1
|
Xie Y, Chen Y, Li Z, Zhu J, Liu M, Zhang Y, Dong Z. Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat. Genome Biol 2022; 23:109. [PMID: 35501845 PMCID: PMC9063354 DOI: 10.1186/s13059-022-02675-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/18/2022] [Indexed: 12/15/2022] Open
Abstract
The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epigenome profiling, we detect active transcription of enhancers from the complex bread wheat genome. We find that genes associated with transcriptional enhancers are expressed at significantly higher levels, and enhancer RNA is more precise and robust in predicting enhancer activity compared to chromatin features. We demonstrate that sub-genome-biased enhancer transcription could drive sub-genome-biased gene expression. This study highlights enhancer transcription as a hallmark in regulating gene expression in wheat.
Collapse
Affiliation(s)
- Yilin Xie
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Zijuan Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiafu Zhu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Min Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
| |
Collapse
|
2
|
Zhang Y, Hu L, Yu D, Xu K, Zhang J, Li X, Wang P, Chen G, Liu Z, Peng C, Li C, Guo T. Integrative Analysis of the Wheat PHT1 Gene Family Reveals A Novel Member Involved in Arbuscular Mycorrhizal Phosphate Transport and Immunity. Cells 2019; 8:E490. [PMID: 31121904 PMCID: PMC6562588 DOI: 10.3390/cells8050490] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/18/2019] [Accepted: 05/20/2019] [Indexed: 11/16/2022] Open
Abstract
Phosphorus (P) deficiency is one of the main growth-limiting factors for plants. However, arbuscular mycorrhizal (AM) symbiosis can significantly promote P uptake. Generally, PHT1 transporters play key roles in plants' P uptake, and thus, PHT1 genes have been investigated in some plants, but the regulation and functions of these genes in wheat (TaPHT1) during AM symbiosis have not been studied in depth. Therefore, a comprehensive analysis of TaPHT1 genes was performed, including sequence, phylogeny, cis-elements, expression, subcellular localization and functions, to elucidate their roles in AM-associated phosphate transport and immunity. In total, 35 TaPHT1s were identified in the latest high-quality bread wheat genome, 34 of which were unevenly distributed on 13 chromosomes, and divided into five groups. Sequence analysis indicated that there are 11 types of motif architectures and five types of exon-intron structures in the TaPHT1 family. Duplication mode analysis indicated that the TaPHT1 family has expanded mainly through segmental and tandem duplication events, and that all duplicated gene pairs have been under purifying selection. Transcription analysis of the 35 TaPHT1s revealed that not only known the mycorrhizal-specific genes TaPht-myc, TaPT15-4B (TaPT11) and TaPT19-4D (TaPT10), but also four novel mycorrhizal-specific/inducible genes (TaPT3-2D, TaPT11-4A, TaPT29-6A, and TaPT31-7A) are highly up-regulated in AM wheat roots. Furthermore, the mycorrhizal-specific/inducible genes are significantly induced in wheat roots at different stages of infection by colonizing fungi. Transient Agrobacterium tumefaciens-mediated transformation expression in onion epidermal cells showed that TaPT29-6A is a membrane-localized protein. In contrast to other AM-specific/inducible PHT1 genes, TaPT29-6A is apparently required for the symbiotic and direct Pi pathway. TaPT29-6A-silenced lines exhibited reduced levels of AM fungal colonization and arbuscules, but increased susceptibility to biotrophic, hemi-biotrophic and necrotrophic pathogens. In conclusion, TaPT29-6A was not only essential for the AM symbiosis, but also played vital roles in immunity.
Collapse
Affiliation(s)
- Yi Zhang
- The Collaborative Innovation Center of Henan Food Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, China.
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou Normal University, Zhoukou 466001, China.
| | - Lizong Hu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou Normal University, Zhoukou 466001, China.
| | - Deshui Yu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou Normal University, Zhoukou 466001, China.
| | - Kedong Xu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou Normal University, Zhoukou 466001, China.
| | - Ju Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou Normal University, Zhoukou 466001, China.
| | - Xiaoli Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou Normal University, Zhoukou 466001, China.
| | - Pengfei Wang
- The Collaborative Innovation Center of Henan Food Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, China.
| | - Guo Chen
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou Normal University, Zhoukou 466001, China.
| | - Zhihui Liu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou Normal University, Zhoukou 466001, China.
| | - Chunfeng Peng
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou Normal University, Zhoukou 466001, China.
| | - Chengwei Li
- The Collaborative Innovation Center of Henan Food Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, China.
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou Normal University, Zhoukou 466001, China.
- Henan Engineering Research Center of Grain Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Tiancai Guo
- The Collaborative Innovation Center of Henan Food Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, China.
| |
Collapse
|
3
|
Zou B, Ding Y, Liu H, Hua J. Silencing of copine genes confers common wheat enhanced resistance to powdery mildew. MOLECULAR PLANT PATHOLOGY 2018; 19:1343-1352. [PMID: 28941084 PMCID: PMC6638117 DOI: 10.1111/mpp.12617] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/01/2017] [Accepted: 09/20/2017] [Indexed: 05/09/2023]
Abstract
Powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt), is a major threat to the production of wheat (Triticum aestivum). It is of great importance to identify new resistance genes for the generation of Bgt-resistant or Bgt-tolerant wheat varieties. Here, we show that the wheat copine genes TaBON1 and TaBON3 negatively regulate wheat disease resistance to Bgt. Two copies of TaBON1 and three copies of TaBON3, located on chromosomes 6AS, 6BL, 1AL, 1BL and 1DL, respectively, were identified from the current common wheat genome sequences. The expression of TaBON1 and TaBON3 is responsive to both pathogen infection and temperature changes. Knocking down of TaBON1 or TaBON3 by virus-induced gene silencing (VIGS) induces the up-regulation of defence responses in wheat. These TaBON1- or TaBON3-silenced plants exhibit enhanced wheat disease resistance to Bgt, accompanied by greater accumulation of hydrogen peroxide and heightened cell death. In addition, high temperature has little effect on the up-regulation of defence response genes conferred by the silencing of TaBON1 or TaBON3. Our study shows a conserved function of plant copine genes in plant immunity and provides new genetic resources for the improvement of resistance to powdery mildew in wheat.
Collapse
Affiliation(s)
- Baohong Zou
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing 210095China
| | - Yuan Ding
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing 210095China
| | - He Liu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing 210095China
| | - Jian Hua
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing 210095China
- Plant Biology Section, School of Integrated Plant ScienceCornell UniversityIthacaNY 14853USA
| |
Collapse
|
4
|
Ge F, Luo X, Huang X, Zhang Y, He X, Liu M, Lin H, Peng H, Li L, Zhang Z, Pan G, Shen Y. Genome-wide analysis of transcription factors involved in maize embryonic callus formation. PHYSIOLOGIA PLANTARUM 2016; 158:452-462. [PMID: 27194582 DOI: 10.1111/ppl.12470] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/21/2016] [Accepted: 04/22/2016] [Indexed: 05/20/2023]
Abstract
In this study, a maize inbred line with a strong capacity to induce embryonic callus, 18-599R, was used to analyze the transcription factors expressed during embryonic callus formation. A total of 1180 transcription factors were found to be expressed during three key stages of callus induction. Of these, compared with control, 361, 346 and 328 transcription factors were significantly downregulated during stages I, II and III, respectively. In contrast, 355, 372 and 401 transcription factors (TFs) were upregulated during the respective stages. We constructed a transcription factor-mediated regulatory network and found that plant hormone signal transduction was the pathway most significantly enriched among TFs. This pathway includes 48 TFs regulating cell enlargement, cell differentiation, cell division and cell dedifferentiation via the response to plant hormones. Through real-time polymerase chain reaction (PCR) and degradome sequencing, we identified 23 transcription factors that are regulated by miRNA. Through further analysis, ZmMYB138, a member of the MYB transcription factor family localized in the nucleus, was verified to promote embryonic callus formation in the maize embryo through GA signal transduction.
Collapse
Affiliation(s)
- Fei Ge
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xu Luo
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xing Huang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanling Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiujing He
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Min Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Haijian Lin
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Huanwei Peng
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an 625014, China
| | - Lujiang Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhiming Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
5
|
Quijano CD, Wichmann F, Schlaich T, Fammartino A, Huckauf J, Schmidt K, Unger C, Broer I, Sautter C. KP4 to control Ustilago tritici in wheat: Enhanced greenhouse resistance to loose smut and changes in transcript abundance of pathogen related genes in infected KP4 plants. ACTA ACUST UNITED AC 2016; 11:90-98. [PMID: 28352545 PMCID: PMC5042339 DOI: 10.1016/j.btre.2016.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/12/2016] [Accepted: 08/22/2016] [Indexed: 11/28/2022]
Abstract
Ustilago tritici causes loose smut, which is a seed-borne fungal disease of wheat, and responsible for yield losses up to 40%. Loose smut is a threat to seed production in developing countries where small scale farmers use their own harvest as seed material. The killer protein 4 (KP4) is a virally encoded toxin from Ustilago maydis and inhibits growth of susceptible races of fungi from the Ustilaginales. Enhanced resistance in KP4 wheat to stinking smut, which is caused by Tilletia caries, had been reported earlier. We show that KP4 in genetically engineered wheat increased resistance to loose smut up to 60% compared to the non-KP4 control under greenhouse conditions. This enhanced resistance is dose and race dependent. The overexpression of the transgene kp4 and its effect on fungal growth have indirect effects on the expression of endogenous pathogen defense genes.
Collapse
Affiliation(s)
- Carolina Diaz Quijano
- Plant Biotechnology, Department of Biology, ETH Zurich, Universitätsstrasse 2, CH-8092 Zurich, Switzerland
| | - Fabienne Wichmann
- Plant Biotechnology, Department of Biology, ETH Zurich, Universitätsstrasse 2, CH-8092 Zurich, Switzerland
| | - Thomas Schlaich
- Plant Biotechnology, Department of Biology, ETH Zurich, Universitätsstrasse 2, CH-8092 Zurich, Switzerland
| | - Alessandro Fammartino
- Plant Biotechnology, Department of Biology, ETH Zurich, Universitätsstrasse 2, CH-8092 Zurich, Switzerland
| | - Jana Huckauf
- Agrobiotechnology, University of Rostock, Justus-von-Liebig-Weg 8, D-18059 Rostock, Germany
| | - Kerstin Schmidt
- biovativ GmbH, Thuneneplatz 1, D-18190, Gross Lusewitz, Germany
| | - Christoph Unger
- Agrobiotechnology, University of Rostock, Justus-von-Liebig-Weg 8, D-18059 Rostock, Germany
| | - Inge Broer
- Agrobiotechnology, University of Rostock, Justus-von-Liebig-Weg 8, D-18059 Rostock, Germany
| | - Christof Sautter
- Plant Biotechnology, Department of Biology, ETH Zurich, Universitätsstrasse 2, CH-8092 Zurich, Switzerland
| |
Collapse
|
6
|
Chen T, Xu G, Wang Z, Zhang H, Yang J, Zhang J. Expression of proteins in superior and inferior spikelets of rice during grain filling under different irrigation regimes. Proteomics 2015; 16:102-21. [PMID: 26442785 DOI: 10.1002/pmic.201500070] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 12/21/2022]
Abstract
Poor grain filling of later-flowering inferior spikelets is a serious problem in modern rice cultivars, but the reason and regulation remain unclear. This study investigated post-anthesis protein expression in relation with grain filling and the possibility to use irrigation methods to enhance grain filling through regulating protein expression. One japonica rice cultivar was field-grown under three irrigation treatments imposed during the grain filling period: alternate wetting and moderate soil-drying (WMD), alternate wetting and severe soil-drying (WSD), and conventional irrigation. High resolution 2DE, combined with MALDI/TOF, was used to compare differential protein expression between superior and inferior spikelets. Results showed that the expression of proteins that function in photosynthesis, carbohydrate and energy metabolism, amino acids metabolism and defense responses were largely down-regulated in inferior spikelets compared to those in superior spikelets. The WMD treatment enhanced grain filling rate and the expression of these proteins, whereas the WSD treatment decreased them. Similar results were observed for transcript levels of the genes encoding these proteins. These results suggest that down-regulated expression of the proteins associated with grain filling contribute to the poor grain filling of inferior spikelets, and post-anthesis WMD could improve grain filling through regulating protein expression in the spikelets.
Collapse
Affiliation(s)
- Tingting Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China.,State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, P. R. China
| | - Genwen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Zhiqin Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Hao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Jianchang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, P. R. China
| |
Collapse
|
7
|
Pathogenesis related-10 proteins are small, structurally similar but with diverse role in stress signaling. Mol Biol Rep 2013; 41:599-611. [PMID: 24343423 DOI: 10.1007/s11033-013-2897-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 12/09/2013] [Indexed: 10/25/2022]
Abstract
Pathogenesis related-10 proteins are small proteins with cytosolic localization, conserved three dimensional structures and single intron at 185 bp position. These proteins have a broad spectrum of roles significantly in biotic and abiotic stresses. The RNase activity, ligand binding activity, posttranslational modification (phosphorylation) and phytohormone signaling provide some information into the mechanism of the regulation of PR-10 proteins, however the presence of isoforms makes it difficult to decipher its exact mode of function. The involvement of phosphorylation/dephosphorylation events in its activation is interesting and provides unique and unbiased insights into the complexity of its regulation. Studies on upstream region of different PR-10 genes indicate the presence of cis-acting elements for WRKY, RAVI, bZ1P, ERF, SEBF and Pti4 transcription factors indicating their role in regulating PR-10 promoter. In this review, we discuss in detail the structure and mechanism of regulation of PR-10 proteins.
Collapse
|