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Yu W, Cai S, Zhao J, Hu S, Zang C, Xu J, Hu L. Beyond genome: Advanced omics progress of Panax ginseng. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112022. [PMID: 38311250 DOI: 10.1016/j.plantsci.2024.112022] [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: 10/12/2023] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Ginseng is a perennial herb of the genus Panax in the family Araliaceae as one of the most important traditional medicine. Genomic studies of ginseng assist in the systematic discovery of genes related to bioactive ginsenosides biosynthesis and resistance to stress, which are of great significance in the conservation of genetic resources and variety improvement. The transcriptome reflects the difference and consistency of gene expression, and transcriptomics studies of ginseng assist in screening ginseng differentially expressed genes to further explore the powerful gene source of ginseng. Protein is the ultimate bearer of ginseng life activities, and proteomic studies of ginseng assist in exploring the biosynthesis and regulation of secondary metabolites like ginsenosides and the molecular mechanism of ginseng adversity adaptation at the overall level. In this review, we summarize the current status of ginseng research in genomics, transcriptomics and proteomics, respectively. We also discuss and look forward to the development of ginseng genome allele mapping, ginseng spatiotemporal, single-cell transcriptome, as well as ginseng post-translational modification proteome. We hope that this review will contribute to the in-depth study of ginseng and provide a reference for future analysis of ginseng from a systems biology perspective.
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Affiliation(s)
- Wenjing Yu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Siyuan Cai
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiali Zhao
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Shuhan Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Chen Zang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China.
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Saha B, Nayak J, Srivastava R, Samal S, Kumar D, Chanwala J, Dey N, Giri MK. Unraveling the involvement of WRKY TFs in regulating plant disease defense signaling. PLANTA 2023; 259:7. [PMID: 38012461 DOI: 10.1007/s00425-023-04269-y] [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: 06/30/2023] [Accepted: 10/18/2023] [Indexed: 11/29/2023]
Abstract
MAIN CONCLUSION This review article explores the intricate role, regulation, and signaling mechanisms of WRKY TFs in response to biotic stress, particularly emphasizing their pivotal role in the trophism of plant-pathogen interactions. Transcription factors (TFs) play a vital role in governing both plant defense and development by controlling the expression of various downstream target genes. Early studies have shown the differential expression of certain WRKY transcription factors by microbial infections. Several transcriptome-wide studies later demonstrated that diverse sets of WRKYs are significantly activated in the early stages of viral, bacterial, and fungal infections. Furthermore, functional investigations indicated that overexpression or silencing of certain WRKY genes in plants can drastically alter disease symptoms as well as pathogen multiplication rates. Hence the new aspects of pathogen-triggered WRKY TFs mediated regulation of plant defense can be explored. The already recognized roles of WRKYs include transcriptional regulation of defense-related genes, modulation of hormonal signaling, and participation in signal transduction pathways. Some WRKYs have been shown to directly bind to pathogen effectors, acting as decoys or resistance proteins. Notably, the signaling molecules like salicylic acid, jasmonic acid, and ethylene which are associated with plant defense significantly increase the expression of several WRKYs. Moreover, induction of WRKY genes or heightened WRKY activities is also observed during ISR triggered by the beneficial microbes which protect the plants from subsequent pathogen infection. To understand the contribution of WRKY TFs towards disease resistance and their exact metabolic functions in infected plants, further studies are required. This review article explores the intrinsic transcriptional regulation, signaling mechanisms, and hormonal crosstalk governed by WRKY TFs in plant disease defense response, particularly emphasizing their specific role against different biotrophic, hemibiotrophic, and necrotrophic pathogen infections.
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Affiliation(s)
- Baisista Saha
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, Odisha, 751024, India
| | - Jagatjeet Nayak
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, Odisha, 751024, India
| | - Richa Srivastava
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, UP, India
| | - Swarnmala Samal
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, UP, India
| | - Deepak Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, UP, India
| | - Jeky Chanwala
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Nrisingha Dey
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Mrunmay Kumar Giri
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, Odisha, 751024, India.
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Yu J, Zhang X, Cao J, Bai H, Wang R, Wang C, Xu Z, Li C, Liu G. Genome-Wide Identification and Characterization of WRKY Transcription Factors in Betula platyphylla Suk. and Their Responses to Abiotic Stresses. Int J Mol Sci 2023; 24:15000. [PMID: 37834448 PMCID: PMC10573109 DOI: 10.3390/ijms241915000] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/02/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
The WRKY transcription factor (TF) family is one the largest plant-specific transcription factor families. It has been proven to play significant roles in multiple plant biological processes, especially stress response. Although many WRKY TFs have been identified in various plant species, WRKYs in white birch (Betula platyphylla Suk.) remain to be studied. Here, we identified a total of 68 BpWRKYs, which could be classified into four main groups. The basic physiochemical properties of these TFs were analyzed using bioinformatics tools, including molecular weight, isoelectric point, chromosome location, and predicted subcellular localization. Most BpWRKYs were predicted to be located in the nucleus. Synteny analysis found 17 syntenic gene pairs among BpWRKYs and 52 syntenic gene pairs between BpWRKYs and AtWRKYs. The cis-acting elements in the promoters of BpWRKYs could be enriched in multiple plant biological processes, including stress response, hormone response, growth and development, and binding sites. Tissue-specific expression analysis using qRT-PCR showed that most BpWRKYs exhibited highest expression levels in the root. After ABA, salt (NaCl), or cold treatment, different BpWRKYs showed different expression patterns at different treatment times. Furthermore, the results of the Y2H assay proved the interaction between BpWRKY17 and a cold-responsive TF, BpCBF7. By transient expression assay, BpWRKY17 and BpWRKY67 were localized in the nucleus, consistent with the previous prediction. Our study hopes to shed light for research on WRKY TFs and plant stress response.
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Affiliation(s)
- Jiajie Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Xiang Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Jiayu Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Heming Bai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Chunming Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
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Zheng H, Fu X, Shao J, Tang Y, Yu M, Li L, Huang L, Tang K. Transcriptional regulatory network of high-value active ingredients in medicinal plants. TRENDS IN PLANT SCIENCE 2023; 28:429-446. [PMID: 36621413 DOI: 10.1016/j.tplants.2022.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 05/14/2023]
Abstract
High-value active ingredients in medicinal plants have attracted research attention because of their benefits for human health, such as the antimalarial artemisinin, anticardiovascular disease tanshinones, and anticancer Taxol and vinblastine. Here, we review how hormones and environmental factors promote the accumulation of active ingredients, thereby providing a strategy to produce high-value drugs at a low cost. Focusing on major hormone signaling events and environmental factors, we review the transcriptional regulatory network mediating biosynthesis of representative active ingredients. In this network, many transcription factors (TFs) simultaneously control multiple synthase genes; thus, understanding the molecular mechanisms affecting transcriptional regulation of active ingredients will be crucial to developing new breeding possibilities.
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Affiliation(s)
- Han Zheng
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xueqing Fu
- School of Design, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Shao
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yueli Tang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), SWU-TAAHC Medicinal Plant Joint R&D Centre,School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Muyao Yu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ling Li
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Kexuan Tang
- Frontiers Science Center for Transformative Molecules, Joint International Research Laboratory of Metabolic and Developmental Sciences, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), SWU-TAAHC Medicinal Plant Joint R&D Centre,School of Life Sciences, Southwest University, Chongqing 400715, China.
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Goyal P, Devi R, Verma B, Hussain S, Arora P, Tabassum R, Gupta S. WRKY transcription factors: evolution, regulation, and functional diversity in plants. PROTOPLASMA 2023; 260:331-348. [PMID: 35829836 DOI: 10.1007/s00709-022-01794-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues into digital data to express both qualitative and quantitative forms. The transcriptomic approach, in particular, has added new dimensions to the versatile essence of plant genomics through the large and deep transcripts generated in the process. This has enabled the mining of super families from the sequenced plants, both model and non-model, understanding their ancestry, diversity, and evolution. The elucidation of the crystal structure of the WRKY proteins and recent advancement in computational prediction through homology modeling and molecular dynamic simulation has provided an insight into the DNA-protein complex formation, stability, and interaction, thereby giving a new dimension in understanding the WRKY regulation. The present review summarizes the functional aspects of the high volume of sequence data of WRKY transcription factors studied from different species, till date. The review focuses on the dynamics of structural classification and lineage in light of the recent information. Additionally, a comparative analysis approach was incorporated to understand the functions of the identified WRKY transcription factors subjected to abiotic (heat, cold, salinity, senescence, dark, wounding, UV, and carbon starvation) stresses as revealed through various sets of studies on different plant species. The review will be instrumental in understanding the events of evolution and the importance of WRKY TFs under the threat of climate change, considering the new scientific evidences to propose a fresh perspective.
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Affiliation(s)
- Pooja Goyal
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Registered from Guru Nanak Dev University, Amritsar, India
| | - Ritu Devi
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bhawana Verma
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shahnawaz Hussain
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Palak Arora
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Rubeena Tabassum
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Suphla Gupta
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India.
- Faculty, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Zhang C, Wang W, Wang D, Hu S, Zhang Q, Wang Z, Cui L. Genome-Wide Identification and Characterization of the WRKY Gene Family in Scutellaria baicalensis Georgi under Diverse Abiotic Stress. Int J Mol Sci 2022; 23:ijms23084225. [PMID: 35457040 PMCID: PMC9029115 DOI: 10.3390/ijms23084225] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023] Open
Abstract
The WRKY gene family is an important inducible regulatory factor in plants, which has been extensively studied in many model plants. It has progressively become the focus of investigation for the secondary metabolites of medicinal plants. Currently, there is no systematic analysis of the WRKY gene family in Scutellaria baicalensis Georgi. For this study, a systematic and comprehensive bioinformatics analysis of the WRKY gene family was conducted based on the genomic data of S. baicalensis. A total of 77 WRKY members were identified and 75 were mapped onto nine chromosomes, respectively. Their encoded WRKY proteins could be classified into three subfamilies: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III, based on the characteristics of the amino acid sequences of the WRKY domain and genetic structure. Syntenic analysis revealed that there were 35 pairs of repetitive fragments. Furthermore, the transcriptome data of roots, stems, leaves, and flowers showed that the spatial expression profiles of WRKYs were different. qRT-PCR analysis revealed that 11 stress-related WRKYs exhibited specific expression patterns under diverse treatments. In addition, sub cellular localization analysis indicated that SbWRKY26 and SbWRKY41 were localized in nucleus. This study is the first to report the identification and characterization of the WRKY gene family in S. baicalensis, which is valuable for the further exploration of the biological function of SbWRKYs. It also provides valuable bioinformatics data for S. baicalensis and provides a reference for assessing the medicinal properties of the genus.
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Di P, Wang P, Yan M, Han P, Huang X, Yin L, Yan Y, Xu Y, Wang Y. Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng. BMC Genomics 2021; 22:834. [PMID: 34794386 PMCID: PMC8600734 DOI: 10.1186/s12864-021-08145-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Panax ginseng is a well-known medicinal plant worldwide. As an herbal medicine, ginseng is also known for its long lifecycle, which can reach several decades. WRKY proteins play regulatory roles in many aspects of biological processes in plants, such as responses to biotic or abiotic stress, plant development, and adaptation to environmental challenges. Genome-wide analyses of WRKY genes in P. ginseng have not been reported. RESULTS In this study, 137 PgWRKY genes were identified from the ginseng genome. Phylogenetic analysis showed that the PgWRKYs could be clustered into three primary groups and five subgroups. Most of the PgWRKY gene promoters contained several kinds of hormone- and stress-related cis-regulatory elements. The expression patterns of PgWRKY genes in 14 different tissues were analyzed based on the available public RNA-seq data. The responses of the PgWRKY genes to heat, cold, salt and drought treatment were also investigated. Most of the PgWRKY genes were expressed differently after heat treatment, and expression trends changed significantly under drought and cold treatment but only slightly under salt treatment. The coexpression analysis of PgWRKY genes with the ginsenoside biosynthesis pathway genes identified 11 PgWRKYs that may have a potential regulatory role in the biosynthesis process of ginsenoside. CONCLUSIONS This work provides insights into the evolution, modulation and distribution of the WRKY gene family in ginseng and extends our knowledge of the molecular basis along with modulatory mechanisms of WRKY transcription factors in ginsenoside biosynthesis.
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Affiliation(s)
- Peng Di
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, 130118, Changchun, China. .,State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China.
| | - Ping Wang
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, 130118, Changchun, China
| | - Min Yan
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, 130118, Changchun, China
| | - Peng Han
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, 130118, Changchun, China
| | - Xinyi Huang
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, 130118, Changchun, China
| | - Le Yin
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, 130118, Changchun, China
| | - Yan Yan
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, 130118, Changchun, China
| | - Yonghua Xu
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, 130118, Changchun, China.
| | - Yingping Wang
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, 130118, Changchun, China
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Zhou T, Yang X, Wang G, Cao F. Molecular cloning and expression analysis of a WRKY transcription factor gene, GbWRKY20, from Ginkgo biloba. PLANT SIGNALING & BEHAVIOR 2021; 16:1930442. [PMID: 34024256 PMCID: PMC8331020 DOI: 10.1080/15592324.2021.1930442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 05/17/2023]
Abstract
WRKY transcription factors are important regulators of diverse plant life processes. Our aim was to clone and characterize GbWRKY20, a WRKY gene of group IIc, derived from Ginkgo biloba. The cDNA sequence of GbWRKY20 was 818 bp long, encoding a 271-amino acid proteins and containing two introns and three exons. The proteinic molecular weight was 30.99 kDa, with a relevant theoretical isoelectric point of 8.15. Subcellular localization analysis confirmed that the GbWRKY20 protein localized to the nucleus. In total, 75 cis-regulatory elements of 19 different types were identified in the GbWRKY20 promoter sequence, including some elements involved in light responsiveness, anaerobic induction and circadian control, low-temperature responsiveness, as well as salicylic acid (SA) and auxin responsiveness. Expression pattern analysis of plant samples from different developmental stages and tissue types, revealed differential GbWRKY20 expression. The GbWRKY20 transcript was downregulated 12 h after heat treatment and at 4-12 h after drought treatment, but was upregulated 12 h after NaCl, cold and methyl jasmonate treatments. For abscisic acid and SA treatments, the GbWRKY20 transcript was upregulated at 24 h. In summary, GbWRKY20 encoded a newly cloned WRKY transcription factor of G. biloba that might be involved in plant growth and plant responses to abiotic stresses and hormones treatments.
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Affiliation(s)
- Tingting Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China; College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xiaoming Yang
- Co-Innovation Center for Sustainable Forestry in Southern China; College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Guibin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China; College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Fuliang Cao
- Co-Innovation Center for Sustainable Forestry in Southern China; College of Forestry, Nanjing Forestry University, Nanjing, China
- CONTACT Fuliang Cao Co-Innovation Center for Sustainable Forestry in Southern China; College of Forestry, Nanjing Forestry University, NanjingChina
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Amin I, Rasool S, Mir MA, Wani W, Masoodi KZ, Ahmad P. Ion homeostasis for salinity tolerance in plants: a molecular approach. PHYSIOLOGIA PLANTARUM 2021; 171:578-594. [PMID: 32770745 DOI: 10.1111/ppl.13185] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/23/2020] [Accepted: 08/06/2020] [Indexed: 05/07/2023]
Abstract
Soil salinity is one of the major environmental stresses faced by the plants. Sodium chloride is the most important salt responsible for inducing salt stress by disrupting the osmotic potential. Due to various innate mechanisms, plants adapt to the sodic niche around them. Genes and transcription factors regulating ion transport and exclusion such as salt overly sensitive (SOS), Na+ /H+ exchangers (NHXs), high sodium affinity transporter (HKT) and plasma membrane protein (PMP) are activated during salinity stress and help in alleviating cells of ion toxicity. For salt tolerance in plants signal transduction and gene expression is regulated via transcription factors such as NAM (no apical meristem), ATAF (Arabidopsis transcription activation factor), CUC (cup-shaped cotyledon), Apetala 2/ethylene responsive factor (AP2/ERF), W-box binding factor (WRKY) and basic leucine zipper domain (bZIP). Cross-talk between all these transcription factors and genes aid in developing the tolerance mechanisms adopted by plants against salt stress. These genes and transcription factors regulate the movement of ions out of the cells by opening various membrane ion channels. Mutants or knockouts of all these genes are known to be less salt-tolerant compared to wild-types. Using novel molecular techniques such as analysis of genome, transcriptome, ionome and metabolome of a plant, can help in expanding the understanding of salt tolerance mechanism in plants. In this review, we discuss the genes responsible for imparting salt tolerance under salinity stress through transport dynamics of ion balance and need to integrate high-throughput molecular biology techniques to delineate the issue.
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Affiliation(s)
- Insha Amin
- Molecular Biology Lab, Division of Veterinary Biochemistry, FVSc & A.H., SKUAST, Shuhama, India
| | - Saiema Rasool
- Department of School Education, Govt. of Jammu & Kashmir, Srinagar, 190001, India
| | - Mudasir A Mir
- Transcriptomics Lab, Division of Plant Biotechnology, SKUAST-Kashmir, Shalimar, 190025, India
| | - Wasia Wani
- Transcriptomics Lab, Division of Plant Biotechnology, SKUAST-Kashmir, Shalimar, 190025, India
| | - Khalid Z Masoodi
- Transcriptomics Lab, Division of Plant Biotechnology, SKUAST-Kashmir, Shalimar, 190025, India
| | - Parvaiz Ahmad
- Botany and Microbiology Department, College of Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
- Department of Botany, S. P. College, Srinagar, Jammu and Kashmir, 190001, India
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Yao L, Lu J, Wang J, Gao WY. Advances in biosynthesis of triterpenoid saponins in medicinal plants. Chin J Nat Med 2020; 18:417-424. [PMID: 32503733 DOI: 10.1016/s1875-5364(20)30049-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Indexed: 12/13/2022]
Abstract
In recent years, biosynthesis of triterpenoid saponins in medicinal plants has been widely studied because of their active ingredients with diverse pharmacological activities. Various oxidosqualene cyclases, cytochrome P450 monooxygenases, uridine diphosphate glucuronosyltransferases, and transcription factors related to triterpenoid saponins biosynthesis have been explored and identified. In the biosynthesis of triterpenoid saponins, the progress of gene mining by omics-based sequencing, gene screening, gene function verification, catalyzing mechanism of key enzymes and gene regulation are summarized and discussed. By the progress of the biosynthesis pathway of triterpenoid saponins, the large-scale production of some triterpenoid saponins and aglycones has been achieved through plant tissue culture, transgenic plants and engineered yeast cells. However, the complex biosynthetic pathway and structural diversity limit the biosynthesis of triterpenoid saponins in different system. Special focus can further be placed on the systematic botany information of medicinal plants obtained from omics large dataset, and triterpenoid saponins produced by synthetic biology strategies, gene mutations and gene editing technology.
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Affiliation(s)
- Lu Yao
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Jun Lu
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Juan Wang
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
| | - Wen-Yuan Gao
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
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11
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Penicillium sp. YJM-2013 induces ginsenosides biosynthesis in Panax ginseng adventitious roots by inducing plant resistance responses. CHINESE HERBAL MEDICINES 2020; 12:257-264. [PMID: 36119014 PMCID: PMC9476754 DOI: 10.1016/j.chmed.2020.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 10/19/2019] [Accepted: 02/12/2020] [Indexed: 01/30/2023] Open
Abstract
Objective Fusarium oxysporum is a common pathogenic fungus in ginseng cultivation. Both pathogens and antagonistic fungi have been reported to induce plant resistance responses, thereby promoting the accumulation of secondary metabolites. The purpose of this experiment is to compare the advantages of one of the two fungi, in order to screen out more effective elicitors. The mechanism of fungal elicitor-induced plant resistance response is supplemented. Methods A gradient dilution and the dural culture were carried out to screen strains. The test strain was identified by morphology and 18 s rDNA. The effect of different concentrations (0, 50, 100, 200, 400 mg/L) of Penicillium sp. YJM-2013 and F. oxysporum on fresh weight and ginsenosides accumulation were tested. Signal molecules transduction, expression of transcription factors and functional genes were investigated to study the induction mechanism of fungal elicitors. Results Antagonistic fungi of F. oxysporum was identified as Penicillium sp. YJM-2013, which reduced root biomass. The total ginsenosides content of Panax ginseng adventitious roots reached the maximum (48.95 ± 0.97 mg/g) treated with Penicillium sp. YJM-2013 at 200 mg/L, higher than control by 2.59-fold, in which protopanoxadiol-type ginsenosides (PPD) were increased by 4.57 times. Moreover, Penicillium sp. YJM-2013 activated defense signaling molecules, up-regulated the expression of PgWRKY 1, 2, 3, 5, 7, 9 and functional genes in ginsenosides synthesis. Conclusion Compared with the pathogenic fungi F. oxysporum, antagonistic fungi Penicillium sp. YJM-2013 was more conducive to the accumulation of ginsenosides in P. ginseng adventitious roots. Penicillium sp. YJM-2013 promoted the accumulation of ginsenosides by intensifying the generation of signal molecules, activating the expression of transcription factors and functional genes.
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12
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Yang Y, Wang N, Zhao S. Functional characterization of a WRKY family gene involved in somatic embryogenesis in Panax ginseng. PROTOPLASMA 2020; 257:449-458. [PMID: 31760482 DOI: 10.1007/s00709-019-01455-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
As a perennial herbaceous species, Panax ginseng is widely cultivated and used as traditional herbal medicine. The root of Panax ginseng commonly remains expensive as conventional breeding of Panax ginseng is difficult. Somatic embryogenesis (S.E.) is a useful tool for plant propagation and optimal model for understanding the mechanisms of plant embryogenesis. In Panax ginseng, increasing studies have been widely performed to optimize the technology of S.E., while the underlying mechanism remains unclear. In this paper, we cloned and identified a WRKY family gene named PgWRKY6 which is upregulated in response to 2,4-D (2,4-dichlorophenoxyacetic acid)-induced embryogenic callus development. The silencing of PgWRKY6 obviously reduces the induction rate of embryogenic callus, indicating its crucial role in S.E. of Panax ginseng hairy root. The expressions of several ROS-scavenging genes are also inducible during embryogenic callus development, and the transcriptions of PgGST, PgAPX1, and PgSOD are demonstrated to be regulated by PgWRKY6. Recombinant PgWRKY6, an approximate 40-KDa protein purified from Escherichia coli, shows a specific DNA-binding activity with a potential recognition site of TTGAC(C/T). This work demonstrated that as a conserved WRKY family transcription factor, PgWRKY6 functions upstream of PgGST, PgAPX1, and PgSOD, and potentially mediated auxins -ROS signaling pathway in the process of S.E. in Panax species.
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Affiliation(s)
- Yu Yang
- Shandong Collaborative Innovation Center for Diagnosis, Treatment and Behavioral Interventions, Jining Medical University, No. 133 Hehua Street, Jining, China
- School of Life Sciences, Jilin University, No. 5988, Renmin Street, Nanguan District, Changchun, China
| | - Ni Wang
- Changchun Vocational Institute of Technology, No. 3278 Weixing Street, Changchun, China
| | - Shoujing Zhao
- School of Life Sciences, Jilin University, No. 5988, Renmin Street, Nanguan District, Changchun, China.
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Till 2018: a survey of biomolecular sequences in genus Panax. J Ginseng Res 2020; 44:33-43. [PMID: 32095095 PMCID: PMC7033366 DOI: 10.1016/j.jgr.2019.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022] Open
Abstract
Ginseng is popularly known to be the king of ancient medicines and is used widely in most of the traditional medicinal compositions due to its various pharmaceutical properties. Numerous studies are being focused on this plant's curative effects to discover their potential health benefits in most human diseases, including cancer- the most life-threatening disease worldwide. Modern pharmacological research has focused mainly on ginsenosides, the major bioactive compounds of ginseng, because of their multiple therapeutic applications. Various issues on ginseng plant development, physiological processes, and agricultural issues have also been studied widely through state-of-the-art, high-throughput sequencing technologies. Since the beginning of the 21st century, the number of publications on ginseng has rapidly increased, with a recent count of more than 6,000 articles and reviews focusing notably on ginseng. Owing to the implementation of various technologies and continuous efforts, the ginseng plant genomes have been decoded effectively in recent years. Therefore, this review focuses mainly on the cellular biomolecular sequences in ginseng plants from the perspective of the central molecular dogma, with an emphasis on genomes, transcriptomes, and proteomes, together with a few other related studies.
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14
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Kochan E, Balcerczak E, Szymczyk P, Sienkiewicz M, Zielińska-Bliźniewska H, Szymańska G. Abscisic Acid Regulates the 3-Hydroxy-3-methylglutaryl CoA Reductase Gene Promoter and Ginsenoside Production in Panax quinquefolium Hairy Root Cultures. Int J Mol Sci 2019; 20:ijms20061310. [PMID: 30875925 PMCID: PMC6471273 DOI: 10.3390/ijms20061310] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/22/2022] Open
Abstract
Panax quinquefolium hairy root cultures synthesize triterpenoid saponins named ginsenosides, that have multidirectional pharmacological activity. The first rate-limiting enzyme in the process of their biosynthesis is 3-hydroxy-3-methylglutaryl CoA reductase (HMGR). In this study, a 741 bp fragment of the P. quinquefoliumHMGR gene (PqHMGR), consisting of a proximal promoter, 5′UTR (5′ untranslated region) and 5′CDS (coding DNA sequence) was isolated. In silico analysis of an isolated fragment indicated a lack of tandem repeats, miRNA binding sites, and CpG/CpNpG elements. However, the proximal promoter contained potential cis-elements involved in the response to light, salicylic, and abscisic acid (ABA) that was represented by the motif ABRE (TACGTG). The functional significance of ABA on P. quinquefolium HMGR gene expression was evaluated, carrying out quantitative RT-PCR experiments at different ABA concentrations (0.1, 0.25, 0.5, and 1 mg·L−1). Additionally, the effect of abscisic acid and its time exposure on biomass and ginsenoside level in Panax quinquefolium hairy root was examined. The saponin content was determined using HPLC. The 28 day elicitation period with 1 mg·L−1 ABA was the most efficient for Rg2 and Re (17.38 and 1.83 times increase, respectively) accumulation; however, the protopanaxadiol derivative content decreased in these conditions.
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Affiliation(s)
- Ewa Kochan
- Department of Pharmaceutical Biotechnology, Medical University of Lodz, Muszyńskiego l, 90-151 Lodz, Poland.
| | - Ewa Balcerczak
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Interfaculty Cathedral of Laboratory and Molecular Diagnostics, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland.
| | - Piotr Szymczyk
- Department of Pharmaceutical Biotechnology, Medical University of Lodz, Muszyńskiego l, 90-151 Lodz, Poland.
| | - Monika Sienkiewicz
- Department of Allergology and Respiratory Rehabilitation, 2nd Chair of Otolaryngology, Medical University of Lodz, Żeligowskiego 7/9, 90-725, Lodz, Poland.
| | - Hanna Zielińska-Bliźniewska
- Department of Allergology and Respiratory Rehabilitation, 2nd Chair of Otolaryngology, Medical University of Lodz, Żeligowskiego 7/9, 90-725, Lodz, Poland.
| | - Grażyna Szymańska
- Department of Pharmaceutical Biotechnology, Medical University of Lodz, Muszyńskiego l, 90-151 Lodz, Poland.
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Zeng X, Luo T, Li J, Li G, Zhou D, Liu T, Zou X, Pandey A, Luo Z. Transcriptomics-based identification and characterization of 11 CYP450 genes of Panax ginseng responsive to MeJA. Acta Biochim Biophys Sin (Shanghai) 2018; 50:1094-1103. [PMID: 30321253 DOI: 10.1093/abbs/gmy120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Indexed: 11/14/2022] Open
Abstract
Cytochromes P450 (CYP450s), a superfamily of mono-oxygenases, are essential to generate highly functionalized secondary metabolites in plants and contribute to the diversification of specialized triterpenoid biosynthesis in eudicots. However, screening and identifying the exact CYP450 genes in ginsenoside biosynthesis is extremely challenging due to existence of large quantities of members in CYP450 superfamily. Therefore, to screen the CYP450 genes involved in ginsenoside biosynthesis, transcriptome dataset of Panax ginseng was created in our previous work using the technique of the next-generation sequencing. On the basis of bioinformatics analysis, 16 putative CYP450 genes with significant differential expression were screened from the dataset and submitted to GenBank, in which 11 of them have been cloned. Methyl jasmonate (MeJA) was used as an elicitor to analyze the expression profiles of candidate CYP450 genes by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). The results of qRT-PCR analysis revealed that the expression of some CYP450 genes were strongly induced by MeJA and showed different transcription levels at different treatment time points. Homology analysis indicated that each putative CYP450 protein of P. ginseng has a conserved domain consisting of E-E-R-F-P-R-G. The CYP450 genes were screened and cloned here to enrich the resources of CYP450 genes, and the results of bioinformatics analysis provided a foundation to further identify the function of CYP450s involved in ginsenoside biosynthesis. Furthermore, this study facilitated the construction of microbial cell factories for increasing the production of ginsenosides by means of metabolic engineering.
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Affiliation(s)
- Xu Zeng
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Tiao Luo
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Jijia Li
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Gui Li
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Donghua Zhou
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Tuo Liu
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Xian Zou
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Aparna Pandey
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Zhiyong Luo
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
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16
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Ali MA, Azeem F, Nawaz MA, Acet T, Abbas A, Imran QM, Shah KH, Rehman HM, Chung G, Yang SH, Bohlmann H. Transcription factors WRKY11 and WRKY17 are involved in abiotic stress responses in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2018; 226:12-21. [PMID: 29689430 DOI: 10.1016/j.jplph.2018.04.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 03/14/2018] [Accepted: 04/14/2018] [Indexed: 05/28/2023]
Abstract
Plant WRKY transcription factors play a vital role in abiotic stress tolerance and regulation of plant defense responses. This study examined AtWRKY11 and AtWRKY17 expression under ABA, salt, and osmotic stress at different developmental stages in Arabidopsis. We used reverse transcriptase PCR, quantitative real-time PCR, and promoter:GUS lines to analyze expression. Both genes were upregulated in response to abiotic stress. Next, we applied the same stressors to seedlings of T-DNA insertion wrky11 and 17 knock-out mutants (single and double). Under stress, the mutants exhibited slower germination and compromised root growth compared with the wild type. In most cases, double-mutant seedlings were more affected than single mutants. These results suggest that wrky11 and wrky17 are not strictly limited to plant defense responses but are also involved in conferring stress tolerance.
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Affiliation(s)
- Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, 38040 Faisalabad, Pakistan; Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, 38040 Faisalabad, Pakistan.
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Tuba Acet
- Department of Genetic and Bioengineering, Faculty of Engineering and Natural Sciences, Gumusahne University, 29100, Gumushane, Turkey
| | - Amjad Abbas
- Department of Plant Pathology, University of Agriculture, 38040 Faisalabad, Pakistan
| | - Qari Muhammad Imran
- Laboratory of Plant Functional Genomics, College of Agriculture & Life Sciences, Kyngpook National University, Buk-gu Daegu, 702-701, South Korea
| | - Kausar Hussain Shah
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea.
| | - Holger Bohlmann
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
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17
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Lu J, Li J, Wang S, Yao L, Liang W, Wang J, Gao W. Advances in ginsenoside biosynthesis and metabolic regulation. Biotechnol Appl Biochem 2018; 65:514-522. [DOI: 10.1002/bab.1649] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 01/24/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Jun Lu
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency; School of Pharmaceutical Science and Technology; Tianjin University; Tianjin People's Republic of China
- Key Laboratory of Systems Bioengineering; Ministry of Education; Tianjin University; Tianjin People's Republic of China
| | - Jinxin Li
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency; School of Pharmaceutical Science and Technology; Tianjin University; Tianjin People's Republic of China
- Key Laboratory of Systems Bioengineering; Ministry of Education; Tianjin University; Tianjin People's Republic of China
| | - Shihui Wang
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education; Tianjin University of Science and Technology; Tianjin People's Republic of China
| | - Lu Yao
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency; School of Pharmaceutical Science and Technology; Tianjin University; Tianjin People's Republic of China
- Key Laboratory of Systems Bioengineering; Ministry of Education; Tianjin University; Tianjin People's Republic of China
| | - Wenxia Liang
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education; Tianjin University of Science and Technology; Tianjin People's Republic of China
| | - Juan Wang
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency; School of Pharmaceutical Science and Technology; Tianjin University; Tianjin People's Republic of China
- Key Laboratory of Systems Bioengineering; Ministry of Education; Tianjin University; Tianjin People's Republic of China
| | - Wenyuan Gao
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency; School of Pharmaceutical Science and Technology; Tianjin University; Tianjin People's Republic of China
- Key Laboratory of Systems Bioengineering; Ministry of Education; Tianjin University; Tianjin People's Republic of China
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18
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Jo IH, Lee J, Hong CE, Lee DJ, Bae W, Park SG, Ahn YJ, Kim YC, Kim JU, Lee JW, Hyun DY, Rhee SK, Hong CP, Bang KH, Ryu H. Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome. Genes (Basel) 2017; 8:E228. [PMID: 28914759 PMCID: PMC5615361 DOI: 10.3390/genes8090228] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/17/2017] [Accepted: 09/12/2017] [Indexed: 11/17/2022] Open
Abstract
Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness. Of those unigenes, 67.5% were predicted to be complete full-length (FL) open reading frames (ORFs) and exhibited a high gene annotation rate. Furthermore, we successfully identified unique full-length genes involved in triterpenoid saponin synthesis and plant hormonal signaling pathways, including auxin and cytokinin. Studies on the functional genomics of P. ginseng seedlings have confirmed the rapid upregulation of negative feed-back loops by auxin and cytokinin signaling cues. The conserved evolutionary mechanisms in the auxin and cytokinin canonical signaling pathways of P. ginseng are more complex than those in Arabidopsis thaliana. Our analysis also revealed a more detailed view of transcriptome-wide alternative isoforms for 88 genes. Finally, transposable elements (TEs) were also identified, suggesting transcriptional activity of TEs in P. ginseng. In conclusion, our results suggest that long-read, full-length or partial-unigene data with high-quality assemblies are invaluable resources as transcriptomic references in P. ginseng and can be used for comparative analyses in closely related medicinal plants.
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Affiliation(s)
- Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Chi Eun Hong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | | | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Sin-Gi Park
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Yong Ju Ahn
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Young Chang Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jang Uk Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jung Woo Lee
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Dong Yun Hyun
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea.
| | | | - Kyong Hwan Bang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
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Xiu H, Nuruzzaman M, Guo X, Cao H, Huang J, Chen X, Wu K, Zhang R, Huang Y, Luo J, Luo Z. Molecular Cloning and Expression Analysis of Eight PgWRKY Genes in Panax ginseng Responsive to Salt and Hormones. Int J Mol Sci 2016; 17:319. [PMID: 26959011 PMCID: PMC4813182 DOI: 10.3390/ijms17030319] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 02/03/2016] [Accepted: 02/22/2016] [Indexed: 12/11/2022] Open
Abstract
Despite the importance of WRKY genes in plant physiological processes, little is known about their roles in Panax ginseng C.A. Meyer. Forty-eight unigenes on this species were previously reported as WRKY transcripts using the next-generation sequencing (NGS) technology. Subsequently, one gene that encodes PgWRKY1 protein belonging to subgroup II-d was cloned and functionally characterized. In this study, eight WRKY genes from the NGS-based transcriptome sequencing dataset designated as PgWRKY2-9 have been cloned and characterized. The genes encoding WRKY proteins were assigned to WRKY Group II (one subgroup II-c, four subgroup II-d, and three subgroup II-e) based on phylogenetic analysis. The cDNAs of the cloned PgWRKYs encode putative proteins ranging from 194 to 358 amino acid residues, each of which includes one WRKYGQK sequence motif and one C2H2-type zinc-finger motif. Quantitative real-time PCR (qRT-PCR) analysis demonstrated that the eight analyzed PgWRKY genes were expressed at different levels in various organs including leaves, roots, adventitious roots, stems, and seeds. Importantly, the transcription responses of these PgWRKYs to methyl jasmonate (MeJA) showed that PgWRKY2, PgWRKY3, PgWRKY4, PgWRKY5, PgWRKY6, and PgWRKY7 were downregulated by MeJA treatment, while PgWRKY8 and PgWRKY9 were upregulated to varying degrees. Moreover, the PgWRKY genes increased or decreased by salicylic acid (SA), abscisic acid (ABA), and NaCl treatments. The results suggest that the PgWRKYs may be multiple stress–inducible genes responding to both salt and hormones.
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Affiliation(s)
- Hao Xiu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Mohammed Nuruzzaman
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Xiangqian Guo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Hongzhe Cao
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Jingjia Huang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Xianghui Chen
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Kunlu Wu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Ru Zhang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Yuzhao Huang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Junli Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Zhiyong Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
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20
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Phukan UJ, Jeena GS, Shukla RK. WRKY Transcription Factors: Molecular Regulation and Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:760. [PMID: 27375634 PMCID: PMC4891567 DOI: 10.3389/fpls.2016.00760] [Citation(s) in RCA: 390] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/17/2016] [Indexed: 05/17/2023]
Abstract
Plants in their natural habitat have to face multiple stresses simultaneously. Evolutionary adaptation of developmental, physiological, and biochemical parameters give advantage over a single window of stress but not multiple. On the other hand transcription factors like WRKY can regulate diverse responses through a complicated network of genes. So molecular orchestration of WRKYs in plant may provide the most anticipated outcome of simultaneous multiple responses. Activation or repression through W-box and W-box like sequences is regulated at transcriptional, translational, and domain level. Because of the tight regulation involved in specific recognition and binding of WRKYs to downstream promoters, they have become promising candidate for crop improvement. Epigenetic, retrograde and proteasome mediated regulation enable WRKYs to attain the dynamic cellular homeostatic reprograming. Overexpression of several WRKYs face the paradox of having several beneficial affects but with some unwanted traits. These overexpression-associated undesirable phenotypes need to be identified and removed for proper growth, development and yeild. Taken together, we have highlighted the diverse regulation and multiple stress response of WRKYs in plants along with the future prospects in this field of research.
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