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Yang Z, Gu J, Zhao M, Fan X, Guo H, Xie Y, Zhang J, Xiong H, Zhao L, Zhao S, Ding Y, Kong F, Sui L, Xu L, Liu L. Genetic Analysis and Fine Mapping of QTL for the Erect Leaf in Mutant mths29 Induced through Fast Neutron in Wheat. BIOLOGY 2024; 13:430. [PMID: 38927310 PMCID: PMC11201221 DOI: 10.3390/biology13060430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
The erect leaf plays a crucial role in determining plant architecture, with its growth and development regulated by genetic factors. However, there has been a lack of comprehensive studies on the regulatory mechanisms governing wheat lamina joint development, thus failing to meet current breeding demands. In this study, a wheat erect leaf mutant, mths29, induced via fast neutron mutagenesis, was utilized for QTL fine mapping and investigation of lamina joint development. Genetic analysis of segregating populations derived from mths29 and Jimai22 revealed that the erect leaf trait was controlled by a dominant single gene. Using BSR sequencing and map-based cloning techniques, the QTL responsible for the erect leaf trait was mapped to a 1.03 Mb physical region on chromosome 5A. Transcriptome analysis highlighted differential expression of genes associated with cell division and proliferation, as well as several crucial transcription factors and kinases implicated in lamina joint development, particularly in the boundary cells of the preligule zone in mths29. These findings establish a solid foundation for understanding lamina joint development and hold promise for potential improvements in wheat plant architecture.
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Affiliation(s)
- Zhixin Yang
- College of Agriculture, Yangtze University, Jingzhou 434023, China; (Z.Y.); (X.F.); (L.X.)
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, CAEA Research and Development Center on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (H.G.); (Y.X.); (H.X.); (L.Z.); (S.Z.); (Y.D.)
| | - Jiayu Gu
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, CAEA Research and Development Center on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (H.G.); (Y.X.); (H.X.); (L.Z.); (S.Z.); (Y.D.)
| | - Minghui Zhao
- Dry-Land Farming Institute of Hebei Academy of Agricultural and Forestry Sciences, Hengshui 053000, China
| | - Xiaofeng Fan
- College of Agriculture, Yangtze University, Jingzhou 434023, China; (Z.Y.); (X.F.); (L.X.)
| | - Huijun Guo
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, CAEA Research and Development Center on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (H.G.); (Y.X.); (H.X.); (L.Z.); (S.Z.); (Y.D.)
| | - Yongdun Xie
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, CAEA Research and Development Center on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (H.G.); (Y.X.); (H.X.); (L.Z.); (S.Z.); (Y.D.)
| | - Jinfeng Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, CAEA Research and Development Center on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (H.G.); (Y.X.); (H.X.); (L.Z.); (S.Z.); (Y.D.)
| | - Hongchun Xiong
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, CAEA Research and Development Center on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (H.G.); (Y.X.); (H.X.); (L.Z.); (S.Z.); (Y.D.)
| | - Linshu Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, CAEA Research and Development Center on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (H.G.); (Y.X.); (H.X.); (L.Z.); (S.Z.); (Y.D.)
| | - Shirong Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, CAEA Research and Development Center on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (H.G.); (Y.X.); (H.X.); (L.Z.); (S.Z.); (Y.D.)
| | - Yuping Ding
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, CAEA Research and Development Center on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (H.G.); (Y.X.); (H.X.); (L.Z.); (S.Z.); (Y.D.)
| | - Fuquan Kong
- China Institute of Atomic Energy, Beijing 102413, China; (F.K.); (L.S.)
| | - Li Sui
- China Institute of Atomic Energy, Beijing 102413, China; (F.K.); (L.S.)
| | - Le Xu
- College of Agriculture, Yangtze University, Jingzhou 434023, China; (Z.Y.); (X.F.); (L.X.)
| | - Luxiang Liu
- State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, CAEA Research and Development Center on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.G.); (H.G.); (Y.X.); (H.X.); (L.Z.); (S.Z.); (Y.D.)
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2
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Xu F, Dong H, Guo W, Le L, Jing Y, Fletcher JC, Sun J, Pu L. The trxG protein ULT1 regulates Arabidopsis organ size by interacting with TCP14/15 to antagonize the LIM peptidase DA1 for H3K4me3 on target genes. PLANT COMMUNICATIONS 2024; 5:100819. [PMID: 38217289 PMCID: PMC11009162 DOI: 10.1016/j.xplc.2024.100819] [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: 07/21/2023] [Revised: 08/18/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Plant organ size is an important agronomic trait that makes a significant contribution to plant yield. Despite its central importance, the genetic and molecular mechanisms underlying organ size control remain to be fully clarified. Here, we report that the trithorax group protein ULTRAPETALA1 (ULT1) interacts with the TEOSINTE BRANCHED1/CYCLOIDEA/PCF14/15 (TCP14/15) transcription factors by antagonizing the LIN-11, ISL-1, and MEC-3 (LIM) peptidase DA1, thereby regulating organ size in Arabidopsis. Loss of ULT1 function significantly increases rosette leaf, petal, silique, and seed size, whereas overexpression of ULT1 results in reduced organ size. ULT1 associates with TCP14 and TCP15 to co-regulate cell size by affecting cellular endoreduplication. Transcriptome analysis revealed that ULT1 and TCP14/15 regulate common target genes involved in endoreduplication and leaf development. ULT1 can be recruited by TCP14/15 to promote lysine 4 of histone H3 trimethylation at target genes, activating their expression to determine final cell size. Furthermore, we found that ULT1 influences the interaction of DA1 and TCP14/15 and antagonizes the effect of DA1 on TCP14/15 degradation. Collectively, our findings reveal a novel epigenetic mechanism underlying the regulation of organ size in Arabidopsis.
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Affiliation(s)
- Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huixue Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yexing Jing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jennifer C Fletcher
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Plant Gene Expression Center, United States Department of Agriculture - Agricultural Research Service, Albany, CA 94710, USA
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Ochoa-Alejo N, Reyes-Valdés MH, Martínez O. Estimating Transcriptome Diversity and Specialization in Capsicum annuum L. PLANTS (BASEL, SWITZERLAND) 2024; 13:983. [PMID: 38611513 PMCID: PMC11013594 DOI: 10.3390/plants13070983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
Chili pepper fruits of the genus Capsicum represent excellent experimental models to study the growth, development, and ripening processes in a non-climacteric species at the physiological, biochemical, and molecular levels. Fruit growth, development, and ripening involve a complex, harmonious, and finely controlled regulation of gene expression. The purpose of this study was to estimate the changes in transcriptome diversity and specialization, as well as gene specificities during fruit development in this crop, and to illustrate the advantages of estimating these parameters. To achieve these aims, we programmed and made publicly available an R package. In this study, we applied these methods to a set of 179 RNA-Seq libraries from a factorial experiment that includes 12 different genotypes at various stages of fruit development. We found that the diversity of the transcriptome decreases linearly from the flower to the mature fruit, while its specialization follows a complex and non-linear behavior during this process. Additionally, by defining sets of genes with different degrees of specialization and applying Gene Ontology enrichment analysis, we identified processes, functions, and components that play a central role in particular fruit development stages. In conclusion, the estimation of diversity, specialization, and specificity summarizes the global properties of the transcriptomes, providing insights that are difficult to achieve by other means.
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Affiliation(s)
- Neftalí Ochoa-Alejo
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico;
| | - M. Humberto Reyes-Valdés
- Department of Plant Breeding, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Coahuila, Mexico;
| | - Octavio Martínez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Guanajuato, Mexico
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Hu G, Zhang D, Luo D, Sun W, Zhou R, Hong Z, Munir S, Ye Z, Yang C, Zhang J, Wang T. SlTCP24 and SlTCP29 synergistically regulate compound leaf development through interacting with SlAS2 and activating transcription of SlCKX2 in tomato. THE NEW PHYTOLOGIST 2023; 240:1275-1291. [PMID: 37615215 DOI: 10.1111/nph.19221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023]
Abstract
The complexity of compound leaves results primarily from the leaflet initiation and arrangement during leaf development. However, the molecular mechanism underlying compound leaf development remains a central research question. SlTCP24 and SlTCP29, two plant-specific transcription factors with the conserved TCP motif, are shown here to synergistically regulate compound leaf development in tomato. When both of them were knocked out simultaneously, the number of leaflets significantly increased, and the shape of the leaves became more complex. SlTCP24 and SlTCP29 could form both homodimers and heterodimers, and such dimerization was impeded by the leaf polarity regulator SlAS2, which interacted with SlTCP24 and SlTCP29. SlTCP24 and SlTCP29 could bind to the TCP-binding cis-element of the SlCKX2 promoter and activate its transcription. Transgenic plants with SlTCP24 and SlTCP29 double-gene knockout had a lowered transcript level of SlCKX2 and an elevated level of cytokinin. This work led to the identification of two key regulators of tomato compound leaf development and their targeted genes involved in cytokinin metabolic pathway. A model of regulation of compound leaf development was proposed based on observations of this study.
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Affiliation(s)
- Guoyu Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Danqiu Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Dan Luo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Wenhui Sun
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Rijin Zhou
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Shoaib Munir
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Zhibiao Ye
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Changxian Yang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Junhong Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Taotao Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
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Shi T, Bai Y, Wu X, Wang Y, Iqbal S, Tan W, Ni Z, Gao Z. PmAGAMOUS recruits polycomb protein PmLHP1 to regulate single-pistil morphogenesis in Japanese apricot. PLANT PHYSIOLOGY 2023; 193:466-482. [PMID: 37204822 DOI: 10.1093/plphys/kiad292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/31/2023] [Accepted: 04/12/2023] [Indexed: 05/20/2023]
Abstract
Japanese apricot (Prunus mume Sieb. et Zucc.) is a traditional fruit tree with a long history. Multiple pistils (MP) lead to the formation of multiple fruits, decreasing fruit quality and yield. In this study, the morphology of flowers was observed at 4 stages of pistil development: undifferentiated stage (S1), predifferentiation stage (S2), differentiation stage (S3), and late differentiation stage (S4). In S2 and S3, the expression of PmWUSCHEL (PmWUS) in the MP cultivar was significantly higher than that in the single-pistil (SP) cultivar, and the gene expression of its inhibitor, PmAGAMOUS (PmAG), also showed the same trend, indicating that other regulators participate in the regulation of PmWUS during this period. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) showed that PmAG could bind to the promoter and the locus of PmWUS, and H3K27me3 repressive marks were also detected at these sites. The SP cultivar exhibited an elevated level of DNA methylation in the promoter region of PmWUS, which partially overlapped with the region of histone methylation. This suggests that the regulation of PmWUS involves both transcription factors and epigenetic modifications. Also, the gene expression of Japanese apricot LIKE HETEROCHROMATIN PROTEIN (PmLHP1), an epigenetic regulator, in MP was significantly lower than that in SP in S2 to 3, contrary to the trend in expression of PmWUS. Our results showed that PmAG recruited sufficient PmLHP1 to maintain the level of H3K27me3 on PmWUS during the S2 of pistil development. This recruitment of PmLHP1 by PmAG inhibits the expression of PmWUS at the precise time, leading to the formation of 1 normal pistil primordium.
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Affiliation(s)
- Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinxin Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- College of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Yike Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shahid Iqbal
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL 32351, USA
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Kupriyanova E, Manakhov A, Ezhova T. PARG1 and EXA1 genes as possible components of the facultative epigenetic control of plant development. PHYSIOLOGIA PLANTARUM 2023; 175:e13959. [PMID: 37350155 DOI: 10.1111/ppl.13959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
Plants are able to adjust their developmental program in response to incremental environmental changes by reprogramming the epigenomes of the cells. This process, known as facultative epigenetic developmental control, underlies plant developmental plasticity and the amazing diversity of morphotypes, which arises from the changes in cell fates. How plants determine when epigenome reprogramming should occur is largely unclear. Here, we show that the Arabidopsis PARG1 and EXA1 genes, encoding poly(ADP-ribose) glycohydrolase and GYF domain protein involved in nonsense-mediated mRNA decay, respectively, act synergistically in maintaining leaf cell identity. Loss of their function in Arabidopsis tae mutant triggers autoimmunity and wounding response, alters transcription of a number of epigenetic regulators, initiates the acquisition of pluripotency by cells of the developed leaf and ectopic outgrowths and buds formation. The dependence of the cell fate on the activity level of PARG1 and EXA1 genes indicates that these interacting genes may function as an important regulator of facultative epigenetic control of plant development.
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Affiliation(s)
- Evgenia Kupriyanova
- Faculty of Biology, Department of Genetics, Lomonosov Moscow State University, Moscow, Russia
| | - Andrey Manakhov
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Ezhova
- Faculty of Biology, Department of Genetics, Lomonosov Moscow State University, Moscow, Russia
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7
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Bai Y, Shi T, Huang X, Zhou P, Ouma KO, Ni Z, Gao F, Tan W, Ma C, Ma Y, Gao Z. Genome-Wide Identification of the KNOX Gene Family in Japanese Apricot ( Prunus mume Sieb. et Zucc.) and Functional Characterization of PmKNAT2 Genes. Genes (Basel) 2023; 14:genes14040939. [PMID: 37107697 PMCID: PMC10138190 DOI: 10.3390/genes14040939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The Knotted1-like Homeobox gene is crucial for plant morphological development and growth. Physicochemical characteristics, phylogenetic relationships, chromosomal localization, cis-acting elements, and tissue-specific expression patterns of the 11 PmKNOX genes found in the Japanese apricot genome in this study were examined. Proteins of 11 PmKNOX were soluble proteins with isoelectric points between 4.29 and 6.53, molecular masses between 15.732 and 44.011 kDa, and amino acid counts between 140 and 430. The identified PmKNOX gene family was split into three subfamilies by jointly constructing the phylogenetic tree of KNOX proteins in Japanese apricot and Arabidopsis thaliana. Combined outcomes of the analyzed conserved motifs and gene structures of the 11 PmKNOX genes from the same subfamily displayed comparable gene structure and motif patterns. The 11 PmKNOX members were distributed across six chromosomes, while two sets of PmKNOX genes were found to be collinear. Analysis of the 2000 bp promoter upstream of the coding region of the PmKNOX gene revealed that most PmKNOX genes might be involved in the physiological metabolism, growth and development processes of plants. The PmKNOX gene expression profile revealed that these genes were expressed at varying levels in different tissues, and most of them were linked to the meristems of leaf and flower buds, suggesting that PmKNOX may be involved in plants' apical meristems. In Arabidopsis thaliana, functional validation of PmKNAT2a and PmKNAT2b revealed that these two genes might be involved in regulating leaf and stem development. In addition to laying the groundwork for future research on the function of these genes, understanding the evolutionary relationships between members of the PmKNOX gene family provides opportunities for future breeding in Japanese apricots.
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Affiliation(s)
- Yang Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengyu Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kenneth Omondi Ouma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengdong Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufan Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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8
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Zhang Y, Ma M, Liu M, Sun A, Zheng X, Liu K, Yin C, Li C, Jiang C, Tu X, Fang Y. Histone H2A monoubiquitination marks are targeted to specific sites by cohesin subunits in Arabidopsis. Nat Commun 2023; 14:1209. [PMID: 36869051 PMCID: PMC9984397 DOI: 10.1038/s41467-023-36788-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/16/2023] [Indexed: 03/05/2023] Open
Abstract
Histone H2A monoubiquitination (H2Aub1) functions as a conserved posttranslational modification in eukaryotes to maintain gene expression and guarantee cellular identity. Arabidopsis H2Aub1 is catalyzed by the core components AtRING1s and AtBMI1s of polycomb repressive complex 1 (PRC1). Because PRC1 components lack known DNA binding domains, it is unclear how H2Aub1 is established at specific genomic locations. Here, we show that the Arabidopsis cohesin subunits AtSYN4 and AtSCC3 interact with each other, and AtSCC3 binds to AtBMI1s. H2Aub1 levels are reduced in atsyn4 mutant or AtSCC3 artificial microRNA knockdown plants. ChIP-seq assays indicate that most binding events of AtSYN4 and AtSCC3 are associated with H2Aub1 along the genome where transcription is activated independently of H3K27me3. Finally, we show that AtSYN4 binds directly to the G-box motif and directs H2Aub1 to these sites. Our study thus reveals a mechanism for cohesin-mediated recruitment of AtBMI1s to specific genomic loci to mediate H2Aub1.
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Affiliation(s)
- Yu Zhang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Min Ma
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Meng Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 200065, Shanghai, China
| | - Aiqing Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xiaoyun Zheng
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Kunpeng Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Chunmei Yin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Chuanshun Li
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 200065, Shanghai, China.
| | - Xiaoyu Tu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China.
| | - Yuda Fang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China.
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9
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Zhou R, Fan M, Zhao M, Jiang X, Liu Q. Overexpression of LtKNOX1 from Lilium tsingtauense in Nicotiana benthamiana affects the development of leaf morphology. PLANT SIGNALING & BEHAVIOR 2022; 17:2031783. [PMID: 35139775 PMCID: PMC9176240 DOI: 10.1080/15592324.2022.2031783] [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: 11/21/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 05/27/2023]
Abstract
Leaves are the main vegetative organs of the aboveground part of plants and play an important role in plant morphogenesis. KNOTTED-LIKE HOMEOBOX (KNOX) plays a crucial role in regulating leaf cell fate and maintaining leaf development. In this study, we analyzed LtKNOX1 from Lilium tsingtauense and illustrated its function in transgenic plants. Tissue-specific expression analysis indicated that LtKNOX1 was highly expressed in stems, young flower buds, and shoot apical meristems (SAMs). Ectopic overexpression of LtKNOX1 in Nicotiana benthamiana suggested that transformants with mild phenotypes were characterized by foliar wrinkles and mildly curled leaves; transformants with intermediate phenotypes showed severely crimped blades and narrow leaf angles, and the most severe phenotypes lacked normal SAMs and leaves. Moreover, the expression levels of genes involved in the regulation of KNOX in transgenic plants were detected, including ASYMMETRIC LEAVES1, PIN-FORMED 1, GA20-oxidase, CUP-SHAPED COTYLEDON 2, CLAVATA 1 and WUSCHEL(WUS), and the expression of other genes were down-regulated except WUS. This study contributes to our understanding of the LtKNOX1 function.
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Affiliation(s)
- Rui Zhou
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Menglong Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Mei Zhao
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xinqiang Jiang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qinghua Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
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10
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Müller-Xing R, Xing Q. The plant stem-cell niche and pluripotency: 15 years of an epigenetic perspective. FRONTIERS IN PLANT SCIENCE 2022; 13:1018559. [PMID: 36388540 PMCID: PMC9659954 DOI: 10.3389/fpls.2022.1018559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Pluripotent stem-cells are slowly dividing cells giving rise to daughter cells that can either differentiate to new tissues and organs, or remain stem-cells. In plants, stem-cells are located in specific niches of the shoot and root apical meristems (SAMs and RAMs). After ablation of stem-cell niches, pluripotent meristematic cells can establish new stem-cells, whereas the removal of the whole meristem destructs the regeneration process. In tissue cultures, after detached plant organs are transferred to rooting or callus induction medium (G5 or CIM), vasculature-associated pluripotent cells (VPCs) immediately start proliferation to form adventitious roots or callus, respectively, while other cell types of the organ explants basically play no part in the process. Hence, in contrast to the widely-held assumption that all plant cells have the ability to reproduce a complete organism, only few cell types are pluripotent in practice, raising the question how pluripotent stem-cells differ from differentiated cells. It is now clear that, in addition to gene regulatory networks of pluripotency factors and phytohormone signaling, epigenetics play a crucial role in initiation, maintenance and determination of plant stem-cells. Although, more and more epigenetic regulators have been shown to control plant stem-cell fate, only a few studies demonstrate how they are recruited and how they change the chromatin structure and transcriptional regulation of pluripotency factors. Here, we highlight recent breakthroughs but also revisited classical studies of epigenetic regulation and chromatin dynamics of plant stem-cells and their pluripotent precursor-cells, and point out open questions and future directions.
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11
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Borah P, Ni F, Ying W, Zhuang H, Chong SL, Hu XG, Yang J, Lin EP, Huang H. Genome-wide identification and characterization of OVATE family proteins in Betula luminifera reveals involvement of BlOFP3 and BlOFP5 genes in leaf development. FRONTIERS IN PLANT SCIENCE 2022; 13:950936. [PMID: 36311104 PMCID: PMC9613114 DOI: 10.3389/fpls.2022.950936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Ovate family proteins (OFP) are plant-specific transcription factors involved in regulating morphologies of the lateral organs, plant growth and development. However, the functional roles of OFP genes in Betula luminifera, an important timber tree species, are not well studied. In this study, we identified 20 BlOFP genes and analyzed their phylogenetic relationship, gene structure, conserved motifs, and cis-elements. Further, expression analysis indicates that BlOFP genes were up-regulated in leaves on the one-year-old branch compared to leaves on the current-year branch and bract, except BlOFP7, BlOFP11, BlOFP14 and BlOFP12. The overexpression of BlOFP3 and BlOFP5 in Arabidopsis thaliana not only resulted in a slower growth rate but also produced sawtooth shape, flatter and darker green rosette leaves. Further investigation showed that the leaf thickness of the transgenic plants was more than double that of the wild type, which was caused by the increasement in the number and size of palisade tissue cells. Furthermore, the expression analysis also indicated that the expressions of several genes related to leaf development were significantly changed in the transgene plants. These results suggested the significant roles of BlOFP3 and BlOFP5 in leaf development. Moreover, protein-protein interaction studies showed that BlOFP3 interacts with BlKNAT5, and BlOFP5 interacts with BlKNAT5, BlBLH6 and BlBLH7. In conclusion, our study demonstrates that BlOFP3 and BlOFP5 were involved in leaf shape and thickness regulation by forming a complex with BlKNAT5, BlBLH6 and BlBLH7. In addition, our study serves as a guide for future functional genomic studies of OFP genes of the B. luminifera.
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Affiliation(s)
- Priyanka Borah
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Fei Ni
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Weiyang Ying
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Hebi Zhuang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Sun-Li Chong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Xian-Ge Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Er-pei Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Huahong Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
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12
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Chen W, Tamada Y, Yamane H, Matsushita M, Osako Y, Gao-Takai M, Luo Z, Tao R. H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1015-1031. [PMID: 35699670 DOI: 10.1111/tpj.15868] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Bud dormancy helps woody perennials survive winter and activate robust plant development in the spring. For apple (Malus × domestica), short-term chilling induces bud dormancy in autumn, then prolonged chilling leads to dormancy release and a shift to a quiescent state in winter, with subsequent warm periods promoting bud break in spring. Epigenetic regulation contributes to seasonal responses such as vernalization. However, how histone modifications integrate seasonal cues and internal signals during bud dormancy in woody perennials remains largely unknown. Here, we show that H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. The global changes in gene expression strongly correlated with changes in H3K4me3, but not H3K27me3. High expression of DORMANCY-ASSOCIATED MADS-box (DAM) genes, key regulators of dormancy, in autumn was associated with high H3K4me3 levels. In addition, known DAM/SHORT VEGETATIVE PHASE (SVP) target genes significantly overlapped with H3K4me3-modified genes as bud dormancy progressed. These data suggest that H3K4me3 contributes to the central dormancy circuit, consisting of DAM/SVP and abscisic acid (ABA), in autumn. In winter, the lower expression and H3K4me3 levels at DAMs and gibberellin metabolism genes control chilling-induced release of dormancy. Warming conditions in spring facilitate the expression of genes related to phytohormones, the cell cycle, and cell wall modification by increasing H3K4me3 toward bud break. Our study also revealed that activation of auxin and repression of ABA sensitivity in spring are conditioned at least partly through temperature-mediated epigenetic regulation in winter.
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Affiliation(s)
- Wenxing Chen
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China
| | - Yosuke Tamada
- School of Engineering, Utsunomiya University, Utsunomiya, Japan
- National Institute for Basic Biology, Okazaki, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Miura-gun, Japan
| | - Hisayo Yamane
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Yutaro Osako
- Faculty of Agriculture, Shinshu University, Kamiina-gun, Japan
| | - Mei Gao-Takai
- Agricultural Experimental Station, Ishikawa Prefectural University, Nonoichi, Japan
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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13
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Mo W, Zhang J, Zhang L, Yang Z, Yang L, Yao N, Xiao Y, Li T, Li Y, Zhang G, Bian M, Du X, Zuo Z. Arabidopsis cryptochrome 2 forms photobodies with TCP22 under blue light and regulates the circadian clock. Nat Commun 2022; 13:2631. [PMID: 35551190 PMCID: PMC9098493 DOI: 10.1038/s41467-022-30231-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cryptochromes are blue light receptors that regulate plant growth and development. They also act as the core components of the central clock oscillator in animals. Although plant cryptochromes have been reported to regulate the circadian clock in blue light, how they do so is unclear. Here we show that Arabidopsis cryptochrome 2 (CRY2) forms photobodies with the TCP22 transcription factor in response to blue light in plant cells. We provide evidence that PPK kinases influence the characteristics of these photobodies and that together these components, along with LWD transcriptional regulators, can positively regulate the expression of CCA1 encoding a central component of the circadian oscillator. Cryptochrome signaling has been reported to regulate circadian oscillations in plants. Here the authors show that CRY2 and the TCP22 transcription factors can form photobodies in a blue light dependent manner and induce expression of CCA1, a core component of the circadian oscillator.
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Affiliation(s)
- Weiliang Mo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Junchuan Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Li Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Zhenming Yang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Liang Yang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Nan Yao
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yong Xiao
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Tianhong Li
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Yaxing Li
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guangmei Zhang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingdi Bian
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Xinglin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Zecheng Zuo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China. .,Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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14
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Godwin J, Farrona S. The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors. EPIGENOMES 2022; 6:epigenomes6010008. [PMID: 35323212 PMCID: PMC8948837 DOI: 10.3390/epigenomes6010008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation.
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15
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Rodriguez-Granados NY, Ramirez-Prado JS, Brik-Chaouche R, An J, Manza-Mianza D, Sircar S, Troadec C, Hanique M, Soulard C, Costa R, Dogimont C, Latrasse D, Raynaud C, Boualem A, Benhamed M, Bendahmane A. CmLHP1 proteins play a key role in plant development and sex determination in melon (Cucumis melo). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1213-1228. [PMID: 34897855 DOI: 10.1111/tpj.15627] [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: 05/04/2021] [Revised: 11/26/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
In monoecious melon (Cucumis melo), sex is determined by the differential expression of sex determination genes (SDGs) and adoption of sex-specific transcriptional programs. Histone modifications such as H3K27me3 have been previously shown to be a hallmark associated to unisexual flower development in melon; yet, no genetic approaches have been conducted for elucidating the roles of H3K27me3 writers, readers, and erasers in this process. Here we show that melon homologs to Arabidopsis LHP1, CmLHP1A and B, redundantly control several aspects of plant development, including sex expression. Cmlhp1ab double mutants displayed an overall loss and redistribution of H3K27me3, leading to a deregulation of genes involved in hormone responses, plant architecture, and flower development. Consequently, double mutants display pleiotropic phenotypes and, interestingly, a general increase of the male:female ratio. We associated this phenomenon with a general deregulation of some hormonal response genes and a local activation of male-promoting SDGs and MADS-box transcription factors. Altogether, these results reveal a novel function for CmLHP1 proteins in maintenance of monoecy and provide novel insights into the polycomb-mediated epigenomic regulation of sex lability in plants.
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Affiliation(s)
- Natalia Yaneth Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Juan Sebastian Ramirez-Prado
- Centre of Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Jing An
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Sanchari Sircar
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Christelle Troadec
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Melissa Hanique
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Camille Soulard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Rafael Costa
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Catherine Dogimont
- INRA, UR 1052, Unité de Génétique et d'Amélioration des Fruits et Légumes, BP 94, F-84143, Montfavet, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Adnane Boualem
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
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Liu Y, Yang X, Zhou M, Yang Y, Li F, Yan X, Zhang M, Wei Z, Qin S, Min J. Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain. J Biol Chem 2022; 298:101623. [PMID: 35074427 PMCID: PMC8861120 DOI: 10.1016/j.jbc.2022.101623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Arabidopsis LHP1 (LIKE HETEROCHROMATIN PROTEIN 1), a unique homolog of HP1 in Drosophila, plays important roles in plant development, growth, and architecture. In contrast to specific binding of the HP1 chromodomain to methylated H3K9 histone tails, the chromodomain of LHP1 has been shown to bind to both methylated H3K9 and H3K27 histone tails, and LHP1 carries out its function mainly via its interaction with these two epigenetic marks. However, the molecular mechanism for the recognition of methylated histone H3K9/27 by the LHP1 chromodomain is still unknown. In this study, we characterized the binding ability of LHP1 to histone H3K9 and H3K27 peptides and found that the chromodomain of LHP1 binds to histone H3K9me2/3 and H3K27me2/3 peptides with comparable affinities, although it exhibited no binding or weak binding to unmodified or monomethylated H3K9/K27 peptides. Our crystal structures of the LHP1 chromodomain in peptide-free and peptide-bound forms coupled with mutagenesis studies reveal that the chromodomain of LHP1 bears a slightly different chromodomain architecture and recognizes methylated H3K9 and H3K27 peptides via a hydrophobic clasp, similar to the chromodomains of human Polycomb proteins, which could not be explained only based on primary structure analysis. Our binding and structural studies of the LHP1 chromodomain illuminate a conserved ligand interaction mode between chromodomains of both animals and plants, and shed light on further functional study of the LHP1 protein.
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Affiliation(s)
- Yanli Liu
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China.
| | - Xiajie Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Mengqi Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Yinxue Yang
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | - Fangzhou Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Xuemei Yan
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | | | - Zhengguo Wei
- School of Biology and Basic Medical Science, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | - Su Qin
- Life Science Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China.
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17
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Machida Y, Suzuki T, Sasabe M, Iwakawa H, Kojima S, Machida C. Arabidopsis ASYMMETRIC LEAVES2 (AS2): roles in plant morphogenesis, cell division, and pathogenesis. JOURNAL OF PLANT RESEARCH 2022; 135:3-14. [PMID: 34668105 PMCID: PMC8755679 DOI: 10.1007/s10265-021-01349-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/21/2021] [Indexed: 05/26/2023]
Abstract
The ASYMMETRIC LEAVES2 (AS2) gene in Arabidopsis thaliana is responsible for the development of flat, symmetric, and extended leaf laminae and their vein systems. AS2 protein is a member of the plant-specific AS2/LOB protein family, which includes 42 members comprising the conserved amino-terminal domain referred to as the AS2/LOB domain, and the variable carboxyl-terminal region. Among the members, AS2 has been most intensively investigated on both genetic and molecular levels. AS2 forms a complex with the myb protein AS1, and is involved in epigenetic repression of the abaxial genes ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3), ARF4, and class 1 KNOX homeobox genes. The repressed expression of these genes by AS2 is markedly enhanced by the cooperative action of various modifier genes, some of which encode nucleolar proteins. Further downstream, progression of the cell division cycle in the developing organs is stimulated; meristematic states are suppressed in determinate leaf primordia; and the extension of leaf primordia is induced. AS2 binds the specific sequence in exon 1 of ETT/ARF3 and maintains methylated CpGs in several exons of ETT/ARF3. AS2 forms bodies (designated as AS2 bodies) at nucleolar peripheries. AS2 bodies partially overlap chromocenters, including inactive 45S ribosomal DNA repeats, suggesting the presence of molecular and functional links among AS2, the 45S rDNAs, and the nucleolus to exert the repressive regulation of ETT/ARF3. The AS2/LOB domain is characterized by three subdomains, the zinc finger (ZF) motif, the internally conserved-glycine containing (ICG) region, and the leucine-zipper-like (LZL) region. Each of these subdomains is essential for the formation of AS2 bodies. ICG to LZL are required for nuclear localization, but ZF is not. LZL intrinsically has the potential to be exported to the cytoplasm. In addition to its nuclear function, it has been reported that AS2 plays a positive role in geminivirus infection: its protein BV1 stimulates the expression of AS2 and recruits AS2 to the cytoplasm, which enhances virus infectivity by suppression of cytoplasmic post transcriptional gene silencing.
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Affiliation(s)
- Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan.
| | - Takanori Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
- Central Research Institute, Ishihara Sangyo Kaisha, Ltd., 2-3-1 Nishi-Shibukawa, Kusatsu, Shiga, 525-0025, Japan
| | - Michiko Sasabe
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, 036-8561, Japan
| | - Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan
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Boher P, Soler M, Fernández-Piñán S, Torrent X, Müller SY, Kelly KA, Serra O, Figueras M. Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress. BMC PLANT BIOLOGY 2021; 21:409. [PMID: 34493224 PMCID: PMC8424952 DOI: 10.1186/s12870-021-03141-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The periderm is a protective barrier crucial for land plant survival, but little is known about genetic factors involved in its development and regulation. Using a transcriptomic approach in the cork oak (Q. suber) periderm, we previously identified an RS2-INTERACTING KH PROTEIN (RIK) homologue of unknown function containing a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. RESULTS To gain insight into the function of RIK in the periderm, potato (S. tuberosum) tuber periderm was used as a model: the full-length coding sequence of RIK, hereafter referred to as StRIK, was isolated, the transcript profile analyzed and gene silencing in potato performed to analyze the silencing effects on periderm anatomy and transcriptome. The StRIK transcript accumulated in all vegetative tissues studied, including periderm and other suberized tissues such as root and also in wounded tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show any obvious effects on tuber periderm anatomy but, unlike Wild type, transgenic plants flowered. Global transcript profiling of the StRIK-RNAi periderm did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis orthologue. CONCLUSIONS The ubiquitous expression of StRIK transcript, the flower associated phenotype and the differential expression of StRIK-RNAi periderm point out to a general regulatory role of StRIK in diverse plant developmental processes. The transcriptome analysis suggests that StRIK might play roles in RNA maturation and stress response in the periderm.
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Affiliation(s)
- Pau Boher
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Marçal Soler
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Sandra Fernández-Piñán
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Xènia Torrent
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Sebastian Y. Müller
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA UK
| | - Krystyna A. Kelly
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA UK
| | - Olga Serra
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
| | - Mercè Figueras
- Laboratori del Suro, Biology Department, Universitat de Girona, Campus Montilivi, E-17071 Girona, Catalonia Spain
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19
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Shen Q, Lin Y, Li Y, Wang G. Dynamics of H3K27me3 Modification on Plant Adaptation to Environmental Cues. PLANTS 2021; 10:plants10061165. [PMID: 34201297 PMCID: PMC8228231 DOI: 10.3390/plants10061165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022]
Abstract
Given their sessile nature, plants have evolved sophisticated regulatory networks to confer developmental plasticity for adaptation to fluctuating environments. Epigenetic codes, like tri-methylation of histone H3 on Lys27 (H3K27me3), are evidenced to account for this evolutionary benefit. Polycomb repressive complex 2 (PRC2) and PRC1 implement and maintain the H3K27me3-mediated gene repression in most eukaryotic cells. Plants take advantage of this epigenetic machinery to reprogram gene expression in development and environmental adaption. Recent studies have uncovered a number of new players involved in the establishment, erasure, and regulation of H3K27me3 mark in plants, particularly highlighting new roles in plants’ responses to environmental cues. Here, we review current knowledge on PRC2-H3K27me3 dynamics occurring during plant growth and development, including its writers, erasers, and readers, as well as targeting mechanisms, and summarize the emerging roles of H3K27me3 mark in plant adaptation to environmental stresses.
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20
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Zhang C, Cheng Q, Wang H, Gao H, Fang X, Chen X, Zhao M, Wei W, Song B, Liu S, Wu J, Zhang S, Xu P. GmBTB/POZ promotes the ubiquitination and degradation of LHP1 to regulate the response of soybean to Phytophthora sojae. Commun Biol 2021; 4:372. [PMID: 33742112 PMCID: PMC7979691 DOI: 10.1038/s42003-021-01907-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/24/2021] [Indexed: 01/07/2023] Open
Abstract
Phytophthora sojae is a pathogen that causes stem and root rot in soybean (Glycine max [L.] Merr.). We previously demonstrated that GmBTB/POZ, a BTB/POZ domain-containing nuclear protein, enhances resistance to P. sojae in soybean, via a process that depends on salicylic acid (SA). Here, we demonstrate that GmBTB/POZ associates directly with soybean LIKE HETEROCHROMATIN PROTEIN1 (GmLHP1) in vitro and in vivo and promotes its ubiquitination and degradation. Both overexpression and RNA interference analysis of transgenic lines demonstrate that GmLHP1 negatively regulates the response of soybean to P. sojae by reducing SA levels and repressing GmPR1 expression. The WRKY transcription factor gene, GmWRKY40, a SA-induced gene in the SA signaling pathway, is targeted by GmLHP1, which represses its expression via at least two mechanisms (directly binding to its promoter and impairing SA accumulation). Furthermore, the nuclear localization of GmLHP1 is required for the GmLHP1-mediated negative regulation of immunity, SA levels and the suppression of GmWRKY40 expression. Finally, GmBTB/POZ releases GmLHP1-regulated GmWRKY40 suppression and increases resistance to P. sojae in GmLHP1-OE hairy roots. These findings uncover a regulatory mechanism by which GmBTB/POZ-GmLHP1 modulates resistance to P. sojae in soybean, likely by regulating the expression of downstream target gene GmWRKY40.
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Affiliation(s)
- Chuanzhong Zhang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qun Cheng
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Huiyu Wang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Hong Gao
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Xin Fang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Xi Chen
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Ming Zhao
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Wanling Wei
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Bo Song
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Shanshan Liu
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Junjiang Wu
- Soybean Research Institute of Heilongjiang Academy of Agricultural Sciences, Key Laboratory of Soybean Cultivation of Ministry of Agriculture, Harbin, China
| | - Shuzhen Zhang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China.
| | - Pengfei Xu
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China.
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21
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Iwakawa H, Takahashi H, Machida Y, Machida C. Roles of ASYMMETRIC LEAVES2 (AS2) and Nucleolar Proteins in the Adaxial-Abaxial Polarity Specification at the Perinucleolar Region in Arabidopsis. Int J Mol Sci 2020; 21:E7314. [PMID: 33022996 PMCID: PMC7582388 DOI: 10.3390/ijms21197314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
Leaves of Arabidopsis develop from a shoot apical meristem grow along three (proximal-distal, adaxial-abaxial, and medial-lateral) axes and form a flat symmetric architecture. ASYMMETRIC LEAVES2 (AS2), a key regulator for leaf adaxial-abaxial partitioning, encodes a plant-specific nuclear protein and directly represses the abaxial-determining gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). How AS2 could act as a critical regulator, however, has yet to be demonstrated, although it might play an epigenetic role. Here, we summarize the current understandings of the genetic, molecular, and cellular functions of AS2. A characteristic genetic feature of AS2 is the presence of a number of (about 60) modifier genes, mutations of which enhance the leaf abnormalities of as2. Although genes for proteins that are involved in diverse cellular processes are known as modifiers, it has recently become clear that many modifier proteins, such as NUCLEOLIN1 (NUC1) and RNA HELICASE10 (RH10), are localized in the nucleolus. Some modifiers including ribosomal proteins are also members of the small subunit processome (SSUP). In addition, AS2 forms perinucleolar bodies partially colocalizing with chromocenters that include the condensed inactive 45S ribosomal RNA genes. AS2 participates in maintaining CpG methylation in specific exons of ETT/ARF3. NUC1 and RH10 genes are also involved in maintaining the CpG methylation levels and repressing ETT/ARF3 transcript levels. AS2 and nucleolus-localizing modifiers might cooperatively repress ETT/ARF3 to develop symmetric flat leaves. These results raise the possibility of a nucleolus-related epigenetic repression system operating for developmental genes unique to plants and predict that AS2 could be a molecule with novel functions that cannot be explained by the conventional concept of transcription factors.
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Affiliation(s)
- Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200, Matsumoto-cho, Kasugai, Aichi 487-8501, Japan;
| | - Hiro Takahashi
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan;
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200, Matsumoto-cho, Kasugai, Aichi 487-8501, Japan;
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22
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Garrido AN, Supijono E, Boshara P, Douglas SJ, Stronghill PE, Li B, Nambara E, Kliebenstein DJ, Riggs CD. flasher, a novel mutation in a glucosinolate modifying enzyme, conditions changes in plant architecture and hormone homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1989-2006. [PMID: 32529723 DOI: 10.1111/tpj.14878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Meristem function is underpinned by numerous genes that affect hormone levels, ultimately controlling phyllotaxy, the transition to flowering and general growth properties. Class I KNOX genes are major contributors to this process, promoting cytokinin biosynthesis but repressing gibberellin production to condition a replication competent state. We identified a suppressor mutant of the KNOX1 mutant brevipedicellus (bp) that we termed flasher (fsh), which promotes stem and pedicel elongation, suppresses early senescence, and negatively affects reproductive development. Map-based cloning and complementation tests revealed that fsh is due to an E40K change in the flavin monooxygenase GS-OX5, a gene encoding a glucosinolate (GSL) modifying enzyme. In vitro enzymatic assays revealed that fsh poorly converts substrate to product, yet the levels of several GSLs are higher in the suppressor line, implicating FSH in feedback control of GSL flux. FSH is expressed predominantly in the vasculature in patterns that do not significantly overlap those of BP, implying a non-cell autonomous mode of meristem control via one or more GSL metabolites. Hormone analyses revealed that cytokinin levels are low in bp, but fsh restores cytokinin levels to near normal by activating cytokinin biosynthesis genes. In addition, jasmonate levels in the fsh suppressor are significantly lower than in bp, which is likely due to elevated expression of JA inactivating genes. These observations suggest the involvement of the GSL pathway in generating one or more negative effectors of growth that influence inflorescence architecture and fecundity by altering the balance of hormonal regulators.
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Affiliation(s)
- Ameth N Garrido
- Department of Biological Sciences, University of Toronto, Toronto, ON, Canada
| | - Esther Supijono
- Department of Biological Sciences, University of Toronto, Toronto, ON, Canada
| | - Peter Boshara
- Department of Biological Sciences, University of Toronto, Toronto, ON, Canada
| | - Scott J Douglas
- Department of Biological Sciences, University of Toronto, Toronto, ON, Canada
| | - Patti E Stronghill
- Department of Biological Sciences, University of Toronto, Toronto, ON, Canada
| | - Baohua Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Eiji Nambara
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - C Daniel Riggs
- Department of Biological Sciences, University of Toronto, Toronto, ON, Canada
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
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23
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Yan B, Lv Y, Zhao C, Wang X. Knowing When to Silence: Roles of Polycomb-Group Proteins in SAM Maintenance, Root Development, and Developmental Phase Transition. Int J Mol Sci 2020; 21:E5871. [PMID: 32824274 PMCID: PMC7461556 DOI: 10.3390/ijms21165871] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 01/01/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) and PRC2 are the major complexes composed of polycomb-group (PcG) proteins in plants. PRC2 catalyzes trimethylation of lysine 27 on histone 3 to silence target genes. Like Heterochromatin Protein 1/Terminal Flower 2 (LHP1/TFL2) recognizes and binds to H3K27me3 generated by PRC2 activities and enrolls PRC1 complex to further silence the chromatin through depositing monoubiquitylation of lysine 119 on H2A. Mutations in PcG genes display diverse developmental defects during shoot apical meristem (SAM) maintenance and differentiation, seed development and germination, floral transition, and so on so forth. PcG proteins play essential roles in regulating plant development through repressing gene expression. In this review, we are focusing on recent discovery about the regulatory roles of PcG proteins in SAM maintenance, root development, embryo development to seedling phase transition, and vegetative to reproductive phase transition.
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Affiliation(s)
| | | | | | - Xiaoxue Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China; (B.Y.); (Y.L.); (C.Z.)
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24
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Chen C, Kim D, Yun HR, Lee YM, Yogendra B, Bo Z, Kim HE, Min JH, Lee YS, Rim YG, Kim HU, Sung S, Heo JB. Nuclear import of LIKE HETEROCHROMATIN PROTEIN1 is redundantly mediated by importins α-1, α-2 and α-3. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1205-1214. [PMID: 32365248 PMCID: PMC7810169 DOI: 10.1111/tpj.14796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 04/09/2020] [Accepted: 04/24/2020] [Indexed: 05/19/2023]
Abstract
LIKE HETEROCHROMATIN PROTEIN1 (LHP1) encodes the only plant homologue of the metazoan HETEROCHROMATIN PROTEIN1 (HP1) protein family. The LHP1 protein is necessary for proper epigenetic regulation of a range of developmental processes in plants. LHP1 is a transcriptional repressor of flowering-related genes, such as FLOWERING LOCUS T (FT), FLOWERING LOCUS C (FLC), AGAMOUS (AG) and APETALA 3 (AP3). We found that LHP1 interacts with importin α-1 (IMPα-1), importin α-2 (IMPα-2) and importin α-3 (IMPα-3) both in vitro and in vivo. A genetic approach revealed that triple mutation of impα-1, impα-2 and impα-3 resulted in Arabidopsis plants with a rapid flowering phenotype similar to that of plants with mutations in lhp1 due to the upregulation of FT expression. Nuclear targeting of LHP1 was severely impaired in the impα triple mutant, resulting in the de-repression of LHP1 target genes AG, AP3 and SHATTERPROOF 1 as well as FT. Therefore, the importin proteins IMPα-1, -2 and -3 are necessary for the nuclear import of LHP1.
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Affiliation(s)
- Chong Chen
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Daewon Kim
- Department of Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Hee Rang Yun
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Yun Mi Lee
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Bordiya Yogendra
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - Zhao Bo
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - Hae Eun Kim
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Jun Hong Min
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Yong-Suk Lee
- Department of Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Yeong Gil Rim
- Systems & Synthetic Agrobiotech Center, Gyeongsang National University, Jinju 660-701 Korea
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Sejong University, Seoul, 05006 Korea
| | - Sibum Sung
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
- International Scholar, Kyung-Hee University, Suwon, Korea
- Corresponding author: Tel: +82 51 200 7520; Fax: +82 51 200 7505. ;
| | - Jae Bok Heo
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
- Corresponding author: Tel: +82 51 200 7520; Fax: +82 51 200 7505. ;
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25
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Ali S, Khan N, Xie L. Molecular and Hormonal Regulation of Leaf Morphogenesis in Arabidopsis. Int J Mol Sci 2020; 21:ijms21145132. [PMID: 32698541 PMCID: PMC7404056 DOI: 10.3390/ijms21145132] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/28/2022] Open
Abstract
Shoot apical meristems (SAM) are tissues that function as a site of continuous organogenesis, which indicates that a small pool of pluripotent stem cells replenishes into lateral organs. The coordination of intercellular and intracellular networks is essential for maintaining SAM structure and size and also leads to patterning and formation of lateral organs. Leaves initiate from the flanks of SAM and then develop into a flattened structure with variable sizes and forms. This process is mainly regulated by the transcriptional regulators and mechanical properties that modulate leaf development. Leaf initiation along with proper orientation is necessary for photosynthesis and thus vital for plant survival. Leaf development is controlled by different components such as hormones, transcription factors, miRNAs, small peptides, and epigenetic marks. Moreover, the adaxial/abaxial cell fate, lamina growth, and shape of margins are determined by certain regulatory mechanisms. The over-expression and repression of various factors responsible for leaf initiation, development, and shape have been previously studied in several mutants. However, in this review, we collectively discuss how these factors modulate leaf development in the context of leaf initiation, polarity establishment, leaf flattening and shape.
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Affiliation(s)
- Shahid Ali
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Correspondence: (S.A.); (L.X.)
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA;
| | - Linan Xie
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence: (S.A.); (L.X.)
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26
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Zhu Y, Luo X, Liu X, Wu W, Cui X, He Y, Huang J. Arabidopsis PEAPODs function with LIKE HETEROCHROMATIN PROTEIN1 to regulate lateral organ growth. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:812-831. [PMID: 31099089 DOI: 10.1111/jipb.12841] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
In higher plants, lateral organs are usually of determinate growth. It remains largely elusive how the determinate growth is achieved and maintained. Previous reports have shown that Arabidopsis PEAPOD (PPD) proteins suppress proliferation of dispersed meristematic cells partly through a TOPLESS corepressor complex. Here, we identified a new PPD-interacting partner, LIKE HETEROCHROMATIN PROTEIN1 (LHP1), using the yeast two-hybrid system, and their interaction is mediated by the chromo shadow domain and the Jas domain in LHP1 and PPD2, respectively. Our genetic data demonstrate that the phenotype of ppd2 lhp1 is more similar to lhp1 than to ppd2, indicating epistasis of lhp1 to ppd2. Microarray analysis reveals that PPD2 and LHP1 can regulate expression of a common set of genes directly or indirectly. Consistently, chromatin immunoprecipitation results confirm that PPD2 and LHP1 are coenriched at the promoter region of their targets such as D3-TYPE CYCLINS and HIGH MOBILITY GROUP A, which are upregulated in ppd2, lhp1 and ppd2 lhp1 mutants, and that PPDs mediate repressive histone 3 lysine-27 trimethylation at these loci. Taken together, our data provide evidence that PPD and LHP1 form a corepressor complex that regulates lateral organ growth.
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Affiliation(s)
- Ying Zhu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiao Luo
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Xuxin Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wenjuan Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences,, Shanghai Normal University,, Shanghai, 200234, China
| | - Xiaofeng Cui
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuehui He
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences,, Shanghai Normal University,, Shanghai, 200234, China
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27
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Singh S, Singh A, Singh A, Yadav S, Bajaj I, Kumar S, Jain A, Sarkar AK. Role of chromatin modification and remodeling in stem cell regulation and meristem maintenance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:778-792. [PMID: 31793642 DOI: 10.1093/jxb/erz459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
In higher plants, pluripotent stem cells reside in the specialized microenvironment called stem cell niches (SCNs) harbored at the shoot apical meristem (SAM) and root apical meristem (RAM), which give rise to the aerial and underground parts of a plant, respectively. The model plant Arabidopsis thaliana (Arabidopsis) has been extensively studied to decipher the intricate regulatory mechanisms involving some key transcriptions factors and phytohormones that play pivotal roles in stem cell homeostasis, meristem maintenance, and organ formation. However, there is increasing evidence to show the epigenetic regulation of the chromatin architecture, gene expression exerting an influence on an innate balance between the self-renewal of stem cells, and differentiation of the progeny cells to a specific tissue type or organ. Post-translational histone modifications, ATP-dependent chromatin remodeling, and chromatin assembly/disassembly are some of the key features involved in the modulation of chromatin architecture. Here, we discuss the major epigenetic regulators and illustrate their roles in the regulation of stem cell activity, meristem maintenance, and related organ patterning in Arabidopsis.
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Affiliation(s)
- Sharmila Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Alka Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Archita Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sandeep Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Ishita Bajaj
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Shailendra Kumar
- Amity School of Architecture and Planning, Amity University, Kant Kalwar, Rajasthan, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University, Kant Kalwar, Rajasthan, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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28
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Overexpression of a Novel LcKNOX Transcription Factor from Liriodendron chinense Induces Lobed Leaves in Arabidopsis thaliana. FORESTS 2019. [DOI: 10.3390/f11010033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Liriodendron chinense is a common ornamental tree that has attractive leaves, which is a valuable trait for use in landscape architecture. In this work, we aimed to identify the potential genes that control and regulate the development of L. chinense leaf lobes. Based on the transcriptome data for the leaf developmental stages we previously generated, two candidate genes were identified in this study. KNOTTED-LIKE HOMEOBOX(KNOX), encoding homeobox family proteins, play a large role in leaf lobe and leaf complexity regulation. Here, two full length KNOX genes from L. chinense were amplified and named LcKNOX1 and LcKNOX6 according to their sequence similarities with the respective Arabidopsis thaliana KNOX family genes. Overexpression vectors were constructed and subsequently transformed into wild type (WT) A. thaliana. Additionally, LcKNOX6 was expressed in tobacco leaves to examine its subcellular localization, and the 35S::LcKNOX6 transgenic A. thaliana leaf cells were imaged with the use of SEM. The expression of several genes that participate in KNOX gene regulation were validated by quantitative real-time PCR. The results show that LcKNOX1 produces almost the same phenotype as that found in WT A. thaliana. Notably, the LcKNOX6-1 lines presented deep leaf lobes that were similar to L. chinense leaf lobes. Two 35S::LcKNOX6 lines induced an abnormal growth phenotype whose seeds were abortive. In short, these results indicate that the LcKNOX6 gene might affect leaf development in A. thaliana and provide insights into the regulation of L. chinense leaf shaping.
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Satterlee JW, Scanlon MJ. Coordination of Leaf Development Across Developmental Axes. PLANTS 2019; 8:plants8100433. [PMID: 31652517 PMCID: PMC6843618 DOI: 10.3390/plants8100433] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 02/06/2023]
Abstract
Leaves are initiated as lateral outgrowths from shoot apical meristems throughout the vegetative life of the plant. To achieve proper developmental patterning, cell-type specification and growth must occur in an organized fashion along the proximodistal (base-to-tip), mediolateral (central-to-edge), and adaxial–abaxial (top-bottom) axes of the developing leaf. Early studies of mutants with defects in patterning along multiple leaf axes suggested that patterning must be coordinated across developmental axes. Decades later, we now recognize that a highly complex and interconnected transcriptional network of patterning genes and hormones underlies leaf development. Here, we review the molecular genetic mechanisms by which leaf development is coordinated across leaf axes. Such coordination likely plays an important role in ensuring the reproducible phenotypic outcomes of leaf morphogenesis.
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Affiliation(s)
- James W Satterlee
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Michael J Scanlon
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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Transcriptomic analysis of contrasting inbred lines and F 2 segregant of Chinese cabbage provides valuable information on leaf morphology. Genes Genomics 2019; 41:811-829. [PMID: 30900192 DOI: 10.1007/s13258-019-00809-7] [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: 10/15/2018] [Accepted: 03/07/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Leaf morphology influences plant growth and productivity and is controlled by genetic and environmental cues. The various morphotypes of Brassica rapa provide an excellent resource for genetic and molecular studies of morphological traits. OBJECTIVE This study aimed to identify genes regulating leaf morphology using segregating B. rapa p F2 population. METHODS Phenotyping and transcriptomic analyses were performed on an F2 population derived from a cross between Rapid cycling B. rapa (RCBr) and B. rapa ssp. penkinensis, inbred line Kenshin. Analyses focused on four target traits: lamina (leaf) length (LL), lamina width (LW), petiole length (PL), and leaf margin (LM). RESULTS All four traits were controlled by multiple QTLs, and expression of 466 and 602 genes showed positive and negative correlation with leaf phenotypes, respectively. From this microarray analysis, large numbers of genes were putatively identified as leaf morphology-related genes. The Gene Ontology (GO) category containing the highest number of differentially expressed genes (DEGs) was "phytohormones". The sets of genes enriched in the four leaf phenotypes did not overlap, indicating that each phenotype was regulated by a different set of genes. The expression of BrAS2, BrAN3, BrCYCB1;2, BrCYCB2;1,4, BrCYCB3;1, CrCYCBD3;2, BrULT1, and BrANT seemed to be related to leaf size traits (LL and LW), whereas BrCUC1, BrCUC2, and BrCUC3 expression for LM trait. CONCLUSION An analysis integrating the results of the current study with previously published data revealed that Kenshin alleles largely determined LL and LW but LM resulted from RCBr alleles. Genes identified in this study could be used to develop molecular markers for use in Brassica breeding projects and for the dissection of gene function.
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Chromatin modulation and gene regulation in plants: insight about PRC1 function. Biochem Soc Trans 2018; 46:957-966. [DOI: 10.1042/bst20170576] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 02/07/2023]
Abstract
In plant and metazoan, Polycomb Group (PcG) proteins play key roles in regulating developmental processes by repression of gene expression. PcG proteins function as multi-protein complexes; among them the best characterized ones are Polycomb Repressive Complex 1 (PRC1) and PRC2. PRC2 catalyzes histone H3 lysine 27 trimethylation (H3K27me3), and PRC1 can bind H3K27me3 and catalyzes H2A monoubiquitination. While the PRC2 components and molecular functions are evolutionarily conserved, varied PRC1 complexes are found and they show high divergences between animals and plants. In addition to the core subunits, an exponentially increasing number of PRC1-associated factors have been identified in Arabidopsis thaliana. Recent studies have also unraveled cross-component interactions and intertwined roles of PRC1 and PRC2 in chromatin modulation. In addition, complexities of interactions and functions between PcG and Trithorax Group proteins have been observed. This short review summarizes up current knowledge to provide insight about repressive functional mechanism of PRC1 and its interplay with other factors.
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Guo L, Cao X, Liu Y, Li J, Li Y, Li D, Zhang K, Gao C, Dong A, Liu X. A chromatin loop represses WUSCHEL expression in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:1083-1097. [PMID: 29660180 DOI: 10.1111/tpj.13921] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 05/27/2023]
Abstract
WUSCHEL (WUS) is critical for plant meristem maintenance and determinacy in Arabidopsis, and the regulation of its spatiotemporal expression patterns is complex. We previously found that AGAMOUS (AG), a key MADS-domain transcription factor in floral organ identity and floral meristem determinacy, can directly suppress WUS expression through the recruitment of the Polycomb group (PcG) protein TERMINAL FLOWER 2 (TFL2, also known as LIKE HETEROCHROMATIN PROTEIN 1, LHP1) at the WUS locus; however, the mechanism by which WUS is repressed remains unclear. Here, using chromosome conformation capture (3C) and chromatin immunoprecipitation 3C, we found that two specific regions flanking the WUS gene body bound by AG and TFL2 form a chromatin loop that is directly promoted by AG during flower development in a manner independent of the physical distance and sequence content of the intervening region. Moreover, AG physically interacts with TFL2, and TFL2 binding to the chromatin loop is dependent on AG. Transgenic and CRISPR/Cas9-edited lines showed that the WUS chromatin loop represses gene expression by blocking the recruitment of RNA polymerase II at the locus. The findings uncover the WUS chromatin loop as another regulatory mechanism controlling WUS expression, and also shed light on the factors required for chromatin conformation change and their recruitment.
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Affiliation(s)
- Lin Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
| | - Xiuwei Cao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
| | - Yuhao Liu
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jun Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongpeng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
| | - Dongming Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
| | - Ke Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Xigang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
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Lin X, Gu D, Zhao H, Peng Y, Zhang G, Yuan T, Li M, Wang Z, Wang X, Cui S. LFR is functionally associated with AS2 to mediate leaf development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:598-612. [PMID: 29775508 DOI: 10.1111/tpj.13973] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 06/08/2023]
Abstract
Leaves are essential organs for plants. We previously identified a functional gene possibly encoding a component of the SWI/SNF complex named Leaf and Flower Related (LFR) in Arabidopsis thaliana. Loss-of-function mutants of LFR displayed obvious defects in leaf morphogenesis, indicating its vital role in leaf development. Here an allelic null mutant of ASYMMETRIC LEAVES2 (AS2), as2-6, was isolated as an enhancer of lfr-1 in petiole length, vasculature pattern and leaf margin development. The lfr as2 double-mutants showed enhanced ectopic expression of BREVIPEDICELLUS (BP) compared with each of the single-mutants, which is consistent with their synergistic genetic enhancement in multiple BP-dependent development processes. Moreover, LFR and several putative subunits of the SWI/SNF complex interacted physically with AS2. LFR associated with BP chromatin in an AS1-AS2-dependent manner to promote the nucleosome occupancy for appropriate BP repression in leaves. Taken together, our findings reveal that LFR and the SWI/SNF complex play roles in leaf development at least partly by repressing BP transcription as interacting factors of AS2, which expounds our understanding of BP repression at the chromatin structure level in leaf development.
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Affiliation(s)
- Xiaowei Lin
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Dandan Gu
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Hongtao Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Yue Peng
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Guofang Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Tingting Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Mengge Li
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Zhijuan Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Xiutang Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
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Xiao J, Jin R, Wagner D. Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants. Genome Biol 2017; 18:88. [PMID: 28490341 PMCID: PMC5425979 DOI: 10.1186/s13059-017-1228-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Run Jin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Yang X, Tong A, Yan B, Wang X. Governing the Silencing State of Chromatin: The Roles of Polycomb Repressive Complex 1 in Arabidopsis. PLANT & CELL PHYSIOLOGY 2017; 58:198-206. [PMID: 28069891 DOI: 10.1093/pcp/pcw209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
Polycomb group proteins form multiple protein complexes such as Polycomb Repressive Complex (PRC) 1 and PRC2, which repress the expression of thousands of genes. PRC1 and PRC2 are essential for normal development in Arabidopsis. Recently, significant progress has been made in understanding the functions and regulatory mechanisms of PRC1. In this review, we focus on the discovery of the composition of PRC1, functions of its components, the recruitment of PRC1 to target genes and the control of PRC1 function in Arabidopsis. Perspectives on dissecting the roles of PRC1 in plant gene expression and development are also given.
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Affiliation(s)
- Xianli Yang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Aizi Tong
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Bowen Yan
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Xiaoxue Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
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Feng J, Lu J. LHP1 Could Act as an Activator and a Repressor of Transcription in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:2041. [PMID: 29234344 PMCID: PMC5712405 DOI: 10.3389/fpls.2017.02041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/14/2017] [Indexed: 05/19/2023]
Abstract
Polycomb group (PcG) proteins within the polycomb repressive complex 1 (PRC1) and PRC2 are significant epigenetic regulatory factors involved in important cellular and developmental processes in eukaryotes. In Arabidopsis, LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), also known as TERMINAL FLOWER 2, has been proposed as a plant specific subunit of PRC1 that could bind the trimethylated lysine 27 of histone H3 (H3K27me3), which is established by PRC2 and is required for a functional plant PcG system. LHP1 not only interacts with PRC1 to catalyze monoubiquitination at lysine 119 of histone H2A but also functions with PRC2 to establish H3K27me3. This review is about the interaction of LHP1 with PRC1 and PRC2, in which LHP1 may act as a bridge between the two. Meantime, this review highlights that LHP1 could act as an activator and a repressor of transcription.
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Affiliation(s)
- Jing Feng
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
- *Correspondence: Jiang Lu, Jing Feng,
| | - Jiang Lu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Jiang Lu, Jing Feng,
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Chen D, Molitor AM, Xu L, Shen WH. Arabidopsis PRC1 core component AtRING1 regulates stem cell-determining carpel development mainly through repression of class I KNOX genes. BMC Biol 2016; 14:112. [PMID: 28007029 PMCID: PMC5178098 DOI: 10.1186/s12915-016-0336-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/25/2016] [Indexed: 11/27/2022] Open
Abstract
Background Polycomb repressive complex 2 (PRC2)-catalyzed H3K27me3 marks are tightly associated with the WUS-AG negative feedback loop to terminate floral stem cell fate to promote carpel development, but the roles of Polycomb repressive complex 1 (PRC1) in this event remain largely uncharacterized. Results Here we show conspicuous variability in the morphology and number of carpels among individual flowers in the absence of the PRC1 core components AtRING1a and AtRING1b, which contrasts with the wild-type floral meristem consumed by uniform carpel production in Arabidopsis thaliana. Promoter-driven GUS reporter analysis showed that AtRING1a and AtRING1b display a largely similar expression pattern, except in the case of the exclusively maternal-preferred expression of AtRING1b, but not AtRING1a, in the endosperm. Indeterminate carpel development in the atring1a;atring1b double mutant is due to replum/ovule-to-carpel conversion in association with ectopic expression of class I KNOX (KNOX-I) genes. Moreover, AtRING1a and AtRING1b also play a critical role in ovule development, mainly through promoting the degeneration of non-functional megaspores and proper integument formation. Genetic interaction analysis indicates that the AtRING1a/b-regulated KNOX-I pathway acts largely in a complementary manner with the WUS-AG pathway in controlling floral stem cell maintenance and proper carpel development. Conclusions Our study uncovers a novel mechanistic pathway through which AtRING1a and AtRING1b repress KNOX-I expression to terminate floral stem cell activities and establish carpel cell fate identities. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0336-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Donghong Chen
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 du CNRS, Université de Strasbourg, 12 rue du Général ZIMMER, 67084, Strasbourg, France. .,College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Hunan Agricultural University, Changsha, 410128, China.
| | - Anne M Molitor
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 du CNRS, Université de Strasbourg, 12 rue du Général ZIMMER, 67084, Strasbourg, France.,Present address: Institut de Genetique et de Biologie Moleculaire et Cellulaire, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 du CNRS, Université de Strasbourg, 12 rue du Général ZIMMER, 67084, Strasbourg, France.
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