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Wu M, Zhang Y, Guo P, Liu H, Xia L, Wang M, Zeng C, Wang H, Shang F. Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analyses Provide Comprehensive Insight into Molecular Mechanisms of Flavonoid Metabolites Biosynthesis in Styphnolobium japonicum. Genes (Basel) 2024; 15:329. [PMID: 38540388 PMCID: PMC10970609 DOI: 10.3390/genes15030329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 06/14/2024] Open
Abstract
Styphnolobium japonicum L. is a commonly consumed plant in China, known for its medicinal and nutritional benefits. This study focuses on the medicinal properties influenced by flavonoid metabolites, which vary during flower development. Utilizing full-length transcriptome sequencing on S. japonicum flowers, we observed changes in gene expression levels as the flowers progressed through growth stages. During stages S1 and S2, key genes related to flavonoid synthesis (PAL, 4CL, CHS, F3H, etc.) exhibited heightened expression. A weighted gene co-expression network analysis (WGCNA) identified regulatory genes (MYB, bHLH, WRKY) potentially involved in the regulatory network with flavonoid biosynthesis-related genes. Our findings propose a regulatory mechanism for flavonoid synthesis in S. japonicum flowers, elucidating the genetic underpinnings of this process. The identified candidate genes present opportunities for genetic enhancements in S. japonicum, offering insights into potential applications for improving its medicinal attributes.
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Affiliation(s)
- Miao Wu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Yu Zhang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
| | - Peng Guo
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
| | - Huiyuan Liu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Linkui Xia
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Mengyuan Wang
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Chuqi Zeng
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Hongwei Wang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
| | - Fude Shang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
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2
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Liu Z, Wang Y, Guan P, Hu J, Sun L. Interaction of VvDELLA2 and VvCEB1 Mediates Expression of Expansion-Related Gene during GA-Induced Enlargement of Grape Fruit. Int J Mol Sci 2023; 24:14870. [PMID: 37834318 PMCID: PMC10573625 DOI: 10.3390/ijms241914870] [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: 08/08/2023] [Revised: 09/30/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
Exogenous gibberellin treatment can promote early growth of grape fruit, but the underlying regulatory mechanisms are not well understood. Here, we show that VvDELLA2 directly regulates the activity of the VvCEB1 transcription factor, a key regulator in the control of cell expansion in grape fruit. Our results show that VvCEB1 binds directly to the promoters of cell expansion-related genes in grape fruit and acts as a transcriptional activator, while VvDELLA2 blocks VvCEB1 function by binding to its activating structural domain. The exogenous gibberellin treatment relieved this inhibition by promoting the degradation of VvDELLA2 protein, thus, allowing VvCEB1 to transcriptionally activate the expression of cell expansion-related genes. In conclusion, we conclude that exogenous GA3 treatment regulates early fruit expansion by affecting the VvDELLA-VvCEB1 interaction in grape fruit development.
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Affiliation(s)
- Zhenhua Liu
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China; (Z.L.); (Y.W.)
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China
| | - Yan Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China; (Z.L.); (Y.W.)
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China
| | - Pingyin Guan
- College of Horticulture, China Agricultural University, Beijing 100193, China;
| | - Jianfang Hu
- College of Horticulture, China Agricultural University, Beijing 100193, China;
| | - Lei Sun
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China; (Z.L.); (Y.W.)
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China
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Jiang L, Gao Y, Han L, Zhang W, Fan P. Designing plant flavonoids: harnessing transcriptional regulation and enzyme variation to enhance yield and diversity. FRONTIERS IN PLANT SCIENCE 2023; 14:1220062. [PMID: 37575923 PMCID: PMC10420081 DOI: 10.3389/fpls.2023.1220062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023]
Abstract
Plant synthetic biology has emerged as a powerful and promising approach to enhance the production of value-added metabolites in plants. Flavonoids, a class of plant secondary metabolites, offer numerous health benefits and have attracted attention for their potential use in plant-based products. However, achieving high yields of specific flavonoids remains challenging due to the complex and diverse metabolic pathways involved in their biosynthesis. In recent years, synthetic biology approaches leveraging transcription factors and enzyme diversity have demonstrated promise in enhancing flavonoid yields and expanding their production repertoire. This review delves into the latest research progress in flavonoid metabolic engineering, encompassing the identification and manipulation of transcription factors and enzymes involved in flavonoid biosynthesis, as well as the deployment of synthetic biology tools for designing metabolic pathways. This review underscores the importance of employing carefully-selected transcription factors to boost plant flavonoid production and harnessing enzyme promiscuity to broaden flavonoid diversity or streamline the biosynthetic steps required for effective metabolic engineering. By harnessing the power of synthetic biology and a deeper understanding of flavonoid biosynthesis, future researchers can potentially transform the landscape of plant-based product development across the food and beverage, pharmaceutical, and cosmetic industries, ultimately benefiting consumers worldwide.
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Affiliation(s)
- Lina Jiang
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Yifei Gao
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Leiqin Han
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Wenxuan Zhang
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
| | - Pengxiang Fan
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Hangzhou, China
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4
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Cannavò S, Bertoldi A, Valeri MC, Damiani F, Reale L, Brilli F, Paolocci F. Impact of High Light Intensity and Low Temperature on the Growth and Phenylpropanoid Profile of Azolla filiculoides. Int J Mol Sci 2023; 24:ijms24108554. [PMID: 37239901 DOI: 10.3390/ijms24108554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Exposure to high light intensity (HL) and cold treatment (CT) induces reddish pigmentation in Azolla filiculoides, an aquatic fern. Nevertheless, how these conditions, alone or in combination, influence Azolla growth and pigment synthesis remains to be fully elucidated. Likewise, the regulatory network underpinning the accumulation of flavonoids in ferns is still unclear. Here, we grew A. filiculoides under HL and/or CT conditions for 20 days and evaluated the biomass doubling time, relative growth rate, photosynthetic and non-photosynthetic pigment contents, and photosynthetic efficiency by chlorophyll fluorescence measurements. Furthermore, from the A. filiculoides genome, we mined the homologs of MYB, bHLH, and WDR genes, which form the MBW flavonoid regulatory complex in higher plants, to investigate their expression by qRT-PCR. We report that A. filiculoides optimizes photosynthesis at lower light intensities, regardless of the temperature. In addition, we show that CT does not severely hamper Azolla growth, although it causes the onset of photoinhibition. Coupling CT with HL stimulates the accumulation of flavonoids, which likely prevents irreversible photoinhibition-induced damage. Although our data do not support the formation of MBW complexes, we identified candidate MYB and bHLH regulators of flavonoids. Overall, the present findings are of fundamental and pragmatic relevance to Azolla's biology.
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Affiliation(s)
- Sara Cannavò
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Agnese Bertoldi
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Maria Cristina Valeri
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, 06123 Perugia, Italy
- Institute of Bioscience and Bioresources (IBBR), National Research Council of Italy (CNR), 06128 Perugia, Italy
| | - Francesco Damiani
- Institute of Bioscience and Bioresources (IBBR), National Research Council of Italy (CNR), 06128 Perugia, Italy
| | - Lara Reale
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Federico Brilli
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), 50017 Sesto Fiorentino, Italy
| | - Francesco Paolocci
- Institute of Bioscience and Bioresources (IBBR), National Research Council of Italy (CNR), 06128 Perugia, Italy
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Zhang L, Li S, Shan C, Liu Y, Zhang Y, Ye L, Lin Y, Xiong G, Ma J, Adnan M, Shi X, Sun X, Kuang W, Cui R. Integrated transcriptome and metabolome analysis revealed that flavonoids enhanced the resistance of Oryza sativa against Meloidogyne graminicola. FRONTIERS IN PLANT SCIENCE 2023; 14:1137299. [PMID: 37063174 PMCID: PMC10102519 DOI: 10.3389/fpls.2023.1137299] [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: 01/04/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Rice is a crucial food crop worldwide, but its yield and quality are significantly affected by Meloidogyne graminicola is a root knot nematode. No rice variety is entirely immune to this nematode disease in agricultural production. Thus, the fundamental strategy to combat this disease is to utilize rice resistance genes. In this study, we conducted transcriptome and metabolome analyses on two rice varieties, ZH11 and IR64. The results indicated that ZH11 showed stronger resistance than IR64. Transcriptome analysis revealed that the change in gene expression in ZH11 was more substantial than that in IR64 after M. graminicola infection. Moreover, GO and KEGG enrichment analysis of the upregulated genes in ZH11 showed that they were primarily associated with rice cell wall construction, carbohydrate metabolism, and secondary metabolism relating to disease resistance, which effectively enhanced the resistance of ZH11. However, in rice IR64, the number of genes enriched in disease resistance pathways was significantly lower than that in ZH11, which further explained susceptibility to IR64. Metabolome analysis revealed that the metabolites detected in ZH11 were enriched in flavonoid metabolism and the pentose phosphate pathway, compared to IR64, after M. graminicola infection. The comprehensive analysis of transcriptome and metabolome data indicated that flavonoid metabolism plays a crucial role in rice resistance to M. graminicola infection. The content of kaempferin, apigenin, and quercetin in ZH11 significantly increased after M. graminicola infection, and the expression of genes involved in the synthetic pathway of flavonoids also significantly increased in ZH11. Our study provides theoretical guidance for the precise analysis of rice resistance and disease resistance breeding in further research.
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Affiliation(s)
- Lianhu Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Songyan Li
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Chonglei Shan
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yankun Liu
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yifan Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Lifang Ye
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yachun Lin
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Guihong Xiong
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Jian Ma
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Muhammad Adnan
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xugen Shi
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Xiaotang Sun
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
| | - Weigang Kuang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Ruqiang Cui
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
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Metabolomics integrated with transcriptomics unveil the regulatory pathways of modified atmosphere packaging–maintained leaf quality of Chinese flowering cabbage. Food Chem 2023. [DOI: 10.1016/j.foodchem.2022.134910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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7
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Jia S, Liu X, Wen X, Waheed A, Ding Y, Kahar G, Li X, Zhang D. Genome-Wide Identification of bHLH Transcription Factor Family in Malus sieversii and Functional Exploration of MsbHLH155.1 Gene under Valsa Canker Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:620. [PMID: 36771705 PMCID: PMC9919239 DOI: 10.3390/plants12030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/15/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Xinjiang wild apple (Malus sieversii) is an ancient relic; a plant with abundant genetic diversity and disease resistance. Several transcription factors were studied in response to different biotic and abiotic stresses on the wild apple. Basic/helix-loop-helix (bHLH) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, no study has yet been conducted on the bHLH gene in M. sieversii. Based on the genome of M. sieversii, 184 putative MsbHLH genes were identified, and their physicochemical properties were studied. MsbHLH covered 23 subfamilies and lacked two subfamily genes of Arabidopsis thaliana based on the widely used classification method. Moreover, MsbHLH exon-intron structures matched subfamily classification, as evidenced by the analysis of their protein motifs. The analysis of cis-acting elements revealed that many MsbHLH genes share stress- and hormone-related cis-regulatory elements. These MsbHLH transcription factors were found to be involved in plant defense responses based on the protein-protein interactions among the differentially expressed MsbHLHs. Furthermore, 94 MsbHLH genes were differentially expressed in response to pathogenic bacteria. The qRT-PCR results also showed differential expression of MsbHLH genes. To further verify the gene function of bHLH, our study used the transient transformation method to obtain the overexpressed MsbHLH155.1 transgenic plants and inoculated them. Under Valsa canker infection, the lesion phenotype and physiological and biochemical indexes indicated that the antioxidant capacity of plants could increase and reduce the damage caused by membrane peroxidation. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of bHLH genes in M. sieversii and lays a foundation for a better understanding disease resistance in plants, as well as providing candidate genes for the development of M. sieversii resistance breeding.
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Affiliation(s)
- Shanshan Jia
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xiaojie Liu
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Xuejing Wen
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Abdul Waheed
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Yu Ding
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Gulnaz Kahar
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xiaoshuang Li
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
| | - Daoyuan Zhang
- National Key Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi 830000, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838000, China
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8
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Gao Q, Song W, Li X, Xiang C, Chen G, Xiang G, Liu X, Zhang G, Li X, Yang S, Zhai C, Zhao Y. Genome-wide identification of bHLH transcription factors: Discovery of a candidate regulator related to flavonoid biosynthesis in Erigeron breviscapus. FRONTIERS IN PLANT SCIENCE 2022; 13:977649. [PMID: 36186051 PMCID: PMC9515989 DOI: 10.3389/fpls.2022.977649] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Erigeron breviscapus is a Compositae plant, and its rich flavonoids have shown strong preventative and curative effects in the treatment of cardio- and cerebrovascular diseases. bHLH genes play a crucial role in plant growth and development. There are 116 EbbHLH genes in E. breviscapus, and each gene has been named based on its chromosome location. Our phylogenetic analysis divided these genes into 18 subfamilies. To further investigate its function, EbbHLH80 was isolated from E. breviscapus leaves. Next, transcriptomic and metabolomic analyses of tobacco leaves were performed. Among 421 differentially accumulated compounds, 98 flavonoids were identified. In addition, differentially expressed genes were identified using RNA-seq, and further analysis suggested that EbbHLH80-OE could not only regulate the expression of some structural genes in the flavonoid biosynthesis pathway to achieve flavonoid accumulation but also be involved in the regulation of a series of downstream pathways, such as stress response, ABA and ethylene signal transduction, to affect plant growth and development. The results of our analysis provide new insights into the function of EbbHLH80 and lay the foundation for future functional studies on E. breviscapus.
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Affiliation(s)
- Qingqing Gao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Wanling Song
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Xia Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Chunfan Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Geng Chen
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Guisheng Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Xiangyu Liu
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Guanghui Zhang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Xiaoning Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Shengchao Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Chenxi Zhai
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, United States
| | - Yan Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
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9
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Integrated Metabolomic and Transcriptomic Analysis Reveals Differential Flavonoid Accumulation and Its Underlying Mechanism in Fruits of Distinct Canarium album Cultivars. Foods 2022; 11:foods11162527. [PMID: 36010527 PMCID: PMC9407539 DOI: 10.3390/foods11162527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/11/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022] Open
Abstract
Canarium album fruit has great potential to be consumed as a raw material not only for food but also medicine. The diverse active metabolites composition and content of C. album fruits greatly affect their pharmacological effects. However, up to now, there has been no report on the global metabolome differences among fruits from distinct C. album cultivars. In our present study, by using non-targeted metabolomics techniques, we identified 87 DAMs (differentially accumulated metabolites) including 17 types of flavonoids from fruits of four different C. album cultivars. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis revealed that the flavone and flavonol biosynthesis- and flavonoid biosynthesis-related DAMs were major factors determining their metabolome differences. Comparative transcriptomic analysis revealed that 15 KEGG pathways were significantly enriched by genes of the identified 3655 DEGs (differentially expressed genes) among different C. album cultivars. Consistent with the metabolome data, flavonoid biosynthesis-related DEGs, including eight key structural genes (such as FLS, CCoAOMT, CHI, C4H, DFR, LAR, and C3′H, etc.) and several regulatory transcription factor (TF) genes (including 32 MYBs and 34 bHLHs, etc.), were found to be significantly enriched (p < 0.01). Our study indicated that the differential expression of flavonoid biosynthesis-related genes and accumulation of flavonoids played dominant roles in the various metabolome compositions of fruits from different C. album cultivars.
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10
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Reboledo G, Agorio A, Ponce De León I. Moss transcription factors regulating development and defense responses to stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4546-4561. [PMID: 35167679 DOI: 10.1093/jxb/erac055] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Transcription factors control gene expression, leading to regulation of biological processes that determine plant development and adaptation to the environment. Land colonization by plants occurred 450-470 million years ago and was accompanied by an increase in the complexity of transcriptional regulation associated to transcription factor gene expansions. AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY transcription factor families increased in land plants compared with algae. In angiosperms, they play crucial roles in regulating plant growth and responses to environmental stressors. However, less information is available in bryophytes and only in a few cases is the functional role of moss transcription factors in stress mechanisms known. In this review, we discuss current knowledge of the transcription factor families involved in development and defense responses to stress in mosses and other bryophytes. By exploring and analysing the Physcomitrium patens public database and published transcriptional profiles, we show that a high number of AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY genes are differentially expressed in response to abiotic stresses and during biotic interactions. Expression profiles together with a comprehensive analysis provide insights into relevant transcription factors involved in moss defenses, and hint at distinct and conserved biological roles between bryophytes and angiosperms.
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Affiliation(s)
- Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Astrid Agorio
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Inés Ponce De León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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11
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Martínez-Abaigar J, Núñez-Olivera E. Bryophyte ultraviolet-omics: from genes to the environment. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4412-4426. [PMID: 35274697 DOI: 10.1093/jxb/erac090] [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: 01/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Ultraviolet (UV) radiation has contributed to the evolution of organisms since the origins of life. Bryophytes also have evolutionary importance as the first clearly identified lineage of land plants (embryophytes) colonizing the terrestrial environment, thus facing high UV and water scarcity, among other new challenges. Here we review bryophyte UV-omics, the discipline relating bryophytes and UV, with an integrative perspective from genes to the environment. We consider species and habitats investigated, methodology, response variables, protection mechanisms, environmental interactions, UV biomonitoring, molecular and evolutionary aspects, and applications. Bryophyte UV-omics shows convergences and divergences with the UV-omics of other photosynthetic organisms, from algae to tracheophytes. All these organisms converge in that UV damage may be limited under realistic UV levels, due to structural protection and/or physiological acclimation capacity. Nevertheless, bryophytes diverge because they have a unique combination of vegetative and reproductive characteristics to cope with high UV and other concomitant adverse processes, such as desiccation. This interaction has both evolutionary and ecological implications. In addition, UV effects on bryophytes depend on the species and the evolutionary lineage considered, with mosses more UV-tolerant than liverworts. Thus, bryophytes do not constitute a homogeneous functional type with respect to their UV tolerance.
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Affiliation(s)
- Javier Martínez-Abaigar
- Faculty of Science and Technology, University of La Rioja, Madre de Dios 53, 26006 Logroño, Spain
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12
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Yin DJ, Ye SJ, Sun XY, Chen QY, Min T, Wang HX, Wang LM. Integrative Analysis of the Transcriptome and Metabolome Reveals Genes Involved in Phenylpropanoid and Flavonoid Biosynthesis in the Trapa bispinosa Roxb. FRONTIERS IN PLANT SCIENCE 2022; 13:913265. [PMID: 35873984 PMCID: PMC9302371 DOI: 10.3389/fpls.2022.913265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Trapa bispinosa Roxb. is grown worldwide as an important aquatic cash crop. Current research on Trapa bispinosa primarily focuses on the separation and identification of active ingredients, as well as the inhibitory effect on tumors; however, research on the molecular mechanism of secondary metabolite accumulation is rather limited. Consequently, an integrative analysis of transcriptome and metabolome is required to identify the key metabolic pathways, and key genes, and to explain the molecular mechanism of Trapa bispinosa. RESULTS The biosynthesis pathways of phenolics in Trapa bispinosa were examined through transcriptome and metabolome analyses. Transcriptome analysis yielded 42.76 million clean reads representing 81,417 unigenes with an average length of 1,752 bp. KEGG pathway analysis revealed that 1,623 unigenes, including 88 candidate unigenes related to phenolics biosynthesis, were up-regulated in Trapa bispinosa shell (FR) when compared to leaves (LF), root (RT), and stem (ST). The FR vs. LF group had the highest number of specific genes involved in phenylpropanoid, flavonoid, flavone, and flavonol biosynthesis pathways compared to all other comparison groups. In addition, RNA sequencing revealed 18,709 SSRs spanning 14,820 unigenes and 4,387 unigenes encoding transcription factors. Metabolome analysis identified 793 metabolites, including 136 flavonoids and 31 phenylpropane compounds. In the FR group compared to the LF group, there were 202 differentially accumulated metabolites (DAMs). The combined transcriptome and metabolome analyses indicated a significant correlation between 1,050 differentially expressed genes (DEGs) and 62 DAMs. This view proposes a schematic of flavonoid biosynthesis in the FR vs. LF group, providing evidence for the differences in genes and metabolites between FR and LF. CONCLUSION In this study, through de novo transcriptome assembly and metabolome analysis, several DEGs and DAMs were identified, which were subsequently used to build flavonoid biosynthesis pathways and a correlation network. The findings pave the way for future research into the molecular mechanisms and functional characterization of Trapa bispinosa candidate genes for phenolics biosynthesis.
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Affiliation(s)
- Dong-Jie Yin
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Shi-Jie Ye
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Xiao-Yan Sun
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Qin-Yi Chen
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Ting Min
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Hong-Xun Wang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Li-Mei Wang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
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13
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Wu Y, Zhang C, Huang Z, Lyu L, Li W, Wu W. Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of flavonoid biosynthesis in blackberry. Food Res Int 2022; 153:110948. [DOI: 10.1016/j.foodres.2022.110948] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/28/2022]
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14
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An F, Xiao X, Chen T, Xue J, Luo X, Ou W, Li K, Cai J, Chen S. Systematic Analysis of bHLH Transcription Factors in Cassava Uncovers Their Roles in Postharvest Physiological Deterioration and Cyanogenic Glycosides Biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:901128. [PMID: 35789698 PMCID: PMC9249602 DOI: 10.3389/fpls.2022.901128] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/09/2022] [Indexed: 05/15/2023]
Abstract
The basic helix-loop-helix (bHLH) proteins are a large superfamily of transcription factors, and play a central role in a wide range of metabolic, physiological, and developmental processes in higher organisms. However, systematic investigation of bHLH gene family in cassava (Manihot esculenta Crantz) has not been reported. In the present study, we performed a genome-wide survey and identified 148 MebHLHs genes were unevenly harbored in 18 chromosomes. Through phylogenetic analyses along with Arabidopsis counterparts, these MebHLHs genes were divided into 19 groups, and each gene contains a similar structure and conserved motifs. Moreover, many cis-acting regulatory elements related to various defense and stress responses showed in MebHLH genes. Interestingly, transcriptome data analyses unveiled 117 MebHLH genes during postharvest physiological deterioration (PPD) process of cassava tuberous roots, while 65 MebHLH genes showed significantly change. Meanwhile, the relative quantitative analysis of 15 MebHLH genes demonstrated that they were sensitive to PPD, suggesting they may involve in PPD process regulation. Cyanogenic glucosides (CGs) biosynthesis during PPD process was increased, silencing of MebHLH72 and MebHLH114 showed that linamarin content was significantly decreased in the leaves. To summarize, the genome-wide identification and expression profiling of MebHLH candidates pave a new avenue for uderstanding their function in PPD and CGs biosynthesis, which will accelerate the improvement of PPD tolerance and decrease CGs content in cassava tuberous roots.
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Affiliation(s)
- Feifei An
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
- School of Life Sciences, Hainan University, Haikou, China
| | - Xinhui Xiao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
| | - Ting Chen
- Postgraduate Department, Hainan Normal University, Haikou, China
| | - Jingjing Xue
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
| | - Xiuqin Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
| | - Wenjun Ou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
| | - Kaimian Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
| | - Jie Cai
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
- Jie Cai,
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Haikou, China
- *Correspondence: Songbi Chen,
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Shi M, Ali MM, He Y, Ma S, Rizwan HM, Yang Q, Li B, Lin Z, Chen F. Flavonoids Accumulation in Fruit Peel and Expression Profiling of Related Genes in Purple ( Passiflora edulis f. edulis) and Yellow ( Passiflora edulis f. flavicarpa) Passion Fruits. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112240. [PMID: 34834602 PMCID: PMC8620868 DOI: 10.3390/plants10112240] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 05/14/2023]
Abstract
Flavonoids play a key role as a secondary antioxidant defense system against different biotic and abiotic stresses, and also act as coloring compounds in various fruiting plants. In this study, fruit samples of purple (Passiflora edulis f. edulis) and yellow (Passiflora edulis f. flavicarpa) passion fruit were collected at five developmental stages (i.e., fruitlet, green, veraison, maturation, and ripening stage) from an orchard located at Nanping, Fujian, China. The contents of flavonoid, anthocyanin, proanthocyanin, and their metabolites were determined using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS), activities of key enzymes involved in flavonoid metabolism were measured, and expression profiling of related genes was done using quantitative real-time PCR (qRT-PCR). The results revealed that total flavonoids, anthocyanins, and procyanidins were found to be increased in the fruit peel of both cultivars with fruit maturity. Total flavonoids, anthocyanins, procyanidins, flavonoid metabolites (i.e., rutin, luteolin, and quercetin), and anthocyanin metabolites (i.e., cyanidin-3-O-glucoside chloride, peonidin-3-O-glucoside, and pelargonidin-3-O-glucoside) were found abundant in the peel of purple passion fruit, as compared to yellow passion fruit. Principle component analysis showed that the enzymes, i.e., C4H, 4CL, UFGT, and GST were maybe involved in the regulation of flavonoids metabolism in the peel of passion fruit cultivars. Meanwhile, PePAL4, Pe4CL2,3, PeCHS2, and PeGST7 may play an important role in flavonoid metabolism in fruit peel of the passion fruit. This study provides new insights for future elucidation of key mechanisms regulating flavonoids biosynthesis in passion fruit.
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Affiliation(s)
- Meng Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Muhammad Moaaz Ali
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Yinying He
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Songfeng Ma
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Hafiz Muhammad Rizwan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Qiang Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Binqi Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
| | - Zhimin Lin
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
- Correspondence: (Z.L.); (F.C.)
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (M.M.A.); (Y.H.); (S.M.); (H.M.R.); (Q.Y.); (B.L.)
- Correspondence: (Z.L.); (F.C.)
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Yuan JC, Xiong RL, Zhu TT, Ni R, Fu J, Lou HX, Cheng AX. Cloning and functional characterization of three flavonoid O-glucosyltransferase genes from the liverworts Marchantia emarginata and Marchantia paleacea. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:495-504. [PMID: 34166976 DOI: 10.1016/j.plaphy.2021.06.009] [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: 03/09/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Flavonoid glycosides are important plant secondary metabolites with broad pharmacological activities. Flavonoid glycosides are generated from aglycones, in reactions catalyzed by typical uridine diphosphate-dependent glycosyltransferases (UGTs). Liverworts produce various types of flavonoid glycosides; however, only two UGTs have been characterized from liverworts to date. Here, we isolated three genes encoding UGTs (MeUGT1, MeUGT2, and MpalUGT1) from the liverwort species Marchantia emarginata and Marchantia paleacea through transcriptome sequencing. Recombinant MeUGT1, MeUGT2, and MpalUGT1 proteins heterologously produced in Escherichia coli exhibited catalytic activity towards multiple flavonoids. MeUGT1 and MpalUGT1 catalyzed the glycosylation of flavonols into the corresponding 3-O-glucosides with UDP-glucose as the sugar donor, while MeUGT2 exhibited a wider substrate specificity that included flavonols, flavones, and flavanones. When MeUGT2 was expressed in E. coli, the yield of flavonol 3-O-glucosides reached to 40-60% with feeding of the substrates kaempferol or quercetin under optimal conditions. Furthermore, heterologous expression of MeUGT1 in Arabidopsis thaliana increased the flavonol glycoside contents in the plants. Therefore, the UGTs characterized in this study could provide new data that will be useful for examining flavonoid biosynthesis in liverworts.
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Affiliation(s)
- Jing-Cong Yuan
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Rui-Lin Xiong
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Ting-Ting Zhu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Rong Ni
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Jie Fu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China.
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Bano N, Patel P, Chakrabarty D, Bag SK. Genome-wide identification, phylogeny, and expression analysis of the bHLH gene family in tobacco ( Nicotiana tabacum). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1747-1764. [PMID: 34539114 PMCID: PMC8405835 DOI: 10.1007/s12298-021-01042-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 05/05/2023]
Abstract
UNLABELLED The basic helix-loop-helix (bHLH) is the second-largest TF family in plants that play important roles in plant growth, development, and stress responses. In this study, a total of 100 bHLHs were identified using Hidden Markov Model profiles in the Nicotiana tabacum genome, clustered into 15 major groups (I-XV) based on their conserved domains and phylogenetic relationships. Group VIII genes were found to be the most abundant, with 27 NtbHLH members. The expansion of NtbHLHs in the genome was due to segmental and tandem duplication. The purifying selection was found to have an important role in the evolution of NtHLHs. Subsequent qRT-PCR validation of five selected genes from transcriptome data revealed that NtbHLH3.1, NtbHLH3.2, NtbHLH24, NtbHLH50, and NtbHLH59.2 have higher expressions at 12 and 24 h in comparison to 0 h (control) of chilling stress. The validated results demonstrated that NtbHLH3.2 and NtbHLH24 genes have 3 and fivefold higher expression at 12 h and 2 and threefold higher expression at 24 h than control plant, shows high sensitivity towards chilling stress. Moreover, the co-expression of positively correlated genes of NtbHLH3.2 and NtbHLH24 confirmed their functional significance in chilling stress response. Therefore, suggesting the importance of NtbHLH3.2 and NtbHLH24 genes in exerting control over the chilling stress responses in tobacco. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01042-x.
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Affiliation(s)
- Nasreen Bano
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Preeti Patel
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
| | - Debasis Chakrabarty
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Sumit Kumar Bag
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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Qian Y, Zhang T, Yu Y, Gou L, Yang J, Xu J, Pi E. Regulatory Mechanisms of bHLH Transcription Factors in Plant Adaptive Responses to Various Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:677611. [PMID: 34220896 PMCID: PMC8250158 DOI: 10.3389/fpls.2021.677611] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/19/2021] [Indexed: 05/05/2023]
Abstract
Basic helix-loop-helix proteins (bHLHs) comprise one of the largest families of transcription factors in plants. They have been shown to be involved in responses to various abiotic stresses, such as drought, salinity, chilling, heavy metal toxicity, iron deficiency, and osmotic damages. By specifically binding to cis-elements in the promoter region of stress related genes, bHLHs can regulate their transcriptional expression, thereby regulating the plant's adaptive responses. This review focuses on the structural characteristics of bHLHs, the regulatory mechanism of how bHLHs are involved transcriptional activation, and the mechanism of how bHLHs regulate the transcription of target genes under various stresses. Finally, as increasing research demonstrates that flavonoids are usually induced under fluctuating environments, the latest research progress and future research prospects are described on the mechanisms of how flavonoid biosynthesis is regulated by bHLHs in the regulation of the plant's responses to abiotic stresses.
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Affiliation(s)
| | | | | | | | | | | | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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Aslam M, Jakada BH, Fakher B, Greaves JG, Niu X, Su Z, Cheng Y, Cao S, Wang X, Qin Y. Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response. BMC Genomics 2020; 21:735. [PMID: 33092537 PMCID: PMC7583237 DOI: 10.1186/s12864-020-07152-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory functions. Cryptochrome-interacting bHLH (CIB) and cryptochromes form an extensive regulatory network to mediate a plethora of pathways. Although bHLHs regulate critical biological processes in plants, the information about pineapple bHLHs remains unexplored. RESULTS Here, we identified a total of 121 bHLH proteins in the pineapple genome. The identified genes were renamed based on the ascending order of their gene ID and classified into 18 subgroups by phylogenetic analysis. We found that bHLH genes are expressed in different organs and stages of pineapple development. Furthermore, by the ectopic expression of AcCIB2 in Arabidopsis and complementation of Atcib2 mutant, we verified the involvement of AcCIB2 in photomorphogenesis and abiotic stress response. CONCLUSIONS Our findings revealed that AcCIB2 plays an essential role in flowering time regulation and abiotic stress response. The present study provides additional insights into the current knowledge of bHLH genes and suggests their potential role in various biological processes during pineapple development.
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Affiliation(s)
- Mohammad Aslam
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Bello Hassan Jakada
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Beenish Fakher
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Joseph G Greaves
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xiaoping Niu
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Zhenxia Su
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yan Cheng
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, 530007, China.
| | - Yuan Qin
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
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20
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Wang PY, Ni R, Zhu TT, Sun CJ, Lou HX, Zhang X, Cheng AX. Isolation and functional characterization of four microbial type terpene synthases from ferns. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:716-724. [PMID: 32862021 DOI: 10.1016/j.plaphy.2020.08.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 07/28/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Typical plant terpene synthases (TPSs) are responsible for the production of terpenes, a major class of plant secondary metabolites. However, various nonseed plants also harbor genes encoding microbial terpene synthase-like (MTPSL) enzymes. Here, a scan of 31 ferns transcriptomes revealed 40 sequences putatively encoding MTPSLs. Two groups of sequences were recognized based on the key conserved motifs. Four representative genes were isolated from each of the four species Adiantum capillus-veneris, Cyclosorus parasiticus, Drynaria bonii and Microlepia platyphylla. Following their heterologous expression in E. coli, the recombinant proteins were tested for monoterpene synthase and sesquiterpene synthase activity. These enzymatic products were typical monoterpenes and sesquiterpenes that have been previous shown to be generated by classical plant TPSs when provided with GPP and FPP as substrates. Subcellular localization experiments in the leaf epidermis of Nicotiana benthamiana and onion (Allium cepa) inner epidermal cells indicated that AcMTPSL1 and DbMTPSL were deposited in both the cytoplasm and nucleus, whereas CpMTPSL1 and MpMTPSL were localized in the cytoplasm, chloroplasts and nucleus. AcMTPSL1 was up-regulated in plants exposed to methyl jasmonate treatment, suggesting a role for this gene in host defense. This study provides more information about the catalytic function of MTPSLs in nonseed plants and for the first time, the subcellular localization of MTPSLs was experimentally characterized.
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Affiliation(s)
- Piao-Yi Wang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Rong Ni
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Ting-Ting Zhu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Chun-Jing Sun
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Xuebin Zhang
- Henan Joint International Laboratory for Crop Multi-Omics Research, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China.
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China.
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Peng JJ, Wu YC, Wang SQ, Niu JF, Cao XY. SmbHLH53 is relevant to jasmonate signaling and plays dual roles in regulating the genes for enzymes in the pathway for salvianolic acid B biosynthesis in Salvia miltiorrhiza. Gene 2020; 756:144920. [PMID: 32593720 DOI: 10.1016/j.gene.2020.144920] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 11/26/2022]
Abstract
Basic helix-loop-helix (bHLH) transcription factors play essential roles in myriad regulatory processes, including secondary metabolism. In this study with Salvia miltiorrhiza, we isolated and characterized SmbHLH53, which encodes a bHLH family member. Expression of this gene was significantly induced by wounding and multiple hormones, including methyl jasmonic acid; transcript levels were highest in the leaves and roots. Phylogenetic analysis indicated that SmbHLH53 clusters withAtbHLH17 and AtbHLH13, two negative regulators of jasmonate (JA) responses, and is localized in the nucleus and cell membrane. Yeast two-hybrid and bimolecular fluorescent complementation assays indicated that SmbHLH53 forms a homodimer as well as a heterodimer with SmbHLH37. It also interacts with both SmJAZs1/3/8 and SmMYC2, the core members of the JA signal pathway. Unexpectedly, we noted that overexpression of SmbHLH53 did not significantly influence the concentrations of rosmarinic acid and salvianolic acid B in transgenic plants. Results from yeast one-hybrid assays showed that SmbHLH53 binds to the promoters of SmTAT1, SmPAL1, and Sm4CL9, the key genes for enzymes in the pathway for phenolic acid synthesis. Assays of transient transcriptional activity demonstrated that SmbHLH53 represses the promoter of SmTAT1 while activating the promoter of Sm4CL9. Thus, the present work revealed that SmbHLH53 may play dual roles in regulating the genes for enzymes in the pathway for Sal B biosynthesis.
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Affiliation(s)
- Jing-Jing Peng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, 710062 Xi'an, China
| | - Yu-Cui Wu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, 056038 Handan, China
| | - Shi-Qiang Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, 710062 Xi'an, China
| | - Jun-Feng Niu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, 710062 Xi'an, China.
| | - Xiao-Yan Cao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, 710062 Xi'an, China.
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