleyanum. Also, we summarized the progress made in metabolic engineering for bioactive molecule enhancement in T. hemsleyanum. It may lead to reducing the destruction of the natural habitat of T. hemsleyanum and conserving them through the cost-effective production of bioactive molecules in the future.
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Affiliation(s)
- T.P. Ajeesh Krishna
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India
| | - T. Maharajan
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India
| | - T.P. Adarsh Krishna
- Research & Development Division, Sreedhareeyam Farmherbs India Pvt. Ltd, Ernakulam, 686-662, Kerala, India
| | - S. Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India
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15
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Tian C, Quan H, Jiang R, Zheng Q, Huang S, Tan G, Yan C, Zhou J, Liao H. Differential roles of Cassia tora 1-deoxy-D-xylulose-5-phosphate synthase and 1-deoxy-D-xylulose-5-phosphate reductoisomerase in trade-off between plant growth and drought tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1270396. [PMID: 37929171 PMCID: PMC10623318 DOI: 10.3389/fpls.2023.1270396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023]
Abstract
Due to global climate change, drought is emerging as a major threat to plant growth and agricultural productivity. Abscisic acid (ABA) has been implicated in plant drought tolerance, however, its retarding effects on plant growth cannot be ignored. The reactions catalyzed by 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) proteins are critical steps within the isoprenoid biosynthesis in plants. Here, five DXS (CtDXS1-5) and two DXR (CtDXR1-2) genes were identified from Cassia tora genome. Based on multiple assays including the phylogeny, cis-acting element, expression pattern, and subcellular localization, CtDXS1 and CtDXR1 genes might be potential candidates controlling the isoprenoid biosynthesis. Intriguingly, CtDXS1 transgenic plants resulted in drought tolerance but retardant growth, while CtDXR1 transgenic plants exhibited both enhanced drought tolerance and increased growth. By comparison of β-carotene, chlorophyll, abscisic acid (ABA) and gibberellin 3 (GA3) contents in wild-type and transgenic plants, the absolute contents and (or) altered GA3/ABA levels were suggested to be responsible for the balance between drought tolerance and plant growth. The transcriptome of CtDXR1 transgenic plants suggested that the transcript levels of key genes, such as DXS, 9-cis-epoxycarotenoid dioxygenases (NCED), ent-kaurene synthase (KS) and etc, involved with chlorophyll, β-carotene, ABA and GA3 biosynthesis were induced and their contents increased accordingly. Collectively, the trade-off effect induced by CtDXR1 was associated with redesigning architecture in phytohormone homeostasis and thus was highlighted for future breeding purposes.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiayu Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Hai Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
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16
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [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: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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17
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Bae SH, Lee MH, Lee JH, Yu Y, Lee J, Kim TH. The Genome of the Korean Island-Originated Perilla citriodora 'Jeju17' Sheds Light on Its Environmental Adaptation and Fatty Acid and Lipid Production Pathways. Genes (Basel) 2023; 14:1898. [PMID: 37895247 PMCID: PMC10606934 DOI: 10.3390/genes14101898] [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: 08/29/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Perilla is a key component of Korean food. It contains several plant-specialized metabolites that provide medical benefits. In response to an increased interest in healthy supplement food from the public, people are focusing on the properties of Perilla. Nevertheless, unlike rice and soybeans, there are few studies based on molecular genetics on Perilla, so it is difficult to systematically study the molecular breed. The wild Perilla, Perilla citriodora 'Jeju17', was identified a decade ago on the Korean island of Jeju. Using short-reads, long-reads, and Hi-C, a chromosome-scale genome spanning 676 Mbp, with high contiguity, was assembled. Aligning the 'Jeju17' genome to the 'PC002' Chinese species revealed significant collinearity with respect to the total length. A total of 31,769 coding sequences were predicted, among which 3331 were 'Jeju17'-specific. Gene enrichment of the species-specific gene repertoire highlighted environment adaptation, fatty acid metabolism, and plant-specialized metabolite biosynthesis. Using a homology-based approach, genes involved in fatty acid and lipid triacylglycerol biosynthesis were identified. A total of 22 fatty acid desaturases were found and comprehensively characterized. Expression of the FAD genes in 'Jeju17' was examined at the seed level, and hormone signaling factors were identified. The results showed that the expression of FAD genes in 'Jeju17' at the seed level was high 25 days after flowering, and their responses of hormones and stress were mainly associated with hormone signal transduction and abiotic stress via cis-elements patterns. This study presents a chromosome-level genome assembly of P. citriodora 'Jeju17', the first wild Perilla to be sequenced from the Korean island of Jeju. The analyses provided can be useful in designing ALA-enhanced Perilla genotypes in the future.
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Affiliation(s)
- Seon-Hwa Bae
- Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea;
| | - Myoung Hee Lee
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, Rural Development Administration (RDA), Miryang 50424, Republic of Korea;
| | - Jeong-Hee Lee
- SEEDERS Inc., 118, Jungang-ro, Jung-gu, Daejeon 34912, Republic of Korea;
| | - Yeisoo Yu
- DNACARE Co., Ltd., 48, Teheran-ro 25-gil, Gangnam-gu, Seoul 06126, Republic of Korea;
| | - Jundae Lee
- Department of Horticulture, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Tae-Ho Kim
- Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea;
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Li Y, Wang Z, Zhu M, Niu Z, Li M, Zheng Z, Hu H, Lu Z, Zhang J, Wan D, Chen Q, Yang Y. A chromosome-scale Rhubarb (Rheum tanguticum) genome assembly provides insights into the evolution of anthraquinone biosynthesis. Commun Biol 2023; 6:867. [PMID: 37612424 PMCID: PMC10447539 DOI: 10.1038/s42003-023-05248-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Rhubarb is the collective name for various perennial plants from the genus Rheum L. and the Polygonaceae family. They are one of the most ancient, commonly used, and important herbs in traditional Chinese medicine. Rhubarb is a major source of anthraquinones, but how they are synthesized remains largely unknown. Here, we generate a genome sequence assembly of one important medicinal rhubarb R. tanguticum at the chromosome level, with 2.76 Gb assembled into 11 chromosomes. The genome is shaped by two recent whole-genome duplication events and recent bursts of retrotransposons. Metabolic analyses show that the major anthraquinones are mainly synthesized in its roots. Transcriptomic analysis reveals a co-expression module with a high correlation to anthraquinone biosynthesis that includes key chalcone synthase genes. One CHS, four CYP450 and two BGL genes involved in secondary metabolism show significantly upregulated expression levels in roots compared with other tissues and clustered in the co-expression module, which implies that they may also act as candidate genes for anthraquinone biosynthesis. This study provides valuable insights into the genetic bases of anthraquinone biosynthesis that will facilitate improved breeding practices and agronomic properties for rhubarb in the future.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhenyue Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhimin Niu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Minjie Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Jin Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Qiao Chen
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China.
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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Wang P, Wei J, Hua X, Dong G, Dziedzic K, Wahab AT, Efferth T, Sun W, Ma P. Plant anthraquinones: Classification, distribution, biosynthesis, and regulation. J Cell Physiol 2023. [PMID: 37393608 DOI: 10.1002/jcp.31063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/10/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Anthraquinones are polycyclic compounds with an unsaturated diketone structure (quinoid moiety). As important secondary metabolites of plants, anthraquinones play an important role in the response of many biological processes and environmental factors. Anthraquinones are common in the human diet and have a variety of biological activities including anticancer, antibacterial, and antioxidant activities that reduce disease risk. The biological activity of anthraquinones depends on the substitution pattern of their hydroxyl groups on the anthraquinone ring structure. However, there is still a lack of systematic summary on the distribution, classification, and biosynthesis of plant anthraquinones. Therefore, this paper systematically reviews the research progress of the distribution, classification, biosynthesis, and regulation of plant anthraquinones. Additionally, we discuss future opportunities in anthraquinone research, including biotechnology, therapeutic products, and dietary anthraquinones.
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Affiliation(s)
- Peng Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Jia Wei
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xin Hua
- College of Life Sciences, Northeast Forestry University, Harbin, China
| | | | - Krzysztof Dziedzic
- Department of Food Technology of Plant Origin, Poznan' University of Life Sciences, Poznań, Poland
| | - Atia-Tul Wahab
- Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Pengda Ma
- College of Life Sciences, Northwest A&F University, Yangling, China
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20
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Castro DTH, Leite DF, da Silva Baldivia D, Dos Santos HF, Balogun SO, da Silva DB, Carollo CA, de Picoli Souza K, Dos Santos EL. Structural Characterization and Anticancer Activity of a New Anthraquinone from Senna velutina (Fabaceae). Pharmaceuticals (Basel) 2023; 16:951. [PMID: 37513863 PMCID: PMC10385181 DOI: 10.3390/ph16070951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
In this study, a novel compound was isolated, identified, and its chemical structure was determined from the extract of the roots of Senna velutina. In addition, we sought to evaluate the anticancer potential of this molecule against melanoma and leukemic cell lines and identify the pathways of cell death involved. To this end, a novel anthraquinone was isolated from the barks of the roots of S. velutina, analyzed by HPLC-DAD, and its molecular structure was determined by nuclear magnetic resonance (NMR). Subsequently, their cytotoxic activity was evaluated by the (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) method against non-cancerous, melanoma, and leukemic cells. The migration of melanoma cells was evaluated by the scratch assay. The apoptosis process, caspase-3 activation, analysis of mitochondrial membrane potential, and measurement of ROS were evaluated by flow cytometry technique. In addition, the pharmacological cell death inhibitors NEC-1, RIP-1, BAPTA, Z-VAD, and Z-DEVD were used to confirm the related cell death mechanisms. With the results, it was possible to elucidate the novel compound characterized as 2'-OH-Torosaol I. In normal cells, the compound showed no cytotoxicity in PBMC but reduced the cell viability of all melanoma and leukemic cell lines evaluated. 2'-OH-Torosaol I inhibited chemotaxis of B16F10-Nex2, SK-Mel-19, SK-Mel-28 and SK-Mel-103. The cytotoxicity of the compound was induced by apoptosis via the intrinsic pathway with reduced mitochondrial membrane potential, increased levels of reactive oxygen species, and activation of caspase-3. In addition, the inhibitors demonstrated the involvement of necroptosis and Ca2+ in the death process and confirmed caspase-dependent apoptosis death as one of the main programmed cell death pathways induced by 2'-OH-Torosaol I. Taken together, the data characterize the novel anthraquinone 2'-OH-Torosaol I, demonstrating its anticancer activity and potential application in cancer therapy.
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Affiliation(s)
- David Tsuyoshi Hiramatsu Castro
- Research Group on Biotechnology and Bioprospecting Applied to Metabolism (GEBBAM), Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
| | - Daniel Ferreira Leite
- Research Group on Biotechnology and Bioprospecting Applied to Metabolism (GEBBAM), Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
| | - Debora da Silva Baldivia
- Research Group on Biotechnology and Bioprospecting Applied to Metabolism (GEBBAM), Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
| | - Helder Freitas Dos Santos
- Research Group on Biotechnology and Bioprospecting Applied to Metabolism (GEBBAM), Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
| | - Sikiru Olaitan Balogun
- Research Group on Biotechnology and Bioprospecting Applied to Metabolism (GEBBAM), Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
| | - Denise Brentan da Silva
- Laboratory of Natural Products and Mass Spectrometry, Universidade Federal do Mato Grosso do Sul, Cidade Universitária, Campo Grande 79070-900, Brazil
| | - Carlos Alexandre Carollo
- Laboratory of Natural Products and Mass Spectrometry, Universidade Federal do Mato Grosso do Sul, Cidade Universitária, Campo Grande 79070-900, Brazil
| | - Kely de Picoli Souza
- Research Group on Biotechnology and Bioprospecting Applied to Metabolism (GEBBAM), Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
| | - Edson Lucas Dos Santos
- Research Group on Biotechnology and Bioprospecting Applied to Metabolism (GEBBAM), Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados 79804-970, Brazil
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21
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Zheng W, Zhang W, Liu D, Yin M, Wang X, Wang S, Shen S, Liu S, Huang Y, Li X, Zhao Q, Yan L, Xu Y, Yu S, Hu B, Yuan T, Mei Z, Guo L, Luo J, Deng X, Xu Q, Huang L, Ma Z. Evolution-guided multiomics provide insights into the strengthening of bioactive flavone biosynthesis in medicinal pummelo. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37115171 PMCID: PMC10363765 DOI: 10.1111/pbi.14058] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
Pummelo (Citrus maxima or Citrus grandis) is a basic species and an important type for breeding in Citrus. Pummelo is used not only for fresh consumption but also for medicinal purposes. However, the molecular basis of medicinal traits is unclear. Here, compared with wild citrus species/Citrus-related genera, the content of 43 bioactive metabolites and their derivatives increased in the pummelo. Furthermore, we assembled the genome sequence of a variety for medicinal purposes with a long history, Citrus maxima 'Huazhouyou-tomentosa' (HZY-T), at the chromosome level with a genome size of 349.07 Mb. Comparative genomics showed that the expanded gene family in the pummelo genome was enriched in flavonoids-, terpenoid-, and phenylpropanoid biosynthesis. Using the metabolome and transcriptome of six developmental stages of HZY-T and Citrus maxima 'Huazhouyou-smooth' (HZY-S) fruit peel, we generated the regulatory networks of bioactive metabolites and their derivatives. We identified a novel MYB transcription factor, CmtMYB108, as an important regulator of flavone pathways. Both mutations and expression of CmtMYB108, which targets the genes PAL (phenylalanine ammonia-lyase) and FNS (flavone synthase), displayed differential expression between Citrus-related genera, wild citrus species and pummelo species. This study provides insights into the evolution-associated changes in bioactive metabolism during the origin process of pummelo.
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Affiliation(s)
- Weikang Zheng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Wang Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Dahui Liu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Minqiang Yin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Xia Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | | | | | - Shengjun Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Yue Huang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Xinxin Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Qian Zhao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Lu Yan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Yuantao Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Shiqi Yu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Bin Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Tao Yuan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Zhinan Mei
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhaocheng Ma
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
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22
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Cai Z, Zhao X, Zhou C, Fang T, Liu G, Luo J. Genome-Wide Mining of the Tandem Duplicated Type III Polyketide Synthases and Their Expression, Structure Analysis of Senna tora. Int J Mol Sci 2023; 24:ijms24054837. [PMID: 36902267 PMCID: PMC10003783 DOI: 10.3390/ijms24054837] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Senna tora is one of the homologous crops used as a medicinal food containing an abundance of anthraquinones. Type III polyketide synthases (PKSs) are key enzymes that catalyze polyketide formation; in particular, the chalcone synthase-like (CHS-L) genes are involved in anthraquinone production. Tandem duplication is a fundamental mechanism for gene family expansion. However, the analysis of the tandem duplicated genes (TDGs) and the identification and characterization of PKSs have not been reported for S. tora. Herein, we identified 3087 TDGs in the S. tora genome; the synonymous substitution rates (Ks) analysis indicated that the TDGs had recently undergone duplication. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the type III PKSs were the most enriched TDGs involved in the biosynthesis of the secondary metabolite pathways, as evidenced by 14 tandem duplicated CHS-L genes. Subsequently, we identified 30 type III PKSs with complete sequences in the S. tora genome. Based on the phylogenetic analysis, the type III PKSs were classified into three groups. The protein conserved motifs and key active residues showed similar patterns in the same group. The transcriptome analysis showed that the chalcone synthase (CHS) genes were more highly expressed in the leaves than in the seeds in S. tora. The transcriptome and qRT-PCR analysis showed that the CHS-L genes had a higher expression in the seeds than in other tissues, particularly seven tandem duplicated CHS-L2/3/5/6/9/10/13 genes. The key active-site residues and three-dimensional models of the CHS-L2/3/5/6/9/10/13 proteins showed slight variation. These results indicated that the rich anthraquinones in S. tora seeds might be ascribed to the PKSs' expansion from tandem duplication, and the seven key CHS-L2/3/5/6/9/10/13 genes provide candidate genes for further research. Our study provides an important basis for further research on the regulation of anthraquinones' biosynthesis in S. tora.
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Affiliation(s)
- Zeping Cai
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou 570228, China
| | - Xingkun Zhao
- College of Tropical Crops & College of Life Sciences, Hainan University, Haikou 570228, China
| | - Chaoye Zhou
- College of Tropical Crops & College of Life Sciences, Hainan University, Haikou 570228, China
| | - Ting Fang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou 570228, China
| | - Guodao Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (G.L.); (J.L.)
| | - Jiajia Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (G.L.); (J.L.)
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23
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Mund NK, Čellárová E. Recent advances in the identification of biosynthetic genes and gene clusters of the polyketide-derived pathways for anthraquinone biosynthesis and biotechnological applications. Biotechnol Adv 2023; 63:108104. [PMID: 36716800 DOI: 10.1016/j.biotechadv.2023.108104] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/27/2022] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
Natural anthraquinones are represented by a large group of compounds. Some of them are widespread across the kingdoms, especially in bacteria, fungi and plants, while the others are restricted to certain groups of organisms. Despite the significant pharmacological potential of several anthraquinones (hypericin, skyrin and emodin), their biosynthetic pathways and candidate genes coding for key enzymes have not been experimentally validated. Understanding the genetic and epigenetic regulation of the anthraquinone biosynthetic gene clusters in fungal endophytes would help not only understand their pathways in plants, which ensure their commercial availability, but also favor them as promising systems for prospective biotechnological production.
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Affiliation(s)
- Nitesh Kumar Mund
- Pavol Jozef Šafárik University in Košice, Faculty of Science, Institute of Biology and Ecology, Department of Genetics, Mánesova 23, 041 54 Košice, Slovakia
| | - Eva Čellárová
- Pavol Jozef Šafárik University in Košice, Faculty of Science, Institute of Biology and Ecology, Department of Genetics, Mánesova 23, 041 54 Košice, Slovakia.
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24
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He Q, Ma D, Li W, Xing L, Zhang H, Wang Y, Du C, Li X, Jia Z, Li X, Liu J, Liu Z, Miao Y, Feng R, Lv Y, Wang M, Lu H, Li X, Xiao Y, Wang R, Liang H, Zhou Q, Zhang L, Liang C, Du H. High-quality Fagopyrum esculentum genome provides insights into the flavonoid accumulation among different tissues and self-incompatibility. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36680412 DOI: 10.1111/jipb.13459] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/20/2023] [Indexed: 06/17/2023]
Abstract
Common buckwheat (Fagopyrum esculentum) and Tartary buckwheat (Fagopyrum tataricum), the two most widely cultivated buckwheat species, differ greatly in flavonoid content and reproductive mode. Here, we report the first high-quality and chromosome-level genome assembly of common buckwheat with 1.2 Gb. Comparative genomic analysis revealed that common buckwheat underwent a burst of long terminal repeat retrotransposons insertion accompanied by numerous large chromosome rearrangements after divergence from Tartary buckwheat. Moreover, multiple gene families involved in stress tolerance and flavonoid biosynthesis such as multidrug and toxic compound extrusion (MATE) and chalcone synthase (CHS) underwent significant expansion in buckwheat, especially in common buckwheat. Integrated multi-omics analysis identified high expression of catechin biosynthesis-related genes in flower and seed in common buckwheat and high expression of rutin biosynthesis-related genes in seed in Tartary buckwheat as being important for the differences in flavonoid type and content between these buckwheat species. We also identified a candidate key rutin-degrading enzyme gene (Ft8.2377) that was highly expressed in Tartary buckwheat seed. In addition, we identified a haplotype-resolved candidate locus containing many genes reportedly associated with the development of flower and pollen, which was potentially related to self-incompatibility in common buckwheat. Our study provides important resources facilitating future functional genomics-related research of flavonoid biosynthesis and self-incompatibility in buckwheat.
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Affiliation(s)
- Qiang He
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Dan Ma
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Longsheng Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Hongyu Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Cailian Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Xuanzhao Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Zheng Jia
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Xiuxiu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianan Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Ze Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yuqing Miao
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Rui Feng
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yang Lv
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Meijia Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Hongwei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310000, China
| | - Xiaochen Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yao Xiao
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Ruyu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Hanfei Liang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qinghong Zhou
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Lijun Zhang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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25
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Zhang W, Zeng Y, Jiao M, Ye C, Li Y, Liu C, Wang J. Integration of high-throughput omics technologies in medicinal plant research: The new era of natural drug discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1073848. [PMID: 36743502 PMCID: PMC9891177 DOI: 10.3389/fpls.2023.1073848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Medicinal plants are natural sources to unravel novel bioactive compounds to satisfy human pharmacological potentials. The world's demand for herbal medicines is increasing year by year; however, large-scale production of medicinal plants and their derivatives is still limited. The rapid development of modern technology has stimulated multi-omics research in medicinal plants, leading to a series of breakthroughs on key genes, metabolites, enzymes involved in biosynthesis and regulation of active compounds. Here, we summarize the latest research progress on the molecular intricacy of medicinal plants, including the comparison of genomics to demonstrate variation and evolution among species, the application of transcriptomics, proteomics and metabolomics to explore dynamic changes of molecular compounds, and the utilization of potential resources for natural drug discovery. These multi-omics research provide the theoretical basis for environmental adaptation of medicinal plants and allow us to understand the chemical diversity and composition of bioactive compounds. Many medicinal herbs' phytochemical constituents and their potential health benefits are not fully explored. Given their large diversity and global distribution as well as the impacts of growth duration and environmental factors on bioactive phytochemicals in medicinal plants, it is crucial to emphasize the research needs of using multi-omics technologies to address basic and applied problems in medicinal plants to aid in developing new and improved medicinal plant resources and discovering novel medicinal ingredients.
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Affiliation(s)
- Wenting Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Yuan Zeng
- School of Plant and Environmental Sciences, Virginia Tech, VA, Blacksburg, United States
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, VA, Blackstone, United States
| | - Meng Jiao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chanjuan Ye
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yanrong Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chuanguang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
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26
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The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis. Int J Mol Sci 2022; 23:ijms232415932. [PMID: 36555572 PMCID: PMC9781956 DOI: 10.3390/ijms232415932] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.
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27
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Luo R, Pan W, Liu W, Tian Y, Zeng Y, Li Y, Li Z, Cui L. The barley DIR gene family: An expanded gene family that is involved in stress responses. Front Genet 2022; 13:1042772. [PMID: 36406120 PMCID: PMC9667096 DOI: 10.3389/fgene.2022.1042772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/24/2022] [Indexed: 09/09/2023] Open
Abstract
Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses.
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Affiliation(s)
- Ruihan Luo
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenqiang Liu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yuan Tian
- Xintai Urban and Rural Development Group Co., Ltd., Taian, Shandong, China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zhimin Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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Liang W, Zhang W, Chen Y, Guo F, Sun J, Zhang X, Li X, Gao W. Accumulation of functional metabolites and transcriptomics in postharvest fume-drying and air-drying process in rhubarb. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:5628-5641. [PMID: 35373362 DOI: 10.1002/jsfa.11910] [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: 12/23/2021] [Revised: 03/15/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The active component content is an important factor affecting quality of traditional Chinese medicines. The fume-drying process can effectively improve the content of active components in rhubarb, but the accumulation dynamics and molecular mechanisms are not known. In this study, variations in the active components of rhubarb during the drying process were determined, and the most intense changes in the active components were preferred for transcriptome inquiry. RESULTS The results showed that the accumulation of active ingredients could be significantly promoted in the early stage of fume-drying and air-drying. In particular, the active ingredients increased by 61.57% (from 44.58 to 72.02 mg g-1 ) on the fourth day of fume-drying. A total of 4191 DEGs (differentially expressed genes) were identified by transcriptome analysis when the active components changed significantly. Transcriptome data of different dried rhubarb samples revealed, that the fume-drying process could significantly improve the expression of genes relevant to respiration, phenolic acid, and anthraquinone synthesis pathways in rhubarb, which was more conducive to the synthesis and accumulation of the active components. CONCLUSION Fume-drying stimulated respiration and secondary metabolite synthesis in rhubarb cells by exerting strong external stress on freshly harvested rhubarb. This study revealed the variations and molecular mechanism of active component accumulation in the rhubarb drying process and might serve as a guide for the development of alternative methods for rhubarb fumigation and drying process. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Wei Liang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- College of Agronomy, College of Life Science and Technology, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Weimei Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yuan Chen
- College of Agronomy, College of Life Science and Technology, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Fengxia Guo
- College of Agronomy, College of Life Science and Technology, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Jiachen Sun
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Xuemin Zhang
- Key Laboratory of Modern Chinese Medicine Resources Research Enterprises, Tianjin, China
| | - Xia Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- College of Pharmacy, Qinghai Minzu University, Qinhai, China
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Guo L, Yao H, Chen W, Wang X, Ye P, Xu Z, Zhang S, Wu H. Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era. HORTICULTURE RESEARCH 2022; 9:uhac223. [PMID: 36479585 PMCID: PMC9720450 DOI: 10.1093/hr/uhac223] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/22/2022] [Indexed: 06/01/2023]
Abstract
Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face the tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance and surging drug prices etc., harnessing the healing power of medicinal plants gifted from mother nature is more urgent than ever in helping us survive future challenge in a sustainable way. PNP research efforts in the pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, and identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- and inter-disciplinary approaches integrating and interrogating all accessible data from genomics, metabolomics, structural biology, and chemical informatics are necessary to accelerate the full characterization of biosynthetic and regulatory circuitry for producing PNPs in medicinal plants. In this review, we attempt to provide a brief update on the current research of PNPs in medicinal plants by focusing on how different state-of-the-art biotechnologies facilitate their discovery, the molecular basis of their biosynthesis, as well as synthetic biology. Finally, we humbly provide a foresight of the research trend for understanding the biology of medicinal plants in the coming decades.
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Affiliation(s)
- Li Guo
- Corresponding authors. E-mails: ;
| | | | | | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an 710061, China
| | - Peng Ye
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Sisheng Zhang
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hong Wu
- Corresponding authors. E-mails: ;
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Singh KS, van der Hooft JJJ, van Wees SCM, Medema MH. Integrative omics approaches for biosynthetic pathway discovery in plants. Nat Prod Rep 2022; 39:1876-1896. [PMID: 35997060 PMCID: PMC9491492 DOI: 10.1039/d2np00032f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic pathways and their genetic regulation have become increasingly important. While genomes provide clues regarding functional associations between genes based on gene clustering, metabolome mining provides a foundational technology to chart natural product structural diversity in plants, and transcriptomics has been successfully used to identify new members of their biosynthetic pathways based on coexpression. Thus far, most approaches utilizing transcriptomics and metabolomics have been targeted towards specific pathways and use one type of omics data at a time. Recent technological advances now provide new opportunities for integration of multiple omics types and untargeted pathway discovery. Here, we review advances in plant biosynthetic pathway discovery using genomics, transcriptomics, and metabolomics, as well as recent efforts towards omics integration. We highlight how transcriptomics and metabolomics provide complementary information to link genes to metabolites, by associating temporal and spatial gene expression levels with metabolite abundance levels across samples, and by matching mass-spectral features to enzyme families. Furthermore, we suggest that elucidation of gene regulatory networks using time-series data may prove useful for efforts to unwire the complexities of biosynthetic pathway components based on regulatory interactions and events.
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Affiliation(s)
- Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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31
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Comparative Transcriptome Analyses of Different Rheum officinale Tissues Reveal Differentially Expressed Genes Associated with Anthraquinone, Catechin, and Gallic Acid Biosynthesis. Genes (Basel) 2022; 13:genes13091592. [PMID: 36140760 PMCID: PMC9498579 DOI: 10.3390/genes13091592] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022] Open
Abstract
Rheum officinale Baill. is an important traditional Chinese medicinal herb, its dried roots and rhizomes being widely utilized to cure diverse diseases. However, previous studies mainly focused on the active compounds and their pharmacological effects, and the molecular mechanism underlying the biosynthesis of these ingredients in R. officinale is still elusive. Here, we performed comparative transcriptome analyses to elucidate the differentially expressed genes (DEGs) in the root, stem, and leaf of R. officinale. A total of 236,031 unigenes with N50 of 769 bp was generated, 136,329 (57.76%) of which were annotated. A total of 5884 DEGs was identified after the comparative analyses of different tissues; 175 and 126 key enzyme genes with tissue-specific expression were found in the anthraquinone, catechin/gallic acid biosynthetic pathway, respectively, and some of these key enzyme genes were verified by qRT-PCR. The phylogeny of the PKS III family in Polygonaceae indicated that probably only PL_741 PKSIII1, PL_11549 PKSIII5, and PL_101745 PKSIII6 encoded PKSIII in the polyketide pathway. These results will shed light on the molecular basis of the tissue-specific accumulation and regulation of secondary metabolites in R. officinale, and lay a foundation for the future genetic diversity, molecular assisted breeding, and germplasm resource improvement of this essential medicinal plant.
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Sohn SI, Pandian S, Rakkammal K, Largia MJV, Thamilarasan SK, Balaji S, Zoclanclounon YAB, Shilpha J, Ramesh M. Jasmonates in plant growth and development and elicitation of secondary metabolites: An updated overview. FRONTIERS IN PLANT SCIENCE 2022; 13:942789. [PMID: 36035665 PMCID: PMC9407636 DOI: 10.3389/fpls.2022.942789] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Secondary metabolites are incontestably key specialized molecules with proven health-promoting effects on human beings. Naturally synthesized secondary metabolites are considered an important source of pharmaceuticals, food additives, cosmetics, flavors, etc., Therefore, enhancing the biosynthesis of these relevant metabolites by maintaining natural authenticity is getting more attention. The application of exogenous jasmonates (JAs) is well recognized for its ability to trigger plant growth and development. JAs have a large spectrum of action that covers seed germination, hypocotyl growth regulation, root elongation, petal expansion, and apical hook growth. This hormone is considered as one of the key regulators of the plant's growth and development when the plant is under biotic or abiotic stress. The JAs regulate signal transduction through cross-talking with other genes in plants and thereby deploy an appropriate metabolism in the normal or stressed conditions. It has also been found to be an effective chemical elicitor for the synthesis of naturally occurring secondary metabolites. This review discusses the significance of JAs in the growth and development of plants and the successful outcomes of jasmonate-driven elicitation of secondary metabolites including flavonoids, anthraquinones, anthocyanin, xanthonoid, and more from various plant species. However, as the enhancement of these metabolites is essentially measured via in vitro cell culture or foliar spray, the large-scale production is significantly limited. Recent advancements in the plant cell culture technology lay the possibilities for the large-scale manufacturing of plant-derived secondary metabolites. With the insights about the genetic background of the metabolite biosynthetic pathway, synthetic biology also appears to be a potential avenue for accelerating their production. This review, therefore, also discussed the potential manoeuvres that can be deployed to synthesis plant secondary metabolites at the large-scale using plant cell, tissue, and organ cultures.
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Affiliation(s)
- Soo-In Sohn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Subramani Pandian
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | | | | | - Senthil Kumar Thamilarasan
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | | | - Yedomon Ange Bovys Zoclanclounon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Jayabalan Shilpha
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Manikandan Ramesh
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
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33
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Bai G, Chen C, Zhao C, Zhou T, Li D, Zhou T, Li W, Lu Y, Cong X, Jia Y, Li S. The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis. iScience 2022; 25:104512. [PMID: 35733792 PMCID: PMC9207680 DOI: 10.1016/j.isci.2022.104512] [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: 12/29/2021] [Revised: 04/21/2022] [Accepted: 05/27/2022] [Indexed: 12/04/2022] Open
Abstract
The lacquer tree (Toxicodendron vernicifluum (Stokes) F.A. Barkley) is an important tree with economic, industrial, and medicinal values. Here, we generated the reference genome of T. vernicifluum at the chromosome level with 491.93 Mb in size, in which 98.26% of the assembled contigs were anchored onto 15 pseudochromosomes with the scaffold N50 of 32.97 Mb. Comparative genomic analysis revealed the gene families related to urushiol biosynthesis were expanded, contributing to the ecological fitness and biological adaptability of the lacquer tree. We combined multi-omics data to identify genes that encode key enzymes in the T. vernicifluum urushiol and lignin biosynthetic pathways. Furthermore, the unique active metabolites, such as butin and fisetin, in cultivar lacquers were identified by metabolism profiling. Our work would provide crucial insights into metabolite synthesis such as urushiol and lignin, meanwhile offer a basis for further exploration of the cultivation and breeding of T. vernicifluum and other Anacardiaceae members.
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Affiliation(s)
- Guoqing Bai
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Chen Chen
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Chenxi Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an 710061, China
| | - Dan Li
- SDIC Biotech Investment Co., Ltd., Shanghai 200082, China
| | - Tianhua Zhou
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - Weimin Li
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Yuan Lu
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Xiaofeng Cong
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Yun Jia
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Sifeng Li
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
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Löhr NA, Eisen F, Thiele W, Platz L, Motter J, Hüttel W, Gressler M, Müller M, Hoffmeister D. Unprecedented Mushroom Polyketide Synthases Produce the Universal Anthraquinone Precursor. Angew Chem Int Ed Engl 2022; 61:e202116142. [PMID: 35218274 PMCID: PMC9325552 DOI: 10.1002/anie.202116142] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Indexed: 11/11/2022]
Abstract
(Pre-)anthraquinones are widely distributed natural compounds and occur in plants, fungi, microorganisms, and animals, with atrochrysone (1) as the key biosynthetic precursor. Chemical analyses established mushrooms of the genus Cortinarius-the webcaps-as producers of atrochrysone-derived octaketide pigments. However, more recent genomic data did not provide any evidence for known atrochrysone carboxylic acid (4) synthases nor any other polyketide synthase (PKS) producing oligocyclic metabolites. Here, we describe an unprecedented class of non-reducing (NR-)PKS. In vitro assays with recombinant enzyme in combination with in vivo product formation in the heterologous host Aspergillus niger established CoPKS1 and CoPKS4 of C. odorifer as members of a new class of atrochrysone carboxylic acid synthases. CoPKS4 catalyzed both hepta- and octaketide synthesis and yielded 6-hydroxymusizin (6), along with 4. These first mushroom PKSs for oligocyclic products illustrate how the biosynthesis of bioactive natural metabolites evolved independently in various groups of life.
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Affiliation(s)
- Nikolai A Löhr
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Frederic Eisen
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Wiebke Thiele
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lukas Platz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Jonas Motter
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Wolfgang Hüttel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Markus Gressler
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
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Zhao K, Rhee SY. Omics-guided metabolic pathway discovery in plants: Resources, approaches, and opportunities. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102222. [PMID: 35512431 DOI: 10.1016/j.pbi.2022.102222] [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: 11/09/2021] [Revised: 01/30/2022] [Accepted: 03/25/2022] [Indexed: 05/28/2023]
Abstract
Plants produce a vast array of metabolites, the biosynthetic routes of which remain largely undetermined. Genome-scale enzyme and pathway annotations and omics technologies have revolutionized research to decrypt plant metabolism and produced a growing list of functionally characterized metabolic genes and pathways. However, what is known is still a tiny fraction of the metabolic capacity harbored by plants. Here, we review plant enzyme and pathway annotation resources and cutting-edge omics approaches to guide discovery and characterization of plant metabolic pathways. We also discuss strategies for improving enzyme function prediction by integrating protein 3D structure information and single cell omics. This review aims to serve as a primer for plant biologists to leverage omics datasets to facilitate understanding and engineering plant metabolism.
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Affiliation(s)
- Kangmei Zhao
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA.
| | - Seung Y Rhee
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
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Löhr NA, Eisen F, Thiele W, Platz L, Motter J, Hüttel W, Gressler M, Müller M, Hoffmeister D. Unprecedented Mushroom Polyketide Synthases Produce the Universal Anthraquinone Precursor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nikolai A Löhr
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Frederic Eisen
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Wiebke Thiele
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Lukas Platz
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Jonas Motter
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Wolfgang Hüttel
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Markus Gressler
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Michael Müller
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Dirk Hoffmeister
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Pharmaceutical Microbiology at the Hans-Kn�ll-Institute Beutenbergstrasse 11a 07745 Jena GERMANY
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Zhang T, Liu R, Zheng J, Wang Z, Gao T, Qin M, Hu X, Wang Y, Yang S, Li T. Insights into glucosinolate accumulation and metabolic pathways in Isatis indigotica Fort. BMC PLANT BIOLOGY 2022; 22:78. [PMID: 35193497 PMCID: PMC8862337 DOI: 10.1186/s12870-022-03455-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 02/03/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND Glucosinolates (GSLs) play important roles in defending against exogenous damage and regulating physiological activities in plants. However, GSL accumulation patterns and molecular regulation mechanisms are largely unknown in Isatis indigotica Fort. RESULTS Ten GSLs were identified in I. indigotica, and the dominant GSLs were epiprogoitrin (EPI) and indole-3-methyl GSL (I3M), followed by progoitrin (PRO) and gluconapin (GNA). The total GSL content was highest (over 20 μmol/g) in reproductive organs, lowest (less than 1.0 μmol/g) in mature organs, and medium in fresh leaves (2.6 μmol/g) and stems (1.5 μmol/g). In the seed germination process, the total GSL content decreased from 27.2 μmol/g (of seeds) to 2.7 μmol/g (on the 120th day) and then increased to 4.0 μmol/g (180th day). However, the content of indole GSL increased rapidly in the first week after germination and fluctuated between 1.13 μmol/g (28th day) and 2.82 μmol/g (150th day). Under the different elicitor treatments, the total GSL content increased significantly, ranging from 2.9-fold (mechanical damage, 3 h) to 10.7-fold (MeJA, 6 h). Moreover, 132 genes were involved in GSL metabolic pathways. Among them, no homologs of AtCYP79F2 and AtMAM3 were identified, leading to a distinctive GSL profile in I. indigotica. Furthermore, most genes involved in the GSL metabolic pathway were derived from tandem duplication, followed by dispersed duplication and segmental duplication. Purifying selection was observed, although some genes underwent relaxed selection. In addition, three tandem-arrayed GSL-OH genes showed different expression patterns, suggesting possible subfunctionalization during evolution. CONCLUSIONS Ten different GSLs with their accumulation patterns and 132 genes involved in the GSL metabolic pathway were explored, which laid a foundation for the study of GSL metabolism and regulatory mechanisms in I. indigotica.
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Affiliation(s)
- Tianyi Zhang
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Rui Liu
- National Engineering Laboratory for Resources Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Jinyu Zheng
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Zirong Wang
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Tian'e Gao
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Miaomiao Qin
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Xiangyang Hu
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Yuanyuan Wang
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Shu Yang
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an, Shaanxi, 710000, People's Republic of China
| | - Tao Li
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China.
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Wang H, Guo Y, Luo Z, Gao L, Li R, Zhang Y, Kalaji HM, Qiang S, Chen S. Recent Advances in Alternaria Phytotoxins: A Review of Their Occurrence, Structure, Bioactivity and Biosynthesis. J Fungi (Basel) 2022; 8:jof8020168. [PMID: 35205922 PMCID: PMC8878860 DOI: 10.3390/jof8020168] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/04/2022] Open
Abstract
Alternaria is a ubiquitous fungal genus in many ecosystems, consisting of species and strains that can be saprophytic, endophytic, or pathogenic to plants or animals, including humans. Alternaria species can produce a variety of secondary metabolites (SMs), especially low molecular weight toxins. Based on the characteristics of host plant susceptibility or resistance to the toxin, Alternaria phytotoxins are classified into host-selective toxins (HSTs) and non-host-selective toxins (NHSTs). These Alternaria toxins exhibit a variety of biological activities such as phytotoxic, cytotoxic, and antimicrobial properties. Generally, HSTs are toxic to host plants and can cause severe economic losses. Some NHSTs such as alternariol, altenariol methyl-ether, and altertoxins also show high cytotoxic and mutagenic activities in the exposed human or other vertebrate species. Thus, Alternaria toxins are meaningful for drug and pesticide development. For example, AAL-toxin, maculosin, tentoxin, and tenuazonic acid have potential to be developed as bioherbicides due to their excellent herbicidal activity. Like altersolanol A, bostrycin, and brefeldin A, they exhibit anticancer activity, and ATX V shows high activity to inhibit the HIV-1 virus. This review focuses on the classification, chemical structure, occurrence, bioactivity, and biosynthesis of the major Alternaria phytotoxins, including 30 HSTs and 50 NHSTs discovered to date.
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Affiliation(s)
- He Wang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Yanjing Guo
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Zhi Luo
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Liwen Gao
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Rui Li
- Agricultural and Animal Husbandry Ecology and Resource Protection Center, Ordos Agriculture and Animal Husbandry Bureau, Ordos 017010, China;
| | - Yaxin Zhang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Hazem M. Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences SGGW, 159 Nowoursynowska 159, 02-776 Warsaw, Poland;
- Institute of Technology and Life Sciences—National Research Institute, Falenty, Al. Hrabska 3, 05-090 Raszyn, Poland
| | - Sheng Qiang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
| | - Shiguo Chen
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.W.); (Y.G.); (Z.L.); (L.G.); (Y.Z.); (S.Q.)
- Correspondence: ; Tel.: +86-25-84395117
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Transcriptome and HPLC Analysis Reveal the Regulatory Mechanisms of Aurantio-Obtusin in Space Environment-Induced Senna obtusifolia Lines. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19020898. [PMID: 35055719 PMCID: PMC8776150 DOI: 10.3390/ijerph19020898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 01/25/2023]
Abstract
Senna obtusifolia is a famous medicinal plant that is widely used in Asian countries. Its seed plays an important role in the treatment of many diseases because it contains various anthraquinones and flavonoids. Our previous studies have indicated that three space environment-induced S. obtusifolia lines (SP-lines) i.e., QC10, QC29, and QC46, have higher seed yield and aurantio-obtusin (AO) content. However, the underlying mechanism of higher AO content in SP-lines is still unknown. Herein, transcriptome sequencing and HPLC were employed to analyze the differences between SP-lines and ground control (GC3) and elucidate the regulatory mechanisms of AO accumulation in SP-lines. The results show that 4002 differentially expressed genes (DEGs) were identified in SP-lines versus (vs.) GC3. DEGs in the QC10 vs. GC3, QC29 vs. GC3, and QC46 vs. GC3 comparisons were classified into 28, 36, and 81 GO terms and involved in 63, 74, and 107 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. KEGG pathway and gene expression analysis revealed that DEGs involved in anthraquinone pathways were significantly elevated in QC10 and QC46. Integrating the results of GO annotation, KEGG enrichment, and gene expression analysis, we propose that the elevated genes such as DAHPS, DHQS, and MenB enhance the metabolic flux in the anthraquinone pathway and promote AO content in QC10 and QC46. Taken together, this study elucidated the mechanism of AO content in SP-lines and provides valuable genetic information for S. obtusifolia. In addition, to the best of our knowledge, this study presents the first transcriptome analysis of environment-induced medicinal plants and paves the way to select elite S. obtusifolia varieties in the future.
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Kang SH, Lee WH, Sim JS, Thaku N, Chang S, Hong JP, Oh TJ. De novo Transcriptome Assembly of Senna occidentalis Sheds Light on the Anthraquinone Biosynthesis Pathway. FRONTIERS IN PLANT SCIENCE 2022; 12:773553. [PMID: 35046973 PMCID: PMC8761625 DOI: 10.3389/fpls.2021.773553] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Senna occidentalis is an annual leguminous herb that is rich in anthraquinones, which have various pharmacological activities. However, little is known about the genetics of S. occidentalis, particularly its anthraquinone biosynthesis pathway. To broaden our understanding of the key genes and regulatory mechanisms involved in the anthraquinone biosynthesis pathway, we used short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) to perform a spatial and temporal transcriptomic analysis of S. occidentalis. This generated 121,592 RNA-Seq unigenes and 38,440 Iso-Seq unigenes. Comprehensive functional annotation and classification of these datasets using public databases identified unigene sequences related to major secondary metabolite biosynthesis pathways and critical transcription factor families (bHLH, WRKY, MYB, and bZIP). A tissue-specific differential expression analysis of S. occidentalis and measurement of the amount of anthraquinones revealed that anthraquinone accumulation was related to the gene expression levels in the different tissues. In addition, the amounts and types of anthraquinones produced differ between S. occidentalis and S. tora. In conclusion, these results provide a broader understanding of the anthraquinone metabolic pathway in S. occidentalis.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Woo-Haeng Lee
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan, South Korea
| | - Joon-Soo Sim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Niha Thaku
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan, South Korea
| | - Saemin Chang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Jong-Pil Hong
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan, South Korea
- Genome-Based BioIT Convergence Institute, Asan, South Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, South Korea
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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Hou Q, Li S, Shang C, Wen Z, Cai X, Hong Y, Qiao G. Genome-wide characterization of chalcone synthase genes in sweet cherry and functional characterization of CpCHS1 under drought stress. FRONTIERS IN PLANT SCIENCE 2022; 13:989959. [PMID: 36061761 PMCID: PMC9437463 DOI: 10.3389/fpls.2022.989959] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/03/2022] [Indexed: 05/22/2023]
Abstract
Cherries are one of the important fruit trees. The growth of cherry is greatly affected by abiotic stresses such as drought, which hinders its development. Chalcone synthase (CHS, EC 2.3.1.74) is a crucial rate-limiting enzyme in the flavonoid biosynthetic pathway that plays an important role in regulating plant growth, development, and abiotic stress tolerance. In the current study, three genes encoding chalcone synthase were identified in the genome of sweet cherry (Prunus avium L.). The three genes contained fewer introns and showed high homology with CHS genes of other Rosaceae members. All members are predicted to localize in the cytoplasm. The conserved catalytic sites may be located at the Cys163, Phe214, His302, and Asn335 residues. These genes were differentially expressed during flower bud dormancy and fruit development. The total flavonoid content of Chinese cherry (Cerasus pseudocerasus Lindl.) was highest in the leaves and slightly higher in the pulp than in the peel. No significant difference in total flavonoid content was detected between aborted kernels and normally developing kernels. Overexpression of Chinese cherry CpCHS1 in tobacco improved the germination frequency of tobacco seeds under drought stress, and the fresh weight of transgenic seedlings under drought stress was higher than that of the wild type, and the contents of SOD, POD, CAT, and Pro in OE lines were significantly increased and higher than WT under drought stress. These results indicate cherry CHS genes are conserved and functionally diverse and will assist in elucidating the functions of flavonoid synthesis pathways in cherry and other Rosaceae species under drought stress.
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Affiliation(s)
- Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Shuang Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Chunqiong Shang
- College of Forestry, Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang, China
| | - Zhuang Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Xiaowei Cai
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Yi Hong
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- *Correspondence: Guang Qiao,
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Hawkins C, Ginzburg D, Zhao K, Dwyer W, Xue B, Xu A, Rice S, Cole B, Paley S, Karp P, Rhee SY. Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1888-1905. [PMID: 34403192 DOI: 10.1111/jipb.13163] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/14/2021] [Indexed: 05/18/2023]
Abstract
To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.
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Affiliation(s)
- Charles Hawkins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Daniel Ginzburg
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - William Dwyer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Bo Xue
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Angela Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Selena Rice
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley Laboratory, Berkeley, California, 94720, USA
| | - Suzanne Paley
- SRI International, Menlo Park, California, 94025, USA
| | - Peter Karp
- SRI International, Menlo Park, California, 94025, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
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Zhou T, Zhang T, Sun J, Zhu H, Zhang M, Wang X. Tissue-specific transcriptome for Rheum tanguticum reveals candidate genes related to the anthraquinones biosynthesis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2487-2501. [PMID: 34924706 PMCID: PMC8639895 DOI: 10.1007/s12298-021-01099-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 05/09/2023]
Abstract
UNLABELLED Rheum tanguticum (Maxim. ex Regel) Maxim. ex Balf. is a herbaceous perennial plant indigenous to China, and its root and rhizomes were usually used as an important traditional Chinese medicine. However, the genomic resources are still scarce for R. tanguticum and even for Rheum genus. Transcriptome datasets from different tissues of R. tanguticum were obtained to screen the genes related to anthraquinones biosynthesis, and five free anthraquinones were also determined. Nine cDNA libraries of roots, stems and leaves were generated, and a total of 272 million high-quality reads were assembled into 257,942 unigenes. Based on the functional annotation, A total of 227 candidate enzyme genes involved in the MVA, MEP, shikimate and polyketide pathways were identified, and several differentially expressed genes found functionally associated with anthraquinones biosynthesis showed distinct tissue-specific expression patterns. Especially, we found that the expression levels of PKS III genes might result in the content differences of free anthraquinones in different tissues of R. tanguticum. Besides, 137,400 SSR loci were identified, and 64,081 SSR primer pairs were successfully designed based on these loci. Our results not only provide cues for the genetic mechanism of anthraquinone content differences in different tissues of R. tanguticum, but also lay genomic foundation for the subsequent genetic engineering and breeding for Rheum species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01099-8.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Tianyi Zhang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Jiangyan Sun
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Honghong Zhu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Miao Zhang
- Lixian Spring Pharmaceutical Co. Ltd., Longnan, 742200 China
| | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, 710061 China
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Franke J, Zhang Y, Dang TTT. Editorial: Exploring and Engineering Plant Specialized Metabolism: Latest Advances and New Horizons. FRONTIERS IN PLANT SCIENCE 2021; 12:783465. [PMID: 34777454 PMCID: PMC8581220 DOI: 10.3389/fpls.2021.783465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Jakob Franke
- Institute of Botany, Leibniz University Hannover, Hanover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Hanover, Germany
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Thu-Thuy T. Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC, Canada
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Kang JN, Lee WH, Won SY, Chang S, Hong JP, Oh TJ, Lee SM, Kang SH. Systemic Expression of Genes Involved in the Plant Defense Response Induced by Wounding in Senna tora. Int J Mol Sci 2021; 22:ijms221810073. [PMID: 34576236 PMCID: PMC8469979 DOI: 10.3390/ijms221810073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 02/05/2023] Open
Abstract
Wounds in tissues provide a pathway of entry for pathogenic fungi and bacteria in plants. Plants respond to wounding by regulating the expression of genes involved in their defense mechanisms. To analyze this response, we investigated the defense-related genes induced by wounding in the leaves of Senna tora using RNA sequencing. The genes involved in jasmonate and ethylene biosynthesis were strongly induced by wounding, as were a large number of genes encoding transcription factors such as ERFs, WRKYs, MYBs, bHLHs, and NACs. Wounding induced the expression of genes encoding pathogenesis-related (PR) proteins, such as PR-1, chitinase, thaumatin-like protein, cysteine proteinase inhibitor, PR-10, and plant defensin. Furthermore, wounding led to the induction of genes involved in flavonoid biosynthesis and the accumulation of kaempferol and quercetin in S. tora leaves. All these genes were expressed systemically in leaves distant from the wound site. These results demonstrate that mechanical wounding can lead to a systemic defense response in the Caesalpinioideae, a subfamily of the Leguminosae. In addition, a co-expression analysis of genes induced by wounding provides important information about the interactions between genes involved in plant defense responses.
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Affiliation(s)
- Ji-Nam Kang
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (J.-N.K.); (S.Y.W.); (S.C.); (J.-P.H.)
| | - Woo-Haeng Lee
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan 31460, Korea; (W.-H.L.); (T.-J.O.)
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (J.-N.K.); (S.Y.W.); (S.C.); (J.-P.H.)
| | - Saemin Chang
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (J.-N.K.); (S.Y.W.); (S.C.); (J.-P.H.)
| | - Jong-Pil Hong
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (J.-N.K.); (S.Y.W.); (S.C.); (J.-P.H.)
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan 31460, Korea; (W.-H.L.); (T.-J.O.)
| | - Si Myung Lee
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (J.-N.K.); (S.Y.W.); (S.C.); (J.-P.H.)
- Correspondence: (S.M.L.); (S.-H.K.)
| | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (J.-N.K.); (S.Y.W.); (S.C.); (J.-P.H.)
- Correspondence: (S.M.L.); (S.-H.K.)
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Zhu X, Liu X, Liu T, Wang Y, Ahmed N, Li Z, Jiang H. Synthetic biology of plant natural products: From pathway elucidation to engineered biosynthesis in plant cells. PLANT COMMUNICATIONS 2021; 2:100229. [PMID: 34746761 PMCID: PMC8553972 DOI: 10.1016/j.xplc.2021.100229] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 04/11/2021] [Accepted: 08/06/2021] [Indexed: 05/10/2023]
Abstract
Plant natural products (PNPs) are the main sources of drugs, food additives, and new biofuels and have become a hotspot in synthetic biology. In the past two decades, the engineered biosynthesis of many PNPs has been achieved through the construction of microbial cell factories. Alongside the rapid development of plant physiology, genetics, and plant genetic modification techniques, hosts have now expanded from single-celled microbes to complex plant systems. Plant synthetic biology is an emerging field that combines engineering principles with plant biology. In this review, we introduce recent advances in the biosynthetic pathway elucidation of PNPs and summarize the progress of engineered PNP biosynthesis in plant cells. Furthermore, a future vision of plant synthetic biology is proposed. Although we are still a long way from overcoming all the bottlenecks in plant synthetic biology, the ascent of this field is expected to provide a huge opportunity for future agriculture and industry.
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Affiliation(s)
- Xiaoxi Zhu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Xiaonan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Tian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Life Science and Technology College, Guangxi University, Nanning, Guangxi 530004, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yina Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Nida Ahmed
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Zhichao Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
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Chevalier Q, Gallé JB, Wasser N, Mazan V, Villette C, Mutterer J, Elustondo MM, Girard N, Elhabiri M, Schaller H, Hemmerlin A, Vonthron-Sénécheau C. Unravelling the Puzzle of Anthranoid Metabolism in Living Plant Cells Using Spectral Imaging Coupled to Mass Spectrometry. Metabolites 2021; 11:metabo11090571. [PMID: 34564386 PMCID: PMC8472718 DOI: 10.3390/metabo11090571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/16/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Vismione H (VH) is a fluorescent prenylated anthranoid produced by plants from the Hypericaceae family, with antiprotozoal activities against malaria and leishmaniosis. Little is known about its biosynthesis and metabolism in plants or its mode of action against parasites. When VH is isolated from Psorospermum glaberrimum, it is rapidly converted into madagascine anthrone and anthraquinone, which are characterized by markedly different fluorescent properties. To locate the fluorescence of VH in living plant cells and discriminate it from that of the other metabolites, an original strategy combining spectral imaging (SImaging), confocal microscopy, and non-targeted metabolomics using mass spectrometry, was developed. Besides VH, structurally related molecules including madagascine (Mad), emodin (Emo), quinizarin (Qui), as well as lapachol (Lap) and fraxetin (Fra) were analyzed. This strategy readily allowed a spatiotemporal characterization and discrimination of spectral fingerprints from anthranoid-derived metabolites and related complexes with cations and proteins. In addition, our study validates the ability of plant cells to metabolize VH into madagascine anthrone, anthraquinones and unexpected metabolites. These results pave the way for new hypotheses on anthranoid metabolism in plants.
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Affiliation(s)
- Quentin Chevalier
- Centre National de la Recherche Scientifique, Laboratoire d’Innovation Thérapeutique, Université de Strasbourg, CEDEX, F-67401 Illkirch, France; (J.-B.G.); (N.W.); (N.G.); (C.V.-S.)
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, CEDEX, F-67084 Strasbourg, France; (C.V.); (J.M.); (H.S.); (A.H.)
- Correspondence: ; Tel.: +33-367155265
| | - Jean-Baptiste Gallé
- Centre National de la Recherche Scientifique, Laboratoire d’Innovation Thérapeutique, Université de Strasbourg, CEDEX, F-67401 Illkirch, France; (J.-B.G.); (N.W.); (N.G.); (C.V.-S.)
| | - Nicolas Wasser
- Centre National de la Recherche Scientifique, Laboratoire d’Innovation Thérapeutique, Université de Strasbourg, CEDEX, F-67401 Illkirch, France; (J.-B.G.); (N.W.); (N.G.); (C.V.-S.)
| | - Valérie Mazan
- Centre National de la Recherche Scientifique, Laboratoire d’Innovation Moléculaire et Applications, Université de Strasbourg-Université de Haute Alsace, CEDEX, F-67087 Strasbourg, France; (V.M.); (M.E.)
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, CEDEX, F-67084 Strasbourg, France; (C.V.); (J.M.); (H.S.); (A.H.)
| | - Jérôme Mutterer
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, CEDEX, F-67084 Strasbourg, France; (C.V.); (J.M.); (H.S.); (A.H.)
| | | | - Nicolas Girard
- Centre National de la Recherche Scientifique, Laboratoire d’Innovation Thérapeutique, Université de Strasbourg, CEDEX, F-67401 Illkirch, France; (J.-B.G.); (N.W.); (N.G.); (C.V.-S.)
| | - Mourad Elhabiri
- Centre National de la Recherche Scientifique, Laboratoire d’Innovation Moléculaire et Applications, Université de Strasbourg-Université de Haute Alsace, CEDEX, F-67087 Strasbourg, France; (V.M.); (M.E.)
| | - Hubert Schaller
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, CEDEX, F-67084 Strasbourg, France; (C.V.); (J.M.); (H.S.); (A.H.)
| | - Andréa Hemmerlin
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, CEDEX, F-67084 Strasbourg, France; (C.V.); (J.M.); (H.S.); (A.H.)
| | - Catherine Vonthron-Sénécheau
- Centre National de la Recherche Scientifique, Laboratoire d’Innovation Thérapeutique, Université de Strasbourg, CEDEX, F-67401 Illkirch, France; (J.-B.G.); (N.W.); (N.G.); (C.V.-S.)
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Wang J, Xu S, Mei Y, Cai S, Gu Y, Sun M, Liang Z, Xiao Y, Zhang M, Yang S. A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China. HORTICULTURE RESEARCH 2021; 8:135. [PMID: 34059651 PMCID: PMC8166937 DOI: 10.1038/s41438-021-00551-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/23/2021] [Accepted: 03/22/2021] [Indexed: 05/03/2023]
Abstract
Morinda officinalis is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of southern China. Its dried roots (called bajitian in traditional Chinese medicine) are broadly used to treat various diseases, such as impotence and rheumatism. Here, we report a high-quality chromosome-scale genome assembly of M. officinalis using Nanopore single-molecule sequencing and Hi-C technology. The assembled genome size was 484.85 Mb with a scaffold N50 of 40.97 Mb, and 90.77% of the assembled sequences were anchored on eleven pseudochromosomes. The genome includes 27,698 protein-coding genes, and most of the assemblies are repetitive sequences. Genome evolution analysis revealed that M. officinalis underwent core eudicot γ genome triplication events but no recent whole-genome duplication (WGD). Likewise, comparative genomic analysis showed no large-scale structural variation after species divergence between M. officinalis and Coffea canephora. Moreover, gene family analysis indicated that gene families associated with plant-pathogen interactions and sugar metabolism were significantly expanded in M. officinalis. Furthermore, we identified many candidate genes involved in the biosynthesis of major active components such as anthraquinones, iridoids and polysaccharides. In addition, we also found that the DHQS, GGPPS, TPS-Clin, TPS04, sacA, and UGDH gene families-which include the critical genes for active component biosynthesis-were expanded in M. officinalis. This study provides a valuable resource for understanding M. officinalis genome evolution and active component biosynthesis. This work will facilitate genetic improvement and molecular breeding of this commercially important plant.
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Affiliation(s)
- Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Yu Mei
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Shike Cai
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Yan Gu
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Minyang Sun
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Zhan Liang
- DongFuhang High-tech Agricultural Planting and Management Co., Ltd, 526000, Zhaoqing, China
| | - Yong Xiao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, China.
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, 530005, Nanning, China.
| | - Shaohai Yang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China.
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Bisht R, Bhattacharyya A, Shrivastava A, Saxena P. An Overview of the Medicinally Important Plant Type III PKS Derived Polyketides. FRONTIERS IN PLANT SCIENCE 2021; 12:746908. [PMID: 34721474 PMCID: PMC8551677 DOI: 10.3389/fpls.2021.746908] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/08/2021] [Indexed: 05/06/2023]
Abstract
Plants produce interesting secondary metabolites that are a valuable source of both medicines for human use, along with significant advantages for the manufacturer species. The active compounds which lead to these instrumental effects are generally secondary metabolites produced during various plant growth phases, which provide the host survival advantages while affecting human health inadvertently. Different chemical classes of secondary metabolites are biosynthesized by the plant type III polyketide synthases (PKSs). They are simple homodimeric proteins with the unique mechanistic potential to produce a broad array of secondary metabolites by utilizing simpler starter and extender units. These PKS derived products are majorly the precursors of some important secondary metabolite pathways leading to products such as flavonoids, stilbenes, benzalacetones, chromones, acridones, xanthones, cannabinoids, aliphatic waxes, alkaloids, anthrones, and pyrones. These secondary metabolites have various pharmaceutical, medicinal and industrial applications which make biosynthesizing type III PKSs an important tool for bioengineering purposes. Because of their structural simplicity and ease of manipulation, these enzymes have garnered interest in recent years due to their application in the generation of unnatural natural polyketides and modified products in the search for newer drugs for a variety of health problems. The following review covers the biosynthesis of a variety of type III PKS-derived secondary metabolites, their biological relevance, the associated enzymes, and recent research.
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