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Wang D, Coleman HD. The transcriptional regulation of a putative hemicellulose gene, PtrPARVUS2 in poplar. Sci Rep 2024; 14:12592. [PMID: 38824196 PMCID: PMC11144201 DOI: 10.1038/s41598-024-63408-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024] Open
Abstract
The plant cell wall serves as a critical interface between the plant and its environment, offering protection against various stresses and contributing to biomass production. Hemicellulose is one of the major components of the cell wall, and understanding the transcriptional regulation of its production is essential to fully understanding cell wall formation. This study explores the regulatory mechanisms underlying one of the genes involved in hemicellulose biosynthesis, PtrPARVUS2. Six transcription factors (TFs) were identified from a xylem-biased library to negatively regulate PtrPARVUS2 expression. These TFs, belonging to diverse TF families, were confirmed to bind to specific cis-elements in the PtrPARVUS2 promoter region, as validated by Yeast One-Hybrid (Y1H) assays, transient expression analysis, and Chromatin Immunoprecipitation sequencing (ChIP-seq) assays. Furthermore, motif analysis identified putative cis-regulatory elements bound by these TFs, shedding light on the transcriptional regulation of SCW biosynthesis genes. Notably, several TFs targeted genes encoding uridine diphosphate glycosyltransferases (UGTs), crucial enzymes involved in hemicellulose glycosylation. Phylogenetic analysis of UGTs regulated by these TFs highlighted their diverse roles in modulating hemicellulose synthesis. Overall, this study identifies a set of TFs that regulate PARVUS2 in poplar, providing insights into the intricate coordination of TFs and PtrPARVUS2 in SCW formation. Understanding these regulatory mechanisms enhances our ability to engineer plant biomass for tailored applications, including biofuel production and bioproduct development.
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Affiliation(s)
- Dan Wang
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
| | - Heather D Coleman
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA.
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Zhang B, Wang Z, Dai X, Gao J, Zhao J, Ma R, Chen Y, Sun Y, Ma H, Li S, Zhou C, Wang JP, Li W. A COMPASS histone H3K4 trimethyltransferase pentamer transactivates drought tolerance and growth/biomass production in Populus trichocarpa. THE NEW PHYTOLOGIST 2024; 241:1950-1972. [PMID: 38095236 DOI: 10.1111/nph.19481] [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: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Histone H3 lysine-4 trimethylation (H3K4me3) activating drought-responsive genes in plants for drought adaptation has long been established, but the underlying regulatory mechanisms are unknown. Here, using yeast two-hybrid, bimolecular fluorescence complementation, biochemical analyses, transient and CRISPR-mediated transgenesis in Populus trichocarpa, we unveiled in this adaptation a regulatory interplay between chromatin regulation and gene transactivation mediated by an epigenetic determinant, a PtrSDG2-1-PtrCOMPASS (complex proteins associated with Set1)-like H3K4me3 complex, PtrSDG2-1-PtrWDR5a-1-PtrRbBP5-1-PtrAsh2-2 (PtrSWRA). Under drought conditions, a transcription factor PtrAREB1-2 interacts with PtrSWRA, forming a PtrSWRA-PtrAREB1-2 pentamer, to recruit PtrSWRA to specific promoter elements of drought-tolerant genes, such as PtrHox2, PtrHox46, and PtrHox52, for depositing H3K4me3 to promote and maintain activated state of such genes for tolerance. CRISPR-edited defects in the pentamer impaired drought tolerance and elevated expression of PtrHox2, PtrHox46, or PtrHox52 improved the tolerance as well as growth in P. trichocarpa. Our findings revealed the identity of the underlying H3K4 trimethyltransferase and its interactive arrangement with the COMPASS for catalysis specificity and efficiency. Furthermore, our study uncovered how the H3K4 trimethyltransferase-COMPASS complex is recruited to the effector genes for elevating H3K4me3 marks for improved drought tolerance and growth/biomass production in plants.
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Affiliation(s)
- Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhuwen Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinfeng Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Rong Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yanjie Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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Zhou H, Song X, Lu MZ. Growth-regulating factor 15-mediated vascular cambium differentiation positively regulates wood formation in hybrid poplar ( Populus alba × P. glandulosa). FRONTIERS IN PLANT SCIENCE 2024; 15:1343312. [PMID: 38425797 PMCID: PMC10902170 DOI: 10.3389/fpls.2024.1343312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
Introduction Hybrid poplars are industrial trees in China. An understanding of the molecular mechanism underlying wood formation in hybrid poplars is necessary for molecular breeding. Although the division and differentiation of vascular cambial cells is important for secondary growth and wood formation, the regulation of this process is largely unclear. Methods In this study, mPagGRF15 OE and PagGRF15-SRDX transgenic poplars were generated to investigate the function of PagGRF15. RNA-seq and qRT-PCR were conducted to analyze genome-wide gene expression, while ChIP‒seq and ChIP-PCR were used to identified the downstream genes regulated by PagGRF15. Results and discussion We report that PagGRF15 from hybrid poplar (Populus alba × P. glandulosa), a growth-regulating factor, plays a critical role in the regulation of vascular cambium activity. PagGRF15 was expressed predominantly in the cambial zone of vascular tissue. Overexpression of mPagGRF15 (the mutated version of GRF15 in the miR396 target sequence) in Populus led to decreased plant height and internode number. Further stem cross sections showed that the mPagGRF15 OE plants exhibited significant changes in vascular pattern with an increase in xylem and a reduction in phloem. In addition, cambium cell files were decreased in the mPagGRF15 OE plants. However, dominant suppression of the downstream genes of PagGRF15 using PagGRF15-SRDX showed an opposite phenotype. Based on the RNA-seq and ChIP-seq results, combining qRT-PCR and ChIP-PCR analysis, candidate genes, such as WOX4b, PXY and GID1.3, were obtained and found to be mainly involved in cambial activity and xylem differentiation. Accordingly, we speculated that PagGRF15 functions as a positive regulator mediating xylem differentiation by repressing the expression of the WOX4a and PXY genes to set the pace of cambial activity. In contrast, PagGRF15 mediated the GA signaling pathway by upregulating GID1.3 expression to stimulate xylem differentiation. This study provides valuable information for further studies on vascular cambium differentiation mechanisms and genetic improvement of the specific gravity of wood in hybrid poplars.
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Affiliation(s)
- Houjun Zhou
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Li W, Lin YCJ, Chen YL, Zhou C, Li S, De Ridder N, Oliveira DM, Zhang L, Zhang B, Wang JP, Xu C, Fu X, Luo K, Wu AM, Demura T, Lu MZ, Zhou Y, Li L, Umezawa T, Boerjan W, Chiang VL. Woody plant cell walls: Fundamentals and utilization. MOLECULAR PLANT 2024; 17:112-140. [PMID: 38102833 DOI: 10.1016/j.molp.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Cell walls in plants, particularly forest trees, are the major carbon sink of the terrestrial ecosystem. Chemical and biosynthetic features of plant cell walls were revealed early on, focusing mostly on herbaceous model species. Recent developments in genomics, transcriptomics, epigenomics, transgenesis, and associated analytical techniques are enabling novel insights into formation of woody cell walls. Here, we review multilevel regulation of cell wall biosynthesis in forest tree species. We highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic trees. We outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | | | - Ying-Lan Chen
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Nette De Ridder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dyoni M Oliveira
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaokang Fu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Taku Demura
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Laigeng Li
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Toshiaki Umezawa
- Laboratory of Metabolic Science of Forest Plants and Microorganisms, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
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Yu W, Kong G, Ya H, He L, Wu Y, Zhang H. Comprehensive Analysis of the Catalase ( CAT) Gene Family and Expression Patterns in Rubber Tree ( Hevea brasiliensis) under Various Abiotic Stresses and Multiple Hormone Treatments. Int J Mol Sci 2023; 25:70. [PMID: 38203241 PMCID: PMC10779098 DOI: 10.3390/ijms25010070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
Catalase (CAT) is one of the key enzymes involved in antioxidant defense systems and mainly scavenges H2O2 and plays a vital role in plant growth, development, and various adverse stresses. To date, a systematic study of the CAT gene family in rubber tree has not been reported. In this study, five HbCAT gene family members were identified from the rubber tree genome, and these were mainly clustered into two subfamilies. Gene structure and motif analysis showed that exon-intron and motif patterns were conserved across different plant species. Sequence analysis revealed that HbCAT proteins contain one active catalytic site, one heme-ligand signature sequence, three conserved amino acid residues (His, Tyr, and Asn), and one peroxisome-targeting signal 1 (PTS1) sequence. Fragment duplication is a selection pressure for the evolution of the HbCAT family based on Ka/Ks values. Analysis of cis-acting elements in the promoters indicated that HbCAT gene expression might be regulated by abscisic acid (ABA), salicylic acid (SA), and MYB transcription factors; furthermore, these genes might be involved in plant growth, development, and abiotic stress responses. A tissue-specific expression analysis showed that HbCATs gradually increased with leaf development and were highly expressed in mature leaves. Gene expression profiling exhibited the differential expression of the HbCATs under cold, heat, drought, and NaCl stresses. Our results provide comprehensive information about the HbCAT gene family, laying the foundation for further research on its function in rubber tree.
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Affiliation(s)
- Wencai Yu
- Yunnan Key Laboratory of Sustainable Utilization Research on Rubber Tree, National and Local Joint Engineering Research Center of Breeding and Cultivation Technology of Rubber Tree, Yunnan Institute of Tropical Crops, Jinghong 666100, China; (W.Y.); (G.K.); (H.Y.); (L.H.)
- Key Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Guanghong Kong
- Yunnan Key Laboratory of Sustainable Utilization Research on Rubber Tree, National and Local Joint Engineering Research Center of Breeding and Cultivation Technology of Rubber Tree, Yunnan Institute of Tropical Crops, Jinghong 666100, China; (W.Y.); (G.K.); (H.Y.); (L.H.)
| | - Huajin Ya
- Yunnan Key Laboratory of Sustainable Utilization Research on Rubber Tree, National and Local Joint Engineering Research Center of Breeding and Cultivation Technology of Rubber Tree, Yunnan Institute of Tropical Crops, Jinghong 666100, China; (W.Y.); (G.K.); (H.Y.); (L.H.)
| | - Ligang He
- Yunnan Key Laboratory of Sustainable Utilization Research on Rubber Tree, National and Local Joint Engineering Research Center of Breeding and Cultivation Technology of Rubber Tree, Yunnan Institute of Tropical Crops, Jinghong 666100, China; (W.Y.); (G.K.); (H.Y.); (L.H.)
| | - Yu Wu
- Yunnan Key Laboratory of Sustainable Utilization Research on Rubber Tree, National and Local Joint Engineering Research Center of Breeding and Cultivation Technology of Rubber Tree, Yunnan Institute of Tropical Crops, Jinghong 666100, China; (W.Y.); (G.K.); (H.Y.); (L.H.)
| | - Hanyao Zhang
- Key Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, China
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6
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Wei M, Zhang M, Sun J, Zhao Y, Pak S, Ma M, Chen Y, Lu H, Yang J, Wei H, Li Y, Li C. PuHox52 promotes coordinated uptake of nitrate, phosphate, and iron under nitrogen deficiency in Populus ussuriensis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:791-809. [PMID: 36226597 DOI: 10.1111/jipb.13389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
It is of great importance to better understand how trees regulate nitrogen (N) uptake under N deficiency conditions which severely challenge afforestation practices, yet the underlying molecular mechanisms have not been well elucidated. Here, we functionally characterized PuHox52, a Populus ussuriensis HD-ZIP transcription factor, whose overexpression greatly enhanced nutrient uptake and plant growth under N deficiency. We first conducted an RNA sequencing experiment to obtain root transcriptome using PuHox52-overexpression lines of P. ussuriensis under low N treatment. We then performed multiple genetic and phenotypic analyses to identify key target genes of PuHox52 and validated how they acted against N deficiency under PuHox52 regulation. PuHox52 was specifically induced in roots by N deficiency, and overexpression of PuHox52 promoted N uptake, plant growth, and root development. We demonstrated that several nitrate-responsive genes (PuNRT1.1, PuNRT2.4, PuCLC-b, PuNIA2, PuNIR1, and PuNLP1), phosphate-responsive genes (PuPHL1A and PuPHL1B), and an iron transporter gene (PuIRT1) were substantiated to be direct targets of PuHox52. Among them, PuNRT1.1, PuPHL1A/B, and PuIRT1 were upregulated to relatively higher levels during PuHox52-mediated responses against N deficiency in PuHox52-overexpression lines compared to WT. Our study revealed a novel regulatory mechanism underlying root adaption to N deficiency where PuHox52 modulated a coordinated uptake of nitrate, phosphate, and iron through 'PuHox52-PuNRT1.1', 'PuHox52-PuPHL1A/PuPHL1B', and 'PuHox52-PuIRT1' regulatory relationships in poplar roots.
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Affiliation(s)
- Ming Wei
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Mengqiu Zhang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Jiali Sun
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Ying Zhao
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Solme Pak
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Miaomiao Ma
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Yingxi Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Han Lu
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Jingli Yang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Yuhua Li
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, 150040, China
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7
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Dai X, Zhai R, Lin J, Wang Z, Meng D, Li M, Mao Y, Gao B, Ma H, Zhang B, Sun Y, Li S, Zhou C, Lin YCJ, Wang JP, Chiang VL, Li W. Cell-type-specific PtrWOX4a and PtrVCS2 form a regulatory nexus with a histone modification system for stem cambium development in Populus trichocarpa. NATURE PLANTS 2023; 9:96-111. [PMID: 36624255 PMCID: PMC9873556 DOI: 10.1038/s41477-022-01315-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 11/17/2022] [Indexed: 05/20/2023]
Abstract
Stem vascular cambium cells in forest trees produce wood for materials and energy. WOX4 affects the proliferation of such cells in Populus. Here we show that PtrWOX4a is the most highly expressed stem vascular-cambium-specific (VCS) gene in P. trichocarpa, and its expression is controlled by the product of the second most highly expressed VCS gene, PtrVCS2, encoding a zinc finger protein. PtrVCS2 binds to the PtrWOX4a promoter as part of a PtrWOX13a-PtrVCS2-PtrGCN5-1-PtrADA2b-3 protein tetramer. PtrVCS2 prevented the interaction between PtrGCN5-1 and PtrADA2b-3, resulting in H3K9, H3K14 and H3K27 hypoacetylation at the PtrWOX4a promoter, which led to fewer cambium cell layers. These effects on cambium cell proliferation were consistent across more than 20 sets of transgenic lines overexpressing individual genes, gene-edited mutants and RNA interference lines in P. trichocarpa. We propose that the tetramer-PtrWOX4a system may coordinate genetic and epigenetic regulation to maintain normal vascular cambium development for wood formation.
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Affiliation(s)
- Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Rui Zhai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jiaojiao Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dekai Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Meng Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yuli Mao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Boyuan Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
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Song S, Ge M, Wang W, Gu C, Chen K, Zhang Q, Yu Q, Liu G, Jiang J. BpEIN3.1 represses leaf senescence by inhibiting synthesis of ethylene and abscisic acid in Betula platyphylla. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111330. [PMID: 35696929 DOI: 10.1016/j.plantsci.2022.111330] [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: 02/10/2022] [Revised: 05/12/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023]
Abstract
Leaf senescence and abscission play crucial role in annual plant adapting to seasonal alteration and climate changes by shortening life cycle and development process in response to abiotic and/or biotic stressors underlying phytohormones and environmental signals. Ethylene and abscisic acid are the major phytohormones that promotes leaf senescence, involving various transcription factors, such as EIN3 (ethylene-insensitive 3) and EIL (ethylene-insensitive 3-like) gene family, controlling leaf senescence through metabolite biosynthesis and signal transduction pathways. However, the roles of EIN3 regulating leaf senescence responding to environmental changes in perennial plant, especially forestry tree, remain unclear. In this study, we found that BpEIN3.1 from a subordinated to EIL3 subclade, is a transcription repressor and regulated light-dependent premature leaf senescence in birch (Betula platyphylla). BpEIN3.1 might inhibits the transcription of BpATPS1 by binding to its promoter. Shading suppressed premature leaf senescence in birch ein3.1 mutant line. Ethylene and abscisic acid biosynthesis were also reduced. In addition, abscisic acid positively regulated the expression of BpEIN3.1. This was demonstrated by the hormone-response element analysis of BpEIN3.1 promoter and its gene expression after the hormone treatments. Moreover, our results showed that abscisic acid is also involved in maintaining homeostasis. The molecular mechanism of leaf senescence provides a possibility to increasing wood production by delaying of leaf senescence.
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Affiliation(s)
- Shiyu Song
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Mengyan Ge
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Wei Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chenrui Gu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Kun Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Qibin Yu
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, United States
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.
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9
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Wang H, Pak S, Yang J, Wu Y, Li W, Feng H, Yang J, Wei H, Li C. Two high hierarchical regulators, PuMYB40 and PuWRKY75, control the low phosphorus driven adventitious root formation in Populus ussuriensis. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1561-1577. [PMID: 35514032 PMCID: PMC9342623 DOI: 10.1111/pbi.13833] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 04/11/2022] [Accepted: 04/28/2022] [Indexed: 05/20/2023]
Abstract
Adventitious rooting is an essential biological process in the vegetative propagation of economically important horticultural and forest tree species. It enables utilization of the elite genotypes in breeding programmes and production. Promotion of adventitious root (AR) formation has been associated with starvation of inorganic phosphate and some factors involved in low phosphorus (LP) signalling. However, the regulatory mechanism underlying LP-mediated AR formation remains largely elusive. We established an efficient experimental system that guaranteed AR formation through short-term LP treatment in Populus ussuriensis. We then generated a time-course RNA-seq data set to recognize key regulatory genes and regulatory cascades positively regulating AR formation through data analysis and gene network construction, which were followed by experimental validation and characterization. We constructed a multilayered hierarchical gene regulatory network, from which PuMYB40, a typical R2R3-type MYB transcription factor (TF), and its interactive partner, PuWRKY75, as well as their direct targets, PuLRP1 and PuERF003, were identified to function upstream of the known adventitious rooting genes. These regulatory genes were functionally characterized and proved their roles in promoting AR formation in P. ussuriensis. In conclusion, our study unveiled a new hierarchical regulatory network that promoted AR formation in P. ussuriensis, which was activated by short-term LP stimulus and primarily governed by PuMYB40 and PuWRKY75.
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Affiliation(s)
- Hanzeng Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
- College of AgricultureJilin Agricultural Science and Technology UniversityJilinChina
| | - Solme Pak
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Jia Yang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Ye Wu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Wenlong Li
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - He Feng
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Jingli Yang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Hairong Wei
- College of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMIUSA
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
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10
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Role of PsnWRKY70 in Regulatory Network Response to Infection with Alternaria alternata (Fr.) Keissl in Populus. Int J Mol Sci 2022; 23:ijms23147537. [PMID: 35886886 PMCID: PMC9324512 DOI: 10.3390/ijms23147537] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
WRKY is an important complex family of transcription factors involved in plant immune responses. Among them, WRKY70 plays an important role in the process of the plant defense response to the invasion of pathogens. However, the defense mechanism of PsnWRKY70 is not clear in Populus nigra. In this study, we showed that PsnWRKY70-overexpression lines (OE) had fewer leaf blight symptoms than PsnWRKY70-repressing lines (RE). PsnWRKY70 activated MAP kinase cascade genes (PsnM2K4, PsnMPK3, PsnM3K18), calcium channel proteins-related genes (PsnCNG3, PsnCNGC1, PsnCNG4), and calcium-dependent protein kinases genes (PsnCDPKL, PsnCDPKW, PsnCDPKS, PsnCDPKQ). Furthermore, 129 genes of PsnWRKY70 putative genome-wide direct targets (DTGs) were identified by using transcriptome (RNA-seq) and DNA affinity purification sequencing (DAP-seq). PsnWRKY70 directly binds to the promoters of homologous genes and LRR domain proteins to promote the expression of WRKY6, WRKY18, WRKY22, and WRKY22–1, LRR domain proteins LRR8, LRR-RLK, ADR1-like 2, NB-ARC, etc. Our study suggests that PsnWRKY70 enhances the resistance of A. alternata in poplar by activating genes in both pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI).
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11
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Liu H, Gao J, Sun J, Li S, Zhang B, Wang Z, Zhou C, Sulis DB, Wang JP, Chiang VL, Li W. Dimerization of PtrMYB074 and PtrWRKY19 mediates transcriptional activation of PtrbHLH186 for secondary xylem development in Populus trichocarpa. THE NEW PHYTOLOGIST 2022; 234:918-933. [PMID: 35152419 PMCID: PMC9314101 DOI: 10.1111/nph.18028] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/02/2022] [Indexed: 05/28/2023]
Abstract
Wood formation is controlled by transcriptional regulatory networks (TRNs) involving regulatory homeostasis determined by combinations of transcription factor (TF)-DNA and TF-TF interactions. Functions of TF-TF interactions in wood formation are still in the early stages of identification. PtrMYB074 is a woody dicot-specific TF in a TRN for wood formation in Populus trichocarpa. Here, using yeast two-hybrid and bimolecular fluorescence complementation, we conducted a genome-wide screening for PtrMYB074 interactors and identified 54 PtrMYB074-TF pairs. Of these pairs, 53 are novel. We focused on the PtrMYB074-PtrWRKY19 pair, the most highly expressed and xylem-specific interactor, and its direct transregulatory target, PtrbHLH186, the xylem-specific one of the pair's only two direct TF target genes. Using transient and CRISPR-mediated transgenesis in P. trichocarpa coupled with chromatin immunoprecipitation and electrophoretic mobility shift assays, we demonstrated that PtrMYB074 is recruited by PtrWRKY19 and that the PtrMYB074-PtrWRKY19 dimers are required to transactive PtrbHLH186. Overexpressing PtrbHLH186 in P. trichocarpa resulted in retarded plant growth, increased guaiacyl lignin, a higher proportion of smaller stem vessels and strong drought-tolerant phenotypes. Knowledge of the PtrMYB074-PtrWRKY19-PtrbHLH186 regulation may help design genetic controls of optimal growth and wood formation to maximize beneficial wood properties while minimizing negative effects on growth.
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Affiliation(s)
- Huizi Liu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Jiatong Sun
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Baofeng Zhang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Zhuwen Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
| | - Daniel Barletta Sulis
- Forest Biotechnology GroupDepartment of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC27695USA
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
- Forest Biotechnology GroupDepartment of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC27695USA
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
- Forest Biotechnology GroupDepartment of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC27695USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbin150040China
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12
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Yu J, Zhou C, Li D, Li S, Jimmy Lin YC, Wang JP, Chiang VL, Li W. A PtrLBD39-mediated transcriptional network regulates tension wood formation in Populus trichocarpa. PLANT COMMUNICATIONS 2022; 3:100250. [PMID: 35059630 PMCID: PMC8760142 DOI: 10.1016/j.xplc.2021.100250] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/10/2021] [Accepted: 10/19/2021] [Indexed: 05/29/2023]
Abstract
Tension wood (TW) is a specialized xylem tissue formed in angiosperm trees under gravitational stimulus or mechanical stresses (e.g., bending). The genetic regulation that underlies this important mechanism remains poorly understood. Here, we used laser capture microdissection of stem xylem cells coupled with full transcriptome RNA-sequencing to analyze TW formation in Populus trichocarpa. After tree bending, PtrLBD39 was the most significantly induced transcription factor gene; it has a phylogenetically paired homolog, PtrLBD22. CRISPR-based knockout of PtrLBD39/22 severely inhibited TW formation, reducing cellulose and increasing lignin content. Transcriptomic analyses of CRISPR-based PtrLBD39/22 double mutants showed that these two genes regulate a set of TW-related genes. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify direct targets of PtrLBD39. We integrated transcriptomic analyses and ChIP-seq assays to construct a transcriptional regulatory network (TRN) mediated by PtrLBD39. In this TRN, PtrLBD39 directly regulates 26 novel TW-responsive transcription factor genes. Our work suggests that PtrLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Danning Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan 10617, China
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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13
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Zhang X, Guo Q, Qin L, Li L. A Cys2His2 Zinc Finger Transcription Factor BpSZA1 Positively Modulates Salt Stress in Betula platyphylla. FRONTIERS IN PLANT SCIENCE 2022; 13:823547. [PMID: 35693173 PMCID: PMC9174930 DOI: 10.3389/fpls.2022.823547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/29/2022] [Indexed: 05/07/2023]
Abstract
Zinc finger proteins (ZFPs) are widely involved in plant growth and abiotic stress responses, however, few of these proteins have been functionally characterized in tree species. In this study, we cloned and characterized the BpSZA1 gene encoding a C2H2-type ZFP from Betula platyphylla. BpSZA1 is a transcription factor localized in the nucleus, with a transcription activation domain located at the N-terminus. BpSZA1 was predominantly expressed in stems and was induced by salt. We generated transgenic birch lines displaying overexpression (OE) or RNAi silencing (Ri) of BpSZA1 and exposed these along with wild-type birch seedlings to salinity. Phenotypic and physiological parameters such as superoxide dismutase, peroxisome, H2O2 content, proline content, water loss rate, and malondialdehyde content were examined. Overexpression of BpSZA1 in birch conferred increased salt tolerance. Chromatin immunoprecipitation-qPCR and RNA-seq showed that BpSZA1 binds to the GAGA-motif in the promoter of downstream target genes including BpAPX1, BpAPX2, BpCAT, and Bp6PGDH to activate their transcription. BpSZA1 also participates in abscisic acid (ABA) biosynthesis, proline biosynthesis, and the ABA/jasmonic acid pathway to enhance the salt stress of B. platyphylla.
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14
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Li D, Yang J, Pak S, Zeng M, Sun J, Yu S, He Y, Li C. PuC3H35 confers drought tolerance by enhancing lignin and proanthocyanidin biosynthesis in the roots of Populus ussuriensis. THE NEW PHYTOLOGIST 2022; 233:390-408. [PMID: 34643281 DOI: 10.1111/nph.17799] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Since the roots are the very organ where plants first sense and respond drought stress, it is of great importance to better understand root responses to drought. Yet the underlying molecular mechanisms governing root responses to drought stress have been poorly understood. Here, we identified and functionally characterized a CCCH type transcription factor, PuC3H35, and its targets, anthocyanin reductase (PuANR) and early Arabidopsis aluminum induced1 (PuEARLI1), which are involved in mediating proanthocyanidin (PA) and lignin biosynthesis in response to drought stress in Populus ussuriensis root. PuC3H35 was root-specifically induced upon drought stress. Overexpressing PuC3H35 promoted PA and lignin biosynthesis and vascular tissue development, resulting in enhanced tolerance to drought stress by the means of anti-oxidation and mechanical supporting. We further demonstrated that PuC3H35 directly bound to the promoters of PuANR and PuEARLI1 and overexpressing PuANR or PuEARLI1 increased root PA or lignin levels, respectively, under drought stress. Taken together, these results revealed a novel regulatory pathway for drought tolerance, in which PuC3H35 mediated PA and lignin biosynthesis by collaboratively regulating 'PuC3H35-PuANR-PA' and 'PuC3H35-PuEARLI1-PuCCRs-lignin' modules in poplar roots.
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Affiliation(s)
- Dandan Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Key Lab Forest Tree Genetics and Breeding of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jingli Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Solme Pak
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Minzhen Zeng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jiali Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Sen Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yuting He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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15
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He H, Song XQ, Jiang C, Liu YL, Wang D, Wen SS, Chai GH, Zhao ST, Lu MZ. The role of senescence-associated gene101 (PagSAG101a) in the regulation of secondary xylem formation in poplar. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:73-86. [PMID: 34845845 DOI: 10.1111/jipb.13195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Wood is produced by the accumulation of secondary xylem via proliferation and differentiation of the cambium cells in woody plants. Identifying the regulators involved in this process remains a challenging task. In this study, we isolated PagSAG101a, the homolog of Arabidopsis thaliana SAG101, from a hybrid poplar (Populus alba × Populus glandulosa) clone 84K and investigated its role in secondary xylem development. PagSAG101a was expressed predominantly in lignified stems and localized in the nucleus. Compared with non-transgenic 84K plants, transgenic plants overexpressing PagSAG101a displayed increased plant height, internode number, stem diameter, xylem width, and secondary cell wall thickness, while opposite phenotypes were observed for PagSAG101a knock-out plants. Transcriptome analyses revealed that differentially expressed genes were enriched for those controlling cambium cell division activity and subsequent secondary cell wall deposition during xylem formation. In addition, the tandem CCCH zinc finger protein PagC3H17, which positively regulates secondary xylem width and secondary wall thickening in poplar, could bind to the promoter of PagSAG101a and mediate the regulation of xylem differentiation. Our results support that PagSAG101a, downstream of PagC3H17, functions in wood development.
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Affiliation(s)
- Hui He
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xue-Qin Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Cheng Jiang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Ying-Li Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Dian Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shuang-Shuang Wen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Guo-Hua Chai
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shu-Tang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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16
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Wang YM, Zhang YM, Zhang X, Zhao X, Zhang Y, Wang C, Wang YC, Wang LQ. Poplar PsnICE1 enhances cold tolerance by binding to different cis-acting elements to improve reactive oxygen species-scavenging capability. TREE PHYSIOLOGY 2021; 41:2424-2437. [PMID: 34185092 DOI: 10.1093/treephys/tpab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Low temperature is a major stress that severely affects plant growth and development. Inducer of CBF expression 1 (ICE1) plays a key role in plant cold tolerance by regulating the expression of cold stress-responsive genes. In the present study, we characterized the function and underlying regulatory mechanism of PsnICE1 from Xiaohei poplar (Populus simonii × Populus nigra). PsnICE1 was significantly induced in response to cold stress in the roots, stems and leaves. PsnICE1 proteins were found to localize to the nucleus and exert transactivation activity via their N-terminal transactivation domain. Compared with non-transgenic poplar, transgenic poplar overexpressing PsnICE1 showed substantially enhanced tolerance to cold stress, with higher survival rates and antioxidant enzyme activity levels and reduced reactive oxygen species (ROS) accumulation. In contrast, plants with RNA inhibition-mediated silencing of PsnICE1 showed the opposite phenotype. PsnICE1 can bind to H-box element and abscisic acid-responsive element (ABRE), and more importantly, it mainly binds to IBS1 (a newly discovered cis-acting element) and E-box elements to regulate stress-related genes involved in ROS scavenging. Overall, these results indicated that PsnICE1 functions as a positive regulator of cold tolerance and serves as a potential candidate gene for plant cold tolerance improvement via molecular breeding.
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Affiliation(s)
- Yan-Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Dongxiaofu 1, Xiangshan Road, Beijing 100091, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
- Key Laboratory of Fast-Growing Tree Cultivating of Heilongjiang Province, Forestry Science Research Institute of Heilongjiang Province, 134 haping Road, Harbin 150081, China
| | - Yi-Ming Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
| | - Xin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
| | - Xin Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
| | - Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Dongxiaofu 1, Xiangshan Road, Beijing 100091, China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
| | - Yu-Cheng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin 150040, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 Beijingnan Road, Urumqi 830011, China
| | - Liu-Qiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Dongxiaofu 1, Xiangshan Road, Beijing 100091, China
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17
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Shen T, Xu M, Qi H, Feng Y, Yang Z, Xu M. Protoplast isolation and transcriptome analysis of developing xylem in Pinus massoniana (Pinaceae). Mol Biol Rep 2021; 49:1857-1869. [PMID: 34826048 DOI: 10.1007/s11033-021-06995-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/19/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND With active physiological and biochemical activities, tissue-specific protoplasts from cambial derivatives, could serve as a specific source for information on xylogenesis for softwood species resistant to stable genetic transformation and lacking available mutants. METHODS AND RESULTS In this study, protoplasts were isolated from developing xylem of the Chinese red pine, Pinus massoniana, by enzymolysis. High-quality RNAs were extracted from developing xylem and their protoplasts for constructing transcriptome libraries. Using Illumina HiSeq 2500 PE150 platform, a total of 362,328,426 clean paired-end reads (54.35G) were generated from multiple cDNA libraries and assembled into 146,422 unigenes. The transcriptome data were further analysed to identify 1567 differentially expressed genes (DEGs) between the isolated protoplasts and developing xylem of P. massoniana (Masson pine), 1126 DEGs were upregulated in protoplasts relative to developing xylem cells and 441 were downregulated. Most of the differentially expressed genes in biological process terms are related to plant response, which may be due to the response to cell wall removal. Further, the expression pattern of 71 unigenes involved in lignin biosynthesis was verified by RNA-seq. CONCLUSIONS This study is the first to report the transcriptome profiles of the developing xylem and its protoplasts of coniferous trees, which provide a new perspective and valuable resource for tracking transcriptional regulatory events in wood formation of Masson pine.
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Affiliation(s)
- Tengfei Shen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Mengxuan Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Haoran Qi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuanheng Feng
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002, China
| | - Zhangqi Yang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning, 530002, China
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China.
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18
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Wang L, Wen S, Wang R, Wang C, Gao B, Lu M. PagWOX11/12a activates PagCYP736A12 gene that facilitates salt tolerance in poplar. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2249-2260. [PMID: 34170605 PMCID: PMC8541782 DOI: 10.1111/pbi.13653] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 05/19/2023]
Abstract
The WUSCHEL-related homeobox (WOX) transcription factors WOX11 and WOX12 regulate adventitious rooting and responses to stress. The underlying physiological and molecular regulatory mechanisms in salt stress tolerance remain largely unexplored. Here, we characterized the roles of PagWOX11/12a from 84K poplar (Populus alba × P. glandulosa) and the underlying regulatory mechanism in salt stress. PagWOX11/12a was strongly induced by salt stress in roots. Overexpression of PagWOX11/12a in poplar enhanced salt tolerance, as evident by the promotion of growth-related biomass. In contrast, salt-treated PagWOX11/12a dominant repression plants displayed reduced biomass growth. Under salt stress conditions, PagWOX11/12a-overexpressed lines showed higher reactive oxygen species (ROS) scavenging capacity and lower accumulation of hydrogen peroxide (H2 O2 ) than non-transgenic 84K plants, whereas the suppressors displayed the opposite phenotype. In addition, PagWOX11/12a directly bound to the promoter region of PagCYP736A12 and regulated PagCYP736A12 expression. The activated PagCYP736A12 could enhance ROS scavenging, thus reducing H2 O2 levels in roots under salt stress in PagWOX11/12a-overexpressed poplars. The collective results support the important role of PagWOX11/12a in salt acclimation of poplar trees, indicating that PagWOX11/12a enhances salt tolerance through modulation of ROS scavenging by directly regulating PagCYP736A12 expression in poplar.
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Affiliation(s)
- Liu‐Qiang Wang
- State Key Laboratory of Tree Genetics and BreedingKey Laboratory of Tree Breeding and Cultivation of the State Forestry AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Shuang‐Shuang Wen
- State Key Laboratory of Tree Genetics and BreedingKey Laboratory of Tree Breeding and Cultivation of the State Forestry AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijingChina
| | - Rui Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Chao Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Bei Gao
- State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongHong KongChina
| | - Meng‐Zhu Lu
- State Key Laboratory of Tree Genetics and BreedingKey Laboratory of Tree Breeding and Cultivation of the State Forestry AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijingChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- State Key Laboratory of Subtropical SilvicultureCollege of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
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19
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Wang J, Zhou H, Zhao Y, Jiang C, Li J, Tang F, Liu Y, Zhao S, Hu J, Song X, Lu MZ. PagGRF12a interacts with PagGIF1b to regulate secondary xylem development through modulating PagXND1a expression in Populus alba × P. glandulosa. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1683-1694. [PMID: 33913591 DOI: 10.1111/jipb.13102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Growth-regulating factors (GRFs) are important regulators of plant development and growth, but their possible roles in xylem development in woody plants remain unclear. Here, we report that Populus alba × Papulus glandulosa PagGRF12a negatively regulates xylem development in poplar. PagGRF12a is expressed in vascular tissues. Compared to non-transgenic control plants, transgenic poplar plants overexpressing PagGRF12a exhibited reduced xylem width and plants with repressed expression of PagGRF12a exhibited increased xylem width. Xylem NAC domain 1 (XND1) encodes a NAC domain transcription factor that regulates xylem development and transcriptional analyses revealed that PagXND1a is highly upregulated in PagGRF12a-overexpressing plants and downregulated in PagGRF12a-suppressed plants, indicating that PagGRF12a may regulate xylem development through PagXND1a. Transient transcriptional assays and chromatin immunoprecipitation-polymerase chain reaction assays confirmed that PagGRF12a directly upregulates PagXND1a. In addition, PagGRF12a interacts with the GRF-Interacting Factor (GIF) PagGIF1b, and this interaction enhances the effects of PagGRF12a on PagXND1a. Our results indicate that PagGRF12a inhibits xylem development by upregulating the expression of PagXND1a.
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Affiliation(s)
- Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China
| | - Houjun Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Cheng Jiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Jihong Li
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yingli Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Shutang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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Gao Y, Yang Q, Yan X, Wu X, Yang F, Li J, Wei J, Ni J, Ahmad M, Bai S, Teng Y. High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy. HORTICULTURE RESEARCH 2021; 8:197. [PMID: 34465760 PMCID: PMC8408243 DOI: 10.1038/s41438-021-00632-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 06/09/2021] [Accepted: 06/13/2021] [Indexed: 05/26/2023]
Abstract
Dormancy-associated MADS-box (DAM) genes serve as crucial regulators of the endodormancy cycle in rosaceous plants. Although pear DAM genes have been identified previously, the lack of a high-quality reference genome and techniques to study gene function have prevented accurate genome-wide analysis and functional verification of such genes. Additionally, the contribution of other genes to the regulation of endodormancy release remains poorly understood. In this study, a high-quality genome assembly for 'Cuiguan' pear (Pyrus pyrifolia), which is a leading cultivar with a low chilling requirement cultivated in China, was constructed using PacBio and Hi-C technologies. Using this genome sequence, we revealed that pear DAM genes were tandemly clustered on Chr8 and Chr15 and were differentially expressed in the buds between 'Cuiguan' and the high-chilling-requirement cultivar 'Suli' during the dormancy cycle. Using a virus-induced gene silencing system, we determined the repressive effects of DAM genes on bud break. Several novel genes potentially involved in the regulation of endodormancy release were identified by RNA sequencing and H3K4me3 chromatin immunoprecipitation sequencing analyses of 'Suli' buds during artificial chilling using the new reference genome. Our findings enrich the knowledge of the regulatory mechanism underlying endodormancy release and chilling requirements and provide a foundation for the practical regulation of dormancy release in fruit trees as an adaptation to climate change.
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Affiliation(s)
- Yuhao Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Qinsong Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Haidian District, Beijing, 100083, China
| | - Xinhui Yan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyue Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Feng Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jianzhao Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- College of Agriculture, Ludong University, Yantai, Shandong, 264025, China
| | - Jia Wei
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Junbei Ni
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Mudassar Ahmad
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Songling Bai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Yuanwen Teng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, 572000, China
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21
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Song X, Zhao Y, Wang J, Lu MZ. The transcription factor KNAT2/6b mediates changes in plant architecture in response to drought via down-regulating GA20ox1 in Populus alba × P. glandulosa. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5625-5637. [PMID: 33987654 DOI: 10.1093/jxb/erab201] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 05/11/2023]
Abstract
Plant architecture is genetically controlled, but is influenced by environmental factors. Plants have evolved adaptive mechanisms that allow changes in their architecture under stress, in which phytohormones play a central role. However, the gene regulators that connect growth and stress signals are rarely reported. Here, we report that a class I KNOX gene, PagKNAT2/6b, can directly inhibit the synthesis of gibberellin (GA), altering plant architecture and improving drought resistance in Populus. Expression of PagKNAT2/6b was significantly induced under drought conditions, and transgenic poplars overexpressing PagKNAT2/6b exhibited shorter internode length and smaller leaf size with short or even absent petioles. Interestingly, these transgenic plants showed improved drought resistance under both short- and long-term drought stress. Histological observations indicated that decreased internode length and leaf size were mainly caused by the inhibition of cell elongation and expansion. GA content was reduced, and the GA20-oxidase gene PagGA20ox1 was down-regulated in overexpressing plants. Expression of PagGA20ox1 was negatively related to that of PagKNAT2/6b under drought stress. ChIP and transient transcription activity assays revealed that PagGA20ox1 was directly targeted by PagKNAT2/6b. Therefore, this study provides evidence that PagKNAT2/6b mediates stress signals and changes in plant architecture via GA signaling by down-regulating PagGA20ox1.
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Affiliation(s)
- Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, China
| | - Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
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22
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Wang R, Zhang Y, Wang C, Wang YC, Wang LQ. ThNAC12 from Tamarix hispida directly regulates ThPIP2;5 to enhance salt tolerance by modulating reactive oxygen species. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 163:27-35. [PMID: 33812224 DOI: 10.1016/j.plaphy.2021.03.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
NAC (NAM, ATAF1/2 and CUC2) transcription factors play critical roles in plant development and abiotic stress responses, and aquaporins have diverse functions in environmental stress responses. In this study, we described the salt-induced transcriptional responses of ThNAC12 and ThPIP2;5 in Tamarix hispida, and their regulatory mechanisms in response to salt stress. Using yeast one-hybrid (Y1H), chromatin immunoprecipitation (ChIP) and dual-luciferase reporter assays, we identified that ThNAC12 directly binds to the NAC recognition sequence (NACRS) of the ThPIP2;5 promoter and then activates the ThPIP2;5 expression. Subcellular localization and transcriptional activation assays demonstrated that ThNAC12 was a nuclear protein with a C-terminal transactivation domain. Compared with the corresponding control plants, transgenic plants overexpressing ThNAC12 exhibited enhanced salt tolerance and displayed increased reactive oxygen species (ROS) scavenging capability and antioxidant enzyme activity levels under salt stress. All results suggested that overexpression of ThNAC12 in plants enhanced salt tolerance through modulation of ROS scavenging via direct regulation of ThPIP2;5 expression in T. hispida.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yu-Cheng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Liu-Qiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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23
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Liu B, Liu J, Yu J, Wang Z, Sun Y, Li S, Lin YCJ, Chiang VL, Li W, Wang JP. Transcriptional reprogramming of xylem cell wall biosynthesis in tension wood. PLANT PHYSIOLOGY 2021; 186:250-269. [PMID: 33793955 PMCID: PMC8154086 DOI: 10.1093/plphys/kiab038] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/04/2021] [Indexed: 05/02/2023]
Abstract
Tension wood (TW) is a specialized xylem tissue developed under mechanical/tension stress in angiosperm trees. TW development involves transregulation of secondary cell wall genes, which leads to altered wood properties for stress adaptation. We induced TW in the stems of black cottonwood (Populus trichocarpa, Nisqually-1) and identified two significantly repressed transcription factor (TF) genes: class B3 heat-shock TF (HSFB3-1) and MYB092. Transcriptomic analysis and chromatin immunoprecipitation (ChIP) were used to identify direct TF-DNA interactions in P. trichocarpa xylem protoplasts overexpressing the TFs. This analysis established a transcriptional regulatory network in which PtrHSFB3-1 and PtrMYB092 directly activate 8 and 11 monolignol genes, respectively. The TF-DNA interactions were verified for their specificity and transactivator roles in 35 independent CRISPR-based biallelic mutants and overexpression transgenic lines of PtrHSFB3-1 and PtrMYB092 in P. trichocarpa. The gene-edited trees (mimicking the repressed PtrHSFB3-1 and PtrMYB092 under tension stress) have stem wood composition resembling that of TW during normal growth and under tension stress (i.e., low lignin and high cellulose), whereas the overexpressors showed an opposite effect (high lignin and low cellulose). Individual overexpression of the TFs impeded lignin reduction under tension stress and restored high levels of lignin biosynthesis in the TW. This study offers biological insights to further uncover how metabolism, growth, and stress adaptation are coordinately regulated in trees.
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Affiliation(s)
- Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry, Beihua University, Jilin 132013, China
| | - Juan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- Department of Life Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Author for communication:
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24
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Sun TT, Wang C, Liu R, Zhang Y, Wang YC, Wang LQ. ThHSFA1 Confers Salt Stress Tolerance through Modulation of Reactive Oxygen Species Scavenging by Directly Regulating ThWRKY4. Int J Mol Sci 2021; 22:ijms22095048. [PMID: 34068763 PMCID: PMC8126225 DOI: 10.3390/ijms22095048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/26/2021] [Accepted: 05/06/2021] [Indexed: 01/03/2023] Open
Abstract
Heat shock transcription factors (HSFs) play critical roles in several types of environmental stresses. However, the detailed regulatory mechanisms in response to salt stress are still largely unknown. In this study, we examined the salt-induced transcriptional responses of ThHSFA1-ThWRKY4 in Tamarix hispida and their functions and regulatory mechanisms in salt tolerance. ThHSFA1 protein acts as an upstream regulator that can directly activate ThWRKY4 expression by binding to the heat shock element (HSE) of the ThWRKY4 promoter using yeast one-hybrid (Y1H), chromatin immunoprecipitation (ChIP), and dual-luciferase reporter assays. ThHSFA1 and ThWRKY4 expression was significantly induced by salt stress and abscisic acid (ABA) treatment in the roots and leaves of T. hispida. ThHSFA1 is a nuclear-localized protein with transactivation activity at the C-terminus. Compared to nontransgenic plants, transgenic plants overexpressing ThHSFA1 displayed enhanced salt tolerance and exhibited reduced reactive oxygen species (ROS) levels and increased antioxidant enzyme activity levels under salt stress. Therefore, we further concluded that ThHSFA1 mediated the regulation of ThWRKY4 in response to salt stress in T. hispida.
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Affiliation(s)
- Ting-Ting Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (T.-T.S.); (R.L.); (Y.Z.)
- Beijing Academy of Forestry and Pomology Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100093, China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (C.W.); (Y.-C.W.)
| | - Rui Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (T.-T.S.); (R.L.); (Y.Z.)
| | - Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (T.-T.S.); (R.L.); (Y.Z.)
| | - Yu-Cheng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (C.W.); (Y.-C.W.)
| | - Liu-Qiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (T.-T.S.); (R.L.); (Y.Z.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel.: +86-10-62889687
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25
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Wang H, Liu S, Dai X, Yang Y, Luo Y, Gao Y, Liu X, Wei W, Wang H, Xu X, Reddy ASN, Jaiswal P, Li W, Liu B, Gu L. PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:655565. [PMID: 34122478 PMCID: PMC8195342 DOI: 10.3389/fpls.2021.655565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/26/2021] [Indexed: 05/16/2023]
Abstract
Populus trichocarpa (P. trichocarpa) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new P. trichocarpa Stem Differentiating Xylem (PSDX) database (http://forestry.fafu.edu.cn/db/SDX), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in P. trichocarpa, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants.
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Affiliation(s)
- Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yongkang Yang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunjun Luo
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yubang Gao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Xu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Bo Liu,
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Lianfeng Gu,
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Lv K, Wei H, Liu G. A R2R3-MYB Transcription Factor Gene, BpMYB123, Regulates BpLEA14 to Improve Drought Tolerance in Betula platyphylla. FRONTIERS IN PLANT SCIENCE 2021; 12:791390. [PMID: 34956289 PMCID: PMC8702527 DOI: 10.3389/fpls.2021.791390] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/18/2021] [Indexed: 05/07/2023]
Abstract
Drought stress causes various negative impacts on plant growth and crop production. R2R3-MYB transcription factors (TFs) play crucial roles in the response to abiotic stress. However, their functions in Betula platyphylla haven't been fully investigated. In this study, a R2R3 MYB transcription factor gene, BpMYB123, was identified from Betula platyphylla and reveals its significant role in drought stress. Overexpression of BpMYB123 enhances tolerance to drought stress in contrast to repression of BpMYB123 by RNA interference (RNAi) in transgenic experiment. The overexpression lines increased peroxidase (POD) and superoxide dismatase (SOD) activities, while decreased hydrogen peroxide (H2O2), superoxide radicals (O2 -), electrolyte leakage (EL) and malondialdehyde (MDA) contents. Our study showed that overexpression of BpMYB123 increased BpLEA14 gene expression up to 20-fold due to BpMYB123 directly binding to the MYB1AT element of BpLEA14 promoter. These results indicate that BpMYB123 acts as a regulator via regulating BpLEA14 to improve drought tolerance in birch.
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Affiliation(s)
- Kaiwen Lv
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, United States
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- *Correspondence: Guifeng Liu,
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27
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García-García I, Méndez-Cea B, Martín-Gálvez D, Seco JI, Gallego FJ, Linares JC. Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline. FRONTIERS IN PLANT SCIENCE 2021; 12:797958. [PMID: 35058957 PMCID: PMC8764141 DOI: 10.3389/fpls.2021.797958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/13/2021] [Indexed: 05/14/2023]
Abstract
Forest tree species are highly vulnerable to the effects of climate change. As sessile organisms with long generation times, their adaptation to a local changing environment may rely on epigenetic modifications when allele frequencies are not able to shift fast enough. However, the current lack of knowledge on this field is remarkable, due to many challenges that researchers face when studying this issue. Huge genome sizes, absence of reference genomes and annotation, and having to analyze huge amounts of data are among these difficulties, which limit the current ability to understand how climate change drives tree species epigenetic modifications. In spite of this challenging framework, some insights on the relationships among climate change-induced stress and epigenomics are coming. Advances in DNA sequencing technologies and an increasing number of studies dealing with this topic must boost our knowledge on tree adaptive capacity to changing environmental conditions. Here, we discuss challenges and perspectives in the epigenetics of climate change-induced forests decline, aiming to provide a general overview of the state of the art.
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Affiliation(s)
- Isabel García-García
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: Isabel García-García,
| | - Belén Méndez-Cea
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- Belén Méndez-Cea,
| | - David Martín-Gálvez
- Departamento de Biodiversidad, Ecología y Evolución, UD Zoología, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - José Ignacio Seco
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
| | - Francisco Javier Gallego
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Carlos Linares
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
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Wei M, Liu Q, Wang Z, Yang J, Li W, Chen Y, Lu H, Nie J, Liu B, Lv K, Mao X, Chen S, Sanders J, Wei H, Li C. PuHox52-mediated hierarchical multilayered gene regulatory network promotes adventitious root formation in Populus ussuriensis. THE NEW PHYTOLOGIST 2020; 228:1369-1385. [PMID: 32589766 DOI: 10.1111/nph.16778] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/15/2020] [Indexed: 05/25/2023]
Abstract
Adventitious root (AR) formation is critically important in vegetative propagation through cuttings in some plants, especially woody species. However, the underlying molecular mechanisms remain elusive. Here, we report the identification of a poplar homeobox gene, PuHox52, which was induced rapidly (within 15 min) at the basal ends of stems upon cutting and played a key regulatory role in adventitious rooting. We demonstrated that overexpression of PuHox52 significantly increased the number of ARs while suppression of PuHox52 had the opposite effect. A multilayered hierarchical gene regulatory network (ML-hGRN) mediated by PuHox52 was reverse-engineered and demonstrated to govern AR formation. PuHox52 regulated AR formation through upregulation of nine hub regulators, including a jasmonate signaling pathway gene, PuMYC2, and an auxin signaling pathway gene, PuAGL12. We also identified coherent type 4 feed-forward loops within this ML-hGRN; PuHox52 repressed PuHDA9, which encodes a histone deacetylase, and led to an increase in acetylation and presumably expression of three hub regulators, PuWRKY51, PuLBD21 and PuIAA7. Our results indicate that the ML-hGRN mediated by PuHox52 governs AR formation at the basal ends of stem cuttings from poplar trees.
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Affiliation(s)
- Ming Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Quangang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhanchao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jingli Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Wenlong Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yingxi Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Han Lu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinfu Nie
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230000, China
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Kaiwen Lv
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xuliang Mao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jennifer Sanders
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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Lv K, Li J, Zhao K, Chen S, Nie J, Zhang W, Liu G, Wei H. Overexpression of an AP2/ERF family gene, BpERF13, in birch enhances cold tolerance through upregulating CBF genes and mitigating reactive oxygen species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110375. [PMID: 32005381 DOI: 10.1016/j.plantsci.2019.110375] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/27/2019] [Accepted: 12/07/2019] [Indexed: 05/20/2023]
Abstract
The AP2/ERF (APETALA2/ethylene-responsive factor) family of transcription factors (TF) is involved in regulating biotic and abiotic stress responses in plants. To explore the role of AP2/ERFs in cold tolerance in woody plants, BpERF13 was cloned and characterized in Betula platyphylla (white birch), a species primarily found in Asia in temperate and boreal climates. Based on phylogenetic analysis, BpERF13 is a member of the IXb subfamily of ERFs. Using qRT-PCR, we found that BpERF13 was differentially expressed in different tissues, and its expression could be induced by cold treatment (4 °C). BpERF13 protein, fused with GFP, was exclusively localized to nuclei. To further assess the role of BpERF13 in cold tolerance, BpERF13 overexpression (OE) transgenic lines were generated in B. platyphylla and used for cold stress treatment and biochemical/physiological studies. BpERF13 overexpression lines had significantly increased tolerance to subfreezing treatment and reduced reactive oxygen species. Using a TF-centered yeast one-hybrid (Y1H) experimental system, we showed that BpERF13 could bind to LTRECOREATCOR15 and MYBCORE cis-elements to activate a reporter gene. ChIP-seq and ChIP-PCR experiments further demonstrated that BpERF13 bound to these cis-elements when present in the 5' proximal regions of superoxide dismutase (SOD), peroxidase (POD), and C-repeat-binding factor (CBF) genes. qRT-PCR was employed to examine the expression levels of these genes in response to cold stress; SOD, POD, and CBF genes were significantly upregulated in BpERF13 transgenic lines compared to wild-type plants in response to cold stress. These results indicate that the transcription factor BpERF13 regulates physiological processes underlying cold tolerance in woody plants.
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Affiliation(s)
- Kaiwen Lv
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, PR China
| | - Jiang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, PR China
| | - Kai Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, PR China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, PR China
| | - Jeff Nie
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu, 210095, PR China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, PR China.
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, United States.
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Wang S, Huang H, Han R, Liu C, Qiu Z, Liu G, Chen S, Jiang J. Negative feedback loop between BpAP1 and BpPI/BpDEF heterodimer in Betula platyphylla × B. pendula. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110280. [PMID: 31623773 DOI: 10.1016/j.plantsci.2019.110280] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/25/2019] [Accepted: 09/18/2019] [Indexed: 05/15/2023]
Abstract
MADS-box genes encode transcription factors involved in the control of many important developmental processes, especially the flower development of angiosperms. Analysis on gene regulatory relationship between MADS-box genes is useful for understanding the molecular mechanism of flower development. In this study, we focused on the regulatory relationship between MADS-box transcription factors APETALA1 (AP1) and PISTILLATA(PI)/DEFICIENS (DEF) in birch. We found that BpPI was an authentic target gene of BpAP1, and BpAP1 activated the expression of BpPI via directly binding to the CArG box motif. Functional analysis of BpPI showed that overexpression of BpPI may delay flowering via restricting flowering activators, in which BpAP1 was significantly down-regulated. We further investigated the regulatory of BpAP1 by BpPI, and found that BpPI could directly bind to the promoter of BpAP1 to restrict BpAP1 expression. In addition, we also found that BpPI could interact with its hypothetical partner BpDEF to co-regulate BpAP1 in birch. Our results suggested that overexpression of BpPI may delay flowering via restricting flowering activators, and there is a negative feedback loop between BpAP1 and BpPI/BpDEF heterodimer in birch. Our results will bring new evidences for further analysis of the molecular mechanism of flower formation in plants that produced unisexual flowers.
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Affiliation(s)
- Shuo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Haijiao Huang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Rui Han
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Chaoyi Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Zhinan Qiu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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31
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Gang H, Li R, Zhao Y, Liu G, Chen S, Jiang J. Loss of GLK1 transcription factor function reveals new insights in chlorophyll biosynthesis and chloroplast development. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3125-3138. [PMID: 30921458 DOI: 10.1093/jxb/erz128] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/06/2019] [Indexed: 05/14/2023]
Abstract
Birch (Betula platyphylla × B. pendula) is an important tree for landscaping due to its attractive white bark and straight trunk. In this study, we characterized a T-DNA yellow-green leaf mutant, yl. We identified six insertion sites (ISs) in the mutant by genome resequencing and found a 40-kb deletion containing BpGLK1 around IS2 on chromosome 2. Complementation experiments with the yl mutant and repression of BpGLK1 in wild-type plants confirmed that BpGLK1 was responsible for the mutated phenotype. Physiological and ultrastructural analyses showed that the leaves of the yl mutant and BpGLK1-repression lines had decreased chlorophyll content and defective chloroplast development compared to the wild-type. Furthermore, the loss function of BpGLK1 also affected photosynthesis in leaves. Transcriptomics, proteomics, and ChIP-PCR analysis revealed that BpGLK1 directly interacted with the promoter of genes related to antenna proteins, chlorophyll biosynthesis, and photosystem subunit synthesis, and regulated their expression. Overall, our research not only provides new insights into the mechanism of chloroplast development and chlorophyll biosynthesis regulated by BpGLK1, but also provides new transgenic birch varieties with various levels of yellowing leaves by repressing BpGLK1 expression.
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Affiliation(s)
- Huixin Gang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ranhong Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yuming Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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32
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Yeh CS, Wang Z, Miao F, Ma H, Kao CT, Hsu TS, Yu JH, Hung ET, Lin CC, Kuan CY, Tsai NC, Zhou C, Qu GZ, Jiang J, Liu G, Wang JP, Li W, Chiang VL, Chang TH, Lin YCJ. A novel synthetic-genetic-array-based yeast one-hybrid system for high discovery rate and short processing time. Genome Res 2019; 29:1343-1351. [PMID: 31186303 PMCID: PMC6673709 DOI: 10.1101/gr.245951.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/06/2019] [Indexed: 12/18/2022]
Abstract
Eukaryotic gene expression is often tightly regulated by interactions between transcription factors (TFs) and their DNA cis targets. Yeast one-hybrid (Y1H) is one of the most extensively used methods to discover these interactions. We developed a high-throughput meiosis-directed yeast one-hybrid system using the Magic Markers of the synthetic genetic array analysis. The system has a transcription factor–DNA interaction discovery rate twice as high as the conventional diploid-mating approach and a processing time nearly one-tenth of the haploid-transformation method. The system also offers the highest accuracy in identifying TF–DNA interactions that can be authenticated in vivo by chromatin immunoprecipitation. With these unique features, this meiosis-directed Y1H system is particularly suited for constructing novel and comprehensive genome-scale gene regulatory networks for various organisms.
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Affiliation(s)
- Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Fang Miao
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chung-Ting Kao
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Shu Hsu
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Institute of Biomedical Informatics and Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Jhong-He Yu
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Er-Tsi Hung
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Chang Lin
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chen-Yu Kuan
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Ni-Chiao Tsai
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guan-Zheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
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Wang S, Huang H, Han R, Chen J, Jiang J, Li H, Liu G, Chen S. BpAP1 directly regulates BpDEF to promote male inflorescence formation in Betula platyphylla × B. pendula. TREE PHYSIOLOGY 2019; 39:1046-1060. [PMID: 30976801 DOI: 10.1093/treephys/tpz021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/28/2019] [Indexed: 05/15/2023]
Abstract
Flowering is a crucial process for plants that is under complex genetic control. AP1 acts as an organizer and a switch for the transition from vegetative to reproductive growth. In our previous study, we found that overexpression of BpAP1 significantly promoted the formation of male inflorescence in birch (Betula platyphlla × B. pendula). In this study, we aimed at investigating the molecular regulatory mechanism of BpAP1 during the process of male inflorescence formation in birch. We found that overexpression of BpAP1 affected the expression of many flowering-related genes, and had significant effect on B class MADS-box genes. A BpAP1-mediated gene regulatory network was constructed and B class gene BpDEF was finally predicted as a key target gene of BpAP1. Chromatin immunoprecipitation results indicated that BpAP1 could directly regulate BpDEF during the process of male inflorescence formation. Yeast one-hybrid assays and its validation in tobacco results suggested that BpAP1 regulated BpDEF via binding to a consensus DNA sequence known as CArG box. Gene function analysis of BpDEF indicated that BpDEF may function in sex-determination, and in particular specify the identity of male inflorescence in birch. Our results provide valuable clues for our understanding of the molecular mechanism of BpAP1 during the process of male inflorescence formation in birch.
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Affiliation(s)
- Shuo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, China
| | - Haijiao Huang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, China
| | - Rui Han
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, China
| | - Jiying Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, China
| | - Huiyu Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, China
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Lin J, Cai Y, Huang G, Yang Y, Li Y, Wang K, Wu Z. Analysis of the chromatin binding affinity of retrotransposases reveals novel roles in diploid and tetraploid cotton. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:32-44. [PMID: 30421576 DOI: 10.1111/jipb.12740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
LTR-retrotransposable elements are major components of diploid (Gossypium arboreum) and tetraploid (Gossypium hirsutum) cotton genomes that have undergone dramatic increases in copy number during the course of evolution. However, little is known about the biological functions of LTR-retrotransposable elements in cotton. Here, we show that a copia-like LTR-retrotransposable element has maintained considerable activity in both G. arboreum and G. hirsutum. We identified two functional domains of the retrotransposon and analyzed their expression levels in various cotton tissues, including leaves, ovules, and germinating seeds. ChIP-qPCR (chromatin immunoprecipitation followed by quantitative PCR), using a copia-specific antibody, established that copia-like proteins primarily bind to the first exons of several protein-coding genes in cotton cells. This finding suggests that retrotransposons play a novel, important role in regulating the transcriptional activities of protein-coding genes with various biological activities.
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Affiliation(s)
- Jing Lin
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ying Cai
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Gai Huang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yan Yang
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yang Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
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Capote T, Barbosa P, Usié A, Ramos AM, Inácio V, Ordás R, Gonçalves S, Morais-Cecílio L. ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber). BMC PLANT BIOLOGY 2018; 18:198. [PMID: 30223777 PMCID: PMC6142680 DOI: 10.1186/s12870-018-1403-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 08/30/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Gene activity is largely controlled by transcriptional regulation through the action of transcription factors and other regulators. QsMYB1 is a member of the R2R3-MYB transcription factor family related to secondary growth, and in particular, with the cork development process. In order to identify the putative gene targets of QsMYB1 across the cork oak genome we developed a ChIP-Seq strategy. RESULTS Results provide direct evidence that QsMY1B targets genes encoding for enzymes involved in the lignin and suberin pathways as well as gene encoding for ABCG transporters and LTPs implicated in the transport of monomeric suberin units across the cellular membrane. These results highlight the role of QsMYB1 as a regulator of lignin and suberin biosynthesis, transport and assembly. CONCLUSION To our knowledge, this work constitutes the first ChIP-Seq experiment performed in cork oak, a non-model plant species with a long-life cycle, and these results will contribute to deepen the knowledge about the molecular mechanisms of cork formation and differentiation.
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Affiliation(s)
- Tiago Capote
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
- Linking Landscape, Environment, Agriculture and Food (LEAF) Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal
| | - Pedro Barbosa
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Ana Usié
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - António Marcos Ramos
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Vera Inácio
- Linking Landscape, Environment, Agriculture and Food (LEAF) Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal
| | - Ricardo Ordás
- Departamento BOS, Escuela Politécnica de Mieres, Oviedo University, Oviedo, Spain
| | - Sónia Gonçalves
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL) / Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- Present Address: Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB101SA UK
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF) Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal
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Haque ME, Han B, Wang B, Wang Y, Liu A. Development of an efficient chromatin immunoprecipitation method to investigate protein-DNA interaction in oleaginous castor bean seeds. PLoS One 2018; 13:e0197126. [PMID: 29738563 PMCID: PMC5940234 DOI: 10.1371/journal.pone.0197126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/26/2018] [Indexed: 11/19/2022] Open
Abstract
Chromatin immunoprecipitation (ChIP) is usually a reliable technique to find the binding sites of a transcription factor. In the current study, we developed a suitable ChIP method using developing castor bean seeds. A castor bean seed with large and persistent endosperm contains high amounts of storage lipids (ca. 50-60%) and is often considered as a model material to studying seed biology. In oleaginous seeds, due to the rich oils which could seriously affect immunoprecipitation and DNA isolation, it is often difficult to carry out a successful ChIP experiment. Thus, the development of an efficient ChIP method for oleaginous seeds is required. In this study, we modified different steps, including tissue preparation for cross-linking, chromatin washing, sonication and immunoprecipitation of other existing methods. As exemplified by the targeted gene identification of a master regulator WRI1, which regulates fatty acid biosynthesis, we found that the improved ChIP method worked well. We analyzed percentage input and fold changes of the ChIPed DNA. We also made successful ChIP-seq libraries using this method. This method provides a technical support not only for use on castor bean seeds; it might be used equally to analyze protein-DNA interaction in vivo in other oleaginous seeds.
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Affiliation(s)
- Mohammad Enamul Haque
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bing Han
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bin Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yue Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Aizhong Liu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis. Nat Commun 2018; 9:1579. [PMID: 29679008 PMCID: PMC5910405 DOI: 10.1038/s41467-018-03863-z] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 03/16/2018] [Indexed: 11/21/2022] Open
Abstract
A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to lignin and affecting wood properties. We perturb these 21 pathway genes and integrate transcriptomic, proteomic, fluxomic and phenomic data from 221 lines selected from ~2000 transgenics (6-month-old). The integrative analysis estimates how changing expression of pathway gene or gene combination affects protein abundance, metabolic-flux, metabolite concentrations, and 25 wood traits, including lignin, tree-growth, density, strength, and saccharification. The analysis then predicts improvements in any of these 25 traits individually or in combinations, through engineering expression of specific monolignol genes. The analysis may lead to greater understanding of other pathways for improved growth and adaptation. A systematic analysis of lignin biosynthetic genes to quantitatively understand their effect on wood properties is still lacking. Here, the authors integrate transcriptomic, proteomic, fluxomic and phenomic data to quantify the impact of perturbations of transcript abundance on lignin biosynthesis and wood properties.
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López-Galiano MJ, González-Hernández AI, Crespo-Salvador O, Rausell C, Real MD, Escamilla M, Camañes G, García-Agustín P, González-Bosch C, García-Robles I. Epigenetic regulation of the expression of WRKY75 transcription factor in response to biotic and abiotic stresses in Solanaceae plants. PLANT CELL REPORTS 2018; 37:167-176. [PMID: 29079899 DOI: 10.1007/s00299-017-2219-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/05/2017] [Indexed: 05/12/2023]
Abstract
SlyWRKY75: gene expression was induced in response to biotic stresses, especially in Botrytis cinerea-infected tomato plants, in which Sly-miR1127-3p is a putative SlyWRKY75 regulator and epigenetic marks were detected. WRKY75 transcription factor involved in Pi homeostasis was recently found also induced in defense against necrotrophic pathogens. In this study, we analyzed by RT-qPCR the expression of SlyWRKY75 gene in tomato plants in response to abiotic stresses (drought or heat) and biotic stresses (Colorado potato beetle larvae infestation, Pseudomonas syringae or Botrytis cinerea infection) being only differentially expressed following biotic stresses, especially upon B. cinerea infection (55-fold induction). JA and JA-Ile levels were significantly increased in tomato plants under biotic stresses compared with control plants, indicating that SlyWRKY75 might be a transcriptional regulator of the JA pathway. The contribution of miRNAs and epigenetic molecular mechanisms to the regulation of this gene in B. cinerea-infected tomato plants was explored. We identified a putative Sly-miR1127-3p miRNA predicted to bind the intronic region of the SlyWRKY75 genomic sequence. Sly-miR1127-3p miRNA was repressed in infected plants (0.4-fold) supporting that it might act as an epigenetic regulation factor of SlyWRKY75 gene expression rather than via the post-transcriptional mechanisms of canonical miRNAs. It has been proposed that certain miRNAs can mediate DNA methylation in the plant nucleus broadening miRNA functions with transcriptional gene silencing by targeting intron-containing pre-mRNAs. Histone modifications analysis by chromatin immunoprecipitation (ChIP) demonstrated the presence of the activator histone modification H3K4me3 on SlyWRKY75 transcription start site and gene body. The induction of this gene in response to B. cinerea correlates with the presence of an activator mark. Thus, miRNAs and chromatin modifications might cooperate as epigenetic factors to modulate SlyWRKY75 gene expression.
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Affiliation(s)
- María José López-Galiano
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| | - Ana I González-Hernández
- Plant Physiology Area, Biochemistry and Biotechnology Laboratory, Department CAMN, University Jaume I, 12071, Castellón, Spain
| | - Oscar Crespo-Salvador
- Department of Biochemistry and Molecular Biology, University of Valencia, IATA (CSIC), 46980, Paterna, Valencia, Spain
| | - Carolina Rausell
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| | - M Dolores Real
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| | - Mónica Escamilla
- Department of Biochemistry and Molecular Biology, University of Valencia, IATA (CSIC), 46980, Paterna, Valencia, Spain
| | - Gemma Camañes
- Plant Physiology Area, Biochemistry and Biotechnology Laboratory, Department CAMN, University Jaume I, 12071, Castellón, Spain
| | - Pilar García-Agustín
- Plant Physiology Area, Biochemistry and Biotechnology Laboratory, Department CAMN, University Jaume I, 12071, Castellón, Spain
| | - Carmen González-Bosch
- Department of Biochemistry and Molecular Biology, University of Valencia, IATA (CSIC), 46980, Paterna, Valencia, Spain
| | - Inmaculada García-Robles
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain.
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Crespo-Salvador Ó, Escamilla-Aguilar M, López-Cruz J, López-Rodas G, González-Bosch C. Determination of histone epigenetic marks in Arabidopsis and tomato genes in the early response to Botrytis cinerea. PLANT CELL REPORTS 2018; 37:153-166. [PMID: 29119291 DOI: 10.1007/s00299-017-2218-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/05/2017] [Indexed: 05/25/2023]
Abstract
Determination of histone epigenetic marks in Arabidopsis and tomato genes in the early response to Botrytis cinerea may contribute to find biomarkers of the early detection of this devastating pathogen. Recent studies have linked epigenetic modifications with plant responses to biotic stresses. Information about specific histone marks upon necrotrophic pathogens is scarce. Here we wondered whether the altered responsiveness of specific genes in plants infected with Botrytis cinerea was associated with changes in chromatin structure. We performed a chromatin immunoprecipitation analysis that obtained differential epigenetic signature of activating marks H3K4me3, H3K9ac, and the repressor one H3K27me3 on both the promoter and the body of the highly induced PR1 in Arabidopsis plants infected with B. cinerea at 24 and 33 h after inoculation. We also determined the histone marks' profile in two differentially expressed genes in response to B. cinerea, as well as to oxidative stress, given its relevance in this infection. These are both the induced CYP71A13, which encodes a cytochrome P450 involved in camalexin synthesis, and is essential against this necrotroph and the repressed EXL7 (Exordium-like 1). We also adapted our protocol in tomato plants infected with B. cinerea. At 24 hpi, H3K4me3 level increased on the promoter and at different locations of the body of the genes induced upon B. cinerea, including DES (divinyl ethyl synthase), LoxD (lipoxygenase D), DOX1 (α-dioxygenase 1), PR2 (pathogenesis-related protein2), WRKY53 and WRKY33. The histone modifications determined herein will allow future studies on epigenetic marks and their transgenerational inheritance in plants infected with B. cinerea. In addition, the analyzed genes are potential biomarkers of B. cinerea infection that could contribute to its early detection in tomato and related crops.
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Affiliation(s)
- Óscar Crespo-Salvador
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, 46980, Paterna, Valencia, Spain
| | - Mónica Escamilla-Aguilar
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, 46980, Paterna, Valencia, Spain
| | - Jaime López-Cruz
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, 46980, Paterna, Valencia, Spain
| | - Gerardo López-Rodas
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Dr. Moliner 50, Burjassot, Valencia, Spain
- Institute of health research INCLIVA, Valencia, Spain
| | - Carmen González-Bosch
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, 46980, Paterna, Valencia, Spain.
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Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa. Proc Natl Acad Sci U S A 2017; 114:E9722-E9729. [PMID: 29078399 DOI: 10.1073/pnas.1714422114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Secondary cell wall (SCW) biosynthesis is the biological process that generates wood, an important renewable feedstock for materials and energy. NAC domain transcription factors, particularly Vascular-Related NAC-Domain (VND) and Secondary Wall-Associated NAC Domain (SND) proteins, are known to regulate SCW differentiation. The regulation of VND and SND is important to maintain homeostasis for plants to avoid abnormal growth and development. We previously identified a splice variant, PtrSND1-A2IR , derived from PtrSND1-A2 as a dominant-negative regulator, which suppresses the transactivation of all PtrSND1 family members. PtrSND1-A2IR also suppresses the self-activation of the PtrSND1 family members except for its cognate transcription factor, PtrSND1-A2, suggesting the existence of an unknown factor needed to regulate PtrSND1-A2 Here, a splice variant, PtrVND6-C1IR , derived from PtrVND6-C1 was discovered that suppresses the protein functions of all PtrVND6 family members. PtrVND6-C1IR also suppresses the expression of all PtrSND1 members, including PtrSND1-A2, demonstrating that PtrVND6-C1IR is the previously unidentified regulator of PtrSND1-A2 We also found that PtrVND6-C1IR cannot suppress the expression of its cognate transcription factor, PtrVND6-C1PtrVND6-C1 is suppressed by PtrSND1-A2IR Both PtrVND6-C1IR and PtrSND1-A2IR cannot suppress their cognate transcription factors but can suppress all members of the other family. The results indicate that the splice variants from the PtrVND6 and PtrSND1 family may exert reciprocal cross-regulation for complete transcriptional regulation of these two families in wood formation. This reciprocal cross-regulation between families suggests a general mechanism among NAC domain proteins and likely other transcription factors, where intron-retained splice variants provide an additional level of regulation.
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Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem. Sci Rep 2017; 7:3370. [PMID: 28611454 PMCID: PMC5469831 DOI: 10.1038/s41598-017-03665-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/02/2017] [Indexed: 01/10/2023] Open
Abstract
Despite the considerable contribution of xylem development (xylogenesis) to plant biomass accumulation, its epigenetic regulation is poorly understood. Furthermore, the relative contributions of histone modifications to transcriptional regulation is not well studied in plants. We investigated the biological relevance of H3K4me3 and H3K27me3 in secondary xylem development using ChIP-seq and their association with transcript levels among other histone modifications in woody and herbaceous models. In developing secondary xylem of the woody model Eucalyptus grandis, H3K4me3 and H3K27me3 genomic spans were distinctly associated with xylogenesis-related processes, with (late) lignification pathways enriched for putative bivalent domains, but not early secondary cell wall polysaccharide deposition. H3K27me3-occupied genes, of which 753 (~31%) are novel targets, were enriched for transcriptional regulation and flower development and had significant preferential expression in roots. Linear regression models of the ChIP-seq profiles predicted ~50% of transcript abundance measured with strand-specific RNA-seq, confirmed in a parallel analysis in Arabidopsis where integration of seven additional histone modifications each contributed smaller proportions of unique information to the predictive models. This study uncovers the biological importance of histone modification antagonism and genomic span in xylogenesis and quantifies for the first time the relative correlations of histone modifications with transcript abundance in plants.
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Moreno-Romero J, Santos-González J, Hennig L, Köhler C. Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles. Nat Protoc 2017; 12:238-254. [PMID: 28055034 DOI: 10.1038/nprot.2016.167] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The early endosperm tissue of dicot species is very difficult to isolate by manual dissection. This protocol details how to apply the INTACT (isolation of nuclei tagged in specific cell types) system for isolating early endosperm nuclei of Arabidopsis at high purity and how to generate parental-specific epigenome profiles. As a Protocol Extension, this article describes an adaptation of an existing Nature Protocol that details the use of the INTACT method for purification of root nuclei. We address how to obtain the INTACT lines, generate the starting material and purify the nuclei. We describe a method that allows purity assessment, which has not been previously addressed. The purified nuclei can be used for ChIP and DNA bisulfite treatment followed by next-generation sequencing (seq) to study histone modifications and DNA methylation profiles, respectively. By using two different Arabidopsis accessions as parents that differ by a large number of single-nucleotide polymorphisms (SNPs), we were able to distinguish the parental origin of epigenetic modifications. Our protocol describes the only working method to our knowledge for generating parental-specific epigenome profiles of the early Arabidopsis endosperm. The complete protocol, from silique collection to finished libraries, can be completed in 2 d for bisulfite-seq (BS-seq) and 3 to 4 d for ChIP-seq experiments.This protocol is an extension to: Nat. Protoc. 6, 56-68 (2011); doi:10.1038/nprot.2010.175; published online 16 December 2010.
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Affiliation(s)
- Jordi Moreno-Romero
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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Li Y, Dong XM, Jin F, Shen Z, Chao Q, Wang BC. Histone Acetylation Modifications Affect Tissue-Dependent Expression of Poplar Homologs of C 4 Photosynthetic Enzyme Genes. FRONTIERS IN PLANT SCIENCE 2017; 8:950. [PMID: 28642769 PMCID: PMC5462996 DOI: 10.3389/fpls.2017.00950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/22/2017] [Indexed: 05/18/2023]
Abstract
Histone modifications play important roles in regulating the expression of C4 photosynthetic genes. Given that all enzymes required for the C4 photosynthesis pathway are present in C3 plants, it has been hypothesized that this expression regulatory mechanism has been conserved. However, the relationship between histone modification and the expression of homologs of C4 photosynthetic enzyme genes has not been well determined in C3 plants. In the present study, we cloned nine hybrid poplar (Populus simonii × Populus nigra) homologs of maize (Zea mays) C4 photosynthetic enzyme genes, carbonic anhydrase (CA), pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxykinase (PCK), and phosphoenolpyruvate carboxylase (PEPC), and investigated the correlation between the expression levels of these genes and the levels of promoter histone acetylation modifications in four vegetative tissues. We found that poplar homologs of C4 homologous genes had tissue-dependent expression patterns that were mostly well-correlated with the level of histone acetylation modification (H3K9ac and H4K5ac) determined by chromatin immunoprecipitation assays. Treatment with the histone deacetylase inhibitor trichostatin A further confirmed the role of histone acetylation in the regulation of the nine target genes. Collectively, these results suggest that both H3K9ac and H4K5ac positively regulate the tissue-dependent expression pattern of the PsnCAs, PsnPPDKs, PsnPCKs, and PsnPEPCs genes and that this regulatory mechanism seems to be conserved among the C3 and C4 species. Our findings provide new insight that will aid efforts to modify the expression pattern of these homologs of C4 genes to engineer C4 plants from C3 plants.
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Affiliation(s)
- Yuan Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry UniversityHarbin, China
| | - Xiu-Mei Dong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Feng Jin
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Zhuo Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
- *Correspondence: Bai-Chen Wang,
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Latrasse D, Benhamed M, Bergounioux C, Raynaud C, Delarue M. Plant programmed cell death from a chromatin point of view. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5887-5900. [PMID: 27639093 DOI: 10.1093/jxb/erw329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Programmed cell death (PCD) is a ubiquitous genetically regulated process consisting of the activation of finely controlled signalling pathways that lead to cellular suicide. PCD can be part of a developmental programme (dPCD) or be triggered by environmental conditions (ePCD). In plant cells, as in animal cells, extensive chromatin condensation and degradation of the nuclear DNA are among the most conspicuous features of cells undergoing PCD. Changes in chromatin condensation could either reflect the structural changes required for internucleosomal fragmentation of nuclear DNA or relate to large-scale chromatin rearrangements associated with a major transcriptional switch occurring during cell death. The aim of this review is to give an update on plant PCD processes from a chromatin point of view. The first part will be dedicated to chromatin conformational changes associated with cell death observed in various developmental and physiological conditions, whereas the second part will be devoted to histone dynamics and DNA modifications associated with critical changes in genome expression during the cell death process.
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Affiliation(s)
- D Latrasse
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - M Benhamed
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - C Bergounioux
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - C Raynaud
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - M Delarue
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
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Hussey SG, Mizrachi E, Groover A, Berger DK, Myburg AA. Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem. BMC PLANT BIOLOGY 2015; 15:117. [PMID: 25957781 PMCID: PMC4425858 DOI: 10.1186/s12870-015-0499-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/21/2015] [Indexed: 05/15/2023]
Abstract
BACKGROUND Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. RESULTS Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A "nano-ChIP-seq" procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. CONCLUSIONS In this first genome-wide analysis of a modified histone in a woody tissue, we optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation.
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Affiliation(s)
- Steven G Hussey
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - Andrew Groover
- US Forest Service, Pacific Southwest Research Station, Davis, CA, USA.
- Department of Plant Biology, University of California, Davis, USA.
| | - Dave K Berger
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
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