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Xu X, Passalacqua M, Rice B, Demesa-Arevalo E, Kojima M, Takebayashi Y, Harris B, Sakakibara H, Gallavotti A, Gillis J, Jackson D. Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583414. [PMID: 38496543 PMCID: PMC10942292 DOI: 10.1101/2024.03.04.583414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Stem cells in plant shoots are a rare population of cells that produce leaves, fruits and seeds, vital sources for food and bioethanol. Uncovering regulators expressed in these stem cells will inform crop engineering to boost productivity. Single-cell analysis is a powerful tool for identifying regulators expressed in specific groups of cells. However, accessing plant shoot stem cells is challenging. Recent single-cell analyses of plant shoots have not captured these cells, and failed to detect stem cell regulators like CLAVATA3 and WUSCHEL . In this study, we finely dissected stem cell-enriched shoot tissues from both maize and arabidopsis for single-cell RNA-seq profiling. We optimized protocols to efficiently recover thousands of CLAVATA3 and WUSCHEL expressed cells. A cross-species comparison identified conserved stem cell regulators between maize and arabidopsis. We also performed single-cell RNA-seq on maize stem cell overproliferation mutants to find additional candidate regulators. Expression of candidate stem cell genes was validated using spatial transcriptomics, and we functionally confirmed roles in shoot development. These candidates include a family of ribosome-associated RNA-binding proteins, and two families of sugar kinase genes related to hypoxia signaling and cytokinin hormone homeostasis. These large-scale single-cell profiling of stem cells provide a resource for mining stem cell regulators, which show significant association with yield traits. Overall, our discoveries advance the understanding of shoot development and open avenues for manipulating diverse crops to enhance food and energy security.
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Simonini S, Bencivenga S, Grossniklaus U. A paternal signal induces endosperm proliferation upon fertilization in Arabidopsis. Science 2024; 383:646-653. [PMID: 38330116 DOI: 10.1126/science.adj4996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024]
Abstract
In multicellular organisms, sexual reproduction relies on the formation of highly differentiated cells, the gametes, which await fertilization in a quiescent state. Upon fertilization, the cell cycle resumes. Successful development requires that male and female gametes are in the same phase of the cell cycle. The molecular mechanisms that reinstate cell division in a fertilization-dependent manner are poorly understood in both animals and plants. Using Arabidopsis, we show that a sperm-derived signal induces the proliferation of a female gamete, the central cell, precisely upon fertilization. The central cell is arrested in S phase by the activity of the RETINOBLASTOMA RELATED1 (RBR1) protein. Upon fertilization, delivery of the core cell cycle component CYCD7;1 causes RBR1 degradation and thus S phase progression, ensuring the formation of functional endosperm and, consequently, viable seeds.
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Affiliation(s)
- Sara Simonini
- Institute of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland
| | - Stefano Bencivenga
- Institute of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland
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3
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Yoon J, Min CW, Kim J, Baek G, Kim D, Jang JW, Gupta R, Kim ST, Cho LH. Quantitative Proteomic Analysis Deciphers the Molecular Mechanism for Endosperm Nuclear Division in Early Rice Seed Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3715. [PMID: 37960070 PMCID: PMC10650807 DOI: 10.3390/plants12213715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Understanding the molecular mechanisms underlying early seed development is important in improving the grain yield and quality of crop plants. We performed a comparative label-free quantitative proteomic analysis of developing rice seeds for the WT and osctps1-2 mutant, encoding a cytidine triphosphate synthase previously reported as the endospermless 2 (enl2) mutant in rice, harvested at 0 and 1 d after pollination (DAP) to understand the molecular mechanism of early seed development. In total, 5231 proteins were identified, of which 902 changed in abundance between 0 and 1 DAP seeds. Proteins that preferentially accumulated at 1 DAP were involved in DNA replication and pyrimidine biosynthetic pathways. Notably, an increased abundance of OsCTPS1 was observed at 1 DAP; however, no such changes were observed at the transcriptional level. We further observed that the inhibition of phosphorylation increased the stability of this protein. Furthermore, in osctps1-2, minichromosome maintenance (MCM) proteins were significantly reduced compared with those in the WT at 1 DAP, and mutations in OsMCM5 caused defects in seed development. These results highlight the molecular mechanisms underlying early seed development in rice at the post-transcriptional level.
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Affiliation(s)
- Jinmi Yoon
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea;
- Department of Biological Sciences and Bioengineering, Industry-Academia Interactive R&E Center for Bioprocess Innovation, Inha University, Incheon 22212, Republic of Korea
| | - Cheol Woo Min
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
| | - Jiyoung Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Gibeom Baek
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Dohyeon Kim
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Jeong Woo Jang
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea;
| | - Sun Tae Kim
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
| | - Lae-Hyeon Cho
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, Republic of Korea; (J.K.); (G.B.); (D.K.); (J.W.J.)
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Yang Z, Qin T, Jin H, Wang J, Li C, Lim KJ, Wang Z. Quantitative Phosphoproteomic Analysis Reveals Potential Regulatory Mechanisms of Early Fruit Enlargement in Pecan ( Carya illinoinensis). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4901-4914. [PMID: 36938622 DOI: 10.1021/acs.jafc.2c08876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Pecan (Carya illinoinensis) is a popular tree nut. Its fruit development undergoes slow growth, rapid expansion, core hardening, and kernel maturation stages. However, little is known about how pecan initiates fruit development and enlargement after pollination. In this study, we performed the first large-scale identification of potential phosphorylation sites and proteins at early development of pecan fruit by a label-free phosphoproteomic quantification technique. A total of 2155 phosphosites were identified from 1953 phosphopeptides covering 1311 phosphoproteins in unpollinated pistils and fruits at 5 and 9 weeks after pollination. Of these, 699 nonredundant phosphoproteins were differentially phosphorylated (DP). Furthermore, the phosphorylation intensity of DP proteins in brassinolide (BR) and auxin signaling were analyzed, and the function of CiBZR1 was investigated. Ectopic expression of CiBZR1 resulted in BR response phenotypes with curled leaves and fruit, while enlarged seed size in Arabidopsis. Subcellular localization and transcriptional activation activity assay demonstrated that CiBZR1 distributed in both the nucleus and cytoplasm with transcriptional activity. When two phosphosites mutated, CiBZR1S201P,S205G moved to the nucleus completely, while the transcriptional activity remained unchanged. Taken together, our data reveal extensive phosphoproteins and lay a foundation to comprehensively dissect the potential post-translational regulation mechanism of early development of pecan fruit.
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Affiliation(s)
- Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Tao Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Hongmiao Jin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Jiani Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Caiyun Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
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5
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Jin HL, Duan S, Zhang P, Yang Z, Zeng Y, Chen Z, Hong L, Li M, Luo L, Chang Z, Hu J, Wang HB. Dual roles for CND1 in maintenance of nuclear and chloroplast genome stability in plants. Cell Rep 2023; 42:112268. [PMID: 36933214 DOI: 10.1016/j.celrep.2023.112268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 12/19/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
The coordination of chloroplast and nuclear genome status is critical for plant cell function. Here, we report that Arabidopsis CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in the chloroplast and the nucleus. CND1 localizes to both compartments, and complete loss of CND1 results in embryo lethality. Partial loss of CND1 disturbs nuclear cell-cycle progression and photosynthetic activity. CND1 binds to nuclear pre-replication complexes and DNA replication origins and regulates nuclear genome stability. In chloroplasts, CND1 interacts with and facilitates binding of the regulator of chloroplast genome stability WHY1 to chloroplast DNA. The defects in nuclear cell-cycle progression and photosynthesis of cnd1 mutants are respectively rescued by compartment-restricted CND1 localization. Light promotes the association of CND1 with HSP90 and its import into chloroplasts. This study provides a paradigm of the convergence of genome status across organelles to coordinately regulate cell cycle to control plant growth and development.
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Affiliation(s)
- Hong-Lei Jin
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China; Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 263, Longxi Avenue, Guangzhou, China.
| | - Sujuan Duan
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Pengxiang Zhang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ziyue Yang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Yunping Zeng
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ziqi Chen
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Liu Hong
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Mengshu Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Lujun Luo
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Zhenyi Chang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Jiliang Hu
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Hong-Bin Wang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.
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6
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Lardon R, Trinh HK, Xu X, Vu LD, Van De Cotte B, Pernisová M, Vanneste S, De Smet I, Geelen D. Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants. FRONTIERS IN PLANT SCIENCE 2022; 13:894208. [PMID: 36684719 PMCID: PMC9847488 DOI: 10.3389/fpls.2022.894208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/27/2022] [Indexed: 06/17/2023]
Abstract
Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.
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Affiliation(s)
- Robin Lardon
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Hoang Khai Trinh
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Biotechnology Research and Development Institute, Can Tho University, Can Tho, Vietnam
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Brigitte Van De Cotte
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Markéta Pernisová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Steffen Vanneste
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon, South Korea
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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7
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Gao J, Zhang K, Cheng YJ, Yu S, Shang GD, Wang FX, Wu LY, Xu ZG, Mai YX, Zhao XY, Zhai D, Lian H, Wang JW. A robust mechanism for resetting juvenility during each generation in Arabidopsis. NATURE PLANTS 2022; 8:257-268. [PMID: 35318444 DOI: 10.1038/s41477-022-01110-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 02/10/2022] [Indexed: 05/02/2023]
Abstract
Multicellular organisms undergo several developmental transitions during their life cycles. In contrast to animals, the plant germline is derived from adult somatic cells. As such, the juvenility of a plant must be reset in each generation. Previous studies have demonstrated that the decline in the levels of miR156/7 with age drives plant maturation. Here we show that the resetting of plant juvenility during each generation is mediated by de novo activation of MIR156/7 in Arabidopsis. Blocking this process leads to a shortened juvenile phase and premature flowering in the offspring. In particular, an Arabidopsis plant devoid of miR156/7 flowers even without formation of rosette leaves in long days. Mechanistically, we find that different MIR156/7 genes are reset at different developmental stages through distinct reprogramming routes. Among these genes, MIR156A, B and C are activated de novo during sexual reproduction and embryogenesis, while MIR157A and C are reset upon seed germination. This redundancy generates a robust reset mechanism that ensures accurate restoration of the juvenile phase in each plant generation.
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Affiliation(s)
- Jian Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Ke Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ying-Juan Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Sha Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Guan-Dong Shang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Fu-Xiang Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Lian-Yu Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhou-Geng Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Yan-Xia Mai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xin-Yan Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai, China
| | - Dong Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Heng Lian
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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8
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Telomerase Interaction Partners-Insight from Plants. Int J Mol Sci 2021; 23:ijms23010368. [PMID: 35008793 PMCID: PMC8745574 DOI: 10.3390/ijms23010368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 12/29/2022] Open
Abstract
Telomerase, an essential enzyme that maintains chromosome ends, is important for genome integrity and organism development. Various hypotheses have been proposed in human, ciliate and yeast systems to explain the coordination of telomerase holoenzyme assembly and the timing of telomerase performance at telomeres during DNA replication or repair. However, a general model is still unclear, especially pathways connecting telomerase with proposed non-telomeric functions. To strengthen our understanding of telomerase function during its intracellular life, we report on interactions of several groups of proteins with the Arabidopsis telomerase protein subunit (AtTERT) and/or a component of telomerase holoenzyme, POT1a protein. Among these are the nucleosome assembly proteins (NAP) and the minichromosome maintenance (MCM) system, which reveal new insights into the telomerase interaction network with links to telomere chromatin assembly and replication. A targeted investigation of 176 candidate proteins demonstrated numerous interactions with nucleolar, transport and ribosomal proteins, as well as molecular chaperones, shedding light on interactions during telomerase biogenesis. We further identified protein domains responsible for binding and analyzed the subcellular localization of these interactions. Moreover, additional interaction networks of NAP proteins and the DOMINO1 protein were identified. Our data support an image of functional telomerase contacts with multiprotein complexes including chromatin remodeling and cell differentiation pathways.
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Van de Peer Y, Ashman TL, Soltis PS, Soltis DE. Polyploidy: an evolutionary and ecological force in stressful times. THE PLANT CELL 2021; 33:11-26. [PMID: 33751096 PMCID: PMC8136868 DOI: 10.1093/plcell/koaa015] [Citation(s) in RCA: 238] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
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Affiliation(s)
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
- Department of Biology, University of Florida, Gainesville, Florida 32611
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10
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Duan S, Hu L, Dong B, Jin HL, Wang HB. Signaling from Plastid Genome Stability Modulates Endoreplication and Cell Cycle during Plant Development. Cell Rep 2021; 32:108019. [PMID: 32783941 DOI: 10.1016/j.celrep.2020.108019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/08/2020] [Accepted: 07/20/2020] [Indexed: 01/10/2023] Open
Abstract
Plastid-nucleus genome coordination is crucial for plastid activity, but the mechanisms remain unclear. By treating Arabidopsis plants with the organellar genome-damaging agent ciprofloxacin, we found that plastid genome instability can alter endoreplication and the cell cycle. Similar results are observed in the plastid genome instability mutants of reca1why1why3. Cell division and embryo development are disturbed in the reca1why1why3 mutant. Notably, SMR5 and SMR7 genes, which encode cell-cycle kinase inhibitors, are upregulated in plastid genome instability plants, and the mutation of SMR7 can restore the endoreplication and growth phenotype of reca1why1why3 plants. Furthermore, we establish that the DNA damage response transcription factor SOG1 mediates the alteration of endoreplication and cell cycle triggered by plastid genome instability. Finally, we demonstrate that reactive oxygen species produced in plastids are important for plastid-nucleus genome coordination. Our findings uncover a molecular mechanism for the coordination of plastid and nuclear genomes during plant growth and development.
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Affiliation(s)
- Sujuan Duan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China; Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China
| | - Lili Hu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China
| | - Beibei Dong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China
| | - Hong-Lei Jin
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China.
| | - Hong-Bin Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China; Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China.
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11
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Comparative genomic analysis reveals evolutionary and structural attributes of MCM gene family in Arabidopsis thaliana and Oryza sativa. J Biotechnol 2020; 327:117-132. [PMID: 33373625 DOI: 10.1016/j.jbiotec.2020.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/16/2020] [Accepted: 12/17/2020] [Indexed: 11/20/2022]
Abstract
The mini-chromosome maintenance (MCM) family, a large and functionally diverse protein family belonging to the AAA+ superfamily, is essential for DNA replication in all eukaryotic organisms. The MCM 2-7 form a hetero-hexameric complex which serves as licensing factor necessary to ensure the proper genomic DNA replication during the S phase of cell cycle. MCM 8-10 are also associated with the DNA replication process though their roles are particularly unclear. In this study, we report an extensive in silico analysis of MCM gene family (MCM 2-10) in Arabidopsis and rice. Comparative analysis of genomic distribution across eukaryotes revealed conservation of core MCMs 2-7 while MCMs 8-10 are absent in some taxa. Domain architecture analysis underlined MCM 2-10 subfamily specific features. Phylogenetic analyses clustered MCMs into 9 clades as per their subfamily. Duplication events are prominent in plant MCM family, however no duplications are observed in Arabidopsis and rice MCMs. Synteny analysis among Arabidopsis thaliana, Oryza sativa, Glycine max and Zea mays MCMs demonstrated orthologous relationships and duplication events. Further, estimation of synonymous and non-synonymous substitution rates illustrated evolution of MCM family under strong constraints. Expression profiling using available microarray data and qRT-PCR revealed differential expression under various stress conditions, hinting at their potential use to develop stress resilient crops. Homology modeling of Arabidopsis and rice MCM 2-7 and detailed comparison with yeast MCMs identified conservation of eukaryotic specific insertions and extensions as compared to archeal MCMs. Protein-protein interaction analysis revealed an extensive network of putative interacting partners mainly involved in DNA replication and repair. The present study provides novel insights into the MCM family in Arabidopsis and rice and identifies unique features, thus opening new perspectives for further targeted analyses.
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12
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Hale B, Phipps C, Rao N, Wijeratne A, Phillips GC. Differential Expression Profiling Reveals Stress-Induced Cell Fate Divergence in Soybean Microspores. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1510. [PMID: 33171842 PMCID: PMC7695151 DOI: 10.3390/plants9111510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 01/01/2023]
Abstract
Stress-induced microspore embryogenesis is a widely employed method to achieve homozygosity in plant breeding programs. However, the molecular mechanisms that govern gametophyte de- and redifferentiation are understood poorly. In this study, RNA-Seq was used to evaluate global changes across the microspore transcriptome of soybean (Glycine max [L.] Merrill) as a consequence of pretreatment low-temperature stress. Expression analysis revealed more than 20,000 differentially expressed genes between treated and control microspore populations. Functional enrichment illustrated that many of these genes (e.g., those encoding heat shock proteins and cytochrome P450s) were upregulated to maintain cellular homeostasis through the mitigation of oxidative damage. Moreover, transcripts corresponding to saccharide metabolism, vacuolar transport, and other pollen-related developmental processes were drastically downregulated among treated microspores. Temperature stress also triggered cell wall modification and cell proliferation-characteristics that implied putative commitment to an embryonic pathway. These findings collectively demonstrate that pretreatment cold stress induces soybean microspore reprogramming through suppression of the gametophytic program while concomitantly driving sporophytic development.
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Affiliation(s)
- Brett Hale
- College of Science and Mathematics, Arkansas State University, Jonesboro, AR 72467-1080, USA;
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR 72467-0639, USA; (C.P.); (N.R.); (G.C.P.)
| | - Callie Phipps
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR 72467-0639, USA; (C.P.); (N.R.); (G.C.P.)
| | - Naina Rao
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR 72467-0639, USA; (C.P.); (N.R.); (G.C.P.)
| | - Asela Wijeratne
- College of Science and Mathematics, Arkansas State University, Jonesboro, AR 72467-1080, USA;
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR 72467-0639, USA; (C.P.); (N.R.); (G.C.P.)
| | - Gregory C. Phillips
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR 72467-0639, USA; (C.P.); (N.R.); (G.C.P.)
- College of Agriculture, Arkansas State University, Jonesboro, AR 72467-1080, USA
- Agricultural Experiment Station, University of Arkansas System Division of Agriculture, Jonesboro, AR 72467-2340, USA
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13
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González R, Butković A, Rivarez MPS, Elena SF. Natural variation in Arabidopsis thaliana rosette area unveils new genes involved in plant development. Sci Rep 2020; 10:17600. [PMID: 33077802 PMCID: PMC7788084 DOI: 10.1038/s41598-020-74723-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/06/2020] [Indexed: 11/08/2022] Open
Abstract
Growth is a complex trait influenced by multiple genes that act at different moments during the development of an organism. This makes it difficult to spot its underlying genetic mechanisms. Since plant growth is intimately related to the effective leaf surface area (ELSA), identifying genes controlling this trait will shed light on our understanding of plant growth. To find new genes with a significant contribution to plant growth, here we used the natural variation in Arabidopsis thaliana to perform a genome-wide association study of ELSA. To do this, the projected rosette area of 710 worldwide distributed natural accessions was measured and analyzed using the genome-wide efficient mixed model association algorithm. From this analysis, ten genes were identified having SNPs with a significant association with ELSA. To validate the implication of these genes into A. thaliana growth, six of them were further studied by phenotyping knock-out mutant plants. It was observed that rem1.2, orc1a, ppd1, and mcm4 mutants showed different degrees of reduction in rosette size, thus confirming the role of these genes in plant growth. Our study identified genes already known to be involved in plant growth but also assigned this role, for the first time, to other genes.
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Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980, Valencia, Spain.
| | - Anamarija Butković
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980, Valencia, Spain
| | - Mark Paul Selda Rivarez
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980, Valencia, Spain
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980, Valencia, Spain
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
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14
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Almeida FA, Passamani LZ, Santa-Catarina C, Mooney BP, Thelen JJ, Silveira V. Label-Free Quantitative Phosphoproteomics Reveals Signaling Dynamics Involved in Embryogenic Competence Acquisition in Sugarcane. J Proteome Res 2020; 19:4145-4157. [PMID: 32964716 DOI: 10.1021/acs.jproteome.0c00652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this study, a label-free quantitative phosphoproteomic analysis was performed to identify and quantify signaling events related to the acquisition of embryogenic competence in sugarcane. Embryogenic and nonembryogenic calli were compared at the multiplication phase, resulting in the identification of 163 phosphoproteins unique to embryogenic calli, 9 unique to nonembryogenic calli, and 51 upregulated and 40 downregulated in embryogenic calli compared to nonembryogenic calli. Data are available via ProteomeXchange with identifier PXD018054. Motif-x analysis revealed the enrichment of [xxxpSPxxx], [RxxpSxxx], and [xxxpSDxxx] motifs, which are predicted phosphorylation sites for several kinases related to stress responses. The embryogenic-related phosphoproteins (those unique and upregulated in embryogenic calli) identified in the present study are related to abscisic acid-induced signaling and abiotic stress response; they include OSK3, ABF1, LEAs, and RD29Bs. On the other hand, the nonembryogenic-related phosphoproteins EDR1 and PP2Ac-2 are negative regulators of abscisic acid signaling, suggesting a relationship between phosphoproteins involved in the abscisic acid and stress responses in the acquisition of embryogenic competence. Moreover, embryogenic-related phosphoproteins associated with epigenetic modifications, such as HDA6, HDA19, and TOPLESS, and with RNA metabolism, including AGO1, DEAH5, SCL30, UB2C, and SR45, were identified to play potential roles in embryogenic competence. These results reveal novel phosphorylation sites for several proteins and identify potential candidate biomarkers for the acquisition of embryogenic competence in sugarcane.
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Affiliation(s)
- Felipe A Almeida
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil.,Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Lucas Z Passamani
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil.,Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual, CBB-UENF, Campos dos Goytacazes 28013-602, Rio de Janeiro, Brazil
| | - Brian P Mooney
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, 65211 Columbia, Missouri, United States
| | - Jay J Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, 65211 Columbia, Missouri, United States
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil.,Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
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15
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Zhang M, Li W, Feng J, Gong Z, Yao Y, Zheng C. Integrative transcriptomics and proteomics analysis constructs a new molecular model for ovule abortion in the female-sterile line of Pinus tabuliformis Carr. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110462. [PMID: 32234230 DOI: 10.1016/j.plantsci.2020.110462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 06/11/2023]
Abstract
Ovule development is critical to plant reproduction and free nuclear mitosis of megagametophyte (FNMM) is vital for ovule development. However, most results of ovule development were based on the studies in angiosperms, and its molecular regulation remained largely unknown in gymnosperms, particularly, during FNMM. In this context, we studied the genome-wide difference between sterile line (SL) and fertile line (FL) ovules using transcriptomics and proteomics approaches in Pinus tabuliformis Carr. Comparative analyses revealed that genes involved in DNA replication, DNA damage repair, Cell cycle, Apoptosis and Energy metabolism were highlighted. Further results showed the low expressions of MCM 2-7, RRM1, etc. perhaps led to abnormal DNA replication and damage repair, and the significantly different expressions of PARP2, CCs1, CCs3, etc. implied that the accumulated DNA double-stranded breaks were failed to be repaired and the cell cycle was arrested at G2/M in SL ovules, potentially resulting in the occurrence of apoptosis. Moreover, the deficiency of ETF-QO might hinder FNMM. Consequently, FNMM stopped and ovule aborted in SL ovules. Our results suggested a selective regulatory mechanism led to FNMM half-stop and ovule abortion in P. tabuliformis and these insights could be exploited to investigate the molecular regulations of ovule development in woody gymnosperms.
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Affiliation(s)
- Min Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Wenhai Li
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Jun Feng
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Zaixin Gong
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Yang Yao
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China
| | - Caixia Zheng
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, China.
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16
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Wu ZG, Jiang W, Tao ZM, Pan XJ, Yu WH, Huang HL. Morphological and stage-specific transcriptome analyses reveal distinct regulatory programs underlying yam (Dioscorea alata L.) bulbil growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1899-1914. [PMID: 31832647 PMCID: PMC7242083 DOI: 10.1093/jxb/erz552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/12/2019] [Indexed: 06/09/2023]
Abstract
In yam (Dioscorea spp) species, bulbils at leaf axils are the most striking species-specific axillary structure and exhibit important ecological niches. Genetic regulation underlying bulbil growth remains largely unclear so far. Here, we characterize yam (Dioscorea alata L.) bulbil development using histological analysis, and perform full transcriptional profiling on key developmental stages together with phytohormone analyses. Using the stage-specific scoring algorithm, we have identified 3451 stage-specifically expressed genes that exhibit a tight link between major transcriptional changes and stages. Co-expressed gene clusters revealed an obvious over-representation of genes associated with cell division and expansion at the initiation stage of bulbils (T1). Transcriptional changes of hormone-related genes highly coincided with hormone levels, indicating that bulbil initiation and growth are coordinately controlled by multiple phytohormones. In particular, localized auxin is transiently required to trigger bulbil initiation, and be further depleted or exported from bulbils to promote growth by up-regulation of genes involved in auxinconjugation and efflux. The sharp increase in supply of sucrose and an enhanced trehalose-6-phophate pathway at T1 were observed, suggesting that sucrose probably functions as a key signal and promotes bulbil initiation. Analysis of the expression of transcription factors (TFs) predicated 149 TFs as stage-specifically expressed; several T1-specific TFs (from Aux/IAA, E2F, MYB, and bHLH families) have been shown to play key roles in triggering bulbil formation. Together, our work provides a crucial angle for in-depth understanding of the molecular programs underlying yam's unique bulbil development processes. Stage-specific gene sets can be queried to obtain key candidates regulating bulbil growth, serving as valuable resources for further functional research.
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Affiliation(s)
- Zhi-Gang Wu
- Key Laboratory for Plant Genetic Improvement, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Wu Jiang
- Key Laboratory for Plant Genetic Improvement, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Zheng-Ming Tao
- Key Laboratory for Plant Genetic Improvement, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Xiao-Jun Pan
- School of Pharmacy, Wenzhou Medical University, Wenzhou, China
| | - Wen-Hui Yu
- Quzhou Academy of Agricultural Sciences, Quzhou, China
| | - Hui-Lian Huang
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
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17
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DNA Helicases as Safekeepers of Genome Stability in Plants. Genes (Basel) 2019; 10:genes10121028. [PMID: 31835565 PMCID: PMC6947026 DOI: 10.3390/genes10121028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 02/07/2023] Open
Abstract
Genetic information of all organisms is coded in double-stranded DNA. DNA helicases are essential for unwinding this double strand when it comes to replication, repair or transcription of genetic information. In this review, we will focus on what is known about a variety of DNA helicases that are required to ensure genome stability in plants. Due to their sessile lifestyle, plants are especially exposed to harmful environmental factors. Moreover, many crop plants have large and highly repetitive genomes, making them absolutely dependent on the correct interplay of DNA helicases for safeguarding their stability. Although basic features of a number of these enzymes are conserved between plants and other eukaryotes, a more detailed analysis shows surprising peculiarities, partly also between different plant species. This is additionally of high relevance for plant breeding as a number of these helicases are also involved in crossover control during meiosis and influence the outcome of different approaches of CRISPR/Cas based plant genome engineering. Thus, gaining knowledge about plant helicases, their interplay, as well as the manipulation of their pathways, possesses the potential for improving agriculture. In the long run, this might even help us cope with the increasing obstacles of climate change threatening food security in completely new ways.
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18
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Abstract
Maintenance of genome integrity is a key process in all organisms. DNA polymerases (Pols) are central players in this process as they are in charge of the faithful reproduction of the genetic information, as well as of DNA repair. Interestingly, all eukaryotes possess a large repertoire of polymerases. Three protein complexes, DNA Pol α, δ, and ε, are in charge of nuclear DNA replication. These enzymes have the fidelity and processivity required to replicate long DNA sequences, but DNA lesions can block their progression. Consequently, eukaryotic genomes also encode a variable number of specialized polymerases (between five and 16 depending on the organism) that are involved in the replication of damaged DNA, DNA repair, and organellar DNA replication. This diversity of enzymes likely stems from their ability to bypass specific types of lesions. In the past 10–15 years, our knowledge regarding plant DNA polymerases dramatically increased. In this review, we discuss these recent findings and compare acquired knowledge in plants to data obtained in other eukaryotes. We also discuss the emerging links between genome and epigenome replication.
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19
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Wang R, Lin Y, Jin Q, Yao C, Zhong Y, Wu T. RNA-Seq analysis of gynoecious and weak female cucumber revealing the cell cycle pathway may regulate sex determination in cucumber. Gene 2019; 687:289-297. [DOI: 10.1016/j.gene.2018.11.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 11/13/2018] [Accepted: 11/20/2018] [Indexed: 10/27/2022]
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20
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Collum TD, Lutton E, Raines CD, Dardick C, Culver JN. Identification of phloem-associated translatome alterations during leaf development in Prunus domestica L. HORTICULTURE RESEARCH 2019; 6:16. [PMID: 30729006 PMCID: PMC6355854 DOI: 10.1038/s41438-018-0092-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 06/01/2023]
Abstract
Phloem plays a fundamental role in plants by transporting hormones, nutrients, proteins, RNAs, and carbohydrates essential for plant growth and development. However, the identity of the underlying phloem genes and pathways remain enigmatic especially in agriculturally important perennial crops, in part, due to the technical difficulty of phloem sampling. Here, we used two phloem-specific promoters and a translating ribosome affinity purification (TRAP) strategy to characterize the phloem translatome during leaf development at 2, 4, and 6 weeks post vernalization in plum (Prunus domestica L.). Results provide insight into the changing phloem processes that occur during leaf development. These processes included the early activation of DNA replication genes that are likely involved in phloem cell division during leaf expansion, as well as the upregulation of phloem genes associated with sink to source conversion, induction of defense processes, and signaling for reproduction. Combined these results reveal the dynamics of phloem gene expression during leaf development and establish the TRAP system as a powerful tool for studying phloem-specific functions and responses in trees.
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Affiliation(s)
- Tamara D. Collum
- Institute for Bioscience and Biotechnology Research, College Park, MD USA
| | - Elizabeth Lutton
- USDA-ARS, Appalachian Fruit Research Laboratory, Kearneysville, WV USA
| | - C. Douglas Raines
- USDA-ARS, Appalachian Fruit Research Laboratory, Kearneysville, WV USA
| | | | - James N. Culver
- Institute for Bioscience and Biotechnology Research, College Park, MD USA
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD USA
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21
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Bélanger S, Marchand S, Jacques PÉ, Meyers B, Belzile F. Differential Expression Profiling of Microspores During the Early Stages of Isolated Microspore Culture Using the Responsive Barley Cultivar Gobernadora. G3 (BETHESDA, MD.) 2018; 8:1603-1614. [PMID: 29531122 PMCID: PMC5940152 DOI: 10.1534/g3.118.200208] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/06/2018] [Indexed: 11/18/2022]
Abstract
In barley, it is possible to induce embryogenesis in the haploid and uninucleate microspore to obtain a diploid plant that is perfectly homozygous. To change developmental fates in this fashion, microspores need to engage in cellular de-differentiation, interrupting the pollen formation, and restore totipotency prior to engaging in embryogenesis. In this work, we used the barley cultivar Gobernadora to characterize the transcriptome of microspores prior to (day 0) and immediately after (days 2 and 5) the application of a stress pretreatment. A deep RNA-seq analysis revealed that microspores at these three time points exhibit a transcriptome of ∼14k genes, ∼90% of which were shared. An expression analysis identified a total of 3,382 differentially expressed genes (DEGs); of these, 2,155 and 2,281 DEGs were respectively identified when contrasting expression at days 0 and 2 and at days 2 and 5. These define 8 expression profiles in which DEGs share a common up- or down-regulation at these time points. Up-regulation of numerous glutathione S-transferase and heat shock protein genes as well as down-regulation of ribosomal subunit protein genes was observed between days 0 and 2. The transition from microspores to developing embryos (days 2 vs. 5) was marked by the induction of transcription factor genes known to play important roles in early embryogenesis, numerous genes involved in hormone biosynthesis and plant hormonal signal transduction in addition to genes involved in secondary metabolism. This work sheds light on transcriptional changes accompanying an important developmental shift and provides candidate biomarkers for embryogenesis in barley.
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Affiliation(s)
- Sébastien Bélanger
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, Quebec, Canada, G1V 0A6
| | - Suzanne Marchand
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, Quebec, Canada, G1V 0A6
| | | | - Blake Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211
| | - François Belzile
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, Quebec, Canada, G1V 0A6
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22
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Qian J, Chen Y, Hu Y, Deng Y, Liu Y, Li G, Zou W, Zhao J. Arabidopsis replication factor C4 is critical for DNA replication during the mitotic cell cycle. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:288-303. [PMID: 29406597 DOI: 10.1111/tpj.13855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/16/2018] [Accepted: 01/23/2018] [Indexed: 06/07/2023]
Abstract
Replication factor C (RFC) is a conserved eukaryotic complex consisting of RFC1/2/3/4/5. It plays important roles in DNA replication and the cell cycle in yeast and fruit fly. However, it is not very clear how RFC subunits function in higher plants, except for the Arabidopsis (At) subunits AtRFC1 and AtRFC3. In this study, we investigated the functions of AtRFC4 and found that loss of function of AtRFC4 led to an early sporophyte lethality that initiated as early as the elongated zygote stage, all defective embryos arrested at the two- to four-cell embryo proper stage, and the endosperm possessed six to eight free nuclei. Complementation of rfc4-1/+ with AtRFC4 expression driven through the embryo-specific DD45pro and ABI3pro or the endosperm-specific FIS2pro could not completely restore the defective embryo or endosperm, whereas a combination of these three promoters in rfc4-1/+ enabled the aborted ovules to develop into viable seeds. This suggests that AtRFC4 functions simultaneously in endosperm and embryo and that the proliferation of endosperm is critical for embryo maturation. Assays of DNA content in rfc4-1/+ verified that DNA replication was disrupted in endosperm and embryo, resulting in blocked mitosis. Moreover, we observed a decreased proportion of late S-phase and M-phase cells in the rfc4-1/-FIS2;DD45;ABI3pro::AtRFC4 seedlings, suggesting that incomplete DNA replication triggered cell cycle arrest in cells of the root apical meristem. Therefore, we conclude that AtRFC4 is a crucial gene for DNA replication.
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Affiliation(s)
- Jie Qian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yueyue Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ying Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yingtian Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yang Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Gang Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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23
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French E, Kim BS, Rivera-Zuluaga K, Iyer-Pascuzzi AS. Whole Root Transcriptomic Analysis Suggests a Role for Auxin Pathways in Resistance to Ralstonia solanacearum in Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:432-444. [PMID: 29153016 DOI: 10.1094/mpmi-08-17-0209-r] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt and causes significant crop loss in the Solanaceae family. The pathogen first infects roots, which are a critical source of resistance in tomato (Solanum lycopersicum L.). Roots of both resistant and susceptible plants are colonized by the pathogen, yet rootstocks can provide significant levels of resistance. Currently, mechanisms of this 'root-mediated resistance' remain largely unknown. To identify the molecular basis of this resistance, we analyzed the genome-wide transcriptional response of roots of resistant 'Hawaii 7996' and susceptible 'West Virginia 700' (WV) tomatoes at multiple timepoints after inoculation with R. solanacearum. We found that defense pathways in roots of the resistant Hawaii 7996 are activated earlier and more strongly than roots of susceptible WV. Further, auxin signaling and transport pathways are suppressed in roots of the resistant variety. Functional analysis of an auxin transport mutant in tomato revealed a role for auxin pathways in bacterial wilt. Together, our results suggest that roots mediate resistance to R. solanacearum through genome-wide transcriptomic changes that result in strong activation of defense genes and alteration of auxin pathways.
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Affiliation(s)
- Elizabeth French
- Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, U.S.A
| | - Bong-Suk Kim
- Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, U.S.A
| | - Katherine Rivera-Zuluaga
- Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, U.S.A
| | - Anjali S Iyer-Pascuzzi
- Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, U.S.A
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Leisner CP, Yendrek CR, Ainsworth EA. Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress. BMC PLANT BIOLOGY 2017; 17:242. [PMID: 29233093 PMCID: PMC5727933 DOI: 10.1186/s12870-017-1188-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/30/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Understanding how intensification of abiotic stress due to global climate change affects crop yields is important for continued agricultural productivity. Coupling genomic technologies with physiological crop responses in a dynamic field environment is an effective approach to dissect the mechanisms underpinning crop responses to abiotic stress. Soybean (Glycine max L. Merr. cv. Pioneer 93B15) was grown in natural production environments with projected changes to environmental conditions predicted for the end of the century, including decreased precipitation, increased tropospheric ozone concentrations ([O3]), or increased temperature. RESULTS All three environmental stresses significantly decreased leaf-level photosynthesis and stomatal conductance, leading to significant losses in seed yield. This was driven by a significant decrease in the number of pods per node for all abiotic stress treatments. To understand the underlying transcriptomic response involved in the yield response to environmental stress, RNA-Sequencing analysis was performed on the soybean seed coat, a tissue that plays an essential role in regulating carbon and nitrogen transport to developing seeds. Gene expression analysis revealed 49, 148 and 1,576 differentially expressed genes in the soybean seed coat in response to drought, elevated [O3] and elevated temperature, respectively. CONCLUSIONS Elevated [O3] and drought did not elicit substantive transcriptional changes in the soybean seed coat. However, this may be due to the timing of sampling and does not preclude impacts of those stresses on different tissues or different stages in seed coat development. Expression of genes involved in DNA replication and metabolic processes were enriched in the seed coat under high temperate stress, suggesting that the timing of events that are important for cell division and proper seed development were altered in a stressful growth environment.
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Affiliation(s)
- Courtney P. Leisner
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
- Current address: Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Craig R. Yendrek
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
- Current address: The Scotts Company, Marysville, OH 43040 USA
| | - Elizabeth A. Ainsworth
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
- USDA ARS Global Change and Photosynthesis Research Unit, 1201 W Gregory Drive, Urbana, IL 61801 USA
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Brasil JN, Costa CNM, Cabral LM, Ferreira PCG, Hemerly AS. The plant cell cycle: Pre-Replication complex formation and controls. Genet Mol Biol 2017; 40:276-291. [PMID: 28304073 PMCID: PMC5452130 DOI: 10.1590/1678-4685-gmb-2016-0118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 08/16/2016] [Indexed: 01/07/2023] Open
Abstract
The multiplication of cells in all living organisms requires a tight regulation of DNA replication. Several mechanisms take place to ensure that the DNA is replicated faithfully and just once per cell cycle in order to originate through mitoses two new daughter cells that contain exactly the same information from the previous one. A key control mechanism that occurs before cells enter S phase is the formation of a pre-replication complex (pre-RC) that is assembled at replication origins by the sequential association of the origin recognition complex, followed by Cdt1, Cdc6 and finally MCMs, licensing DNA to start replication. The identification of pre-RC members in all animal and plant species shows that this complex is conserved in eukaryotes and, more importantly, the differences between kingdoms might reflect their divergence in strategies on cell cycle regulation, as it must be integrated and adapted to the niche, ecosystem, and the organism peculiarities. Here, we provide an overview of the knowledge generated so far on the formation and the developmental controls of the pre-RC mechanism in plants, analyzing some particular aspects in comparison to other eukaryotes.
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Affiliation(s)
- Juliana Nogueira Brasil
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Centro Universitário Christus, Fortaleza, CE, Brazil
| | - Carinne N Monteiro Costa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Luiz Mors Cabral
- Departamento de Biologia Celular e Molecular, Universidade Federal Fluminense, Niteroi, RJ, Brazil
| | - Paulo C G Ferreira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Adriana S Hemerly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Fu S, Shao J, Zhou C, Hartung JS. Co-infection of Sweet Orange with Severe and Mild Strains of Citrus tristeza virus Is Overwhelmingly Dominated by the Severe Strain on Both the Transcriptional and Biological Levels. FRONTIERS IN PLANT SCIENCE 2017; 8:1419. [PMID: 28912786 PMCID: PMC5583216 DOI: 10.3389/fpls.2017.01419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/31/2017] [Indexed: 05/18/2023]
Abstract
Citrus tristeza is one of the most destructive citrus diseases and is caused by the phloem-restricted Closterovirus, Citrus tristeza virus. Mild strain CTV-B2 does not cause obvious symptoms on indicators whereas severe strain CTV-B6 causes symptoms, including stem pitting, cupping, yellowing, and stiffening of leaves, and vein corking. Our laboratory has previously characterized changes in transcription in sweet orange separately infected with CTV-B2 and CTV-B6. In the present study, transcriptome analysis of Citrus sinensis in response to double infection by CTV-B2 and CTV-B6 was carried out. Four hundred and eleven transcripts were up-regulated and 356 transcripts were down-regulated prior to the onset of symptoms. Repressed genes were overwhelmingly associated with photosynthesis, and carbon and nucleic acid metabolism. Expression of genes related to the glycolytic, oxidative pentose phosphate (OPP), tricarboxylic acid cycle (TCA) pathways, tetrapyrrole synthesis, redox homeostasis, nucleotide metabolism, protein synthesis and post translational protein modification and folding, and cell organization were all reduced. Ribosomal composition was also greatly altered in response to infection by CTV-B2/CTV-B6. Genes that were induced were related to cell wall structure, secondary and hormone metabolism, responses to biotic stress, regulation of transcription, signaling, and secondary metabolism. Transport systems dedicated to metal ions were especially disturbed and ZIPs (Zinc Transporter Precursors) showed different expression patterns in response to co-infection by CTV-B2/CTV-B6 and single infection by CTV-B2. Host plants experienced root decline that may have contributed to Zn, Fe, and other nutrient deficiencies. Though defense responses, such as, strengthening of the cell wall, alteration of hormone metabolism, secondary metabolites, and signaling pathways, were activated, these defense responses did not suppress the spread of the pathogens and the development of symptoms. The mild strain CTV-B2 did not provide a useful level of cross-protection to citrus against the severe strain CTV-B6.
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Affiliation(s)
- Shimin Fu
- Citrus Research Institute, Southwest UniversityChongqing, China
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research ServiceBeltsville, MD, United States
| | - Jonathan Shao
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research ServiceBeltsville, MD, United States
| | - Changyong Zhou
- Citrus Research Institute, Southwest UniversityChongqing, China
| | - John S. Hartung
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research ServiceBeltsville, MD, United States
- *Correspondence: John S. Hartung
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Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size. Sci Rep 2016; 6:36304. [PMID: 27824099 PMCID: PMC5099886 DOI: 10.1038/srep36304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/13/2016] [Indexed: 11/21/2022] Open
Abstract
Litchi chinensis is a subtropical fruit crop, popular for its nutritional value and taste. Fruits with small seed size and thick aril are desirable in litchi. To gain molecular insight into gene expression that leads to the reduction in the size of seed in Litchi chinensis, transcriptomes of two genetically closely related genotypes, with contrasting seed size were compared in developing ovules. The cDNA library constructed from early developmental stages of ovules (0, 6, and 14 days after anthesis) of bold- and small-seeded litchi genotypes yielded 303,778,968 high quality paired-end reads. These were de-novo assembled into 1,19,939 transcripts with an average length of 865 bp. A total of 10,186 transcripts with contrast in expression were identified in developing ovules between the small- and large- seeded genotypes. A majority of these differences were present in ovules before anthesis, thus suggesting the role of maternal factors in seed development. A number of transcripts indicative of metabolic stress, expressed at higher level in the small seeded genotype. Several differentially expressed transcripts identified in such ovules showed homology with Arabidopsis genes associated with different stages of ovule development and embryogenesis.
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Pedroza-Garcia JA, Domenichini S, Mazubert C, Bourge M, White C, Hudik E, Bounon R, Tariq Z, Delannoy E, Del Olmo I, Piñeiro M, Jarillo JA, Bergounioux C, Benhamed M, Raynaud C. Role of the Polymerase ϵ sub-unit DPB2 in DNA replication, cell cycle regulation and DNA damage response in Arabidopsis. Nucleic Acids Res 2016; 44:7251-66. [PMID: 27193996 PMCID: PMC5009731 DOI: 10.1093/nar/gkw449] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/09/2016] [Indexed: 12/24/2022] Open
Abstract
Faithful DNA replication maintains genome stability in dividing cells and from one generation to the next. This is particularly important in plants because the whole plant body and reproductive cells originate from meristematic cells that retain their proliferative capacity throughout the life cycle of the organism. DNA replication involves large sets of proteins whose activity is strictly regulated, and is tightly linked to the DNA damage response to detect and respond to replication errors or defects. Central to this interconnection is the replicative polymerase DNA Polymerase ϵ (Pol ϵ) which participates in DNA replication per se, as well as replication stress response in animals and in yeast. Surprisingly, its function has to date been little explored in plants, and notably its relationship with DNA Damage Response (DDR) has not been investigated. Here, we have studied the role of the largest regulatory sub-unit of Arabidopsis DNA Pol ϵ: DPB2, using an over-expression strategy. We demonstrate that excess accumulation of the protein impairs DNA replication and causes endogenous DNA stress. Furthermore, we show that Pol ϵ dysfunction has contrasting outcomes in vegetative and reproductive cells and leads to the activation of distinct DDR pathways in the two cell types.
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Affiliation(s)
- José Antonio Pedroza-Garcia
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Séverine Domenichini
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Christelle Mazubert
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Mickael Bourge
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Charles White
- Génétique, Reproduction et Développement, UMR CNRS 6293/Clermont Université/INSERM U1103, 63000 Clermont-Ferrand, France
| | - Elodie Hudik
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Rémi Bounon
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Zakia Tariq
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Ivan Del Olmo
- CBGP (INIA-UPM) Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Madrid 28223, Spain
| | - Manuel Piñeiro
- CBGP (INIA-UPM) Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Madrid 28223, Spain
| | - Jose Antonio Jarillo
- CBGP (INIA-UPM) Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Madrid 28223, Spain
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
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Rizvi I, Choudhury NR, Tuteja N. Arabidopsis thaliana MCM3 single subunit of MCM2-7 complex functions as 3' to 5' DNA helicase. PROTOPLASMA 2016; 253:467-75. [PMID: 25944245 DOI: 10.1007/s00709-015-0825-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/27/2015] [Indexed: 05/09/2023]
Abstract
Minichromosome maintenance 2-7 (MCM2-7) proteins are conserved eukaryotic replicative factors essential for the DNA replication at its initiation and elongation step, and act as a licensing factor. The MCM2-7 and MCM4/6/7subcomplex exhibit DNA helicase activity, and are therefore regarded as the replicative helicase. The MCM proteins have not been studied in detail in plant system. Here, we present the biochemical characterization of Arabidopsis thaliana MCM3 single subunit and show that it exhibits in vitro unwinding and ATPase activities. AtMCM3 shows a greater unwinding activity with 5' forked partial DNA duplex substrate as compared to 3' forked and non-forked substrates. ATP and magnesium ion are indispensable for its DNA helicase activity. Specifically, ATP and dATP are the preferred nucleotides for its unwinding activity. The directionality of the AtMCM3 has been determined to be in 3' to 5' direction. The oligomerization status of AtMCM3 single subunit protein indicates that it is present in different multimeric forms. The unraveling of the helicase activity of AtMCM3 will provide better insights into the plant DNA replication.
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Affiliation(s)
- Irum Rizvi
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nirupam Roy Choudhury
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Jégu T, Domenichini S, Blein T, Ariel F, Christ A, Kim SK, Crespi M, Boutet-Mercey S, Mouille G, Bourge M, Hirt H, Bergounioux C, Raynaud C, Benhamed M. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture. PLoS One 2015; 10:e0138276. [PMID: 26457678 PMCID: PMC4601769 DOI: 10.1371/journal.pone.0138276] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/26/2015] [Indexed: 02/07/2023] Open
Abstract
Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.
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Affiliation(s)
- Teddy Jégu
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Séverine Domenichini
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Thomas Blein
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Federico Ariel
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Aurélie Christ
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Soon-Kap Kim
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Martin Crespi
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | | | - Grégory Mouille
- Institut Jean-Pierre Bourgin, UMR1318 INRA/AgroParisTech, Versailles, France
| | - Mickaël Bourge
- Pôle de Biologie Cellulaire, Imagif, Centre de Recherche de Gif, CNRS, IFR87, Gif-sur-Yvette, France
| | - Heribert Hirt
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
- * E-mail:
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Yang Y, Yang S, Li J, Deng Y, Zhang Z, Xu S, Guo W, Zhong C, Zhou R, Shi S. Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones. BMC Genomics 2015; 16:605. [PMID: 26272068 PMCID: PMC4536770 DOI: 10.1186/s12864-015-1813-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 08/03/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Acanthus is a unique genus consisting of both true mangrove and terrestrial species; thus, it represents an ideal system for studying the origin and adaptive evolution of mangrove plants to intertidal environments. However, little is known regarding the two respects of mangrove species in Acanthus. In this study, we sequenced the transcriptomes of the pooled roots and leaves tissues for a mangrove species, Acanthus ilicifolius, and its terrestrial congener, A. leucostachyus, to illustrate the origin of the mangrove species in this genus and their adaptive evolution to harsh habitats. RESULTS We obtained 73,039 and 69,580 contigs with N50 values of 741 and 1557 bp for A. ilicifolius and A. leucostachyus, respectively. Phylogenetic analyses based on four nuclear segments and three chloroplast fragments revealed that mangroves and terrestrial species in Acanthus fell into different clades, indicating a single origin of the mangrove species in Acanthus. Based on 6634 orthologs, A. ilicifolius and A. leucostachyus were found to be highly divergent, with a peak of synonymous substitution rate (Ks) distribution of 0.145 and an estimated divergence time of approximately 16.8 million years ago (MYA). The transgression in the Early to Middle Miocene may be the major reason for the entry of the mangrove lineage of Acanthus into intertidal environments. Gene ontology (GO) classifications of the full transcriptomes did not show any apparent differences between A. ilicifolius and A. leucostachyus, suggesting the absence of gene components specific to the mangrove transcriptomes. A total of 99 genes in A. ilicifolius were identified with signals of positive selection. Twenty-three of the 99 positively selected genes (PSGs) were found to be involved in salt, heat and ultraviolet stress tolerance, seed germination and embryo development under periodic inundation. These stress-tolerance related PSGs may be crucial for the adaptation of the mangrove species in this genus to stressful marine environments and may contribute to speciation in Acanthus. CONCLUSIONS We characterized the transcriptomes of one mangrove species of Acanthus, A. ilicifolius, and its terrestrial relative, A. leucostachyus, and provided insights into the origin of the mangrove Acanthus species and their adaptive evolution to abiotic stresses in intertidal environments.
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Affiliation(s)
- Yuchen Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Shuhuan Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Jianfang Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Yunfei Deng
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, China.
| | - Zhang Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Wuxia Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve, Haikou, 571129, China.
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
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Shin DH, Cho M, Choi MG, Das PK, Lee SK, Choi SB, Park YI. Identification of genes that may regulate the expression of the transcription factor production of anthocyanin pigment 1 (PAP1)/MYB75 involved in Arabidopsis anthocyanin biosynthesis. PLANT CELL REPORTS 2015; 34:805-15. [PMID: 25604992 DOI: 10.1007/s00299-015-1743-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/19/2014] [Accepted: 01/06/2015] [Indexed: 05/10/2023]
Abstract
A putative RNA-binding protein with a single RNA Recognition Motif (At3G63450) is involved in anthocyanin biosynthesis via its ability to modulate the transcript level of a major positive regulator PAP1 in Arabidopsis. The R2R3 MYB-activator production of anthocyanin pigment 1 (PAP1)/MYB75 plays a major role in anthocyanin biosynthesis in Arabidopsis in combination with one of three bHLH activators including transparent test 8 (TT8), enhancer of glabra3 (EGL3), glabra3 (GL3), and the WD-repeat transcription factor transparent testa 1 (TTG1), forming ternary MYB-basic HLH-WD40 complexes. Transcriptional activation of PAP1 expression is largely triggered by changes in light color and intensity, temperature fluctuations, nutrient status, and sugar and hormone treatments. However, the immediate upstream and downstream regulatory factors for PAP1 transcription are largely unknown. In the present study, using a T-DNA insertional mutagenesis approach, we transformed pap1-Dominant (pap1D) plants to modulate the levels of endogenous PAP1 transcripts. We employed Restriction Site Extension (RSE)-PCR analysis of 247 homogenous T3 genetic mutant lines exhibiting variations in anthocyanin accumulation compared to pap1D and identified 92 lines with T-DNA integrated in either intra- or inter-genic locations. This analysis revealed 80 novel candidate proteins, including a putative RNA-binding protein with a single RNA Recognition Motif (At3G63450), which may directly or indirectly regulate PAP1 expression at the transcriptional level.
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Affiliation(s)
- Dong Ho Shin
- Department of Biological Sciences, Chungnam National University, 99 Daehagro, Youseong, Daejeon, 305-764, Korea
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Hudik E, Yoshioka Y, Domenichini S, Bourge M, Soubigout-Taconnat L, Mazubert C, Yi D, Bujaldon S, Hayashi H, De Veylder L, Bergounioux C, Benhamed M, Raynaud C. Chloroplast dysfunction causes multiple defects in cell cycle progression in the Arabidopsis crumpled leaf mutant. PLANT PHYSIOLOGY 2014; 166:152-67. [PMID: 25037213 PMCID: PMC4149703 DOI: 10.1104/pp.114.242628] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The majority of research on cell cycle regulation is focused on the nuclear events that govern the replication and segregation of the genome between the two daughter cells. However, eukaryotic cells contain several compartmentalized organelles with specialized functions, and coordination among these organelles is required for proper cell cycle progression, as evidenced by the isolation of several mutants in which both organelle function and overall plant development were affected. To investigate how chloroplast dysfunction affects the cell cycle, we analyzed the crumpled leaf (crl) mutant of Arabidopsis (Arabidopsis thaliana), which is deficient for a chloroplastic protein and displays particularly severe developmental defects. In the crl mutant, we reveal that cell cycle regulation is altered drastically and that meristematic cells prematurely enter differentiation, leading to reduced plant stature and early endoreduplication in the leaves. This response is due to the repression of several key cell cycle regulators as well as constitutive activation of stress-response genes, among them the cell cycle inhibitor SIAMESE-RELATED5. One unique feature of the crl mutant is that it produces aplastidic cells in several organs, including the root tip. By investigating the consequence of the absence of plastids on cell cycle progression, we showed that nuclear DNA replication occurs in aplastidic cells in the root tip, which opens future research prospects regarding the dialogue between plastids and the nucleus during cell cycle regulation in higher plants.
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Affiliation(s)
- Elodie Hudik
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Yasushi Yoshioka
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Séverine Domenichini
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Mickaël Bourge
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Ludivine Soubigout-Taconnat
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Christelle Mazubert
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Dalong Yi
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Sandrine Bujaldon
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Hiroyuki Hayashi
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Lieven De Veylder
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Moussa Benhamed
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Cécile Raynaud
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
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Herridge RP, Day RC, Macknight RC. The role of the MCM2-7 helicase complex during Arabidopsis seed development. PLANT MOLECULAR BIOLOGY 2014; 86:69-84. [PMID: 24947836 DOI: 10.1007/s11103-014-0213-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/08/2014] [Indexed: 05/27/2023]
Abstract
The MINICHROMOSOME MAINTENANCE 2-7 (MCM2-7) complex, a ring-shaped heterohexamer, unwinds the DNA double helix ahead of the other replication machinery. Although there is evidence that individual components might have other roles, the essential nature of the MCM2-7 complex in DNA replication has made it difficult to uncover these. Here, we present a detailed analysis of Arabidopsis thaliana mcm2-7 mutants and reveal phenotypic differences. The MCM2-7 genes are coordinately expressed during development, although MCM7 is expressed at a higher level in the egg cell. Consistent with a role in the egg cell, heterozygous mcm7 mutants resulted in frequent ovule abortion, a phenotype that does not occur in other mcm mutants. All mutants showed a maternal effect, whereby seeds inheriting a maternal mutant allele occasionally aborted later in seed development with defects in embryo patterning, endosperm nuclear size, and cellularization, a phenotype that is variable between subunit mutants. We provide evidence that this maternal effect is due to the necessity of a maternal store of MCM protein in the central cell that is sufficient for maintaining seed viability and size in the absence of de novo MCM transcription. Reducing MCM levels using endosperm-specific RNAi constructs resulted in the up-regulation of DNA repair transcripts, consistent with the current hypothesis that excess MCM2-7 complexes are loaded during G1 phase, and are required during S phase to overcome replicative stress or DNA damage. Overall, this study demonstrates the importance of the MCM2-7 subunits during seed development and suggests that there are functional differences between the subunits.
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Affiliation(s)
- Rowan P Herridge
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
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Tuteja N, Tran NQ, Dang HQ, Tuteja R. Plant MCM proteins: role in DNA replication and beyond. PLANT MOLECULAR BIOLOGY 2011; 77:537-45. [PMID: 22038093 DOI: 10.1007/s11103-011-9836-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 10/09/2011] [Indexed: 05/18/2023]
Abstract
Mini-chromosome maintenance (MCM) proteins form heterohexameric complex (MCM2-7) to serve as licensing factor for DNA replication to make sure that genomic DNA is replicated completely and accurately once during S phase in a single cell cycle. MCMs were initially identified in yeast for their role in plasmid replication or cell cycle progression. Each of six MCM contains highly conserved sequence called "MCM box", which contains two ATPase consensus Walker A and Walker B motifs. Studies on MCM proteins showed that (a) the replication origins are licensed by stable binding of MCM2-7 to form pre-RC (pre-replicative complex) during G1 phase of the cell cycle, (b) the activation of MCM proteins by CDKs (cyclin-dependent kinases) and DDKs (Dbf4-dependent kinases) and their helicase activity are important for pre-RC to initiate the DNA replication, and (c) the release of MCMs from chromatin renders the origins "unlicensed". DNA replication licensing in plant is, in general, less characterized. The MCMs have been reported from Arabidopsis, maize, tobacco, pea and rice, where they are found to be highly expressed in dividing tissues such as shoot apex and root tips, localized in nucleus and cytosol and play important role in DNA replication, megagametophyte and embryo development. The identification of six MCM coding genes from pea and Arabidopsis suggest six distinct classes of MCM protein in higher plant, and the conserved function right across the eukaryotes. This overview of MCMs contains an emphasis on MCMs from plants and the novel role of MCM6 in abiotic stress tolerance.
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Affiliation(s)
- Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Hsu SC, Belmonte MF, Harada JJ, Inoue K. Indispensable Roles of Plastids in Arabidopsis thaliana Embryogenesis. Curr Genomics 2011; 11:338-49. [PMID: 21286311 PMCID: PMC2944999 DOI: 10.2174/138920210791616716] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 05/18/2010] [Accepted: 05/25/2010] [Indexed: 11/22/2022] Open
Abstract
The plastid is an organelle vital to all photosynthetic and some non-photosynthetic eukaryotes. In the model plant Arabidopsis thaliana, a number of nuclear genes encoding plastid proteins have been found to be necessary for embryo development. However, the exact roles of plastids in this process remain largely unknown. Here we use publicly available datasets to obtain insights into the relevance of plastid activities to A. thaliana embryogenesis. By searching the SeedGenes database (http://www.seedgenes.org) and recent literature, we found that, of the 339 non-redundant genes required for proper embryo formation, 108 genes likely encode plastid-targeted proteins. Nineteen of these genes are necessary for development of preglobular embryos and/or their conversion to globular embryos, of which 13 genes encode proteins involved in non-photosynthetic metabolism. By contrast, among 38 genes which are dispensable for globular embryo formation but necessary for further development, only one codes for a protein involved in metabolism. Products of 21 of the 38 genes play roles in plastid gene expression and maintenance. Examination of RNA profiles of embryos at distinct growth stages obtained in laser-capture microdissection coupled with DNA microarray experiments revealed that most of the identified genes are expressed throughout embryo morphogenesis and maturation. These findings suggest that metabolic activities are required at preglobular and throughout all stages of embryo development, whereas plastid gene expression becomes necessary during and/or after the globular stage to sustain various activities of the organelle including photosynthetic electron transport.
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Affiliation(s)
- Shih-Chi Hsu
- Department of Plant Sciences, University of California, Davis, CA, USA
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Tran NQ, Dang HQ, Tuteja R, Tuteja N. A single subunit MCM6 from pea forms homohexamer and functions as DNA helicase. PLANT MOLECULAR BIOLOGY 2010; 74:327-36. [PMID: 20730596 DOI: 10.1007/s11103-010-9675-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 07/27/2010] [Indexed: 05/18/2023]
Abstract
The initiation of DNA replication starts from origins and is controlled by a multiprotein complex, which involves about twenty protein factors. One of the important factors is hetrohexameric minichromosome maintenance (MCM2-7) protein complex which is evolutionary conserved and functions as essential replicative helicase for DNA replication. Here we report the isolation and characterization of a single subunit of pea MCM protein complex, the MCM6. The deduced amino acid (827) sequence contains all the known canonical MCM motifs including zinc finger, MCM specific Walker A and Walker B and arginine finger. The purified recombinant protein contains ATP-dependent 3'-5' DNA helicase, ATP-binding and ATPase activities. The helicase activity was stimulated by replication fork like substrate and anti-MCM6 antibodies curtail all the enzyme activities of MCM6 protein. In vitro it self-interacts and forms a homohexamer which is active for DNA helicase and ATPase activities. The complete protein is required for self-interaction as the truncated MCM6 proteins were unable to self-interact. Western blot analysis and in vivo immunostaining followed by confocal microscopy showed the localization of MCM6 both in the nucleus and cytosol. These findings provide first direct evidence that single subunit MCM6 contains DNA helicase activity which is unique to plant MCM6 protein, as this activity was only reported for heteromultimers of MCM proteins in animal system. This discovery should make an important contribution to a better understanding of DNA replication in plants.
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Affiliation(s)
- Ngoc Quang Tran
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
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