1
|
Jia X, Gao H, Zhang L, Tang W, Wei G, Sun J, Xiong W. Expression of Foxtail Millet bZIP Transcription Factor SibZIP67 Enhances Drought Tolerance in Arabidopsis. Biomolecules 2024; 14:958. [PMID: 39199345 PMCID: PMC11352937 DOI: 10.3390/biom14080958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 09/01/2024] Open
Abstract
Foxtail millet is a drought-tolerant cereal and forage crop. The basic leucine zipper (bZIP) gene family plays important roles in regulating plant development and responding to stresses. However, the roles of bZIP genes in foxtail millet remain largely uninvestigated. In this study, 92 members of the bZIP transcription factors were identified in foxtail millet and clustered into ten clades. The expression levels of four SibZIP genes (SibZIP11, SibZIP12, SibZIP41, and SibZIP67) were significantly induced after PEG treatment, and SibZIP67 was chosen for further analysis. The studies showed that ectopic overexpression of SibZIP67 in Arabidopsis enhanced the plant drought tolerance. Detached leaves of SibZIP67 overexpressing plants had lower leaf water loss rates than those of wild-type plants. SibZIP67 overexpressing plants improved survival rates under drought conditions compared to wild-type plants. Additionally, overexpressing SibZIP67 in plants displayed reduced malondialdehyde (MDA) levels and enhanced activities of antioxidant enzymes, including catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) under drought stress. Furthermore, the drought-related genes, such as AtRD29A, AtRD22, AtNCED3, AtABF3, AtABI1, and AtABI5, were found to be regulated in SibZIP67 transgenic plants than in wild-type Arabidopsis under drought conditions. These data suggested that SibZIP67 conferred drought tolerance in transgenic Arabidopsis by regulating antioxidant enzyme activities and the expression of stress-related genes. The study reveals that SibZIP67 plays a beneficial role in drought response in plants, offering a valuable genetic resource for agricultural improvement in arid environments.
Collapse
Affiliation(s)
- Xinfeng Jia
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (X.J.); (H.G.); (L.Z.); (W.T.)
| | - Hanchi Gao
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (X.J.); (H.G.); (L.Z.); (W.T.)
| | - Lingxin Zhang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (X.J.); (H.G.); (L.Z.); (W.T.)
| | - Wei Tang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (X.J.); (H.G.); (L.Z.); (W.T.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, China
| | - Guo Wei
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
| | - Juan Sun
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (X.J.); (H.G.); (L.Z.); (W.T.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, China
| | - Wangdan Xiong
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China; (X.J.); (H.G.); (L.Z.); (W.T.)
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, China
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Parajuli A, Borphukan B, Sanguinet KA, Zhang Z. In silico analysis identified bZIP transcription factors genes responsive to abiotic stress in Alfalfa (Medicago sativa L.). BMC Genomics 2024; 25:497. [PMID: 38773372 PMCID: PMC11106943 DOI: 10.1186/s12864-024-10277-3] [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: 03/23/2023] [Accepted: 04/02/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies including, but not limited to, differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa. RESULT In the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in A. thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physico-chemical properties, motif analysis and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance. RT-qPCR analysis on selected genes further verified these differential expression patterns. CONCLUSIONS Taken together, this work provides a framework for the future study of bZIPs in alfalfa and presents candidate bZIPs involved in stress-response signaling.
Collapse
Affiliation(s)
- Atit Parajuli
- Department of Crop and Soil Science, Washington State University, 99164, Pullman, WA, USA
| | - Bhabesh Borphukan
- Department of Crop and Soil Science, Washington State University, 99164, Pullman, WA, USA
| | - Karen A Sanguinet
- Department of Crop and Soil Science, Washington State University, 99164, Pullman, WA, USA.
| | - Zhiwu Zhang
- Department of Crop and Soil Science, Washington State University, 99164, Pullman, WA, USA.
| |
Collapse
|
4
|
Zhao Q, Xiong H, Yu H, Wang C, Zhang S, Hao J, Wang J, Zhang H, Zhang L. Function of MYB8 in larch under PEG simulated drought stress. Sci Rep 2024; 14:11290. [PMID: 38760385 PMCID: PMC11101485 DOI: 10.1038/s41598-024-61510-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
Larch, a prominent afforestation, and timber species in northeastern China, faces growth limitations due to drought. To further investigate the mechanism of larch's drought resistance, we conducted full-length sequencing on embryonic callus subjected to PEG-simulated drought stress. The sequencing results revealed that the differentially expressed genes (DEGs) primarily played roles in cellular activities and cell components, with molecular functions such as binding, catalytic activity, and transport activity. Furthermore, the DEGs showed significant enrichment in pathways related to protein processing, starch and sucrose metabolism, benzose-glucuronic acid interconversion, phenylpropyl biology, flavonoid biosynthesis, as well as nitrogen metabolism and alanine, aspartic acid, and glutamic acid metabolism. Consequently, the transcription factor T_transcript_77027, which is involved in multiple pathways, was selected as a candidate gene for subsequent drought stress resistance tests. Under PEG-simulated drought stress, the LoMYB8 gene was induced and showed significantly upregulated expression compared to the control. Physiological indices demonstrated an improved drought resistance in the transgenic plants. After 48 h of PEG stress, the transcriptome sequencing results of the transiently transformed LoMYB8 plants and control plants exhibited that genes were significantly enriched in biological process, cellular component and molecular function. Function analyses indicated for the enrichment of multiple KEGG pathways, including energy synthesis, metabolic pathways, antioxidant pathways, and other relevant processes. The pathways annotated by the differential metabolites mainly encompassed signal transduction, carbohydrate metabolism, amino acid metabolism, and flavonoid metabolism.
Collapse
Affiliation(s)
- Qingrong Zhao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Huanhuan Xiong
- Forestry Research Institute in Heilongjiang Province, Harbin, China
| | - Hongying Yu
- State Administration of Forestry and Grassland, Harbin Research Institute of Forestry Machinery, Harbin, China
| | - Chen Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Sufang Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Junfei Hao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding (Chinese Academy of Forestry), Beijing, China
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China.
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China.
| |
Collapse
|
5
|
Liu X, Sukumaran S, Viitanen E, Naik N, Hassan S, Aronsson H. An Accurate Representation of the Number of bZIP Transcription Factors in the Triticum aestivum (Wheat) Genome and the Regulation of Functional Genes during Salt Stress. Curr Issues Mol Biol 2024; 46:4417-4436. [PMID: 38785536 PMCID: PMC11120151 DOI: 10.3390/cimb46050268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024] Open
Abstract
Climate change is dramatically increasing the overall area of saline soils around the world, which is increasing by approximately two million hectares each year. Soil salinity decreases crop yields and, thereby, makes farming less profitable, potentially causing increased poverty and hunger in many areas. A solution to this problem is increasing the salt tolerance of crop plants. Transcription factors (TFs) within crop plants represent a key to understanding salt tolerance, as these proteins play important roles in the regulation of functional genes linked to salt stress. The basic leucine zipper (bZIP) TF has a well-documented role in the regulation of salt tolerance. To better understand how bZIP TFs are linked to salt tolerance, we performed a genome-wide analysis in wheat using the Chinese spring wheat genome, which has been assembled by the International Wheat Genome Sequencing Consortium. We identified 89 additional bZIP gene sequences, which brings the total of bZIP gene sequences in wheat to 237. The majority of these 237 sequences included a single bZIP protein domain; however, different combinations of five other domains also exist. The bZIP proteins are divided into ten subfamily groups. Using an in silico analysis, we identified five bZIP genes (ABF2, ABF4, ABI5, EMBP1, and VIP1) that were involved in regulating salt stress. By scrutinizing the binding properties to the 2000 bp upstream region, we identified putative functional genes under the regulation of these TFs. Expression analyses of plant tissue that had been treated with or without 100 mM NaCl revealed variable patterns between the TFs and functional genes. For example, an increased expression of ABF4 was correlated with an increased expression of the corresponding functional genes in both root and shoot tissues, whereas VIP1 downregulation in root tissues strongly decreased the expression of two functional genes. Identifying strategies to sustain the expression of the functional genes described in this study could enhance wheat's salt tolerance.
Collapse
Affiliation(s)
- Xin Liu
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China
| | - Selvakumar Sukumaran
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
| | - Esteri Viitanen
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
| | - Nupur Naik
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
| | - Sameer Hassan
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
| | - Henrik Aronsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Huang X, Zhou Y, Shi X, Wen J, Sun Y, Chen S, Hu T, Li R, Wang J, Jia X. PfbZIP85 Transcription Factor Mediates ω-3 Fatty Acid-Enriched Oil Biosynthesis by Down-Regulating PfLPAT1B Gene Expression in Plant Tissues. Int J Mol Sci 2024; 25:4375. [PMID: 38673960 PMCID: PMC11050522 DOI: 10.3390/ijms25084375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The basic leucine zipper (bZIP) transcription factor (TF) family is one of the biggest TF families identified so far in the plant kingdom, functioning in diverse biological processes including plant growth and development, signal transduction, and stress responses. For Perilla frutescens, a novel oilseed crop abundant in polyunsaturated fatty acids (PUFAs) (especially α-linolenic acid, ALA), the identification and biological functions of bZIP members remain limited. In this study, 101 PfbZIPs were identified in the perilla genome and classified into eleven distinct groups (Groups A, B, C, D, E, F, G, H, I, S, and UC) based on their phylogenetic relationships and gene structures. These PfbZIP genes were distributed unevenly across 18 chromosomes, with 83 pairs of them being segmental duplication genes. Moreover, 78 and 148 pairs of orthologous bZIP genes were detected between perilla and Arabidopsis or sesame, respectively. PfbZIP members belonging to the same subgroup exhibited highly conserved gene structures and functional domains, although significant differences were detected between groups. RNA-seq and RT-qPCR analysis revealed differential expressions of 101 PfbZIP genes during perilla seed development, with several PfbZIPs exhibiting significant correlations with the key oil-related genes. Y1H and GUS activity assays evidenced that PfbZIP85 downregulated the expression of the PfLPAT1B gene by physical interaction with the promoter. PfLPAT1B encodes a lysophosphatidate acyltransferase (LPAT), one of the key enzymes for triacylglycerol (TAG) assembly. Heterogeneous expression of PfbZIP85 significantly reduced the levels of TAG and UFAs (mainly C18:1 and C18:2) but enhanced C18:3 accumulation in both seeds and non-seed tissues in the transgenic tobacco lines. Furthermore, these transgenic tobacco plants showed no significantly adverse phenotype for other agronomic traits such as plant growth, thousand seed weight, and seed germination rate. Collectively, these findings offer valuable perspectives for understanding the functions of PfbZIPs in perilla, particularly in lipid metabolism, showing PfbZIP85 as a suitable target in plant genetic improvement for high-value vegetable oil production.
Collapse
Affiliation(s)
- Xusheng Huang
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Yali Zhou
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Xianfei Shi
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Jing Wen
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Yan Sun
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Shuwei Chen
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Ting Hu
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Runzhi Li
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Jiping Wang
- College of Agronomy/Institute of Molecular Agriculture & Bioenergy, Shanxi Agricultural University, Shanxi Engineering Research Center for Genetics and Metabolism of Specific Crops, Jinzhong 030801, China; (X.H.); (Y.Z.); (J.W.)
| | - Xiaoyun Jia
- College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, China
| |
Collapse
|
9
|
Yang F, Sun X, Wu G, He X, Liu W, Wang Y, Sun Q, Zhao Y, Xu D, Dai X, Ma W, Zeng J. Genome-Wide Identification and Expression Profiling of the ABF Transcription Factor Family in Wheat ( Triticum aestivum L.). Int J Mol Sci 2024; 25:3783. [PMID: 38612594 PMCID: PMC11011718 DOI: 10.3390/ijms25073783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Members of the abscisic acid (ABA)-responsive element (ABRE) binding factor (ABF) and ABA-responsive element binding protein (AREB) families play essential roles in the regulation of ABA signaling pathway activity and shape the ability of plants to adapt to a range of stressful environmental conditions. To date, however, systematic genome-wide analyses focused on the ABF/AREB gene family in wheat are lacking. Here, we identified 35 ABF/AREB genes in the wheat genome, designated TaABF1-TaABF35 according to their chromosomal distribution. These genes were further classified, based on their phylogenetic relationships, into three groups (A-C), with the TaABF genes in a given group exhibiting similar motifs and similar numbers of introns/exons. Cis-element analyses of the promoter regions upstream of these TaABFs revealed large numbers of ABREs, with the other predominant elements that were identified differing across these three groups. Patterns of TaABF gene expansion were primarily characterized by allopolyploidization and fragment duplication, with purifying selection having played a significant role in the evolution of this gene family. Further expression profiling indicated that the majority of the TaABF genes from groups A and B were highly expressed in various tissues and upregulated following abiotic stress exposure such as drought, low temperature, low nitrogen, etc., while some of the TaABF genes in group C were specifically expressed in grain tissues. Regulatory network analyses revealed that four of the group A TaABFs (TaABF2, TaABF7, TaABF13, and TaABF19) were centrally located in protein-protein interaction networks, with 13 of these TaABF genes being regulated by 11 known miRNAs, which play important roles in abiotic stress resistance such as drought and salt stress. The two primary upstream transcription factor types found to regulate TaABF gene expression were BBR/BPC and ERF, which have previously been reported to be important in the context of plant abiotic stress responses. Together, these results offer insight into the role that the ABF/AREB genes play in the responses of wheat to abiotic stressors, providing a robust foundation for future functional studies of these genes.
Collapse
Affiliation(s)
- Fuhui Yang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xuelian Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Gang Wu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyan He
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenxing Liu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yongmei Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qingyi Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yan Zhao
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Dengan Xu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xuehuan Dai
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Wujun Ma
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
| | - Jianbin Zeng
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
| |
Collapse
|
10
|
Jha DK, Chanwala J, Barla P, Dey N. "Genome-wide identification of bZIP gene family in Pearl millet and transcriptional profiling under abiotic stress, phytohormonal treatments; and functional characterization of PgbZIP9". FRONTIERS IN PLANT SCIENCE 2024; 15:1352040. [PMID: 38469329 PMCID: PMC10925649 DOI: 10.3389/fpls.2024.1352040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024]
Abstract
Abiotic stresses are major constraints in crop production, and are accountable for more than half of the total crop loss. Plants overcome these environmental stresses using coordinated activities of transcription factors and phytohormones. Pearl millet an important C4 cereal plant having high nutritional value and climate resilient features is grown in marginal lands of Africa and South-East Asia including India. Among several transcription factors, the basic leucine zipper (bZIP) is an important TF family associated with diverse biological functions in plants. In this study, we have identified 98 bZIP family members (PgbZIP) in pearl millet. Phylogenetic analysis divided these PgbZIP genes into twelve groups (A-I, S, U and X). Motif analysis has shown that all the PgbZIP proteins possess conserved bZIP domains and the exon-intron organization revealed conserved structural features among the identified genes. Cis-element analysis, RNA-seq data analysis, and real-time expression analysis of PgbZIP genes suggested the potential role of selected PgbZIP genes in growth/development and abiotic stress responses in pearl millet. Expression profiling of selected PgbZIPs under various phytohormones (ABA, SA and MeJA) treatment showed differential expression patterns of PgbZIP genes. Further, PgbZIP9, a homolog of AtABI5 was found to localize in the nucleus and modulate gene expression in pearl millet under stresses. Our present findings provide a better understanding of bZIP genes in pearl millet and lay a good foundation for the further functional characterization of multi-stress tolerant PgbZIP genes, which could become efficient tools for crop improvement.
Collapse
Affiliation(s)
- Deepak Kumar Jha
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Jeky Chanwala
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Preeti Barla
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
| |
Collapse
|
11
|
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.
Collapse
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.)
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Huang X, Zhang W, Liao Y, Ye J, Xu F. Contemporary understanding of transcription factor regulation of terpenoid biosynthesis in plants. PLANTA 2023; 259:2. [PMID: 37971670 DOI: 10.1007/s00425-023-04268-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
KEY MESSAGE This review summarized how TFs function independently or in response to environmental factors to regulate terpenoid biosynthesis via fine-tuning the expression of rate-limiting enzymes. Terpenoids are derived from various species and sources. They are essential for interacting with the environment and defense mechanisms, such as antimicrobial, antifungal, antiviral, and antiparasitic properties. Almost all terpenoids have high medicinal value and economic performance. Recently, the control of enzyme genes on terpenoid biosynthesis has received a great deal of attention, but transcriptional factors regulatory network on terpenoid biosynthesis and accumulation has yet to get a thorough review. Transcription factors function as activators or suppressors independently or in response to environmental stimuli, fine-tuning terpenoid accumulation through regulating rate-limiting enzyme expression. This study investigates the advancements in transcription factors related to terpenoid biosynthesis and systematically summarizes previous works on the specific mechanisms of transcription factors that regulate terpenoid biosynthesis via hormone signal-transcription regulatory networks in plants. This will help us to better comprehend the regulatory network of terpenoid biosynthesis and build the groundwork for terpenoid development and effective utilization.
Collapse
Affiliation(s)
- Xinru Huang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yongling Liao
- 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.
| |
Collapse
|
14
|
Lu M, Chen Z, Dang Y, Li J, Wang J, Zheng H, Li S, Wang X, Du X, Sui N. Identification of the MYB gene family in Sorghum bicolor and functional analysis of SbMYBAS1 in response to salt stress. PLANT MOLECULAR BIOLOGY 2023; 113:249-264. [PMID: 37964053 DOI: 10.1007/s11103-023-01386-w] [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: 05/02/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023]
Abstract
Salt stress adversely affects plant growth and development. It is necessary to understand the underlying salt response mechanism to improve salt tolerance in plants. MYB transcription factors can regulate plant responses to salt stress. However, only a few studies have explored the role of MYB TFs in Sorghum bicolor (L.) Moench. So we decided to make a systematic analysis and research on the sorghum MYB family. A total of 210 MYB genes in sorghum were identified in this study. Furthermore, 210 MYB genes were distributed across ten chromosomes, named SbMYB1-SbMYB210. To study the phylogeny of the identified TFs, 210 MYB genes were divided into six subfamilies. We further demonstrated that SbMYB genes have evolved under strong purifying selection. SbMYBAS1 (SbMYB119) was chosen as the study object, which the expression decreased under salt stress conditions. Further study of the SbMYBAS1 showed that SbMYBAS1 is located in the nucleus. Under salt stress conditions, Arabidopsis plants overexpressed SbMYBAS1 showed significantly lower dry/fresh weight and chlorophyll content but significantly higher membrane permeability, MDA content, and Na+/K+ ratio than the wild-type Arabidopsis plants. Yeast two-hybrid screening result showed that SbMYBAS1 might interact with proteins encoded by SORBI_302G184600, SORBI_3009G247900 and SORBI_3004G59600. Results also showed that SbMYBAS1 could regulate the expression of AtGSTU17, AtGSTU16, AtP5CS2, AtUGT88A1, AtUGT85A2, AtOPR2 and AtPCR2 under salt stress conditions. This work laid a foundation for the study of the response mechanism of sorghum MYB gene family to salt stress.
Collapse
Affiliation(s)
- Mei Lu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, No.88, East Wenhua Road, Jinan, 250014, China
| | - Zengting Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, No.88, East Wenhua Road, Jinan, 250014, China
- Dongying Institute, Shandong Normal University, Dongying, 257000, China
| | - Yingying Dang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, No.88, East Wenhua Road, Jinan, 250014, China
| | - Jinlu Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, No.88, East Wenhua Road, Jinan, 250014, China
| | - Jingyi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, No.88, East Wenhua Road, Jinan, 250014, China
| | - Hongxiang Zheng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, No.88, East Wenhua Road, Jinan, 250014, China
| | - Simin Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, No.88, East Wenhua Road, Jinan, 250014, China
| | - Xuemei Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, No.88, East Wenhua Road, Jinan, 250014, China
| | - Xihua Du
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, No.88, East Wenhua Road, Jinan, 250014, China.
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, No.88, East Wenhua Road, Jinan, 250014, China.
| |
Collapse
|
15
|
Zhou R, Zhao G, Zheng S, Xie S, Lu C, Liu S, Wang Z, Niu J. Comprehensive Functional Analysis of the bZIP Family in Bletilla striata Reveals That BsbZIP13 Could Respond to Multiple Abiotic Stresses. Int J Mol Sci 2023; 24:15202. [PMID: 37894883 PMCID: PMC10607107 DOI: 10.3390/ijms242015202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Basic leucine zipper (bZIP) transcription factors (TFs) are one of the largest families involved in plant physiological processes such as biotic and abiotic responses, growth, and development, etc. In this study, 66 members of the bZIP family were identified in Bletilla striata, which were divided into 10 groups based on their phylogenetic relationships with AtbZIPs. A structural analysis of BsbZIPs revealed significant intron-exon differences among BsbZIPs. A total of 63 bZIP genes were distributed across 16 chromosomes in B. striata. The tissue-specific and germination stage expression patterns of BsbZIPs were based on RNA-seq. Stress-responsive expression analysis revealed that partial BsbZIPs were highly expressed under low temperatures, wounding, oxidative stress, and GA treatments. Furthermore, subcellular localization studies indicated that BsbZIP13 was localized in the nucleus. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays suggested that BsbZIP13 could interact with multiple BsSnRK2s. The results of this study provide insightful data regarding bZIP TF as one of the stress response regulators in B. striata, while providing a theoretical basis for transgenic and functional studies of the bZIP gene family in B. striata.
Collapse
Affiliation(s)
- Ru Zhou
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Xi’an 710119, China; (R.Z.); (G.Z.); (S.Z.); (S.X.); (C.L.); (S.L.)
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Guangming Zhao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Xi’an 710119, China; (R.Z.); (G.Z.); (S.Z.); (S.X.); (C.L.); (S.L.)
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Siting Zheng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Xi’an 710119, China; (R.Z.); (G.Z.); (S.Z.); (S.X.); (C.L.); (S.L.)
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Siyuan Xie
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Xi’an 710119, China; (R.Z.); (G.Z.); (S.Z.); (S.X.); (C.L.); (S.L.)
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Chan Lu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Xi’an 710119, China; (R.Z.); (G.Z.); (S.Z.); (S.X.); (C.L.); (S.L.)
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Shuai Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Xi’an 710119, China; (R.Z.); (G.Z.); (S.Z.); (S.X.); (C.L.); (S.L.)
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Zhezhi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Xi’an 710119, China; (R.Z.); (G.Z.); (S.Z.); (S.X.); (C.L.); (S.L.)
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Junfeng Niu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Xi’an 710119, China; (R.Z.); (G.Z.); (S.Z.); (S.X.); (C.L.); (S.L.)
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| |
Collapse
|
16
|
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.
Collapse
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.)
| |
Collapse
|
17
|
Aslam MM, Fritschi FB, Di Z, Wang G, Li H, Lam HM, Waseem M, Weifeng X, Zhang J. Overexpression of LaGRAS enhances phosphorus acquisition via increased root growth of phosphorus-deficient white lupin. PHYSIOLOGIA PLANTARUM 2023; 175:e13962. [PMID: 37343119 DOI: 10.1111/ppl.13962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
The GRAS transcription factors play an indispensable role in plant growth and responses to environmental stresses. The GRAS gene family has extensively been explored in various plant species; however, the comprehensive investigation of GRAS genes in white lupin remains insufficient. In this study, bioinformatics analysis of white lupin genome revealed 51 LaGRAS genes distributed into 10 distinct phylogenetic clades. Gene structure analyses revealed that LaGRAS proteins were considerably conserved among the same subfamilies. Notably, 25 segmental duplications and a single tandem duplication showed that segmental duplication was the major driving force for the expansion of GRAS genes in white lupin. Moreover, LaGRAS genes exhibited preferential expression in young cluster root and mature cluster roots and may play key roles in nutrient acquisition, particularly phosphorus (P). To validate this, RT-qPCR analysis of white lupin plants grown under +P (normal P) and -P (P deficiency) conditions elucidated significant differences in the transcript level of GRAS genes. Among them, LaGRAS38 and LaGRAS39 were identified as potential candidates with induced expression in MCR under -P. Additionally, white lupin transgenic hairy root overexpressing OE-LaGRAS38 and OE-LaGRAS39 showed increased root growth, and P concentration in root and leaf compared to those with empty vector control, suggesting their role in P acquisition. We believe this comprehensive analysis of GRAS members in white lupin is a first step in exploring their role in the regulation of root growth, tissue development, and ultimately improving P use efficiency in legume crops under natural environments.
Collapse
Affiliation(s)
- Mehtab Muhammad Aslam
- College of Agriculture, Yangzhou University, Yangzhou, China
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Felix B Fritschi
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Zhang Di
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Muhammad Waseem
- College of Horticulture, Hainan University, Haikou, China
- Department of Botany, University of Narowal, Narowal, Pakistan
| | - Xu Weifeng
- College of Agriculture, Yangzhou University, Yangzhou, China
- Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| |
Collapse
|
18
|
Zhao Z, Zhang R, Wang D, Zhang J, Zang S, Zou W, Feng A, You C, Su Y, Wu Q, Que Y. Dissecting the features of TGA gene family in Saccharum and the functions of ScTGA1 under biotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 200:107760. [PMID: 37207494 DOI: 10.1016/j.plaphy.2023.107760] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/22/2023] [Accepted: 05/11/2023] [Indexed: 05/21/2023]
Abstract
Sugarcane is an important sugar and energy crop and smut disease caused by Sporisorium scitamineum is a major fungal disease which can seriously reduce the yield and quality of sugarcane. In plants, TGACG motif binding (TGA) transcription factors are involved in the regulation of salicylic acid (SA) and methyl jasmonate (MeJA) signaling pathways, as well as in response to various biotic and abiotic stresses. However, no TGA-related transcription factor has been reported in Saccharum. In the present study, 44 SsTGA genes were identified from Saccharum spontaneum, and were assorted into three clades (I, II, III). Cis-regulatory elements (CREs) analysis revealed that SsTGA genes may be involved in hormone and stress response. RNA-seq data and RT-qPCR analysis indicated that SsTGAs were constitutively expressed in different tissues and induced by S. scitamineum stress. In addition, a ScTGA1 gene (GenBank accession number ON416997) was cloned from the sugarcane cultivar ROC22, which was homologous to SsTGA1e in S. spontaneum and encoded a nucleus protein. It was constitutively expressed in sugarcane tissues and up-regulated by SA, MeJA and S. scitamineum stresses. Furthermore, transient overexpression of ScTGA1 in Nicotiana benthamiana could enhance its resistance to the infection of Ralstonia solanacearum and Fusarium solani var. coeruleum, by regulating the expression of immune genes related to hypersensitive response (HR), ethylene (ET), SA and jasmonic acid (JA) pathways. This study should contribute to our understanding on the evolution and function of the SsTGA gene family in Saccharum, and provide a basis for the functional identification of ScTGA1 under biotic stresses.
Collapse
Affiliation(s)
- Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Renren Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Aoyin Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chuihuai You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China.
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China.
| |
Collapse
|
19
|
Liu W, Mei Z, Yu L, Gu T, Li Z, Zou Q, Zhang S, Fang H, Wang Y, Zhang Z, Chen X, Wang N. The ABA-induced NAC transcription factor MdNAC1 interacts with a bZIP-type transcription factor to promote anthocyanin synthesis in red-fleshed apples. HORTICULTURE RESEARCH 2023; 10:uhad049. [PMID: 37200839 PMCID: PMC10186271 DOI: 10.1093/hr/uhad049] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/07/2023] [Indexed: 05/20/2023]
Abstract
Anthocyanins are valuable compounds in red-fleshed apples. The MdMYB10 transcription factor is an important regulator of the anthocyanin synthesis pathway. However, other transcription factors are key components of the complex network controlling anthocyanin synthesis and should be more thoroughly characterized. In this study, we used a yeast-based screening technology to identify MdNAC1 as a transcription factor that positively regulates anthocyanin synthesis. The overexpression of MdNAC1 in apple fruits and calli significantly promoted the accumulation of anthocyanins. In binding experiments, we demonstrated that MdNAC1 combines with the bZIP-type transcription factor MdbZIP23 to activate the transcription of MdMYB10 and MdUFGT. Our analyses also indicated that the expression of MdNAC1 is strongly induced by ABA because of the presence of an ABRE cis-acting element in its promoter. Additionally, the accumulation of anthocyanins in apple calli co-transformed with MdNAC1 and MdbZIP23 increased in the presence of ABA. Therefore, we revealed a novel anthocyanin synthesis mechanism involving the ABA-induced transcription factor MdNAC1 in red-fleshed apples.
Collapse
Affiliation(s)
- Wenjun Liu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Zhuoxin Mei
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Lei Yu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Tingting Gu
- College of Agricultural Science and Technology, Shandong Agricultural and Engineering University, Jinan, Shandong 250100, China
| | - Zhiqiang Li
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Qi Zou
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Shuhui Zhang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Hongcheng Fang
- StateForestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Yicheng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Zongying Zhang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | | | - Nan Wang
- Corresponding authors. E-mails: ;
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Aslam MM, Deng L, Meng J, Wang Y, Pan L, Niu L, Lu Z, Cui G, Zeng W, Wang Z. Characterization and expression analysis of basic leucine zipper (bZIP) transcription factors responsive to chilling injury in peach fruit. Mol Biol Rep 2023; 50:361-376. [PMID: 36334232 DOI: 10.1007/s11033-022-08035-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/17/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Peach (Prunus persica L.) is prone to chilling injury as exhibited by inhibition of the ethylene production, failure in softening, and the manifestation of internal browning. The basic leucine zipper (bZIP) transcription factors play an essential role in regulatory networks that control many processes associated with physiological, abiotic and biotic stress responses in fruits. Formerly, the underlying molecular and regulatory mechanism of (bZIP) transcription factors responsive to chilling injury in peach fruit is still elusive. METHODS AND RESULTS In the current experiment, the solute peach 'Zhongyou Peach No. 13' was used as the test material and cold storage at low temperature (4 °C). It was found that long-term low-temperature storage induced the production of ethylene, the hardness of the pulp decreased, and the low temperature also induced ABA accumulation. The changes of ABA and ethylene in peach fruits during low-temperature storage were clarified. Since the bZIP transcription factor is involved in the regulation of downstream pathways of ABA signals, 47 peach bZIP transcription factor family genes were identified through bioinformatics analysis. Further based on RT-qPCR analysis, 18 PpbZIP genes were discovered to be expressed in refrigerated peach fruits. Among them, the expression of PpbZIP23 and PpbZIP25 was significantly reduced during the refrigeration process, the promoter analysis of these genes found that this region contains the MYC/MYB/ABRES binding element, but not the DRES/CBFS element, indicating that the expression may be regulated by the ABA-dependent cold induction pathway, thereby responding to chilling injury in peach fruit. CONCLUSIONS Over investigation will provide new insights for further postharvest protocols related to molecular changes during cold storage and will prove a better cope for chilling injury.
Collapse
Affiliation(s)
- Muhammad Muzammal Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Li Deng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Junren Meng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Yan Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Lei Pan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Liang Niu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Zhenhua Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Guochao Cui
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China
| | - Wenfang Zeng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China.
| | - Zhiqiang Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, People's Republic of China.
| |
Collapse
|
22
|
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.
Collapse
|
23
|
Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet. Int J Mol Sci 2022; 23:ijms231911573. [PMID: 36232881 PMCID: PMC9569505 DOI: 10.3390/ijms231911573] [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: 07/30/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 12/04/2022] Open
Abstract
As one of the largest transcription factor families in plants, bZIP transcription factors play important regulatory roles in different biological processes, especially in the process of stress response. Salt stress inhibits the growth and yield of sugar beet. However, bZIP-related studies in sugar beet (Beta vulgaris L.) have not been reported. This study aimed to identify the bZIP transcription factors in sugar beet and analyze their biological functions and response patterns to salt stress. Using bioinformatics, 48 BvbZIP genes were identified in the genome of sugar beet, encoding 77 proteins with large structural differences. Collinearity analysis showed that three pairs of BvbZIP genes were fragment replication genes. The BvbZIP genes were grouped according to the phylogenetic tree topology and conserved structures, and the results are consistent with those reported in Arabidopsis. Under salt stress, the expression levels of most BvbZIP genes were decreased, and only eight genes were up-regulated. GO analysis showed that the BvbZIP genes were mainly negatively regulated in stress response. Protein interaction prediction showed that the BvbZIP genes were mainly involved in light signaling and ABA signal transduction, and also played a certain role in stress responses. In this study, the structures and biological functions of the BvbZIP genes were analyzed to provide foundational data for further mechanistic studies and for facilitating the efforts toward the molecular breeding of stress-resilient sugar beet.
Collapse
|
24
|
Genome-Wide Identification and Analysis of the Aureochrome Gene Family in Saccharina japonica and a Comparative Analysis with Six Other Algae. PLANTS 2022; 11:plants11162088. [PMID: 36015392 PMCID: PMC9416419 DOI: 10.3390/plants11162088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
Aureochrome (AUREO) is a kind of blue light photoreceptor with both LOV and bZIP structural domains, identified only in Stramenopiles. It functions as a transcription factor that responds to blue light, playing diverse roles in the growth, development, and reproduction of Stramenopiles. Most of its functions are currently unknown, especially in the economically important alga S. japonica farmed on a large scale. This study provided a comprehensive analysis of the characteristics of AUREO gene families in seven algae, focusing on the AUREOs of S. japonica. AUREO genes were strictly identified from seven algal genomes. Then AUREO phylogenetic tree was constructed from 44 conserved AUREO genes collected. These AUREO genes were divided into five groups based on phylogenetic relationships. A total of 28 genes unnamed previously were named according to the phylogenetic tree. A large number of different cis-acting elements, especially bZIP transcription factors, were discovered upstream of AUREO genes in brown algae. Different intron/exon structural patterns were identified among all AUREOs. Transcriptomic data indicated that the expression of Sj AUREO varied significantly during the different development stages of S. japonica gametophytes. Periodic rhythms of light induction experiments indicate that Sj AUREO existed in a light-dependent circadian expression pattern, differing from other similar studies in the past. This may indicate that blue light affects gametophyte development through AUREO as a light signal receptor. This study systematically identified and analyzed the AUREO gene family in seven representative brown algae, which lay a good foundation for further study and understanding of AUERO functions in agal growth and development.
Collapse
|
25
|
Mao Y, Chen X, Yan K, Liang Z, Xia P. Multi-algorithm cooperation comprehensive research of bZIP genes under Nitrogen stress in Panax notoginseng. Gene X 2022; 841:146768. [PMID: 35905849 DOI: 10.1016/j.gene.2022.146768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/30/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
Basic leucine zipper (bZIP) transcription factors play an irreplaceable position in the regulation of plant secondary metabolism, growth and development, and resistance to abiotic stress. Panax notoginseng is a traditional medicinal plant in China, but the systematic identification and the resistance of Panax notoginseng bZIP (PnbZIP) family under nitrogen stress have not been reported before, considering the excessive application of N fertilizers. In this study, we conducted a genome-wide identification of the PnbZIP family and analyzed its phylogeny, tissue selectivity, and abiotic resistence. 74 PnbZIPs were distributed on 12 chromosomes and 8 were not successfully located. Through phylogenetic analysis of Arabidopsis and Panax notoginseng, we divided them into 14 subgroups. In the same subgroup, bZIPs had similiar intron/exon structure and conserved motifs. In the analysis of chromosome structure, two PnbZIP genes were duplicated in tandem on chromosome 3. Intraspecific collinearity analysis showed that 28 PnbZIPs participated in segmental replication. Each PnbZIP promoter contained at least one stress response element or stress-related hormone response element. RNA-seq and qRT-PCR methods were used to analyze the expression patterns of the PnbZIP gene in different tissues (roots, flowers, and leaves) and under different nitrogen stresses. The results showed that the PnbZIP gene had the highest expression level in flowers and reflected tissue-specific expressions. Meanwhile, under the stress of ammonium nitrogen fertilizer and nitrate nitrogen fertilizer, PnbZIPs in roots were differently expressed. 10 PnbZIP stress-responsive genes were screened for significant expression, among which PnbZIP46 was significantly up-regulated, which could be a candidate gene for resistance to Nitrogen stress. This study laid the foundation for functional identification of PnbZIPs and improved the cultivation of Panax notoginseng.
Collapse
Affiliation(s)
- Yucheng Mao
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiang Chen
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Kaijing Yan
- Tasly Pharmaceutical Group Co., Ltd, Tianjin 300410, China
| | - Zongsuo Liang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Pengguo Xia
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| |
Collapse
|
26
|
Herath V, Connolly K, Roach A, Ausekar A, Persky T, Verchot J. The plant endoplasmic reticulum UPRome: A repository and pathway browser for genes involved in signaling networks linked to the endoplasmic reticulum. PLANT DIRECT 2022; 6:e431. [PMID: 35875835 PMCID: PMC9300056 DOI: 10.1002/pld3.431] [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: 03/15/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The endoplasmic reticulum (ER) houses sensors that respond to environmental stress and underly plants' adaptative responses. These sensors transduce signals that lead to changes in nuclear gene expression. The ER to nuclear signaling pathways are primarily attributed to the unfolded protein response (UPR) and are also integrated with a wide range of development, hormone, immune, and stress signaling pathways. Understanding the role of the UPR in signaling network mechanisms that associate with particular phenotypes is crucially important. While UPR-associated genes are the subject of ongoing investigations in a few model plant systems, most remain poorly annotated, hindering the identification of candidates across plant species. This open-source curated database provides a centralized resource of peer reviewed knowledge of ER to nuclear signaling pathways for the plant community. We provide a UPRome interactive viewer for users to navigate through the pathways and to access annotated information. The plant ER UPRome website is located at http://uprome.tamu.edu. We welcome contributions from the researchers studying the ER UPR to incorporate additional genes into the database through the "contact us" page.
Collapse
Affiliation(s)
- Venura Herath
- Department of Plant Pathology & MicrobiologyTexas A&M UniversityCollege StationTexasUSA
- Department of Agriculture Biology, Faculty of AgricultureUniversity of PeridaniyaPeradeniyaSri Lanka
| | - Kaylee Connolly
- Department of Plant Pathology & MicrobiologyTexas A&M UniversityCollege StationTexasUSA
| | - Anna Roach
- Department of Plant Pathology & MicrobiologyTexas A&M UniversityCollege StationTexasUSA
| | - Ashish Ausekar
- Division of Information TechnologyTexas A&M UniversityCollege StationTexasUSA
| | - Tracy Persky
- Division of Information TechnologyTexas A&M UniversityCollege StationTexasUSA
| | - Jeanmarie Verchot
- Department of Plant Pathology & MicrobiologyTexas A&M UniversityCollege StationTexasUSA
| |
Collapse
|
27
|
Zhang W, Ye S, Du Y, Zhao Q, Du J, Zhang Q. Identification and Expression Analysis of bZIP Members under Abiotic Stress in Mung Bean ( Vigna radiata). Life (Basel) 2022; 12:938. [PMID: 35888028 PMCID: PMC9316212 DOI: 10.3390/life12070938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023] Open
Abstract
The main aim of this study was to identify the bZIP family members in mung bean and explore their expression patterns under several abiotic stresses, with the overarching goal of elucidating their biological functions. Results identified 75 bZIP members in mung bean, which were unevenly distributed in the chromosomes (1-11), and all had a highly conserved bZIP domain. Phylogenetic analysis divided the members into 10 subgroups, with members in the same subgroup having similar structure and motif. The cis-acting elements in the promoter region revealed that most of the bZIP members might have the connection with abscisic acid, ethylene, and stress responsive elements. The transcriptome data demonstrated that bZIP members could respond to salt stress at different degrees in leaves, but the expression patterns could vary at different time points under stress. Differentially expressed genes (DEGs), such as VrbZIP12, VrbZIP37, and VrZIP45, were annotated into the plant hormone signal transduction pathway, which might be regulated the expression of abiotic stress-related gene (ABF). Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to determine the expression of bZIP members in roots and leaves under drought, alkali, and low-temperature stress. Results showed that bZIP members respond differently to diverse stresses, and their expression was tissue-specific, which suggests that they may have different regulatory mechanism in different tissues. Overall, this study will provide a reference for further research on the functions of bZIP members in mung bean.
Collapse
Affiliation(s)
- Wenhui Zhang
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
- National Coarse Cereals Engineering Research Center, Daqing 163319, China
| | - Shijia Ye
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
| | - Yanli Du
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
- National Coarse Cereals Engineering Research Center, Daqing 163319, China
| | - Qiang Zhao
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
- Research Center of Saline and Alkali Land Improvement Engineering Technology in Heilongjiang Province, Daqing 163319, China
| | - Jidao Du
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
- Research Center of Saline and Alkali Land Improvement Engineering Technology in Heilongjiang Province, Daqing 163319, China
| | - Qi Zhang
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
| |
Collapse
|
28
|
Samtani H, Sharma A, Khurana P. Wheat ocs-Element Binding Factor 1 Enhances Thermotolerance by Modulating the Heat Stress Response Pathway. FRONTIERS IN PLANT SCIENCE 2022; 13:914363. [PMID: 35712575 PMCID: PMC9194769 DOI: 10.3389/fpls.2022.914363] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/28/2022] [Indexed: 05/26/2023]
Abstract
The basic leucine zipper family (bZIP) represents one of the largest families of transcription factors that play an important role in plant responses to abiotic stresses. However, their role in contributing to thermotolerance in plants is not well explored. In this article, two homoeologs of wheat ocs-element binding factor 1 (TaOBF1-5B and TaOBF1-5D) were found to be heat-responsive TabZIP members. Their expression analysis in Indian wheat cultivars revealed their differential expression pattern and TaOBF1-5B was found to be more receptive to heat stress. Consistent with this, the heterologous overexpression of TaOBF1-5B in Arabidopsis thaliana and Oryza sativa promoted the expression of stress-responsive genes, which contributed to thermotolerance in transgenic plants. TaOBF1-5B was seen to interact with TaHSP90 in the nucleus and TaSTI in the nucleolus and the ER. Thus, the results suggest that TaOBF1-5B might play an important regulatory role in the heat stress response and is a major factor governing thermotolerance in plants.
Collapse
Affiliation(s)
| | | | - Paramjit Khurana
- *Correspondence: Paramjit Khurana ; orcid.org/0000-0002-8629-1245
| |
Collapse
|
29
|
Bai H, Liao X, Li X, Wang B, Luo Y, Yang X, Tian Y, Zhang L, Zhang F, Pan Y, Jiang B, Jia Y, Liu Q. DgbZIP3 interacts with DgbZIP2 to increase the expression of DgPOD for cold stress tolerance in chrysanthemum. HORTICULTURE RESEARCH 2022; 9:uhac105. [PMID: 35821702 PMCID: PMC9271009 DOI: 10.1093/hr/uhac105] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 04/23/2022] [Indexed: 06/15/2023]
Abstract
The bZIP transcription factor plays a very important role in abiotic stresses, e.g. drought, salt, and low-temperature stress, but the mechanism of action at low temperature is still unclear. In this study, overexpression of DgbZIP3 led to increased tolerance of chrysanthemum (Chrysanthemum morifolium Ramat.) to cold stress, whereas antisense suppression of DgbZIP3 resulted in decreased tolerance. Electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP), luciferase complementary imaging analysis (LCI), and dual-luciferase reporter gene detection (DLA) experiments indicated that DgbZIP3 directly bound to the promoter of DgPOD and activated its expression. DgbZIP2 was identified as a DgbZIP3-interacting protein using yeast two-hybrid, co-immunoprecipitation, LCI, and bimolecular fluorescence complementation assays. Overexpression of DgbZIP2 led to increased tolerance of chrysanthemum to cold stress, whereas antisense suppression of DgbZIP2 resulted in decreased tolerance. A ChIP-qPCR experiment showed that DgbZIP2 was highly enriched in the promoter of DgPOD, while DLA, EMSA, and LCI experiments further showed that DgbZIP2 could not directly regulate the expression of DgPOD. The above results show that DgbZIP3 interacts with DgbZIP2 to regulate the expression of DgPOD to promote an increase in peroxidase activity, thereby regulating the balance of reactive oxygen species and improving the tolerance of chrysanthemum to low-temperature stress.
Collapse
Affiliation(s)
- Huiru Bai
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Xiaoqin Liao
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Xin Li
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Bei Wang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Yunchen Luo
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Xiaohan Yang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Yuchen Tian
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Lei Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Fan Zhang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Yuanzhi Pan
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Beibei Jiang
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | - Yin Jia
- Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, China
| | | |
Collapse
|
30
|
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.
Collapse
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.
| |
Collapse
|
31
|
Khan Y, Xiong Z, Zhang H, Liu S, Yaseen T, Hui T. Expression and roles of GRAS gene family in plant growth, signal transduction, biotic and abiotic stress resistance and symbiosis formation-a review. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:404-416. [PMID: 34854195 DOI: 10.1111/plb.13364] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
The GRAS (derived from GAI, RGA and SCR) gene family consists of plant-specific genes, works as a transcriptional regulator and plays a key part in the regulation of plant growth and development. The past decade has witnessed significant progress in understanding and advances on GRAS transcription factors in various plants. A notable concern is to what extent the mechanisms found in plants, particularly crops, are shared by other species, and what other characteristics are dependent on GRAS transcription factor (TFS)-mediated gene expression. GRAS are involved in many processes that are intimately linked to plant growth regulation. However, GRAS also perform additional roles against environmental stresses, allowing plants to function more efficiently. GRAS increase plant growth and development by improving several physiological processes, such as phytohormone, biosynthetic and signalling pathways. Furthermore, the GRAS gene family plays an important role in response to abiotic stresses, e.g. photooxidative stress. Moreover, evidence shows the involvement of GRAS in arbuscule development during plant-mycorrhiza associations. In this review, the diverse roles of GRAS in plant systems are highlighted that could be useful in enhancing crop productivity through genetic modification, especially of crops. This is the first review to report the role and function of the GRAS gene family in plant systems. Furthermore, a large number of studies are reviewed, and several limitations and research gaps identified that must be addressed in future studies.
Collapse
Affiliation(s)
- Y Khan
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Z Xiong
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - H Zhang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - S Liu
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - T Yaseen
- Department of Botany, Bacha Khan University, Charsadda, Khyber Pakhtunkhwa, Pakistan
| | - T Hui
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
32
|
Liang Y, Xia J, Jiang Y, Bao Y, Chen H, Wang D, Zhang D, Yu J, Cang J. Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 ( TabZIP96) under Freezing Stress in Wheat ( Triticum aestivum). Int J Mol Sci 2022; 23:2351. [PMID: 35216467 PMCID: PMC8874521 DOI: 10.3390/ijms23042351] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/02/2022] [Accepted: 02/15/2022] [Indexed: 01/07/2023] Open
Abstract
The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat and the gene structure, physicochemical properties, cis-acting elements, and gene collinearity were analyzed. RNA-Seq and qRT-PCR analysis showed that ABA and abiotic stress induced most TabZIP genes expression. The ectopic expression of TaABI5 up-regulated the expression of several cold-responsive genes in Arabidopsis. Physiological indexes of seedlings of different lines under freezing stress showed that TaABI5 enhanced the freezing tolerance of plants. Subcellular localization showed that TaABI5 is localized in the nucleus. Furthermore, TaABI5 physically interacted with cold-resistant transcription factor TaICE1 in yeast two-hybrid system. In conclusion, this study identified and analyzed members of the TabZIP gene family in wheat. It proved for the first time that the gene TaABI5 affected the cold tolerance of transgenic plants and was convenient for us to understand the cold resistance molecular mechanism of TaABI5. These results will provide a new inspiration for further study on improving plant abiotic stress resistance.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Jing Cang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (J.X.); (Y.J.); (Y.B.); (H.C.); (D.W.); (D.Z.); (J.Y.)
| |
Collapse
|
33
|
Liu L, Zhang Y, Wang Q, Tao X, Fang J, Zheng W, Zhu L, Jia B, Heng W, Li S. Identification of bZIP transcription factors and their responses to brown spot in pear. Genet Mol Biol 2022; 45:e20210175. [PMID: 35099498 PMCID: PMC8802300 DOI: 10.1590/1678-4685-gmb-2021-0175] [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: 06/15/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022] Open
Abstract
Basic leucine zipper (bZIP) is a conserved transcription factor (TF) widely
present in eukaryotes, and it plays an important role in regulating plant growth
and stress responses. To better understand the white pear bZIP
gene family, comprehensive bioinformatics analysis of the pear genome was
performed. A total of 84 PbbZIP genes were identified, which
were divided into 13 subfamilies by phylogenetic analysis. The 84
PbbZIP genes were all located in the nucleus, and 77 of
those genes were unevenly distributed across the 17 chromosomes of white pear.
The other 7 PbbZIP genes were located on the scaffold.
Subsequent expression profile analysis showed that PbbZIP genes
in exocarp were significantly upregulated or downregulated in ‘Huangguan’ pear
with brown spot (BS) compared with healthy pear and in response to hormonal
treatment with gibberellin A3 (GA3). These results provide
helpful insights into the characteristics of PbbZIP genes and
their responses to BS in ‘Huangguan’ pear.
Collapse
Affiliation(s)
- Li Liu
- Anhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China
| | - Yuxin Zhang
- Anhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China
| | - Qi Wang
- Anhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China
| | - Xingyu Tao
- Anhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China
| | - Jing Fang
- Anhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China
| | - Wenjuan Zheng
- Anhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China
| | - Liwu Zhu
- Anhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China
| | - Bing Jia
- Anhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China
| | - Wei Heng
- Anhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China
| | - Shaowen Li
- Anhui Agriculture University, School of Information and Computer Science, Hefei, Anhui, P. R. China
| |
Collapse
|
34
|
Wang H, Zhang Y, Norris A, Jiang CZ. S1-bZIP Transcription Factors Play Important Roles in the Regulation of Fruit Quality and Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 12:802802. [PMID: 35095974 PMCID: PMC8795868 DOI: 10.3389/fpls.2021.802802] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Sugar metabolism not only determines fruit sweetness and quality but also acts as signaling molecules to substantially connect with other primary metabolic processes and, therefore, modulates plant growth and development, fruit ripening, and stress response. The basic region/leucine zipper motif (bZIP) transcription factor family is ubiquitous in eukaryotes and plays a diverse array of biological functions in plants. Among the bZIP family members, the smallest bZIP subgroup, S1-bZIP, is a unique one, due to the conserved upstream open reading frames (uORFs) in the 5' leader region of their mRNA. The translated small peptides from these uORFs are suggested to mediate Sucrose-Induced Repression of Translation (SIRT), an important mechanism to maintain sucrose homeostasis in plants. Here, we review recent research on the evolution, sequence features, and biological functions of this bZIP subgroup. S1-bZIPs play important roles in fruit quality, abiotic and biotic stress responses, plant growth and development, and other metabolite biosynthesis by acting as signaling hubs through dimerization with the subgroup C-bZIPs and other cofactors like SnRK1 to coordinate the expression of downstream genes. Direction for further research and genetic engineering of S1-bZIPs in plants is suggested for the improvement of quality and safety traits of fruit.
Collapse
Affiliation(s)
- Hong Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States
| | - Yunting Zhang
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ayla Norris
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, United States
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, United States
| |
Collapse
|
35
|
Ahad A, Aslam R, Gul A, Amir R, Munir F, Batool TS, Ilyas M, Sarwar M, Nadeem MA, Baloch FS, Fiaz S, Zia MAB. Genome-wide analysis of bZIP, BBR, and BZR transcription factors in Triticum aestivum. PLoS One 2021; 16:e0259404. [PMID: 34847173 PMCID: PMC8631640 DOI: 10.1371/journal.pone.0259404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
Transcription factors are regulatory proteins known to modulate gene expression. These are the critical component of signaling pathways and help in mitigating various developmental and stress responses. Among them, bZIP, BBR, and BZR transcription factor families are well known to play a crucial role in regulating growth, development, and defense responses. However, limited data is available on these transcription factors in Triticum aestivum. In this study, bZIP, BBR, and BZR sequences from Brachypodium distachyon, Oryza sativa, Oryza barthii, Oryza brachyantha, T. aestivum, Triticum urartu, Sorghum bicolor, Zea mays were retrieved, and dendrograms were constructed to analyze the evolutionary relatedness among them. The sequences clustered into one group indicated a degree of evolutionary correlation highlighting the common lineage of cereal grains. This analysis also exhibited that these genes were highly conserved among studied monocots emphasizing their common ancestry. Furthermore, these transcription factor genes were evaluated for envisaging conserved motifs, gene structure, and subcellular localization in T. aestivum. This comprehensive computational analysis has provided an insight into transcription factor evolution that can also be useful in developing approaches for future functional characterization of these genes in T. aestivum. Furthermore, the data generated can be beneficial in future for genetic manipulation of economically important plants.
Collapse
Affiliation(s)
- Arzoo Ahad
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Roohi Aslam
- NUTECH School of Applied Sciences and Humanities, National University of Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Tuba Sharf Batool
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Mahnoor Ilyas
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Sarwar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Hyber Pakhtunkhwa, Pakistan
| | - Muhammad Abu Bakar Zia
- College of Agriculture, Bahauddin Zakariya University, Bahadur sub–Campus Layyah, Punjab, Pakistan
| |
Collapse
|
36
|
Cui M, Haider MS, Chai P, Guo J, Du P, Li H, Dong W, Huang B, Zheng Z, Shi L, Zhang X, Han S. Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut ( Arachis hypogaea L.). Front Genet 2021; 12:750761. [PMID: 34721538 PMCID: PMC8548641 DOI: 10.3389/fgene.2021.750761] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
APETALA2/ethylene response element-binding factor (AP2/ERF) transcription factors (TFs) have been found to regulate plant growth and development and response to various abiotic stresses. However, detailed information of AP2/ERF genes in peanut against drought has not yet been performed. Herein, 185 AP2/ERF TF members were identified from the cultivated peanut (A. hypogaea cv. Tifrunner) genome, clustered into five subfamilies: AP2 (APETALA2), ERF (ethylene-responsive-element-binding), DREB (dehydration-responsive-element-binding), RAV (related to ABI3/VP), and Soloist (few unclassified factors)). Subsequently, the phylogenetic relationship, intron-exon structure, and chromosomal location of AhAP2/ERF were further characterized. All of these AhAP2/ERF genes were distributed unevenly across the 20 chromosomes, and 14 tandem and 85 segmental duplicated gene pairs were identified which originated from ancient duplication events. Gene evolution analysis showed that A. hypogaea cv. Tifrunner were separated 64.07 and 66.44 Mya from Medicago truncatula L. and Glycine max L., respectively. Promoter analysis discovered many cis-acting elements related to light, hormones, tissues, and stress responsiveness process. The protein interaction network predicted the exitance of functional interaction among families or subgroups. Expression profiles showed that genes from AP2, ERF, and dehydration-responsive-element-binding subfamilies were significantly upregulated under drought stress conditions. Our study laid a foundation and provided a panel of candidate AP2/ERF TFs for further functional validation to uplift breeding programs of drought-resistant peanut cultivars.
Collapse
Affiliation(s)
- Mengjie Cui
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | | | - Pengpei Chai
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Junjia Guo
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Pei Du
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Hongyan Li
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Wenzhao Dong
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Bingyan Huang
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Zheng Zheng
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Lei Shi
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Xinyou Zhang
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Suoyi Han
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| |
Collapse
|
37
|
Wang S, Zhang R, Zhang Z, Zhao T, Zhang D, Sofkova S, Wu Y, Wang Y. Genome-wide analysis of the bZIP gene lineage in apple and functional analysis of MhABF in Malus halliana. PLANTA 2021; 254:78. [PMID: 34536142 DOI: 10.1007/s00425-021-03724-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/06/2021] [Indexed: 05/23/2023]
Abstract
51 MdbZIP genes were identified from the apple genome by bioinformatics methods. MhABF-OE improved tolerance to saline-alkali stress in Arabidopsis, indicating it is involved in positive regulation of saline-alkali stress response. Saline-alkali stress is a major abiotic stress limiting plant growth all over the world. Members of the bZIP family play an important role in regulating gene expression in response to many kinds of biotic and abiotic stress, including salt stress. According to the transcriptome data, 51 MdbZIP genes responding to saline-alkali stress were identified in apple genome, and their gene structures, conserved protein motifs, phylogenetic analysis, chromosome localization, and promoter cis-acting elements were analyzed. Based on transcriptome data analysis, a MdbZIP family gene (MD15G1081800), which was highly expressed under stress, was selected to isolate and named as MhABF. Expression profile analysis by quantitative real-time PCR confirmed that the expression of MhABF in the leaves of Malus halliana was 10.6-fold higher than that of the control (0 days) after 2 days of stress. Then an MhABF gene was isolated from apple rootstock M. halliana. CaMV35S promoter drived MhABF gene expression vector was constructed to infect Arabidopsis with Agrobacterium-mediated infection. And overexpression MhABF gene plants were obtained. Compared with wild type, transgenic plants grew better under saline-alkali stress and the MhABF-OE lines showed higher chlorophyll content, POD, SOD and CAT activity, which indicated that they had strong resistance to stress. These results indicate that MhABF plays an important role in plant resistance to saline-alkali stress, which lays a foundation for further study on the functions in apple.
Collapse
Affiliation(s)
- Shuangcheng Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Rui Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Zhongxing Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Ting Zhao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - De Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Svetla Sofkova
- Institute of Agriculture and Environment, Massey University, Palmerston North, 4442, New Zealand
| | - Yuxia Wu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.
| | - Yanxiu Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.
| |
Collapse
|
38
|
Manzoor MA, Manzoor MM, Li G, Abdullah M, Han W, Wenlong H, Shakoor A, Riaz MW, Rehman S, Cai Y. Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri). BMC PLANT BIOLOGY 2021; 21:413. [PMID: 34503442 PMCID: PMC8427902 DOI: 10.1186/s12870-021-03191-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/28/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values. RESULTS In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate in pear fruits by real-time qRT-PCR. CONCLUSIONS Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.
Collapse
Affiliation(s)
| | | | - Guohui Li
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wang Han
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Han Wenlong
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Awais Shakoor
- Department of Environment and Soil Sciences, University of Lleida, Avinguda Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | | | - Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| |
Collapse
|
39
|
Wang M, Qiu X, Pan X, Li C. Transcriptional Factor-Mediated Regulation of Active Component Biosynthesis in Medicinal Plants. Curr Pharm Biotechnol 2021; 22:848-866. [PMID: 32568019 DOI: 10.2174/1389201021666200622121809] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/06/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022]
Abstract
Plants produce thousands of chemically diverse secondary metabolites, many of which have valuable pharmaceutical properties. There is much interest in the synthesis of these pharmaceuticallyvaluable compounds, including the key enzymes and the transcription factors involved. The function and regulatory mechanism of transcription factors in biotic and abiotic stresses have been studied in depth. However, their regulatory roles in the biosynthesis of bioactive compounds, especially in medicinal plants, have only begun. Here, we review what is currently known about how transcription factors contribute to the synthesis of bioactive compounds (alkaloids, terpenoids, flavonoids, and phenolic acids) in medicinal plants. Recent progress has been made in the cloning and characterization of transcription factors in medicinal plants on the genome scale. So far, several large transcription factors have been identified in MYB, WRKY, bHLH, ZIP, AP2/ERF transcription factors. These transcription factors have been predicted to regulate bioactive compound production. These transcription factors positively or negatively regulate the expression of multiple genes encoding key enzymes, and thereby control the metabolic flow through the biosynthetic pathway. Although the research addressing this niche topic is in its infancy, significant progress has been made, and advances in high-throughput sequencing technology are expected to accelerate the discovery of key regulatory transcription factors in medicinal plants. This review is likely to be useful for those interested in the synthesis of pharmaceutically- valuable plant compounds, especially those aiming to breed or engineer plants that produce greater yields of these compounds.
Collapse
Affiliation(s)
- Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xian Pan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| |
Collapse
|
40
|
Manna M, Thakur T, Chirom O, Mandlik R, Deshmukh R, Salvi P. Transcription factors as key molecular target to strengthen the drought stress tolerance in plants. PHYSIOLOGIA PLANTARUM 2021; 172:847-868. [PMID: 33180329 DOI: 10.1111/ppl.13268] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/23/2020] [Accepted: 11/07/2020] [Indexed: 05/03/2023]
Abstract
Amid apprehension of global climate change, crop plants are inevitably confronted with a myriad of abiotic stress factors during their growth that inflicts a serious threat to their development and overall productivity. These abiotic stresses comprise extreme temperature, pH, high saline soil, and drought stress. Among different abiotic stresses, drought is considered the most calamitous stressor with its serious impact on the crops' yield stability. The development of climate-resilient crops that withstands reduced water availability is a major focus of the scientific fraternity to ensure the food security of the sharply increasing population. Numerous studies aim to recognize the key regulators of molecular and biochemical processes associated with drought stress tolerance response. A few potential candidates are now considered as promising targets for crop improvement. Transcription factors act as a key regulatory switch controlling the gene expression of diverse biological processes and, eventually, the metabolic processes. Understanding the role and regulation of the transcription factors will facilitate the crop improvement strategies intending to develop and deliver agronomically-superior crops. Therefore, in this review, we have emphasized the molecular avenues of the transcription factors that can be exploited to engineer drought tolerance potential in crop plants. We have discussed the molecular role of several transcription factors, such as basic leucine zipper (bZIP), dehydration responsive element binding (DREB), DNA binding with one finger (DOF), heat shock factor (HSF), MYB, NAC, TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP), and WRKY. We have also highlighted candidate transcription factors that can be used for the development of drought-tolerant crops.
Collapse
Affiliation(s)
- Mrinalini Manna
- National Institute of Plant Genome Research, New Delhi, India
| | - Tanika Thakur
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Oceania Chirom
- National Institute of Plant Genome Research, New Delhi, India
| | - Rushil Mandlik
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Rupesh Deshmukh
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Prafull Salvi
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| |
Collapse
|
41
|
Zhong X, Feng X, Li Y, Guzmán C, Lin N, Xu Q, Zhang Y, Tang H, Qi P, Deng M, Ma J, Wang J, Chen G, Lan X, Wei Y, Zheng Y, Jiang Q. Genome-wide identification of bZIP transcription factor genes related to starch synthesis in barley ( Hordeum vulgare L.). Genome 2021; 64:1067-1080. [PMID: 34058097 DOI: 10.1139/gen-2020-0195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The basic leucine zipper (bZIP) family of genes encode transcription factors that play key roles in plant growth and development. In this study, a total of 92 HvbZIP genes were identified and compared with previous studies using recently released barley genome data. Two novel genes were characterized in this study, and some misannotated and duplicated genes from previous studies have been corrected. Phylogenetic analysis results showed that 92 HvbZIP genes were classified into 10 groups and three unknown groups. The gene structure and motif distribution of the three unknown groups implied that the genes of the three groups may be functionally different. Expression profiling indicated that the HvbZIP genes exhibited different patterns of spatial and temporal expression. Using qRT-PCR, more than 10 HvbZIP genes were identified with expression patterns similar to those of starch synthase genes in barley. Yeast one-hybrid analysis revealed that two of the HvbZIP genes exhibited in vitro binding activity to the promoter of HvAGP-S. The two HvbZIP genes may be candidate genes for further study to explore the mechanism by which they regulate the synthesis of barley starch.
Collapse
Affiliation(s)
- Xiaojuan Zhong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiuqin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yulong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, Cordoba, 14071, Spain
| | - Na Lin
- College of Sichuan Tea, Yibin University, Yibin, Sichuan 644000, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| |
Collapse
|
42
|
Wang Q, Guo C, Li Z, Sun J, Wang D, Xu L, Li X, Guo Y. Identification and Analysis of bZIP Family Genes in Potato and Their Potential Roles in Stress Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:637343. [PMID: 34122468 PMCID: PMC8193719 DOI: 10.3389/fpls.2021.637343] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/19/2021] [Indexed: 05/27/2023]
Abstract
The bZIP proteins comprise one of the largest transcription factor families and play important roles in plant growth and development, senescence, metabolic reactions, and stress responses. In this study, 49 bZIP transcription factor-encoding genes (StbZIP genes) on the potato genome were identified and analyzed. The 49 StbZIP genes, which are located on 12 chromosomes of the potato genome, were divided into 11 subgroups together with their Arabidopsis homologs based on the results of phylogenetic analysis. Gene structure and protein motif analysis revealed that members from the same subgroup often possessed similar exon/intron structures and motif organizations, further supporting the results of the phylogenetic analysis. Syntenic analysis indicated the existence of gene duplication events, which might play an important role in the expansion of the bZIP gene family in potato. Expressions of the StbZIP genes were analyzed in a variety of tissues via RNA-Seq data, suggesting functional diversity. Several StbZIP genes were found to be induced by different stress conditions. For example, the expression of StbZIP25, the close homolog of AtbZIP36/ABF2, was significantly upregulated by salt stress treatments. The StbZIP25 protein was found to be located in the nucleus and function as a transcriptional activator. Overexpression of StbZIP25 enhanced salt tolerance in Arabidopsis. The results from this study imply potential roles of the bZIP family genes in the stress response of potato.
Collapse
Affiliation(s)
- Qi Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cun Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinhao Sun
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Wang
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Liangtao Xu
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Xiaoxu Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| |
Collapse
|
43
|
Plant Transcription Factors Involved in Drought and Associated Stresses. Int J Mol Sci 2021; 22:ijms22115662. [PMID: 34073446 PMCID: PMC8199153 DOI: 10.3390/ijms22115662] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors (TFs) play a significant role in signal transduction networks spanning the perception of a stress signal and the expression of corresponding stress-responsive genes. TFs are multi-functional proteins that may simultaneously control numerous pathways during stresses in plants-this makes them powerful tools for the manipulation of regulatory and stress-responsive pathways. In recent years, the structure-function relationships of numerous plant TFs involved in drought and associated stresses have been defined, which prompted devising practical strategies for engineering plants with enhanced stress tolerance. Vast data have emerged on purposely basic leucine zipper (bZIP), WRKY, homeodomain-leucine zipper (HD-Zip), myeloblastoma (MYB), drought-response elements binding proteins/C-repeat binding factor (DREB/CBF), shine (SHN), and wax production-like (WXPL) TFs that reflect the understanding of their 3D structure and how the structure relates to function. Consequently, this information is useful in the tailored design of variant TFs that enhances our understanding of their functional states, such as oligomerization, post-translational modification patterns, protein-protein interactions, and their abilities to recognize downstream target DNA sequences. Here, we report on the progress of TFs based on their interaction pathway participation in stress-responsive networks, and pinpoint strategies and applications for crops and the impact of these strategies for improving plant stress tolerance.
Collapse
|
44
|
Wang Z, Zhu J, Yuan W, Wang Y, Hu P, Jiao C, Xia H, Wang D, Cai Q, Li J, Wang C, Zhang X, Chen Y, Wang Z, Ou Z, Xu Z, Shi J, Chen J. Genome-wide characterization of bZIP transcription factors and their expression patterns in response to drought and salinity stress in Jatropha curcas. Int J Biol Macromol 2021; 181:1207-1223. [PMID: 33971233 DOI: 10.1016/j.ijbiomac.2021.05.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 11/18/2022]
Abstract
The basic leucine zipper (bZIP) family is one of the largest families of transcription factors (TFs) in plants and is responsible for various functions, including regulating development and responses to abiotic/biotic stresses. However, the roles of bZIPs in the regulation of responses to drought stress and salinity stress remain poorly understood in Jatropha curcas L., a biodiesel crop. In the present study, 50 JcbZIP genes were identified and classified into ten groups. Cis-element analysis indicated that JcbZIP genes are associated with abiotic stress. Gene expression patterns and quantitative real-time PCR (qRT-PCR) showed that four JcbZIP genes (JcbZIPs 34, 36, 49 and 50) are key resistance-related genes under both drought and salinity stress conditions. On the basis of the results of cis-element and phylogenetic analyses, JcbZIP49 and JcbZIP50 are likely involved in responses to drought and salinity stress; moreover, JcbZIP34 and JcbZIP36 might also play important roles in seed development and response to abiotic stress. These findings advance our understanding of the comprehensive characteristics of JcbZIP genes and provide new insights for functional validation in the further.
Collapse
Affiliation(s)
- Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei 230601, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jin Zhu
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Wenya Yuan
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Ying Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Peipei Hu
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Chunyan Jiao
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Haimeng Xia
- School of Biosciences, University of Nottingham, Sutton Bonington 999020, UK
| | - Dandan Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qianwen Cai
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Jie Li
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Chenchen Wang
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Xie Zhang
- Institute of Botany, Hunan Academy of Forestry, Changsha 410004, China
| | - Yansong Chen
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Zhaoxia Wang
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Zulan Ou
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Zhongdong Xu
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Jisen Shi
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jinhui Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| |
Collapse
|
45
|
Li H, Chen J, Zhao Q, Han Y, Li L, Sun C, Wang K, Wang Y, Zhao M, Chen P, Lei J, Wang Y, Zhang M. Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer. BMC Genomics 2021; 22:316. [PMID: 33932982 PMCID: PMC8088647 DOI: 10.1186/s12864-021-07624-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 04/16/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Ginseng is an important medicinal herb in Asia and Northern America. The basic leucine zipper (bZIP) transcription factor genes play important roles in many biological processes and plant responses to abiotic and biotic stresses, such as drought stress. Nevertheless, the genes remain unknown in ginseng. RESULTS Here, we report 91 bZIP genes identified from ginseng, designated PgbZIP genes. These PgbZIP genes were alternatively spliced into 273 transcripts. Phylogenetic analysis grouped the PgbZIP genes into ten groups, including A, B, C, D, E, F, G, H, I and S. Gene Ontology (GO) categorized the PgbZIP genes into five functional subcategories, suggesting that they have diversified in functionality, even though their putative proteins share a number of conserved motifs. These 273 PgbZIP transcripts expressed differentially across 14 tissues, the roots of different ages and the roots of different genotypes. However, the transcripts of the genes expressed coordinately and were more likely to form a co-expression network. Furthermore, we studied the responses of the PgbZIP genes to drought stress in ginseng using a random selection of five PgbZIP genes, including PgbZIP25, PgbZIP38, PgbZIP39, PgbZIP53 and PgbZIP54. The results showed that all five PgbZIP genes responded to drought stress in ginseng, indicating that the PgbZIP genes play important roles in ginseng responses to drought stress. CONCLUSIONS These results provide knowledge and gene resources for deeper functional analysis of the PgbZIP genes and molecular tools for enhanced drought tolerance breeding in ginseng.
Collapse
Affiliation(s)
- Hongjie Li
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Jing Chen
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Qi Zhao
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Yilai Han
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Li Li
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Chunyu Sun
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China.,Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China.,Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Yanfang Wang
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China.,College of Chinese Medicinal Materials, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China.,Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Ping Chen
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Jun Lei
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China. .,Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China.
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China. .,Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, 2888 Xincheng Street, 130118, Changchun, Jilin, China.
| |
Collapse
|
46
|
Joo H, Baek W, Lim CW, Lee SC. Post-translational Modifications of bZIP Transcription Factors in Abscisic Acid Signaling and Drought Responses. Curr Genomics 2021; 22:4-15. [PMID: 34045920 PMCID: PMC8142349 DOI: 10.2174/1389202921999201130112116] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/25/2020] [Accepted: 10/03/2020] [Indexed: 11/22/2022] Open
Abstract
Under drought stress, plants have developed various mechanisms to survive in the reduced water supply, of which the regulation of stress-related gene expression is responsible for several transcription factors. The basic leucine zippers (bZIPs) are one of the largest and most diverse transcription factor families in plants. Among the 10 Arabidopsis bZIP groups, group A bZIP transcription factors function as a positive or negative regulator in ABA signal transduction and drought stress response. These bZIP transcription factors, which are involved in the drought response, have also been isolated in various plant species such as rice, pepper, potato, and maize. Recent studies have provided substantial evidence that many bZIP transcription factors undergo the post-translational modifications, through which the regulation of their activity or stability affects plant responses to various intracellular or extracellular stimuli. This review aims to address the modulation of the bZIP proteins in ABA signaling and drought responses through phosphorylation, ubiquitination and sumoylation.
Collapse
Affiliation(s)
- Hyunhee Joo
- Department of Life Science (BK21 Program), Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul 06974, Republic of Korea
| | - Woonhee Baek
- Department of Life Science (BK21 Program), Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul 06974, Republic of Korea
| | - Chae Woo Lim
- Department of Life Science (BK21 Program), Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul 06974, Republic of Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 Program), Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul 06974, Republic of Korea
| |
Collapse
|
47
|
Genome-wide identification and expression profiling of basic leucine zipper transcription factors following abiotic stresses in potato (Solanum tuberosum L.). PLoS One 2021; 16:e0247864. [PMID: 33711039 PMCID: PMC7954325 DOI: 10.1371/journal.pone.0247864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/15/2021] [Indexed: 11/29/2022] Open
Abstract
Potato (Solanum tuberosum L.) is an important food crop that is grown and consumed worldwide. The growth and productivity of this crop are severely affected by various abiotic stresses. Basic leucine zipper (bZIP) transcription factors (TFs) in plants are well known for their function during growth and development. However, systematic and in-depth identification and functional characterization of the bZIP gene family of potato is lacking. In the current study, we identified a total of 90 bZIPs (StbZIP) distributed on 12 linkage groups of potato. Based on the previous functional annotation and classification of bZIPs in Arabidopsis, wheat, and rice, a phylogenetic tree of potato bZIPs was constructed and genes were categorized into various functional groups (A to I, S, and U) as previously annotated in Arabidopsis thaliana. Analyses of the transcript sequence (RNA-seq) data led to identifying a total of 18 candidate StbZIPs [four in roots, eight in the tuber, six in mesocarp and endocarp] that were expressed in a tissue-specific manner. Differential expression analysis under the various abiotic conditions (salt, mannitol, water, and heat stress) and treatment with phytohormones (ABA, GA, IAA, and BAP) led to the identification of forty-two [thirteen under salt stress, two under mannitol stress, ten under water stress, and eighteen under heat stress], and eleven [eight and three StbZIPs upon treatment with ABA, and IAA, respectively] candidate StbZIPs, respectively. Using sequence information of candidate StbZIPs, a total of 22 SSR markers were also identified in this study. In conclusion, the genome-wide identification analysis coupled with RNA-Seq expression data led to identifying candidate StbZIPs, which are dysregulated, and may play a pivotal role under various abiotic stress conditions. This study will pave the way for future functional studies using forward and reverse genetics to improve abiotic stress tolerance in potato.
Collapse
|
48
|
Kumar P, Kumar P, Sharma D, Verma SK, Halterman D, Kumar A. Genome-wide identification and expression profiling of basic leucine zipper transcription factors following abiotic stresses in potato (Solanum tuberosum L.). PLoS One 2021. [PMID: 33711039 DOI: 10.1371/journal.pone.0247864]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Potato (Solanum tuberosum L.) is an important food crop that is grown and consumed worldwide. The growth and productivity of this crop are severely affected by various abiotic stresses. Basic leucine zipper (bZIP) transcription factors (TFs) in plants are well known for their function during growth and development. However, systematic and in-depth identification and functional characterization of the bZIP gene family of potato is lacking. In the current study, we identified a total of 90 bZIPs (StbZIP) distributed on 12 linkage groups of potato. Based on the previous functional annotation and classification of bZIPs in Arabidopsis, wheat, and rice, a phylogenetic tree of potato bZIPs was constructed and genes were categorized into various functional groups (A to I, S, and U) as previously annotated in Arabidopsis thaliana. Analyses of the transcript sequence (RNA-seq) data led to identifying a total of 18 candidate StbZIPs [four in roots, eight in the tuber, six in mesocarp and endocarp] that were expressed in a tissue-specific manner. Differential expression analysis under the various abiotic conditions (salt, mannitol, water, and heat stress) and treatment with phytohormones (ABA, GA, IAA, and BAP) led to the identification of forty-two [thirteen under salt stress, two under mannitol stress, ten under water stress, and eighteen under heat stress], and eleven [eight and three StbZIPs upon treatment with ABA, and IAA, respectively] candidate StbZIPs, respectively. Using sequence information of candidate StbZIPs, a total of 22 SSR markers were also identified in this study. In conclusion, the genome-wide identification analysis coupled with RNA-Seq expression data led to identifying candidate StbZIPs, which are dysregulated, and may play a pivotal role under various abiotic stress conditions. This study will pave the way for future functional studies using forward and reverse genetics to improve abiotic stress tolerance in potato.
Collapse
Affiliation(s)
- Pankaj Kumar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Pankaj Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Dennis Halterman
- U.S. Department of Agriculture-Agricultural Research Service, Madison, Wisconsin, United States of America
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| |
Collapse
|
49
|
Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function. Int J Mol Sci 2020; 22:ijms22010253. [PMID: 33383823 PMCID: PMC7796262 DOI: 10.3390/ijms22010253] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022] Open
Abstract
The basic region-leucine zipper (bZIP) transcription factors (TFs) form homodimers and heterodimers via the coil–coil region. The bZIP dimerization network influences gene expression across plant development and in response to a range of environmental stresses. The recent release of the most comprehensive potato reference genome was used to identify 80 StbZIP genes and to characterize their gene structure, phylogenetic relationships, and gene expression profiles. The StbZIP genes have undergone 22 segmental and one tandem duplication events. Ka/Ks analysis suggested that most duplications experienced purifying selection. Amino acid sequence alignments and phylogenetic comparisons made with the Arabidopsis bZIP family were used to assign the StbZIP genes to functional groups based on the Arabidopsis orthologs. The patterns of introns and exons were conserved within the assigned functional groups which are supportive of the phylogeny and evidence of a common progenitor. Inspection of the leucine repeat heptads within the bZIP domains identified a pattern of attractive pairs favoring homodimerization, and repulsive pairs favoring heterodimerization. These patterns of attractive and repulsive heptads were similar within each functional group for Arabidopsis and S. tuberosum orthologs. High-throughput RNA-seq data indicated the most highly expressed and repressed genes that might play significant roles in tissue growth and development, abiotic stress response, and response to pathogens including Potato virus X. These data provide useful information for further functional analysis of the StbZIP gene family and their potential applications in crop improvement.
Collapse
|
50
|
Li H, Li L, ShangGuan G, Jia C, Deng S, Noman M, Liu Y, Guo Y, Han L, Zhang X, Dong Y, Ahmad N, Du L, Li H, Yang J. Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L. Sci Rep 2020; 10:15521. [PMID: 32968100 PMCID: PMC7511407 DOI: 10.1038/s41598-020-72390-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 08/31/2020] [Indexed: 12/18/2022] Open
Abstract
The basic leucine zipper (bZIP) is a widely known transcription factors family in eukaryotes. In plants, the role of bZIP proteins are crucial in various biological functions such as plant growth and development, seed maturation, response to light signal and environmental stress. To date, bZIP protein family has been comprehensively identified in Arabidopsis, castor, rice, ramie, soybean and other plant species, however, the complete genome-wide investigation of Carthamus tinctorius-bZIP family still remains unexplained. Here, we identified 52 putative bZIP genes from Carthamus tinctorius using a draft genome assembly and further analyzed their evolutionary classification, physicochemical properties, Conserved domain analysis, functional differentiation and the investigation of expression level in different tissues. Based on the common bZIP domain, CtbZIP family were clustered into 12 subfamilies renamed as (A-J, S, X), of which the X is a unique subfamily to Carthamus tinctorius. A total of 20 conserved protein motifs were found in CtbZIP proteins. The expression profiling of CtbZIP genes deciphered their tissue-specific pattern. Furthermore, the changes in CtbZIP transcript abundance suggested that their transcription regulation could be highly influenced by light intensity and hormones. Collectively, this study highlights all functional and regulatory elements of bZIP transcription factors family in Carthamus tinctorius which may serve as potential candidates for functional characterization in future.
Collapse
Affiliation(s)
- Haoyang Li
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Lixia Li
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Guodong ShangGuan
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Chang Jia
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Sinan Deng
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Muhammad Noman
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Yilin Liu
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Yongxin Guo
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Long Han
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Xiaomei Zhang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Yuanyuan Dong
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Naveed Ahmad
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Linna Du
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China.
| | - Haiyan Li
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China.
| | - Jing Yang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China.
| |
Collapse
|