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Shahzad A, Fan Y, Qian M, Khan SU, Mahmood U, Wei L, Qu C, Lu K. Genome-wide characterization of Related to ABI3/VP1 transcription factors among U's triangle Brassica species reveals a negative role for BnaA06.RAV3L in seed size. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108854. [PMID: 38901228 DOI: 10.1016/j.plaphy.2024.108854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/01/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
The transcription factors Related to ABI3/VP1 (RAV) are crucial for various plant processes and stress responses. Although the U's triangle Brassica species genomes have been released, the knowledge regarding the RAV family is still limited. In this study, we identified 123 putative RAV genes across the six U's triangle Brassica species (Brassica rapa, 14; Brassica oleracea, 14; Brassica nigra, 13; Brassica carinata, 27; Brassica juncea, 28; Brassica napus, 27). Phylogenetic analysis categorized them into three groups. The RAV genes exhibited diversity in both functional and structural aspects, particularly in gene structure and cis-acting elements within their promoters. The expression analysis revealed that BnaRAV genes in Group 1/2 exhibited diverse expression patterns across various tissues, while those in Group 3 did not show expression except for BnaRAV3L-2 and BnaRAV3L-6, which were exclusively expressed in seeds. Furthermore, the seed-specific expression of BnaA06. RAV3L (BnaRAV3L-2) was confirmed through promoter-GUS staining. Subcellular localization studies demonstrated that BnaA06.RAV3L is localized to the nucleus. The overexpression of BnaA06. RAV3L in Arabidopsis led to a remarkable inhibition of seed-specific traits such as seed width, seed length, seed area, and seed weight. This study provides insights into the functional evolution of the RAV gene family in U triangle Brassica species. It establishes a foundation for uncovering the molecular mechanisms underlying the negative role of RAV3L in seed development.
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Affiliation(s)
- Ali Shahzad
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Yonghai Fan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Mingchao Qian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Umer Mahmood
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Lijuan Wei
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Cunmin Qu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715, China.
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Wei Y, Kong Y, Li H, Yao A, Han J, Zhang W, Li X, Li W, Han D. Genome-Wide Characterization and Expression Profiling of the AP2/ERF Gene Family in Fragaria vesca L. Int J Mol Sci 2024; 25:7614. [PMID: 39062854 DOI: 10.3390/ijms25147614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
The wild strawberry (Fragaria vesca L.; F. vesca) represents a resilient and extensively studied model organism. While the AP2/ERF gene family plays a pivotal role in plant development, its exploration within F. vesca remains limited. In this study, we characterized the AP2/ERF gene family in wild strawberries using the recently released genomic data (F. vesca V6.0). We conducted an analysis of the gene family expansion pattern, we examined gene expression in stem segments and leaves under cold conditions, and we explored its functional attributes. Our investigation revealed that the FvAP2/ERF family comprises 86 genes distributed among four subfamilies: AP2 (17), RAV (6), ERF (62), and Soloist (1). Tandem and segmental duplications significantly contributed to the growth of this gene family. Furthermore, predictive analysis identified several cis-acting elements in the promoter region associated with meristematic tissue expression, hormone regulation, and resistance modulation. Transcriptomic analysis under cold stress unveiled diverse responses among multiple FvAP2/ERFs in stem segments and leaves. Real-time fluorescence quantitative reverse transcription PCR (RT-qPCR) results confirmed elevated expression levels of select genes following the cold treatment. Additionally, overexpression of FvERF23 in Arabidopsis enhanced cold tolerance, resulting in significantly increased fresh weight and root length compared to the wild-type control. These findings lay the foundation for further exploration into the functional roles of FvAP2/ERF genes.
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Affiliation(s)
- Yangfan Wei
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Yihan Kong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Huiwen Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Anqi Yao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Jiaxin Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Wenhao Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xingguo Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Wenhui Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Deguo Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
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Feng Y, Li X, Qin Y, Li Y, Yang Z, Xiong X, Wan J, Qiu M, Hou Q, Zhang Z, Guo Z, Zhang X, Niu J, Zhou Q, Tang J, Fu Z. Identification of anther thermotolerance genes by the integration of linkage and association analysis in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38943629 DOI: 10.1111/tpj.16900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/24/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Maize is one of the world's most important staple crops, yet its production is increasingly threatened by the rising frequency of high-temperature stress (HTS). To investigate the genetic basis of anther thermotolerance under field conditions, we performed linkage and association analysis to identify HTS response quantitative trait loci (QTL) using three recombinant inbred line (RIL) populations and an association panel containing 375 diverse maize inbred lines. These analyses resulted in the identification of 16 co-located large QTL intervals. Among the 37 candidate genes identified in these QTL intervals, five have rice or Arabidopsis homologs known to influence pollen and filament development. Notably, one of the candidate genes, ZmDUP707, has been subject to selection pressure during breeding. Its expression is suppressed by HTS, leading to pollen abortion and barren seeds. We also identified several additional candidate genes potentially underly QTL previously reported by other researchers. Taken together, our results provide a pool of valuable candidate genes that could be employed by future breeding programs aiming at enhancing maize HTS tolerance.
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Affiliation(s)
- Yijian Feng
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xinlong Li
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yongtian Qin
- Hebi Academy of Agricultural Sciences, Hebi, 458030, Henan, China
| | - Yibo Li
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zeyuan Yang
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jiong Wan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Meng Qiu
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qiuchan Hou
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jishan Niu
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qingqian Zhou
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy/The Shennong Laboratory, Henan Agricultural University, Zhengzhou, 450046, China
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Cui T, Zang S, Sun X, Zhang J, Su Y, Wang D, Wu G, Chen R, Que Y, Lin Q, You C. Molecular identification and functional characterization of a transcription factor GeRAV1 from Gelsemium elegans. BMC Genomics 2024; 25:22. [PMID: 38166591 PMCID: PMC10759518 DOI: 10.1186/s12864-023-09919-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Gelsemium elegans is a traditional Chinese medicinal plant and temperature is one of the key factors affecting its growth. RAV (related to ABI3/VP1) transcription factor plays multiple roles in higher plants, including the regulation of plant growth, development, and stress response. However, RAV transcription factor in G. elegans has not been reported. RESULTS In this study, three novel GeRAV genes (GeRAV1-GeRAV3) were identified from the transcriptome of G. elegans under low temperature stress. Phylogenetic analysis showed that GeRAV1-GeRAV3 proteins were clustered into groups II, IV, and V, respectively. RNA-sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) analyses indicated that the expression of GeRAV1 and GeRAV2 was increased in response to cold stress. Furthermore, the GeRAV1 gene was successfully cloned from G. elegans leaf. It encoded a hydrophilic, unstable, and non-secretory protein that contained both AP2 and B3 domains. The amino acid sequence of GeRAV1 protein shared a high similarity of 81.97% with Camptotheca acuminata CaRAV. Subcellular localization and transcriptional self-activation experiments demonstrated that GeRAV1 was a nucleoprotein without self-activating activity. The GeRAV1 gene was constitutively expressed in the leaves, stems, and roots of the G. elegans, with the highest expression levels in roots. In addition, the expression of the GeRAV1 gene was rapidly up-regulated under abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (MeJA) stresses, suggesting that it may be involved in hormonal signaling pathways. Moreover, GeRAV1 conferred improved cold and sodium chloride tolerance in Escherichia coli Rosetta cells. CONCLUSIONS These findings provided a foundation for further understanding on the function and regulatory mechanism of the GeRAV1 gene in response to low-temperature stress in G. elegans.
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Affiliation(s)
- Tianzhen Cui
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinlu Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guran Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruiqi Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qing Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- The Second People's Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350003, China.
| | - Chuihuai You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- The Second People's Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350003, China.
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Tang M, Zhao G, Awais M, Gao X, Meng W, Lin J, Zhao B, Lai Z, Lin Y, Chen Y. Genome-Wide Identification and Expression Analysis Reveals the B3 Superfamily Involved in Embryogenesis and Hormone Responses in Dimocarpus longan Lour. Int J Mol Sci 2023; 25:127. [PMID: 38203301 PMCID: PMC10779397 DOI: 10.3390/ijms25010127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
B3 family transcription factors play an essential regulatory role in plant growth and development processes. This study performed a comprehensive analysis of the B3 family transcription factor in longan (Dimocarpus longan Lour.), and a total of 75 DlB3 genes were identified. DlB3 genes were unevenly distributed on the 15 chromosomes of longan. Based on the protein domain similarities and functional diversities, the DlB3 family was further clustered into four subgroups (ARF, RAV, LAV, and REM). Bioinformatics and comparative analyses of B3 superfamily expression were conducted in different light and with different temperatures and tissues, and early somatic embryogenesis (SE) revealed its specific expression profile and potential biological functions during longan early SE. The qRT-PCR results indicated that DlB3 family members played a crucial role in longan SE and zygotic embryo development. Exogenous treatments of 2,4-D (2,4-dichlorophenoxyacetic acid), NPA (N-1-naphthylphthalamic acid), and PP333 (paclobutrazol) could significantly inhibit the expression of the DlB3 family. Supplementary ABA (abscisic acid), IAA (indole-3-acetic acid), and GA3 (gibberellin) suppressed the expressions of DlLEC2, DlARF16, DlTEM1, DlVAL2, and DlREM40, but DlFUS3, DlARF5, and DlREM9 showed an opposite trend. Furthermore, subcellular localization indicated that DlLEC2 and DlFUS3 were located in the nucleus, suggesting that they played a role in the nucleus. Therefore, DlB3s might be involved in complex plant hormone signal transduction pathways during longan SE and zygotic embryo development.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.T.); (G.Z.); (M.A.); (X.G.); (W.M.); (J.L.); (B.Z.); (Z.L.)
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.T.); (G.Z.); (M.A.); (X.G.); (W.M.); (J.L.); (B.Z.); (Z.L.)
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Park S, Shi A, Meinhardt LW, Mou B. Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa). Sci Rep 2023; 13:21990. [PMID: 38081919 PMCID: PMC10713603 DOI: 10.1038/s41598-023-49245-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) gene family plays vital roles in plants, serving as a key regulator in responses to abiotic stresses. Despite its significance, a comprehensive understanding of this family in lettuce remains incomplete. In this study, we performed a genome-wide search for the AP2/ERF family in lettuce and identified a total of 224 members. The duplication patterns provided evidence that both tandem and segmental duplications contributed to the expansion of this family. Ka/Ks ratio analysis demonstrated that, following duplication events, the genes have been subjected to purifying selection pressure, leading to selective constraints on their protein sequence. This selective pressure provides a dosage benefit against stresses in plants. Additionally, a transcriptome analysis indicated that some duplicated genes gained novel functions, emphasizing the contribution of both dosage effect and functional divergence to the family functionalities. Furthermore, an orthologous relationship study showed that 60% of genes descended from a common ancestor of Rosid and Asterid lineages, 28% from the Asterid ancestor, and 12% evolved in the lettuce lineage, suggesting lineage-specific roles in adaptive evolution. These results provide valuable insights into the evolutionary mechanisms of the AP2/ERF gene family in lettuce, with implications for enhancing abiotic stress tolerance, ultimately contributing to the genetic improvement of lettuce crop production.
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Affiliation(s)
- Sunchung Park
- US Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705, USA.
| | - Ainong Shi
- Horticulture Department, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Lyndel W Meinhardt
- US Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Beiquan Mou
- US Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA
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Jin Y, Zeng L, Xiao M, Feng Y, Gao Z, Wei J. Exploration of the B3 transcription factor superfamily in Aquilaria sinensis reveal their involvement in seed recalcitrance and agarwood formation. PLoS One 2023; 18:e0294358. [PMID: 37972007 PMCID: PMC10653465 DOI: 10.1371/journal.pone.0294358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
The endangered tree species of the Aquilaria genus produce agarwood, a high value material produced only after wounding; however, conservation of Aquilaria seeds is difficult. The B3 transcription factor family has diverse important functions in plant development, especially in seed development, although their functions in other areas, such as stress responses, remain to be revealed. Here germination tests proved that the seeds of A. sinensis were recalcitrant seeds. To provide insights into the B3 superfamily, the members were identified and characterized by bioinformatic approaches and classified by phylogenetic analysis and domain structure. In total, 71 members were identified and classified into four subfamilies. Each subfamily not only had similar domains, but also had conserved motifs in their B3 domains. For the seed-related LAV subfamily, the B3 domain of AsLAV3 was identical to that of AsVALs but lacked a typical zf-CW domain such as VALs. AsLAV5 lacks a typical PHD-L domain present in Arabidopsis VALs. qRT-PCR expression analysis showed that the LEC2 ortholog AsLAV4 was not expressed in seeds. RAVs and REMs induced after wound treatment were also identified. These findings provide insights into the functions of B3 genes and seed recalcitrance of A. sinensis and indicate the role of B3 genes in wound response and agarwood formation.This is the first work to investigate the B3 family in A. sinensis and to provide insights of the molecular mechanism of seed recalcitrance.This will be a valuable guidance for studies of B3 genes in stress responses, secondary metabolite biosynthesis, and seed development.
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Affiliation(s)
- Yue Jin
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Zeng
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & Key Laboratory of State Administration of Traditional Chinese Medicine for Agarwood Sustainable Utilization, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Mengjun Xiao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanan Feng
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhihui Gao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhe Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & Key Laboratory of State Administration of Traditional Chinese Medicine for Agarwood Sustainable Utilization, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
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Yue E, Rong F, Liu Z, Ruan S, Lu T, Qian H. Cadmium induced a non-coding RNA microRNA535 mediates Cd accumulation in rice. J Environ Sci (China) 2023; 130:149-162. [PMID: 37032032 DOI: 10.1016/j.jes.2022.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 06/19/2023]
Abstract
Identifying key regulators related to cadmium (Cd) tolerance and accumulation is the main factor for genetic engineering to improve plants for bioremediation and ensure crop food safety. MicroRNAs (miRNAs), as fine-tuning regulators of genes, participate in various abiotic stress processes. MiR535 is an ancient conserved non-coding small RNA in land plants, positively responding to Cd stress. We investigated the effects of knocking out (mir535) and overexpressing miR535 (mir535 and OE535) under Cd stress in rice plants in this study. The mir535 plants showed better Cd tolerance than wild type (WT), whereas the OE535 showed the opposite effect. Cd accumulated approximately 71.9% and 127% in the roots of mir535 and OE535 plants, respectively, compared to WT, after exposure to 2 µmol/L Cd. In brown rice, the total Cd accumulation of OE535 and mir535 was about 78% greater and 35% lower than WT. When growing in 2 mg/kg Cd of soil, the Cd concentration was significantly lower in mir535 and higher in OE535 than in the WT; afterward, we further revealed the most possible target gene SQUAMOSA promoter binding-like transcription factor 7(SPL7) and it negatively regulates Nramp5 expression, which in turn regulates Cd metabolism. Therefore, the CRISPR/Cas9 technology may be a valuable strategy for creating new rice varieties to ensure food safety.
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Affiliation(s)
- Erkui Yue
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China; Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Institute of Crops, Hangzhou Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fuxi Rong
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhen Liu
- Hainan Institute, Zhejiang University, Hainan 572000, China
| | - Songlin Ruan
- Institute of Crops, Hangzhou Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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9
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Ren C, Wang H, Zhou Z, Jia J, Zhang Q, Liang C, Li W, Zhang Y, Yu G. Genome-wide identification of the B3 gene family in soybean and the response to melatonin under cold stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1091907. [PMID: 36714689 PMCID: PMC9880549 DOI: 10.3389/fpls.2022.1091907] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Melatonin is a multipotent molecule that exists widely in animals and plants and plays an active regulatory role in abiotic stresses. The B3 superfamily is a ubiquitous transcription factor with a B3 functional domain in plants, which can respond temporally to abiotic stresses by activating defense compounds and plant hormones. Despite the fact that the B3 genes have been studied in a variety of plants, their role in soybean is still unknown. METHODS The regulation of melatonin on cold resistance of soybean and the response of B3 genes to cold stress were investigated by measuring biochemical indexes of soybean. Meanwhile, the genome-wide identification of B3 gene family was conducted in soybean, and B3 genes were analyzed based on phylogeny, motifs, gene structure, collinearity, and cis-regulatory elements analysis. RESULTS We found that cold stress-induced oxidative stress in soybean by producing excessive reactive oxygen species. However, exogenous melatonin treatment could increase the content of endogenous melatonin and other hormones, including IAA and ABA, and enhance the antioxidative system, such as POD activity, CAT activity, and GSH/GSSG, to scavenge ROS. Furthermore, the present study first revealed that melatonin could alleviate the response of soybean to cold stress by inducing the expression of B3 genes. In addition, we first identified 145 B3 genes in soybean that were unevenly distributed on 20 chromosomes. The B3 gene family was divided into 4 subgroups based on the phylogeny tree constructed with protein sequence and a variety of plant hormones and stress response cis-elements were discovered in the promoter region of the B3 genes, indicating that the B3 genes were involved in several aspects of the soybean stress response. Transcriptome analysis and results of qRT-PCR revealed that most GmB3 genes could be induced by cold, the expression of which was also regulated by melatonin. We also found that B3 genes responded to cold stress in plants by interacting with other transcription factors. DISCUSSION We found that melatonin regulates the response of soybean to cold stress by regulating the expression of the transcription factor B3 gene, and we identified 145 B3 genes in soybean. These findings further elucidate the potential role of the B3 gene family in soybean to resist low-temperature stress and provide valuable information for soybean functional genomics study.
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Affiliation(s)
- Chunyuan Ren
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Huamei Wang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Zhiheng Zhou
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Jingrui Jia
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Qi Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Changzhi Liang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Wanting Li
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Yuxian Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Gaobo Yu
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
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10
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Nicolas A, Maugarny-Calès A, Adroher B, Chelysheva L, Li Y, Burguet J, Bågman AM, Smit ME, Brady SM, Li Y, Laufs P. De novo stem cell establishment in meristems requires repression of organ boundary cell fate. THE PLANT CELL 2022; 34:4738-4759. [PMID: 36029254 PMCID: PMC9709991 DOI: 10.1093/plcell/koac269] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/24/2022] [Indexed: 05/27/2023]
Abstract
Stem cells play important roles in animal and plant biology, as they sustain morphogenesis and tissue replenishment following aging or injury. In plants, stem cells are embedded in multicellular structures called meristems. The formation of new meristems is essential for the plastic expansion of the highly branched shoot and root systems. In particular, axillary meristems (AMs) that produce lateral shoots arise from the division of boundary domain cells at the leaf base. The CUP-SHAPED COTYLEDON (CUC) genes are major determinants of the boundary domain and are required for AM initiation. However, how AMs get structured and how stem cells become established de novo remain elusive. Here, we show that two NGATHA-LIKE (NGAL) transcription factors, DEVELOPMENT-RELATED PcG TARGET IN THE APEX4 (DPA4)/NGAL3 and SUPPRESSOR OF DA1-1 7 (SOD7)/NGAL2, redundantly repress CUC expression in initiating AMs of Arabidopsis thaliana. Ectopic boundary fate leads to abnormal growth and organization of the AM and prevents de novo stem cell establishment. Floral meristems of the dpa4 sod7 double mutant show a similar delay in de novo stem cell establishment. Altogether, while boundary fate is required for the initiation of AMs, our work reveals how it is later repressed to allow proper meristem establishment and de novo stem cell niche formation.
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Affiliation(s)
- Antoine Nicolas
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
- Université Paris-Saclay, Orsay, 91405, France
| | - Aude Maugarny-Calès
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
- Université Paris-Saclay, Orsay, 91405, France
| | - Bernard Adroher
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Liudmila Chelysheva
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Yu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jasmine Burguet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Margot E Smit
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Patrick Laufs
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
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11
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Allen M, Hulse-Kemp AM, Storm AR. Gossypium hirsutum gene of unknown function, Gohir.A02G044702.1, encodes a potential B3 Transcription Factor of the REM subfamily. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000574. [PMID: 35996691 PMCID: PMC9391945 DOI: 10.17912/micropub.biology.000574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/28/2022] [Accepted: 07/26/2022] [Indexed: 11/06/2022]
Abstract
A gene of unknown function, Gohir.A02G044702.1, identified in Gossypium hirsutum was studied using sequence and structure bioinformatic tools. The encoded protein (UniProt A0A1U8MGX4) was predicted to localize to the nucleus, was found to retain the B3 transcription factor domain with conserved DNA-binding residues and to most closely cluster with REM subfamily members of B3-domain containing proteins.
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Affiliation(s)
- Michael Allen
- Department of Biology, Western Carolina University, Cullowhee, NC
| | - Amanda M. Hulse-Kemp
- Genomics and Bioinformatics Research Unit, The Agricultural Research Service of U.S. Department of Agriculture, Raleigh, NC
,
Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC
,
Correspondence to: Amanda M. Hulse-Kemp (
)
| | - Amanda R. Storm
- Department of Biology, Western Carolina University, Cullowhee, NC
,
Correspondence to: Amanda R. Storm (
)
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12
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Zhang C, Wang X, Li H, Wang J, Zeng Q, Huang W, Huang H, Xie Y, Yu S, Kan Q, Wang Q, Cheng Y. GLRaV-2 protein p24 suppresses host defenses by interaction with a RAV transcription factor from grapevine. PLANT PHYSIOLOGY 2022; 189:1848-1865. [PMID: 35485966 PMCID: PMC9237672 DOI: 10.1093/plphys/kiac181] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/24/2022] [Indexed: 05/27/2023]
Abstract
Grapevine leafroll-associated virus 2 (GLRaV-2) is a prevalent virus associated with grapevine leafroll disease, but the molecular mechanism underlying GLRaV-2 infection is largely unclear. Here, we report that 24-kDa protein (p24), an RNA-silencing suppressor (RSS) encoded by GLRaV-2, promotes GLRaV-2 accumulation via interaction with the B3 DNA-binding domain of grapevine (Vitis vinifera) RELATED TO ABSCISIC ACID INSENSITIVE3/VIVIPAROUS1 (VvRAV1), a transcription factor belonging to the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) superfamily. Salicylic acid-inducible VvRAV1 positively regulates the grapevine pathogenesis-related protein 1 (VvPR1) gene by directly binding its promoter, indicating that VvRAV1 may function in the regulation of host basal defense responses. p24 hijacks VvRAV1 to the cytoplasm and employs the protein to sequester 21-nt double-stranded siRNA together, thereby enhancing its own RSS activity. Moreover, p24 enters the nucleus via interaction with VvRAV1 and weakens the latter's binding affinity to the VvPR1 promoter, leading to decreased expression of VvPR1. Our results provide a mechanism by which a viral RSS interferes with both the antiviral RNA silencing and the AP2/ERF-mediated defense responses via the targeting of one specific host factor.
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Affiliation(s)
| | - Xianyou Wang
- Department of Pomology/Lab of Stress Physiology and Molecular Biology for Tree Fruits, Key Lab of Beijing Municipality, China Agricultural University, Beijing 100193, China
| | - Hanwei Li
- Department of Pomology/Lab of Stress Physiology and Molecular Biology for Tree Fruits, Key Lab of Beijing Municipality, China Agricultural University, Beijing 100193, China
| | - Jinying Wang
- Department of Pomology/Lab of Stress Physiology and Molecular Biology for Tree Fruits, Key Lab of Beijing Municipality, China Agricultural University, Beijing 100193, China
| | - Qi Zeng
- Department of Pomology/Lab of Stress Physiology and Molecular Biology for Tree Fruits, Key Lab of Beijing Municipality, China Agricultural University, Beijing 100193, China
| | - Wenting Huang
- Department of Pomology/Lab of Stress Physiology and Molecular Biology for Tree Fruits, Key Lab of Beijing Municipality, China Agricultural University, Beijing 100193, China
| | - Haoqiang Huang
- Department of Pomology/Lab of Stress Physiology and Molecular Biology for Tree Fruits, Key Lab of Beijing Municipality, China Agricultural University, Beijing 100193, China
| | - Yinshuai Xie
- Department of Pomology/Lab of Stress Physiology and Molecular Biology for Tree Fruits, Key Lab of Beijing Municipality, China Agricultural University, Beijing 100193, China
| | - Shangzhen Yu
- Department of Pomology/Lab of Stress Physiology and Molecular Biology for Tree Fruits, Key Lab of Beijing Municipality, China Agricultural University, Beijing 100193, China
| | - Qing Kan
- Department of Pomology/Lab of Stress Physiology and Molecular Biology for Tree Fruits, Key Lab of Beijing Municipality, China Agricultural University, Beijing 100193, China
| | - Qi Wang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
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13
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Abstract
Winter wheat growing areas in the Northern hemisphere are regularly exposed to heavy frost. Due to the negative impact on yield, the identification of genetic factors controlling frost tolerance (FroT) and development of tools for breeding is of prime importance. Here, we detected QTL associated with FroT by genome wide association studies (GWAS) using a diverse panel of 276 winter wheat genotypes that was phenotyped at five locations in Germany and Russia in three years. The panel was genotyped using the 90 K iSelect array and SNPs in FroT candidate genes. In total, 17,566 SNPs were used for GWAS resulting in the identification of 53 markers significantly associated (LOD ≥ 4) to FroT, corresponding to 23 QTL regions located on 11 chromosomes (1A, 1B, 2A, 2B, 2D, 3A, 3D, 4A, 5A, 5B and 7D). The strongest QTL effect confirmed the importance of chromosome 5A for FroT. In addition, to our best knowledge, eight FroT QTLs were discovered for the first time in this study comprising one QTL on chromosomes 3A, 3D, 4A, 7D and two on chromosomes 1B and 2D. Identification of novel FroT candidate genes will help to better understand the FroT mechanism in wheat and to develop more effective combating strategies.
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14
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Wang WB, Ao T, Zhang YY, Wu D, Xu W, Han B, Liu AZ. Genome-wide analysis of the B3 transcription factors reveals that RcABI3/VP1 subfamily plays important roles in seed development and oil storage in castor bean ( Ricinus communis). PLANT DIVERSITY 2022; 44:201-212. [PMID: 35505987 PMCID: PMC9043308 DOI: 10.1016/j.pld.2021.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 06/14/2023]
Abstract
The B3 transcription factors (TFs) in plants play vital roles in numerous biological processes. Although B3 genes have been broadly identified in many plants, little is known about their potential functions in mediating seed development and material accumulation. Castor bean (Ricinus communis) is a non-edible oilseed crop considered an ideal model system for seed biology research. Here, we identified a total of 61 B3 genes in the castor bean genome, which can be classified into five subfamilies, including ABI3/VP1, HSI, ARF, RAV and REM. The expression profiles revealed that RcABI3/VP1 subfamily genes are significantly up-regulated in the middle and later stages of seed development, indicating that these genes may be associated with the accumulation of storage oils. Furthermore, through yeast one-hybrid and tobacco transient expression assays, we detected that ABI3/VP1 subfamily member RcLEC2 directly regulates the transcription of RcOleosin2, which encodes an oil-body structural protein. This finding suggests that RcLEC2, as a seed-specific TF, may be involved in the regulation of storage materials accumulation. This study provides novel insights into the potential roles and molecular basis of B3 family proteins in seed development and material accumulation.
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Affiliation(s)
- Wen-Bo Wang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Ao
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Mengla, 666303, China
| | - Yan-Yu Zhang
- Northwest A&F University, Yangling, 712100, China
| | - Di Wu
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Xu
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
| | - Bing Han
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650204, China
| | - Ai-Zhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), Southwest Forestry University, Kunming, 650224, China
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15
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Kabir N, Lin H, Kong X, Liu L, Qanmber G, Wang Y, Zhang L, Sun Z, Yang Z, Yu Y, Zhao N. Identification, evolutionary analysis and functional diversification of RAV gene family in cotton (G. hirsutum L.). PLANTA 2021; 255:14. [PMID: 34862931 DOI: 10.1007/s00425-021-03782-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Genome wide analysis, expression pattern analysis, and functional characterization of RAV genes highlight their roles in roots, stem development and hormonal response. RAV (Related to ABI3 and VP1) gene family members have been involved in tissues/organs growth and hormone signaling in various plant species. Here, we identified 247 RAVs from 12 different species with 33 RAV genes from G. hirsutum. Phylogenetic analysis classified RAV genes into four distinct groups. Analysis of gene structure showed that most GhRAVs lack introns. Motif distribution pattern and protein sequence logos indicated that GhRAV genes were highly conserved during the process of evolution. Promotor cis-acting elements revealed that promotor regions of GhRAV genes encode numerous elements related to plant growth, abiotic stresses and phytohormones. Chromosomal location information showed uneven distribution of 33 GhRAV genes on different chromosomes. Collinearity analysis identified 628 and 52 orthologous/ paralogous gene pairs in G. hirsutum and G. barbadense, respectively. Ka/Ks values indicated that GhRAV and GbRAV genes underwent strong purifying selection pressure. Selecton model and codon model selection revealed that GhRAV amino acids were under purifying selection and adaptive evolution exists among GhRAV proteins. Three dimensional structure of GhRAVs indicated the presence of numerous alpha helix and beta-barrels. Expression level revealed that some GhRAV genes exhibited high expression in roots (GhRAV3, GhRAV4, GhRAV11, GhRAV18, GhRAV20 and GhRAV30) and stem (GhRAV3 and GhRAV18), indicating their potential role in roots and stem development. GhRAV genes can be regulated by phytohormonal stresses (BL, JA and IAA). Our study provides a reference for future studies related to the functional analysis of GhRAVs in cotton.
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Affiliation(s)
- Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hai Lin
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Xianhui Kong
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Le Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - YuXuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lian Zhang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100122, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Yu Yu
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
| | - Na Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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16
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Li Y, Ng EY, Loh YR, Gea CY, Huang Q, Li Q, Kang C. Secondary structures, dynamics, and DNA binding of the homeodomain of human SIX1. J Pept Sci 2021; 28:e3376. [PMID: 34713534 DOI: 10.1002/psc.3376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 11/09/2022]
Abstract
Human sine oculis homeobox homolog (SIX) 1 contains a homeodomain (HD), which is important for binding to DNA. In this study, we carried out structural studies on the HD of human SIX1 using nuclear magnetic resonance (NMR) spectroscopy. Its secondary structures and dynamics in solution were explored. HD is well-structured in solution, and our study shows that it contains three α-helices. Dynamics study indicates that the N- and C-terminal residues of HD are flexible in solution. HD of human SIX1 exhibits molecular interactions with a short double-strand DNA sequence evidenced by the 1 H-15 N-heteronuclear single quantum correlation (HSQC) and 19 F-NMR experiments. Our current study provides structural information for HD of human SIX1. Further studies indicate that this construct can be utilized to study SIX1 and DNA interactions.
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Affiliation(s)
- Yan Li
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Elizabeth YiHui Ng
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ying Ru Loh
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chong Yu Gea
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Qiwei Huang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore
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17
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Smolikova G, Strygina K, Krylova E, Leonova T, Frolov A, Khlestkina E, Medvedev S. Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects. PLANTS (BASEL, SWITZERLAND) 2021; 10:1884. [PMID: 34579418 PMCID: PMC8467299 DOI: 10.3390/plants10091884] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 01/21/2023]
Abstract
Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network-the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes-POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ksenia Strygina
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Ekaterina Krylova
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; (T.L.); (A.F.)
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; (T.L.); (A.F.)
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Khlestkina
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
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18
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Liu M, Li Y, Ma Y, Zhao Q, Stiller J, Feng Q, Tian Q, Liu D, Han B, Liu C. The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:443-456. [PMID: 31314154 PMCID: PMC6953193 DOI: 10.1111/pbi.13210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 07/13/2019] [Indexed: 05/06/2023]
Abstract
Wild barley (Hordeum spontaneum) is the progenitor of cultivated barley (Hordeum vulgare) and provides a rich source of genetic variations for barley improvement. Currently, the genome sequences of wild barley and its differences with cultivated barley remain unclear. In this study, we report a high-quality draft assembly of wild barley accession (AWCS276; henceforth named as WB1), which consists of 4.28 Gb genome and 36 395 high-confidence protein-coding genes. BUSCO analysis revealed that the assembly included full lengths of 95.3% of the 956 single-copy plant genes, illustrating that the gene-containing regions have been well assembled. By comparing with the genome of the cultivated genotype Morex, it is inferred that the WB1 genome contains more genes involved in resistance and tolerance to biotic and abiotic stresses. The presence of the numerous WB1-specific genes indicates that, in addition to enhance allele diversity for genes already existing in the cultigen, exploiting the wild barley taxon in breeding should also allow the incorporation of novel genes. Furthermore, high levels of genetic variation in the pericentromeric regions were detected in chromosomes 3H and 5H between the wild and cultivated genotypes, which may be the results of domestication. This H. spontaneum draft genome assembly will help to accelerate wild barley research and be an invaluable resource for barley improvement and comparative genomics research.
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Affiliation(s)
- Miao Liu
- CSIRO Agriculture and FoodSt LuciaQldAustralia
- Crop Research InstituteSichuan Academy of Agricultural SciencesJinjiang District, ChengduChina
- Triticeae Research InstituteSichuan Agricultural UniversityWenjiang, ChengduChina
| | - Yan Li
- National Center for Gene ResearchChinese Academy of SciencesShanghaiChina
| | - Yanling Ma
- CSIRO Agriculture and FoodSt LuciaQldAustralia
- Institute of Crop SciencesChinese Academy of Agricultural SciencesHaidian District, BeijingChina
| | - Qiang Zhao
- National Center for Gene ResearchChinese Academy of SciencesShanghaiChina
| | | | - Qi Feng
- National Center for Gene ResearchChinese Academy of SciencesShanghaiChina
| | - Qilin Tian
- National Center for Gene ResearchChinese Academy of SciencesShanghaiChina
| | - Dengcai Liu
- Triticeae Research InstituteSichuan Agricultural UniversityWenjiang, ChengduChina
| | - Bin Han
- National Center for Gene ResearchChinese Academy of SciencesShanghaiChina
| | - Chunji Liu
- CSIRO Agriculture and FoodSt LuciaQldAustralia
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19
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Wang J, Wang R, Mao X, Li L, Chang X, Zhang X, Jing R. TaARF4 genes are linked to root growth and plant height in wheat. ANNALS OF BOTANY 2019; 124:903-915. [PMID: 30590478 PMCID: PMC6881231 DOI: 10.1093/aob/mcy218] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 12/08/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Auxin response factors (ARFs) as transcription activators or repressors have important roles in plant growth and development, but knowledge about the functions of wheat ARF members is limited. A novel ARF member in wheat (Triticum aestivum), TaARF4, was identified, and its protein function, haplotype geographic distribution and allelic frequencies were investigated. METHODS Tissue expression of TaARF4 was analysed by real-time PCR. Sub-cellular localization was performed using green fluorescent protein (GFP)-tagged TaARF4. Ectopic expression of TaARF4-A in arabidopsis was used to study its functions. Electrophoretic mobility shift assays (EMSAs), chromatin immunoprecipitation (ChIP) analyses and gene expression were performed to detect TaARF4 target genes. A dCAPS (derived cleaved amplified polymorphic sequence) marker developed from TaARF4-B was used to identify haplotypes and association analysis between haplotypes and agronomic traits. KEY RESULTS TaARF4-A was constitutively expressed and its protein was localized in the nucleus. Ectopic expression of TaARF4-A in arabidopsis caused abscisic acid (ABA) insensitivity, shorter primary root length and reduced plant height (PH). Through expression studies and ChIP assays, TaARF4-A was shown to regulate HB33 expression which negatively responded to ABA, and reduced root length and plant height by repressing expression of Gretchen Hagen 3 (GH3) genes that in turn upregulated indole-3-acetic acid content in arabidopsis. Association analysis showed that TaARF4-B was strongly associated with PH and root depth at the tillering, jointing and grain fill stages. Geographic distribution and allelic frequencies suggested that TaARF4-B haplotypes were selected in Chinese wheat breeding programmes. An amino acid change (threonine to alanine) at position 158 might be the cause of phenotype variation in accessions possessing different haplotypes. CONCLUSIONS Ectopic expression and association analysis indicate that TaARF4 may be involved in root length and plant height determination in wheat. This work is helpful for selection of wheat genotypes with optimal root and plant architecture.
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Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruitong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- For correspondence. E-mail
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20
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Baison J, Vidalis A, Zhou L, Chen Z, Li Z, Sillanpää MJ, Bernhardsson C, Scofield D, Forsberg N, Grahn T, Olsson L, Karlsson B, Wu H, Ingvarsson PK, Lundqvist S, Niittylä T, García‐Gil MR. Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:83-100. [PMID: 31166032 PMCID: PMC6852177 DOI: 10.1111/tpj.14429] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/16/2019] [Accepted: 05/20/2019] [Indexed: 05/26/2023]
Abstract
Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome-wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO-based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.
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Affiliation(s)
- John Baison
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Amaryllis Vidalis
- Section of Population Epigenetics and EpigenomicsCentre of Life and Food Sciences WeihenstephanTechnische Universität MünchenLichtenbergstr. 2aMünchen85748Germany
| | - Linghua Zhou
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Zhi‐Qiang Chen
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Zitong Li
- Ecological Genetics Research UnitDepartment of BiosciencesUniversity of HelsinkiP.O. Box 65FI‐00014HelsinkiFinland
| | - Mikko J. Sillanpää
- Department of Mathematical SciencesBiocenter OuluUniversity of OuluPentti Kaiteran katu 1OuluFinland
| | - Carolina Bernhardsson
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
- Department of Ecology and Environmental ScienceUmeå UniversityLinnaeus väg 4-6Umeå907 36Sweden
| | - Douglas Scofield
- Uppsala Multidisciplinary Centre for Advanced Computational ScienceUppsala UniversityLägerhyddsvägen 2Uppsala752 37Sweden
| | - Nils Forsberg
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Thomas Grahn
- RISE BioeconomyDrottning Kristinas väg 61SE‐114 86StockholmSweden
| | - Lars Olsson
- RISE BioeconomyDrottning Kristinas väg 61SE‐114 86StockholmSweden
| | | | - Harry Wu
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Pär K. Ingvarsson
- Department of Ecology and Environmental ScienceUmeå UniversityLinnaeus väg 4-6Umeå907 36Sweden
- Department of Ecology and Genetics: Evolutionary BiologyUppsala UniversityKåbovägen 4Uppsala752 36Sweden
| | - Sven‐Olof Lundqvist
- RISE BioeconomyDrottning Kristinas väg 61SE‐114 86StockholmSweden
- IICRosenlundsgatan 48BSE‐118 63StockholmSweden
| | - Totte Niittylä
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - M Rosario García‐Gil
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
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21
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Tao Z, Hu H, Luo X, Jia B, Du J, He Y. Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis. NATURE PLANTS 2019; 5:424-435. [PMID: 30962525 DOI: 10.1038/s41477-019-0402-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/06/2019] [Indexed: 05/02/2023]
Abstract
Some overwintering plants acquire competence to flower, after experiencing prolonged cold in winter, through a process termed vernalization. In the crucifer plant Arabidopsis thaliana, prolonged cold induces chromatin-mediated silencing of the potent floral repressor FLOWERING LOCUS C (FLC) by Polycomb proteins. This vernalized state is epigenetically maintained or 'memorized' in warm rendering plants competent to flower in spring, but is reset in the next generation. Here, we show that in early embryogenesis, two homologous B3 domain transcription factors LEAFY COTYLEDON 2 (LEC2) and FUSCA3 (FUS3) compete against two repressive B3-containing epigenome readers and Polycomb partners known as VAL1 and VAL2 for the cis-regulatory cold memory element (CME) of FLC to disrupt Polycomb silencing. Consistently, crystal structures of B3-CME complexes show that B3FUS3, B3LEC2 and B3VAL1 employ a nearly identical binding interface for CME. We further found that LEC2 and FUS3 recruit the scaffold protein FRIGIDA in association with active chromatin modifiers to establish an active chromatin state at FLC, which results in resetting of the silenced FLC to active and erasing the epigenetic parental memory of winter cold in early embryos. Following embryo development, LEC2 and FUS3 are developmentally silenced throughout post-embryonic stages, enabling VALs to bind to the CME again at seedling stages at which plants experience winter cold. Our findings illustrate how overwintering crucifer annuals or biennials in temperate climates employ a subfamily of B3 domain proteins to switch on, off and on again the expression of a key flowering gene in the embryo-to-plant-to-embryo cycle, and thus to synchronize growth and development with seasonal temperature changes in their life cycles.
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Affiliation(s)
- Zeng Tao
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hongmiao Hu
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Luo
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Bei Jia
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jiamu Du
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China.
| | - Yuehui He
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China.
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China.
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22
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Tavares EQP, De Souza AP, Romim GH, Grandis A, Plasencia A, Gaiarsa JW, Grima-Pettenati J, de Setta N, Van Sluys MA, Buckeridge MS. The control of endopolygalacturonase expression by the sugarcane RAV transcription factor during aerenchyma formation. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:497-506. [PMID: 30605523 PMCID: PMC6322575 DOI: 10.1093/jxb/ery362] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 10/10/2018] [Indexed: 05/22/2023]
Abstract
The development of lysigenous aerenchyma starts with cell expansion and degradation of pectin from the middle lamella, leading to cell wall modification, and culminating with cell separation. Here we report that nutritional starvation of sugarcane induced gene expression along sections of the first 5 cm of the root and between treatments. We selected two candidate genes: a RAV transcription factor, from the ethylene response factors superfamily, and an endopolygalacturonase (EPG), a glycosyl hydrolase related to homogalacturonan hydrolysis from the middle lamella. epg1 and rav1 transcriptional patterns suggest they are essential genes at the initial steps of pectin degradation during aerenchyma development in sugarcane. Due to the high complexity of the sugarcane genome, rav1 and epg1 were sequenced from 17 bacterial artificial chromosome clones containing hom(e)ologous genomic regions, and the sequences were compared with those of Sorghum bicolor. We used one hom(e)olog sequence from each gene for transactivation assays in tobacco. rav1 was shown to bind to the epg1 promoter, repressing β-glucuronidase activity. RAV repression upon epg1 transcription is the first reported link between ethylene regulation and pectin hydrolysis during aerenchyma formation. Our findings may help to elucidate cell wall degradation in sugarcane and therefore contribute to second-generation bioethanol production.
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Affiliation(s)
- Eveline Q P Tavares
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Amanda P De Souza
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Grayce H Romim
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Adriana Grandis
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Anna Plasencia
- LRSV, Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Paul Sabatier Toulouse III/CNRS Castanet-Tolosan, France
| | - Jonas W Gaiarsa
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
- Tau Bioinformatics, São Paulo, SP, Brazil
| | - Jacqueline Grima-Pettenati
- LRSV, Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Paul Sabatier Toulouse III/CNRS Castanet-Tolosan, France
| | - Nathalia de Setta
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
- Centro de Ciências Naturais e Humanas. Universidade Federal do ABC, São André, SP, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Marcos S Buckeridge
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
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23
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Chen WF, Wei XB, Rety S, Huang LY, Liu NN, Dou SX, Xi XG. Structural analysis reveals a "molecular calipers" mechanism for a LATERAL ORGAN BOUNDARIES DOMAIN transcription factor protein from wheat. J Biol Chem 2018; 294:142-156. [PMID: 30425099 DOI: 10.1074/jbc.ra118.003956] [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: 05/16/2018] [Revised: 11/10/2018] [Indexed: 01/13/2023] Open
Abstract
LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a family of plant-specific transcription factors harboring a conserved Lateral Organ Boundaries (LOB) domain, are regulators of plant organ development. Recent studies have unraveled additional pivotal roles of the LBD protein family beyond defining lateral organ boundaries, such as pollen development and nitrogen metabolism. The structural basis for the molecular network of LBD-dependent processes remains to be deciphered. Here, we solved the first structure of the homodimeric LOB domain of Ramosa2 from wheat (TtRa2LD) to 1.9 Å resolution. Our crystal structure reveals structural features shared with other zinc-finger transcriptional factors, as well as some features unique to LBD proteins. Formation of the TtRa2LD homodimer relied on hydrophobic interactions of its coiled-coil motifs. Several specific motifs/domains of the LBD protein were also involved in maintaining its overall conformation. The intricate assembly within and between the monomers determined the precise spatial configuration of the two zinc fingers that recognize palindromic DNA sequences. Biochemical, molecular modeling, and small-angle X-ray scattering experiments indicated that dimerization is important for cooperative DNA binding and discrimination of palindromic DNA through a molecular calipers mechanism. Along with previously published data, this study enables us to establish an atomic-scale mechanistic model for LBD proteins as transcriptional regulators in plants.
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Affiliation(s)
- Wei-Fei Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiao-Bin Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, 467044, China
| | - Stephane Rety
- University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France.
| | - Ling-Yun Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, 61 Avenue du Président Wilson, F-94235 Cachan, France.
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24
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Sasnauskas G, Manakova E, Lapėnas K, Kauneckaitė K, Siksnys V. DNA recognition by Arabidopsis transcription factors ABI3 and NGA1. FEBS J 2018; 285:4041-4059. [PMID: 30183137 DOI: 10.1111/febs.14649] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/24/2018] [Accepted: 08/31/2018] [Indexed: 01/31/2023]
Abstract
B3 transcription factors constitute a large plant-specific protein superfamily, which plays a central role in plant life. Family members are characterized by the presence of B3 DNA-binding domains (DBDs). To date, only a few B3 DBDs were structurally characterized; therefore, the DNA recognition mechanism of other family members remains to be elucidated. Here, we analyze DNA recognition mechanism of two structurally uncharacterized B3 transcription factors, ABI3 and NGA1. Guided by the structure of the DNA-bound B3 domain of Arabidopsis transcriptional repressor VAL1, we have performed mutational analysis of the ABI3 B3 domain. We demonstrate that both VAL1-B3 and ABI3-B3 recognize the Sph/RY DNA sequence 5'-TGCATG-3' via a conserved set of base-specific contacts. We have also solved a 1.8 Å apo-structure of NGA1-B3, DBD of Arabidopsis transcription factor NGA1. We show that NGA1-B3, like the structurally related RAV1-B3 domain, is specific for the 5'-CACCTG-3' DNA sequence, albeit tolerates single base pair substitutions at the 5'-terminal half of the recognition site. Employing distance-dependent fluorophore quenching, we show that NGA1-B3 binds the asymmetric recognition site in a defined orientation, with the 'N-arm' and 'C-arm' structural elements interacting with the 5'- and 3'-terminal nucleotides of the 5'-CACCTG-3' sequence, respectively. Mutational analysis guided by the model of DNA-bound NGA1-B3 helped us identify NGA1-B3 residues involved in base-specific and DNA backbone contacts, providing new insights into the mechanism of DNA recognition by plant B3 domains of RAV and REM families. DATABASES: RCSB Protein Data Bank, accession number 5OS9.
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Affiliation(s)
| | - Elena Manakova
- Institute of Biotechnology, Vilnius University, Lithuania
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25
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Hosford CJ, Chappie JS. The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding. J Biol Chem 2018; 293:11758-11771. [PMID: 29895618 PMCID: PMC6066307 DOI: 10.1074/jbc.ra118.001888] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/04/2018] [Indexed: 12/11/2022] Open
Abstract
Restriction modification systems consist of an endonuclease that cleaves foreign DNA site-specifically and an associated methyltransferase that protects the corresponding target site in the host genome. Modification-dependent restriction systems, in contrast, specifically recognize and cleave methylated and/or glucosylated DNA. The LlaJI restriction system contains two 5-methylcytosine (5mC) methyltransferases (LlaJI.M1 and LlaJI.M2) and two restriction proteins (LlaJI.R1 and LlaJI.R2). LlaJI.R1 and LlaJI.R2 are homologs of McrB and McrC, respectively, which in Escherichia coli function together as a modification-dependent restriction complex specific for 5mC-containing DNA. Lactococcus lactis LlaJI.R1 binds DNA site-specifically, suggesting that the LlaJI system uses a different mode of substrate recognition. Here we present the structure of the N-terminal DNA-binding domain of Helicobacter pylori LlaJI.R1 at 1.97-Å resolution, which adopts a B3 domain fold. Structural comparison to B3 domains in plant transcription factors and other restriction enzymes identifies key recognition motifs responsible for site-specific DNA binding. Moreover, biochemistry and structural modeling provide a rationale for how H. pylori LlaJI.R1 may bind a target site that differs from the 5-bp sequence recognized by other LlaJI homologs and identify residues critical for this recognition activity. These findings underscore the inherent structural plasticity of B3 domains, allowing recognition of a variety of substrates using the same structural core.
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Affiliation(s)
- Christopher J Hosford
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Joshua S Chappie
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
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26
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Chen N, Veerappan V, Abdelmageed H, Kang M, Allen RD. HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis. THE PLANT CELL 2018; 30:600-619. [PMID: 29475938 PMCID: PMC5894832 DOI: 10.1105/tpc.17.00655] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/30/2018] [Accepted: 02/20/2018] [Indexed: 05/18/2023]
Abstract
Gene expression during seed development in Arabidopsis thaliana is controlled by transcription factors including LEAFY COTYLEDON1 (LEC1) and LEC2, ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), known as LAFL proteins, and AGAMOUS-LIKE15 (AGL15). The transition from seed maturation to germination and seedling growth requires the transcriptional silencing of these seed maturation-specific factors leading to downregulation of structural genes including those that encode seed storage proteins, oleosins, and dehydrins. During seed germination and vegetative growth, B3-domain protein HSI2/VAL1 is required for the transcriptional silencing of LAFL genes. Here, we report chromatin immunoprecipitation analysis indicating that HSI2/VAL1 binds to the upstream sequences of the AGL15 gene but not at LEC1, ABI3, FUS3, or LEC2 loci. Functional analysis indicates that the HSI2/VAL1 B3 domain interacts with two RY elements upstream of the AGL15 coding region and at least one of them is required for HSI2/VAL1-dependent AGL15 repression. Expression analysis of the major seed maturation regulatory genes LEC1, ABI3, FUS3, and LEC2 in different genetic backgrounds demonstrates that HSI2/VAL1 is epistatic to AGL15 and represses the seed maturation regulatory program through downregulation of AGL15 by deposition of H3K27me3 at this locus. This hypothesis is further supported by results that show that HSI2/VAL1 physically interacts with the Polycomb Repressive Complex 2 component protein MSI1, which is also enriched at the AGL15 locus.
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Affiliation(s)
- Naichong Chen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74074
| | - Vijaykumar Veerappan
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
- Department of Biology, Eastern Connecticut State University, Willimantic, Connecticut 06226
| | - Haggag Abdelmageed
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
- Department of Agricultural Botany, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Miyoung Kang
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74074
| | - Randy D Allen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74074
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Boulard C, Fatihi A, Lepiniec L, Dubreucq B. Regulation and evolution of the interaction of the seed B3 transcription factors with NF-Y subunits. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1069-1078. [PMID: 28866096 DOI: 10.1016/j.bbagrm.2017.08.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 12/14/2022]
Abstract
The LAFL genes (LEC2, ABI3, FUS3, LEC1) encode transcription factors that regulate different aspects of seed development, from early to late embryogenesis and accumulation of storage compounds. These transcription factors form a complex network, with members able to interact with various other players to control the switch between embryo development and seed maturation and, at a later stage in the plant life cycle, between the mature seed and germination. In this review, we first summarize our current understanding of the role of each member in the network in the light of recent advances regarding their regulation and structure/function relationships. In a second part, we discuss new insights concerning the evolution of the LAFL genes to address the more specific question of the conservation of LEAFY COTYLEDONS 2 in both dicots and monocots and the putative origin of the network. Last we examine the current major limitations to current knowledge and future prospects to improve our understanding of this regulatory network.
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Affiliation(s)
- C Boulard
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, ERL-CNRS, Saclay Plant Sciences (SPS), Université Paris-Saclay, RD10, F-78026 Versailles, France
| | - A Fatihi
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, ERL-CNRS, Saclay Plant Sciences (SPS), Université Paris-Saclay, RD10, F-78026 Versailles, France
| | - L Lepiniec
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, ERL-CNRS, Saclay Plant Sciences (SPS), Université Paris-Saclay, RD10, F-78026 Versailles, France
| | - B Dubreucq
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, ERL-CNRS, Saclay Plant Sciences (SPS), Université Paris-Saclay, RD10, F-78026 Versailles, France.
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Yu LX. Identification of Single-Nucleotide Polymorphic Loci Associated with Biomass Yield under Water Deficit in Alfalfa ( Medicago sativa L.) Using Genome-Wide Sequencing and Association Mapping. FRONTIERS IN PLANT SCIENCE 2017; 8:1152. [PMID: 28706532 PMCID: PMC5489703 DOI: 10.3389/fpls.2017.01152] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/15/2017] [Indexed: 05/08/2023]
Abstract
Alfalfa is a worldwide grown forage crop and is important due to its high biomass production and nutritional value. However, the production of alfalfa is challenged by adverse environmental factors such as drought and other stresses. Developing drought resistance alfalfa is an important breeding target for enhancing alfalfa productivity in arid and semi-arid regions. In the present study, we used genotyping-by-sequencing and genome-wide association to identify marker loci associated with biomass yield under drought in the field in a panel of diverse germplasm of alfalfa. A total of 28 markers at 22 genetic loci were associated with yield under water deficit, whereas only four markers associated with the same trait under well-watered condition. Comparisons of marker-trait associations between water deficit and well-watered conditions showed non-similarity except one. Most of the markers were identical across harvest periods within the treatment, although different levels of significance were found among the three harvests. The loci associated with biomass yield under water deficit located throughout all chromosomes in the alfalfa genome agreed with previous reports. Our results suggest that biomass yield under drought is a complex quantitative trait with polygenic inheritance and may involve a different mechanism compared to that of non-stress. BLAST searches of the flanking sequences of the associated loci against DNA databases revealed several stress-responsive genes linked to the drought resistance loci, including leucine-rich repeat receptor-like kinase, B3 DNA-binding domain protein, translation initiation factor IF2, and phospholipase-like protein. With further investigation, those markers closely linked to drought resistance can be used for MAS to accelerate the development of new alfalfa cultivars with improved resistance to drought and other abiotic stresses.
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Affiliation(s)
- Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction Testing and ResearchProsser, WA, United States
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Ibryashkina EM, Solonin AS, Zakharova MV. Protein NCRII-18: the role of gene fusion in the molecular evolution of restriction endonucleases. FEBS Lett 2017; 591:1702-1711. [DOI: 10.1002/1873-3468.12669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Elena M. Ibryashkina
- FSBIS G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms; Russian Academy of Sciences; Pushchino Moscow Region Russia
| | - Alexander S. Solonin
- FSBIS G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms; Russian Academy of Sciences; Pushchino Moscow Region Russia
| | - Marina V. Zakharova
- FSBIS G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms; Russian Academy of Sciences; Pushchino Moscow Region Russia
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Zhao SP, Xu ZS, Zheng WJ, Zhao W, Wang YX, Yu TF, Chen M, Zhou YB, Min DH, Ma YZ, Chai SC, Zhang XH. Genome-Wide Analysis of the RAV Family in Soybean and Functional Identification of GmRAV-03 Involvement in Salt and Drought Stresses and Exogenous ABA Treatment. FRONTIERS IN PLANT SCIENCE 2017; 8:905. [PMID: 28634481 PMCID: PMC5459925 DOI: 10.3389/fpls.2017.00905] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/15/2017] [Indexed: 05/21/2023]
Abstract
Transcription factors play vital roles in plant growth and in plant responses to abiotic stresses. The RAV transcription factors contain a B3 DNA binding domain and/or an APETALA2 (AP2) DNA binding domain. Although genome-wide analyses of RAV family genes have been performed in several species, little is known about the family in soybean (Glycine max L.). In this study, a total of 13 RAV genes, named as GmRAVs, were identified in the soybean genome. We predicted and analyzed the amino acid compositions, phylogenetic relationships, and folding states of conserved domain sequences of soybean RAV transcription factors. These soybean RAV transcription factors were phylogenetically clustered into three classes based on their amino acid sequences. Subcellular localization analysis revealed that the soybean RAV proteins were located in the nucleus. The expression patterns of 13 RAV genes were analyzed by quantitative real-time PCR. Under drought stresses, the RAV genes expressed diversely, up- or down-regulated. Following NaCl treatments, all RAV genes were down-regulated excepting GmRAV-03 which was up-regulated. Under abscisic acid (ABA) treatment, the expression of all of the soybean RAV genes increased dramatically. These results suggested that the soybean RAV genes may be involved in diverse signaling pathways and may be responsive to abiotic stresses and exogenous ABA. Further analysis indicated that GmRAV-03 could increase the transgenic lines resistance to high salt and drought and result in the transgenic plants insensitive to exogenous ABA. This present study provides valuable information for understanding the classification and putative functions of the RAV transcription factors in soybean.
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Affiliation(s)
- Shu-Ping Zhao
- College of Agronomy/College of Life Sciences, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
| | - Zhao-Shi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
| | - Wei-Jun Zheng
- College of Agronomy/College of Life Sciences, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
| | - Wan Zhao
- College of Agronomy/College of Life Sciences, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
| | - Yan-Xia Wang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Research Center of Wheat Engineering Technology of HebeiShijiazhuang, China
| | - Tai-Fei Yu
- College of Agronomy/College of Life Sciences, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
| | - Yong-Bin Zhou
- College of Agronomy/College of Life Sciences, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
| | - Dong-Hong Min
- College of Agronomy/College of Life Sciences, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
| | - You-Zhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
| | - Shou-Cheng Chai
- College of Agronomy/College of Life Sciences, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
- *Correspondence: Xiao-Hong Zhang, Shou-Cheng Chai,
| | - Xiao-Hong Zhang
- College of Agronomy/College of Life Sciences, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid AreasYangling, China
- *Correspondence: Xiao-Hong Zhang, Shou-Cheng Chai,
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Yuan W, Luo X, Li Z, Yang W, Wang Y, Liu R, Du J, He Y. A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis. Nat Genet 2016; 48:1527-1534. [DOI: 10.1038/ng.3712] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/07/2016] [Indexed: 12/16/2022]
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Baud S, Kelemen Z, Thévenin J, Boulard C, Blanchet S, To A, Payre M, Berger N, Effroy-Cuzzi D, Franco-Zorrilla JM, Godoy M, Solano R, Thevenon E, Parcy F, Lepiniec L, Dubreucq B. Deciphering the Molecular Mechanisms Underpinning the Transcriptional Control of Gene Expression by Master Transcriptional Regulators in Arabidopsis Seed. PLANT PHYSIOLOGY 2016; 171:1099-112. [PMID: 27208266 PMCID: PMC4902591 DOI: 10.1104/pp.16.00034] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/07/2016] [Indexed: 05/20/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), transcriptional control of seed maturation involves three related regulators with a B3 domain, namely LEAFY COTYLEDON2 (LEC2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (ABI3/FUS3/LEC2 [AFLs]). Although genetic analyses have demonstrated partially overlapping functions of these regulators, the underlying molecular mechanisms remained elusive. The results presented here confirmed that the three proteins bind RY DNA elements (with a 5'-CATG-3' core sequence) but with different specificities for flanking nucleotides. In planta as in the moss Physcomitrella patens protoplasts, the presence of RY-like (RYL) elements is necessary but not sufficient for the regulation of the OLEOSIN1 (OLE1) promoter by the B3 AFLs. G box-like domains, located in the vicinity of the RYL elements, also are required for proper activation of the promoter, suggesting that several proteins are involved. Consistent with this idea, LEC2 and ABI3 showed synergistic effects on the activation of the OLE1 promoter. What is more, LEC1 (a homolog of the NF-YB subunit of the CCAAT-binding complex) further enhanced the activation of this target promoter in the presence of LEC2 and ABI3. Finally, recombinant LEC1 and LEC2 proteins produced in Arabidopsis protoplasts could form a ternary complex with NF-YC2 in vitro, providing a molecular explanation for their functional interactions. Taken together, these results allow us to propose a molecular model for the transcriptional regulation of seed genes by the L-AFL proteins, based on the formation of regulatory multiprotein complexes between NF-YBs, which carry a specific aspartate-55 residue, and B3 transcription factors.
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Affiliation(s)
- Sébastien Baud
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Zsolt Kelemen
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Johanne Thévenin
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Céline Boulard
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Sandrine Blanchet
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Alexandra To
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Manon Payre
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Nathalie Berger
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Delphine Effroy-Cuzzi
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Jose Manuel Franco-Zorrilla
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Marta Godoy
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Roberto Solano
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Emmanuel Thevenon
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - François Parcy
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Loïc Lepiniec
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, F-78026 Versailles cedex, France (S.Ba., Z.K., J.T., C.B., A.T., M.P., N.B., D.E.-C., L.L., B.D.);Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5168, Commissariat à l'Energie Atomique/DRF/BIG, Institut National de la Recherche Agronomique Unité Mixte de Recherche 1417, 38054 Grenoble, France (S.Bl., E.T., F.P.); andGenomics Unit (J.M.F.-Z., M.G.) and Plant Molecular Genetics Department (R.S.), Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
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Duan YB, Li J, Qin RY, Xu RF, Li H, Yang YC, Ma H, Li L, Wei PC, Yang JB. Identification of a regulatory element responsible for salt induction of rice OsRAV2 through ex situ and in situ promoter analysis. PLANT MOLECULAR BIOLOGY 2016; 90:49-62. [PMID: 26482477 DOI: 10.1007/s11103-015-0393-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/14/2015] [Indexed: 05/21/2023]
Abstract
Salt is a major environmental stress factor that can affect rice growth and yields. Recent studies suggested that members of the AP2/ERF domain-containing RAV (related to ABI3/VP1) TF family are involved in abiotic stress adaptation. However, the transcriptional response of rice RAV genes (OsRAVs) to salt has not yet been fully characterized. In this study, the expression patterns of all five OsRAVs were examined under salt stress. Only one gene, OsRAV2, was stably induced by high-salinity treatment. Further expression profile analyses indicated that OsRAV2 is transcriptionally regulated by salt, but not KCl, osmotic stress, cold or ABA (abscisic acid) treatment. To elucidate the regulatory mechanism of the stress response at the transcriptional level, we isolated and characterized the promoter region of OsRAV2 (P OsRAV2 ). Transgenic analysis indicated that P OsRAV2 is induced by salt stress but not osmotic stress or ABA treatment. Serial 5' deletions and site-specific mutations in P OsRAV2 revealed that a GT-1 element located at position -664 relative to the putative translation start site is essential for the salt induction of P OsRAV2 . The regulatory function of the GT-1 element in the salt induction of OsRAV2 was verified in situ in plants with targeted mutations generated using the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system. Taken together, our results indicate that the GT-1 element directly controls the salt response of OsRAV2. This study provides a better understanding of the putative functions of OsRAVs and the molecular regulatory mechanisms of plant genes under salt stress.
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Affiliation(s)
- Yong-Bo Duan
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Juan Li
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Rui-Ying Qin
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Rong-Fang Xu
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Hao Li
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Ya-Chun Yang
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Hui Ma
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Li Li
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Peng-Cheng Wei
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
| | - Jian-Bo Yang
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
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Barah P, B N MN, Jayavelu ND, Sowdhamini R, Shameer K, Bones AM. Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses. Nucleic Acids Res 2015; 44:3147-64. [PMID: 26681689 PMCID: PMC4838348 DOI: 10.1093/nar/gkv1463] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 11/28/2015] [Indexed: 11/25/2022] Open
Abstract
Differentially evolved responses to various stress conditions in plants are controlled by complex regulatory circuits of transcriptional activators, and repressors, such as transcription factors (TFs). To understand the general and condition-specific activities of the TFs and their regulatory relationships with the target genes (TGs), we have used a homogeneous stress gene expression dataset generated on ten natural ecotypes of the model plant Arabidopsis thaliana, during five single and six combined stress conditions. Knowledge-based profiles of binding sites for 25 stress-responsive TF families (187 TFs) were generated and tested for their enrichment in the regulatory regions of the associated TGs. Condition-dependent regulatory sub-networks have shed light on the differential utilization of the underlying network topology, by stress-specific regulators and multifunctional regulators. The multifunctional regulators maintain the core stress response processes while the transient regulators confer the specificity to certain conditions. Clustering patterns of transcription factor binding sites (TFBS) have reflected the combinatorial nature of transcriptional regulation, and suggested the putative role of the homotypic clusters of TFBS towards maintaining transcriptional robustness against cis-regulatory mutations to facilitate the preservation of stress response processes. The Gene Ontology enrichment analysis of the TGs reflected sequential regulation of stress response mechanisms in plants.
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Affiliation(s)
- Pankaj Barah
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| | - Mahantesha Naika B N
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK campus, Bangalore 560 065, India
| | - Naresh Doni Jayavelu
- Department of Chemical Engineering, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK campus, Bangalore 560 065, India
| | - Khader Shameer
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK campus, Bangalore 560 065, India
| | - Atle M Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim N-7491, Norway
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Wang Y, Cao L, Zhang Y, Cao C, Liu F, Huang F, Qiu Y, Li R, Lou X. Map-based cloning and characterization of BPH29, a B3 domain-containing recessive gene conferring brown planthopper resistance in rice. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6035-45. [PMID: 26136269 PMCID: PMC4566989 DOI: 10.1093/jxb/erv318] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Rice (Oryza sativa L.) production, essential for global food security, is threatened by the brown planthopper (BPH). The breeding of host-resistant crops is an economical and environmentally friendly strategy for pest control, but few resistance gene resources have thus far been cloned. An indica rice introgression line RBPH54, derived from wild rice Oryza rufipogon, has been identified with sustainable resistance to BPH, which is governed by recessive alleles at two loci. In this study, a map-based cloning approach was used to fine-map one resistance gene locus to a 24kb region on the short arm of chromosome 6. Through genetic analysis and transgenic experiments, BPH29, a resistance gene containing a B3 DNA-binding domain, was cloned. The tissue specificity of BPH29 is restricted to vascular tissue, the location of BPH attack. In response to BPH infestation, RBPH54 activates the salicylic acid signalling pathway and suppresses the jasmonic acid/ethylene-dependent pathway, similar to plant defence responses to biotrophic pathogens. The cloning and characterization of BPH29 provides insights into molecular mechanisms of plant-insect interactions and should facilitate the breeding of rice host-resistant varieties.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Liming Cao
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yuexiong Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Agriculture, Guangxi University, Nanning 530004, China
| | - Changxiang Cao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Agriculture, Guangxi University, Nanning 530004, China
| | - Fengkuan Huang
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yongfu Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Agriculture, Guangxi University, Nanning 530004, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xiaojin Lou
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
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Zhang Y, Du L, Xu R, Cui R, Hao J, Sun C, Li Y. Transcription factors SOD7/NGAL2 and DPA4/NGAL3 act redundantly to regulate seed size by directly repressing KLU expression in Arabidopsis thaliana. THE PLANT CELL 2015; 27:620-32. [PMID: 25783029 PMCID: PMC4558667 DOI: 10.1105/tpc.114.135368] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 02/10/2015] [Accepted: 02/26/2015] [Indexed: 05/18/2023]
Abstract
Although seed size is one of the most important agronomic traits in plants, the genetic and molecular mechanisms that set the final size of seeds are largely unknown. We previously identified the ubiquitin receptor DA1 as a negative regulator of seed size, and the Arabidopsis thaliana da1-1 mutant produces larger seeds than the wild type. Here, we describe a B3 domain transcriptional repressor NGATHA-like protein (NGAL2), encoded by the suppressor of da1-1 (SOD7), which acts maternally to regulate seed size by restricting cell proliferation in the integuments of ovules and developing seeds. Overexpression of SOD7 significantly decreases seed size of wild-type plants, while the simultaneous disruption of SOD7 and its closest homolog DEVELOPMENT-RELATED PcG TARGET IN THE APEX4 (DPA4/NGAL3) increases seed size. Genetic analyses indicate that SOD7 and DPA4 act in a common pathway with the seed size regulator KLU to regulate seed growth, but do so independently of DA1. Further results show that SOD7 directly binds to the promoter of KLUH (KLU) in vitro and in vivo and represses the expression of KLU. Therefore, our findings reveal the genetic and molecular mechanisms of SOD7, DPA4, and KLU in seed size regulation and suggest that they are promising targets for seed size improvement in crops.
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Affiliation(s)
- Yueying Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100039, China
| | - Liang Du
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rongfeng Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianjun Hao
- College of Life and Health Sciences, Northeastern University, Shenyang 110004, China
| | - Caixia Sun
- College of Life and Health Sciences, Northeastern University, Shenyang 110004, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Li XJ, Li M, Zhou Y, Hu S, Hu R, Chen Y, Li XB. Overexpression of cotton RAV1 gene in Arabidopsis confers transgenic plants high salinity and drought sensitivity. PLoS One 2015; 10:e0118056. [PMID: 25710493 PMCID: PMC4340050 DOI: 10.1371/journal.pone.0118056] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/03/2015] [Indexed: 11/18/2022] Open
Abstract
RAV (related to ABI3/VP1) protein containing an AP2 domain in the N-terminal region and a B3 domain in the C-terminal region, which belongs to AP2 transcription factor family, is unique in higher plants. In this study, a gene (GhRAV1) encoding a RAV protein of 357 amino acids was identified in cotton (Gossypium hirsutum). Transient expression analysis of the eGFP:GhRAV1 fusion genes in tobacco (Nicotiana tabacum) epidermal cells revealed that GhRAV1 protein was localized in the cell nucleus. Quantitative RT-PCR analysis indicated that expression of GhRAV1 in cotton is induced by abscisic acid (ABA), NaCl and polyethylene glycol (PEG). Overexpression of GhRAV1 in Arabidopsis resulted in plant sensitive to ABA, NaCl and PEG. With abscisic acid (ABA) treatment, seed germination and green seedling rates of the GhRAV1 transgenic plants were remarkably lower than those of wild type. In the presence of NaCl, the seed germination and seedling growth of the GhRAV1 transgenic lines were inhibited greater than those of wild type. And chlorophyll content and maximum photochemical efficiency of the transgenic plants were significantly lower than those of wild type. Under drought stress, the GhRAV1 transgenic plants displayed more severe wilting than wild type. Furthermore, expressions of the stress-related genes were altered in the GhRAV1 transgenic Arabidopsis plants under high salinity and drought stresses. Collectively, our data suggested that GhRAV1 may be involved in response to high salinity and drought stresses through regulating expressions of the stress-related genes during cotton development.
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Affiliation(s)
- Xiao-Jie Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Mo Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ying Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Shan Hu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Rong Hu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yun Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xue-Bao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
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38
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Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V. Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII. Nucleic Acids Res 2014; 42:14022-30. [PMID: 25429979 PMCID: PMC4267654 DOI: 10.1093/nar/gku1237] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba et al., 2014). Here we present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII REases, and in plant transcription factors. Structural comparison of the B3-like domains of R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII, EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the majority of the contacts to the target site is much longer. The overall structures of R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity, R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to cleave DNA at the target site. The structures we present will help formulate future experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA cleavage by R.NgoAVII and related endonucleases.
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Affiliation(s)
- Giedre Tamulaitiene
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Arunas Silanskas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Saulius Grazulis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Virginijus Siksnys
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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Wakabayashi T, Oh H, Kawaguchi M, Harada K, Sato S, Ikeda H, Setoguchi H. Polymorphisms of E1 and GIGANTEA in wild populations of Lotus japonicus. JOURNAL OF PLANT RESEARCH 2014; 127:651-60. [PMID: 25117507 DOI: 10.1007/s10265-014-0649-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 05/13/2014] [Indexed: 05/21/2023]
Abstract
In plants, timing of flowering is an essential factor that controls the survival rates of descendants. The circadian clock genes E1 and GIGANTEA (GI) play a central role in transmitting signals to flowering locus T (FT) in leguminous plants. Lotus japonicus is a wild Japanese species that ranges from northern Hokkaido to the southern Ryukyus and exhibits a wide range in terms of the time between seeding and first flowering. In this study, we first identified LjGI and analyzed polymorphisms of LjE1 and LjGI among wild populations covering the entire distribution range of this species in Japan. LjGI had a coding sequence (CDS) length of 3495 bp and included 14 exons. The homologies of DNA and amino acid sequences between LjGI and GmGI were 89 and 88% (positive rate was 92%), respectively. LjE1 harbored five nucleic acid changes in a 552 bp CDS, all of which were nonsynonymous; four of the changes were located in the core function area. LjE1 alleles exhibited partial north-south differentiation and non-neutrality. In contrast, the LjGI harbored one synonymous and one nonsynonymous change. Thus, our study suggests that LjE1 may be involved in the control of flowering times, whereas LjGI may be under strong purifying selection.
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Affiliation(s)
- Tomomi Wakabayashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsucho, Sakyo-ku, Kyoto, 606-8501, Japan,
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40
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Matías-Hernández L, Aguilar-Jaramillo AE, Marín-González E, Suárez-López P, Pelaz S. RAV genes: regulation of floral induction and beyond. ANNALS OF BOTANY 2014; 114:1459-70. [PMID: 24812253 PMCID: PMC4204781 DOI: 10.1093/aob/mcu069] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/12/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Transcription factors of the RAV (RELATED TO ABI3 AND VP1) family are plant-specific and possess two DNA-binding domains. In Arabidopsis thaliana, the family comprises six members, including TEMPRANILLO 1 (TEM1) and TEM2. Arabidopsis RAV1 and TEM1 have been shown to bind bipartite DNA sequences, with the consensus motif C(A/C/G)ACA(N)2-8(C/A/T)ACCTG. Through direct binding to DNA, RAV proteins act as transcriptional repressors, probably in complexes with other co-repressors. SCOPE AND CONCLUSIONS In this review, a summary is given of current knowledge of the regulation and function of RAV genes in diverse plant species, paying particular attention to their roles in the control of flowering in arabidopsis. TEM1 and TEM2 delay flowering by repressing the production of two florigenic molecules, FLOWERING LOCUS T (FT) and gibberellins. In this way, TEM1 and TEM2 prevent precocious flowering and postpone floral induction until the plant has accumulated enough reserves or has reached a growth stage that ensures survival of the progeny. Recent results indicate that TEM1 and TEM2 are regulated by genes acting in several flowering pathways, suggesting that TEMs may integrate information from diverse pathways. However, flowering is not the only process controlled by RAV proteins. Family members are involved in other aspects of plant development, such as bud outgrowth in trees and leaf senescence, and possibly in general growth regulation. In addition, they respond to pathogen infections and abiotic stresses, including cold, dehydration, high salinity and osmotic stress.
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Affiliation(s)
- Luis Matías-Hernández
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
| | | | - Esther Marín-González
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
| | - Paula Suárez-López
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain ICREA (Institució Catalana de Recerca i Estudis Avançats), Barcelona, Spain
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41
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Characterization of putative cis-regulatory elements in genes preferentially expressed in Arabidopsis male meiocytes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:708364. [PMID: 25250331 PMCID: PMC4163388 DOI: 10.1155/2014/708364] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/19/2014] [Accepted: 07/20/2014] [Indexed: 11/18/2022]
Abstract
Meiosis is essential for plant reproduction because it is the process during which homologous chromosome pairing, synapsis, and meiotic recombination occur. The meiotic transcriptome is difficult to investigate because of the size of meiocytes and the confines of anther lobes. The recent development of isolation techniques has enabled the characterization of transcriptional profiles in male meiocytes of Arabidopsis. Gene expression in male meiocytes shows unique features. The direct interaction of transcription factors (TFs) with DNA regulatory sequences forms the basis for the specificity of transcriptional regulation. Here, we identified putative cis-regulatory elements (CREs) associated with male meiocyte-expressed genes using in silico tools. The upstream regions (1 kb) of the top 50 genes preferentially expressed in Arabidopsis meiocytes possessed conserved motifs. These motifs are putative binding sites of TFs, some of which share common functions, such as roles in cell division. In combination with cell-type-specific analysis, our findings could be a substantial aid for the identification and experimental verification of the protein-DNA interactions for the specific TFs that drive gene expression in meiocytes.
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42
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Suzuki M, Wu S, Li Q, McCarty DR. Distinct functions of COAR and B3 domains of maize VP1 in induction of ectopic gene expression and plant developmental phenotypes in Arabidopsis. PLANT MOLECULAR BIOLOGY 2014; 85:179-191. [PMID: 24473899 DOI: 10.1007/s11103-014-0177-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/18/2014] [Indexed: 06/03/2023]
Abstract
Arabidopsis ABI3 and maize VP1 are orthologous transcription factors that regulate seed maturation. ABI3 and VP1 have a C-terminal B3 DNA binding domain and a conserved N-terminal co-activator/co-repressor (COAR) domain consisting of A1, B1, B2 sub-domains. The COAR domain mediates abscisic acid signaling via a physical interaction with ABI5-related bZIP proteins. In order to delineate the COAR and B3 domain dependent functions of VP1, we created site directed mutations in the B3 domain that disrupted DNA binding activity and characterized gene regulation by the mutant proteins in transgenic abi3 mutant Arabidopsis plants. In seeds, COAR domain function of VP1 mutants that lacked B3 DNA binding activity was sufficient for complementation of the desiccation intolerant seed phenotype of abi3. Similarly in seedlings, the B3 domain was dispensable for most VP1 induced gene expression and ectopic developmental phenotypes, except for a small subset of the genes that showed B3 dependent regulation. Unexpectedly, over-expression of the DNA-binding deficient VP1-K519R mutant protein caused quantitative changes in floral organ size including elongation of pistils and shortened stamen filaments that resulted in a self-incompatible longistyly flower morphology, a key component of heterostyly type self-incompatibility.
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Affiliation(s)
- Masaharu Suzuki
- PMCB Program, Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA,
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43
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Boer DR, Freire-Rios A, van den Berg WAM, Saaki T, Manfield IW, Kepinski S, López-Vidrieo I, Franco-Zorrilla JM, de Vries SC, Solano R, Weijers D, Coll M. Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors. Cell 2014; 156:577-89. [PMID: 24485461 DOI: 10.1016/j.cell.2013.12.027] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/22/2013] [Accepted: 12/11/2013] [Indexed: 10/25/2022]
Abstract
Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function. Strikingly, DNA-contacting residues are conserved between ARFs, and we discover that monomers have the same intrinsic specificity. ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites. Our data identify the DNA-binding domain as an ARF dimerization domain, suggest that ARF dimers bind complex sites as molecular calipers with ARF-specific spacing preference, and provide an atomic-scale mechanistic model for specificity in auxin response.
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Affiliation(s)
- D Roeland Boer
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain; Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Alejandra Freire-Rios
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Willy A M van den Berg
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Terrens Saaki
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology (IWM) and Centre for Plant Sciences (SK), Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Stefan Kepinski
- Astbury Centre for Structural Molecular Biology (IWM) and Centre for Plant Sciences (SK), Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Irene López-Vidrieo
- Genomics Unit and Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Jose Manuel Franco-Zorrilla
- Genomics Unit and Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Sacco C de Vries
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Roberto Solano
- Genomics Unit and Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands.
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain; Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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Abstract
From mammals to plants, the Polycomb Group (PcG) machinery plays a crucial role in maintaining the repression of genes that are not required in a specific differentiation status. However, the mechanism by which PcG machinery mediates gene repression is still largely unknown in plants. Compared to animals, few PcG proteins have been identified in plants, not only because just some of these proteins are clearly conserved to their animal counterparts, but also because some PcG functions are carried out by plant-specific proteins, most of them as yet uncharacterized. For a long time, the apparent lack of Polycomb Repressive Complex (PRC)1 components in plants was interpreted according to the idea that plants, as sessile organisms, do not need a long-term repression, as they must be able to respond rapidly to environmental signals; however, some PRC1 components have been recently identified, indicating that this may not be the case. Furthermore, new data regarding the recruitment of PcG complexes and maintenance of PcG repression in plants have revealed important differences to what has been reported so far. This review highlights recent progress in plant PcG function, focusing on the role of the putative PRC1 components.
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Affiliation(s)
- Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF), Avenida América Vespucio, 49, Isla de La Cartuja, 41092 Seville, Spain
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Golovenko D, Manakova E, Zakrys L, Zaremba M, Sasnauskas G, Gražulis S, Siksnys V. Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme. Nucleic Acids Res 2014; 42:4113-22. [PMID: 24423868 PMCID: PMC3973309 DOI: 10.1093/nar/gkt1368] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The B3 DNA-binding domains (DBDs) of plant transcription factors (TF) and DBDs of EcoRII and BfiI restriction endonucleases (EcoRII-N and BfiI-C) share a common structural fold, classified as the DNA-binding pseudobarrel. The B3 DBDs in the plant TFs recognize a diverse set of target sequences. The only available co-crystal structure of the B3-like DBD is that of EcoRII-N (recognition sequence 5'-CCTGG-3'). In order to understand the structural and molecular mechanisms of specificity of B3 DBDs, we have solved the crystal structure of BfiI-C (recognition sequence 5'-ACTGGG-3') complexed with 12-bp cognate oligoduplex. Structural comparison of BfiI-C-DNA and EcoRII-N-DNA complexes reveals a conserved DNA-binding mode and a conserved pattern of interactions with the phosphodiester backbone. The determinants of the target specificity are located in the loops that emanate from the conserved structural core. The BfiI-C-DNA structure presented here expands a range of templates for modeling of the DNA-bound complexes of the B3 family of plant TFs.
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Affiliation(s)
- Dmitrij Golovenko
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graičiūno 8, LT-02241, Vilnius, Lithuania
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46
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Peng FY, Weselake RJ. Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1305-19. [PMID: 23377560 DOI: 10.1007/s00122-013-2054-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 01/09/2013] [Indexed: 05/04/2023]
Abstract
The plant-specific B3 superfamily of transcription factors has diverse functions in plant growth and development. Using a genome-wide domain analysis, we identified 92, 187, 58, 90, 81, 55, and 77 B3 transcription factor genes in the sequenced genome of Arabidopsis, Brassica rapa, castor bean (Ricinus communis), cocoa (Theobroma cacao), soybean (Glycine max), maize (Zea mays), and rice (Oryza sativa), respectively. The B3 superfamily has substantially expanded during the evolution in eudicots particularly in Brassicaceae, as compared to monocots in the analysis. We observed domain duplication in some of these B3 proteins, forming more complex domain architectures than currently understood. We found that the length of B3 domains exhibits a large variation, which may affect their exact number of α-helices and β-sheets in the core structure of B3 domains, and possibly have functional implications. Analysis of the public microarray data indicated that most of the B3 gene pairs encoding Arabidopsis-rice orthologs are preferentially expressed in different tissues, suggesting their different roles in these two species. Using ESTs in crops, we identified many B3 genes preferentially expressed in reproductive tissues. In a sequence-based quantitative trait loci analysis in rice and maize, we have found many B3 genes associated with traits such as grain yield, seed weight and number, and protein content. Our results provide a framework for future studies into the function of B3 genes in different phases of plant development, especially the ones related to traits in major crops.
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Affiliation(s)
- Fred Y Peng
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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47
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Yamasaki K, Kigawa T, Seki M, Shinozaki K, Yokoyama S. DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. TRENDS IN PLANT SCIENCE 2013; 18:267-76. [PMID: 23040085 DOI: 10.1016/j.tplants.2012.09.001] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 08/10/2012] [Accepted: 09/04/2012] [Indexed: 05/02/2023]
Abstract
The families of the plant-specific transcription factors (TFs) are defined by their characteristic DNA-binding domains (DBDs), such as AP2/ERF, B3, NAC, SBP, and WRKY. Recently, three-dimensional structures of the DBDs, including those in complexes with DNA, were determined by NMR spectroscopy and X-ray crystallography. In this review we summarize the functional and evolutionary implications arising from structure analyses. The unexpected structural similarity between B3 and the noncatalytic DBD of the restriction endonuclease EcoRII allowed us to build structural models of the B3/DNA complex. Most of the DBDs of plant-specific TFs are likely to have originated from endonucleases associated with transposable elements. After the DBDs have been established in unicellular eukaryotes, they experienced extensive plant-specific expansion, by acquiring new functions.
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Affiliation(s)
- Kazuhiko Yamasaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology-AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
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48
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Kaas Q, Craik DJ. NMR of plant proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:1-34. [PMID: 23611313 DOI: 10.1016/j.pnmrs.2013.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
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49
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King GJ, Chanson AH, McCallum EJ, Ohme-Takagi M, Byriel K, Hill JM, Martin JL, Mylne JS. The Arabidopsis B3 domain protein VERNALIZATION1 (VRN1) is involved in processes essential for development, with structural and mutational studies revealing its DNA-binding surface. J Biol Chem 2013; 288:3198-207. [PMID: 23255593 PMCID: PMC3561541 DOI: 10.1074/jbc.m112.438572] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Indexed: 11/06/2022] Open
Abstract
The B3 DNA-binding domain is a plant-specific domain found throughout the plant kingdom from the alga Chlamydomonas to grasses and flowering plants. Over 100 B3 domain-containing proteins are found in the model plant Arabidopsis thaliana, and one of these is critical for accelerating flowering in response to prolonged cold treatment, an epigenetic process called vernalization. Despite the specific phenotype of genetic vrn1 mutants, the VERNALIZATION1 (VRN1) protein localizes throughout the nucleus and shows sequence-nonspecific binding in vitro. In this work, we used a dominant repressor tag that overcomes genetic redundancy to show that VRN1 is involved in processes beyond vernalization that are essential for Arabidopsis development. To understand its sequence-nonspecific binding, we crystallized VRN1(208-341) and solved its crystal structure to 1.6 Å resolution using selenium/single-wavelength anomalous diffraction methods. The crystallized construct comprises the second VRN1 B3 domain and a preceding region conserved among VRN1 orthologs but absent in other B3 domains. We established the DNA-binding face using NMR and then mutated positively charged residues on this surface with a series of 16 Ala and Glu substitutions, ensuring that the protein fold was not disturbed using heteronuclear single quantum correlation NMR spectra. The triple mutant R249E/R289E/R296E was almost completely incapable of DNA binding in vitro. Thus, we have revealed that although VRN1 is sequence-nonspecific in DNA binding, it has a defined DNA-binding surface.
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Affiliation(s)
| | | | | | - Masaru Ohme-Takagi
- the Bioproduction Research Institute, AIST4, Higashi 1-1-1, Tsukuba City, Ibaraki 305–8562, Japan
| | | | - Justine M. Hill
- the School of Chemistry and Molecular Biosciences, and
- the Centre for Advanced Imaging, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia and
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50
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Iyer LM, Aravind L. ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons. Biol Direct 2012; 7:39. [PMID: 23146749 PMCID: PMC3537659 DOI: 10.1186/1745-6150-7-39] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 10/30/2012] [Indexed: 11/10/2022] Open
Abstract
Members of the Arabidopsis LSH1 and Oryza G1 (ALOG) family of proteins have been shown to function as key developmental regulators in land plants. However, their precise mode of action remains unclear. Using sensitive sequence and structure analysis, we show that the ALOG domains are a distinct version of the N-terminal DNA-binding domain shared by the XerC/D-like, protelomerase, topoisomerase-IA, and Flp tyrosine recombinases. ALOG domains are distinguished by the insertion of an additional zinc ribbon into this DNA-binding domain. In particular, we show that the ALOG domain is derived from the XerC/D-like recombinases of a novel class of DIRS-1-like retroposons. Copies of this element, which have been recently inactivated, are present in several marine metazoan lineages, whereas the stramenopile Ectocarpus, retains an active copy of the same. Thus, we predict that ALOG domains help establish organ identity and differentiation by binding specific DNA sequences and acting as transcription factors or recruiters of repressive chromatin. They are also found in certain plant defense proteins, where they are predicted to function as DNA sensors. The evolutionary history of the ALOG domain represents a unique instance of a domain, otherwise exclusively found in retroelements, being recruited as a specific transcription factor in the streptophyte lineage of plants. Hence, they add to the growing evidence for derivation of DNA-binding domains of eukaryotic specific TFs from mobile and selfish elements.
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Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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