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Zheng H, Xie Y, Mu C, Cheng W, Bai Y, Gao J. Deciphering the regulatory role of PheSnRK genes in Moso bamboo: insights into hormonal, energy, and stress responses. BMC Genomics 2024; 25:252. [PMID: 38448813 PMCID: PMC10916206 DOI: 10.1186/s12864-024-10176-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
The SnRK (sucrose non-fermentation-related protein kinase) plays an important role in regulating various signals in plants. However, as an important bamboo shoot and wood species, the response mechanism of PheSnRK in Phyllostachys edulis to hormones, low energy and stress remains unclear. In this paper, we focused on the structure, expression, and response of SnRK to hormones and sugars. In this study, we identified 75 PheSnRK genes from the Moso bamboo genome, which can be divided into three groups according to the evolutionary relationship. Cis-element analysis has shown that the PheSnRK gene can respond to various hormones, light, and stress. The PheSnRK2.9 proteins were localized in the nucleus and cytoplasm. Transgenic experiments showed that overexpression of PheSnRK2.9 inhibited root development, the plants were salt-tolerant and exhibited slowed starch consumption in Arabidopsis in the dark. The results of yeast one-hybrid and dual luciferase assay showed that PheIAAs and PheNACs can regulate PheSnRK2.9 gene expression by binding to the promoter of PheSnRK2.9. This study provided a comprehensive understanding of PheSnRK genes of Moso bamboo, which provides valuable information for further research on energy regulation mechanism and stress response during the growth and development of Moso bamboo.
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Affiliation(s)
- Huifang Zheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
- College of Life Science, Leshan Normal University, Leshan, China
| | - Yali Xie
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China.
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Wang W, Li Y, Cai C, Zhu Q. Auxin response factors fine-tune lignin biosynthesis in response to mechanical bending in bamboo. THE NEW PHYTOLOGIST 2024; 241:1161-1176. [PMID: 37964659 DOI: 10.1111/nph.19398] [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: 08/08/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023]
Abstract
Lignin contributes to plant mechanical properties during bending loads. Meanwhile, phytohormone auxin controls various plant biological processes. However, the mechanism of auxin's role in bending-induced lignin biosynthesis was unclear, especially in bamboo, celebrated for its excellent deformation stability. Here, we reported that auxin response factors (ARF) 3 and ARF6 from Moso bamboo (Phyllostachys edulis (Carrière) J. Houz) directly regulate lignin biosynthesis pathway genes, and affect lignin biosynthesis in bamboo. Auxin and lignin exhibited asymmetric distribution patterns, and auxin promoted lignin biosynthesis in response to bending loads in bamboo. Employing transcriptomic and weighted gene co-expression network analysis approach, we discovered that expression patterns of ARF3 and ARF6 strongly correlated with lignin biosynthesis genes. ARF3 and ARF6 directly bind to the promoter regions of 4-coumarate: coenzyme A ligase (4CL3, 4CL7, and 4CL9) or caffeoyl-CoA O-methyltransferase (CCoAOMT2) genes, pivotal to lignin biosynthesis, and activate their expressions. Notably, the efficacy of this binding hinges on auxin levels. Alternation of the expressions of ARF3 and ARF6 substantially altered lignin accumulation in transgenic bamboo. Collectively, our study shed light on bamboo lignification genetics. Auxin signaling could directly modulate lignin biosynthesis genes to impact plant lignin content.
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Affiliation(s)
- Wenjia Wang
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Haixia Institute for Science and Technology, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Yigang Li
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Haixia Institute for Science and Technology, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Changyang Cai
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Haixia Institute for Science and Technology, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Qiang Zhu
- Basic Forestry and Proteomics Center (BFPC), College of Forestry, Haixia Institute for Science and Technology, Fujian Agriculture and Forestry University, 350002, Fujian, China
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Zhang P, Liu D, Ma J, Sun C, Wang Z, Zhu Y, Zhang X, Liu Y. Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe. BMC Genomics 2024; 25:83. [PMID: 38245685 PMCID: PMC10799369 DOI: 10.1186/s12864-024-09966-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Protein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published. RESULTS In this study, 97 ZoPP2C genes were identified based on the ginger genome. These genes were classified into 15 branches (A-O) according to the phylogenetic analysis and distributed unevenly on 11 ginger chromosomes. The proteins mainly functioned in the nucleus. Similar motif patterns and exon/intron arrangement structures were identified in the same subfamily of ZoPP2Cs. Collinearity analysis indicated that ZoPP2Cs had 33 pairs of fragment duplicated events uniformly distributed on the corresponding chromosomes. Furthermore, ZoPP2Cs showed greater evolutionary proximity to banana's PP2Cs. The forecast of cis-regulatory elements and transcription factor binding sites demonstrated that ZoPP2Cs participate in ginger growth, development, and responses to hormones and stresses. ZoERFs have plenty of binding sites of ZoPP2Cs, suggesting a potential synergistic contribution between ZoERFs and ZoPP2Cs towards regulating growth/development and adverse conditions. The protein-protein interaction network displayed that five ZoPP2Cs (9/23/26/49/92) proteins have robust interaction relationship and potential function as hub proteins. Furthermore, the RNA-Seq and qRT-PCR analyses have shown that ZoPP2Cs exhibit various expression patterns during ginger maturation and responses to environmental stresses such as chilling, drought, flooding, salt, and Fusarium solani. Notably, exogenous application of melatonin led to notable up-regulation of ZoPP2Cs (17/59/11/72/43) under chilling stress. CONCLUSIONS Taken together, our investigation provides significant insights of the ginger PP2C gene family and establishes the groundwork for its functional validation and genetic engineering applications.
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Affiliation(s)
- Pan Zhang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Deqi Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jiawei Ma
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Chong Sun
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Zhaofei Wang
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Yongxing Zhu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xuemei Zhang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yiqing Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
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Hu X, Liang J, Wang W, Cai C, Ye S, Wang N, Han F, Wu Y, Zhu Q. Comprehensive genome-wide analysis of the DREB gene family in Moso bamboo (Phyllostachys edulis): evidence for the role of PeDREB28 in plant abiotic stress response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1248-1270. [PMID: 37566437 DOI: 10.1111/tpj.16420] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/16/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Dehydration response element binding (DREB) proteins are vital for plant abiotic stress responses, but the understanding of DREBs in bamboo, an important sustainable non-timber forest product, is limited. Here we conducted a comprehensive genome-wide analysis of the DREB gene family in Moso bamboo, representing the most important running bamboo species in Asia. In total, 44 PeDREBs were identified, and information on their gene structures, protein motifs, phylogenetic relationships, and stress-related cis-regulatory elements (CREs) was provided. Based on the bioinformatical analysis, we further analyzed PeDREBs from the A5 group and found that four of five PeDREB transcripts were induced by salt, drought, and cold stresses, and their proteins could bind to stress-related CREs. Among these, PeDREB28 was selected as a promising candidate for further functional characterization. PeDREB28 is localized in nucleus, has transcriptional activation activity, and could bind to the DRE- and coupling element 1- (CE1) CREs. Overexpression of PeDREB28 in Arabidopsis and bamboo improved plant abiotic stress tolerance. Transcriptomic analysis showed that broad changes due to the overexpression of PeDREB28. Furthermore, 628 genes that may act as the direct PeDREB28 downstream genes were identified by combining DAP-seq and RNA-seq analysis. Moreover, we confirmed that PeDREB28 could bind to the promoter of pyrabactin-resistance-like gene (DlaPYL3), which is a homolog of abscisic acid receptor in Arabidopsis, and activates its expression. In summary, our study provides important insights into the DREB gene family in Moso bamboo, and contributes to their functional verification and genetic engineering applications in the future.
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Affiliation(s)
- Xin Hu
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Jianxiang Liang
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Wenjia Wang
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Changyang Cai
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Shanwen Ye
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Nannan Wang
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Fangying Han
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Yuxin Wu
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Qiang Zhu
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
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Sun H, Wang J, Li H, Li T, Gao Z. Advancements and challenges in bamboo breeding for sustainable development. TREE PHYSIOLOGY 2023; 43:1705-1717. [PMID: 37471643 DOI: 10.1093/treephys/tpad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/14/2023] [Accepted: 06/27/2023] [Indexed: 07/22/2023]
Abstract
Bamboo is a highly renewable biomass resource with outstanding ecological, economic and social benefits. However, its lengthy vegetative growth stage and uncertain flowering period have hindered the application of traditional breeding methods. In recent years, significant progress has been made in bamboo breeding. While technical advances in bamboo breeding have been impressive, it is essential to also consider the broader implications we can learn from bamboo's extraordinary features for sustainable development. This review provides an overview of the current status of bamboo breeding technology, including a detailed history of bamboo breeding divided into four eras, a comprehensive map of bamboo germplasm gardens worldwide, with a focus on China, and a summary of available transgenic technologies for gene function verification and genetic improvement. As the demand for bamboo as a sustainable and renewable resource increases continuously, breeding objectives should be focused on enhancing yield, wood properties and adaptability to diverse environmental conditions. In particular, priority should be given to improving fiber length, internode length and wall thickness, as well as regulating lignin and cellulose content for papermaking, substitute for plastic and other applications. Furthermore, we highlight the challenges and opportunities for future research and development in bamboo breeding, including the application of omics technologies, artificial intelligence and the development of new breeding methods. Finally, by integrating the technical advances in bamboo breeding with a discussion of its broader implications for sustainable development, this review provides a comprehensive framework for the development of bamboo industry.
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Affiliation(s)
- Huayu Sun
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Jiangfei Wang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Hui Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Tiankuo Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
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Li K, Ji L, Xing Y, Zuo Z, Zhang L. Data-Independent Acquisition Proteomics Reveals the Effects of Red and Blue Light on the Growth and Development of Moso Bamboo ( Phyllostachys edulis) Seedlings. Int J Mol Sci 2023; 24:ijms24065103. [PMID: 36982175 PMCID: PMC10049362 DOI: 10.3390/ijms24065103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/30/2023] Open
Abstract
Moso bamboo is a rapidly growing species with significant economic, social, and cultural value. Transplanting moso bamboo container seedlings for afforestation has become a cost-effective method. The growth and development of the seedlings is greatly affected by the quality of light, including light morphogenesis, photosynthesis, and secondary metabolite production. Therefore, studies on the effects of specific light wavelengths on the physiology and proteome of moso bamboo seedlings are crucial. In this study, moso bamboo seedlings were germinated in darkness and then exposed to blue and red light conditions for 14 days. The effects of these light treatments on seedling growth and development were observed and compared through proteomics analysis. Results showed that moso bamboo has higher chlorophyll content and photosynthetic efficiency under blue light, while it displays longer internode and root length, more dry weight, and higher cellulose content under red light. Proteomics analysis reveals that these changes under red light are likely caused by the increased content of cellulase CSEA, specifically expressed cell wall synthetic proteins, and up-regulated auxin transporter ABCB19 in red light. Additionally, blue light is found to promote the expression of proteins constituting photosystem II, such as PsbP and PsbQ, more than red light. These findings provide new insights into the growth and development of moso bamboo seedlings regulated by different light qualities.
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Affiliation(s)
- Ke Li
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Luyao Ji
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yaoyun Xing
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zecheng Zuo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
| | - Li Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China
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Sun H, Wang S, Zhu C, Yang K, Liu Y, Gao Z. A new biotechnology for in-planta gene editing and its application in promoting flavonoid biosynthesis in bamboo leaves. PLANT METHODS 2023; 19:20. [PMID: 36864483 PMCID: PMC9979463 DOI: 10.1186/s13007-023-00993-4] [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: 10/31/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Bamboo is a perennial and renewable biomass forest resource and its leaf flavonoid is an antioxidant for biological and pharmacological research. The established genetic transformation and gene editing systems in bamboo are significantly limited by the dependence on bamboo regeneration capability. The way to improve the flavonoid content in bamboo leaves through biotechnology is still not feasible. RESULTS Here, we developed an in-planta, Agrobacterium-mediated gene expression method for exogenous genes via wounding and vacuum in bamboo. We demonstrated that the RUBY served as a reporter efficiently expressed in bamboo leaves and shoots, albeit unable to integrate into the chromosome. We have also developed a gene editing system by creating an in situ mutant of the bamboo violaxanthin de-epoxidase (PeVDE) gene in bamboo leaves, with lower NPQ values under the fluorometer, which can serve as a native reporter for gene editing. Furthermore, the bamboo leaves with increased flavonoid content were achieved by knocking out the cinnamoyl-CoA reductase genes. CONCLUSIONS Our method can be applied for the functional characterization of novel genes in a short time and is helpful for bamboo leaf flavonoid biotechnology breeding in the future.
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Affiliation(s)
- Huayu Sun
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, 100102 China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102 China
| | - Sining Wang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, 100102 China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102 China
| | - Chenglei Zhu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, 100102 China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102 China
| | - Kebin Yang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, 100102 China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102 China
| | - Yan Liu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, 100102 China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102 China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, 100102 China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102 China
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Jin Y, Wang B, Bao M, Li Y, Xiao S, Wang Y, Zhang J, Zhao L, Zhang H, Hsu YH, Li M, Gu L. Development of an efficient expression system with large cargo capacity for interrogation of gene function in bamboo based on bamboo mosaic virus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36794821 DOI: 10.1111/jipb.13468] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Bamboo is one of the fastest growing plants among monocotyledonous species and is grown extensively in subtropical regions. Although bamboo has high economic value and produces much biomass quickly, gene functional research is hindered by the low efficiency of genetic transformation in this species. We therefore explored the potential of a bamboo mosaic virus (BaMV)-mediated expression system to investigate genotype-phenotype associations. We determined that the sites between the triple gene block proteins (TGBps) and the coat protein (CP) of BaMV are the most efficient insertion sites for the expression of exogenous genes in both monopodial and sympodial bamboo species. Moreover, we validated this system by individually overexpressing the two endogenous genes ACE1 and DEC1, which resulted in the promotion and suppression of internode elongation, respectively. In particular, this system was able to drive the expression of three 2A-linked betalain biosynthesis genes (more than 4 kb in length) to produce betalain, indicating that it has high cargo capacity and may provide the prerequisite basis for the development of a DNA-free bamboo genome editing platform in the future. Since BaMV can infect multiple bamboo species, we anticipate that the system described in this study will greatly contribute to gene function research and further promote the molecular breeding of bamboo.
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Affiliation(s)
- Yandong Jin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baijie Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingchuan Bao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yujie Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shengwu Xiao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuhua Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jun Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangzhen Zhao
- Basic Forestry and Proteomics Research Center, School of Future Technology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, School of Future Technology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, Chung Hsing University, Taichung, 40227, China
| | - Mingjie Li
- College of crop science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, School of Future Technology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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9
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Kor SD, Chowdhury N, Keot AK, Yogendra K, Chikkaputtaiah C, Sudhakar Reddy P. RNA Pol III promoters-key players in precisely targeted plant genome editing. Front Genet 2023; 13:989199. [PMID: 36685866 PMCID: PMC9845283 DOI: 10.3389/fgene.2022.989199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/15/2022] [Indexed: 01/05/2023] Open
Abstract
The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool in basic and applied research for crop improvement programs. CRISPR/Cas tool is being extensively used in plants to improve crop yield, quality, and nutritional value and make them tolerant to environmental stresses. CRISPR/Cas system consists of a Cas protein with DNA endonuclease activity and one CRISPR RNA transcript that is processed to form one or several short guide RNAs that direct Cas9 to the target DNA sequence. The expression levels of Cas proteins and gRNAs significantly influence the editing efficiency of CRISPR/Cas-mediated genome editing. This review focuses on insights into RNA Pol III promoters and their types that govern the expression levels of sgRNA in the CRISPR/Cas system. We discussed Pol III promoters structural and functional characteristics and their comparison with Pol II promoters. Further, the use of synthetic promoters to increase the targeting efficiency and overcome the structural, functional, and expressional limitations of RNA Pol III promoters has been discussed. Our review reports various studies that illustrate the use of endogenous U6/U3 promoters for improving editing efficiency in plants and the applicative approach of species-specific RNA pol III promoters for genome editing in model crops like Arabidopsis and tobacco, cereals, legumes, oilseed, and horticultural crops. We further highlight the significance of optimizing these species-specific promoters' systematic identification and validation for crop improvement and biotic and abiotic stress tolerance through CRISPR/Cas mediated genome editing.
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Affiliation(s)
- Sakshi Dharmendra Kor
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Ajay Kumar Keot
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kalenahalli Yogendra
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India,*Correspondence: Palakolanu Sudhakar Reddy, ,
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Wu M, Liu H, Wang L, Zhang X, He W, Xiang Y. Comparative genomic analysis of the CPK gene family in Moso bamboo (Phyllostachys edulis) and the functions of PheCPK1 in drought stress. PROTOPLASMA 2023; 260:171-187. [PMID: 35503386 DOI: 10.1007/s00709-022-01765-y] [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: 01/13/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Calcium-dependent protein kinases (CPKs) play an important role in plant regulation of growth and development, and in the responses to biotic and abiotic stresses. In the present study, we analyzed Moso bamboo (Phyllostachys edulis) CPK genes and their closely related five gene families (Brachypodium distachyon, Hordeum vulgare L., Oryza sativa, Setaria italica, and Zea mays) comprehensively, including phylogenetic relationships, gene structures, and synteny analysis. Thirty Moso bamboo CPKs were divided into four subgroups; in each subgroup, the constituent parts of gene structure were relatively conserved. Furthermore, analysis of expression profiles showed that most PheCPK genes are significantly upregulated under drought and cold stress, especially PheCPK1. Overexpression of PheCPK1 in Arabidopsis reduced plant tolerance to drought stress, as determined through physiological analyses of the relative water content, relative electrical leakage, and malondialdehyde content. It also activated the expressions of stress-related genes. In addition, overexpression of PheCPK1 in Arabidopsis exhibited significantly decreased reactive oxygen species (ROS)-scavenging ability. Taken together, these results suggest that PheCPK1 may act as a negative regulator involved in the drought stress responses.
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Affiliation(s)
- Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Hongxia Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Linna Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaoyue Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Wei He
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China.
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Green Revolution to Gene Revolution: Technological Advances in Agriculture to Feed the World. PLANTS 2022; 11:plants11101297. [PMID: 35631721 PMCID: PMC9146367 DOI: 10.3390/plants11101297] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/26/2022]
Abstract
Technological applications in agriculture have evolved substantially to increase crop yields and quality to meet global food demand. Conventional techniques, such as seed saving, selective breeding, and mutation breeding (variation breeding), have dramatically increased crop production, especially during the ‘Green Revolution’ in the 1990s. However, newer issues, such as limited arable lands, climate change, and ever-increasing food demand, pose challenges to agricultural production and threaten food security. In the following ‘Gene Revolution’ era, rapid innovations in the biotechnology field provide alternative strategies to further improve crop yield, quality, and resilience towards biotic and abiotic stresses. These innovations include the introduction of DNA recombinant technology and applications of genome editing techniques, such as transcription activator-like effector (TALEN), zinc-finger nucleases (ZFN), and clustered regularly interspaced short palindromic repeats/CRISPR associated (CRISPR/Cas) systems. However, the acceptance and future of these modern tools rely on the regulatory frameworks governing their development and production in various countries. Herein, we examine the evolution of technological applications in agriculture, focusing on the motivations for their introduction, technical challenges, possible benefits and concerns, and regulatory frameworks governing genetically engineered product development and production.
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