1
|
Wang Z, Peng Y, Li J, Li J, Yuan H, Yang S, Ding X, Xie A, Zhang J, Wang S, Li K, Shi J, Xing G, Shi W, Yan J, Liu J. DeepCBA: A deep learning framework for gene expression prediction in maize based on DNA sequences and chromatin interactions. PLANT COMMUNICATIONS 2024:100985. [PMID: 38859587 DOI: 10.1016/j.xplc.2024.100985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/25/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Abstract
Chromatin interactions create spatial proximity between distal regulatory elements and target genes in the genome, which has an important impact on gene expression, transcriptional regulation, and phenotypic traits. To date, several methods have been developed for predicting gene expression. However, existing methods do not take into consideration the effect of chromatin interactions on target gene expression, thus potentially reducing the accuracy of gene expression prediction and mining of important regulatory elements. In this study, we developed a highly accurate deep learning-based gene expression prediction model (DeepCBA) based on maize chromatin interaction data. Compared with existing models, DeepCBA exhibits higher accuracy in expression classification and expression value prediction. The average Pearson correlation coefficients (PCCs) for predicting gene expression using gene promoter proximal interactions, proximal-distal interactions, and both proximal and distal interactions were 0.818, 0.625, and 0.929, respectively, representing an increase of 0.357, 0.16, and 0.469 over the PCCs obtained with traditional methods that use only gene proximal sequences. Some important motifs were identified through DeepCBA; they were enriched in open chromatin regions and expression quantitative trait loci and showed clear tissue specificity. Importantly, experimental results for the maize flowering-related gene ZmRap2.7 and the tillering-related gene ZmTb1 demonstrated the feasibility of DeepCBA for exploration of regulatory elements that affect gene expression. Moreover, promoter editing and verification of two reported genes (ZmCLE7 and ZmVTE4) demonstrated the utility of DeepCBA for the precise design of gene expression and even for future intelligent breeding. DeepCBA is available at http://www.deepcba.com/ or http://124.220.197.196/.
Collapse
Affiliation(s)
- Zhenye Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jie Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiying Li
- Microsoft Corporation, Redmond, WA 98052, USA
| | - Hao Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shangpo Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinru Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ao Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiangling Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shouzhe Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; WIMI Biotechnology Co., Ltd., Changzhou 213000, China
| | - Keqin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaqi Shi
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangjie Xing
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Weihan Shi
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jianxiao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| |
Collapse
|
2
|
Duan S, Guan S, Fei R, Sun T, Kang X, Xin R, Song W, Sun X. Unraveling the role of PlARF2 in regulating deed formancy in Paeonia lactiflora. PLANTA 2024; 259:133. [PMID: 38668881 DOI: 10.1007/s00425-024-04411-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/10/2024] [Indexed: 05/01/2024]
Abstract
MAIN CONCLUSION PlARF2 can positively regulate the seed dormancy in Paeonia lactiflora Pall. and bind the RY cis-element. Auxin, a significant phytohormone influencing seed dormancy, has been demonstrated to be regulated by auxin response factors (ARFs), key transcriptional modulators in the auxin signaling pathway. However, the role of this class of transcription factors (TFs) in perennials with complex seed dormancy mechanisms remains largely unexplored. Here, we cloned and characterized an ARF gene from Paeonia lactiflora, named PlARF2, which exhibited differential expression levels in the seeds during the process of seed dormancy release. The deduced amino acid sequence of PlARF2 had high homology with those of other plants and contained typical conserved Auxin_resp domain of the ARF family. Phylogenetic analysis revealed that PlARF2 was closely related to VvARF3 in Vitis vinifera. The subcellular localization and transcriptional activation assay showed that PlARF2 is a nuclear protein possessing transcriptional activation activity. The expression levels of dormancy-related genes in transgenic callus indicated that PlARF2 was positively correlated with the contents of PlABI3 and PlDOG1. The germination assay showed that PlARF2 promoted seed dormancy. Moreover, TF Centered Yeast one-hybrid assay (TF-Centered Y1H), electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter assay analysis (Dual-Luciferase) provided evidence that PlARF2 can bind to the 'CATGCATG' motif. Collectively, our findings suggest that PlARF2, as TF, could be involved in the regulation of seed dormancy and may act as a repressor of germination.
Collapse
Affiliation(s)
- Siyang Duan
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, 110866, China
| | - Shixin Guan
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, 110866, China
| | - Riwen Fei
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, 110866, China
| | - Tianyi Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, 110866, China
| | - Xuening Kang
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, 110866, China
| | - Rujie Xin
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, 110866, China
| | - Wenhui Song
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, 110866, China
| | - Xiaomei Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China.
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang, 110866, China.
| |
Collapse
|
3
|
Turkan S, Kulasek M, Zienkiewicz A, Mierek-Adamska A, Skrzypek E, Warchoł M, Szydłowska-Czerniak A, Bartoli J, Field B, Dąbrowska GB. Guanosine tetraphosphate (ppGpp) is a new player in Brassica napus L. seed development. Food Chem 2024; 436:137648. [PMID: 37852071 DOI: 10.1016/j.foodchem.2023.137648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/23/2023] [Accepted: 09/30/2023] [Indexed: 10/20/2023]
Abstract
Rapeseed oil, constituting 12% of global vegetable oil production, is susceptible to quality degradation due to stress-induced incomplete seed degreening, fatty acid oxidation, or poor nutrient accumulation. We hypothesise that the hyperphosphorylated nucleotide alarmone ppGpp (guanosine tetraphosphate), acts as a pivotal regulator of these processes, given its established roles in nutrient management, degreening, and ROS regulation in leaves. Using qPCR, UHPLC-MS/MS, and biochemical methods, our study delves into the impact of ppGpp on seed nutritional value. We observed a positive correlation between ppGpp levels and desiccation, and a negative correlation with photosynthetic pigment levels. Trends in antioxidant activity suggest that ppGpp may negatively influence peroxidases, which are safeguarding against chlorophyll decomposition. Notably, despite increasing ppGpp levels, sugars, proteins and oils appear unaffected. This newfound role of ppGpp in seed development suggests it regulates the endogenous antioxidant system during degreening and desiccation, preserving nutritional quality. Further validation through mutant-based research is needed.
Collapse
Affiliation(s)
- Sena Turkan
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland.
| | - Milena Kulasek
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland.
| | - Agnieszka Zienkiewicz
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland.
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland.
| | - Edyta Skrzypek
- Department of Biotechnology, The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland.
| | - Marzena Warchoł
- Department of Biotechnology, The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland.
| | - Aleksandra Szydłowska-Czerniak
- Department of Analytical Chemistry and Applied Spectroscopy, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland.
| | - Julia Bartoli
- Aix Marseille Univ, CNRS, LISM, UMR7255, IMM FR 3479, 31 Chemin Joseph Aiguier, 13009 Marseille, France.
| | - Ben Field
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, 13009 Marseille, France.
| | - Grażyna B Dąbrowska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland.
| |
Collapse
|
4
|
Xu M, Zuo D, Wang Q, Lv L, Zhang Y, Jiao H, Zhang X, Yang Y, Song G, Cheng H. Identification and molecular evolution of the GLX genes in 21 plant species: a focus on the Gossypium hirsutum. BMC Genomics 2023; 24:474. [PMID: 37608304 PMCID: PMC10464159 DOI: 10.1186/s12864-023-09524-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/19/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND The glyoxalase system includes glyoxalase I (GLXI), glyoxalase II (GLXII) and glyoxalase III (GLXIII), which are responsible for methylglyoxal (MG) detoxification and involved in abiotic stress responses such as drought, salinity and heavy metal. RESULTS In this study, a total of 620 GLX family genes were identified from 21 different plant species. The results of evolutionary analysis showed that GLX genes exist in all species from lower plants to higher plants, inferring that GLX genes might be important for plants, and GLXI and GLXII account for the majority. In addition, motif showed an expanding trend in the process of evolution. The analysis of cis-acting elements in 21 different plant species showed that the promoter region of the GLX genes were rich in phytohormones and biotic and abiotic stress-related elements, indicating that GLX genes can participate in a variety of life processes. In cotton, GLXs could be divided into two groups and most GLXIs distributed in group I, GLXIIs and GLXIIIs mainly belonged to group II, indicating that there are more similarities between GLXII and GLXIII in cotton evolution. The transcriptome data analysis and quantitative real-time PCR analysis (qRT-PCR) show that some members of GLX family would respond to high temperature treatment in G.hirsutum. The protein interaction network of GLXs in G.hirsutum implied that most members can participate in various life processes through protein interactions. CONCLUSIONS The results elucidated the evolutionary history of GLX family genes in plants and lay the foundation for their functions analysis in cotton.
Collapse
Affiliation(s)
- Menglin Xu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Limin Lv
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Huixin Jiao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiang Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yi Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Guoli Song
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Hailiang Cheng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| |
Collapse
|
5
|
Wang Y, Fan J, Wu X, Guan L, Li C, Gu T, Li Y, Ding J. Genome-Wide Characterization and Expression Profiling of HD-Zip Genes in ABA-Mediated Processes in Fragaria vesca. PLANTS (BASEL, SWITZERLAND) 2022; 11:3367. [PMID: 36501406 PMCID: PMC9737017 DOI: 10.3390/plants11233367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Members of homeodomain-leucine zipper (HD-Zip) transcription factors can play their roles by modulating abscisic acid (ABA) signaling in Arabidopsis. So far, our knowledge of the functions of HD-Zips in woodland strawberries (Fragaria vesca), a model plant for studying ABA-mediated fruit ripening, is limited. Here, we identified a total of 31 HD-Zip genes (FveHDZ1-31) in F. vesca, and classified them into four subfamilies (I to IV). Promoter analyses show that the ABA-responsive element, ABRE, is prevalent in the promoters of subfamily I and II FveHDZs. RT-qPCR results demonstrate that 10 of the 14 investigated FveHDZs were consistently >1.5-fold up-regulated or down-regulated in expression in response to exogenous ABA, dehydration, and ABA-induced senescence in leaves. Five of the six consistently up-regulated genes are from subfamily I and II. Thereinto, FveHDZ4, and 20 also exhibited significantly enhanced expression along with increased ABA content during fruit ripening. In yeast one-hybrid assays, FveHDZ4 proteins could bind the promoter of an ABA signaling gene FvePP2C6. Collectively, our results strongly support that the FveHDZs, particularly those from subfamilies I and II, are involved in the ABA-mediated processes in F. vesca, providing a basis for further functional characterization of the HD-Zips in strawberry and other plants.
Collapse
Affiliation(s)
- Yong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Junmiao Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Xinjie Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Ling Guan
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Chun Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Tingting Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Jing Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210023, China
| |
Collapse
|
6
|
Zhang B, Guo Y, Wang H, Wang X, Lv M, Yang P, Zhang L. Identification and Characterization of Shaker K + Channel Gene Family in Foxtail Millet ( Setaria italica) and Their Role in Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 13:907635. [PMID: 35755660 PMCID: PMC9218596 DOI: 10.3389/fpls.2022.907635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Potassium (K+) is one of the indispensable elements in plant growth and development. The Shaker K+ channel protein family is involved in plant K+ uptake and distribution. Foxtail millet (Setaria italica), as an important crop, has strong tolerance and adaptability to abiotic stresses. However, no systematic study focused on the Shaker K+ channel family in foxtail millet. Here, ten Shaker K+ channel genes in foxtail millet were identified and divided into five groups through phylogenetic analysis. Gene structures, chromosome locations, cis-acting regulatory elements in promoter, and post-translation modification sites of Shaker K+ channels were analyzed. In silico analysis of transcript level demonstrated that the expression of Shaker K+ channel genes was tissue or developmental stage specific. The transcription levels of Shaker K+ channel genes in foxtail millet under different abiotic stresses (cold, heat, NaCl, and PEG) and phytohormones (6-BA, BR, MJ, IAA, NAA, GA3, SA, and ABA) treatments at 0, 12, and 24 h were detected by qRT-PCR. The results showed that SiAKT1, SiKAT3, SiGORK, and SiSKOR were worth further research due to their significant responses after most treatments. The yeast complementation assay verified the inward K+ transport activities of detectable Shaker K+ channels. Finally, we found interactions between SiKAT2 and SiSNARE proteins. Compared to research in Arabidopsis, our results showed a difference in SYP121 related Shaker K+ channel regulation mechanism in foxtail millet. Our results indicate that Shaker K+ channels play important roles in foxtail millet and provide theoretical support for further exploring the K+ absorption mechanism of foxtail millet under abiotic stress.
Collapse
Affiliation(s)
- Ben Zhang
- State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, China
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Yue Guo
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Hui Wang
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Xiaoxia Wang
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Mengtao Lv
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Pu Yang
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Lizhen Zhang
- School of Life Sciences, Shanxi University, Taiyuan, China
| |
Collapse
|
7
|
Gomez-Cano F, Chu YH, Cruz-Gomez M, Abdullah HM, Lee YS, Schnell DJ, Grotewold E. Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:589-606. [PMID: 35064997 DOI: 10.1111/tpj.15682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Camelina (Camelina sativa) is an annual oilseed plant that is gaining momentum as a biofuel cover crop. Understanding gene regulatory networks is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. We identified approximately 350 TFs highly co-expressed with lipid-related genes (LRGs). These TFs are highly represented in the MYB, AP2/ERF, bZIP, and bHLH families, including a significant number of homologs of well-known Arabidopsis lipid and seed developmental regulators. After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16 out of the 22 TFs tested using DNA affinity purification followed by sequencing (DAP-seq). Enrichment analyses of targets supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes, but also aspects unique to Camelina. Within the top potential lipid regulators, we identified CsaMYB1, CsaABI3AVP1-2, CsaHB1, CsaNAC2, CsaMYB3, and CsaNAC1 as likely involved in the control of seed fatty acid elongation and CsaABI3AVP1-2 and CsabZIP1 as potential regulators of the synthesis and degradation of triacylglycerols (TAGs), respectively. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confidence and short list of Camelina TFs involved in the control of lipid metabolism during seed development.
Collapse
Affiliation(s)
- Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Yi-Hsuan Chu
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Mariel Cruz-Gomez
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Hesham M Abdullah
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824-1312, USA
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, 11651, Egypt
| | - Yun Sun Lee
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Danny J Schnell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824-1312, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Sengupta S, Ray A, Mandal D, Nag Chaudhuri R. ABI3 mediated repression of RAV1 gene expression promotes efficient dehydration stress response in Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194582. [DOI: 10.1016/j.bbagrm.2020.194582] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/01/2020] [Accepted: 05/14/2020] [Indexed: 01/19/2023]
|
10
|
Lyall R, Schlebusch SA, Proctor J, Prag M, Hussey SG, Ingle RA, Illing N. Vegetative desiccation tolerance in the resurrection plant Xerophyta humilis has not evolved through reactivation of the seed canonical LAFL regulatory network. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1349-1367. [PMID: 31680354 PMCID: PMC7187197 DOI: 10.1111/tpj.14596] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 10/09/2019] [Accepted: 10/21/2019] [Indexed: 05/25/2023]
Abstract
It has been hypothesised that vegetative desiccation tolerance in resurrection plants evolved via reactivation of the canonical LAFL (i.e. LEC1, ABI3, FUS3 and LEC2) transcription factor (TF) network that activates the expression of genes during the maturation of orthodox seeds leading to desiccation tolerance of the plant embryo in most angiosperms. There is little direct evidence to support this, however, and the transcriptional changes that occur during seed maturation in resurrection plants have not previously been studied. Here we performed de novo transcriptome assembly for Xerophyta humilis, and analysed gene expression during seed maturation and vegetative desiccation. Our results indicate that differential expression of a set of 4205 genes is common to maturing seeds and desiccating leaves. This shared set of genes is enriched for gene ontology terms related to abiotic stress, including water stress and abscisic acid signalling, and includes many genes that are seed-specific in Arabidopsis thaliana and targets of ABI3. However, while we observed upregulation of orthologues of the canonical LAFL TFs and ABI5 during seed maturation, similar to what is seen in A. thaliana, this did not occur during desiccation of leaf tissue. Thus, reactivation of components of the seed desiccation program in X. humilis vegetative tissues likely involves alternative transcriptional regulators.
Collapse
Affiliation(s)
- Rafe Lyall
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| | - Stephen A. Schlebusch
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| | - Jessica Proctor
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| | - Mayur Prag
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| | - Steven G. Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoria0002South Africa
| | - Robert A. Ingle
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| | - Nicola Illing
- Department of Molecular and Cell BiologyUniversity of Cape TownRondebosch7701South Africa
| |
Collapse
|
11
|
O'Neill JP, Colon KT, Jenik PD. The onset of embryo maturation in Arabidopsis is determined by its developmental stage and does not depend on endosperm cellularization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:286-301. [PMID: 30900325 PMCID: PMC6635039 DOI: 10.1111/tpj.14324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/12/2019] [Accepted: 03/18/2019] [Indexed: 05/06/2023]
Abstract
Seeds are dormant and desiccated structures, filled with storage products to be used after germination. These properties are determined by the maturation program, which starts, in Arabidopsis thaliana, mid-embryogenesis, at about the same time and developmental stage in all the seeds in a fruit. The two factors, chronological and developmental time, are closely entangled during seed development, so their relative contribution to the transition to maturation is not well understood. It is also unclear whether that transition is determined autonomously by each seed or whether it depends on signals from the fruit. The onset of maturation follows the cellularization of the endosperm, and it has been proposed that there exists a causal relationship between both processes. We explored all these issues by analyzing markers for maturation in Arabidopsis mutant seeds that develop at a slower pace, or where endosperm cellularization happens too early, too late, or not at all. Our data show that the developmental stage of the embryo is the key determinant of the initiation of maturation, and that each seed makes that transition autonomously. We also found that, in contrast with previous models, endosperm cellularization is not required for the onset of maturation, suggesting that this transition is independent of the hexose/sucrose ratio in the seed. Our observations indicate that the mechanisms that control endosperm cellularization, embryo growth, and embryo maturation act independently of each other.
Collapse
Affiliation(s)
- John P O'Neill
- Department of Biology, Franklin & Marshall College, P.O. Box 3003, Lancaster, PA, 17604-3003, USA
| | - Kristen T Colon
- Department of Biology, Franklin & Marshall College, P.O. Box 3003, Lancaster, PA, 17604-3003, USA
| | - Pablo D Jenik
- Department of Biology, Franklin & Marshall College, P.O. Box 3003, Lancaster, PA, 17604-3003, USA
| |
Collapse
|
12
|
Bedi S, Nag Chaudhuri R. Transcription factor
ABI
3 auto‐activates its own expression during dehydration stress response. FEBS Lett 2018; 592:2594-2611. [DOI: 10.1002/1873-3468.13194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/28/2018] [Accepted: 07/06/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Sonia Bedi
- Department of Biotechnology St. Xavier's College Kolkata India
| | | |
Collapse
|
13
|
Bollhöner B, Jokipii-Lukkari S, Bygdell J, Stael S, Adriasola M, Muñiz L, Van Breusegem F, Ezcurra I, Wingsle G, Tuominen H. The function of two type II metacaspases in woody tissues of Populus trees. THE NEW PHYTOLOGIST 2018; 217:1551-1565. [PMID: 29243818 DOI: 10.1111/nph.14945] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 11/07/2017] [Indexed: 05/03/2023]
Abstract
Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs in hybrid aspen (Populus tremula × tremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNA interference construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins, as well as novel proteins, such as homologs of the PUTATIVE ASPARTIC PROTEASE3 (PASPA3) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in downstream proteolytic processes and cell death of xylem elements. This work provides a valuable reference dataset on xylem-specific metacaspase functions for future functional and biochemical analyses.
Collapse
Affiliation(s)
- Benjamin Bollhöner
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Soile Jokipii-Lukkari
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Joakim Bygdell
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden
| | - Simon Stael
- VIB-Ugent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Mathilda Adriasola
- School of Biotechnology, Royal Institute of Technology (KTH), 10691, Stockholm, Sweden
| | - Luis Muñiz
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Frank Van Breusegem
- VIB-Ugent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Inés Ezcurra
- School of Biotechnology, Royal Institute of Technology (KTH), 10691, Stockholm, Sweden
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Hannele Tuominen
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| |
Collapse
|
14
|
Huang KL, Zhang ML, Ma GJ, Wu H, Wu XM, Ren F, Li XB. Transcriptome profiling analysis reveals the role of silique in controlling seed oil content in Brassica napus. PLoS One 2017; 12:e0179027. [PMID: 28594951 PMCID: PMC5464616 DOI: 10.1371/journal.pone.0179027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/23/2017] [Indexed: 12/13/2022] Open
Abstract
Seed oil content is an important agronomic trait in oilseed rape. However, the molecular mechanism of oil accumulation in rapeseeds is unclear so far. In this report, RNA sequencing technique (RNA-Seq) was performed to explore differentially expressed genes in siliques of two Brassica napus lines (HFA and LFA which contain high and low oil contents in seeds, respectively) at 15 and 25 days after pollination (DAP). The RNA-Seq results showed that 65746 and 66033 genes were detected in siliques of low oil content line at 15 and 25 DAP, and 65236 and 65211 genes were detected in siliques of high oil content line at 15 and 25 DAP, respectively. By comparative analysis, the differentially expressed genes (DEGs) were identified in siliques of these lines. The DEGs were involved in multiple pathways, including metabolic pathways, biosynthesis of secondary metabolic, photosynthesis, pyruvate metabolism, fatty metabolism, glycophospholipid metabolism, and DNA binding. Also, DEGs were related to photosynthesis, starch and sugar metabolism, pyruvate metabolism, and lipid metabolism at different developmental stage, resulting in the differential oil accumulation in seeds. Furthermore, RNA-Seq and qRT-PCR data revealed that some transcription factors positively regulate seed oil content. Thus, our data provide the valuable information for further exploring the molecular mechanism of lipid biosynthesis and oil accumulation in B. nupus.
Collapse
Affiliation(s)
- Ke-Lin Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Mei-Li Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Guang-Jing Ma
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Huan Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xiao-Ming Wu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- * E-mail: (XBL); (FR)
| | - Xue-Bao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- * E-mail: (XBL); (FR)
| |
Collapse
|
15
|
Pawar PMA, Ratke C, Balasubramanian VK, Chong SL, Gandla ML, Adriasola M, Sparrman T, Hedenström M, Szwaj K, Derba-Maceluch M, Gaertner C, Mouille G, Ezcurra I, Tenkanen M, Jönsson LJ, Mellerowicz EJ. Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification. THE NEW PHYTOLOGIST 2017; 214:1491-1505. [PMID: 28257170 DOI: 10.1111/nph.14489] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/23/2017] [Indexed: 05/17/2023]
Abstract
High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21. Histochemical analysis of promoter::GUS lines in hybrid aspen (Populus tremula × tremuloides) showed activation of RWA-A and -B promoters in the secondary wall formation zone, while RWA-C and -D promoter activity was diffuse. Ectopic downregulation of either clade reduced wood xylan and xyloglucan acetylation. Suppressing both clades simultaneously using the wood-specific promoter reduced wood acetylation by 25% and decreased acetylation at position 2 of Xylp in the dimethyl sulfoxide-extracted xylan. This did not affect plant growth but decreased xylose and increased glucose contents in the noncellulosic monosaccharide fraction, and increased glucose and xylose yields of wood enzymatic hydrolysis without pretreatment. Both RWA clades regulate wood xylan acetylation in aspen and are promising targets to improve wood saccharification.
Collapse
Affiliation(s)
- Prashant Mohan-Anupama Pawar
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, S-901 83, Sweden
| | - Christine Ratke
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, S-901 83, Sweden
| | - Vimal K Balasubramanian
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, S-901 83, Sweden
| | - Sun-Li Chong
- Department of Food and Environmental Sciences, University of Helsinki, PO Box 27, FI-Helsinki, 00014, Finland
| | | | - Mathilda Adriasola
- School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91, Stockholm, Sweden
| | - Tobias Sparrman
- Department of Chemistry, Umeå University, Umeå, S-901 87, Sweden
| | | | - Klaudia Szwaj
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, S-901 83, Sweden
| | - Marta Derba-Maceluch
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, S-901 83, Sweden
| | - Cyril Gaertner
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, ERL3559 CNRS, Saclay Plant Sciences, INRA, Versailles, 78026, France
| | - Gregory Mouille
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, ERL3559 CNRS, Saclay Plant Sciences, INRA, Versailles, 78026, France
| | - Ines Ezcurra
- School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91, Stockholm, Sweden
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, PO Box 27, FI-Helsinki, 00014, Finland
| | - Leif J Jönsson
- Department of Chemistry, Umeå University, Umeå, S-901 87, Sweden
| | - Ewa J Mellerowicz
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, S-901 83, Sweden
| |
Collapse
|
16
|
Carbonero P, Iglesias-Fernández R, Vicente-Carbajosa J. The AFL subfamily of B3 transcription factors: evolution and function in angiosperm seeds. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:871-880. [PMID: 28007955 DOI: 10.1093/jxb/erw458] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Seed development follows zygotic embryogenesis; during the maturation phase reserves accumulate and desiccation tolerance is acquired. This is tightly regulated at the transcriptional level and the AFL (ABI3/FUS3/LEC2) subfamily of B3 transcription factors (TFs) play a central role. They alter hormone biosynthesis, mainly in regards to abscisic acid and gibberellins, and also regulate the expression of other TFs and/or modulate their downstream activity via protein-protein interactions. This review deals with the origin of AFL TFs, which can be traced back to non-vascular plants such as Physcomitrella patens and achieves foremost expansion in the angiosperms. In green algae, like the unicellular Chlamydomonas reinhardtii or the pluricellular Klebsormidium flaccidum, a single B3 gene and four B3 paralogous genes are annotated, respectively. However, none of them present with the structural features of the AFL subfamily, with the exception of the B3 DNA-binding domain. Phylogenetic analysis groups the AFL TFs into four Major Clusters of Ortologous Genes (MCOGs). The origin and function of these genes is discussed in view of their expression patterns and in the context of major regulatory interactions in seeds of monocotyledonous and dicotyledonous species.
Collapse
Affiliation(s)
- Pilar Carbonero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| |
Collapse
|
17
|
Devic M, Roscoe T. Seed maturation: Simplification of control networks in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:335-346. [PMID: 27717470 DOI: 10.1016/j.plantsci.2016.08.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 08/05/2016] [Accepted: 08/21/2016] [Indexed: 05/09/2023]
Abstract
Networks controlling developmental or metabolic processes in plants are often complex as a consequence of the duplication and specialisation of the regulatory genes as well as the numerous levels of transcriptional and post-transcriptional controls added during evolution. Networks serve to accommodate multicellular complexity and increase robustness to environmental changes. Mathematical simplification by regrouping genes or pathways in a limited number of hubs has facilitated the construction of models for complex traits. In a complementary approach, a biological simplification can be achieved by using genetic modification to understand the core and singular ancestral function of the network, which is likely to be more prevalent within the plant kingdom rather than specific to a species. With this viewpoint, we review examples of simplification successfully undertaken in yeast and other organisms. A strategy of progressive complementation of single, double and triple mutants of seed maturation confirmed the fundamental role of the AFL sub-family of B3 transcription factors as master regulators of seed maturation, illustrating that biological simplification of complex networks could be more widely applied in plants. Defining minimal control networks will facilitate evolutionary comparisons of regulatory processes and the identification of an essential gene set for synthetic biology.
Collapse
Affiliation(s)
- Martine Devic
- Régulations Epigénétiques et Développement de la Graine, ERL 3500 CNRS-IRD UMR DIADE, Centre IRD de Montpellier, 911 avenue Agropolis BP64501, 34394, Montpellier, France.
| | - Thomas Roscoe
- Régulations Epigénétiques et Développement de la Graine, ERL 3500 CNRS-IRD UMR DIADE, Centre IRD de Montpellier, 911 avenue Agropolis BP64501, 34394, Montpellier, France
| |
Collapse
|
18
|
Chhun T, Chong SY, Park BS, Wong ECC, Yin JL, Kim M, Chua NH. HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth. PLANT & CELL PHYSIOLOGY 2016; 57:1689-706. [PMID: 27335347 DOI: 10.1093/pcp/pcw095] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/01/2016] [Indexed: 05/25/2023]
Abstract
Arabidopsis HSI2 (HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE 2) which carries a EAR (ERF-associated amphiphilic repression) motif acts as a repressor of seed maturation genes and lipid biosynthesis, whereas MEDIATOR (MED) is a conserved multiprotein complex linking DNA-bound transcription factors to RNA polymerase II transcription machinery. How HSI2 executes its repressive function through MED is hitherto unknown. Here, we show that HSI2 and its homolog, HSI2-lik (HSL1), are able to form homo- and heterocomplexes. Both factors bind to the TRAP240 domain of MED13, a subunit of the MED CDK8 module. Mutant alleles of the med13 mutant show elevated seed maturation gene expression and increased lipid accumulation in cotyledons; in contrast, HSI2- or MED13-overexpressing plants display the opposite phenotypes. The overexpression phenotypes of HSI2 and MED13 are abolished in med13 and hsi2 hsl1, respectively, indicating that HSI2 and MED13 together are required for these functions. The HSI2 C-terminal region interacts with HDA6, whose overexpression also reduces seed maturation gene expression and lipid accumulation. Moreover, HSI2, MED13 and HDA6 bind to the proximal promoter and 5'-coding regions of seed maturation genes. Taken together, our results suggest that HSI2 recruits MED13 and HDA6 to suppress directly a subset of seed maturation genes post-germination.
Collapse
Affiliation(s)
- Tory Chhun
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Suet Yen Chong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Bong Soo Park
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Eriko Chi Cheng Wong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Jun-Lin Yin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Mijung Kim
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065-6399, USA
| |
Collapse
|
19
|
Schneider A, Aghamirzaie D, Elmarakeby H, Poudel AN, Koo AJ, Heath LS, Grene R, Collakova E. Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:305-19. [PMID: 26678037 DOI: 10.1111/tpj.13106] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/28/2015] [Accepted: 12/01/2015] [Indexed: 05/06/2023]
Abstract
Developing Arabidopsis seeds accumulate oils and seed storage proteins synthesized by the pathways of primary metabolism. Seed development and metabolism are positively regulated by transcription factors belonging to the LAFL (LEC1, AB13, FUSCA3 and LEC2) regulatory network. The VAL gene family encodes repressors of the seed maturation program in germinating seeds, although they are also expressed during seed maturation. The possible regulatory role of VAL1 in seed development has not been studied to date. Reverse genetics revealed that val1 mutant seeds accumulated elevated levels of proteins compared with the wild type, suggesting that VAL1 functions as a repressor of seed metabolism; however, in the absence of VAL1, the levels of metabolites, ABA, auxin and jasmonate derivatives did not change significantly in developing embryos. Two VAL1 splice variants were identified through RNA sequencing analysis: a full-length form and a truncated form lacking the plant homeodomain-like domain associated with epigenetic repression. None of the transcripts encoding the core LAFL network transcription factors were affected in val1 embryos. Instead, activation of VAL1 by FUSCA3 appears to result in the repression of a subset of seed maturation genes downstream of core LAFL regulators, as 39% of transcripts in the FUSCA3 regulon were derepressed in the val1 mutant. The LEC1 and LEC2 regulons also responded, but to a lesser extent. Additional 832 transcripts that were not LAFL targets were derepressed in val1 mutant embryos. These transcripts are candidate targets of VAL1, acting through epigenetic and/or transcriptional repression.
Collapse
Affiliation(s)
- Andrew Schneider
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Delasa Aghamirzaie
- Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Haitham Elmarakeby
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Arati N Poudel
- Division of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Abraham J Koo
- Division of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
| |
Collapse
|
20
|
Merini W, Calonje M. PRC1 is taking the lead in PcG repression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:110-20. [PMID: 25754661 DOI: 10.1111/tpj.12818] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/17/2015] [Accepted: 03/02/2015] [Indexed: 05/28/2023]
Abstract
Polycomb group (PcG) proteins constitute a major epigenetic mechanism for gene repression throughout the plant life. For a long time, the PcG mechanism has been proposed to follow a hierarchical recruitment of PcG repressive complexes (PRCs) to target genes in which the binding of PRC2 and the incorporation of H3 lysine 27 trimethyl marks led to recruitment of PRC1, which in turn mediated H2A monoubiquitination. However, recent studies have turned this model upside-down by showing that PRC1 activity can be required for PRC2 recruitment and H3K27me3 marking. Here, we review the current knowledge on plant PRC1 composition and mechanisms of repression, as well as its role during plant development.
Collapse
Affiliation(s)
- Wiam Merini
- Institute of Plant Biochemistry and Photosynthesis, IBVF-CSIC-University of Seville, Avenida América Vespucio, 49, Isla de La Cartuja, 41092, Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis, IBVF-CSIC-University of Seville, Avenida América Vespucio, 49, Isla de La Cartuja, 41092, Seville, Spain
| |
Collapse
|
21
|
Roscoe TT, Guilleminot J, Bessoule JJ, Berger F, Devic M. Complementation of Seed Maturation Phenotypes by Ectopic Expression of ABSCISIC ACID INSENSITIVE3, FUSCA3 and LEAFY COTYLEDON2 in Arabidopsis. PLANT & CELL PHYSIOLOGY 2015; 56:1215-28. [PMID: 25840088 DOI: 10.1093/pcp/pcv049] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/19/2015] [Indexed: 05/20/2023]
Abstract
ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3) and LEAFY COTYLEDON2 (LEC2), collectively the AFL, are master regulators of seed maturation processes. This study examined the role of AFL in the production of seed reserves in Arabidopsis. Quantification of seed reserves and cytological observations of afl mutant embryos show that protein and lipid but not starch reserves are spatially regulated by AFL. Although AFL contribute to a common regulation of reserves, ABI3 exerts a quantitatively greater control over storage protein content whereas FUS3 controls lipid content to a greater extent. Although ABI3 controls the reserve content throughout the embryo, LEC2 and FUS3 regulate reserves in distinct embryonic territories. By analyzing the ability of an individual ectopically expressed AFL to suppress afl phenotypes genetically, we show that conserved domains common to each component of the AFL are sufficient for the initiation of storage product synthesis and the establishment of embryo morphology. This confirms redundancy among the AFL and indicates a threshold necessary for function within the AFL pool. Since no individual AFL was able to suppress the tolerance to desiccation, mid- and late-maturation programs were uncoupled.
Collapse
Affiliation(s)
- Thomas T Roscoe
- Régulations Epignetiques et Développement de la Graine, ERL 3500 CNRS-IRD, UMR DIADE, IRD centre de Montpellier, 911 avenue Agropolis, BP64501, 34394 Montpellier, France
| | - Jocelyne Guilleminot
- Laboratoire Genome et Développement des Plantes, UMR 5096 CNRS-UPVD, 58 Avenue P. Alduy, 66860 Perpignan, France
| | - Jean-Jacques Bessoule
- Université de Bordeaux, Laboratoire de Biogenèse Membranaire, UMR 5200, Bâtiment A3-INRA Bordeaux Aquitaine, 71 Avenue Edouard Bourlaux CS 20032, 33140 Villenave d'Ornon, France CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, Bâtiment A3-INRA Bordeaux Aquitaine, 71 Avenue Edouard Bourlaux CS 20032, 33140 Villenave d'Ornon, France
| | - Frédéric Berger
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Dr. Bohr-Gasse, 31030 Vienna, Austria
| | - Martine Devic
- Régulations Epignetiques et Développement de la Graine, ERL 3500 CNRS-IRD, UMR DIADE, IRD centre de Montpellier, 911 avenue Agropolis, BP64501, 34394 Montpellier, France
| |
Collapse
|
22
|
PcG and trxG in plants - friends or foes. Trends Genet 2015; 31:252-62. [PMID: 25858128 DOI: 10.1016/j.tig.2015.03.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 03/07/2015] [Accepted: 03/09/2015] [Indexed: 01/07/2023]
Abstract
The highly-conserved Polycomb group (PcG) and trithorax group (trxG) proteins play major roles in regulating gene expression and maintaining developmental states in many organisms. However, neither the recruitment of Polycomb repressive complexes (PRC) nor the mechanisms of PcG and trxG-mediated gene silencing and activation are well understood. Recent progress in Arabidopsis research challenges the dominant model of PRC2-dependent recruitment of PRC1 to target genes. Moreover, evidence indicates that diverse forms of PRC1, with shared components, are a common theme in plants and mammals. Although trxG is known to antagonize PcG, emerging data reveal that trxG can also repress gene expression, acting cooperatively with PcG. We discuss these recent findings and highlight the employment of diverse epigenetic mechanisms during development in plants and animals.
Collapse
|
23
|
Ratke C, Pawar PMA, Balasubramanian VK, Naumann M, Duncranz ML, Derba-Maceluch M, Gorzsás A, Endo S, Ezcurra I, Mellerowicz EJ. Populus GT43 family members group into distinct sets required for primary and secondary wall xylan biosynthesis and include useful promoters for wood modification. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:26-37. [PMID: 25100045 DOI: 10.1111/pbi.12232] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/24/2014] [Accepted: 06/29/2014] [Indexed: 05/05/2023]
Abstract
The plant GT43 protein family includes xylosyltransferases that are known to be required for xylan backbone biosynthesis, but have incompletely understood specificities. RT-qPCR and histochemical (GUS) analyses of expression patterns of GT43 members in hybrid aspen, reported here, revealed that three clades of the family have markedly differing specificity towards secondary wall-forming cells (wood and extraxylary fibres). Intriguingly, GT43A and B genes (corresponding to the Arabidopsis IRX9 clade) showed higher specificity for secondary-walled cells than GT43C and D genes (IRX14 clade), although both IRX9 and IRX14 are required for xylosyltransferase activity. The remaining genes, GT43E, F and G (IRX9-L clade), showed broad expression patterns. Transient transactivation analyses of GT43A and B reporters demonstrated that they are activated by PtxtMYB021 and PNAC085 (master secondary wall switches), mediated in PtxtMYB021 activation by an AC element. The high observed secondary cell wall specificity of GT43B expression prompted tests of the efficiency of its promoter (pGT43B), relative to the CaMV 35S (35S) promoter, for overexpressing a xylan acetyl esterase (CE5) or downregulating REDUCED WALL ACETYLATION (RWA) family genes and thus engineering wood acetylation. CE5 expression was weaker when driven by pGT43B, but it reduced wood acetyl content substantially more efficiently than the 35S promoter. RNAi silencing of the RWA family, which was ineffective using 35S, was achieved when using GT43B promoter. These results show the utility of the GT43B promoter for genetically engineering properties of wood and fibres.
Collapse
Affiliation(s)
- Christine Ratke
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
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.
Collapse
Affiliation(s)
- Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF), Avenida América Vespucio, 49, Isla de La Cartuja, 41092 Seville, Spain
| |
Collapse
|
25
|
Delahaie J, Hundertmark M, Bove J, Leprince O, Rogniaux H, Buitink J. LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4559-73. [PMID: 24043848 PMCID: PMC3808335 DOI: 10.1093/jxb/ert274] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In contrast to orthodox seeds that acquire desiccation tolerance during maturation, recalcitrant seeds are unable to survive drying. These desiccation-sensitive seeds constitute an interesting model for comparative analysis with phylogenetically close species that are desiccation tolerant. Considering the importance of LEA (late embryogenesis abundant) proteins as protective molecules both in drought and in desiccation tolerance, the heat-stable proteome was characterized in cotyledons of the legume Castanospermum australe and it was compared with that of the orthodox model legume Medicago truncatula. RNA sequencing identified transcripts of 16 homologues out of 17 LEA genes for which polypeptides are detected in M. truncatula seeds. It is shown that for 12 LEA genes, polypeptides were either absent or strongly reduced in C. australe cotyledons compared with M. truncatula seeds. Instead, osmotically responsive, non-seed-specific dehydrins accumulated to high levels in the recalcitrant cotyledons compared with orthodox seeds. Next, M. truncatula mutants of the abscisic acid insensitive3 (ABI3) gene were characterized. Mature Mtabi3 seeds were found to be desiccation sensitive when dried below a critical water content of 0.4 g H2O g DW(-1). Characterization of the LEA proteome of the Mtabi3 seeds revealed a subset of LEA proteins with severely reduced abundance that were also found to be reduced or absent in C. australe cotyledons. Transcripts of these genes were indeed shown to be ABI3 responsive. The results highlight those LEA proteins that are critical to desiccation tolerance and suggest that comparable regulatory pathways responsible for their accumulation are missing in both desiccation-sensitive genotypes, revealing new insights into the mechanistic basis of the recalcitrant trait in seeds.
Collapse
Affiliation(s)
- Julien Delahaie
- Université d’Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, 49045 Angers, France
| | - Michaela Hundertmark
- Université d’Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, 49045 Angers, France
- * Present address: Vilmorin SA, Route du Manoir, 49250 La Ménitré, France
| | - Jérôme Bove
- Université d’Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, 49045 Angers, France
| | - Olivier Leprince
- Agrocampus Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, 49045 Angers, France
| | - Hélène Rogniaux
- Institut National de la Recherche Agronomique, UR1268 Biopolymères, Interactions, Assemblages, Plate-forme Biopolymères-Biologie Structurale, 44316 Nantes, France
| | - Julia Buitink
- Institut National de la Recherche Agronomique, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, 49045 Angers, France
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
26
|
Sharma N, Bender Y, Boyle K, Fobert PR. High-level expression of sugar inducible gene2 (HSI2) is a negative regulator of drought stress tolerance in Arabidopsis. BMC PLANT BIOLOGY 2013; 13:170. [PMID: 24168327 PMCID: PMC3893512 DOI: 10.1186/1471-2229-13-170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 10/02/2013] [Indexed: 05/08/2023]
Abstract
BACKGROUND HIGH-LEVEL EXPRESSION OF SUGAR INDUCIBLE GENE2 (HSI2), also known as VAL1, is a B3 domain transcriptional repressor that acts redundantly with its closest relative, HSI2-LIKE1 (HSL1), to suppress the seed maturation program following germination. Mutant hsi2 hsl1 seedlings are arrested early in development and differentially express a number of abiotic stress-related genes. To test the potential requirement for HSI2 during abiotic stress, hsi2 single mutants and plants overexpressing HSI2 were subjected to simulated drought stress by withholding watering, and characterized through physiological, metabolic and gene expression studies. RESULTS The hsi2 mutants demonstrated reduced wilting and maintained higher relative water content than wild-type after withholding watering, while the overexpressing lines displayed the opposite phenotype. The hsi2 mutant displayed lower constitutive and ABA-induced stomatal conductance than wild-type and accumulated lower levels of ABA metabolites and several osmolytes and osmoprotectants following water withdrawal. Microarray comparisons between wild-type and the hsi2 mutant revealed that steady-state levels of numerous stress-induced genes were up-regulated in the mutant in the absence of stress but down-regulated at visible wilting. Plants with altered levels of HSI2 responded to exogenous application of ABA and a long-lived ABA analog, but the hsi2 mutant did not show altered expression of several ABA-responsive or ABA signalling genes 4 hr after application. CONCLUSIONS These results implicate HSI2 as a negative regulator of drought stress response in Arabidopsis, acting, at least in part, by regulating transpirational water loss. Metabolic and global transcript profiling comparisons of the hsi2 mutant and wild-type plants do not support a model whereby the greater drought tolerance observed in the hsi2 mutant is conferred by the accumulation of known osmolytes and osmoprotectants. Instead, data are consistent with mutants experiencing a relatively milder dehydration stress following water withdrawal.
Collapse
MESH Headings
- Abscisic Acid/pharmacology
- Adaptation, Physiological/drug effects
- Adaptation, Physiological/genetics
- Arabidopsis/drug effects
- Arabidopsis/genetics
- Arabidopsis/physiology
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- DNA, Bacterial/genetics
- Down-Regulation/drug effects
- Down-Regulation/genetics
- Droughts
- Gene Expression Regulation, Plant/drug effects
- Gene Ontology
- Kinetics
- Metabolome/drug effects
- Metabolome/genetics
- Molecular Sequence Annotation
- Mutagenesis, Insertional/drug effects
- Mutagenesis, Insertional/genetics
- Mutation/genetics
- Oligonucleotide Array Sequence Analysis
- Plant Stomata/drug effects
- Plant Stomata/genetics
- Plant Stomata/physiology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Reproducibility of Results
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Transcriptome/genetics
Collapse
Affiliation(s)
- Nirmala Sharma
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Yarnel Bender
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Kerry Boyle
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Pierre R Fobert
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| |
Collapse
|
27
|
Guo X, Hou X, Fang J, Wei P, Xu B, Chen M, Feng Y, Chu C. The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:403-16. [PMID: 23581288 PMCID: PMC3813988 DOI: 10.1111/tpj.12209] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/08/2013] [Accepted: 04/11/2013] [Indexed: 05/19/2023]
Abstract
It has been shown that seed development is regulated by a network of transcription factors in Arabidopsis including LEC1 (LEAFY COTYLEDON1), L1L (LEC1-like) and the B3 domain factors LEC2, FUS3 (FUSCA3) and ABI3 (ABA-INSENSITIVE3); however, molecular and genetic regulation of seed development in cereals is poorly understood. To understand seed development and seed germination in cereals, a large-scale screen was performed using our T-DNA mutant population, and a mutant germination-defective1 (gd1) was identified. In addition to the severe germination defect, the gd1 mutant also shows a dwarf phenotype and abnormal flower development. Molecular and biochemical analyses revealed that GD1 encodes a B3 domain-containing transcription factor with repression activity. Consistent with the dwarf phenotype of gd1, expression of the gibberelic acid (GA) inactivation gene OsGA2ox3 is increased dramatically, accompanied by reduced expression of GA biosynthetic genes including OsGA20ox1, OsGA20ox2 and OsGA3ox2 in gd1, resulting in a decreased endogenous GA₄ level. Exogenous application of GA not only induced GD1 expression, but also partially rescued the dwarf phenotype of gd1. Furthermore, GD1 binds to the promoter of OsLFL1, a LEC2/FUS3-like gene of rice, via an RY element, leading to significant up-regulation of OsLFL1 and a large subset of seed maturation genes in the gd1 mutant. Plants over-expressing OsLFL1 partly mimic the gd1 mutant. In addition, expression of GD1 was induced under sugar treatment, and the contents of starch and soluble sugar are altered in the gd1 mutant. These data indicate that GD1 participates directly or indirectly in regulating GA and carbohydrate homeostasis, and further regulates rice seed germination and seedling development.
Collapse
Affiliation(s)
- Xiaoli Guo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, 100101, China
| | - Xiaomei Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, 100101, China
- Graduate University of the Chinese Academy of SciencesBeijing, 100049, China
| | - Jun Fang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, 100101, China
- For correspondence (e-mail or )
| | - Piwei Wei
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, 100101, China
| | - Bo Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, 100101, China
- Graduate University of the Chinese Academy of SciencesBeijing, 100049, China
| | - Mingluan Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) Department of Chemistry, Wuhan UniversityWuhan, 430072, China
| | - Yuqi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) Department of Chemistry, Wuhan UniversityWuhan, 430072, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, 100101, China
- For correspondence (e-mail or )
| |
Collapse
|
28
|
Mönke G, Seifert M, Keilwagen J, Mohr M, Grosse I, Hähnel U, Junker A, Weisshaar B, Conrad U, Bäumlein H, Altschmied L. Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res 2012; 40:8240-54. [PMID: 22730287 PMCID: PMC3458547 DOI: 10.1093/nar/gks594] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The plant-specific, B3 domain-containing transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3) is an essential component of the regulatory network controlling the development and maturation of the Arabidopsis thaliana seed. Genome-wide chromatin immunoprecipitation (ChIP-chip), transcriptome analysis, quantitative reverse transcriptase–polymerase chain reaction and a transient promoter activation assay have been combined to identify a set of 98 ABI3 target genes. Most of these presumptive ABI3 targets require the presence of abscisic acid for their activation and are specifically expressed during seed maturation. ABI3 target promoters are enriched for G-box-like and RY-like elements. The general occurrence of these cis motifs in non-ABI3 target promoters suggests the existence of as yet unidentified regulatory signals, some of which may be associated with epigenetic control. Several members of the ABI3 regulon are also regulated by other transcription factors, including the seed-specific, B3 domain-containing FUS3 and LEC2. The data strengthen and extend the notion that ABI3 is essential for the protection of embryonic structures from desiccation and raise pertinent questions regarding the specificity of promoter recognition.
Collapse
Affiliation(s)
- Gudrun Mönke
- Department of Molecular Genetics, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Corrensstr. 3, D-06466 Gatersleben, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Gagete AP, Franco L, Isabel Rodrigo M. The Pisum sativum psp54 gene requires ABI3 and a chromatin remodeller to switch from a poised to a transcriptionally active state. THE NEW PHYTOLOGIST 2011; 192:353-63. [PMID: 21790608 DOI: 10.1111/j.1469-8137.2011.03818.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Aspects of transcriptional regulation in plants, such as the order in which transcriptional factors and the preinitiation complex are assembled, are obscure because studies carried out under conditions in which native chromatin structure is preserved are still few in comparison with those carried out under other conditions. In vivo chromatin immunoprecipitation (ChIP) experiments were used here to study the regulation of Pisum sativum psp54, which codes for the precursor of a chromatin-associated protein in dry seeds. Antibodies against PsSNF5, a component of the SWI/SNF remodelling complex, and against the transcriptional factor Pisum sativum abscisic acid insensitive 3 (PsABI3) were raised and used for ChIP experiments, which showed that both factors are bound to the psp54 promoter only when the gene is actively expressed during seed maturation and germination. However, RNA polymerase II appeared to be bound to the inactive promoter, which was poised for transcription, before the assembly of factors. Micrococcal nuclease protection assays showed that chromatin conformation at the proximal psp54 promoter changes in shifting from the active to inactive state. The changes in the promoter chromatin of psp54 are discussed. Stalled polymerase is described for the first time at the promoter of a non-heat-shock plant gene.
Collapse
Affiliation(s)
- Andrés P Gagete
- Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | | | | |
Collapse
|
30
|
Cândido EDS, Pinto MFS, Pelegrini PB, Lima TB, Silva ON, Pogue R, Grossi-de-Sá MF, Franco OL. Plant storage proteins with antimicrobial activity: novel insights into plant defense mechanisms. FASEB J 2011; 25:3290-305. [PMID: 21746866 DOI: 10.1096/fj.11-184291] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Storage proteins perform essential roles in plant survival, acting as molecular reserves important for plant growth and maintenance, as well as being involved in defense mechanisms by virtue of their properties as insecticidal and antimicrobial proteins. These proteins accumulate in storage vacuoles inside plant cells, and, in response to determined signals, they may be used by the different plant tissues in response to pathogen attack. To shed some light on these remarkable proteins with dual functions, storage proteins found in germinative tissues, such as seeds and kernels, and in vegetative tissues, such as tubercles and leaves, are extensively discussed here, along with the related mechanisms of protein expression. Among these proteins, we focus on 2S albumins, Kunitz proteinase inhibitors, plant lectins, glycine-rich proteins, vicilins, patatins, tarins, and ocatins. Finally, the potential use of these molecules in development of drugs to combat human and plant pathogens, contributing to the development of new biotechnology-based medications and products for agribusiness, is also presented.
Collapse
Affiliation(s)
- Elizabete de Souza Cândido
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Campus Avançado Asa Norte, SGAN 916 Avenida W5, CEP: 70790-160, Brasilia, DF, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Sakata Y, Nakamura I, Taji T, Tanaka S, Quatrano RS. Regulation of the ABA-responsive Em promoter by ABI3 in the moss Physcomitrella patens: role of the ABA response element and the RY element. PLANT SIGNALING & BEHAVIOR 2010; 5:1061-6. [PMID: 20448474 PMCID: PMC3115069 DOI: 10.4161/psb.5.9.11774] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 03/10/2010] [Indexed: 05/19/2023]
Abstract
The plant-specific transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3) or the maize ortholog VIVIPAROUS1 (VP1) is known to regulate seed maturation and germination in concert with the phytohormone abscisic acid (ABA) but is also evolutionarily conserved among land plants including non-seed plants. An ABI3/VP1 ortholog (PpABI3A) from the moss Physcomitrella patens can activate ABA-responsive gene promoters in the moss and angiosperms; however, it failed to fully complement the phenotypes of the Arabidopsis abi3-6 mutant, suggesting that some aspects of ABI3/VP1 functions have diverged during the evolution of land plants. To gain insights into the evolution of ABI3/VP1 function, we performed a comparative analysis of the regulatory elements required for ABI3 activation in Physcomitrella using a wheat Em gene promoter, which is induced by ABA and ABI3/VP1 both in Physcomitrella and in angiosperms. Elimination of either the ACGT core motif in the ABA response element (ABRE) or the RY element, to which ABI3/VP1 binds directly, resulted in a drastic reduction of the ABA response in Physcomitrella. Arabidopsis ABI3 could effectively activate the Em promoter either in an ABRE- or RY-dependent manner, as observed in angiosperms. On the other hand, PpABI3A failed to activate an Em promoter lacking the RY element but not the ABRE. These results suggest that RY-mediated transcriptional regulation of ABI3/VP1 is evolutionarily conserved between the moss and angiosperms, whereas angiosperm ABI3/VP1 has evolved to activate ABA-inducible promoters via the ABRE sequence independently from the RY element.
Collapse
Affiliation(s)
- Yoichi Sakata
- Department of BioScience, Tokyo University of Agriculture, Tokyo Japan.
| | | | | | | | | |
Collapse
|
32
|
Angelovici R, Galili G, Fernie AR, Fait A. Seed desiccation: a bridge between maturation and germination. TRENDS IN PLANT SCIENCE 2010; 15:211-8. [PMID: 20138563 DOI: 10.1016/j.tplants.2010.01.003] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 01/04/2010] [Accepted: 01/07/2010] [Indexed: 05/22/2023]
Abstract
The development of orthodox seeds concludes by a desiccation phase. The dry seeds then enter a phase of dormancy, also called the after-ripening phase, and become competent for germination. We discuss physiological processes as well as gene expression and metabolic programs occurring during the desiccation phase in respect to their contribution to the desiccation tolerance, dormancy competence and successful germination of the dry seeds. The transition of developing seeds from the phase of reserve accumulation to desiccation is associated with distinct gene expression and metabolic switches. Interestingly, a significant proportion of the gene expression and metabolic signatures of seed desiccation resemble those characterizing seed germination, implying that the preparation of the seeds for germination begins already during seed desiccation.
Collapse
Affiliation(s)
- Ruthie Angelovici
- Department of Plant Science, the Weizmann Institute of Science, Rehovot, Israel
| | | | | | | |
Collapse
|
33
|
Winzell A, Aspeborg H, Wang Y, Ezcurra I. Conserved CA-rich motifs in gene promoters of Pt×tMYB021-responsive secondary cell wall carbohydrate-active enzymes in Populus. Biochem Biophys Res Commun 2010; 394:848-53. [DOI: 10.1016/j.bbrc.2010.03.101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 03/17/2010] [Indexed: 11/30/2022]
|