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Huang G, Wan R, Zou L, Ke J, Zhou L, Tan S, Li T, Chen L. The Brachypodium distachyon DREB transcription factor BdDREB-39 confers oxidative stress tolerance in transgenic tobacco. PLANT CELL REPORTS 2024; 43:143. [PMID: 38750149 DOI: 10.1007/s00299-024-03223-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: 01/11/2024] [Accepted: 04/19/2024] [Indexed: 06/18/2024]
Abstract
Key message BdDREB-39 is a DREB/CBF transcription factor, localized in the nucleus with transactivation activity, and BdDREB-39-overexpressing transgenic yeasts and tobacco enhanced the tolerance to oxidative stress.Abstract The DREB/CBF transcription factors are generally recognized to play an important factor in plant growth, development and response to various abiotic stresses. However, the mechanism of DREB/CBFs in oxidative stress response is largely unknown. This study isolated a DREB/CBF gene BdDREB-39 from Brachypodium distachyon (B. distachyon). Multiple sequence alignment and phylogenetic analysis showed that BdDREB-39 was closely related to the DREB proteins of oats, barley, wheat and rye and therefore its study can provide a reference for the excavation and genetic improvement of BdDREB-39 or its homologs in its closely related species. The transcript levels of BdDREB-39 were significantly up-regulated under H2O2 stress. BdDREB-39 was localised in the nucleus and functioned as a transcriptional activator. Overexpression of BdDREB-39 enhanced H2O2 tolerance in yeast. Transgenic tobaccos with BdDREB-39 had higher germination rates, longer root, better growth status, lesser reactive oxygen species (ROS) and malondialdehyde (MDA), and higher superoxide dismutase (SOD) and peroxidase (POD) activities than wild type (WT). The expression levels of ROS-related and stress-related genes were improved by BdDREB-39. In summary, these results revealed that BdDREB-39 can improve the viability of tobacco by regulating the expression of ROS and stress-related genes, allowing transgenic tobacco to accumulate lower levels of ROS and reducing the damage caused by ROS to cells. The BdDREB-39 gene has the potential for developing plant varieties tolerant to stress.
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Affiliation(s)
- Gang Huang
- College of Life Science, Jianghan University, Wuhan, 430056, China
| | - Renjing Wan
- College of Life Science, Jianghan University, Wuhan, 430056, China
| | - Liping Zou
- College of Life Science, Jianghan University, Wuhan, 430056, China
| | - Jie Ke
- College of Life Science, Jianghan University, Wuhan, 430056, China
| | - Lihong Zhou
- College of Life Science, Jianghan University, Wuhan, 430056, China
| | - Shenglong Tan
- School of Information Engineering, Hubei University of Economics, Wuhan, 430205, China.
| | - Tiantian Li
- College of Life Science, Jianghan University, Wuhan, 430056, China.
| | - Lihong Chen
- College of Life Science, Jianghan University, Wuhan, 430056, China.
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2
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Qian Z, Rao X, Zhang R, Gu S, Shen Q, Wu H, Lv S, Xie L, Li X, Wang X, Chen S, Liu L, He L, Li F. Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus. Int J Mol Sci 2023; 24:ijms24087102. [PMID: 37108264 PMCID: PMC10139229 DOI: 10.3390/ijms24087102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
The AP2/ERF transcription factor family is one of the most important gene families in plants and plays a vital role in plant abiotic stress responses. Although Erianthus fulvus is very important in the genetic improvement of sugarcane, there are few studies concerning AP2/ERF genes in E. fulvus. Here, we identified 145 AP2/ERF genes in the E. fulvus genome. Phylogenetic analysis classified them into five subfamilies. Evolutionary analysis showed that tandem and segmental duplication contributed to the expansion of the EfAP2/ERF family. Protein interaction analysis showed that twenty-eight EfAP2/ERF proteins and five other proteins had potential interaction relationships. Multiple cis-acting elements present in the EfAP2/ERF promoter were related to abiotic stress response, suggesting that EfAP2/ERF may contribute to adaptation to environmental changes. Transcriptomic and RT-qPCR analyses revealed that EfDREB10, EfDREB11, EfDREB39, EfDREB42, EfDREB44, EfERF43, and EfAP2-13 responded to cold stress, EfDREB5 and EfDREB42 responded to drought stress, and EfDREB5, EfDREB11, EfDREB39, EfERF43, and EfAP2-13 responded to ABA treatment. These results will be helpful for better understanding the molecular features and biological role of the E. fulvus AP2/ERF genes and lay a foundation for further research on the function of EfAP2/ERF genes and the regulatory mechanism of the abiotic stress response.
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Affiliation(s)
- Zhenfeng Qian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Xibing Rao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Rongqiong Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Shujie Gu
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming 650201, China
| | - Qingqing Shen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Huaying Wu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Shaozhi Lv
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Linyan Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Xianli Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Xianhong Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Shuying Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Lufeng Liu
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming 650201, China
| | - Lilian He
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming 650201, China
| | - Fusheng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming 650201, China
- The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Kunming 650201, China
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3
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Qian C, Li L, Guo H, Zhu G, Yang N, Tan X, Zhao H. Genome-Wide Analysis of DREB Family Genes and Characterization of Cold Stress Responses in the Woody Plant Prunus nana. Genes (Basel) 2023; 14:genes14040811. [PMID: 37107569 PMCID: PMC10137973 DOI: 10.3390/genes14040811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Dehydration response element binding factor (DREB) is a family of plant-specific transcription factors, whose members participate in the regulation of plant responses to various abiotic stresses. Prunus nana, also known as the wild almond, is a member of the Rosaceae family that is rare and found to grow in the wild in China. These wild almond trees are found in hilly regions in northern Xinjiang, and exhibit greater drought and cold stress resistance than cultivated almond varieties. However, the response of P. nana DREBs (PnaDREBs) under low temperature stress is still unclear. In this study, 46 DREB genes were identified in the wild almond genome, with this number being slightly lower than that in the sweet almond (Prunus dulcis cultivar ‘Nonpareil’). These DREB genes in wild almond were separated into two classes. All PnaDREB genes were located on six chromosomes. PnaDREB proteins that were classified in the same groups contained specific shared motifs, and promoter analyses revealed that PnaDREB genes harbored a range of stress-responsive elements associated with drought, low-temperature stress, light responsivity, and hormone-responsive cis-regulatory elements within their promoter regions. MicroRNA target site prediction analyses also suggested that 79 miRNAs may regulate the expression of 40 of these PnaDREB genes, with PnaDREB2. To examine if these identified PnaDREB genes responded to low temperature stress, 15 of these genes were selected including seven homologous to Arabidopsis C-repeat binding factor (CBFs), and their expression was assessed following incubation for 2 h at 25 °C, 5 °C, 0 °C, −5 °C, or −10 °C. In summary, this analysis provides an overview of the P. nana PnaDREB gene family and provides a foundation for further studies of the ability of different PnaDREB genes to regulate cold stress responses in almond plants.
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Affiliation(s)
- Cheng Qian
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Lulu Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Huanhuan Guo
- Zhengzhou Botanical Garden, Zhengzhou 450042, China
| | - Gaopu Zhu
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450014, China
| | - Ning Yang
- Qingdao Landscape and Forestry Integrated Service Center, Qingdao 266003, China
| | - Xiaoyan Tan
- Qingdao Landscape and Forestry Integrated Service Center, Qingdao 266003, China
| | - Han Zhao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450014, China
- Correspondence:
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Vera Hernández PF, Mendoza Onofre LE, Rosas Cárdenas FDF. Responses of sorghum to cold stress: A review focused on molecular breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1124335. [PMID: 36909409 PMCID: PMC9996117 DOI: 10.3389/fpls.2023.1124335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Climate change has led to the search for strategies to acclimatize plants to various abiotic stressors to ensure the production and quality of crops of commercial interest. Sorghum is the fifth most important cereal crop, providing several uses including human food, animal feed, bioenergy, or industrial applications. The crop has an excellent adaptation potential to different types of abiotic stresses, such as drought, high salinity, and high temperatures. However, it is susceptible to low temperatures compared with other monocotyledonous species. Here, we have reviewed and discussed some of the research results and advances that focused on the physiological, metabolic, and molecular mechanisms that determine sorghum cold tolerance to improve our understanding of the nature of such trait. Questions and opportunities for a comprehensive approach to clarify sorghum cold tolerance or susceptibility are also discussed.
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Affiliation(s)
- Pedro Fernando Vera Hernández
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla, Tlaxcala, Mexico
| | | | - Flor de Fátima Rosas Cárdenas
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla, Tlaxcala, Mexico
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DsDBF1, a Type A-5 DREB Gene, Identified and Characterized in the Moss Dicranum scoparium. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010090. [PMID: 36676039 PMCID: PMC9862540 DOI: 10.3390/life13010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022]
Abstract
Plant dehydration-responsive element binding (DREB) transcription factors (TFs) play important roles during stress tolerance by regulating the expression of numerous genes involved in stresses. DREB TFs have been extensively studied in a variety of angiosperms and bryophytes. To date, no information on the identification and characterization of DREB TFs in Dicranum scoparium has been reported. In this study, a new DBF1 gene from D. scoparium was identified by cloning and sequencing. Analysis of the conserved domain and physicochemical properties revealed that DsDBF1 protein has a classic AP2 domain encoding a 238 amino acid polypeptide with a molecular mass of 26 kDa and a pI of 5.98. Subcellular prediction suggested that DsDBF1 is a nuclear and cytoplasmic protein. Phylogenetic analysis showed that DsDBF1 belongs to group A-5 DREBs. Expression analysis by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) revealed that DsDBF1 was significantly upregulated in response to abiotic stresses such as desiccation/rehydration, exposure to paraquat, CdCl2, high and freezing temperatures. Taken together, our data suggest that DsDBF1 could be a promising gene candidate to improve stress tolerance in crop plants, and the characterization of TFs of a stress tolerant moss such as D. scoparium provides a better understanding of plant adaptation mechanisms.
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Sugarcane ScDREB2B-1 Confers Drought Stress Tolerance in Transgenic Nicotiana benthamiana by Regulating the ABA Signal, ROS Level and Stress-Related Gene Expression. Int J Mol Sci 2022; 23:ijms23179557. [PMID: 36076957 PMCID: PMC9455921 DOI: 10.3390/ijms23179557] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
The dehydration-responsive element-binding protein (DREB) is a subgroup member of the AP2/ERF family and actively participates in the response of plants to abiotic stress. Although DREB genes have been studied in a variety of plant species, there are few reports of DREB genes in sugarcane (Saccharum spp.). In this study, a novel full-length cDNA sequence of the ScDREB2B-1 gene was cloned from the Saccharum hybrid ROC22, whose encoding protein contained only one AP2-conserved domain and was clustered into the DREB (A-2) subgroup. The diverse promoter elements in the ScDREB2B-1 gene and the accumulated transcripts of its homologous gene (SsAP2/ERF-107) in S. spontaneum under drought stress suggest that the ScDREB2B-1 gene may play a role in drought response. In addition, reverse transcription quantitative PCR analysis showed that the expression level of the ScDREB2B-1 gene was upregulated in the root and leaf of ROC22 under polyethylene glycol, sodium chloride and abscisic acid (ABA) treatments. The yeast two-hybrid experiment demonstrated that ScDREB2B-1 had transcriptional self-activation activity. Compared with wild-type plants, the overexpression of the ScDREB2B-1 gene improved the drought tolerance of the transgenic Nicotiana benthamiana by activating the ABA pathway to enhance the expression of the ABA-responsive gene (NbNCED) and ABA content, regulate the intracellular reactive oxygen species (ROS) level (enhance the transcripts of ROS synthase-related gene NbRbohB and the activities of catalase, peroxidase and superoxide dismutase) and increase the relative water content, proline content and expression level of osmotic stress-related genes (NbERD and NbLEA). Collectively, our data indicate that ScDREB2B-1 is a stress-inducible and ABA-responsive transcription factor gene that responds to drought stress by regulating ABA signaling, ROS levels and stress-related gene expression. This study contributes to a better understanding of the biological function of ScDREB2B-1, which could serve as a foundation for future resistance breeding in sugarcane.
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7
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Zhang H, Wang Y, Tan J, Weng Y. Functional copy number variation of CsSHINE1 is associated with fruit skin netting intensity in cucumber, Cucumis sativus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2101-2119. [PMID: 35524817 DOI: 10.1007/s00122-022-04100-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Fruit skin netting in cucumber (Cucumis sativus) is associated with important fruit quality attributes. Two simply inherited genes H (Heavy netting) and Rs (Russet skin) control skin netting, but their molecular basis is unknown. Here, we reported map-based cloning and functional characterization of the candidate gene for the Rs locus that encodes CsSHINE1 (CsSHN1), an AP2 domain containing ethylene-responsive transcription factor protein. Comparative phenotypic analysis in near-isogenic lines revealed that fruit with netted skin had different epidermal structures from that with smooth skin including thicker cuticles, smaller, palisade-shaped epidermal and sub-epidermal cells with heavily suberized and lignified cell walls, higher peroxidase activities, which suggests multiple functions of CsSHN1 in regulating fruit skin netting and epidermal cell patterning. Among three representative cucumber inbred lines, three haplotypes at three polymorphic sites were identified inside CsSHN1: a functional copy in Gy14 (wild type) with light fruit skin netting, a copy number variant with two tandemly arrayed functional copies in WI7120 with heavy skin netting, and a loss-of-function copy in 9930 with smooth skin. The expression level of CsSHN1 in fruit exocarp of three lines was positively correlated with the skin netting intensity. Comparative analysis between cucumber and melon revealed conserved and divergent genetic mechanisms underlying fruit skin netting/reticulation that may reflect the different selection histories in the two crops. A discussion was made on genetic basis of fruit skin netting in the context of natural and artificial selections of fruit quality-related epidermal features during cucumber breeding.
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Affiliation(s)
- Huijun Zhang
- School of Life Science, Huaibei Normal University, Huaibei, 10000, China
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Yuhui Wang
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Junyi Tan
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, Madison, WI, 53706, USA.
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Du Y, Li C, Mao X, Wang J, Li L, Yang J, Zhuang M, Sun D, Jing R. TaERF73 is associated with root depth, thousand‐grain weight and plant height in wheat over a range of environmental conditions. Food Energy Secur 2021. [DOI: 10.1002/fes3.325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Yan Du
- College of Agriculture Shanxi Agricultural University Shanxi China
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Jinwen Yang
- College of Agriculture Shanxi Agricultural University Shanxi China
| | - Mengjia Zhuang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Daizhen Sun
- College of Agriculture Shanxi Agricultural University Shanxi China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
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9
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Akdemir H. Evaluation of transcription factor and aquaporin gene expressions in response to Al 2O 3 and ZnO nanoparticles during barley germination. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:466-476. [PMID: 34166973 DOI: 10.1016/j.plaphy.2021.06.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Aluminum oxide and zinc oxide nanoparticles (NPs) are two of the mostly produced engineered metal oxide NPs. Here, barley germination and root elongation as well as gene expressions of the selected aquaporins (HvTip1;1 and HvPip1;1) and transcription factors (HvERFs and HvNFX1) were investigated after exposure to Al2O3 and ZnO NPs for foreseeing the effect of NP exposure. ICP-MS analysis showed that the nanoparticles were taken up into root and leaves. Even the germination analysis and seedling establishment data indicate that the applied NPs do not have any observable inhibitory effects except on root length, the gene expression analysis revealed that these nanoparticle applications lead to a response at the molecular level. The gene expression profiling indicated that aquaporins and transcription factor genes were differentially regulated in leaves and roots in response to NPs treatments. The expressions of aquaporin genes were higher especially in leaves in compared to the control plants. Gradual decrease was obtained in roots by application of the increased levels of Al2O3 NPs. The effects of ZnO NPs on gene expression levels of barley TFs were dramatically more distinctive in comparison with that of Al2O3 NPs. The expression profiles of HvERFs and HvNFX1 transcription factors in response to the Al2O3 and ZnO NPs suggest that these selected TFs can play important roles in shaping abiotic stress tolerance in young barley roots and leaves. Outcomes of the study will allow us to predict complex stress response of barley in response to the nanoparticles.
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Affiliation(s)
- Hulya Akdemir
- Faculty of Science, Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey.
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Lu L, Qanmber G, Li J, Pu M, Chen G, Li S, Liu L, Qin W, Ma S, Wang Y, Chen Q, Liu Z. Identification and Characterization of the ERF Subfamily B3 Group Revealed GhERF13.12 Improves Salt Tolerance in Upland Cotton. FRONTIERS IN PLANT SCIENCE 2021; 12:705883. [PMID: 34434208 PMCID: PMC8382128 DOI: 10.3389/fpls.2021.705883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/05/2021] [Indexed: 06/12/2023]
Abstract
The APETALA2 (AP2)/ethylene response factor plays vital functions in response to environmental stimulus. The ethylene response factor (ERF) subfamily B3 group belongs to the AP2/ERF superfamily and contains a single AP2/ERF domain. Phylogenetic analysis of the ERF subfamily B3 group genes from Arabdiposis thaliana, Gossypium arboreum, Gossypium hirsutum, and Gossypium raimondii made it possible to divide them into three groups and showed that the ERF subfamily B3 group genes are conserved in cotton. Collinearity analysis identified172 orthologous/paralogous gene pairs between G. arboreum and G. hirsutum; 178 between G. hirsutum and G. raimondii; and 1,392 in G. hirsutum. The GhERF subfamily B3 group gene family experienced massive gene family expansion through either segmental or whole genome duplication events, with most genes showing signature compatible with the action of purifying selection during evolution. Most G. hirsutum ERF subfamily B3 group genes are responsive to salt stress. GhERF13.12 transgenic Arabidopsis showed enhanced salt stress tolerance and exhibited regulation of related biochemical parameters and enhanced expression of genes participating in ABA signaling, proline biosynthesis, and ROS scavenging. In addition, the silencing of the GhERF13.12 gene leads to increased sensitivity to salt stress in cotton. These results indicate that the ERF subfamily B3 group had remained conserved during evolution and that GhERF13.12 induces salt stress tolerance in Arabidopsis and cotton.
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Affiliation(s)
- Lili Lu
- Engineering Research Centre of Cotton, Ministry of Education, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jie Li
- Engineering Research Centre of Cotton, Ministry of Education, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Mengli Pu
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
| | - Guoquan Chen
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
| | - Shengdong Li
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
| | - Le Liu
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
| | - Wenqiang Qin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuya Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ye Wang
- Engineering Research Centre of Cotton, Ministry of Education, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education, Xinjiang Agricultural University, Urumqi, China
| | - Zhao Liu
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
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Fan Y, Yan J, Lai D, Yang H, Xue G, He A, Guo T, Chen L, Cheng XB, Xiang DB, Ruan J, Cheng J. Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]. BMC Genomics 2021; 22:509. [PMID: 34229611 PMCID: PMC8259154 DOI: 10.1186/s12864-021-07848-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background GRAS, an important family of transcription factors, have played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. Since the sequencing of the sorghum genome, a plethora of genetic studies were mainly focused on the genomic information. The indepth identification or genome-wide analysis of GRAS family genes, especially in Sorghum bicolor, have rarely been studied. Results A total of 81 SbGRAS genes were identified based on the S. bicolor genome. They were named SbGRAS01 to SbGRAS81 and grouped into 13 subfamilies (LISCL, DLT, OS19, SCL4/7, PAT1, SHR, SCL3, HAM-1, SCR, DELLA, HAM-2, LAS and OS4). SbGRAS genes are not evenly distributed on the chromosomes. According to the results of the gene and motif composition, SbGRAS members located in the same group contained analogous intron/exon and motif organizations. We found that the contribution of tandem repeats to the increase in sorghum GRAS members was slightly greater than that of fragment repeats. By quantitative (q) RT-PCR, the expression of 13 SbGRAS members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. We further investigated the relationship between DELLA genes, GAs and grain development in S. bicolor. The paclobutrazol treatment significantly increased grain weight, and affected the expression levels of all DELLA subfamily genes. SbGRAS03 is the most sensitive to paclobutrazol treatment, but also has a high response to abiotic stresses. Conclusions Collectively, SbGRAs play an important role in plant development and response to abiotic stress. This systematic analysis lays the foundation for further study of the functional characteristics of GRAS genes of S. bicolor. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07848-z.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, 610106, Chengdu, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Tianrong Guo
- Chengdu Institute of Food Inspection, 610030, Chengdu, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, 618200, Mianzhu, People's Republic of China
| | - Xiao-Bin Cheng
- Department of Environmental and Life Sciences, Sichuan MinZu College, 626001, Kangding, People's Republic of China
| | - Da-Bing Xiang
- School of Food and Biological engineering, Chengdu University, 610106, Chengdu, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China.
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Mansour MMF, Emam MM, Salama KHA, Morsy AA. Sorghum under saline conditions: responses, tolerance mechanisms, and management strategies. PLANTA 2021; 254:24. [PMID: 34224010 DOI: 10.1007/s00425-021-03671-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
An overview is presented of recent advances in our knowledge of responses and mechanisms rendering adaptation to saline conditions in sorghum. Different strategies deployed to enhance salinity stress tolerance in sorghum are also pointed out. Salinity stress is a growing problem worldwide. Sorghum is the fifth key crop among cereals. Understanding responses and tolerance strategies in sorghum would be therefore helpful effort for providing biomarkers for designing greatest salinity-tolerant sorghum genotypes. When sorghum exposed to salinity, salinity-tolerant genotypes most probably reprogram their gene expression to activate adaptive biochemical and physiological responses for survival. The review thus discusses the possible physiological and biochemical responses that confer salinity tolerance to sorghum under saline conditions. Although it is not characterized in sorghum, salinity perceiving and transmitting signals to downstream responses via signaling transduction pathways most likely are essential strategy for sorghum adaptation to salinity stress. Sorghum has also shown to withstand moderate saline environments and retain the germination, growth, and photosynthetic activities. Salinity-tolerant sorghum genotypes show the ability to exclude excessive Na+ from reaching shoots and induce ion homeostasis. Osmotic homeostasis and ROS detoxification are also evident as salinity tolerance strategies in sorghum. These above mechanisms lead to re-establishment of cellular ionic, osmotic, and redox homeostasis as well as photosynthesis efficiency. It is noteworthy that these mechanisms act individually or co-operatively to minimize the salinity hazards and enhance acclimation in sorghum. We conclude, however, that although these responses contribute to sorghum tolerance to salinity stress, they seem to be not adequate at higher concentrations of salinity, which agrees with sorghum ranking as moderately salinity-tolerant crop. Also, some of these tolerance strategies reported in other crops are not well studied and documented in sorghum, but most probably have roles in sorghum. Further improvement in sorghum salinity tolerance using different approaches is definitely necessary to meet the requirements of its harsh production environments, and therefore, these approaches are addressed.
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Affiliation(s)
| | - Manal Mohamed Emam
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt
| | | | - Amal Ahmed Morsy
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt
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13
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Fan Y, Yang H, Lai D, He A, Xue G, Feng L, Chen L, Cheng XB, Ruan J, Yan J, Cheng J. Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]. BMC Genomics 2021; 22:415. [PMID: 34090335 PMCID: PMC8178921 DOI: 10.1186/s12864-021-07652-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
Abstract
Background Basic helix-loop-helix (bHLH) is a superfamily of transcription factors that is widely found in plants and animals, and is the second largest transcription factor family in eukaryotes after MYB. They have been shown to be important regulatory components in tissue development and many different biological processes. However, no systemic analysis of the bHLH transcription factor family has yet been reported in Sorghum bicolor. Results We conducted the first genome-wide analysis of the bHLH transcription factor family of Sorghum bicolor and identified 174 SbbHLH genes. Phylogenetic analysis of SbbHLH proteins and 158 Arabidopsis thaliana bHLH proteins was performed to determine their homology. In addition, conserved motifs, gene structure, chromosomal spread, and gene duplication of SbbHLH genes were studied in depth. To further infer the phylogenetic mechanisms in the SbbHLH family, we constructed six comparative syntenic maps of S. bicolor associated with six representative species. Finally, we analyzed the gene-expression response and tissue-development characteristics of 12 typical SbbHLH genes in plants subjected to six different abiotic stresses. Gene expression during flower and fruit development was also examined. Conclusions This study is of great significance for functional identification and confirmation of the S. bicolor bHLH superfamily and for our understanding of the bHLH superfamily in higher plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07652-9.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Liang Feng
- Chengdu Food and Drug Inspection Institute, Chengdu, 610000, P.R. China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, Mianzhu, 618200, P.R. China
| | - Xiao-Bin Cheng
- Department of Environmental and Life Sciences, Sichuan MinZu College, Kangding, 626001, P.R. China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Jun Yan
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106, P.R. China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China.
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14
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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.
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15
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Riaz MW, Lu J, Shah L, Yang L, Chen C, Mei XD, Xue L, Manzoor MA, Abdullah M, Rehman S, Si H, Ma C. Expansion and Molecular Characterization of AP2/ERF Gene Family in Wheat ( Triticum aestivum L.). Front Genet 2021; 12:632155. [PMID: 33868370 PMCID: PMC8044323 DOI: 10.3389/fgene.2021.632155] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/04/2021] [Indexed: 01/02/2023] Open
Abstract
The AP2/ERF is a large protein family of transcription factors, playing an important role in signal transduction, plant growth, development, and response to various stresses. AP2/ERF super-family is identified and functionalized in a different plant but no comprehensive and systematic analysis in wheat (Triticum aestivum L.) has been reported. However, a genome-wide and functional analysis was performed and identified 322 TaAP2/ERF putative genes from the wheat genome. According to the phylogenetic and structural analysis, TaAP2/ERF genes were divided into 12 subfamilies (Ia, Ib, Ic, IIa, IIb, IIc, IIIa, IIIb, IIIc, IVa, IVb, and IVc). Furthermore, conserved motifs and introns/exons analysis revealed may lead to functional divergence within clades. Cis-Acting analysis indicated that many elements were involved in stress-related and plant development. Chromosomal location showed that 320 AP2/ERF genes were distributed among 21 chromosomes and 2 genes were present in a scaffold. Interspecies microsynteny analysis revealed that maximum orthologous between Arabidopsis, rice followed by wheat. Segment duplication events have contributed to the expansion of the AP2/ERF family and made this family larger than rice and Arabidopsis. Additionally, AP2/ERF genes were differentially expressed in wheat seedlings under the stress treatments of heat, salt, and drought, and expression profiles were verified by qRT-PCR. Remarkably, the RNA-seq data exposed that AP2/ERF gene family might play a vital role in stress-related. Taken together, our findings provided useful and helpful information to understand the molecular mechanism and evolution of the AP2/ERF gene family in wheat.
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Affiliation(s)
- Muhammad Waheed Riaz
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Liaqat Shah
- Department of Botany, Mir Chakar Khan Rind University, Sibi, Pakistan
| | - Liu Yang
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Can Chen
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Xu Dong Mei
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Liu Xue
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | | | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Shamsur Rehman
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Hongqi Si
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China.,National United Engineering Laboratory for Crop Stress Resistance Breeding, Hefei, China.,Anhui Key Laboratory of Crop Biology, Hefei, China
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16
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Chai M, Cheng H, Yan M, Priyadarshani S, Zhang M, He Q, Huang Y, Chen F, Liu L, Huang X, Lai L, Chen H, Cai H, Qin Y. Identification and expression analysis of the DREB transcription factor family in pineapple ( Ananas comosus (L.) Merr.). PeerJ 2020; 8:e9006. [PMID: 32377449 PMCID: PMC7194095 DOI: 10.7717/peerj.9006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 03/27/2020] [Indexed: 01/05/2023] Open
Abstract
Background Dehydration responsive element-binding (DREB) transcription factors play a crucial role in plant growth, development and stress responses. Although DREB genes have been characterized in many plant species, genome-wide identification of the DREB gene family has not yet been reported in pineapple (Ananas comosus (L.) Merr.). Results Using comprehensive genome-wide screening, we identified 20 AcoDREB genes on 14 chromosomes. These were categorized into five subgroups. AcoDREBs within a group had similar gene structures and domain compositions. Using gene structure analysis, we showed that most AcoDREB genes (75%) lacked introns, and that the promoter regions of all 20 AcoDREB genes had at least one stress response-related cis-element. We identified four genes with high expression levels and six genes with low expression levels in all analyzed tissues. We detected expression changes under abiotic stress for eight selected AcoDREB genes. Conclusions This report presents the first genome-wide analysis of the DREB transcription factor family in pineapple. Our results provide preliminary data for future functional analysis of AcoDREB genes in pineapple, and useful information for developing new pineapple varieties with key agronomic traits such as stress tolerance.
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Affiliation(s)
- Mengnan Chai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Han Cheng
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Maokai Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi Province, China
| | - Svgn Priyadarshani
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Man Zhang
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Qing He
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Youmei Huang
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Fangqian Chen
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Liping Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Xiaoyi Huang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Linyi Lai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Huihuang Chen
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Hanyang Cai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Yuan Qin
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi Province, China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
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17
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Comprehensive phylogenomic analysis of ERF genes in sorghum provides clues to the evolution of gene functions and redundancy among gene family members. 3 Biotech 2020; 10:139. [PMID: 32158635 DOI: 10.1007/s13205-020-2120-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/05/2020] [Indexed: 10/24/2022] Open
Abstract
APETALA2/Ethylene-Responsive transcription factors (AP2/ERF), with their multifunctional roles in plant development, hormone signaling and stress tolerance, are important candidates for engineering crop plants. Here, we report identification and analysis of gene structure, phylogenetic distribution, expression, chromosomal localization and cis-acting promoter analysis of AP2/ERF genes in the C4 crop plant sorghum. We identified 158 ERF genes in sorghum with 52 of them encoding dehydration-responsive binding elements (DREB) while 106 code for ERF subfamily proteins. Phylogenetic analysis organized sorghum ERF proteins into 11 distinct groups exhibiting clade-specific expansion. About 68% ERF genes have paralogs indicating gene duplications as major cause of expansion of ERF family in sorghum. Analysis of spatiotemporal expression patterns using publicly available data revealed their tissue/genotype-preferential accumulation. In addition, 40 ERF genes exhibited differential accumulation in response to heat and/or drought stress. About 25% of the segmental gene pairs and eleven tandem duplicated genes exhibited high correlation (> 0.7) in their expression patterns indicating genetic redundancy. Comparative phylogenomic analysis of sorghum ERFs with 74 genetically characterized ERF genes from other plant species provided significant clues to sorghum ERF functions. Overall data generated here provides an overview of evolutionary relationship among ERF gene family members in sorghum and with respect to previously characterized ERF genes from other plant species. This information will be instrumental in initiating functional genomic studies of ERF candidates in sorghum.
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18
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Srivastava R, Kumar R. The expanding roles of APETALA2/Ethylene Responsive Factors and their potential applications in crop improvement. Brief Funct Genomics 2019; 18:240-254. [PMID: 30783669 DOI: 10.1093/bfgp/elz001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 11/29/2018] [Accepted: 01/23/2019] [Indexed: 01/10/2023] Open
Abstract
Understanding the molecular basis of the gene-regulatory networks underlying agronomic traits or plant responses to abiotic/biotic stresses is very important for crop improvement. In this context, transcription factors, which either singularly or in conjugation directly control the expression of many target genes, are suitable candidates for improving agronomic traits via genetic engineering. In this regard, members of one of the largest class of plant-specific APETALA2/Ethylene Response Factor (AP2/ERF) superfamily, which is implicated in various aspects of development and plant stress adaptation responses, are considered high-value targets for crop improvement. Besides their long-known regulatory roles in mediating plant responses to abiotic stresses such as drought and submergence, the novel roles of AP2/ERFs during fruit ripening or secondary metabolites production have also recently emerged. The astounding functional plasticity of AP2/ERF members is considered to be achieved by their interplay with other regulatory networks and signalling pathways. In this review, we have integrated the recently accumulated evidence from functional genomics studies and described their newly emerged functions in plants. The key structural features of AP2/ERF proteins and the modes of their action are briefly summarized. The importance of AP2/ERFs in plant development and stress responses and a summary of the event of their successful applications in crop improvement programs are also provided. Altogether, we envisage that the synthesized information presented in this review will be useful to design effective strategies for improving agronomic traits in crop plants.
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Affiliation(s)
- Rajat Srivastava
- Plant Translational Research Laboratory, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Rahul Kumar
- Plant Translational Research Laboratory, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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19
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Baillo EH, Kimotho RN, Zhang Z, Xu P. Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement. Genes (Basel) 2019; 10:E771. [PMID: 31575043 PMCID: PMC6827364 DOI: 10.3390/genes10100771] [Citation(s) in RCA: 229] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 01/24/2023] Open
Abstract
In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.
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Affiliation(s)
- Elamin Hafiz Baillo
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
- Agricultural Research Corporation (ARC), Ministry of Agriculture, Gezira 21111, Sudan.
| | - Roy Njoroge Kimotho
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhengbin Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ping Xu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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20
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Jin X, Yin X, Ndayambaza B, Zhang Z, Min X, Lin X, Wang Y, Liu W. Genome-Wide Identification and Expression Profiling of the ERF Gene Family in Medicago sativa L. Under Various Abiotic Stresses. DNA Cell Biol 2019; 38:1056-1068. [PMID: 31403329 DOI: 10.1089/dna.2019.4881] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The AP2/ERF (APETALA2/ETHYLENE RESPONSE FACTOR) transcription factor represents one of the largest plant-specific transcriptional regulators in plants. ERF plays important roles in the regulation of various developmental processes and acts as a mediator in plant external stress responses. However, the research of the ERF gene family is still limited in alfalfa (Medicago sativa L.), one of the most important forage legume species in the world. In the present study, a total of 159 ERF genes were identified, and the phylogenetic reconstruction, classification, conserved motifs, signal peptide prediction, and expression patterns under salt, drought, and low-temperature stresses of these ERF genes were comprehensively analyzed. The ERF genes family in alfalfa could be classified into 10 groups and predicted to be strongly homologous. Based on the structure and functions relationships, the III and IV subfamilies were more likely to play functions in abiotic stresses and 18 MsERF genes were selected for further quantitative real-time PCR validation in different stresses treatment. The results showed that all these MsERF genes were upregulated under three stresses except MsERF008. This study identified the possibility of abiotic tolerance candidate genes playing various roles in stress resistance at the whole-genome level, which would provide primary understanding for exploring ERF-mediated tolerance in alfalfa.
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Affiliation(s)
- Xiaoyu Jin
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Xiaofan Yin
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Boniface Ndayambaza
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Zhengshe Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Xueyang Min
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Xiaoshan Lin
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
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21
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Zhu Y, Li Y, Zhang S, Zhang X, Yao J, Luo Q, Sun F, Wang X. Genome-wide identification and expression analysis reveal the potential function of ethylene responsive factor gene family in response to Botrytis cinerea infection and ovule development in grapes (Vitis vinifera L.). PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:571-584. [PMID: 30468551 DOI: 10.1111/plb.12943] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 11/16/2018] [Indexed: 05/02/2023]
Abstract
The prevention of Botrytis cinerea infection and the study of grape seedlessness are very important for grape industries. Finding correlated regulatory genes is an important approach towards understanding their molecular mechanisms. Ethylene responsive factor (ERF) gene family play critical roles in defence networks and the growth of plants. To date, no large-scale study of the ERF proteins associated with pathogen defence and ovule development has been performed in grape (Vitis vinifera L.). In the present study, we identified 113 ERF genes (VvERF) and named them based on their chromosome locations. The ERF genes could be divided into 11 groups based on a multiple sequence alignment and a phylogenetic comparison with homologues from Arabidopsis thaliana. Synteny analysis and Ka/Ks ratio calculation suggested that segmental and tandem duplications contributed to the expansion of the ERF gene family. The evolutionary relationships between the VvERF genes were investigated by exon-intron structure characterisation, and an analysis of the cis-acting regulatory elements in their promoters suggested potential regulation after stress or hormone treatments. Expression profiling after infection with the fungus, B. cinerea, indicated that ERF genes function in responses to pathogen attack. In addition, the expression levels of most ERF genes were much higher during ovule development in seedless grapes, suggesting a role in ovule abortion related to seedlessness. Taken together, these results indicate that VvERF proteins are involved in responses to Botrytis cinerea infection and in grape ovule development. This information may help guide strategies to improve grape production.
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Affiliation(s)
- Y Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
| | - Y Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
| | - S Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
| | - X Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
| | - J Yao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
| | - Q Luo
- Research Institute of Grapes and Melon in Xinjiang Uygur Autonomous Region, Shanshan, Xinjiang, China
| | - F Sun
- Research Institute of Grapes and Melon in Xinjiang Uygur Autonomous Region, Shanshan, Xinjiang, China
| | - X Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Shaanxi, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling, China
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22
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Akbudak MA, Filiz E, Kontbay K. DREB2 (dehydration-responsive element-binding protein 2) type transcription factor in sorghum ( Sorghum bicolor): genome-wide identification, characterization and expression profiles under cadmium and salt stresses. 3 Biotech 2018; 8:426. [PMID: 30305995 DOI: 10.1007/s13205-018-1454-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022] Open
Abstract
Biotic and abiotic stresses negatively affect fitness, biomass production, and crop yield in plants. The dehydration-responsive element-binding proteins (DREB) are important transcription factors (TFs), and are induced by abiotic and biotic stresses. In this study, genome-wide identification, in silico sequence, and phylogenetic analyses and expression analyses of DREB2 genes under cadmium (Cd) and salt (NaCl) stresses in sorghum (Sorghum bicolor, Sb) were performed. Six putative SbDREB2 genes were identified in sorghum genome and all contained AP2 domain (PF00847). Nucleotide diversities in SbDREB2 genes were calculated as π: 0.53 and θ: 0.39, respectively. While exon numbers of them were either one or two, length of SbDREB2 proteins ranged from 238 to 388 amino acid residues. Fifty-six cis-acting regulatory elements, which are tissue specific, light, hormone, and stress responsive, were identified in the promotor regions of SbDREB2 genes. Analyses on digital expression data indicated that SbDREB2A and SbDREB2B are more expressed genes than other SbDREB genes in sorghum. Under Cd and NaCl stresses, expressions of SbDREB2 genes were induced at different levels. All SbDREB2 genes in root were up-regulated under salt stress. In case of Cd stress, SbDREB2D gene was particularly up-regulated in leaves and roots. Co-expression analyses revealed four of TFs in co-expression network, indicating that they have roles in transcriptional cascade. Furthermore, five miRNA target regions were identified for four SbDREB2 genes, indicating their roles in post-transcriptional regulation. The predicted 3D structure of SbDREB2 proteins showed some structural divergences and structure overlap between rice and sorghum varied at between 26.58 and 50%. Finally, obtained data could be used in breeding of stress-tolerant plants, particularly genetically engineered DREB2 expressing plants. Findings in this study would also contribute to the understanding of DREB2 genes in plants, especially in sorghum.
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23
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Xing L, Di Z, Yang W, Liu J, Li M, Wang X, Cui C, Wang X, Wang X, Zhang R, Xiao J, Cao A. Overexpression of ERF1-V from Haynaldia villosa Can Enhance the Resistance of Wheat to Powdery Mildew and Increase the Tolerance to Salt and Drought Stresses. FRONTIERS IN PLANT SCIENCE 2017; 8:1948. [PMID: 29238352 PMCID: PMC5712803 DOI: 10.3389/fpls.2017.01948] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/30/2017] [Indexed: 05/04/2023]
Abstract
The APETALA 2/Ethylene-responsive element binding factor (AP2/ERF) transcription factor gene family is widely involved in the biotic and abiotic stress regulation. Haynaldia villosa (VV, 2n = 14), a wild species of wheat, is a potential gene pool for wheat improvement. H. villosa confers high resistance to several wheat diseases and high tolerance to some abiotic stress. In this study, ERF1-V, an ethylene-responsive element-binding factor gene of the AP2/ERF transcription factor gene family from wild H. villosa, was cloned and characterized. Sequence and phylogenetic analysis showed that ERF1-V is a deduced B2 type ERF gene. ERF1-V was first identified as a Blumeria graminis f. sp. tritici (Bgt) up-regulated gene, and later found to be induced by drought, salt and cold stresses. In responses to hormones, ERF1-V was up-regulated by ethylene and abscisic acid, but down-regulated by salicylic acid and jasmonic acid. Over expression of ERF1-V in wheat could improve resistance to powdery mildew, salt and drought stress. Chlorophyll content, malondialdehyde content, superoxide dismutase and peroxidase activity were significantly differences between the recipient Yangmai158 and the transgenic plants following salt treatment. Furthermore, the expression levels of some stress responsive genes were differences after drought or salt treatments. Although ERF1-V was activated by the constitutive promoter, the agronomic traits, including flowering time, plant height, effective tiller number, spikelet number per spike and grain size, did not changed significantly. ERF1-V is a valuable gene for wheat improvement by genetic engineering.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Aizhong Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
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24
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Herath V. Small family, big impact: In silico analysis of DREB2 transcription factor family in rice. Comput Biol Chem 2016; 65:128-139. [PMID: 27816829 DOI: 10.1016/j.compbiolchem.2016.10.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/10/2016] [Accepted: 10/25/2016] [Indexed: 01/15/2023]
Abstract
Dehydration-responsive element- (DREB) proteins are considered as the master regulators of plant abiotic stress responses including drought, salinity and cold. They are also involved in other developmental processes such as embryo and endosperm development. DREB family of transcription factors consist of two sub families namely CBF1/DREB1 and DREB2. In this study, a genome-wide in silico analysis was carried out to dissect the structure and function of DREB2 family transcription factors in the rice genome. Using Arabidopsis DREB2 sequences a total of five rice DREB2 homologs were identified and they were distributed among four chromosomes. All OsDREBs contained the AP2 domain and unique [K/R]GKKGPxN motif characteristic to DREB2 family. During rice growth and development, three OsDREB2s namely OsDREB2A, OsDREB2B and OsABI4 were expressed and their expression was confined to embryo and endosperm tissues. OsDREB2A, OsDREB2B and OsDREB2C were expressed under abiotic stress conditions. OsDREB2B was expressed under drought, salinity and cold stress conditions while OsDREB2A and OsDREB2C were expressed only under drought and salinity conditions. The putative promoter regions of OsDREB2s were enriched with elements related to cellular development, hormonal regulation and stress response validating the observed expression dynamics. Co-expression analysis revealed that embryo development and stress related genes were expressed together with OsDREB2s. Predicted post-translational modifications indicated the fine regulation of OsDREB2s. These findings may shed light in uncovering the complex abiotic stress signaling networks and future genomics studies targeting the development of climate ready crops.
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Affiliation(s)
- Venura Herath
- Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka.
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25
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Guo B, Wei Y, Xu R, Lin S, Luan H, Lv C, Zhang X, Song X, Xu R. Genome-Wide Analysis of APETALA2/Ethylene-Responsive Factor (AP2/ERF) Gene Family in Barley (Hordeum vulgare L.). PLoS One 2016; 11:e0161322. [PMID: 27598245 PMCID: PMC5012588 DOI: 10.1371/journal.pone.0161322] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 08/03/2016] [Indexed: 12/29/2022] Open
Abstract
APETALA2/Ethylene-Responsive Factor (AP2/ERF) gene family is plant specific transcription factor. It plays critical roles in development process, tolerance to biotic and abiotic stresses, and responses to plant hormones. However, limited data are available on the contributions of AP2/ERF gene family in barley (Hordeum vulgare L.). In the present study, 121 HvAP2/ERF genes in barley were identified by using bioinformatics methods. A total of 118 HvAP2/ERF (97.5%) genes were located on seven chromosomes. According to phylogenetic classification of AP2/ERF family in Arabidopsis, HvAP2/ERF proteins were divided into AP2 (APETALA2), RAV (Related to ABI3/VP), DREB (dehydration responsive element binding), ERF (ethylene responsive factors) and soloist sub families. The analysis of duplication events indicated that tandem repeat and segmental duplication contributed to the expansion of the AP2/ERF family in barley. HvDREB1s/2s genes displayed various expression patterns under abiotic stress and phytohormone. Taken together, the data generated in this study will be useful for genome-wide analysis to determine the precise role of the HvAP2/ERF gene during barley development, abiotic stress and phytohormone responses with the ultimate goal of improving crop production.
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Affiliation(s)
- Baojian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yafeng Wei
- JiangSu Yanjiang Institute of Agricultural Sciences, Nantong, China
| | - Ruibin Xu
- College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, China
| | - Shen Lin
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Haiye Luan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Chao Lv
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Xinzhong Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Xiyun Song
- College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, China
| | - Rugen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou, China
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26
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Tang Y, Qin S, Guo Y, Chen Y, Wu P, Chen Y, Li M, Jiang H, Wu G. Genome-Wide Analysis of the AP2/ERF Gene Family in Physic Nut and Overexpression of the JcERF011 Gene in Rice Increased Its Sensitivity to Salinity Stress. PLoS One 2016; 11:e0150879. [PMID: 26943337 PMCID: PMC4778941 DOI: 10.1371/journal.pone.0150879] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/19/2016] [Indexed: 11/19/2022] Open
Abstract
The AP2/ERF transcription factors play crucial roles in plant growth, development and responses to biotic and abiotic stresses. A total of 119 AP2/ERF genes (JcAP2/ERFs) have been identified in the physic nut genome; they include 16 AP2, 4 RAV, 1 Soloist, and 98 ERF genes. Phylogenetic analysis indicated that physic nut AP2 genes could be divided into 3 subgroups, while ERF genes could be classed into 11 groups or 43 subgroups. The AP2/ERF genes are non-randomly distributed across the 11 linkage groups of the physic nut genome and retain many duplicates which arose from ancient duplication events. The expression patterns of several JcAP2/ERF duplicates in the physic nut showed differences among four tissues (root, stem, leaf, and seed), and 38 JcAP2/ERF genes responded to at least one abiotic stressor (drought, salinity, phosphate starvation, and nitrogen starvation) in leaves and/or roots according to analysis of digital gene expression tag data. The expression of JcERF011 was downregulated by salinity stress in physic nut roots. Overexpression of the JcERF011 gene in rice plants increased its sensitivity to salinity stress. The increased expression levels of several salt tolerance-related genes were impaired in the JcERF011-overexpressing plants under salinity stress.
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Affiliation(s)
- Yuehui Tang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Shanshan Qin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yali Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yanbo Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Pingzhi Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Yaping Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Meiru Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Huawu Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Guojiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
- * E-mail:
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27
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Chen L, Han J, Deng X, Tan S, Li L, Li L, Zhou J, Peng H, Yang G, He G, Zhang W. Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon. Sci Rep 2016; 6:21623. [PMID: 26869021 PMCID: PMC4751504 DOI: 10.1038/srep21623] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 01/26/2016] [Indexed: 11/09/2022] Open
Abstract
APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factors constitute one of the largest and most conserved gene families in plant, and play essential roles in growth, development and stress response. Except a few members, the AP2/EREBP family has not been characterized in Brachypodium distachyon, a model plant of Poaceae. We performed a genome-wide study of this family in B. distachyon by phylogenetic analyses, transactivation assays and transcript profiling. A total of 149 AP2/EREBP genes were identified and divided into four subfamilies, i.e., ERF (ethylene responsive factor), DREB (dehydration responsive element binding gene), RAV (related to ABI3/VP) and AP2. Tandem duplication was a major force in expanding B. distachyon AP2/EREBP (BdAP2/EREBP) family. Despite a significant expansion, genomic organizations of BdAP2/EREBPs were monotonous as the majority of them, except those of AP2 subfamily, had no intron. An analysis of transcription activities of several closely related and duplicated BdDREB genes showed their functional divergence and redundancy in evolution. The expression of BdAP2/EREBPs in different tissues and the expression of DREB/ERF subfamilies in B. distachyon, wheat and rice under abiotic stresses were investigated by next-generation sequencing and microarray profiling. Our results are valuable for further function analysis of stress tolerant AP2/EREBP genes in B. distachyon.
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Affiliation(s)
- Lihong Chen
- The Institute for Systems Biology, Jianghan University, Wuhan 430056, China
| | - Jiapeng Han
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science &Technology (HUST), Wuhan 430074, China
| | - Xiaomin Deng
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Shenglong Tan
- School of Information Engineering, Hubei University of Economics, Wuhan 430205, China
| | - Lili Li
- The Institute for Systems Biology, Jianghan University, Wuhan 430056, China
| | - Lun Li
- The Institute for Systems Biology, Jianghan University, Wuhan 430056, China
| | - Junfei Zhou
- The Institute for Systems Biology, Jianghan University, Wuhan 430056, China
| | - Hai Peng
- The Institute for Systems Biology, Jianghan University, Wuhan 430056, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science &Technology (HUST), Wuhan 430074, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, College of Life Science and Technology, Huazhong University of Science &Technology (HUST), Wuhan 430074, China
| | - Weixiong Zhang
- The Institute for Systems Biology, Jianghan University, Wuhan 430056, China.,Department of Computer Science and Engineering and Department of Genetics, Washington University, St. Louis, MO 36130, USA
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28
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Du C, Hu K, Xian S, Liu C, Fan J, Tu J, Fu T. Dynamic transcriptome analysis reveals AP2/ERF transcription factors responsible for cold stress in rapeseed (Brassica napus L.). Mol Genet Genomics 2016; 291:1053-67. [PMID: 26728151 DOI: 10.1007/s00438-015-1161-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/14/2015] [Indexed: 02/02/2023]
Abstract
The APETALA2/ethylene response factor (AP2/ERF) transcription factor (TF) superfamily plays an important regulatory role in signal transduction of the plant responses to various stresses including low temperature. Significant progress has been made in understanding the mechanism of cold resistance in Brassica napus, an important oilseed crop. However, comprehensive studies on the induction and activity of these TFs under low temperature have been lacking. In this study, 132 AP2/ERF genes were identified by transcriptome sequencing of rapeseed leaves exposed to 0, 2, 6, 12, and 24 h of low (4 °C) temperature stress. The genes were classified into 4 subfamilies (AP2, DREB, ERF, and RAV) and 13 subgroups, among which the DREB subfamily and ERF subfamily contained 114 genes, no genes were assigned to soloist or DREB A3 subgroups. One hundred and eighteen genes were located on chromosomes A1 to C9. GO functional analysis and promoter sequence analysis revealed that these genes are involved in many molecular pathways that may enhance cold resistance in plants, such as the low-temperature responsiveness, methyl jasmonate, abscisic acid, and ethylene-responsiveness pathways. Their expression patterns revealed dynamic control at different times following initiation of cold stress; the RAV and DREB subfamilies were expressed at the early stage of cold stress, whereas the AP2 subfamily was expressed later. Quantitative PCR analyses of 13 cold-induced AP2/ERF TFs confirmed the accuracy of above results. This study is the first dynamic analysis of the AP2/ERF TFs responsible for cold stress in rapeseed. These findings will serve as a reference for future functional research on transcription in rapeseed.
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Affiliation(s)
- Chunfang Du
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, People's Republic of China.,Cotton Research Institute, Shanxi Academy of Agricultural Sciences, Yuncheng, 044000, People's Republic of China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shuanshi Xian
- Cotton Research Institute, Shanxi Academy of Agricultural Sciences, Yuncheng, 044000, People's Republic of China
| | - Chunqing Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianchun Fan
- Cotton Research Institute, Shanxi Academy of Agricultural Sciences, Yuncheng, 044000, People's Republic of China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, People's Republic of China
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29
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Pandey B, Sharma P, Tyagi C, Goyal S, Grover A, Sharma I. Structural modeling and molecular simulation analysis of HvAP2/EREBP from barley. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1073630] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Transcriptome-based discovery of AP2/ERF transcription factors related to temperature stress in tea plant (Camellia sinensis). Funct Integr Genomics 2015; 15:741-52. [PMID: 26233577 DOI: 10.1007/s10142-015-0457-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/11/2015] [Accepted: 07/17/2015] [Indexed: 01/01/2023]
Abstract
Tea plant (Camellia sinensis) is an important natural resource for the global supply of non-alcoholic beverage production. The extension of tea plant cultivation is challenged by biotic and abiotic stresses. Transcription factors (TFs) of the APETALA 2 (AP2)/ethylene-responsive factor (ERF) family are involved in growth and anti-stresses through multifaceted transcriptional regulation in plants. This study comprehensively analyzed AP2/ERF family TFs from C. sinensis on the basis of the transcriptome sequencing data of four tea plant cultivars, namely, 'Yunnanshilixiang', 'Chawansanhao', 'Ruchengmaoyecha', and 'Anjibaicha'. A total of 89 putative AP2/ERF transcription factors with full-length AP2 domain were identified from C. sinensis and classified into five subfamilies, namely, AP2, dehydration-responsive-element-binding (DREB), ERF, related to ABI3/VP (RAV), and Soloist. All identified CsAP2/ERF genes presented relatively stable expression levels in the four tea plant cultivars. Many groups also showed cultivar specificity. Five CsAP2/ERF genes from each AP2/ERF subfamily (DREB, ERF, AP2, and RAV) were related to temperature stresses; these results indicated that AP2/ERF TFs may play important roles in abnormal temperature stress response in C. sinensis.
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Wu H, Lv H, Li L, Liu J, Mu S, Li X, Gao J. Genome-Wide Analysis of the AP2/ERF Transcription Factors Family and the Expression Patterns of DREB Genes in Moso Bamboo (Phyllostachys edulis). PLoS One 2015; 10:e0126657. [PMID: 25985202 PMCID: PMC4436012 DOI: 10.1371/journal.pone.0126657] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 04/06/2015] [Indexed: 11/23/2022] Open
Abstract
The AP2/ERF transcription factor family, one of the largest families unique to plants, performs a significant role in terms of regulation of growth and development, and responses to biotic and abiotic stresses. Moso bamboo (Phyllostachys edulis) is a fast-growing non-timber forest species with the highest ecological, economic and social values of all bamboos in Asia. The draft genome of moso bamboo and the available genomes of other plants provide great opportunities to research global information on the AP2/ERF family in moso bamboo. In total, 116 AP2/ERF transcription factors were identified in moso bamboo. The phylogeny analyses indicated that the 116 AP2/ERF genes could be divided into three subfamilies: AP2, RAV and ERF; and the ERF subfamily genes were divided into 11 groups. The gene structures, exons/introns and conserved motifs of the PeAP2/ERF genes were analyzed. Analysis of the evolutionary patterns and divergence showed the PeAP2/ERF genes underwent a large-scale event around 15 million years ago (MYA) and the division time of AP2/ERF family genes between rice and moso bamboo was 15–23 MYA. We surveyed the putative promoter regions of the PeDREBs and showed that largely stress-related cis-elements existed in these genes. Further analysis of expression patterns of PeDREBs revealed that the most were strongly induced by drought, low-temperature and/or high salinity stresses in roots and, in contrast, most PeDREB genes had negative functions in leaves under the same respective stresses. In this study there were two main interesting points: there were fewer members of the PeDREB subfamily in moso bamboo than in other plants and there were differences in DREB gene expression profiles between leaves and roots triggered in response to abiotic stress. The information produced from this study may be valuable in overcoming challenges in cultivating moso bamboo.
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Affiliation(s)
- Huili Wu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People’s Republic of China
| | - Hao Lv
- Hunan Forest Botanical Garden, Changsha, Hunan Province, People’s Republic of China
| | - Long Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People’s Republic of China
| | - Jun Liu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People’s Republic of China
| | - Shaohua Mu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People’s Republic of China
| | - Xueping Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People’s Republic of China
- * E-mail: (XPL); (JG)
| | - Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People’s Republic of China
- * E-mail: (XPL); (JG)
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Anami SE, Zhang L, Xia Y, Zhang Y, Liu Z, Jing H. Sweet sorghum ideotypes: genetic improvement of stress tolerance. Food Energy Secur 2015. [DOI: 10.1002/fes3.54] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Sylvester Elikana Anami
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
- Institute of Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya
| | - Li‐Min Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yan Xia
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yu‐Miao Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Zhi‐Quan Liu
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Hai‐Chun Jing
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
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Yang C, Lu X, Ma B, Chen SY, Zhang JS. Ethylene signaling in rice and Arabidopsis: conserved and diverged aspects. MOLECULAR PLANT 2015; 8:495-505. [PMID: 25732590 DOI: 10.1016/j.molp.2015.01.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 12/16/2014] [Accepted: 01/06/2015] [Indexed: 05/18/2023]
Abstract
Ethylene as a gas phytohormone plays significant roles in the whole life cycle of plants, ranging from growth and development to stress responses. A linear ethylene signaling pathway has been established in the dicotyledonous model plant Arabidopsis. However, the ethylene signaling mechanism in monocotyledonous plants such as rice is largely unclear. In this review, we compare the ethylene response phenotypes of dark-grown seedlings of Arabidopsis, rice, and other monocotyledonous plants (maize, wheat, sorghum, and Brachypodium distachyon) and pinpoint that rice has a distinct phenotype of root inhibition but coleoptile promotion in etiolated seedlings upon ethylene treatment. We further summarize the homologous genes of Arabidopsis ethylene signaling components in these monocotyledonous plants and discuss recent progress. Although conserved in most aspects, ethylene signaling in rice has evolved new features compared with that in Arabidopsis. These analyses provide novel insights into the understanding of ethylene signaling in the dicotyledonous Arabidopsis and monocotyledonous plants, particularly rice. Further characterization of rice ethylene-responsive mutants and their corresponding genes will help us better understand the whole picture of ethylene signaling mechanisms in plants.
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Affiliation(s)
- Chao Yang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiang Lu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Biao Ma
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Rao G, Sui J, Zeng Y, He C, Zhang J. Genome-wide analysis of the AP2/ERF gene family in Salix arbutifolia. FEBS Open Bio 2015; 5:132-7. [PMID: 25830086 PMCID: PMC4354408 DOI: 10.1016/j.fob.2015.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/15/2015] [Accepted: 02/18/2015] [Indexed: 01/08/2023] Open
Abstract
We identified 173 AP2/ERF superfamily genes in Salix arbutifolia. A comparative analysis of AP2/ERF superfamily genes was performed. The phylogenic trees of AP2/ERF superfamily have been constructed.
AP2/ERF genes encode transcriptional regulators with a variety of functions in plant growth and development and in response to biotic and abiotic stresses. To date, there are no detailed classification and expression profiles for AP2/ERF genes in Salix. In this study, a comprehensive computational analysis identified 173 AP2/ERF superfamily genes in willow (Salix arbutifolia), by using in silico cloning methods with the use of the AP2/ERF conserved domain amino acid sequence of Arabidopsis thaliana as a probe. Based on the results of phylogenetic analyses and the number of AP2/ERF domains, the AP2/ERF genes were classified into four groups: AP2, RAV, ERF and Soloist. The expression profile was analyzed using transcriptome data from different tissues. A comparative analysis of AP2/ERF superfamily genes among Salix, Populus and Arabidopsis was performed. The Salix DREB, AP2 and RAV groups had a similar number to those in Arabidopsis, and the size of the ERF subfamily in Salix was about 1.4-fold that of Arabidopsis. The Salix DREB subfamily was smaller compared to Populus, while the other families were similar in size to those in Populus. These results will be useful for future functional analyses of the ERF family genes.
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Affiliation(s)
- Guodong Rao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China ; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China ; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jinkai Sui
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yanfei Zeng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China ; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China ; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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Wang X, Liu S, Tian H, Wang S, Chen JG. The Small Ethylene Response Factor ERF96 is Involved in the Regulation of the Abscisic Acid Response in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2015; 6:1064. [PMID: 26635862 PMCID: PMC4659910 DOI: 10.3389/fpls.2015.01064] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 11/16/2015] [Indexed: 05/22/2023]
Abstract
Ethylene regulates many aspects of plant growth and development including seed germination, leaf senescence, and fruit ripening, and of plant responses to environmental stimuli including both biotic and abiotic stresses. Ethylene response factors (ERFs) are plant-specific transcription factors and are a subfamily of the AP2 (APETALA2)/ERF transcription factor family. The function of many members in this large gene family remains largely unknown. ERF96, a member of the Group IX ERF family transcription factors, has recently been shown to be a transcriptional activator that is involved in plant defense response in Arabidopsis. Here we provide evidence that ERF96 is a positive regulator of abscisic acid (ABA) responses. Bioinformatics analysis indicated that there are a total four small ERFs in Arabidopsis including ERF95, ERF96, ERF97, and ERF98, and that ERF96 forms a cluster with ERF95 and ERF97. By using quantitative RT-PCR, we found that ERF96 is expressed in all tissues and organs examined except roots, with relatively high expression in flowers and seeds. Results from the protoplast transfection assay indicated that the EDLL motif-containing C-terminal domain is responsible for ERF96's transcriptional activity. Although loss-of-function mutant of ERF96 was morphologically similar to wild type plants, transgenic plants overexpressing ERF96 had smaller rosette size and were delayed in flowering time. In ABA sensitivity assays, we found that ERF96 overexpression plants were hypersensitive to ABA in terms of ABA inhibition of seed germination, early seedling development and root elongation. Consistent with these observations, elevated transcript levels of some ABA-responsive genes including RD29A, ABI5, ABF3, ABF4, P5CS, and COR15A were observed in the transgenic plants in the presence of ABA. However, in the absence of ABA treatment, the transcript levels of these ABA-responsive genes remained largely unchanged. Our experiments also showed that water loss in ERF96 overexpression plants was slower than that in Col wild type plants. Stomatal closure assays indicated that ERF96 overexpression plants had reduced stomatal aperture in the presence of ABA. Taken together, our results suggest that ERF96 positively regulates ABA responses in Arabidopsis.
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Affiliation(s)
- Xiaoping Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Shanda Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Hainan Tian
- Key Laboratory of Molecular Epigenetics of Ministry of Education and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- *Correspondence: Shucai Wang,
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Dey S, Corina Vlot A. Ethylene responsive factors in the orchestration of stress responses in monocotyledonous plants. FRONTIERS IN PLANT SCIENCE 2015; 6:640. [PMID: 26379679 PMCID: PMC4552142 DOI: 10.3389/fpls.2015.00640] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/02/2015] [Indexed: 05/18/2023]
Abstract
The APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily of transcription factors (TFs) regulates physiological, developmental and stress responses. Most of the AP2/ERF TFs belong to the ERF family in both dicotyledonous and monocotyledonous plants. ERFs are implicated in the responses to both biotic and abiotic stress and occasionally impart multiple stress tolerance. Studies have revealed that ERF gene function is conserved in dicots and monocots. Moreover, successful stress tolerance phenotypes are observed on expression in heterologous systems, making ERFs promising candidates for engineering stress tolerance in plants. In this review, we summarize the role of ERFs in general stress tolerance, including responses to biotic and abiotic stress factors, and endeavor to understand the cascade of ERF regulation resulting in successful signal-to-response translation in monocotyledonous plants.
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Affiliation(s)
| | - A. Corina Vlot
- *Correspondence: A. Corina Vlot, Helmholtz Zentrum Muenchen, Department of Environmental Sciences, Institute of Biochemical Plant Pathology, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany,
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37
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Makhloufi E, Yousfi FE, Marande W, Mila I, Hanana M, Bergès H, Mzid R, Bouzayen M. Isolation and molecular characterization of ERF1, an ethylene response factor gene from durum wheat (Triticum turgidum L. subsp. durum), potentially involved in salt-stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6359-71. [PMID: 25205575 DOI: 10.1093/jxb/eru352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
As food crop, wheat is of prime importance for human society. Nevertheless, our understanding of the genetic and molecular mechanisms controlling wheat productivity conditions has been, so far, hampered by the lack of sufficient genomic resources. The present work describes the isolation and characterization of TdERF1, an ERF gene from durum wheat (Triticum turgidum L. subsp. durum). The structural features of TdERF1 supported the hypothesis that it is a novel member of the ERF family in durum wheat and, considering its close similarity to TaERF1 of Triticum aestivum, it probably plays a similar role in mediating responses to environmental stresses. TdERF1 displayed an expression pattern that discriminated between two durum wheat genotypes contrasted with regard to salt-stress tolerance. The high number of cis-regulatory elements related to stress responses present in the TdERF1 promoter and the ability of TdERF1 to regulate the transcription of ethylene and drought-responsive promoters clearly indicated its potential role in mediating plant responses to a wide variety of environmental constrains. TdERF1 was also regulated by abscisic acid, ethylene, auxin, and salicylic acid, suggesting that it may be at the crossroads of multiple hormone signalling pathways. Four TdERF1 allelic variants have been identified in durum wheat genome, all shown to be transcriptionally active. Interestingly, the expression of one allelic form is specific to the tolerant genotype, further supporting the hypothesis that this gene is probably associated with the susceptibility/tolerance mechanism to salt stress. In this regard, the TdERF1 gene may provide a discriminating marker between tolerant and sensitive wheat varieties.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Cell Nucleus/drug effects
- Cell Nucleus/metabolism
- Chromosomes, Artificial, Bacterial/metabolism
- DNA, Complementary/genetics
- Droughts
- Ethylenes/metabolism
- Ethylenes/pharmacology
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant
- Genotype
- Molecular Sequence Annotation
- Molecular Sequence Data
- Phylogeny
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Polymerase Chain Reaction
- Promoter Regions, Genetic/genetics
- Protein Transport/drug effects
- Salt Tolerance
- Sequence Alignment
- Sequence Analysis, DNA
- Sodium Chloride/pharmacology
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Transcription, Genetic/drug effects
- Triticum/drug effects
- Triticum/genetics
- Triticum/physiology
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Affiliation(s)
- Emna Makhloufi
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - Fatma-Ezzahra Yousfi
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - William Marande
- Centre National de Ressources Génomiques Végétales, INRA-CNRGV, 24 Chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan, France
| | - Isabelle Mila
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Mohsen Hanana
- Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales, INRA-CNRGV, 24 Chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan, France
| | - Rim Mzid
- Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - Mondher Bouzayen
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
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Jourda C, Cardi C, Mbéguié-A-Mbéguié D, Bocs S, Garsmeur O, D'Hont A, Yahiaoui N. Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage-specific whole-genome duplications. THE NEW PHYTOLOGIST 2014; 202:986-1000. [PMID: 24716518 DOI: 10.1111/nph.12710] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/25/2013] [Indexed: 05/26/2023]
Abstract
Whole-genome duplications (WGDs) are widespread in plants, and three lineage-specific WGDs occurred in the banana (Musa acuminata) genome. Here, we analysed the impact of WGDs on the evolution of banana gene families involved in ethylene biosynthesis and signalling, a key pathway for banana fruit ripening. Banana ethylene pathway genes were identified using comparative genomics approaches and their duplication modes and expression profiles were analysed. Seven out of 10 banana ethylene gene families evolved through WGD and four of them (1-aminocyclopropane-1-carboxylate synthase (ACS), ethylene-insensitive 3-like (EIL), ethylene-insensitive 3-binding F-box (EBF) and ethylene response factor (ERF)) were preferentially retained. Banana orthologues of AtEIN3 and AtEIL1, two major genes for ethylene signalling in Arabidopsis, were particularly expanded. This expansion was paralleled by that of EBF genes which are responsible for control of EIL protein levels. Gene expression profiles in banana fruits suggested functional redundancy for several MaEBF and MaEIL genes derived from WGD and subfunctionalization for some of them. We propose that EIL and EBF genes were co-retained after WGD in banana to maintain balanced control of EIL protein levels and thus avoid detrimental effects of constitutive ethylene signalling. In the course of evolution, subfunctionalization was favoured to promote finer control of ethylene signalling.
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Affiliation(s)
| | | | - Didier Mbéguié-A-Mbéguié
- CIRAD, UMR QUALISUD, F-97130, Capesterre-Belle-Eau, Guadeloupe, France
- CIRAD, UMR QUALISUD, F-34398, Montpellier, France
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