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Wu X, Yang Z, Zhu Y, Zhan Y, Li Y, Teng W, Han Y, Zhao X. Bioinformatics Identification and Expression Analysis of Acetyl-CoA Carboxylase Reveal Its Role in Isoflavone Accumulation during Soybean Seed Development. Int J Mol Sci 2024; 25:10221. [PMID: 39337707 PMCID: PMC11432495 DOI: 10.3390/ijms251810221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/05/2024] [Accepted: 09/20/2024] [Indexed: 09/30/2024] Open
Abstract
Isoflavones belong to the class of flavonoid compounds, which are important secondary metabolites that play a crucial role in plant development and defense. Acetyl-CoA carboxylase (ACCase) is a biotin-dependent enzyme that catalyzes the conversion of Acetyl-CoA into Malonyl-CoA in plants. It is a key enzyme in fatty acid synthesis and also catalyzes the production of various secondary metabolites. However, information on the ACC gene family in the soybean (Glycine max L. Merr.) genome and the specific members involved in isoflavone biosynthesis is still lacking. In this study, we identified 20 ACC family genes (GmACCs) from the soybean genome and further characterized their evolutionary relationships and expression patterns. Phylogenetic analysis showed that the GmACCs could be divided into five groups, and the gene structures within the same groups were highly conserved, indicating that they had similar functions. The GmACCs were randomly distributed across 12 chromosomes, and collinearity analysis suggested that many GmACCs originated from tandem and segmental duplications, with these genes being under purifying selection. In addition, gene expression pattern analysis indicated that there was functional divergence among GmACCs in different tissues. The GmACCs reached their peak expression levels during the early or middle stages of seed development. Based on the transcriptome and isoflavone content data, a weighted gene co-expression network was constructed, and three candidate genes (Glyma.06G105900, Glyma.13G363500, and Glyma.13G057400) that may positively regulate isoflavone content were identified. These results provide valuable information for the further functional characterization and application of GmACCs in isoflavone biosynthesis in soybean.
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Affiliation(s)
| | | | | | | | | | | | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China; (X.W.); (Z.Y.); (Y.Z.); (Y.Z.); (Y.L.); (W.T.)
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China; (X.W.); (Z.Y.); (Y.Z.); (Y.Z.); (Y.L.); (W.T.)
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Wang C, Liu Y, Li Y, Guo L, Li C. Analysis of bZIP transcription factors in Rhododendron simsii and functional study of RsbZIP6 in regulating anthocyanin biosynthesis. Int J Biol Macromol 2024; 280:135889. [PMID: 39307497 DOI: 10.1016/j.ijbiomac.2024.135889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 09/19/2024] [Accepted: 09/19/2024] [Indexed: 09/26/2024]
Abstract
The basic leucine zipper (bZIP) transcription factors play a critical role in various plant biological processes, including anthocyanin biosynthesis. This study focuses on Rhododendron simsii, a notable ornamental species with insufficiently explored bZIP transcription factors. We identified 66 bZIP transcription factors in the R. simsii genome and conducted comprehensive bioinformatics analyses to determine their gene localization, phylogenetic relationships, grouping, gene/protein structure, duplication events, synteny, and expression profiles. Our analysis identified RsbZIP6, a homolog of HY5 known to influence anthocyanin biosynthesis in many plants, as a potential regulator of this pathway. We cloned the complete coding sequence of RsbZIP6, which encodes a 170-amino acid protein spanning 510 bp. Subcellular localization analysis verified the nuclear presence of the RsbZIP6 protein. RT-qPCR analysis revealed the highest expression of RsbZIP6 in petals, which correlated with anthocyanin accumulation. Transgenic experiments indicated that overexpressing RsbZIP6 in Arabidopsis enhanced anthocyanin accumulation by upregulating genes involved in anthocyanin biosynthesis (4CL, CHS, CHI, DFR, F3H, F3'H, ANS and UF3GT). Our findings enhance understanding of the bZIP transcription factor family in R. simsii and underscore the vital role of RsbZIP6 in anthocyanin biosynthesis, providing insights for future genetic enhancement strategies.
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Affiliation(s)
- Cheng Wang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China; Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Xiaogan 432000, China
| | - Yilin Liu
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Yan Li
- Department of Biology and Chemical Engineering, Weihai Vocational College, Weihai 264200, China
| | - Lifan Guo
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Changchun Li
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China; Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Xiaogan 432000, China.
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Hui W, Wu H, Zheng H, Wang K, Yang T, Fan J, Wu J, Wang J, Al Mutairi AA, Yang H, Yang C, Cui B, Loake GJ, Gong W. Genome-wide characterization of RR gene family members in Zanthoxylum armatum and the subsequent functional characterization of the C-type RR. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108943. [PMID: 39032447 DOI: 10.1016/j.plaphy.2024.108943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Response Regulators (RRs) are crucial regulators in plant development and stress responses, comprising A-type, B-type, C-type, and pseudo-RR subfamilies. However, previous studies have often focused on specific subfamilies, which restricts our understanding of the complete RR gene family. In this study, we conducted a comprehensive analysis of 63 RR members from Zanthoxylum armatum, using phylogenetic relationships, motif composition, cis-acting elements, gene duplication and collinearity analyses. Segmental repeats among ZaRR genes enhanced the various environmental adaptabilities of Z. armatum, and the B-type ZaRR exhibited significant collinearity with the RRs in P. trichocarpa and C. sinensis. Cis-element analysis indicated ZaRRs play a significant role in abiotic stress and phytohormone pathways, particularly in light, drought, cold, abscisic acid (ABA) and salicylic acid (SA) responses. Abundant Ethylene Response Factor (ERF) and reproduction-associated binding sites in ZaRR promoters suggested their roles in stress and reproductive processes. A-type ZaRRs were implicated in plant vegetative and reproductive growth, whereas B-type ZaRRs contributed to both growth and stress responses. C-type ZaRRs were associated with plant reproductive growth, whereas pseudo-RRs may function in plant stress responses, such as water logging, cold, and response to ethylene (ETH), SA, and jasmonic acid (JA). Ectopic expression of ZaRR24, a C-type RR, inhibits growth, induces early flowering, and shortens fruit length in Arabidopsis. ZaRR24 overexpression also affected the expression of A- and B-type RRs, as well as floral meristem and organ identity genes. These findings establish a solid and comprehensive foundation for RR gene research in Z. armatum, and provide a platform for investigating signal transduction in other woody plants.
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Affiliation(s)
- Wenkai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Han Wu
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hao Zheng
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiangtao Fan
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaojiao Wu
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingyan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Ahmed A Al Mutairi
- Biology Department, College of Science, Jouf University, Sakaka, 41412, Saudi Arabia
| | - Hua Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunlin Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Beimi Cui
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
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Qu Y, Wang J, Gao T, Qu C, Mo X, Zhang X. Systematic analysis of bZIP gene family in Suaeda australis reveal their roles under salt stress. BMC PLANT BIOLOGY 2024; 24:816. [PMID: 39210264 PMCID: PMC11363414 DOI: 10.1186/s12870-024-05535-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Suaeda australis is one of typical halophyte owing to high levels of salt tolerance. In addition, the bZIP gene family assumes pivotal functions in response to salt stress. However, there are little reports available regarding the bZIP gene family in S. australis. RESULTS In this study, we successfully screened 44 bZIP genes within S. australis genome. Subsequently, we conducted an extensive analysis, encompassing investigations into chromosome location, gene structure, phylogenetic relationship, promoter region, conserved motif, and gene expression profile. The 44 bZIP genes were categorized into 12 distinct groups, exhibiting an uneven distribution among the 9 chromosomes of S. australis chromosomes, but one member (Sau23745) was mapped on unanchored scaffolds. Examination of cis-regulatory elements revealed that bZIP promoters were closely related to anaerobic induction, transcription start, and light responsiveness. Comparative transcriptome analysis between ST1 and ST2 samples identified 2,434 DEGs, which were significantly enriched in some primary biological pathways related to salt response-regulating signaling based on GO and KEGG enrichment analysis. Expression patterns analyses clearly discovered the role of several differently expressed SabZIPs, including Sau08107, Sau08911, Sau11415, Sau16575, and Sau19276, which showed higher expression levels in higher salt concentration than low concentration and a response to salt stress. These expression patterns were corroborated through RT-qPCR analysis. The six differentially expressed SabZIP genes, all localized in the nucleus, exhibited positive regulation involved in the salt stress response. SabZIP14, SabZIP26, and SabZIP36 proteins could bind to the promoter region of downstream salt stress-related genes and activate their expressions. CONCLUSIONS Our findings offer valuable insights into the evolutionary trajectory of the bZIP gene family in S. australis and shed light on their roles in responding to salt stress. In addition to fundamental genomic information, these results would serve as a foundational framework for future investigations into the regulation of salt stress responses in S. australis.
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Affiliation(s)
- Yinquan Qu
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Ji Wang
- School of Teacher Education, Nanjing Xiaozhuang University, Nanjing, 211171, Jiangsu, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Caihui Qu
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Xiaoyun Mo
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Xiumei Zhang
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China.
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Yang X, Gao C, Hu Y, Ma Q, Li Z, Wang J, Li Z, Zhang L, Li D. Identification and expression analysis of bZIP transcription factors in Setaria italica in response to dehydration stress. Front Genet 2024; 15:1466486. [PMID: 39280094 PMCID: PMC11392892 DOI: 10.3389/fgene.2024.1466486] [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: 07/18/2024] [Accepted: 08/19/2024] [Indexed: 09/18/2024] Open
Abstract
Among the largest transcription factor families in plants, bZIPs are crucial for various developmental and physiological processes, particularly abiotic stress resistance. Setaria italica has become a model for understanding stress resistance mechanisms. In this study, we identified 90 bZIP transcription factors in the Setaria italica genome. SibZIPs were classified into 13 groups based on references to Arabidopsis bZIPs. Members in the same group shared similar motifs and gene structure pattern. In addition, gene duplication analysis indenfied 37 pairs of segmental duplicated genes and none tandem duplicated genes in S. italica suggesting segmental duplication contributed to the expansion of the S. italica bZIP gene family. Moreover, the number of SibZIPs genes (39) exhibiting higher expression in roots was significantly more than that in other organs. Twelve SibZIP genes were upregulated in response to dehydration stress. In conclusion, our study advances the current understanding of SibZIP genes and provide a number of candidates for functional analysis of drought tolerance in S. italica.
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Affiliation(s)
- Xuefei Yang
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Changyong Gao
- College of Agriculture and Bioengineering, Heze University, Heze, China
| | - Yaqian Hu
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Qianru Ma
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Zejun Li
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Jing Wang
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Zhaoqun Li
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Li Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Dongming Li
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia Normal University, Hohhot, China
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He S, Xu S, He Z, Hao X. Genome-wide identification, characterization and expression analysis of the bZIP transcription factors in garlic ( Allium sativum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1391248. [PMID: 39148621 PMCID: PMC11324451 DOI: 10.3389/fpls.2024.1391248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024]
Abstract
Introduction The bZIP genes (bZIPs) are essential in numerous biological processes, including development and stress responses. Despite extensive research on bZIPs in many plants, a comprehensive genome-wide analysis of bZIPs in garlic has yet to be undertaken. Methods In this study, we identified and classified 64 AsbZIP genes (AsbZIPs) into 10 subfamilies. A systematic analysis of the evolutionary characteristics of these AsbZIPs, including chromosome location, gene structure, conserved motifs, and gene duplication, was conducted. Furthermore, we also examined the nucleotide diversity, cis-acting elements, and expression profiles of AsbZIPs in various tissues and under different abiotic stresses and hormone treatments. Results and Discussion Our findings revealed that gene replication plays a crucial role in the expansion of AsbZIPs, with a minor genetic bottleneck observed during domestication. Moreover, the identification of cis-acting elements suggested potential associations of AsbZIPs with garlic development, hormone, and stress responses. Several AsbZIPs exhibited tissue-preferential and stress/hormone-responsive expression patterns. Additionally, Asa7G01972 and Asa7G01379 were notably differentially expressed under various stresses and hormone treatments. Subsequent yeast two-hybridization and yeast induction experiments validated their interactions with Asa1G01577, a homologue of ABI5, reinforcing their importance in hormone and abiotic stress responses. This study unveiled the characteristics of the AsbZIP superfamily and lays a solid foundation for further functional analysis of AsbZIP in garlic.
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Affiliation(s)
- Shutao He
- Institute of Neurobiology, Jining Medical University, Jining, China
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing, China
| | - Sen Xu
- Institute of Neurobiology, Jining Medical University, Jining, China
| | - Zhengjie He
- Rehabilitation Department, Traditional Chinese Medicine Hospital of Yanzhou District of Jining City, Jining, China
| | - Xiaomeng Hao
- Institute of Neurobiology, Jining Medical University, Jining, China
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Li X, Gong X, Lin H, Rao S, Shen L, Chen C, Wu Z, Li H, Liu Q, Zhong Y. Genome-wide analysis of the bZIP gene family in Cinnamomum camphora ('Gantong 1') reveals the putative function in anthocyanin biosynthesis. Heliyon 2024; 10:e34311. [PMID: 39082037 PMCID: PMC11284375 DOI: 10.1016/j.heliyon.2024.e34311] [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: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
Basic leucine zipper (bZIP) transcription factors (TFs) regulate plant development, growth, and secondary metabolism. The formation of red bark of new ornamental cultivar 'Gantong 1' is regulated mainly by anthocyanin anabolism. However, it is unclear whether and which bZIP TFs are involved in this process. We identified 89 genes encoding CcbZIP TFs in Cinnamomum camphora genome that could be divided into 14 subfamilies with similar gene structures and conserved motifs. CcbZIP38 and CcbZIP57 were highly conserved compared to HY5 in Arabidopsis thaliana and they were highly expressed in the bark and leaves of 'Gantong 1' at different stages. The target gene enrichment analysis showed that indicating indirect involvement of CcbZIP38 and CcbZIP57 in the regulation of anthocyanin synthesis. Our study contributes to understanding the molecular mechanism of anthocyanin synthesis regulation by CcbZIP TFs and provides a theoretical basis for genetic improvement of ornamental traits in C. camphora.
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Affiliation(s)
- Xiuqi Li
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Xue Gong
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Hanbin Lin
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Shupei Rao
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Le Shen
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Caihui Chen
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Zhaoxiang Wu
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Huihu Li
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Qiaoli Liu
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Yongda Zhong
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China
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Guo Z, Dzinyela R, Yang L, Hwarari D. bZIP Transcription Factors: Structure, Modification, Abiotic Stress Responses and Application in Plant Improvement. PLANTS (BASEL, SWITZERLAND) 2024; 13:2058. [PMID: 39124175 PMCID: PMC11313983 DOI: 10.3390/plants13152058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
Plant growth, yield, and distribution are significantly impacted by abiotic stresses, affecting global ecosystems and forestry practices. However, plants have evolved complex adaptation mechanisms governed by numerous genes and transcription factors (TFs) to manage these stresses. Among these, bZIP (basic leucine zipper) is a crucial regulator orchestrating morphological adaptations. This review aims to elucidate the multifaceted roles of bZIP TFs in plant species. We discuss the morphological changes induced by stress stimuli and the pivotal functions of bZIP TFs in mediating these responses. While several publications have explored the mechanisms of bZIP TFs in response to abiotic stresses, this review delves into the intricate regulatory networks, summarizing alternative splicing and post-translational modifications, signaling networks interacting with bZIP TFs, and genetic engineering of bZIP TFs. By synthesizing current research, this review provides an updated discussion on bZIP interactions with other proteins to regulate stresses such as cold, heat, drought, and salt. Additionally, it offers avenues for future research and applications of bZIP TFs to improve abiotic stress resilience in plants through genetic engineering.
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Affiliation(s)
| | | | | | - Delight Hwarari
- State Key Laboratory of Tree Genetics and Breeding, College of Life Sciences, Nanjing Forestry University, Nanjing 213007, China; (Z.G.); (R.D.); (L.Y.)
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Lan J, Lian C, Shao Y, Chen S, Lu Y, Zhu L, Mu D, Tang Q. Genome-Wide Identification of Seven in Absentia E3 Ubiquitin Ligase Gene Family and Expression Profiles in Response to Different Hormones in Uncaria rhynchophylla. Int J Mol Sci 2024; 25:7636. [PMID: 39062882 PMCID: PMC11277444 DOI: 10.3390/ijms25147636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
SINA (Seven in absentia) E3 ubiquitin ligases are a family of RING (really interesting new gene) E3 ubiquitin ligases, and they play a crucial role in regulating plant growth and development, hormone response, and abiotic and biotic stress. However, there is little research on the SINA gene family in U. rhynchophylla. In this study, a total of 10 UrSINA genes were identified from the U. rhynchophylla genome. The results of multiple sequence alignments and chromosomal locations show that 10 UrSINA genes were unevenly located on 22 chromosomes, and each UrSINA protein contained a SINA domain at the N-terminal and RING domains at the C-terminal. Synteny analysis showed that there are no tandem duplication gene pairs and there are four segmental gene pairs in U. rhynchophylla, contributing to the expansion of the gene family. Furthermore, almost all UrSINA genes contained the same gene structure, with three exons and two introns, and there were many cis-acting elements relating to plant hormones, light responses, and biotic and abiotic stress. The results of qRT-PCR show that most UrSINA genes were expressed in stems, with the least expression in roots; meanwhile, most UrSINA genes and key enzyme genes were responsive to ABA and MeJA hormones with overlapping but different expression patterns. Co-expression analysis showed that UrSINA1 might participate in the TIA pathway under ABA treatment, and UrSINA5 and UrSINA6 might participate in the TIA pathway under MeJA treatment. The mining of UrSINA genes in the U. rhynchophylla provided novel information for understanding the SINA gene and its function in plant secondary metabolites, growth, and development.
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Affiliation(s)
- Jinxu Lan
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China; (J.L.); (C.L.); (S.C.)
| | - Conglong Lian
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China; (J.L.); (C.L.); (S.C.)
| | - Yingying Shao
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (Y.L.); (L.Z.)
| | - Suiqing Chen
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China; (J.L.); (C.L.); (S.C.)
| | - Ying Lu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (Y.L.); (L.Z.)
| | - Lina Zhu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (Y.L.); (L.Z.)
| | - Detian Mu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (Y.L.); (L.Z.)
| | - Qi Tang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (Y.L.); (L.Z.)
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Faiz Z, Parveen S, Saeed S, Tayyab M, Sultana M, Hussain M, Shafqat Z. Comparative genomic studies on the TGF-β superfamily in blue whale. Mamm Genome 2024; 35:228-240. [PMID: 38467865 DOI: 10.1007/s00335-024-10031-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/29/2024] [Indexed: 03/13/2024]
Abstract
TGF-β supergene family has a wide range of physiological functions including cell adhesion, motility, proliferation, apoptosis, and differentiation. We systematically analyzed and characterized the TGF-β gene superfamily from the whole blue whale (Balaenoptera musculus) genome, using comparative genomic and evolutionary analysis. We identified 30 TGF-β genes and were split into two subgroups, BMP-like and TGF-like. All TGF-β proteins demonstrating a basic nature, with the exception of BMP1, BMP2, BMP10, GDF2, MSTN, and NODAL modulator, had acidic characteristics. All the blue whale (B. musculus) TGF-β proteins, excluding BMP1, are thermostable based on aliphatic index. The instability index showed all proteins except the NODAL modulator was unstable. TGF-β proteins showed a hydrophilic character, with the exception of GDF1 and INHBC. Moreover, all the detected TGF-β genes showed evolutionary conserved nature. A segmental duplication was indicated by TGF-β gene family, and the Ka/Ks ratio showed that the duplicated gene pairs were subjected to selection pressure, indicating both purifying and positive selection pressure. Two possible recombination breakpoints were also predicted. This study provides insights into the genetic characterization and evolutionary aspects of the TGF-β superfamily in blue whales (B. musculus).
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Affiliation(s)
- Zunaira Faiz
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Shakeela Parveen
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan.
| | - Saba Saeed
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Tayyab
- Department of Zoology, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Mehwish Sultana
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Hussain
- Department of Veterinary and Animal Sciences, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | - Zainab Shafqat
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
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11
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Tang Q, Wang X, Ma S, Fan S, Chi F, Song Y. Molecular mechanism of abscisic acid signaling response factor VcbZIP55 to promote anthocyanin biosynthesis in blueberry (Vaccinium corymbosum). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108611. [PMID: 38615439 DOI: 10.1016/j.plaphy.2024.108611] [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: 09/27/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024]
Abstract
A high content of anthocyanin in blueberry (Vaccinium corymbosum) is an important indicator to evaluate fruit quality. Abscisic acid (ABA) can promote anthocyanin biosynthesis, but since the molecular mechanism is unclear, clarifying the mechanism will improve for blueberry breeding and cultivation regulation. VcbZIP55 regulating anthocyanin synthesis in blueberry were screened and mined using the published Isoform-sequencing, RNA-Seq and qRT-PCR at different fruit developmental stages. Blueberry genetic transformation and transgenic experiments confirmed that VcbZIP55 could promote anthocyanin biosynthesis in blueberry adventitious buds, tobacco leaves, blueberry leaves and blueberry fruit. VcbZIP55 responded to ABA signals and its expression was upregulated in blueberry fruit. In addition, using VcbZIP55 for Yeast one hybrid assay (Y1H) and transient expression in tobacco leaves demonstrated an interaction between VcbZIP55 and a G-Box motif on the VcMYB1 promoter to activate the expression of VcMYB1. This study will lay the theoretical foundation for the molecular mechanisms of phytohormone regulation responsible for anthocyanin synthesis and provide theoretical support for blueberry quality improvement.
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Affiliation(s)
- Qi Tang
- Research Institute of Pomology of CAAS, Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng, Liaoning, 125100, China.
| | - Xuan Wang
- Research Institute of Pomology of CAAS, Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng, Liaoning, 125100, China.
| | - Shurui Ma
- Research Institute of Pomology of CAAS, Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng, Liaoning, 125100, China.
| | - Shutian Fan
- Institute of Special Animal and Plant Sciences CAAS, Jilin Changchun, 130122, China.
| | - Fumei Chi
- Research Institute of Pomology of CAAS, Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng, Liaoning, 125100, China.
| | - Yang Song
- Research Institute of Pomology of CAAS, Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Xingcheng, Liaoning, 125100, China.
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12
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Fan J, Chen N, Rao W, Ding W, Wang Y, Duan Y, Wu J, Xing S. Genome-wide analysis of bZIP transcription factors and their expression patterns in response to methyl jasmonate and low-temperature stresses in Platycodon grandiflorus. PeerJ 2024; 12:e17371. [PMID: 38708338 PMCID: PMC11067905 DOI: 10.7717/peerj.17371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
Background Platycodon grandiflorus belongs to the genus Platycodon and has many pharmacological effects, such as expectorant, antitussive, and anti-tumor properties. Among transcription factor families peculiar to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important, which exists widely in plants and participates in many biological processes, such as plant growth, development, and stress responses. However, genomic analysis of the bZIP gene family and related stress response genes has not yet been reported in P. grandiflorus. Methods P. grandiflorus bZIP (PgbZIP) genes were first identified here, and the phylogenetic relationships and conserved motifs in the PgbZIPs were also performed. Meanwhile, gene structures, conserved domains, and the possible protein subcellular localizations of these PgbZIPs were characterized. Most importantly, the cis-regulatory elements and expression patterns of selected genes exposed to two different stresses were analyzed to provide further information on PgbZIPs potential biological roles in P. grandiflorus upon exposure to environmental stresses. Conclusions Forty-six PgbZIPs were identified in P. grandiflorus and divided into nine groups, as displayed in the phylogenetic tree. The results of the chromosomal location and the collinearity analysis showed that forty-six PgbZIP genes were distributed on eight chromosomes, with one tandem duplication event and eleven segmental duplication events identified. Most PgbZIPs in the same phylogenetic group have similar conserved motifs, domains, and gene structures. There are cis-regulatory elements related to the methyl jasmonate (MeJA) response, low-temperature response, abscisic acid response, auxin response, and gibberellin response. Ten PgbZIP genes were selected to study their expression patterns upon exposure to low-temperature and MeJA treatments, and all ten genes responded to these stresses. The real-time quantitative polymerase chain reaction (RT-qPCR) results suggest that the expression levels of most PgbZIPs decreased significantly within 6 h and then gradually increased to normal or above normal levels over the 90 h following MeJA treatment. The expression levels of all PgbZIPs were significantly reduced after 3 h of the low-temperature treatment. These results reveal the characteristics of the PgbZIP family genes and provide valuable information for improving P. grandiflorus's ability to cope with environmental stresses during growth and development.
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Affiliation(s)
- Jizhou Fan
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Na Chen
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Joint Research Center for Chinese Herbal Medicine of Anhui, Bozhou, Anhui, China
- College of Pharmacy, Bozhou Vocational and Technical College, Bozhou, Anhui, China
| | - Weiyi Rao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
| | - Wanyue Ding
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yuqing Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yingying Duan
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Joint Research Center for Chinese Herbal Medicine of Anhui, Bozhou, Anhui, China
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
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13
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Ayaz A, Jalal A, Zhang X, Khan KA, Hu C, Li Y, Hou X. In-Depth Characterization of bZIP Genes in the Context of Endoplasmic Reticulum (ER) Stress in Brassica campestris ssp. chinensis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1160. [PMID: 38674568 PMCID: PMC11053814 DOI: 10.3390/plants13081160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
Numerous studies have been conducted to investigate the genomic characterization of bZIP genes and their involvement in the cellular response to endoplasmic reticulum (ER) stress. These studies have provided valuable insights into the coordinated cellular response to ER stress, which is mediated by bZIP transcription factors (TFs). However, a comprehensive and systematic investigations regarding the role of bZIP genes and their involvement in ER stress response in pak choi is currently lacking in the existing literature. To address this knowledge gap, the current study was initiated to elucidate the genomic characteristics of bZIP genes, gain insight into their expression patterns during ER stress in pak choi, and investigate the protein-to-protein interaction of bZIP genes with the ER chaperone BiP. In total, 112 members of the BcbZIP genes were identified through a comprehensive genome-wide analysis. Based on an analysis of sequence similarity, gene structure, conserved domains, and responsive motifs, the identified BcbZIP genes were categorized into 10 distinct subfamilies through phylogenetic analysis. Chromosomal location and duplication events provided insight into their genomic context and evolutionary history. Divergence analysis estimated their evolutionary history with a predicted divergence time ranging from 0.73 to 80.71 million years ago (MYA). Promoter regions of the BcbZIP genes were discovered to exhibit a wide variety of cis-elements, including light, hormone, and stress-responsive elements. GO enrichment analysis further confirmed their roles in the ER unfolded protein response (UPR), while co-expression network analysis showed a strong relationship of BcbZIP genes with ER-stress-responsive genes. Moreover, gene expression profiles and protein-protein interaction with ER chaperone BiP further confirmed their roles and capacity to respond to ER stress in pak choi.
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Affiliation(s)
- Aliya Ayaz
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Abdul Jalal
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiaoli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Khalid Ali Khan
- Applied College, Center of Bee Research and Its Products (CBRP), Unit of Bee Research and Honey Production, and Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, Saudi Arabia
| | - Chunmei Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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14
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Qian F, Zuo D, Zeng T, Gu L, Wang H, Du X, Zhu B, Ou J. Identification, Evolutionary Dynamics, and Gene Expression Patterns of the ACP Gene Family in Responding to Salt Stress in Brassica Genus. PLANTS (BASEL, SWITZERLAND) 2024; 13:950. [PMID: 38611479 PMCID: PMC11013218 DOI: 10.3390/plants13070950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Acyl carrier proteins (ACPs) have been reported to play a crucial role in responding to biotic and abiotic stresses, regulating growth and development. However, the biological function of the ACP gene family in the Brassica genus has been limited until now. In this study, we conducted a comprehensive analysis and identified a total of 120 ACP genes across six species in the Brassica genus. Among these, there were 27, 26, and 30 ACP genes in the allotetraploid B. napus, B. juncea, and B. carinata, respectively, and 14, 13, and 10 ACP genes in the diploid B. rapa, B. oleracea, and B. nigra, respectively. These ACP genes were further classified into six subclades, each containing conserved motifs and domains. Interestingly, the majority of ACP genes exhibited high conservation among the six species, suggesting that the genome evolution and polyploidization processes had relatively minor effects on the ACP gene family. The duplication modes of the six Brassica species were diverse, and the expansion of most ACPs in Brassica occurred primarily through dispersed duplication (DSD) events. Furthermore, most of the ACP genes were under purifying selection during the process of evolution. Subcellular localization experiments demonstrated that ACP genes in Brassica species are localized in chloroplasts and mitochondria. Cis-acting element analysis revealed that most of the ACP genes were associated with various abiotic stresses. Additionally, RNA-seq data revealed differential expression levels of BnaACP genes across various tissues in B. napus, with particularly high expression in seeds and buds. qRT-PCR analysis further indicated that BnaACP genes play a significant role in salt stress tolerance. These findings provide a comprehensive understanding of ACP genes in Brassica plants and will facilitate further functional analysis of these genes.
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Affiliation(s)
- Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Dan Zuo
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Tuo Zeng
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Jing Ou
- College of Forestry, Guizhou University, Guiyang 550025, China
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15
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Vera-Maldonado P, Aquea F, Reyes-Díaz M, Cárcamo-Fincheira P, Soto-Cerda B, Nunes-Nesi A, Inostroza-Blancheteau C. Role of boron and its interaction with other elements in plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1332459. [PMID: 38410729 PMCID: PMC10895714 DOI: 10.3389/fpls.2024.1332459] [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: 11/03/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024]
Abstract
Boron (B) is an essential microelement for plants, and its deficiency can lead to impaired development and function. Around 50% of arable land in the world is acidic, and low pH in the soil solution decreases availability of several essential mineral elements, including B, magnesium (Mg), calcium (Ca), and potassium (K). Plants take up soil B in the form of boric acid (H3BO3) in acidic soil or tetrahydroxy borate [B(OH)4]- at neutral or alkaline pH. Boron can participate directly or indirectly in plant metabolism, including in the synthesis of the cell wall and plasma membrane, in carbohydrate and protein metabolism, and in the formation of ribonucleic acid (RNA). In addition, B interacts with other nutrients such as Ca, nitrogen (N), phosphorus (P), K, and zinc (Zn). In this review, we discuss the mechanisms of B uptake, absorption, and accumulation and its interactions with other elements, and how it contributes to the adaptation of plants to different environmental conditions. We also discuss potential B-mediated networks at the physiological and molecular levels involved in plant growth and development.
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Affiliation(s)
- Peter Vera-Maldonado
- Programa de Doctorado en Ciencias Agropecuarias, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Felipe Aquea
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Marjorie Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Paz Cárcamo-Fincheira
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
| | - Braulio Soto-Cerda
- Laboratorio de Fisiología y Biotecnología Vegetal, Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
- Nucleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Claudio Inostroza-Blancheteau
- Laboratorio de Fisiología y Biotecnología Vegetal, Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
- Nucleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
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16
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Zhou Y, Li Z, Xu C, Pan J, Li H, Zhou Y, Zou Y. Genome-wide analysis of bZIP gene family members in Pleurotus ostreatus, and potential roles of PobZIP3 in development and the heat stress response. Microb Biotechnol 2024; 17:e14413. [PMID: 38376071 PMCID: PMC10877997 DOI: 10.1111/1751-7915.14413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/29/2023] [Accepted: 01/08/2024] [Indexed: 02/21/2024] Open
Abstract
The basic leucine zipper (bZIP) transcription factor (TF) is widespread among eukaryotes and serves different roles in fungal processes including nutrient utilization, growth, stress responses and development. The oyster mushroom (Pleurotus ostreatus) is an important and widely cultivated edible mushroom worldwide; nevertheless, reports are lacking on the identification or function of bZIP gene family members in P. ostreatus. Herein, 11 bZIPs on 6 P. ostreatus chromosomes were systematically identified, which were classified into 3 types according to their protein sequences. Phylogenetic analysis of PobZIPs with other fungal bZIPs indicated that PobZIPs may have differentiated late. Cis-regulatory element analysis revealed that at least one type of stress-response-related element was present on each bZIP promoter. RNA-seq and RT-qPCR analyses revealed that bZIP expression patterns were altered under heat stress and different developmental stages. We combined results from GST-Pull-down, EMSA and yeast two-hybrid assays to screen a key heat stress-responsive candidate gene PobZIP3. PobZIP3 overexpression in P. ostreatus enhanced tolerance to high temperature and cultivation assays revealed that PobZIP3 positively regulates the development of P. ostreatus. RNA-seq analysis showed that PobZIP3 plays a role in glucose metabolism pathways, antioxidant enzyme activity and sexual reproduction. These results may support future functional studies of oyster mushroom bZIP TFs.
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Affiliation(s)
- Yuanyuan Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi‐arid ArableLand in Northern ChinaBeijingChina
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Zihao Li
- State Key Laboratory of Efficient Utilization of Arid and Semi‐arid ArableLand in Northern ChinaBeijingChina
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Congtao Xu
- State Key Laboratory of Efficient Utilization of Arid and Semi‐arid ArableLand in Northern ChinaBeijingChina
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Jinlong Pan
- State Key Laboratory of Efficient Utilization of Arid and Semi‐arid ArableLand in Northern ChinaBeijingChina
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Haikang Li
- State Key Laboratory of Efficient Utilization of Arid and Semi‐arid ArableLand in Northern ChinaBeijingChina
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Yi Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi‐arid ArableLand in Northern ChinaBeijingChina
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Yajie Zou
- State Key Laboratory of Efficient Utilization of Arid and Semi‐arid ArableLand in Northern ChinaBeijingChina
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
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17
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Lai H, Wang M, Yan L, Feng C, Tian Y, Tian X, Peng D, Lan S, Zhang Y, Ai Y. Genome-Wide Identification of bZIP Transcription Factors in Cymbidium ensifolium and Analysis of Their Expression under Low-Temperature Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:219. [PMID: 38256772 PMCID: PMC10818551 DOI: 10.3390/plants13020219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
The basic leucine zipper (bZIP) transcription factors constitute the most widely distributed and conserved eukaryotic family. They play crucial roles in plant growth, development, and responses to both biotic and abiotic stresses, exerting strong regulatory control over the expression of downstream genes. In this study, a genome-wide characterization of the CebZIP transcription factor family was conducted using bioinformatic analysis. Various aspects, including physicochemical properties, phylogenetics, conserved structural domains, gene structures, chromosomal distribution, gene covariance relationships, promoter cis-acting elements, and gene expression patterns, were thoroughly analyzed. A total of 70 CebZIP genes were identified from the C. ensifolium genome, and they were randomly distributed across 18 chromosomes. The phylogenetic tree clustered them into 11 subfamilies, each exhibiting complex gene structures and conserved motifs arranged in a specific order. Nineteen pairs of duplicated genes were identified among the 70 CebZIP genes, with sixteen pairs affected by purifying selection. Cis-acting elements analysis revealed a plethora of regulatory elements associated with stress response, plant hormones, and plant growth and development. Transcriptome and qRT-PCR results demonstrated that the expression of CebZIP genes was universally up-regulated under low temperature conditions. However, the expression patterns varied among different members. This study provides theoretical references for identifying key bZIP genes in C. ensifolium that confer resistance to low-temperature stress, and lays the groundwork for further research into their broader biological functions.
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Affiliation(s)
- Huiping Lai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Mengyao Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Lu Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Caiyun Feng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Yang Tian
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Xinyue Tian
- Anhui Province Key Laboratory of Forest Resources and Silviculture, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China;
| | - Donghui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
| | - Yanping Zhang
- Anhui Province Key Laboratory of Forest Resources and Silviculture, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China;
| | - Ye Ai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.L.); (M.W.); (L.Y.); (C.F.); (Y.T.); (D.P.); (S.L.)
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18
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Wang L, Mo Z, Yu X, Mao Y. Characterization of the basic leucine zipper transcription factor family of Neoporphyra haitanensis and its role in acclimation to dehydration stress. BMC PLANT BIOLOGY 2023; 23:617. [PMID: 38049766 PMCID: PMC10696790 DOI: 10.1186/s12870-023-04636-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Neoporphyra haitanensis, a major marine crop native to southern China, grows in the harsh intertidal habitats of rocky coasts. The thallus can tolerate fluctuating and extreme environmental stresses, for example, repeated desiccation/rehydration due to the turning tides. It is also a typical model system for investigating stress tolerance mechanisms in intertidal seaweed. The basic leucine zipper (bZIP) transcription factors play important roles in the regulation of plants' responses to environmental stress stimuli. However, little information is available regarding the bZIP family in the marine crop Nh. haitanensis. RESULTS We identified 19 bZIP genes in the Nh. haitanensis genome and described their conserved domains. Based on phylogenetic analysis, these 19 NhhbZIP genes, distributed unevenly on the 11 superscaffolds, were divided into four groups. In each group, there were analogous exon/intron numbers and motif compositions, along with diverse exon lengths. Cross-species collinearity analysis indicated that 17 and 9 NhhbZIP genes were orthologous to bZIP genes in Neopyropia yezoensis and Porphyra umbilicalis, respectively. Evidence from RNA sequencing (RNA-seq) data showed that the majority of NhhbZIP genes (73.68%) exhibited transcript abundance in all treatments. Furthermore, genes NN 2, 4 and 5 showed significantly altered expression in response to moderate dehydration, severe dehydration, and rehydration, respectively. Gene co-expression network analysis of the representative genes was carried out, followed by gene set enrichment analysis. Two NhhbZIP genes collectively responding to dehydration and rehydration and their co-expressing genes mainly participated in DNA repair, DNA metabolic process, and regulation of helicase activity. Two specific NhhbZIP genes responding to severe dehydration and their corresponding network genes were mainly involved in macromolecule modification, cellular catabolic process, and transmembrane transport. Three specific NhhbZIP genes responding to rehydration and their co-expression gene networks were mainly involved in the regulation of the cell cycle process and defense response. CONCLUSIONS This study provides new insights into the structural composition, evolution, and function of the NhhbZIP gene family. Our results will help us to further study the functions of bZIP genes in response to dehydration and rehydration in Nh. haitanensis and improve Nh. haitanensis in southern China.
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Affiliation(s)
- Li Wang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Biotechnology and Bioresources Utilization (Ministry of Education), Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
| | - Zhaolan Mo
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Xinzi Yu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Yazhou Bay Innovation Institute & Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource (Ministry of Education), College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, China.
- Laboratory of Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266700, China.
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Liu W, Wang M, Zhong M, Luo C, Shi S, Qian Y, Kang Y, Jiang B. Genome-wide identification of bZIP gene family and expression analysis of BhbZIP58 under heat stress in wax gourd. BMC PLANT BIOLOGY 2023; 23:598. [PMID: 38017380 PMCID: PMC10685590 DOI: 10.1186/s12870-023-04580-6] [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: 03/12/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND The basic leucine zipper (bZIP) transcription factor family is one of the most abundant and evolutionarily conserved gene families in plants. It assumes crucial functions in the life cycle of plants, including pathogen defense, secondary metabolism, stress response, seed maturation, and flower development. Although the genome of wax gourd has been published, little is known about the functions, evolutionary background, and gene expression patterns of the bZIP gene family, which limits its utilization. RESULTS A total of 61 bZIP genes (BhbZIPs) were identified from wax gourd (Benincasa hispida) genome and divided into 12 subgroups. Whole-genome duplication (WGD) and dispersed duplication (DSD) were the main driving forces of bZIP gene family expansion in wax gourd, and this family may have undergone intense purifying selection pressure during the evolutionary process. We selected BhbZIP58, only one in the member of subgroup B, to study its expression patterns under different stresses, including heat, salt, drought, cold stress, and ABA treatment. Surprisingly, BhbZIP58 had a dramatic response under heat stress. BhbZIP58 showed the highest expression level in the root compared with leaves, stem, stamen, pistil, and ovary. In addition, BhbZIP58 protein was located in the nucleus and had transcriptional activation activity. Overexpression of BhbZIP58 in Arabidopsis enhanced their heat tolerance. CONCLUSIONS In this study, bZIP gene family is systematically bioinformatically in wax gourd for the first time. Particularly, BhbZIP58 may have an important role in heat stress. It will facilitate further research on the bZIP gene family regarding their evolutionary history and biological functions.
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Affiliation(s)
- Wei Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Min Wang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510640, Guangdong, China
| | - Min Zhong
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Chen Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510640, Guangdong, China
| | - Shaoqi Shi
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510640, Guangdong, China
| | - Yulei Qian
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510640, Guangdong, China
| | - Yunyan Kang
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
| | - Biao Jiang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510640, Guangdong, China.
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20
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Wang S, Zhao Y, Chen Y, Gao M, Wang Y. The Association between BZIP Transcription Factors and Flower Development in Litsea cubeba. Int J Mol Sci 2023; 24:16646. [PMID: 38068969 PMCID: PMC10705912 DOI: 10.3390/ijms242316646] [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: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The basic leucine zipper (bZIP) family is one of the largest families of transcription factors among eukaryotic organisms. Members of the bZIP family play various roles in regulating the intricate process of flower development in plants. Litsea cubeba (Lour.) (family: Lauraceae) is an aromatic, dioecious plant used in China for a wide range of applications. However, no study to date has undertaken a comprehensive analysis of the bZIP gene family in L. cubeba. In this work, we identified 68 members of the bZIP gene family in L. cubeba and classified them into 12 subfamilies based on previous studies on Arabidopsis thaliana. Transcriptome data analysis revealed that multiple LcbZIP genes exhibit significantly high expression levels in the flowers of L. cubeba, while some also demonstrate distinct temporal specificity during L. cubeba flower development. In particular, some LcbZIP genes displayed specific and high expression levels during the stamen and pistil degradation process. Using differential gene expression analysis, weighted gene co-expression network analysis, and Gene Ontology enrichment analysis, we identified six candidate LcbZIP genes that potentially regulate stamen or pistil degradation during flower development. In summary, our findings provide a framework for future functional analysis of the LcbZIP gene family in L. cubeba and offer novel insights for investigating the mechanism underlying pistil and stamen degeneration in this plant.
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Affiliation(s)
- Siqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100000, China; (S.W.); (Y.Z.); (Y.C.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310000, China
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21
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Sun T, Sun J, Liu Y, Ren Y, Li Y, Shi C, Nasr A, Tang Z, Abozeid A. Metabolome and transcriptome analyses provide new insights into the mechanisms underlying the enhancement of medicinal component content in the roots of Acanthopanax senticosus (Rupr. et Maxim.) Harms through foliar application of zinc fertilizer. Front Genet 2023; 14:1259674. [PMID: 38046048 PMCID: PMC10690782 DOI: 10.3389/fgene.2023.1259674] [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: 07/16/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023] Open
Abstract
Acanthopanax senticosus (Rupr. et Maxim.) Harms is a perennial shrub of the Acanthopanax genus in the Araliaceae family and has a high medicinal value. The application of zinc fertilizer can improve the yield and quality of medicinal materials. However, there are limited reports on approaches to increase the content of medicinal components in A. senticosus, hindering the improvement of its medicinal quality. In this study, A. senticosus was treated with 0.1% (LZn) and 0.4% (HZn) zinc sprayed on the leaf surface. The effects of zinc treatment on the medicinal components in the roots of A. senticosus were analyzed by comprehensive metabolomics and transcriptomics analyses. A total of 316 metabolites were detected, with a prevailing occurrence of terpenoids and phenylpropanoids. We identified metabolites related to the medicinal components that were upregulated after Zn treatment, including 43 terpenoids, 19 phenylpropanoids, eight phenols, and three flavonoids. Combining differential gene expression and K-means analysis, we found 95, 65, and 25 upregulated genes related to phenylpropanoid biosynthesis, terpenoid biosynthesis, and flavonoid biosynthesis, respectively. Under different concentrations of Zn treatment, the upregulated metabolite biosynthesis-related genes and differentially expressed transcription factors varied. Pearson correlation network analysis revealed significant correlations among terpenoids, phenylpropanoids, flavonoids biosynthetic genes, and several transcription factors (ERFs, WRKYs, bHLHs, NACs, and MYBs). This study lays the foundation for understanding the metabolic processes in response to varying levels of zinc foliar spray and provides a theoretical basis for enhancing the efficiency of zinc fertilizer utilization in A. senticosus.
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Affiliation(s)
- Tongze Sun
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
| | - Jialin Sun
- Biological Science and Technology Department, Heilongjiang Vocational College for Nationalities, Harbin, China
| | - Yuli Liu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
| | - Yanjun Ren
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
| | - Yifeng Li
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- College of Life Science, Kim Il Sung University, Pyongyang, Democratic People’s Republic of Korea
| | - Chang Shi
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
| | - Alyaa Nasr
- Botany and Microbiology Department, Faculty of Science, Menoufia University, Shebeen El-Kom, Egypt
| | - Zhonghua Tang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
| | - Ann Abozeid
- Botany and Microbiology Department, Faculty of Science, Menoufia University, Shebeen El-Kom, Egypt
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22
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Wu M, Chen J, Tang W, Jiang Y, Hu Z, Xu D, Hou K, Chen Y, Wu W. Genome-Wide Identification and Expression Analysis of bZIP Family Genes in Stevia rebaudiana. Genes (Basel) 2023; 14:1918. [PMID: 37895267 PMCID: PMC10606749 DOI: 10.3390/genes14101918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors widely distributed in eukaryotic organisms. In plants, they are not only involved in growth and development, defense and stress responses and regulation of physiological processes but also play a pivotal role in regulating secondary metabolism. To explore the function related to the bZIP gene family in Stevia rebaudiana Bertoni, we identified 105 SrbZIP genes at the genome-wide level and classified them into 12 subfamilies using bioinformation methods. Three main classes of cis-acting elements were found in the SrbZIP promoter regions, including development-related elements, defense and stress-responsive elements and phytohormone-responsive elements. Through protein-protein interaction network of 105 SrbZIP proteins, SrbZIP proteins were mainly classified into four major categories: ABF2/ABF4/ABI5 (SrbZIP51/SrbZIP38/SrbZIP7), involved in phytohormone signaling, GBF1/GBF3/GBF4 (SrbZIP29/SrbZIP63/SrbZIP60) involved in environmental signaling, AREB3 (SrbZIP88), PAN (SrbZIP12), TGA1 (SrbZIP69), TGA4 (SrbZIP82), TGA7 (SrbZIP31), TGA9 (SrbZIP95), TGA10 (SrbZIP79) and HY5 (SrbZIP96) involved in cryptochrome signaling, and FD (SrbZIP72) promoted flowering. The transcriptomic data showed that SrbZIP genes were differentially expressed in six S. rebaudiana cultivars ('023', '110', 'B1188', '11-14', 'GP' and 'GX'). Moreover, the expression levels of selected 15 SrbZIP genes in response to light, abiotic stress (low temperature, salt and drought), phytohormones (methyl jasmonate, gibberellic acid and salicylic acid) treatment and in different tissues were analyzed utilizing qRT-PCR. Some SrbZIP genes were further identified to be highly induced by factors affecting glycoside synthesis. Among them, three SrbZIP genes (SrbZIP54, SrbZIP63 and SrbZIP32) were predicted to be related to stress-responsive terpenoid synthesis in S. rebaudiana. The protein-protein interaction network expanded the potential functions of SrbZIP genes. This study firstly provided the comprehensive genome-wide report of the SrbZIP gene family, laying a foundation for further research on the evolution, function and regulatory role of the bZIP gene family in terpenoid synthesis in S. rebaudiana.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wei Wu
- Agronomy College, Sichuan Agricultural University, Chengdu 611130, China; (M.W.); (J.C.); (W.T.); (Y.J.); (Z.H.); (D.X.); (K.H.); (Y.C.)
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23
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Wu Q, Yin J, Jiang M, Zhang J, Sui Z. Identification, characterization and expression profiles of E2 and E3 gene superfamilies during the development of tetrasporophytes in Gracilariopsis lemaneiformis (Rhodophyta). BMC Genomics 2023; 24:549. [PMID: 37723489 PMCID: PMC10506303 DOI: 10.1186/s12864-023-09639-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023] Open
Abstract
E2 ubiquitin conjugating enzymes and E3 ubiquitin ligases play important roles in the growth and development of plants and animals. To date, the systematic analysis of E2 and E3 genes in Rhodophyta is limited. In this study, 14 E2 genes and 51 E3 genes were identified in Gracilariopsis lemaneiformis, an economically important red alga. E2 genes were classified into four classes according to the structure of the conserved domain, UBC. E3 genes were classified into 12 subfamilies according to individual conserved domains. A phylogenetic tree of seven algae species showed that functional differentiation of RING-type E3s was the highest, and the similarity between orthologous genes was high except in Chlamydomonas reinhardtii and Chara braunii. RNA-seq data analysis showed significant differential expression levels of E2 and E3 genes under the life stages of tetraspore formation and release, especially GlUBCN and GlAPC3. According to GO and KEGG analysis of two transcriptomes, GlUBCN and GlAPC3 were involved in ubiquitin-mediated proteolysis, and other subunits of the anaphase promoting complex or cyclosome (APC/C) and its activators GlCDC20 and GlCDH1 were also enriched into this process. The CDH1 and CDC20 in 981 were down-regulated during tetraspores formation and release, with the down-regulation of CDH1 being particularly significant; CDH1 and CDC20 in WLP-1, ZC, and WT were up-regulated during tetraspores formation and release, with CDC20 being more significantly up-regulated. Therefore, GlCDH1, rather than GlCDC20, in '981' might play the leading role in the activation of the APC/C, and GlCDC20 might play the leading role rather than GlCDH1 in strains WLP-1, ZC and wild type. The low fertility of cultivar 981 might be highly correlated with the inactivity of activators CDH1 and CDC20. This study provided a basic and comprehensive understanding of characteristic of E2 and E3 genes in Gp. lemaneiformis and set a foundation for further understanding of E2 ubiquitin conjugating enzymes and E3 ubiquitin ligase in regulating tetrasporophytes development of Gp. lemaneiformis.
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Affiliation(s)
- Qiong Wu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Jingru Yin
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Min Jiang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Jingyu Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China), Qingdao, 266003, China.
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24
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Hua B, Liang F, Zhang W, Qiao D, Wang P, Teng H, Zhang Z, Liu J, Miao M. The Potential Role of bZIP55/65 in Nitrogen Uptake and Utilization in Cucumber Is Revealed via bZIP Gene Family Characterization. PLANTS (BASEL, SWITZERLAND) 2023; 12:3228. [PMID: 37765392 PMCID: PMC10537890 DOI: 10.3390/plants12183228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
Abstract
The bZIP (basic leucine zipper) proteins play crucial roles in various biological functions. Nitrogen (N) is an essential element for plant growth, especially in cucumber (Cucumis sativus) due to its shallow roots. However, the regulation of bZIP genes in cucumber nitrogen metabolism has not been studied yet. In this study, we identified a total of 72 bZIP genes (CsbZIPs) in the cucumber genome that could be classified into 13 groups. These genes were unevenly distributed on seven chromosomes, and synteny analysis showed that the CsbZIP genes were expanded in a segmentally duplicating manner. Furthermore, our genome-wide expression analysis suggested that CsbZIP genes had different patterns and that five CsbZIP genes were regulated by nitrogen treatment in both leaves and roots. Consistent with CsNPF, CsbZIP55 and CsbZIP65 were regulated by nitrogen treatment in leaves and roots. Moreover, the subcellular localization showed that CsbZIP55 and CsbZIP65 were specifically located in the nucleus, and the transcriptional activation assay showed that CsbZIP55 and CsbZIP65 have transcriptional activation activity. Additionally, in the CsbZIP55 and CsbZIP65 overexpression plants, most nitrogen-regulated CsNPF genes were downregulated. Taken together, our comprehensive analysis of the bZIP gene family lays a foundation for understanding the molecular and physiological functions of CsbZIPs.
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Affiliation(s)
- Bing Hua
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (B.H.); (F.L.); (W.Z.); (D.Q.); (P.W.); (H.T.); (Z.Z.); (J.L.)
| | - Fei Liang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (B.H.); (F.L.); (W.Z.); (D.Q.); (P.W.); (H.T.); (Z.Z.); (J.L.)
| | - Wenyan Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (B.H.); (F.L.); (W.Z.); (D.Q.); (P.W.); (H.T.); (Z.Z.); (J.L.)
| | - Dan Qiao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (B.H.); (F.L.); (W.Z.); (D.Q.); (P.W.); (H.T.); (Z.Z.); (J.L.)
| | - Peiqi Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (B.H.); (F.L.); (W.Z.); (D.Q.); (P.W.); (H.T.); (Z.Z.); (J.L.)
| | - Haofeng Teng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (B.H.); (F.L.); (W.Z.); (D.Q.); (P.W.); (H.T.); (Z.Z.); (J.L.)
| | - Zhiping Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (B.H.); (F.L.); (W.Z.); (D.Q.); (P.W.); (H.T.); (Z.Z.); (J.L.)
| | - Jiexia Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (B.H.); (F.L.); (W.Z.); (D.Q.); (P.W.); (H.T.); (Z.Z.); (J.L.)
| | - Minmin Miao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (B.H.); (F.L.); (W.Z.); (D.Q.); (P.W.); (H.T.); (Z.Z.); (J.L.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
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Yuan Y, Zhang W, Pang J, Zhou M, Liu J, Zhao J, Sui J, Huang D, Yang M. Integrated physiological and metabolomic analyses reveal changes during the natural senescence of Quercus mongolica leaves. PLoS One 2023; 18:e0289272. [PMID: 37611226 PMCID: PMC10446833 DOI: 10.1371/journal.pone.0289272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/15/2023] [Indexed: 08/25/2023] Open
Abstract
Quercus mongolica is a common landscape, afforestation, and construction timber species in northern China with high ecological, economic, and ornamental value. Leaf senescence is a complex process that has important implications for plant growth and development. To explore changes of metabolites during the ageing of Quercus mongolica leaves, we investigated physiological responses and metabolite composition in ageing leaves harvested from 15-20-year-old Quercus mongolica. Leaf samples of Q. mongolica were collected when they were still green (at maturity) (stage 1), during early senescence (stage 2), and during late senescence (stage 3). These leaves were then subjected to physiological index and metabolome sequencing analyses. The physiological analysis showed that the leaves of Q. mongolica changed from green to yellow during senescence, which induced significant accumulation of soluble sugar and significant reductions in the concentration of soluble protein and chlorophyll. Peroxidase and catalase were the main antioxidant enzymes mitigating leaf senescence. Metabolomic analysis identified 797 metabolites during leaf senescence. Compared to stage 1, 70 differential metabolites were screened in stage 2 and 72 were screened in stage 3. Differential metabolites in the two senescent stages were principally enriched in amino acid metabolism, lipid metabolism and secondary metabolite biosynthesis. The contents of N-oleoylethanolamine and N, N-dimethylglycine were significantly increased only in stage 2, while the contents of trifolin, astragalin, valine, isoleucine, leucine, and citric acid were significantly increased only in stage 3. Histidine, homoserine, tryptophan, tyrosine, phenylalanine, proline, norleucine, N-glycyl-L-leucine, linoleic acid, linolenic acid, gallic acid, 3-indoleacrylic acid, 3-amino-2-naphthoic acid, 3-hydroxy-3-methylpentane-1,5-dioic acid, 2,3,4-trihydroxybenzoic acid, trifolin, astragalin, DL-2-aminoadipic acid, pinoresinol dimethyl ether, dimethylmatairesinol, and lysophosphatidylcholine increased during both stage 2 and stage 3. Increasing contents of these metabolites may constitute the main mechanism by which Q. mongolica leaves adapt to senescence.
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Affiliation(s)
- Yangchen Yuan
- College of Landscape Architecture and Tourism, Agricultural University of Hebei, Baoding, Hebei, China
- Hongyashan State-Owned Forest Farm, Baoding, Hebei, China
| | - Weiqiang Zhang
- Hongyashan State-Owned Forest Farm, Baoding, Hebei, China
| | - Jiushuai Pang
- Hongyashan State-Owned Forest Farm, Baoding, Hebei, China
| | - Miaomiao Zhou
- Hongyashan State-Owned Forest Farm, Baoding, Hebei, China
| | - Jianying Liu
- Hongyashan State-Owned Forest Farm, Baoding, Hebei, China
| | - Jin Zhao
- Hongyashan State-Owned Forest Farm, Baoding, Hebei, China
| | - Jinming Sui
- Meteorological Bureau of Yi County, Baoding, Hebei, China
| | - Dazhuang Huang
- College of Landscape Architecture and Tourism, Agricultural University of Hebei, Baoding, Hebei, China
| | - Minsheng Yang
- College of Forestry, Agricultural University of Hebei, Baoding, Hebei, China
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Wang H, Peng J, Li Y, Xu L, Dai W, Zhao S. The role of walnut bZIP genes in explant browning. BMC Genomics 2023; 24:377. [PMID: 37407925 DOI: 10.1186/s12864-023-09492-1] [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: 05/23/2023] [Accepted: 06/29/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Basic leucine zipper (bZIP) proteins are important transcription factors in plants. To study the role of bZIP transcription factors in walnut explant browning, this study used bioinformatics software to analyze walnut bZIP gene family members, along with their transcript levels in different walnut tissues, to evaluate the transcriptional expression of this gene family during the primary culture of walnut explants and to reveal the mechanism of action of walnut bZIP genes in walnut explant browning. RESULTS The results identified 65 JrbZIP genes in the walnut genome, which were divided into 8 subfamilies and distributed on 16 chromosomes. The results of transcriptome data analysis showed that there were significant differences in the expression of four genes, namely, JrbZIP55, JrbZIP70, JrbZIP72, and JrbZIP88, under both vermiculite and agar culture conditions. There were multiple hormone (salicylic acid, abscisic acid, auxin, and gibberellin) signaling and regulatory elements that are responsive to stress (low temperature, stress, and defense) located in the promoter regions of JrbZIP55, JrbZIP70, JrbZIP72, and JrbZIP88. The walnut JrbZIP55 protein and Arabidopsis bZIP42 protein are highly homologous, and the proteins interacting with Arabidopsis bZIP42 include the AT2G19940 oxidoreductases, which act on aldehyde or oxygen-containing donors. CONCLUSION It is speculated that JrbZIP55 may participate in the regulation of browning in walnut explants.
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Affiliation(s)
- Hui Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Jiali Peng
- College of Horticulture, Hebei Agricultural University, Baoding, 071001, China
| | - Yaoling Li
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Lishan Xu
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Wenqiang Dai
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Shugang Zhao
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China.
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Han H, Wang C, Yang X, Wang L, Ye J, Xu F, Liao Y, Zhang W. Role of bZIP transcription factors in the regulation of plant secondary metabolism. PLANTA 2023; 258:13. [PMID: 37300575 DOI: 10.1007/s00425-023-04174-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION This study provides an overview of the structure, classification, regulatory mechanisms, and biological functions of the basic (region) leucine zipper transcription factors and their molecular mechanisms in flavonoid, terpenoid, alkaloid, phenolic acid, and lignin biosynthesis. Basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors (TFs) in eukaryotic organisms. The bZIP TFs are widely distributed in plants and play important roles in plant growth and development, photomorphogenesis, signal transduction, resistance to pathogenic microbes, biotic and abiotic stress, and secondary metabolism. Moreover, the expression of bZIP TFs not only promotes or inhibits the accumulation of secondary metabolites in medicinal plants, but also affects the stress response of plants to the external adverse environment. This paper describes the structure, classification, biological function, and regulatory mechanisms of bZIP TFs. In addition, the molecular mechanism of bZIP TFs regulating the biosynthesis of flavonoids, terpenoids, alkaloids, phenolic acids, and lignin are also elaborated. This review provides a summary for in-depth study of the molecular mechanism of bZIP TFs regulating the synthesis pathway of secondary metabolites and plant molecular breeding, which is of significance for the generation of beneficial secondary metabolites and the improvement of plant varieties.
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Affiliation(s)
- Huan Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Caini Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xiaoyan Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Lina Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
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Abdul Aziz M, Masmoudi K. Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms. Int J Mol Sci 2023; 24:9813. [PMID: 37372961 DOI: 10.3390/ijms24129813] [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: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na+ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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Liu H, Tang X, Zhang N, Li S, Si H. Role of bZIP Transcription Factors in Plant Salt Stress. Int J Mol Sci 2023; 24:ijms24097893. [PMID: 37175598 PMCID: PMC10177800 DOI: 10.3390/ijms24097893] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Soil salinity has become an increasingly serious problem worldwide, greatly limiting crop development and yield, and posing a major challenge to plant breeding. Basic leucine zipper (bZIP) transcription factors are the most widely distributed and conserved transcription factors and are the main regulators controlling various plant response processes against external stimuli. The bZIP protein contains two domains: a highly conserved, DNA-binding alkaline region, and a diverse leucine zipper, which is one of the largest transcription factor families in plants. Plant bZIP is involved in many biological processes, such as flower development, seed maturation, dormancy, and senescence, and plays an important role in abiotic stresses such as salt damage, drought, cold damage, osmotic stress, mechanical damage, and ABA signal response. In addition, bZIP is involved in the regulation of plant response to biological stresses such as insect pests and pathogen infection through salicylic acid, jasmonic acid, and ABA signal transduction pathways. This review summarizes and discusses the structural characteristics and functional characterization of the bZIP transcription factor group, the bZIP transcription factor complex and its molecular regulation mechanisms related to salt stress resistance, and the regulation of transcription factors in plant salt stress resistance. This review provides a theoretical basis and research ideas for further exploration of the salt stress-related functions of bZIP transcription factors. It also provides a theoretical basis for crop genetic improvement and green production in agriculture.
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Affiliation(s)
- Haotian Liu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xun Tang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Ning Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Shigui Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Huaijun Si
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
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Lv G, Han R, Shi J, Chen K, Liu G, Yu Q, Yang C, Jiang J. Genome-wide identification of the TIFY family reveals JAZ subfamily function in response to hormone treatment in Betula platyphylla. BMC PLANT BIOLOGY 2023; 23:143. [PMID: 36922795 PMCID: PMC10015818 DOI: 10.1186/s12870-023-04138-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The TIFY family is a plant-specific gene family and plays an important role in plant growth and development. But few reports have been reported on the phylogenetic analysis and gene expression profiling of TIFY family genes in birch (Betula platyphylla). RESULTS In this study, we characterized TIFY family and identified 12 TIFY genes and using phylogeny and chromosome mapping analysis in birch. TIFY family members were divided into JAZ, ZML, PPD and TIFY subfamilies. Phylogenetic analysis revealed that 12 TIFY genes were clustered into six evolutionary branches. The chromosome distribution showed that 12 TIFY genes were unevenly distributed on 5 chromosomes. Some TIFY family members were derived from gene duplication in birch. We found that six JAZ genes from JAZ subfamily played essential roles in response to Methyl jasmonate (MeJA), the JAZ genes were correlated with COI1 under MeJA. Co-expression and GO enrichment analysis further revealed that JAZ genes were related to hormone. JAZ proteins involved in the ABA and SA pathways. Subcellular localization experiments confirmed that the JAZ proteins were localized in the nucleus. Yeast two-hybrid assay showed that the JAZ proteins may form homologous or heterodimers to regulate hormones. CONCLUSION Our results provided novel insights into biological function of TIFY family and JAZ subfamily in birch. It provides the theoretical reference for in-depth analysis of plant hormone and molecular breeding design for resistance.
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Affiliation(s)
- Guanbin Lv
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150036, China
| | - Rui Han
- College of Forestry and Grassland Science, Jilin Agricultural University, Jilin, China
| | - Jingjing Shi
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150036, China
| | - Kun Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150036, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150036, China
| | - Qibin Yu
- University of Florida, Lake Alfred, FL, USA
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150036, China.
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150036, China.
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Medison MB, Pan R, Peng Y, Medison RG, Shalmani A, Yang X, Zhang W. Identification of HQT gene family and their potential function in CGA synthesis and abiotic stresses tolerance in vegetable sweet potato. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:361-376. [PMID: 37033766 PMCID: PMC10073390 DOI: 10.1007/s12298-023-01299-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Hydroxycinnamate-CoA quinate hydroxycinnamoyl transferase (HQT) enzyme affect plant secondary metabolism and are crucial for growth and development. To date, limited research on the genome-wide analysis of HQT family genes and their regulatory roles in chlorogenic acid (CGA) accumulation in leafy vegetable sweet potato is available. Here, a total of 58 HQT family genes in the sweet potato genome (named IbHQT) were identified and analyzed. We studied the chromosomal distribution, phylogenetic relationship, motifs distribution, collinearity, and cis-acting element analysis of HQT family genes. This study used two sweet potato varieties, high CGA content Fushu 7-6-14-7 (HC), and low CGA content Fushu 7-6 (LC). Based on the phylogenetic analysis, clade A was unique among the identified four clades as it contained HQT genes from various species. The chromosomal location and collinearity analysis revealed that tandem gene duplication may promote the IbHQT gene expansion and expression. The expression patterns and profile analysis showed changes in gene expression levels at different developmental stages and under cold, drought, and salt stress conditions. The expression analysis verified by qRT-PCR revealed that IbHQT genes were highly expressed in the HC variety leaves than in the LC variety. Furthermore, cloning and gene function analysis unveiled that IbHQT family genes are involved in the biosynthesis and accumulation of CGA in sweet-potato. This study expands our understanding of the regulatory role of HQT genes in sweet-potato and lays a foundation for further functional characterization and genetic breeding by engineering targeted HQT candidate genes in various sweet-potato varieties and other species. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01299-4.
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Affiliation(s)
- Milca Banda Medison
- Research Center of Crop Stresses Resistance Technologies/ Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025 China
| | - Rui Pan
- Research Center of Crop Stresses Resistance Technologies/ Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025 China
| | - Ying Peng
- Research Center of Crop Stresses Resistance Technologies/ Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025 China
| | - Rudoviko Galileya Medison
- Research Center of Crop Stresses Resistance Technologies/ Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025 China
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100 China
| | - XinSun Yang
- Institute of Food Crops/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei Academy of Agricultural Sciences, Wuhan, 430064 China
| | - Wenying Zhang
- Research Center of Crop Stresses Resistance Technologies/ Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025 China
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Wang Y, Wang R, Yu Y, Gu Y, Wang S, Liao S, Xu X, Jiang T, Yao W. Genome-Wide Analysis of SIMILAR TO RCD ONE (SRO) Family Revealed Their Roles in Abiotic Stress in Poplar. Int J Mol Sci 2023; 24:ijms24044146. [PMID: 36835559 PMCID: PMC9961671 DOI: 10.3390/ijms24044146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
SIMILAR TO RCD ONE (SRO) gene family is a small plant-specific gene family responsible for growth, development, and stress responses. In particular, it plays a vital role in responding to abiotic stresses such as salt, drought, and heavy metals. Poplar SROs are rarely reported to date. In this study, a total of nine SRO genes were identified from Populus simonii × Populus nigra, which are more similar to dicotyledon SRO members. According to phylogenetic analysis, the nine PtSROs can be divided into two groups, and the members in the same cluster have a similar structure. There were some cis-regulatory elements related to abiotic stress response and hormone-induced factors identified in the promoter regions of PtSROs members. Subcellular localization and transcriptional activation activity of PtSRO members revealed a consistent expression profile of the genes with similar structural profiles. In addition, both RT-qPCR and RNA-Seq results indicated that PtSRO members responded to PEG-6000, NaCl, and ABA stress in the roots and leaves of Populus simonii × Populus nigra. The PtSRO genes displayed different expression patterns and peaked at different time points in the two tissues, which was more significant in the leaves. Among them, PtSRO1c and PtSRO2c were more prominent in response to abiotic stress. Furthermore, protein interaction prediction showed that the nine PtSROs might interact with a broad range of transcription factors (TFs) involved in stress responses. In conclusion, the study provides a solid basis for functional analysis of the SRO gene family in abiotic stress responses in poplar.
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Affiliation(s)
- Yuting Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yue Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yongmei Gu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shixian Liao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiaoya Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Correspondence: (T.J.); (W.Y.)
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
- Correspondence: (T.J.); (W.Y.)
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Wang J, Wang Y, Wu X, Wang B, Lu Z, Zhong L, Li G, Wu X. Insight into the bZIP gene family in Lagenaria siceraria: Genome and transcriptome analysis to understand gene diversification in Cucurbitaceae and the roles of LsbZIP gene expression and function under cold stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1128007. [PMID: 36874919 PMCID: PMC9981963 DOI: 10.3389/fpls.2022.1128007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
The basic leucine zipper (bZIP) as a well-known transcription factor family, figures prominently in diverse biological and developmental processes and response to abiotic/biotic stresses. However, no knowledge of the bZIP family is available for the important edible Cucurbitaceae crop bottle gourd. Herein, we identified 65 putative LsbZIP genes and characterized their gene structure, phylogenetic and orthologous relationships, gene expression profiles in different tissues and cultivars, and responsive genes under cold stress. The phylogenetic tree of 16 released Cucurbitaceae plant genomes revealed the evolutionary convergence and divergence of bZIP family. Based on the specific domains, LsbZIP family were classified into 12 clades (A-K, S) with similar motifs and exon-intron distribution. 65 LsbZIP genes have undergone 19 segmental and two tandem duplication events with purifying selection. The expression profiling of LsbZIP genes showed tissue-specific but no cultivar-specific pattern. The cold stress-responsive candidate LsbZIP genes were analyzed and validated by RNA-Seq and RT-PCR, providing new insights of transcriptional regulation of bZIP family genes in bottle gourd and their potential functions in cold-tolerant variety breeding.
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Affiliation(s)
- Jian Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Liping Zhong
- College of Horticulture Science, Zhejiang Agriculture and Forestry (A&F) University, Hangzhou, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Li S, Liu J, Xue C, Lin Y, Yan Q, Chen J, Wu R, Chen X, Yuan X. Identification and Functional Characterization of WRKY, PHD and MYB Three Salt Stress Responsive Gene Families in Mungbean ( Vigna radiata L.). Genes (Basel) 2023; 14:463. [PMID: 36833390 PMCID: PMC9956968 DOI: 10.3390/genes14020463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
WRKY-, PHD-, and MYB-like proteins are three important types of transcription factors in mungbeans, and play an important role in development and stress resistance. The genes' structures and characteristics were clearly reported and were shown to contain the conservative WRKYGQK heptapeptide sequence, Cys4-His-cys3 zinc binding motif, and HTH (helix) tryptophan cluster W structure, respectively. Knowledge on the response of these genes to salt stress is largely unknown. To address this issue, 83 VrWRKYs, 47 VrPHDs, and 149 VrMYBs were identified by using comparative genomics, transcriptomics, and molecular biology methods in mungbeans. An intraspecific synteny analysis revealed that the three gene families had strong co-linearity and an interspecies synteny analysis showed that mungbean and Arabidopsis were relatively close in genetic relationship. Moreover, 20, 10, and 20 genes showed significantly different expression levels after 15 days of salt treatment (p < 0.05; Log2 FC > 0.5), respectively. Additionally, in the qRT-PCR analysis, VrPHD14 had varying degrees of response to NaCl and PEG treatments after 12 h. VrWRKY49 was upregulated by ABA treatment, especially in the beginning (within 24 h). VrMYB96 was significantly upregulated in the early stages of ABA, NaCl, and PEG stress treatments (during the first 4 h). VrWRKY38 was significantly upregulated by ABA and NaCl treatments, but downregulated by PEG treatment. We also constructed a gene network centered on the seven DEGs under NaCl treatment; the results showed that VrWRKY38 was in the center of the PPI network and most of the homologous Arabidopsis genes of the interacted genes were reported to have response to biological stress. Candidate genes identified in this study provide abundant gene resources for the study of salt tolerance in mungbeans.
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Affiliation(s)
- Shicong Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210000, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Jinyang Liu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Chenchen Xue
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Yun Lin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Qiang Yan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Jingbin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Ranran Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
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Tahmasebi A, Niazi A, Akrami S. Integration of meta-analysis, machine learning and systems biology approach for investigating the transcriptomic response to drought stress in Populus species. Sci Rep 2023; 13:847. [PMID: 36646724 PMCID: PMC9842770 DOI: 10.1038/s41598-023-27746-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
In Populus, drought is a major problem affecting plant growth and development which can be closely reflected by corresponding transcriptomic changes. Nevertheless, how these changes in Populus are not fully understood. Here, we first used meta-analysis and machine learning methods to identify water stress-responsive genes and then performed a systematic approach to discover important gene networks. Our analysis revealed that large transcriptional variations occur during drought stress. These changes were more associated with the response to stress, cellular catabolic process, metabolic pathways, and hormone-related genes. The differential gene coexpression analysis highlighted two acetyltransferase NATA1-like and putative cytochrome P450 genes that have a special contribution in response to drought stress. In particular, the findings showed that MYBs and MAPKs have a prominent role in the drought stress response that could be considered to improve the drought tolerance of Populus. We also suggest ARF2-like and PYL4-like genes as potential markers for use in breeding programs. This study provides a better understanding of how Populus responses to drought that could be useful for improving tolerance to stress in Populus.
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Affiliation(s)
- Ahmad Tahmasebi
- Institute of Biotechnology, Shiraz University, Shiraz, 7144165186, Iran.
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, 7144165186, Iran.
| | - Sahar Akrami
- Institute of Biotechnology, Shiraz University, Shiraz, 7144165186, Iran
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Lv T, Liu Q, Xiao H, Fan T, Zhou Y, Wang J, Tian CE. Genome-wide identification and analysis of the IQM gene family in soybean. FRONTIERS IN PLANT SCIENCE 2023; 13:1093589. [PMID: 36684725 PMCID: PMC9853202 DOI: 10.3389/fpls.2022.1093589] [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: 12/13/2022] [Indexed: 05/27/2023]
Abstract
IQM, a plant-specific calmodulin-binding protein, plays multiple roles in plant growth and development. Although a comprehensive analysis has been carried out on the IQM family genes in Arabidopsis and rice, the number and functions of IQM genes in other species have not been explored. In this study, we identified 15 members of the soybean (Glycine max) IQM gene family using BLASTP tools. These members were distributed on 12 soybean chromosomes and constitute six pairs caused by fragment duplication events. According to phylogeny, the 15 genes were divided into three subfamilies (I, II, and III), and members of the same subfamily had similar gene and protein structures. Yeast two-hybrid experiments revealed that the IQ motif is critical for the binding of GmIQM proteins to GmCaM, and its function is conserved in soybean, Arabidopsis, and rice. Based on real-time PCR, the soybean IQM genes were strongly induced by PEG and NaCl, suggesting their important biological functions in abiotic stress responses. Overall, this genome-wide analysis of the soybean IQM gene family lays a solid theoretical foundation for further research on the functions of GmIQM genes and could serve as a reference for the improvement and breeding of soybean stress resistance traits.
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Affiliation(s)
- Tianxiao Lv
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Qiongrui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Hong Xiao
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Tian Fan
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Yuping Zhou
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Jinxing Wang
- Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, Suihua, Heilongjiang, China
| | - Chang-en Tian
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
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Guo Q, Wei R, Xu M, Yao W, Jiang J, Ma X, Qu G, Jiang T. Genome-wide analysis of HSF family and overexpression of PsnHSF21 confers salt tolerance in Populus simonii × P. nigra. FRONTIERS IN PLANT SCIENCE 2023; 14:1160102. [PMID: 37200984 PMCID: PMC10187788 DOI: 10.3389/fpls.2023.1160102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/28/2023] [Indexed: 05/20/2023]
Abstract
Heat shock transcription factor (HSF) is an important TF that performs a dominant role in plant growth, development, and stress response network. In this study, we identified a total of 30 HSF members from poplar, which are unevenly distributed on 17 chromosomes. The poplar HSF family can be divided into three subfamilies, and the members of the same subfamily share relatively conserved domains and motifs. HSF family members are acidic and hydrophilic proteins that are located in the nucleus and mainly carry out gene expansion through segmental replication. In addition, they have rich collinearity across plant species. Based on RNA-Seq analysis, we explored the expression pattern of PtHSFs under salt stress. Subsequently, we cloned the significantly upregulated PtHSF21 gene and transformed it into Populus simonii × P. nigra. Under salt stress, the transgenic poplar overexpressing PtHSF21 had a better growth state and higher reactive oxygen scavenging ability. A yeast one-hybrid experiment indicated PtHSF21 could improve salt tolerance by specifically binding to the anti-stress cis-acting element HSE. This study comprehensively profiled the fundamental information of poplar HSF family members and their responses to salt stress and specifically verified the biological function of PtHSF21, which provides clues for understanding the molecular mechanism of poplar HSF members in response to salt stress.
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Affiliation(s)
- Qing Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- School of Architecture and Civil Engineer, Heilongjiang University of Science and Technology, Harbin, China
| | - Ran Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Min Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
| | - Jiahui Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xujun Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- *Correspondence: Guanzheng Qu, ; Tingbo Jiang,
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- *Correspondence: Guanzheng Qu, ; Tingbo Jiang,
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Guan R, Xu S, Lu Z, Su L, Zhang L, Sun W, Zhang Y, Jiang C, Liu Z, Duan L, Ji A. Genomic characterization of bZIP transcription factors related to andrographolide biosynthesis in Andrographis paniculata. Int J Biol Macromol 2022; 223:1619-1631. [PMID: 36356875 DOI: 10.1016/j.ijbiomac.2022.10.283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022]
Abstract
The basic leucine zipper (bZIP) transcription factor family plays an important role in various biological processes in plants. Andrographis paniculata (Burm.f) Nees, belonging to the family Acanthaceae, has been widely used as an important traditional herb with a wide range of pharmacological activities, such as antivenom, antiretroviral, anticancer and so on. However, there was no comprehensive analysis of bZIP gene family in the Andrographis paniculata been reported. In this study, we identified 62 bZIPs in Andrographis paniculata and grouped them into 12 subfamilies through the phylogenetic tree analysis. The bZIPs in the same groups have similar motif composition, exon-intron structure and domain distribution. In addition, the RNA-seq data gave a reference for selecting candidate bZIPs to make further function verification. Lastly, qRT-PCR analyses revealed seven ApbZIPs (ApbZIP4, ApbZIP19, ApbZIP30, ApbZIP42, ApbZIP50, ApbZIP52, ApbZIP62) were the most highly expressed in leaf and significantly up-regulated with MeJA and ABA treatment which may be involved in biosynthesis regulation of andrographolide. These data pave the way for further revealing the function of the bZIPs in Andrographis paniculata.
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Affiliation(s)
- Rui Guan
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shun Xu
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhimei Lu
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lirong Su
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Libing Zhang
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, 100070 Beijing, China
| | - Yu Zhang
- Shanxi University of Chinese Medicine, 030619 Jinzhong, China
| | - Chunhong Jiang
- State Key Laboratory of Innovative Natural Medicine and TCM Injections, Jiangxi Qingfeng Pharmaceutical Co. Ltd., Ganzhou 100022, China
| | - Zhongqiu Liu
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Lixin Duan
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Aijia Ji
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.
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Zhang B, Feng C, Chen L, Li B, Zhang X, Yang X. Identification and Functional Analysis of bZIP Genes in Cotton Response to Drought Stress. Int J Mol Sci 2022; 23:ijms232314894. [PMID: 36499218 PMCID: PMC9736030 DOI: 10.3390/ijms232314894] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022] Open
Abstract
The basic leucine zipper (bZIP) transcription factors, which harbor a conserved bZIP domain composed of two regions, a DNA-binding basic region and a Leu Zipper region, operate as important switches of transcription networks in eukaryotes. However, this gene family has not been systematically characterized in cotton (Gossypium hirsutum). Here, we identified 197 bZIP family members in cotton. The chromosome distribution pattern indicates that the GhbZIP genes have undergone 53 genome-wide segmental and 7 tandem duplication events which contribute to the expansion of the cotton bZIP family. Phylogenetic analysis showed that cotton GhbZIP proteins cluster into 13 subfamilies, and homologous protein pairs showed similar characteristics. Inspection of the DNA-binding basic region and leucine repeat heptads within the bZIP domains indicated different DNA-binding site specificities as well as dimerization properties among different groups. Comprehensive expression analysis indicated the most highly and differentially expressed genes in root and leaf that might play significant roles in cotton response to drought stress. GhABF3D was identified as a highly and differentially expressed bZIP family gene in cotton leaf and root under drought stress treatments that likely controls drought stress responses in cotton. These data provide useful information for further functional analysis of the GhbZIP gene family and its potential application in crop improvement.
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Tao YT, Chen LX, Jin J, Du ZK, Li JM. Genome-wide identification and analysis of bZIP gene family reveal their roles during development and drought stress in Wheel Wingnut (Cyclocarya paliurus). BMC Genomics 2022; 23:743. [DOI: 10.1186/s12864-022-08978-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/30/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The bZIP gene family has important roles in various biological processes, including development and stress responses. However, little information about this gene family is available for Wheel Wingnut (Cyclocarya paliurus).
Results
In this study, we identified 58 bZIP genes in the C. paliurus genome and analyzed phylogenetic relationships, chromosomal locations, gene structure, collinearity, and gene expression profiles. The 58 bZIP genes could be divided into 11 groups and were unevenly distributed among 16 C. paliurus chromosomes. An analysis of cis-regulatory elements indicated that bZIP promoters were associated with phytohormones and stress responses. The expression patterns of bZIP genes in leaves differed among developmental stages. In addition, several bZIP members were differentially expressed under drought stress. These expression patterns were verified by RT-qPCR.
Conclusions
Our results provide insights into the evolutionary history of the bZIP gene family in C. paliurus and the function of these genes during leaf development and in the response to drought stress. In addition to basic genomic information, our results provide a theoretical basis for further studies aimed at improving growth and stress resistance in C. paliurus, an important medicinal plant.
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Fan G, Xia X, Yao W, Cheng Z, Zhang X, Jiang J, Zhou B, Jiang T. Genome-Wide Identification and Expression Patterns of the F-box Family in Poplar under Salt Stress. Int J Mol Sci 2022; 23:ijms231810934. [PMID: 36142847 PMCID: PMC9505895 DOI: 10.3390/ijms231810934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 12/02/2022] Open
Abstract
The F-box family exists in a wide variety of plants and plays an extremely important role in plant growth, development and stress responses. However, systematic studies of F-box family have not been reported in populus trichocarpa. In the present study, 245 PtrFBX proteins in total were identified, and a phylogenetic tree was constructed on the basis of their C-terminal conserved domains, which was divided into 16 groups (A–P). F-box proteins were located in 19 chromosomes and six scaffolds, and segmental duplication was main force for the evolution of the F-box family in poplar. Collinearity analysis was conducted between poplar and other species including Arabidopsis thaliana, Glycine max, Anemone vitifolia Buch, Oryza sativa and Zea mays, which indicated that poplar has a relatively close relationship with G. max. The promoter regions of PtrFBX genes mainly contain two kinds of cis-elements, including hormone-responsive elements and stress-related elements. Transcriptome analysis indicated that there were 82 differentially expressed PtrFBX genes (DEGs), among which 64 DEGs were in the roots, 17 in the leaves and 26 in the stems. In addition, a co-expression network analysis of four representative PtrFBX genes indicated that their co-expression gene sets were mainly involved in abiotic stress responses and complex physiological processes. Using bioinformatic methods, we explored the structure, evolution and expression pattern of F-box genes in poplar, which provided clues to the molecular function of F-box family members and the screening of salt-tolerant PtrFBX genes.
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Affiliation(s)
- Gaofeng Fan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xinhui Xia
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Zihan Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xuemei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jiahui Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Correspondence: (B.Z.); (T.J.)
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Correspondence: (B.Z.); (T.J.)
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Transcriptome-Wide Identification of CCCH-Type Zinc Finger Proteins Family in Pinus massoniana and RR-TZF Proteins in Stress Response. Genes (Basel) 2022; 13:genes13091639. [PMID: 36140811 PMCID: PMC9498899 DOI: 10.3390/genes13091639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
CCCH-type zinc finger proteins play an important role in multiple biotic and abiotic stresses. More and more reports about CCCH functions in plant development and stress responses have appeared over the past few years, focusing especially on tandem CCCH zinc finger proteins (TZFs). However, this has not been reported in Pinaceae. In this study, we identified 46 CCCH proteins, including 6 plant TZF members in Pinus massoniana, and performed bioinformatic analysis. According to RT-PCR analysis, we revealed the expression patterns of five RR-TZF genes under different abiotic stresses and hormone treatments. Meanwhile, tissue-specific expression analysis suggested that all genes were mainly expressed in needles. Additionally, RR-TZF genes showed transcriptional activation activity in yeast. The results in this study will be beneficial in improving the stress resistance of P. massoniana and facilitating further studies on the biological and molecular functions of CCCH zinc finger proteins.
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Ge H, Xu J, Hua M, An W, Wu J, Wang B, Li P, Fang H. Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench. BMC Genomics 2022; 23:538. [PMID: 35879672 PMCID: PMC9310384 DOI: 10.1186/s12864-022-08776-2] [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: 01/04/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum. RESULTS Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1-3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four α helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What's more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum. CONCLUSIONS In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.
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Affiliation(s)
- Hanqiu Ge
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Jingjing Xu
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Mingzhu Hua
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Wenwen An
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Junping Wu
- Nantong Changjiang Seed Co., Ltd, Nantong, 226368, Jiangsu, People's Republic of China
| | - Baohua Wang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Ping Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Hui Fang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
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Genome-Wide Identification, Classification, Expression and Duplication Analysis of bZIP Family Genes in Juglans regia L. Int J Mol Sci 2022; 23:ijms23115961. [PMID: 35682645 PMCID: PMC9180593 DOI: 10.3390/ijms23115961] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 01/08/2023] Open
Abstract
Basic leucine zipper (bZIP), a conserved transcription factor widely found in eukaryotes, has important regulatory roles in plant growth. To understand the information related to the bZIP gene family in walnut, 88 JrbZIP genes were identified at the genome-wide level and classified into 13 subfamilies (A, B, C, D, E, F, G, H, I, J, K, M, and S) using a bioinformatic approach. The number of exons in JrbZIPs ranged from 1 to 12, the number of amino acids in JrbZIP proteins ranged from 145 to 783, and the isoelectric point ranged from 4.85 to 10.05. The majority of JrbZIP genes were localized in the nucleus. The promoter prediction results indicated that the walnut bZIP gene contains a large number of light-responsive and jasmonate-responsive action elements. The 88 JrbZIP genes were involved in DNA binding and nucleus and RNA biosynthetic processes of three ontological categories, molecular functions, cellular components and biological processes. The codon preference analysis showed that the bZIP gene family has a stronger bias for AGA, AGG, UUG, GCU, GUU, and UCU than other codons. Moreover, the transcriptomic data showed that JrbZIP genes might play an important role in floral bud differentiation. The results of a protein interaction network map and kegg enrichment analysis indicated that bZIP genes were mainly involved in phytohormone signaling, anthocyanin synthesis and flowering regulation. qRT-PCR demonstrated the role of the bZIP gene family in floral bud differentiation. Co-expression network maps were constructed for 29 walnut bZIP genes and 6 flowering genes, and JrCO (a homolog of AtCO) was significantly correlated (p < 0.05) with 13 JrbZIP genes in the level of floral bud differentiation expression, including JrbZIP31 (homolog of AtFD), and JrLFY was significantly and positively correlated with JrbZIP10,11,51,59,67 (p < 0.05), and the above results suggest that bZIP family genes may act together with flowering genes to regulate flower bud differentiation in walnut. This study was the first genome-wide report of the walnut bZIP gene family, which could improve our understanding of walnut bZIP proteins and provide a solid foundation for future cloning and functional analyses of this gene family.
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Yin Z, Meng X, Guo Y, Wei S, Lai Y, Wang Q. The bZIP Transcription Factor Family in Adzuki Bean ( Vigna Angularis): Genome-Wide Identification, Evolution, and Expression Under Abiotic Stress During the Bud Stage. Front Genet 2022; 13:847612. [PMID: 35547244 PMCID: PMC9081612 DOI: 10.3389/fgene.2022.847612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Adzuki bean (Vigna angularis) is an important dietary legume crop that was first cultivated and domesticated in Asia. Currently, little is known concerning the evolution and expression patterns of the basic leucine zipper (bZIP) family transcription factors in the adzuki bean. Through the PFAM search, 72 bZIP members of adzuki bean (VabZIP) were identified from the reference genome. Most of them were located on 11 chromosomes and seven on an unknown chromosome. A comprehensive analysis, including evolutionary, motifs, gene structure, cis-elements, and collinearity was performed to identify VabZIP members. The subcellular localization results showed VabZIPs might locate on the nuclear. Quantitative real-time PCR (qRT-PCR) analysis of the relative expression of VabZIPs in different tissues at the bud stage revealed that VabZIPs had a tissue-specific expression pattern, and its expression was influenced by abiotic stress. These characteristics of VabZIPs provide insights for future research aimed at developing interventions to improve abiotic stress resistance.
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Affiliation(s)
- Zhengong Yin
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences Harbin, Heilongjiang, China
| | - Xianxin Meng
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences Harbin, Heilongjiang, China
| | - Yifan Guo
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences Harbin, Heilongjiang, China
| | - Shuhong Wei
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences Harbin, Heilongjiang, China
| | - Yongcai Lai
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences Harbin, Heilongjiang, China
| | - Qiang Wang
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences Harbin, Heilongjiang, China
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Lu Z, Qiu W, Jin K, Yu M, Han X, He X, Wu L, Wu C, Zhuo R. Identification and Analysis of bZIP Family Genes in Sedum plumbizincicola and Their Potential Roles in Response to Cadmium Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:859386. [PMID: 35574076 PMCID: PMC9094143 DOI: 10.3389/fpls.2022.859386] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/29/2022] [Indexed: 05/23/2023]
Abstract
Sedum plumbizincicola (Crassulaceae), a cadmium (Cd)/zinc (Zn)/lead (Pb) hyperaccumulator native to Southeast China, is potentially useful for the phytoremediation of heavy metal-contaminated soil. Basic leucine zipper (bZIP) transcription factors play vital roles in plant growth, development, and abiotic stress responses. However, there has been minimal research on the effects of Cd stress on the bZIP gene family in S. plumbizincicola. In this study, 92 SpbZIP genes were identified in the S. plumbizincicola genome and then classified into 12 subgroups according to their similarity to bZIP genes in Arabidopsis. Gene structure and conserved motif analyses showed that SpbZIP genes within the same subgroup shared similar intron-exon structures and motif compositions. In total, eight pairs of segmentally duplicated SpbZIP genes were identified, but there were no tandemly duplicated SpbZIP genes. Additionally, the duplicated SpbZIP genes were mainly under purifying selection pressure. Hormone-responsive, abiotic and biotic stress-responsive, and plant development-related cis-acting elements were detected in the SpbZIP promoter sequences. Expression profiles derived from RNA-seq and quantitative real-time PCR analyses indicated that the expression levels of most SpbZIP genes were upregulated under Cd stress conditions. Furthermore, a gene co-expression network analysis revealed that most edge genes regulated by hub genes were related to metal transport, responses to stimuli, and transcriptional regulation. Because its expression was significantly upregulated by Cd stress, the hub gene SpbZIP60 was selected for a functional characterization to elucidate its role in the root response to Cd stress. In a transient gene expression analysis involving Nicotiana benthamiana leaves, SpbZIP60 was localized in the nucleus. The overexpression of SpbZIP60 enhanced the Cd tolerance of transgenic Arabidopsis plants by inhibiting ROS accumulation, protecting the photosynthetic apparatus, and decreasing the Cd content. These findings may provide insights into the potential roles of the bZIP family genes during the S. plumbizincicola response to Cd stress.
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Affiliation(s)
- Zhuchou Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Faculty of Forestry, Nanjing Forestry University, Nanjing, China
| | - Wenmin Qiu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Kangming Jin
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Miao Yu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xiaoyang He
- Agricultural Technology Extension Centre of Dongtai, Yancheng, China
| | - Longhua Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Chao Wu
- Institute of Horticulture, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Renyin Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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Duan L, Mo Z, Fan Y, Li K, Yang M, Li D, Ke Y, Zhang Q, Wang F, Fan Y, Liu R. Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L. BMC Genomics 2022; 23:318. [PMID: 35448973 PMCID: PMC9027840 DOI: 10.1186/s12864-022-08547-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The basic leucine zipper (bZIP) transcription factor (TF) is one of the largest families of transcription factors (TFs). It is widely distributed and highly conserved in animals, plants, and microorganisms. Previous studies have shown that the bZIP TF family is involved in plant growth, development, and stress responses. The bZIP family has been studied in many plants; however, there is little research on the bZIP gene family in tobacco. RESULTS In this study, 77 bZIPs were identified in tobacco and named NtbZIP01 through to NtbZIP77. These 77 genes were then divided into eleven subfamilies according to their homology with Arabidopsis thaliana. NtbZIPs were unevenly distributed across twenty-two tobacco chromosomes, and we found sixteen pairs of segmental duplication. We further studied the collinearity between these genes and related genes of six other species. Quantitative real-time polymerase chain reaction analysis identified that expression patterns of bZIPs differed, including in different organs and under various abiotic stresses. NtbZIP49 might be important in the development of flowers and fruits; NtbZIP18 might be an important regulator in abiotic stress. CONCLUSIONS In this study, the structures and functions of the bZIP family in tobacco were systematically explored. Many bZIPs may play vital roles in the regulation of organ development, growth, and responses to abiotic stresses. This research has great significance for the functional characterisation of the tobacco bZIP family and our understanding of the bZIP family in higher plants.
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Affiliation(s)
- Lili Duan
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Zejun Mo
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, People's Republic of China
| | - Kuiyin Li
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Mingfang Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Dongcheng Li
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yuzhou Ke
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Qian Zhang
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Feiyan Wang
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yu Fan
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Renxiang Liu
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China.
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China.
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Wang S, Zhang X, Li B, Zhao X, Shen Y, Yuan Z. Genome-wide identification and characterization of bZIP gene family and cloning of candidate genes for anthocyanin biosynthesis in pomegranate (Punica granatum). BMC PLANT BIOLOGY 2022; 22:170. [PMID: 35379169 PMCID: PMC8978422 DOI: 10.1186/s12870-022-03560-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/23/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved gene families in eukaryotes. In addition to participating in plant development and growth, bZIP transcription factors play crucial roles in various abiotic stress responses and anthocyanin accumulation. Up to now, analysis of bZIP gene family members in pomegranate (Punica granatum) has not been reported. Three published pomegranate genome sequences provide valuable resources for further gene function analysis. RESULTS Using bioinformatics analysis, 65 PgbZIPs were identified and analyzed from the 'Taishanhong' pomegranate genome. We divided them into 13 groups (A, B, C, D, E, F, G, H, I, J, K, M, and S) according to the phylogenetic relationship with those of Arabidopsis, each containing a different number of genes. The regularity of exon/intron number and distribution was consistent with the classification of groups in the evolutionary tree. Transcriptome analysis of different tissues showed that members of the PgbZIP gene family were differentially expressed in different developmental stages and tissues of pomegranate. Among them, we selected PgbZIP16 and PgbZIP34 as candidate genes which affect anthocyanin accumulation. The full-length CDS region of PgbZIP16 and PgbZIP34 were cloned from pomegranate petals by homologous cloning technique, encoding 170 and 174 amino acids, which were 510 bp and 522 bp, respectively. Subcellular localization assays suggested that both PgbZIP16 and PgbZIP34 were nucleus-localized. Real-time quantitative PCR (qPCR) was used to explore the expression of PgbZIP16 and PgbZIP34 in the petals of three kinds of ornamental pomegranates at the full flowering stage. The results demonstrated that the expression of PgbZIP16 in red petals was 5.83 times of that in white petals, while PgbZIP34 was 3.9 times. The results of transient expression in tobacco showed that consistent trends were observed in anthocyanin concentration and expression levels of related genes, which both increased and then decreased. Both PgbZIP16 and PgbZIP34 could promote anthocyanin accumulation in tobacco leaves. We obtained transgenic strains overexpressing PgbZIP16, and the histochemical staining for GUS activity showed that overexpressed PgbZIP16 seedlings were expressed in the stem. Transgenic experiments indicated that overexpression of PgbZIP16 significantly upregulated UF3GT, ANS and DFR genes in Arabidopsis and enhanced anthocyanin accumulation. CONCLUSIONS The whole genome identification, gene structure, phylogeny, gene cloning, subcellular location and functional verification of the pomegranate bZIP gene family provide a theoretical foundation for the functional study of the PgbZIP gene family and candidate genes for anthocyanin biosynthesis.
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Affiliation(s)
- Sha Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Xinhui Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Bianbian Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Xueqing Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yu Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhaohe Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
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Genome-Wide Identification and Expression Analysis of the Basic Leucine Zipper (bZIP) Transcription Factor Gene Family in Fusarium graminearum. Genes (Basel) 2022; 13:genes13040607. [PMID: 35456413 PMCID: PMC9028111 DOI: 10.3390/genes13040607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/18/2022] [Accepted: 03/26/2022] [Indexed: 12/14/2022] Open
Abstract
The basic leucine zipper (bZIP) is a widely found transcription factor family that plays regulatory roles in a variety of cellular processes including cell growth and development and various stress responses. However, the bZIP gene family has not been well studied at a genome-wide scale in Fusarium graminearum (Fg), a potent pathogen of cereal grains. In the present study, we conducted a genome-wide identification, characterization, and expression profiling of 22 F. graminearum bZIP (FgbZIP) genes at different developmental stages and under various abiotic stresses. All identified FgbZIPs were categorized into nine groups based on their sequence similarity and phylogenetic tree analysis. Furthermore, the gene structure analysis, conserved motif analysis, chromosomal localization, protein network studies, and synteny analysis were performed. The symmetry of the exon and intron varied with the phylogenetic groups. The post-translational modifications (PTMs) analysis also predicted several phosphorylation sites in FgbZIPs, indicating their functional diversity in cellular processes. The evolutionary study identified many orthogroups among eight species and also predicted several gene duplication events in F. graminearum. The protein modeling indicated the presence of a higher number of α-helices and random coils in their structures. The expression patterns of FgbZIP genes showed that 5 FgbZIP genes, including FgbZIP_1.1, FgbZIP_1.3, FgbZIP_2.6 FgbZIP_3.1 and FgbZIP_4.3, had high expression at different growth and conidiogenesis stages. Similarly, eight genes including FgbZIP_1.1, FgbZIP_1.6, FgbZIP_2.3, FgbZIP_2.4, FgbZIP_4.1, FgbZIP_4.2, FgbZIP_4.3 and FgbZIP_4.6 demonstrated their putative role in response to various abiotic stresses. In summary, these results provided basic information regarding FgbZIPs which are helpful for further functional analysis.
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CabZIP23 Integrates in CabZIP63-CaWRKY40 Cascade and Turns CabZIP63 on Mounting Pepper Immunity against Ralstonia solanacearum via Physical Interaction. Int J Mol Sci 2022; 23:ijms23052656. [PMID: 35269798 PMCID: PMC8910381 DOI: 10.3390/ijms23052656] [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: 01/19/2022] [Revised: 02/13/2022] [Accepted: 02/18/2022] [Indexed: 01/25/2023] Open
Abstract
CabZIP63 and CaWRKY40 were previously found to be shared in the pepper defense response to high temperature stress (HTS) and to Ralstonia solanacearum inoculation (RSI), forming a transcriptional cascade. However, how they activate the two distinct defense responses is not fully understood. Herein, using a revised genetic approach, we functionally characterized CabZIP23 in the CabZIP63-CaWRKY40 cascade and its context specific pepper immunity activation against RSI by interaction with CabZIP63. CabZIP23 was originally found by immunoprecipitation-mass spectrometry to be an interacting protein of CabZIP63-GFP; it was upregulated by RSI and acted positively in pepper immunity against RSI by virus induced gene silencing in pepper plants, and transient overexpression in Nicotiana benthamiana plants. By chromatin immunoprecipitation (ChIP)-qPCR and electrophoresis mobility shift assay (EMSA), CabZIP23 was found to be directly regulated by CaWRKY40, and CabZIP63 was directly regulated by CabZIP23, forming a positive feedback loop. CabZIP23-CabZIP63 interaction was confirmed by co-immunoprecipitation (CoIP) and bimolecular fluorescent complimentary (BiFC) assays, which promoted CabZIP63 binding immunity related target genes, including CaPR1, CaNPR1 and CaWRKY40, thereby enhancing pepper immunity against RSI, but not affecting the expression of thermotolerance related CaHSP24. All these data appear to show that CabZIP23 integrates in the CabZIP63-CaWRKY40 cascade and the context specifically turns it on mounting pepper immunity against RSI.
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