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Peng D, Guo Y, Hu H, Wang X, He S, Gao C, Liu Z, Chen M. Functional characterisation of BnaA02.TOP1α and BnaC02.TOP1α involved in true leaf biomass accumulation in Brassica napus L. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39348559 DOI: 10.1111/tpj.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 08/13/2024] [Accepted: 09/18/2024] [Indexed: 10/02/2024]
Abstract
Leaves, as primary photosynthetic organs essential for high crop yield and quality, have attracted significant attention. The functions of DNA topoisomerase 1α (TOP1α) in various biological processes, including leaf development, in Brassica napus remain unknown. Here, four paralogs of BnaTOP1α, namely BnaA01.TOP1α, BnaA02.TOP1α, BnaC01.TOP1α and BnaC02.TOP1α, were identified and cloned in the B. napus inbred line 'K407'. Expression pattern analysis revealed that BnaA02.TOP1α and BnaC02.TOP1α, but not BnaA01.TOP1α and BnaC01.TOP1α, were persistently and highly expressed in B. napus true leaves. Preliminary analysis in Arabidopsis thaliana revealed that BnaA02.TOP1α and BnaC02.TOP1α paralogs, but not BnaA01.TOP1α and BnaC01.TOP1α, performed biological functions. Targeted mutations of four BnaTOP1α paralogs in B. napus using the CRISPR-Cas9 system revealed that BnaA02.TOP1α and BnaC02.TOP1α served as functional paralogs and redundantly promoted true leaf number and size, thereby promoting true leaf biomass accumulation. Moreover, BnaA02.TOP1α modulated the levels of endogenous gibberellins, cytokinins and auxins by indirectly regulating several genes related to their metabolism processes. BnaA02.TOP1α directly activated BnaA03.CCS52A2 and BnaC09.AN3 by facilitating the recruitment of RNA polymerase II and modulating H3K27me3, H3K36me2 and H3K36me3 levels at these loci and indirectly activated the BnaA08.PARL1 expression, thereby positively controlling the true leaf size in B. napus. Additionally, BnaA02.TOP1α indirectly activated the BnaA07.PIN1 expression to positively regulate the true leaf number. These results reveal the important functions of BnaTOP1α and provide insights into the regulatory network controlling true leaf biomass accumulation in B. napus.
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Affiliation(s)
- Danshuai Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuan Guo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huan Hu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuangcheng He
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chenhao Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zijin Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mingxun Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, National Yangling Agricultural Biotechnology & Breeding Center, Shaanxi Key Laboratory of Crop Heterosis, and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
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Pagano P, Bertoncini A, Pagano A, Nisa MU, Raynaud C, Balestrazzi A, Macovei A. Exposure of Arabidopsis thaliana Mutants to Genotoxic Stress Provides New Insights for the Involvement of TDP1α and TDP1β genes in DNA-Damage Response. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39219547 DOI: 10.1111/pce.15128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/17/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Genotoxic stress activates the DNA-damage response (DDR) signalling cascades responsible for maintaining genome integrity. Downstream DNA repair pathways include the tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme that hydrolyses the phosphodiester bond between the tyrosine of topoisomerase I (TopI) and 3'-phosphate of DNA. The plant TDP1 subfamily contains the canonical TDP1α gene and the TDP1β gene whose functions are not fully elucidated. The current study proposes to investigate the involvement of TDP1 genes in DDR-related processes by using Arabidopsis thaliana mutants treated with genotoxic agents. The phenotypic and molecular characterization of tdp1α, tdp1β and tdp1α/β mutants treated with cisplatin (CIS), curcumin (CUR), NSC120686 (NSC), zeocin (ZEO), and camptothecin (CPT), evidenced that while tdp1β was highly sensitive to CIS and CPT, tdp1α was more sensitive to NSC. Gene expression analyses showing upregulation of the TDP2 gene in the double mutant indicate the presence of compensatory mechanisms. The downregulation of POL2A gene in the tdp1β mutant along with the upregulation of the TDP1β gene in pol2a mutants, together with its sensitivity to replication inhibitors (CIS, CTP), point towards a function of this gene in the response to replication stress. Therefore, this study brings novel information relative to the activity of TDP1 genes in plants.
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Affiliation(s)
- Paola Pagano
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Anna Bertoncini
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Maher-Un Nisa
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Paris, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Paris, France
| | - Alma Balestrazzi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
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3
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Elesawi IE, Hashem AM, Yao L, Maher M, Hassanin AA, Abd El-Moneim D, Safhi FA, Al Aboud NM, Alshamrani SM, Shehata WF, Chunli C. The role of DNA topoisomerase 1α (AtTOP1α) in regulating arabidopsis meiotic recombination and chromosome segregation. PeerJ 2024; 12:e17864. [PMID: 39221285 PMCID: PMC11365474 DOI: 10.7717/peerj.17864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024] Open
Abstract
Meiosis is a critical process in sexual reproduction, and errors during this cell division can significantly impact fertility. Successful meiosis relies on the coordinated action of numerous genes involved in DNA replication, strand breaks, and subsequent rejoining. DNA topoisomerase enzymes play a vital role by regulating DNA topology, alleviating tension during replication and transcription. To elucidate the specific function of DNA topoisomerase 1α ( A t T O P 1 α ) in male reproductive development of Arabidopsis thaliana, we investigated meiotic cell division in Arabidopsis flower buds. Combining cytological and biochemical techniques, we aimed to reveal the novel contribution of A t T O P 1 α to meiosis. Our results demonstrate that the absence of A t T O P 1 α leads to aberrant chromatin behavior during meiotic division. Specifically, the top1α1 mutant displayed altered heterochromatin distribution and clustered centromere signals at early meiotic stages. Additionally, this mutant exhibited disruptions in the distribution of 45s rDNA signals and a reduced frequency of chiasma formation during metaphase I, a crucial stage for genetic exchange. Furthermore, the atm-2×top1α1 double mutant displayed even more severe meiotic defects, including incomplete synapsis, DNA fragmentation, and the presence of polyads. These observations collectively suggest that A t T O P 1 α plays a critical role in ensuring accurate meiotic progression, promoting homologous chromosome crossover formation, and potentially functioning in a shared DNA repair pathway with ATAXIA TELANGIECTASIA MUTATED (ATM) in Arabidopsis microspore mother cells.
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Affiliation(s)
- Ibrahim Eid Elesawi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Agricultural Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Ahmed M. Hashem
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Li Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mohamed Maher
- Agricultural Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | - Diaa Abd El-Moneim
- Department of Plant Production, (Genetic Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish, El-Arish, Egypt
| | - Fatmah A. Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nora M. Al Aboud
- Department of Biology Faculty of Science, Umm Al‐Qura University, Makkah, Saudi Arabia
| | - Salha Mesfer Alshamrani
- Department of Biological Science, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Wael F. Shehata
- College of Agriculture and Food Sciences, Department of Agricultural Biotechnology, King Faisal University, Al-Ahsa, Al-Ahsa, Saudi Arabia
- College of Environmental Agricultural Science, Plant Production Department, Arish University, Arish, North Sinai, Egypt
| | - Chen Chunli
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
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Zhang H, Guo L, Li Y, Zhao D, Liu L, Chang W, Zhang K, Zheng Y, Hou J, Fu C, Zhang Y, Zhang B, Ma Y, Niu Y, Zhang K, Xing J, Cui S, Wang F, Tan K, Zheng S, Tang W, Dong J, Liu X. TOP1α fine-tunes TOR-PLT2 to maintain root tip homeostasis in response to sugars. NATURE PLANTS 2022; 8:792-801. [PMID: 35817819 DOI: 10.1038/s41477-022-01179-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Plant development is highly dependent on energy levels. TARGET OF RAPAMYCIN (TOR) activates the proximal root meristem to promote root development in response to photosynthesis-derived sugars during photomorphogenesis in Arabidopsis thaliana. However, the mechanisms of how root tip homeostasis is maintained to ensure proper root cap structure and gravitropism are unknown. PLETHORA (PLT) transcription factors are pivotal for the root apical meristem (RAM) identity by forming gradients, but how PLT gradients are established and maintained, and their roles in COL development are not well known. We demonstrate that endogenous sucrose induces TOPOISOMERASE1α (TOP1α) expression during the skotomorphogenesis-to-photomorphogenesis transition. TOP1α fine-tunes TOR expression in the root tip columella. TOR maintains columella stem cell identity correlating with reduced quiescent centre cell division in a WUSCHEL RELATED HOMEOBOX5-independent manner. Meanwhile, TOR promotes PLT2 expression and phosphorylates and stabilizes PLT2 to maintain its gradient consistent with TOR expression pattern. PLT2 controls cell division and amyloplast formation to regulate columella development and gravitropism. This elaborate mechanism helps maintain root tip homeostasis and gravitropism in response to energy changes during root development.
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Affiliation(s)
- Hao Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Lin Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China.
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China.
| | - Yongpeng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Dan Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
- College of Life Sciences, Hengshui University, Hengshui, China
| | - Luping Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wenwen Chang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Yichao Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Jiajie Hou
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Chenghao Fu
- Food Science College, Shenyang Agricultural University, ShenYang, China
| | - Ying Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Baowen Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Yuru Ma
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Yanxiao Niu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Kang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Jihong Xing
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Sujuan Cui
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Fengru Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Ke Tan
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Shuzhi Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Wenqiang Tang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China.
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China.
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Wang X, Wang L, Huang Y, Deng Z, Li C, Zhang J, Zheng M, Yan S. A plant-specific module for homologous recombination repair. Proc Natl Acad Sci U S A 2022; 119:e2202970119. [PMID: 35412914 PMCID: PMC9169791 DOI: 10.1073/pnas.2202970119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Homologous recombination repair (HR) is an error-free DNA damage repair pathway to maintain genome stability and a basis of gene targeting using genome-editing tools. However, the mechanisms of HR in plants are still poorly understood. Through genetic screens for DNA damage response mutants (DDRM) in Arabidopsis, we find that a plant-specific ubiquitin E3 ligase DDRM1 is required for HR. DDRM1 contains an N-terminal BRCT (BRCA1 C-terminal) domain and a C-terminal RING (really interesting new gene) domain and is highly conserved in plants including mosses. The ddrm1 mutant is defective in HR and thus is hypersensitive to DNA-damaging reagents. Biochemical studies reveal that DDRM1 interacts with and ubiquitinates the transcription factor SOG1, a plant-specific master regulator of DNA damage responses. Interestingly, DDRM1-mediated ubiquitination promotes the stability of SOG1. Consistently, genetic data support that SOG1 functions downstream of DDRM1. Our study reveals that DDRM1-SOG1 is a plant-specific module for HR and highlights the importance of ubiquitination in HR.
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Affiliation(s)
- Xuanpeng Wang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongchi Huang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Cunliang Li
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Zhang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingxi Zheng
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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6
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Gu N, Chen C, Kabeya Y, Hasebe M, Tamada Y. Topoisomerase 1α is required for synchronous spermatogenesis in Physcomitrium patens. THE NEW PHYTOLOGIST 2022; 234:137-148. [PMID: 35067949 DOI: 10.1111/nph.17983] [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: 11/04/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
DNA topoisomerase 1 (TOP1) plays general roles in DNA replication and transcription by regulating DNA topology in land plants and metazoans. TOP1 is also involved in specific developmental events; however, whether TOP1 plays a conserved developmental role among multicellular organisms is unknown. Here, we investigated the developmental roles of TOP1 in the moss Physcomitrium (Physcomitrella) patens with gene targeting, microscopy, 3D image segmentation and crossing experiments. We discovered that the disruption of TOP1α, but not its paralogue TOP1β, leads to a defect in fertilisation and subsequent sporophyte formation in P. patens. In the top1α mutant, the egg cell was functional for fertilisation, while sperm cells were fewer and infertile with disordered structures. We observed that the nuclei volume of wild-type sperm cells synchronously decreases during antheridium development, indicating chromatin condensation towards the compact sperm head. By contrast, the top1α mutant exhibited attenuated cell divisions and asynchronous and defective contraction of the nuclei of sperm cells throughout spermatogenesis. These results indicate that TOP1α is involved in cell division and chromatin condensation during spermatogenesis in P. patens. Our results suggest that the regulation of DNA topology by TOP1 plays a key role in spermatogenesis in both land plants and metazoans.
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Affiliation(s)
- Nan Gu
- Robotics, Engineering and Agriculture-technology Laboratory (REAL), Utsunomiya University, Utsunomiya, 321-8585, Japan
- School of Engineering, Utsunomiya University, Utsunomiya, 321-8585, Japan
- Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Chunli Chen
- Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang, 550025, China
| | - Yukiko Kabeya
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Mitsuyasu Hasebe
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
- School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, 444-8585, Japan
| | - Yosuke Tamada
- Robotics, Engineering and Agriculture-technology Laboratory (REAL), Utsunomiya University, Utsunomiya, 321-8585, Japan
- School of Engineering, Utsunomiya University, Utsunomiya, 321-8585, Japan
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
- School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, 444-8585, Japan
- Center for Optical Research & Education (CORE), Utsunomiya University, Utsunomiya, 321-8585, Japan
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7
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Yin X. Phyllotaxis: from classical knowledge to molecular genetics. JOURNAL OF PLANT RESEARCH 2021; 134:373-401. [PMID: 33550488 DOI: 10.1007/s10265-020-01247-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Plant organs are repetitively generated at the shoot apical meristem (SAM) in recognizable patterns. This phenomenon, known as phyllotaxis, has long fascinated scientists from different disciplines. While we have an enriched body of knowledge on phyllotactic patterns, parameters, and transitions, only in the past 20 years, however, have we started to identify genes and elucidate genetic pathways that involved in phyllotaxis. In this review, I first summarize the classical knowledge of phyllotaxis from a morphological perspective. I then discuss recent advances in the regulation of phyllotaxis, from a molecular genetics perspective. I show that the morphological beauty of phyllotaxis we appreciate is the manifestation of many regulators, in addition to the critical role of auxin as a patterning signal, exerting their respective effects in a coordinated fashion either directly or indirectly in the SAM.
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Affiliation(s)
- Xiaofeng Yin
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Japan Society for the Promotion of Science, Tokyo, Japan.
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Gualtieri C, Gianella M, Pagano A, Cadeddu T, Araújo S, Balestrazzi A, Macovei A. Exploring microRNA Signatures of DNA Damage Response Using an Innovative System of Genotoxic Stress in Medicago truncatula Seedlings. FRONTIERS IN PLANT SCIENCE 2021; 12:645323. [PMID: 33767724 PMCID: PMC7985446 DOI: 10.3389/fpls.2021.645323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/15/2021] [Indexed: 05/08/2023]
Abstract
One of the challenges that living organisms face is to promptly respond to genotoxic stress to avoid DNA damage. To this purpose, all organisms, including plants, developed complex DNA damage response (DDR) mechanisms. These mechanisms are highly conserved among organisms and need to be finely regulated. In this scenario, microRNAs (miRNAs) are emerging as active players, thus attracting the attention of the research community. The involvement of miRNAs in DDR has been investigated prominently in human cells whereas studies in plants are still scarce. To experimentally investigate the involvement of plant miRNAs in the regulation of DDR-associated pathways, an ad hoc system was developed, using the model legume Medicago truncatula. Specific treatments with camptothecin (CPT) and/or NSC120686 (NSC), targeting distinct components of DDR, namely topoisomerase I (TopI) and tyrosyl-DNA phosphodiesterase 1 (TDP1), were used. Phenotypic (germination percentage and speed, seedling growth) and molecular (cell death, DNA damage, and gene expression profiles) analyses demonstrated that the imposed treatments impact DDR. Our results show that these treatments do not influence the germination process but rather inhibit seedling development, causing an increase in cell death and accumulation of DNA damage. Moreover, treatment-specific changes in the expression of suppressor of gamma response 1 (SOG1), master-regulator of plant DDR, were observed. Additionally, the expression of multiple genes playing important roles in different DNA repair pathways and cell cycle regulation were differentially expressed in a treatment-specific manner. Subsequently, specific miRNAs identified from our previous bioinformatics approaches as putatively targeting genes involved in DDR processes were investigated alongside their targets. The obtained results indicate that under most conditions when a miRNA is upregulated the corresponding candidate target gene is downregulated, providing an indirect evidence of miRNAs action over these targets. Hence, the present study extends the present knowledge on the information available regarding the roles played by miRNAs in the post-transcriptional regulation of DDR in plants.
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Affiliation(s)
- Carla Gualtieri
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Maraeva Gianella
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Andrea Pagano
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Tiziano Cadeddu
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Susana Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Association BLC3, Technology and Innovation Campus, Centre BIO- R&D Unit, Lagares da Beira, Portugal
| | - Alma Balestrazzi
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
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9
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Inagaki S, Takahashi M, Takashima K, Oya S, Kakutani T. Chromatin-based mechanisms to coordinate convergent overlapping transcription. NATURE PLANTS 2021; 7:295-302. [PMID: 33649596 DOI: 10.1038/s41477-021-00868-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
In eukaryotic genomes, the transcription units of genes often overlap with other protein-coding and/or noncoding transcription units1,2. In such intertwined genomes, the coordinated transcription of nearby or overlapping genes would be important to ensure the integrity of genome function3-6; however, the mechanisms underlying this coordination are largely unknown. Here, we show in Arabidopsis thaliana that genes with convergent orientation of transcription are major sources of antisense transcripts and that these genes transcribed on both strands are regulated by a putative Lysine-Specific Demethylase 1 family histone demethylase, FLOWERING LOCUS D (FLD)7,8. Our genome-wide chromatin profiling revealed that FLD, as well as its associating factor LUMINIDEPENDENS9, downregulates histone H3K4me1 in regions with convergent overlapping transcription. FLD localizes to actively transcribed genes, where it colocalizes with elongating RNA polymerase II phosphorylated at the Ser2 or Ser5 sites. Genome-wide transcription analyses suggest that FLD-mediated H3K4me1 removal negatively regulates the transcription of genes with high levels of antisense transcription. Furthermore, the effect of FLD on transcription dynamics is antagonized by DNA topoisomerase I. Our study reveals chromatin-based mechanisms to cope with overlapping transcription, which may occur by modulating DNA topology. This global mechanism to cope with overlapping transcription could be co-opted for specific epigenetic processes, such as cellular memory of responses to the environment10.
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Affiliation(s)
- Soichi Inagaki
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan.
- National Institute of Genetics, Mishima, Japan.
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Shonankokusaimura, Hayama, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
| | | | | | - Satoyo Oya
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan
| | - Tetsuji Kakutani
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan
- National Institute of Genetics, Mishima, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Shonankokusaimura, Hayama, Japan
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10
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Vial-Pradel S, Hasegawa Y, Nakagawa A, Miyaki S, Machida Y, Kojima S, Machida C, Takahashi H. SIMON: Simple methods for analyzing DNA methylation by targeted bisulfite next-generation sequencing. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:213-222. [PMID: 31983875 PMCID: PMC6978500 DOI: 10.5511/plantbiotechnology.19.0822a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
DNA methylation in higher organisms has become an expanding field of study as it often involves the regulation of gene expression. Although Whole Genome Bisulfite Sequencing (WG-BS) based on next-generation sequencing (NGS) is the most versatile method, this is a costly technique that lacks in-depth analytic power. There are no conventional methods based on NGS that enable researchers to easily compare the level of DNA methylation from the practical number of samples handled in the laboratory. Although the targeted BS method based on Sanger sequencing is generally used in this case, it lacks in-depth analytic power. Therefore, we propose a new method that combines the high throughput analytic power of NGS and bioinformatics with the specificity and focus offered by PCR-amplification-based bisulfite sequencing methods. We use in silico size sieving of DNA-fragments and primer matchings instead of whole-fragment alignment in our bioinformatics analyses, and named our method SIMON (Simple Inference for Methylome based On NGS). The results of our targeted BS method based on NGS (SIMON method) show that small variations in DNA methylation patterns can be precisely and efficiently measured at a single nucleotide resolution. SIMON method combines pre-existing techniques to provide a cost-effective technique for in-depth studies that focus on pre-identified loci. It offers significant improvements with regard to workflow and the quality of the acquired DNA methylation information. Because of the high accuracy of the analysis, small variations of DNA methylation levels can be precisely determined even with large numbers of samples and loci.
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Affiliation(s)
- Simon Vial-Pradel
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Yoshinori Hasegawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Shido Miyaki
- Graduate School of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba 271-8510, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, 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
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba 271-8510, Japan
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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11
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Zhong P, Li J, Luo L, Zhao Z, Tian Z. TOP1α regulates FLOWERING LOCUS C expression by coupling histone modification and transcription machinery. Development 2019; 146:dev.167841. [PMID: 30705075 DOI: 10.1242/dev.167841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 01/22/2019] [Indexed: 11/20/2022]
Abstract
The key steps of transcription are coupled with the opening of the DNA helical structure and establishment of active chromatin to facilitate the movement of the transcription machinery. Type I topoisomerases cleave one DNA strand and relax the supercoiled structure of transcribed templates. How topoisomerase-mediated DNA topological changes promote transcription and establish a permissive histone modification for transcription elongation is largely unknown. Here, we show that TOPOISOMERASE 1α in plants regulates FLOWERING LOCUS C transcription by coupling histone modification and transcription machinery. We demonstrate that TOP1α directly interacts with the methyltransferase SDG8 to establish high levels of H3K36 methylation downstream of FLC transcription start sites and recruits RNA polymerase II to facilitate transcription elongation. Our results provide a mechanistic framework for TOP1α control of the main steps of early transcription and demonstrate how topoisomerases couple RNA polymerase II and permissive histone modifications to initiate transcription elongation.
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Affiliation(s)
- Peiqiao Zhong
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Jiaojiao Li
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Linjie Luo
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Zhong Zhao
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Zhaoxia Tian
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
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12
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Kupriyanova EV, Albert EV, Bliznina AI, Mamoshina PO, Ezhova TA. Arabidopsis DNA topoisomerase I alpha is required for adaptive response to light and flower development. Biol Open 2017; 6:832-843. [PMID: 28495963 PMCID: PMC5483022 DOI: 10.1242/bio.024422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA topoisomerase I alpha (TOP1α) plays a specific role in Arabidopsis thaliana development and is required for stem cell regulation in shoot and floral meristems. Recently, a new role independent of meristem functioning has been described for TOP1α, namely flowering time regulation. The same feature had been detected by us earlier for fas5, a mutant allele of TOP1α. In this study we clarify the effects of fas5 on bolting initiation and analyze the molecular basis of its role on flowering time regulation. We show that fas5 mutation leads to a constitutive shade avoidance syndrome, accompanied by leaf hyponasty, petiole elongation, lighter leaf color and early bolting. Other alleles of TOP1α demonstrate the same shade avoidance response. RNA sequencing confirmed the activation of shade avoidance gene pathways in fas5 mutant plants. It also revealed the repression of many genes controlling floral meristem identity and organ morphogenesis. Our research further expands the knowledge of TOP1α function in plant development and reveals that besides stem cell maintenance TOP1α plays an important new role in regulating the adaptive plant response to light stimulus and flower development. Summary: This study expands upon the existing knowledge of Arabidopsis DNA topoisomerase gene TOP1α function in plant development and demonstrates its important new role in regulating shade response and flower development.
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Affiliation(s)
- Evgenia V Kupriyanova
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Evgeniy V Albert
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Aleksandra I Bliznina
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Polina O Mamoshina
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Tatiana A Ezhova
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
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13
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Shafiq S, Chen C, Yang J, Cheng L, Ma F, Widemann E, Sun Q. DNA Topoisomerase 1 Prevents R-loop Accumulation to Modulate Auxin-Regulated Root Development in Rice. MOLECULAR PLANT 2017; 10:821-833. [PMID: 28412545 DOI: 10.1016/j.molp.2017.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/02/2017] [Accepted: 04/03/2017] [Indexed: 05/21/2023]
Abstract
R-loop structures (RNA:DNA hybrids) have important functions in many biological processes, including transcriptional regulation and genome instability among diverse organisms. DNA topoisomerase 1 (TOP1), an essential manipulator of DNA topology during RNA transcription and DNA replication processes, can prevent R-loop accumulation by removing the positive and negative DNA supercoiling that is made by RNA polymerases during transcription. TOP1 is required for plant development, but little is known about its function in preventing co-transcriptional R-loop accumulation in various biological processes in plants. Here we show that knockdown of OsTOP1 strongly affects rice development, causing defects in root architecture and gravitropism, which are the consequences of misregulation of auxin signaling and transporter genes. We found that R-loops are naturally formed at rice auxin-related gene loci, and overaccumulate when OsTOP1 is knocked down or OsTOP1 protein activity is inhibited. OsTOP1 therefore sets the accurate expression levels of auxin-related genes by preventing the overaccumulation of inherent R-loops. Our data reveal R-loops as important factors in polar auxin transport and plant root development, and highlight that OsTOP1 functions as a key to link transcriptional R-loops with plant hormone signaling, provide new insights into transcriptional regulation of hormone signaling in plants.
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Affiliation(s)
- Sarfraz Shafiq
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Permanent affiliation: Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad 22060, Pakistan
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jing Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingling Cheng
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fei Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Emilie Widemann
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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14
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Gao C, Qi S, Liu K, Li D, Jin C, Duan S, Zhang M, Chen M. Functional characterization of Brassica napus DNA topoisomerase Iα-1 and its effect on flowering time when expressed in Arabidopsis thaliana. Biochem Biophys Res Commun 2017; 486:124-129. [PMID: 28283390 DOI: 10.1016/j.bbrc.2017.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/06/2017] [Indexed: 01/17/2023]
Abstract
Previous studies have shown that DNA topoisomerase Iα (AtTOP1α) has specific developmental functions during growth and development in Arabidopsis thaliana. However, little is known about the roles of DNA topoisomerases in the closely related and commercially important plant, rapeseed (Brassica napus). Here, the full-length BnTOP1α-1 coding sequence was cloned from the A2 subgenome of the Brassica napus inbred line L111. We determine that all BnTOP1α paralogs showed differing patterns of expression in different organs of L111, and that when expressed in tobacco leaves as a fusion protein with green fluorescent protein, BnTOP1α-1 localized to the nucleus. We further showed that ectopic expression of BnTOP1α-1 in the A. thaliana top1α-7 mutant fully complemented the early flowering phenotype of the mutant. Moreover, altered expression levels in top1α-7 seedlings of several key genes controlling flowering time were restored to wild type levels by ectopic expression of BnTOP1α-1. These results provide valuable insights into the roles of rapeseed DNA topoisomerases in flowering time, and provide a promising target for genetic manipulation of this commercially significant process in rapeseed.
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Affiliation(s)
- Chenhao Gao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuanghui Qi
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaige Liu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dong Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Changyu Jin
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shaowei Duan
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxun Chen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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15
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Gong X, Shen L, Peng YZ, Gan Y, Yu H. DNA Topoisomerase Iα Affects the Floral Transition. PLANT PHYSIOLOGY 2017; 173:642-654. [PMID: 27837087 PMCID: PMC5210759 DOI: 10.1104/pp.16.01603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/08/2016] [Indexed: 05/16/2023]
Abstract
DNA topoisomerases modulate DNA topology to maintain chromosome superstructure and genome integrity, which is indispensable for DNA replication and RNA transcription. Their function in plant development still remains largely unknown. Here, we report a hitherto unidentified role of Topoisomerase Iα (TOP1α) in controlling flowering time in Arabidopsis (Arabidopsis thaliana). Loss of function of TOP1α results in early flowering under both long and short days. This is attributed mainly to a decrease in the expression of a central flowering repressor, FLOWERING LOCUS C (FLC), and its close homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, during the floral transition. TOP1α physically binds to the genomic regions of FLC, MAF4, and MAF5 and promotes the association of RNA polymerase II complexes to their transcriptional start sites. These correlate with the changes in histone modifications but do not directly affect nucleosome occupancy at these loci. Our results suggest that TOP1α mediates DNA topology to facilitate the recruitment of RNA polymerase II at FLC, MAF4, and MAF5 in conjunction with histone modifications, thus facilitating the expression of these key flowering repressors to prevent precocious flowering in Arabidopsis.
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Affiliation(s)
- Ximing Gong
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Lisha Shen
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Ya Zhi Peng
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Yinbo Gan
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
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16
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Li S, Wang P, Yuan W, Su Z, Bullard SH. Endocidal Regulation of Secondary Metabolites in the Producing Organisms. Sci Rep 2016; 6:29315. [PMID: 27389069 PMCID: PMC4937345 DOI: 10.1038/srep29315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/15/2016] [Indexed: 11/30/2022] Open
Abstract
Secondary metabolites are defined as organic compounds that are not directly involved in the normal growth, development, and reproduction of an organism. They are widely believed to be responsible for interactions between the producing organism and its environment, with the producer avoiding their toxicities. In our experiments, however, none of the randomly selected 44 species representing different groups of plants and insects can avoid autotoxicity by its endogenous metabolites once made available. We coined the term endocides (endogenous biocides) to describe such metabolites that can poison or inhibit the parent via induced biosynthesis or external applications. Dosage-dependent endocides can selectively induce morphological mutations in the parent organism (e.g., shrubbiness/dwarfism, pleiocotyly, abnormal leaf morphogenesis, disturbed phyllotaxis, fasciated stems, and variegation in plants), inhibit its growth, development, and reproduction and cause death than non-closely related species. The propagule, as well as the organism itself contains or produces adequate endocides to kill itself.
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Affiliation(s)
- Shiyou Li
- National Center for Pharmaceutical Crops, Arthur Temple College of Forestry and Agriculture, Stephen F. Austin State University, Nacogdoches, TX 75962, USA
| | - Ping Wang
- National Center for Pharmaceutical Crops, Arthur Temple College of Forestry and Agriculture, Stephen F. Austin State University, Nacogdoches, TX 75962, USA
| | - Wei Yuan
- National Center for Pharmaceutical Crops, Arthur Temple College of Forestry and Agriculture, Stephen F. Austin State University, Nacogdoches, TX 75962, USA
| | - Zushang Su
- National Center for Pharmaceutical Crops, Arthur Temple College of Forestry and Agriculture, Stephen F. Austin State University, Nacogdoches, TX 75962, USA
| | - Steven H. Bullard
- National Center for Pharmaceutical Crops, Arthur Temple College of Forestry and Agriculture, Stephen F. Austin State University, Nacogdoches, TX 75962, USA
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17
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Jia N, Liu X, Gao H. A DNA2 Homolog Is Required for DNA Damage Repair, Cell Cycle Regulation, and Meristem Maintenance in Plants. PLANT PHYSIOLOGY 2016; 171:318-33. [PMID: 26951435 PMCID: PMC4854720 DOI: 10.1104/pp.16.00312] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 03/04/2016] [Indexed: 05/18/2023]
Abstract
Plant meristem cells divide and differentiate in a spatially and temporally regulated manner, ultimately giving rise to organs. In this study, we isolated the Arabidopsis jing he sheng 1 (jhs1) mutant, which exhibited retarded growth, an abnormal pattern of meristem cell division and differentiation, and morphological defects such as fasciation, an irregular arrangement of siliques, and short roots. We identified JHS1 as a homolog of human and yeast DNA Replication Helicase/Nuclease2, which is known to be involved in DNA replication and damage repair. JHS1 is strongly expressed in the meristem of Arabidopsis. The jhs1 mutant was sensitive to DNA damage stress and had an increased DNA damage response, including increased expression of genes involved in DNA damage repair and cell cycle regulation, and a higher frequency of homologous recombination. In the meristem of the mutant plants, cell cycle progression was delayed at the G2 or late S phase and genes essential for meristem maintenance were misregulated. These results suggest that JHS1 plays an important role in DNA replication and damage repair, meristem maintenance, and development in plants.
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Affiliation(s)
- Ning Jia
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China (N.J., X.L., H.G.)
| | - Xiaomin Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China (N.J., X.L., H.G.)
| | - Hongbo Gao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China (N.J., X.L., H.G.)
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18
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Zhang Y, Zheng L, Hong JH, Gong X, Zhou C, Pérez-Pérez JM, Xu J. TOPOISOMERASE1α Acts through Two Distinct Mechanisms to Regulate Stele and Columella Stem Cell Maintenance. PLANT PHYSIOLOGY 2016; 171:483-93. [PMID: 26969721 PMCID: PMC4854680 DOI: 10.1104/pp.15.01754] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/10/2016] [Indexed: 05/11/2023]
Abstract
TOPOISOMERASE1 (TOP1), which releases DNA torsional stress generated during replication through its DNA relaxation activity, plays vital roles in animal and plant development. In Arabidopsis (Arabidopsis thaliana), TOP1 is encoded by two paralogous genes (TOP1α and TOP1β), of which TOP1α displays specific developmental functions that are critical for the maintenance of shoot and floral stem cells. Here, we show that maintenance of two different populations of root stem cells is also dependent on TOP1α-specific developmental functions, which are exerted through two distinct novel mechanisms. In the proximal root meristem, the DNA relaxation activity of TOP1α is critical to ensure genome integrity and survival of stele stem cells (SSCs). Loss of TOP1α function triggers DNA double-strand breaks in S-phase SSCs and results in their death, which can be partially reversed by the replenishment of SSCs mediated by ETHYLENE RESPONSE FACTOR115 In the quiescent center and root cap meristem, TOP1α is epistatic to RETINOBLASTOMA-RELATED (RBR) in the maintenance of undifferentiated state and the number of columella stem cells (CSCs). Loss of TOP1α function in either wild-type or RBR RNAi plants leads to differentiation of CSCs, whereas overexpression of TOP1α mimics and further enhances the effect of RBR reduction that increases the number of CSCs Taken together, these findings provide important mechanistic insights into understanding stem cell maintenance in plants.
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Affiliation(s)
- Yonghong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Lanlan Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Jing Han Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Ximing Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Chun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - José Manuel Pérez-Pérez
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Jian Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
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John R, Ganeshan U, Singh BN, Kaul T, Reddy MK, Sopory SK, Rajam MV. Over-expression of Topoisomerase II Enhances Salt Stress Tolerance in Tobacco. FRONTIERS IN PLANT SCIENCE 2016; 7:1280. [PMID: 27630644 PMCID: PMC5006100 DOI: 10.3389/fpls.2016.01280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/11/2016] [Indexed: 05/09/2023]
Abstract
Topoisomerases are unique enzymes having an ability to remove or add DNA supercoils and untangle the snarled DNA. They can cut, shuffle, and religate DNA strands and remove the torsional stress during DNA replication, transcription or recombination events. In the present study, we over-expressed topoisomerase II (TopoII) in tobacco (Nicotiana tabaccum) and examined its role in growth and development as well as salt (NaCl) stress tolerance. Several putative transgenic plants were generated and the transgene integration and expression was confirmed by PCR and Southern blot analyses, and RT-PCR analysis respectively. Percent seed germination, shoot growth, and chlorophyll content revealed that transgenic lines over-expressing the NtTopoIIα-1 gene exhibited enhanced tolerance to salt (150 and 200 mM NaCl) stress. Moreover, over-expression of TopoII lead to the elevation in proline and glycine betaine levels in response to both concentrations of NaCl as compared to wild-type. In response to NaCl stress, TopoII over-expressing lines showed reduced lipid peroxidation derived malondialdehyde (MDA) generation. These results suggest that TopoII plays a pivotal role in salt stress tolerance in plants.
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Affiliation(s)
- Riffat John
- Plant Molecular Biology Laboratory, Department of Botany, University of KashmirSrinagar, India
- *Correspondence: Riffat John
| | - Uma Ganeshan
- Plant Polyamine, Transgenic and RNAi Laboratory, Department of Genetics, University of Delhi South CampusNew Delhi, India
| | - Badri N. Singh
- Plant Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Tanushri Kaul
- Plant Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Malireddy K. Reddy
- Plant Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Sudhir K. Sopory
- Plant Biology, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Manchikatla V. Rajam
- Plant Polyamine, Transgenic and RNAi Laboratory, Department of Genetics, University of Delhi South CampusNew Delhi, India
- Manchikatla V. Rajam
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20
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Singh BN, Mudgil Y, John R, Achary VMM, Tripathy MK, Sopory SK, Reddy MK, Kaul T. Cell cycle stage-specific differential expression of topoisomerase I in tobacco BY-2 cells and its ectopic overexpression and knockdown unravels its crucial role in plant morphogenesis and development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:182-92. [PMID: 26475198 DOI: 10.1016/j.plantsci.2015.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 09/17/2015] [Accepted: 09/19/2015] [Indexed: 05/24/2023]
Abstract
DNA topoisomerases catalyze the inter-conversion of different topological forms of DNA. Cell cycle coupled differential accumulation of topoisomerase I (Topo I) revealed biphasic expression maximum at S-phase and M/G1-phase of cultured synchronized tobacco BY-2 cells. This suggested its active role in resolving topological constrains during DNA replication (S-phase) and chromosome decondensation (M/G1 phase). Immuno-localization revealed high concentrations of Topo I in nucleolus. Propidium iodide staining and Br-UTP incorporation patterns revealed direct correlation between immunofluorescence intensity and rRNA transcription activity within nucleolus. Immuno-stained chromosomes during metaphase and anaphase suggested possible role of Topo I in resolving topological constrains during mitotic chromosome condensation. Inhibitor studies showed that in comparison to Topo I, Topo II was essential in resolving topological constrains during chromosome condensation. Probably, Topo II substituted Topo I functioning to certain extent during chromosome condensation, but not vice-versa. Transgenic Topo I tobacco lines revealed morphological abnormalities and highlighted its crucial role in plant morphogenesis and development.
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Affiliation(s)
- Badri Nath Singh
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Yashwanti Mudgil
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Riffat John
- Department of Botany, University of Kashmir, Hazratbal, Srinagar 190006, Jammu and Kashmir, India
| | - V Mohan Murali Achary
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Manas Kumar Tripathy
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Sudhir K Sopory
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Malireddy K Reddy
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Tanushri Kaul
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India.
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21
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Gaillochet C, Lohmann JU. The never-ending story: from pluripotency to plant developmental plasticity. Development 2015; 142:2237-49. [PMID: 26130755 PMCID: PMC4510588 DOI: 10.1242/dev.117614] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Plants are sessile organisms, some of which can live for over a thousand years. Unlike most animals, plants employ a post-embryonic mode of development driven by the continuous activity of pluripotent stem cells. Consequently, plants are able to initiate new organs over extended periods of time, and many species can readily replace lost body structures by de novo organogenesis. Classical studies have also shown that plant tissues have a remarkable capacity to undergo de-differentiation and proliferation in vitro, highlighting the fact that plant cell fate is highly plastic. This suggests that the mechanisms regulating fate transitions must be continuously active in most plant cells and that the control of cellular pluripotency lies at the core of diverse developmental programs. Here, we review how pluripotency is established in plant stem cell systems, how it is maintained during development and growth and re-initiated during regeneration, and how these mechanisms eventually contribute to the amazing developmental plasticity of plants.
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Affiliation(s)
- Christophe Gaillochet
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
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22
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Cao X, He Z, Guo L, Liu X. Epigenetic Mechanisms Are Critical for the Regulation of WUSCHEL Expression in Floral Meristems. PLANT PHYSIOLOGY 2015; 168:1189-96. [PMID: 25829464 PMCID: PMC4528737 DOI: 10.1104/pp.15.00230] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/25/2015] [Indexed: 05/04/2023]
Abstract
The floral meristem (FM), which develops from the inflorescence meristem upon completion of the floral transition, terminates after producing a defined number of floral organs. This is in contrast to the shoot apical meristem, which is active throughout the entire life span of plants. WUSCHEL (WUS) encodes a homeodomain-containing protein and plays a critical role in shoot apical meristem, inflorescence meristem, and FM establishment and maintenance as well as FM determinacy. Although many genes have been implicated in FM determinacy through the regulation of WUS expression, precisely how these genes are coordinated to regulate WUS and consequently dictate FM fate remains unclear. Emerging lines of evidence indicate that epigenetic mechanisms, such as histone modification, chromatin remodeling, noncoding RNAs, and DNA methylation, play vital roles in meristem maintenance and termination. Here, recent findings demonstrating the involvement of the epigenetic network in the regulation of WUS expression in the context of FM determinacy are summarized and discussed.
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Affiliation(s)
- Xiuwei Cao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
| | - Zishan He
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
| | - Lin Guo
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
| | - Xigang Liu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
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Bonhomme M, Boitard S, San Clemente H, Dumas B, Young N, Jacquet C. Genomic Signature of Selective Sweeps Illuminates Adaptation of Medicago truncatula to Root-Associated Microorganisms. Mol Biol Evol 2015; 32:2097-110. [PMID: 25901015 DOI: 10.1093/molbev/msv092] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Medicago truncatula is a model legume species used to investigate plant-microorganism interactions, notably root symbioses. Massive population genomic and transcriptomic data now available for this species open the way for a comprehensive investigation of genomic variations associated with adaptation of M. truncatula to its environment. Here we performed a fine-scale genome scan of selective sweep signatures in M. truncatula using more than 15 million single nucleotide polymorphisms identified on 283 accessions from two populations (Circum and Far West), and exploited annotation and published transcriptomic data to identify biological processes associated with molecular adaptation. We identified 58 swept genomic regions with a 15 kb average length and comprising 3.3 gene models on average. The unimodal sweep state probability distribution in these regions enabled us to focus on the best single candidate gene per region. We detected two unambiguous species-wide selective sweeps, one of which appears to underlie morphological adaptation. Population genomic analyses of the remaining 56 sweep signatures indicate that sweeps identified in the Far West population are less population-specific and probably more ancient than those identified in the Circum population. Functional annotation revealed a predominance of immunity-related adaptations in the Circum population. Transcriptomic data from accessions of the Far West population allowed inference of four clusters of coregulated genes putatively involved in the adaptive control of symbiotic carbon flow and nodule senescence, as well as in other root adaptations upon infection with soil microorganisms. We demonstrate that molecular adaptations in M. truncatula were primarily triggered by selective pressures from root-associated microorganisms.
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Affiliation(s)
- Maxime Bonhomme
- Laboratoire de Recherche en Sciences Végétales, UPS, Université de Toulouse, Auzeville, Castanet-Tolosan, France Laboratoire de Recherche en Sciences Végétales, CNRS, Auzeville, Castanet-Tolosan, France
| | - Simon Boitard
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique & AgroParisTech, Jouy-en-Josas, France Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle & Ecole Pratique des Hautes Etudes & CNRS & Université Pierre et Marie Curie, Paris, France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, UPS, Université de Toulouse, Auzeville, Castanet-Tolosan, France Laboratoire de Recherche en Sciences Végétales, CNRS, Auzeville, Castanet-Tolosan, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, UPS, Université de Toulouse, Auzeville, Castanet-Tolosan, France Laboratoire de Recherche en Sciences Végétales, CNRS, Auzeville, Castanet-Tolosan, France
| | - Nevin Young
- Department of Plant Biology, University of Minnesota Department of Plant Pathology, University of Minnesota
| | - Christophe Jacquet
- Laboratoire de Recherche en Sciences Végétales, UPS, Université de Toulouse, Auzeville, Castanet-Tolosan, France Laboratoire de Recherche en Sciences Végétales, CNRS, Auzeville, Castanet-Tolosan, France
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Waidmann S, Kusenda B, Mayerhofer J, Mechtler K, Jonak C. A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis. THE PLANT CELL 2014; 26:4328-44. [PMID: 25387881 PMCID: PMC4277211 DOI: 10.1105/tpc.114.129254] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/01/2014] [Accepted: 10/22/2014] [Indexed: 05/19/2023]
Abstract
Chromatin is a major determinant in the regulation of virtually all DNA-dependent processes. Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. The evolutionarily conserved DEK domain-containing protein is implicated in important chromatin-related processes in animals, but little is known about its DNA targets and protein interaction partners. In plants, the role of DEK has remained elusive. In this work, we identified DEK3 as a chromatin-associated protein in Arabidopsis thaliana. DEK3 specifically binds histones H3 and H4. Purification of other proteins associated with nuclear DEK3 also established DNA topoisomerase 1α and proteins of the cohesion complex as in vivo interaction partners. Genome-wide mapping of DEK3 binding sites by chromatin immunoprecipitation followed by deep sequencing revealed enrichment of DEK3 at protein-coding genes throughout the genome. Using DEK3 knockout and overexpressor lines, we show that DEK3 affects nucleosome occupancy and chromatin accessibility and modulates the expression of DEK3 target genes. Furthermore, functional levels of DEK3 are crucial for stress tolerance. Overall, data indicate that DEK3 contributes to modulation of Arabidopsis chromatin structure and function.
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Affiliation(s)
- Sascha Waidmann
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Branislav Kusenda
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Juliane Mayerhofer
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Claudia Jonak
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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25
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Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella P, Li S, Weigel D, Pontes O, Ecker JR, Chen X. DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis. PLoS Genet 2014; 10:e1004446. [PMID: 24992598 PMCID: PMC4080997 DOI: 10.1371/journal.pgen.1004446] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 05/05/2014] [Indexed: 11/18/2022] Open
Abstract
RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) are related transcriptional silencing mechanisms that target transposable elements (TEs) and repeats to maintain genome stability in plants. RdDM is mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α) was able to de-repress LUCL by reducing its DNA methylation and H3K9me2 levels. Further studies with Arabidopsis top1α mutants showed that TOP1α silences endogenous RdDM loci by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at TEs and repeats. This study assigned a new role in epigenetic silencing to an enzyme that affects DNA topology. DNA topoisomerase is an enzyme that releases the torsional stress in DNA generated during DNA replication or transcription. Here, we uncovered an unexpected role of DNA topoisomerase 1α (TOP1α) in the maintenance of genome stability. Eukaryotic genomes are usually littered with transposable elements (TEs) and repeats, which pose threats to genome stability due to their tendency to move or recombine. Mechanisms are in place to silence these elements, such as RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) in plants. Two plant-specific RNA polymerases, Pol IV and Pol V, generate small and long noncoding RNAs, respectively, from TEs and repeats. These RNAs then recruit protein factors to deposit DNA methylation or H3K9me2 to silence the loci. In this study, we found that treatment of plants with camptothecin, a TOP1α inhibitor, or loss of function in TOP1α, led to the de-repression of RdDM target loci, which was accompanied by loss of H3K9me2 or DNA methylation. The role of TOP1α in RdDM could be attributed to its promotion of Pol V, but not Pol IV, transcription to generate long noncoding RNAs.
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Affiliation(s)
- Thanh Theresa Dinh
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- ChemGen IGERT program, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Lei Gao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Xigang Liu
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Dongming Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shengben Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Michael O'Leary
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Brandon Le
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Robert J. Schmitz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Pablo Manavella
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shaofang Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Olga Pontes
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- Howard Hughes Medical Institute, University of California Riverside, Riverside, California, United States of America
- * E-mail:
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26
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Liu X, Gao L, Dinh TT, Shi T, Li D, Wang R, Guo L, Xiao L, Chen X. DNA topoisomerase I affects polycomb group protein-mediated epigenetic regulation and plant development by altering nucleosome distribution in Arabidopsis. THE PLANT CELL 2014; 26:2803-17. [PMID: 25070639 PMCID: PMC4145115 DOI: 10.1105/tpc.114.124941] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
It has been perplexing that DNA topoisomerases, enzymes that release DNA supercoils, play specific roles in development. In this study, using a floral stem cell model in Arabidopsis thaliana, we uncovered a role for TOPOISOMERASE1α (TOP1α) in Polycomb Group (PcG) protein-mediated histone 3 lysine 27 trimethylation (H3K27me3) at, and transcriptional repression of, the stem cell maintenance gene WUSCHEL (WUS). We demonstrated that H3K27me3 deposition at other PcG targets also requires TOP1α. Intriguingly, the repression of some, as well as the expression of many, PcG target genes requires TOP1α. The mechanism that unifies the opposing effects of TOP1α appears to lie in its role in decreasing nucleosome density, which probably allows the binding of factors that either recruit PcG, as we demonstrated for AGAMOUS at the WUS locus, or counteract PcG-mediated regulation. Although TOP1α reduces nucleosome density at all genes, the lack of a 5' nucleosome-free region is a feature that distinguishes PcG targets from nontargets and may condition the requirement for TOP1α for their expression. This study uncovers a connection between TOP1α and PcG, which explains the specific developmental functions of TOP1α.
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Affiliation(s)
- Xigang Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 Key Laboratory of Agricultural Water Resource, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Thanh Theresa Dinh
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Ting Shi
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongming Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 Key Laboratory of Agricultural Water Resource, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Ruozhong Wang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lin Guo
- Key Laboratory of Agricultural Water Resource, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Langtao Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 Howard Hughes Medical Institute, University of California, Riverside, California 92521
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27
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Kumari R, Sharma V, Sharma V, Kumar S. Pleiotropic phenotypes of the salt-tolerant and cytosine hypomethylated leafless inflorescence, evergreen dwarf and irregular leaf lamina mutants of Catharanthus roseus possessing Mendelian inheritance. J Genet 2014; 92:369-94. [PMID: 24371160 DOI: 10.1007/s12041-013-0271-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In Catharanthus roseus, three morphological cum salt-tolerant chemically induced mutants of Mendelian inheritance and their wild-type parent cv Nirmal were characterized for overall cytosine methylation at DNA repeats, expression of 119 protein coding and seven miRNA-coding genes and 50 quantitative traits. The mutants, named after their principal morphological feature(s), were leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill). The Southern-blot analysis of MspI digested DNAs of mutants probed with centromeric and 5S and 18S rDNA probes indicated that, in comparison to wild type, the mutants were extensively demethylated at cytosine sites. Among the 126 genes investigated for transcriptional expression, 85 were upregulated and 41 were downregulated in mutants. All of the five genes known to be stress responsive had increased expression in mutants. Several miRNA genes showed either increased or decreased expression in mutants. The C. roseus counterparts of CMT3, DRM2 and RDR2 were downregulated in mutants. Among the cell, organ and plant size, photosynthesis and metabolism related traits studied, 28 traits were similarly affected in mutants as compared to wild type. Each of the mutants also expressed some traits distinctively. The egd mutant possessed superior photosynthesis and water retention abilities. Biomass was hyperaccumulated in roots, stems, leaves and seeds of the lli mutant. The ill mutant was richest in the pharmaceutical alkaloids catharanthine, vindoline, vincristine and vinblastine. The nature of mutations, origins of mutant phenotypes and evolutionary importance of these mutants are discussed.
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Affiliation(s)
- Renu Kumari
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.
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28
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Mandel T, Moreau F, Kutsher Y, Fletcher JC, Carles CC, Williams LE. The ERECTA receptor kinase regulates Arabidopsis shoot apical meristem size, phyllotaxy and floral meristem identity. Development 2014; 141:830-41. [PMID: 24496620 PMCID: PMC3930468 DOI: 10.1242/dev.104687] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/08/2013] [Indexed: 11/20/2022]
Abstract
In plants, the shoot apical meristem (SAM) serves as a reservoir of pluripotent stem cells from which all above ground organs originate. To sustain proper growth, the SAM must maintain homeostasis between the self-renewal of pluripotent stem cells and cell recruitment for lateral organ formation. At the core of the network that regulates this homeostasis in Arabidopsis are the WUSCHEL (WUS) transcription factor specifying stem cell fate and the CLAVATA (CLV) ligand-receptor system limiting WUS expression. In this study, we identified the ERECTA (ER) pathway as a second receptor kinase signaling pathway that regulates WUS expression, and therefore shoot apical and floral meristem size, independently of the CLV pathway. We demonstrate that reduction in class III HD-ZIP and ER function together leads to a significant increase in WUS expression, resulting in extremely enlarged shoot meristems and a switch from spiral to whorled vegetative phyllotaxy. We further show that strong upregulation of WUS in the inflorescence meristem leads to ectopic expression of the AGAMOUS homeotic gene to a level that switches cell fate from floral meristem founder cell to carpel founder cell, suggesting an indirect role for ER in regulating floral meristem identity. This work illustrates the delicate balance between stem cell specification and differentiation in the meristem and shows that a shift in this balance leads to abnormal phyllotaxy and to altered reproductive cell fate.
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Affiliation(s)
- Tali Mandel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12 Rehovot 76100, Israel
| | | | - Yaarit Kutsher
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12 Rehovot 76100, Israel
| | - Jennifer C. Fletcher
- Plant Gene Expression Center, USDA-ARS/University of California, Berkeley, 800 Buchanan Street, Albany, CA 94710, USA
| | | | - Leor Eshed Williams
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12 Rehovot 76100, Israel
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Bolaños-Villegas P, Yang X, Wang HJ, Juan CT, Chuang MH, Makaroff CA, Jauh GY. Arabidopsis CHROMOSOME TRANSMISSION FIDELITY 7 (AtCTF7/ECO1) is required for DNA repair, mitosis and meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:927-40. [PMID: 23750584 PMCID: PMC3824207 DOI: 10.1111/tpj.12261] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/25/2013] [Accepted: 05/29/2013] [Indexed: 05/21/2023]
Abstract
The proper transmission of DNA in dividing cells is crucial for the survival of eukaryotic organisms. During cell division, faithful segregation of replicated chromosomes requires their tight attachment, known as sister chromatid cohesion, until anaphase. Sister chromatid cohesion is established during S-phase in a process requiring an acetyltransferase that in yeast is known as Establishment of cohesion 1 (Eco1). Inactivation of Eco1 typically disrupts chromosome segregation and homologous recombination-dependent DNA repair in dividing cells, ultimately resulting in lethality. We report here the isolation and detailed characterization of two homozygous T-DNA insertion mutants for the Arabidopsis thaliana Eco1 homolog, CHROMOSOME TRANSMISSION FIDELITY 7/ESTABLISHMENT OF COHESION 1 (CTF7/ECO1), called ctf7-1 and ctf7-2. Mutants exhibited dwarfism, poor anther development and sterility. Analysis of somatic tissues by flow cytometry, scanning electron microscopy and quantitative real-time PCR identified defects in DNA repair and cell division, including an increase in the area of leaf epidermal cells, an increase in DNA content and the upregulation of genes involved in DNA repair including BRCA1 and PARP2. No significant change was observed in the expression of genes that influence entry into the endocycle. Analysis of meiocytes identified changes in chromosome morphology and defective segregation; the abundance of chromosomal-bound cohesion subunits was also reduced. Transcript levels for several meiotic genes, including the recombinase genes DMC1 and RAD51C and the S-phase licensing factor CDC45 were elevated in mutant anthers. Taken together our results demonstrate that Arabidopsis CTF7/ECO1 plays important roles in the preservation of genome integrity and meiosis.
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Affiliation(s)
- Pablo Bolaños-Villegas
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia SinicaTaipei, 11529, Taiwan
| | - Xiaohui Yang
- Department of Chemistry and Biochemistry, Miami UniversityOxford, OH, 45056, USA
| | - Huei-Jing Wang
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, 11529, Taiwan
| | - Chien-Ta Juan
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, 11529, Taiwan
| | - Min-Hsiang Chuang
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, 11529, Taiwan
| | | | - Guang-Yuh Jauh
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia SinicaTaipei, 11529, Taiwan
- Biotechnology Center, Graduate Institute of Biotechnology, National Chung-Hsing UniversityTaichung, 402, Taiwan
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30
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Abstract
The appearance of Fibonacci sequences and the golden ratio in plant structures is one of the great outstanding puzzles of biology. Here I suggest that quasicrystals, which naturally pack in the golden ratio, may be ubiquitous in biological systems and introduce the golden ratio into plant phyllotaxy. The appearance of golden ratio-based structures as beautiful indicates that the golden ratio may play a role in the development of consciousness and lead to the aesthetic natural selection of flowering plants.
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Affiliation(s)
- John Gardiner
- The School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia.
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31
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Hashimura Y, Ueguchi C. The Arabidopsis MERISTEM DISORGANIZATION 1 gene is required for the maintenance of stem cells through the reduction of DNA damage. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:657-69. [PMID: 21781195 DOI: 10.1111/j.1365-313x.2011.04718.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In plants, stem cells reside in apical meristems, and provide the descendants required for post-embryonic growth and development throughout the life of a plant. To identify a novel factor required for the maintenance of stem cells, we isolated an Arabidopsis mutant, named meristem disorganization 1-1 (mdo1-1), that exhibits several developmental defects, such as abnormal phyllotaxy and plastochron, stem fasciation and retarded root growth. We found that the mutant plants fail to maintain stem cells, resulting in the differentiation or death of stem cells. The mutant plants also showed several phenotypes related to DNA damage, suggesting that the mutant cells are exposed constitutively to DNA damage even without external genotoxic stress. The growth defect and the hypersensitivity to DNA-damaging agents of mdo1-1 were enhanced significantly when combined with a lesion of the ATAXIA-TELANGIECTASIA MUTATED (ATM) gene, but not of the ATM/RAD3-RELATED (ATR) gene, suggesting that the function of the MDO1 gene is closely related to that of ATM kinase. The MDO1 gene encodes an unknown protein that is conserved in a wide variety of land plants. The results thus suggested that the MDO1 gene product is required for the maintenance of stem cells through a reduction in DNA damage.
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Affiliation(s)
- Yuma Hashimura
- Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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32
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Sánchez-Pons N, Irar S, García-Muniz N, Vicient CM. Transcriptomic and proteomic profiling of maize embryos exposed to camptothecin. BMC PLANT BIOLOGY 2011; 11:91. [PMID: 21595924 PMCID: PMC3118180 DOI: 10.1186/1471-2229-11-91] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 05/19/2011] [Indexed: 05/23/2023]
Abstract
BACKGROUND Camptothecin is a plant alkaloid that specifically binds topoisomerase I, inhibiting its activity and inducing double stranded breaks in DNA, activating the cell responses to DNA damage and, in response to severe treatments, triggering cell death. RESULTS Comparative transcriptomic and proteomic analyses of maize embryos that had been exposed to camptothecin were conducted. Under the conditions used in this study, camptothecin did not induce extensive degradation in the genomic DNA but induced the transcription of genes involved in DNA repair and repressed genes involved in cell division. Camptothecin also affected the accumulation of several proteins involved in the stress response and induced the activity of certain calcium-dependent nucleases. We also detected changes in the expression and accumulation of different genes and proteins involved in post-translational regulatory processes. CONCLUSIONS This study identified several genes and proteins that participate in DNA damage responses in plants. Some of them may be involved in general responses to stress, but others are candidate genes for specific involvement in DNA repair. Our results open a number of new avenues for researching and improving plant resistance to DNA injury.
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Affiliation(s)
- Nuria Sánchez-Pons
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Sami Irar
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Nora García-Muniz
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Carlos M Vicient
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
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33
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Macovei A, Balestrazzi A, Confalonieri M, Carbonera D. The tyrosyl-DNA phosphodiesterase gene family in Medicago truncatula Gaertn.: bioinformatic investigation and expression profiles in response to copper- and PEG-mediated stress. PLANTA 2010; 232:393-407. [PMID: 20458495 DOI: 10.1007/s00425-010-1179-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Accepted: 04/13/2010] [Indexed: 05/21/2023]
Abstract
The Tdp1 gene encoding tyrosyl-DNA phosphodiesterase has been extensively investigated in animal cells, due to the role of this enzyme in the repair of topoisomerase I-DNA covalent lesions. In contrast, information in this regard is totally missing in plants. We report for the first time in plants on the Tdp1 gene family from barrel medic (Medicago truncatula Gaertn.), composed of two members, hereby named MtTdp1alpha and MtTdp1beta. The expression profiles of MtTdp1alpha and MtTdp1beta genes were evaluated in plantlets grown in vitro using copper and polyethylene glycol (PEG 6000) as stress agents. In situ detection of reactive oxygen species (ROS) was carried out by histochemical staining, while the level of oxidative DNA damage, quantified in terms of 7,8-dihydro-8-oxoguanine (8-oxo-dG), increased up to 7.4- and 6.7-fold in response to copper and PEG 6000 treatments, respectively. Quantitative real-time polymerase chain reaction revealed that both Tdp1 genes were significantly up-regulated in response to copper and PEG. The Tdp1 genes were also significantly up-regulated during seed rehydration, an aspect of seed physiology in which DNA repair is a key component. Thus, the Tdp1 genes might be used as novel tools for improving stress tolerance in crops. The expression patterns of the barrel medic top1alpha and top1beta genes, encoding distinct isoforms of DNA topoisomerase I, were also analyzed and discussed to acquire additional information on their specific functions, closely related to that of the Tdp1 gene in animal cells.
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Affiliation(s)
- Anca Macovei
- Dipartimento di Genetica e Microbiologia, Pavia, Italy
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34
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Graf P, Dolzblasz A, Würschum T, Lenhard M, Pfreundt U, Laux T. MGOUN1 encodes an Arabidopsis type IB DNA topoisomerase required in stem cell regulation and to maintain developmentally regulated gene silencing. THE PLANT CELL 2010; 22:716-28. [PMID: 20228247 PMCID: PMC2861470 DOI: 10.1105/tpc.109.068296] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 02/05/2010] [Accepted: 03/01/2010] [Indexed: 05/18/2023]
Abstract
Maintenance of stem cells in the Arabidopsis thaliana shoot meristem is regulated by signals from the underlying cells of the organizing center, provided through the transcription factor WUSCHEL (WUS). Here, we report the isolation of several independent mutants of MGOUN1 (MGO1) as genetic suppressors of ectopic WUS activity and enhancers of stem cell defects in hypomorphic wus alleles. mgo1 mutants have previously been reported to result in a delayed progression of meristem cells into differentiating organ primordia (Laufs et al., 1998). Genetic analyses indicate that MGO1 functions together with WUS in stem cell maintenance at all stages of shoot and floral meristems. Synergistic interactions of mgo1 with several chromatin mutants suggest that MGO1 affects gene expression together with chromatin remodeling pathways. In addition, the expression states of developmentally regulated genes are randomly switched in mgo1 in a mitotically inheritable way, indicating that MGO1 stabilizes epigenetic states against stochastically occurring changes. Positional cloning revealed that MGO1 encodes a putative type IB topoisomerase, which in animals and yeast has been shown to be required for regulation of DNA coiling during transcription and replication. The specific developmental defects in mgo1 mutants link topoisomerase IB function in Arabidopsis to stable propagation of developmentally regulated gene expression.
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Affiliation(s)
- Philipp Graf
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Alicja Dolzblasz
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Tobias Würschum
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Michael Lenhard
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Ulrike Pfreundt
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Laux
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Freiburg Institute of Advanced Studies, University of Freiburg, 79104 Freiburg, Germany
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35
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Peixoto P, Bailly C, David-Cordonnier MH. Topoisomerase I-mediated DNA relaxation as a tool to study intercalation of small molecules into supercoiled DNA. Methods Mol Biol 2010; 613:235-56. [PMID: 19997888 DOI: 10.1007/978-1-60327-418-0_15] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Several biochemical and biophysical methods are available to study the intercalation of a small molecule between two consecutive base pairs of DNA. Among them, the topoisomerase I-mediated DNA relaxation assay has proved highly efficient, relatively easy to handle and very informative to investigate drug binding to DNA. The test relies on the use of a supercoiled plasmid to mimic the topological constraints of genomic DNA. The three main components of the assay - the topoisomerase I enzyme, DNA helix and intercalating small molecules - are presented here in a structural context. The principle of the assay is described in detail, along with a typical experimental protocol.
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Affiliation(s)
- Paul Peixoto
- INSERM U-837, Jean-Pierre Aubert Research Center (JPARC), Institut de Recherches sur le Cancer de Lille, Lille, France
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36
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Balestrazzi A, Locato V, Bottone MG, De Gara L, Biggiogera M, Pellicciari C, Botti S, Di Gesù D, Donà M, Carbonera D. Response to UV-C radiation in topo I-deficient carrot cells with low ascorbate levels. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:575-85. [PMID: 19917599 DOI: 10.1093/jxb/erp323] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In animal cells, recent studies have emphasized the role played by DNA topoisomerase I (topo I) both as a cofactor of DNA repair complexes and/or as a damage sensor. All these functions are still unexplored in plant cells, where information concerning the relationships between DNA damage, PCD induction, and topo I are also limited. The main goal of this study was to investigate the possible responses activated in topo I-depleted plant cells under oxidative stress conditions which induce DNA damage. The carrot (Daucus carota L.) AT1-beta/22 cell line analysed in this study (characterized by an antisense-mediated reduction of top1beta gene expression of approximately 46% in association with a low ascorbate content) was more sensitive to UV-C radiation than the control line, showing consistent cell death and high levels of 8-oxo-dG accumulation. The topo I-depleted cells were also highly susceptible to the cross-linking agent mitomycin C. The death response was associated with a lack of oxidative burst and there were no changes in ascorbate metabolism in response to UV-C treatment. Electron and fluorescence microscopy suggested the presence of three forms of cell death in the UV-C-treated AT1-beta/22 population: necrosis, apoptotic-like PCD, and autophagy. Taken together, the data reported here support a reduced DNA repair capability in carrot topo I-deficient cells while the putative relationship between topo I-depletion and ascorbate impairment is also discussed.
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Affiliation(s)
- A Balestrazzi
- Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, Pavia, Italy
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37
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38
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Mutations in topoisomerase I as a self-resistance mechanism coevolved with the production of the anticancer alkaloid camptothecin in plants. Proc Natl Acad Sci U S A 2008; 105:6782-6. [PMID: 18443285 DOI: 10.1073/pnas.0801038105] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plants produce a variety of toxic compounds, which are often used as anticancer drugs. The self-resistance mechanism to these toxic metabolites in the producing plants, however, remains unclear. The plant-derived anticancer alkaloid camptothecin (CPT) induces cell death by targeting DNA topoisomerase I (Top1), the enzyme that catalyzes changes in DNA topology. We found that CPT-producing plants, including Camptotheca acuminata, Ophiorrhiza pumila, and Ophiorrhiza liukiuensis, have Top1s with point mutations that confer resistance to CPT, suggesting the effect of an endogenous toxic metabolite on the evolution of the target cellular component. Three amino acid substitutions that contribute to CPT resistance were identified: Asn421Lys, Leu530Ile, and Asn722Ser (numbered according to human Top1). The substitution at position 722 is identical to that found in CPT-resistant human cancer cells. The other mutations have not been found to date in CPT-resistant human cancer cells; this predicts the possibility of occurrence of these mutations in CPT-resistant human cancer patients in the future. Furthermore, comparative analysis of Top1s of CPT-producing and nonproducing plants suggested that the former were partially primed for CPT resistance before CPT biosynthesis evolved. Our results demonstrate the molecular mechanism of self-resistance to endogenously produced toxic compounds and the possibility of adaptive coevolution between the CPT production system and its target Top1 in the producing plants.
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39
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Abstract
Theoretical models of phyllotaxis are based on geometric regularities appearing at the level of the shoot apical meristem (SAM). However, one cannot forget the presence of perturbed patterns in many plants. Disorganized patterns found in mutants of Arabidopsis and Antirrhinum bring new theoretical problems that cannot be solved by using models developed to analyse regular phyllotactic patterns. One way to take into account the perturbed patterns is to use a probabilistic approach to phyllotaxis. This review will focus mainly on recent probabilistic approaches that can be used to analyse perturbed patterns found in the plant kingdom in general and in phyllotactic mutants in particular. More precisely, it will be shown how probabilistic approaches can be used to determine the degree of order of phyllotactic patterns. By using particular tests, it is possible to statistically differentiate between whorled and distichous patterns (aggregated dispersion), spiral patterns (uniform dispersion), and random patterns (random dispersion). The elaboration of a general probabilistic model of phyllotaxis represents a new challenge for both theoretical and experimental research.
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Affiliation(s)
- Denis Barabé
- Institut de Recherche en Biologie Végétale, Jardin botanique de Montréal, Université de Montréal 4101 Sherbrooke Est, Montréal, QC H1X 2B2, Canada (e-mail: )
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40
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Nikovics K, Blein T, Peaucelle A, Ishida T, Morin H, Aida M, Laufs P. The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis. THE PLANT CELL 2006; 18:2929-45. [PMID: 17098808 PMCID: PMC1693934 DOI: 10.1105/tpc.106.045617] [Citation(s) in RCA: 408] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
CUP-SHAPED COTYLEDON1 (CUC1), CUC2, and CUC3 define the boundary domain around organs in the Arabidopsis thaliana meristem. CUC1 and CUC2 transcripts are targeted by a microRNA (miRNA), miR164, encoded by MIR164A, B, and C. We show that each MIR164 is transcribed to generate a large population of primary miRNAs of variable size with a locally conserved secondary structure around the pre-miRNA. We identified mutations in the MIR164A gene that deepen serration of the leaf margin. By contrast, leaves of plants overexpressing miR164 have smooth margins. Enhanced leaf serration was observed following the expression of an miR164-resistant CUC2 but not of an miR164-resistant CUC1. Furthermore, CUC2 inactivation abolished serration in mir164a mutants and the wild type, whereas CUC1 inactivation did not. Thus, CUC2 specifically controls leaf margin development. CUC2 and MIR164A are transcribed in overlapping domains at the margins of young leaf primordia, with transcription gradually restricted to the sinus, where the leaf margins become serrated. We suggest that leaf margin development is controlled by a two-step process in Arabidopsis. The pattern of serration is determined first, independently of CUC2 and miR164. The balance between coexpressed CUC2 and MIR164A then determines the extent of serration.
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Affiliation(s)
- Krisztina Nikovics
- Laboratoire de Biologie Cellulaire, Institut Jean Pierre Bourgin, Institut National de la Recherche Agronomique, 78026 Versailles Cedex, France
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41
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Salceda J, Fernández X, Roca J. Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA. EMBO J 2006; 25:2575-83. [PMID: 16710299 PMCID: PMC1478187 DOI: 10.1038/sj.emboj.7601142] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 04/18/2006] [Indexed: 11/09/2022] Open
Abstract
Eukaryotic topoisomerases I and II efficiently remove helical tension in naked DNA molecules. However, this activity has not been examined in nucleosomal DNA, their natural substrate. Here, we obtained yeast minichromosomes holding DNA under (+) helical tension, and incubated them with topoisomerases. We show that DNA supercoiling density can rise above +0.04 without displacement of the histones and that the typical nucleosome topology is restored upon DNA relaxation. However, in contrast to what is observed in naked DNA, topoisomerase II relaxes nucleosomal DNA much faster than topoisomerase I. The same effect occurs in cell extracts containing physiological dosages of topoisomeraseI and II. Apparently, the DNA strand-rotation mechanism of topoisomerase I does not efficiently relax chromatin, which imposes barriers for DNA twist diffusion. Conversely, the DNA cross-inversion mechanism of topoisomerase II is facilitated in chromatin, which favor the juxtaposition of DNA segments. We conclude that topoisomerase II is the main modulator of DNA topology in chromatin fibers. The nonessential topoisomerase I then assists DNA relaxation where chromatin structure impairs DNA juxtaposition but allows twist diffusion.
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Affiliation(s)
- Javier Salceda
- Institut de Biología Molecular de Barcelona, CSIC, Barcelona, Spain
| | - Xavier Fernández
- Institut de Biología Molecular de Barcelona, CSIC, Barcelona, Spain
| | - Joaquim Roca
- Institut de Biología Molecular de Barcelona, CSIC, Barcelona, Spain
- Institut de Biología Molecular de Barcelona, CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain. Tel.: 34 934 006 178; Fax: 34 932 045 904; E-mail:
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42
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Siddiqui NU, Rusyniak S, Hasenkampf CA, Riggs CD. Disruption of the Arabidopsis SMC4 gene, AtCAP-C, compromises gametogenesis and embryogenesis. PLANTA 2006; 223:990-7. [PMID: 16482433 DOI: 10.1007/s00425-006-0234-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 08/31/2005] [Indexed: 05/06/2023]
Abstract
In higher eukaryotes, the condensin complex is a multisubunit apparatus that plays a pivotal role in the coordinated condensation of chromatin during mitosis. The catalytic subunits, CAP-E and CAP-C, members of the SMC family of ATPases, form a heterodimer, the activity of which is controlled by the non-SMC subunits CAP-D2, CAP-G and CAP-H. Here, we report the characterization of a T-DNA insertion mutant of the Arabidopsis CAP-C gene. Analysis of the progeny of selfed heterozygotes revealed that the homozygous null genotype is embryo lethal, with arrest occurring at or before the globular stage of development. Patterning defects associated with altered planes of cytokinesis were found in both the embryo and the suspensor. Crosses of heterozygotes with wild type plants revealed both male and female gametophytic defects. Stretched chromatin was observed between segregating mitotic chromosomes in pollen produced by selfed heterozygotes. Additionally, some plants heterozygous for the T-DNA insertion exhibited loss of apical dominance and mild fasciation, indicating a semi-dominant effect of the mutation. These results reveal a critical role for AtCAP-C during cell division and, unlike our previous studies on the AtCAP-E genes, suggest that no redundant factors for AtCAP-C exist in the Arabidopsis genome.
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Affiliation(s)
- Najeeb U Siddiqui
- Department of Botany, Division of Life Sciences, University of Toronto, 1265 Military Trail, M1C 1A4, Scarborough, ON, Canada
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43
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Ohtomo I, Ueda H, Shimada T, Nishiyama C, Komoto Y, Hara-Nishimura I, Takahashi T. Identification of an allele of VAM3/SYP22 that confers a semi-dwarf phenotype in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2005; 46:1358-65. [PMID: 15937323 DOI: 10.1093/pcp/pci146] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The short stem and midrib (ssm) mutants of Arabidopsis thaliana show both semi-dwarf and wavy leaf phenotypes due to defects in the elongation of the stem internodes and leaves. Moreover, these abnormalities cannot be recovered by exogenous phytohormones. ssm was originally identified as a single recessive mutant of the ecotype Columbia (Col-0), but genetic crossing experiments have revealed that this mutant phenotype is restored by another gene that is functional in the ecotype Landsberg erecta (Ler) and not in Col-0. Map-based cloning of the gene that is defective in ssm mutants has uncovered a small deletion in the sixth intron of a gene encoding a syntaxin, VAM3/SYP22, which has been implicated in vesicle transport to the vacuole. This mutation appears to cause a peptide insertion in the deduced VAM3/SYP22 polypeptide sequence due to defective splicing of the shortened sixth intron. Significantly, when compared with the wild-type Ler genome, the wild-type Col-0 genome has a single base pair deletion causing a frameshift mutation in SYP23, a gene with the highest known homology to VAM3/SYP22. These findings suggest that VAM3/SYP22 and SYP23 have overlapping functions and that the vesicle transport mediated by these syntaxins is important for shoot morphogenesis.
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Affiliation(s)
- Ichiro Ohtomo
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, N10 W8, Sapporo, 060-0810 Japan
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44
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Cho HS, Lee SS, Kim KD, Hwang I, Lim JS, Park YI, Pai HS. DNA gyrase is involved in chloroplast nucleoid partitioning. THE PLANT CELL 2004; 16:2665-82. [PMID: 15367714 PMCID: PMC520963 DOI: 10.1105/tpc.104.024281] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2004] [Accepted: 07/08/2004] [Indexed: 05/19/2023]
Abstract
DNA gyrase, which catalyzes topological transformation of DNA, plays an essential role in replication and transcription in prokaryotes. Virus-induced gene silencing of NbGyrA or NbGyrB, which putatively encode DNA gyrase subunits A and B, respectively, resulted in leaf yellowing phenotypes in Nicotiana benthamiana. NbGyrA and NbGyrB complemented the gyrA and gyrB temperature-sensitive mutations of Escherichia coli, respectively, which indicates that the plant and bacterial subunits are functionally similar. NbGyrA and NbGyrB were targeted to both chloroplasts and mitochondria, and depletion of these subunits affected both organelles by reducing chloroplast numbers and inducing morphological and physiological abnormalities in both organelles. Flow cytometry analysis revealed that the average DNA content in the affected chloroplasts and mitochondria was significantly higher than in the control organelles. Furthermore, 4',6-diamidino-2-phenylindole staining revealed that the abnormal chloroplasts contained one or a few large nucleoids instead of multiple small nucleoids dispersed throughout the stroma. Pulse-field gel electrophoresis analyses of chloroplasts demonstrated that the sizes and/or structure of the DNA molecules in the abnormal chloroplast nucleoids are highly aberrant. Based on these results, we propose that DNA gyrase plays a critical role in chloroplast nucleoid partitioning by regulating DNA topology.
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Affiliation(s)
- Hye Sun Cho
- Laboratory of Plant Genomics, Korea Research Institute of Bioscience and Biotechnology, Yusong-gu, Taejon 305-333, Korea
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Byrne ME, Groover AT, Fontana JR, Martienssen RA. Phyllotactic pattern and stem cell fate are determined by the Arabidopsis homeobox gene BELLRINGER. Development 2003; 130:3941-50. [PMID: 12874117 DOI: 10.1242/dev.00620] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lateral organs in plants arise from the meristem in a stereotypical pattern known as phyllotaxy. Spiral patterns result from initiation of successive organs at a fixed angle of divergence but variable patterns of physical contact. Such patterns ultimately give rise to individual leaves and flowers at positions related to each other by consecutive terms in the mathematical series first described by Leonardo Fibonacci. We demonstrate that a BELL1 related homeodomain protein in Arabidopsis, BELLRINGER, maintains the spiral phyllotactic pattern. In the absence of BELLRINGER, the regular pattern of organ initiation is disturbed and lateral organs are initiated more frequently. BELLRINGER is also required for maintenance of stem cell fate in the absence of the regulatory genes SHOOT MERISTEMLESS and ASYMMETRIC LEAVES1. We propose a model whereby BELLRINGER coordinates the maintenance of stem cells with differentiation of daughter cells in stem cell lineages.
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Affiliation(s)
- Mary E Byrne
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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Siddiqui NU, Stronghill PE, Dengler RE, Hasenkampf CA, Riggs CD. Mutations in Arabidopsis condensin genes disrupt embryogenesis, meristem organization and segregation of homologous chromosomes during meiosis. Development 2003; 130:3283-95. [PMID: 12783798 DOI: 10.1242/dev.00542] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Proper chromatin condensation and sister chromatid resolution are essential for the maintenance of chromosomal integrity during cell division, and is in part mediated by a conserved multisubunit apparatus termed the condensin complex. The core subunits of the complex are members of the SMC2 (Structural Maintenance of Chromosomes) and SMC4 gene families. We have cloned an Arabidopsis gene, AtCAP-E1, which is a functional ortholog of the yeast SMC2 gene. A second, highly homologous SMC2 gene, AtCAPE-2, was identified by the Arabidopsis genome project. SMC2 gene expression in Arabidopsis was correlated with the mitotic activity of tissues, with high level expression observed in meristematic cells. The two genes are differentially expressed with AtCAP-E1 accounting for more than 85% of the total SMC2 transcript pool. The titan3 mutant is the result of a T-DNA insertion into AtCAP-E1, but other than subtle endosperm defects, titan3 is viable and fecund. We identified a T-DNA insertion mutant of AtCAP-E2, which showed no obvious mutant phenotype, indicating that the two genes are functionally redundant. Genetic crosses were employed to examine the consequences of reduced SMC2 levels. Both male and female gametogenesis were compromised in double mutant spores. Embryo lethality was observed for both double homozygous and AtCAP-E1(-/-), AtCAP-E2(+/-) plants; arrest occurred at or before the globular stage and was associated with altered planes of cell division in both the suspensor and the embryo. Down regulation of both genes by antisense technology, as well as in AtCAP-E1(+/-), AtCAP-E2(-/-) plants results in meristem disorganization and fasciation. Our data are consistent with the interpretation that threshold levels of SMC2 proteins are required for normal development and that AtCAP-E2 may have a higher affinity for its target than AtCAP-E1.
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Affiliation(s)
- Najeeb U Siddiqui
- Department of Botany, Division of Life Sciences, University of Toronto, 1265 Military Trail, West Hill, Ontario M1C 1A4, Canada
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