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Carballo J, Achilli A, Hernández F, Bocchini M, Pasten MC, Marconi G, Albertini E, Zappacosta D, Echenique V. Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes. Plant Reprod 2023:10.1007/s00497-023-00490-7. [PMID: 38055074 DOI: 10.1007/s00497-023-00490-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023]
Abstract
Epigenetics studies changes in gene activity without changes in the DNA sequence. Methylation is an epigenetic mechanism important in many pathways, such as biotic and abiotic stresses, cell division, and reproduction. Eragrostis curvula is a grass species reproducing by apomixis, a clonal reproduction by seeds. This work employed the MCSeEd technique to identify deferentially methylated positions, regions, and genes in the CG, CHG, and CHH contexts in E. curvula genotypes with similar genomic backgrounds but with different reproductive modes and ploidy levels. In this way, we focused the analysis on the cvs. Tanganyika INTA (4x, apomictic), Victoria (2x, sexual), and Bahiense (4x, apomictic). Victoria was obtained from the diploidization of Tanganyika INTA, while Bahiense was produced from the tetraploidization of Victoria. This study showed that polyploid/apomictic genotypes had more differentially methylated positions and regions than the diploid sexual ones. Interestingly, it was possible to observe fewer differentially methylated positions and regions in CG than in the other contexts, meaning CG methylation is conserved across the genotypes regardless of the ploidy level and reproductive mode. In the comparisons between sexual and apomictic genotypes, we identified differentially methylated genes involved in the reproductive pathways, specifically in meiosis, cell division, and fertilization. Another interesting observation was that several differentially methylated genes between the diploid and the original tetraploid genotype recovered their methylation status after tetraploidization, suggesting that methylation is an important mechanism involved in reproduction and ploidy changes.
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Affiliation(s)
- J Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
| | - A Achilli
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
| | - F Hernández
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000, Bahía Blanca, Argentina
| | - M Bocchini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121, Perugia, Italy
| | - M C Pasten
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
| | - G Marconi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121, Perugia, Italy
| | - E Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121, Perugia, Italy.
| | - D Zappacosta
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina.
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000, Bahía Blanca, Argentina.
| | - V Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina.
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000, Bahía Blanca, Argentina.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Pokora W, Tułodziecki S, Dettlaff-Pokora A, Aksmann A. Cross Talk between Hydrogen Peroxide and Nitric Oxide in the Unicellular Green Algae Cell Cycle: How Does It Work? Cells 2022; 11:cells11152425. [PMID: 35954269 PMCID: PMC9368121 DOI: 10.3390/cells11152425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/22/2022] Open
Abstract
The regulatory role of some reactive oxygen species (ROS) and reactive nitrogen species (RNS), such as hydrogen peroxide or nitric oxide, has been demonstrated in some higher plants and algae. Their involvement in regulation of the organism, tissue and single cell development can also be seen in many animals. In green cells, the redox potential is an important photosynthesis regulatory factor that may lead to an increase or decrease in growth rate. ROS and RNS are important signals involved in the regulation of photoautotrophic growth that, in turn, allow the cell to attain the commitment competence. Both hydrogen peroxide and nitric oxide are directly involved in algal cell development as the signals that regulate expression of proteins required for completing the cell cycle, such as cyclins and cyclin-dependent kinases, or histone proteins and E2F complex proteins. Such regulation seems to relate to the direct interaction of these signaling molecules with the redox-sensitive transcription factors, but also with regulation of signaling pathways including MAPK, G-protein and calmodulin-dependent pathways. In this paper, we aim to elucidate the involvement of hydrogen peroxide and nitric oxide in algal cell cycle regulation, considering the role of these molecules in higher plants. We also evaluate the commercial applicability of this knowledge. The creation of a simple tool, such as a precisely established modification of hydrogen peroxide and/or nitric oxide at the cellular level, leading to changes in the ROS-RNS cross-talk network, can be used for the optimization of the efficiency of algal cell growth and may be especially important in the context of increasing the role of algal biomass in science and industry. It could be a part of an important scientific challenge that biotechnology is currently focused on.
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Affiliation(s)
- Wojciech Pokora
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of Gdańsk Wita, Stwosza 59, 83-308 Gdańsk, Poland
- Correspondence:
| | - Szymon Tułodziecki
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of Gdańsk Wita, Stwosza 59, 83-308 Gdańsk, Poland
| | | | - Anna Aksmann
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of Gdańsk Wita, Stwosza 59, 83-308 Gdańsk, Poland
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Li Y, Guo G, Xu H, He T, Zong Y, Zhang S, Faheem M, Lu R, Zhou L, Liu C. Comparative transcriptome analysis reveals compatible and recalcitrant genotypic response of barley microspore-derived embryogenic callus toward Agrobacterium infection. BMC Plant Biol 2021; 21:579. [PMID: 34876002 PMCID: PMC8650547 DOI: 10.1186/s12870-021-03346-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/15/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND The Agrobacterium mediated transformation has been routinely used in lots of plant species as a powerful tool to deliver genes of interest into a host plant. However, the transformation of elite and commercially valuable cultivar is still limited by the genotype-dependency, and the efficiency of Agrobacterium infection efficiency is crucial for the success of transformation. RESULTS In this study, the microspore-derived embryogenic calli (MDEC) of barley elite cultivars and breeding lines were employed as unique subjects to characterize the genotypic response during Agrobacterium infection process. Our results identified compatible barley genotypes (GanPi 6 and L07, assigned as GP6-L07 group) and one recalcitrant genotype (Hong 99, assigned as H99) for the Agrobacterium strain LBA4404 infection using GUS assay. The accumulation trend of reactive oxygen species (ROS) was similar among genotypes across the time course. The results of RNA-seq depicted that the average expressional intensity of whole genomic genes was similar among barley genotypes during Agrobacterium infection. However, the numbers of differentially expressed genes (DEGs) exhibited significant expressional variation between GP6-L07 and H99 groups from 6 to 12 h post-inoculation (hpi). Gene ontology (GO) enrichment analysis revealed different regulation patterns for the predicted biological processes between the early (up-regulated DEGs overrepresented at 2 hpi) and late stages (down-regulated DEGs overrepresented from 6 to 24 hpi) of infection. KEGG analysis predicted 12 pathways during Agrobacterium infection. Among which one pathway related to pyruvate metabolism was enriched in GP6 and L07 at 6 hpi. Two pathways related to plant hormone signal transduction and DNA replication showed expressional variation between GP6-L07 and H99 at 24 hpi. It was further validated by qRT-PCR assay for seven candidate genes (Aldehyde dehydrogenase, SAUR, SAUR50, ARG7, Replication protein A, DNA helicase and DNA replication licensing factor) involved in the three pathways, which are all up-regulated in compatible while down-regulated in recalcitrant genotypes, suggesting the potential compatibility achieved at later stage for the growth of Agrobacterium infected cells. CONCLUSIONS Our findings demonstrated the similarity and difference between compatible and recalcitrant genotypes of barley MDEC upon Agrobacterium infection. Seven candidate genes involved in pyruvate metabolism, hormonal signal transduction and DNA replication were identified, which advocates the genotypic dependency during Agrobacterium infection process.
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Affiliation(s)
- Yingbo Li
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Guimei Guo
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Hongwei Xu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Ting He
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Yingjie Zong
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Shuwei Zhang
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | | | - Ruiju Lu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Longhua Zhou
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
| | - Chenghong Liu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
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Ikui AE, Ueki N, Pecani K, Cross FR. Control of pre-replicative complex during the division cycle in Chlamydomonas reinhardtii. PLoS Genet 2021; 17:e1009471. [PMID: 33909603 PMCID: PMC8081180 DOI: 10.1371/journal.pgen.1009471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/07/2021] [Indexed: 12/31/2022] Open
Abstract
DNA replication is fundamental to all living organisms. In yeast and animals, it is triggered by an assembly of pre-replicative complex including ORC, CDC6 and MCMs. Cyclin Dependent Kinase (CDK) regulates both assembly and firing of the pre-replicative complex. We tested temperature-sensitive mutants blocking Chlamydomonas DNA replication. The mutants were partially or completely defective in DNA replication and did not produce mitotic spindles. After a long G1, wild type Chlamydomonas cells enter a division phase when it undergoes multiple rapid synchronous divisions ('multiple fission'). Using tagged transgenic strains, we found that MCM4 and MCM6 were localized to the nucleus throughout the entire multiple fission division cycle, except for transient cytoplasmic localization during each mitosis. Chlamydomonas CDC6 was transiently localized in nucleus in early division cycles. CDC6 protein levels were very low, probably due to proteasomal degradation. CDC6 levels were severely reduced by inactivation of CDKA1 (CDK1 ortholog) but not the plant-specific CDKB1. Proteasome inhibition did not detectably increase CDC6 levels in the cdka1 mutant, suggesting that CDKA1 might upregulate CDC6 at the transcriptional level. All of the DNA replication proteins tested were essentially undetectable until late G1. They accumulated specifically during multiple fission and then were degraded as cells completed their terminal divisions. We speculate that loading of origins with the MCM helicase may not occur until the end of the long G1, unlike in the budding yeast system. We also developed a simple assay for salt-resistant chromatin binding of MCM4, and found that tight MCM4 loading was dependent on ORC1, CDC6 and MCM6, but not on RNR1 or CDKB1. These results provide a microbial framework for approaching replication control in the plant kingdom.
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Affiliation(s)
- Amy E. Ikui
- Department of Biology, Brooklyn College, The City University of New York, New York City, New York, United States of America
- * E-mail: (AEI); (FRC)
| | - Noriko Ueki
- Department of Biology, Brooklyn College, The City University of New York, New York City, New York, United States of America
| | - Kresti Pecani
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York City, New York, United States of America
| | - Frederick R. Cross
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York City, New York, United States of America
- * E-mail: (AEI); (FRC)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cabral LM, Masuda HP, Ballesteros HF, de Almeida-Engler J, Alves-Ferreira M, De Toni KLG, Bizotto FM, Ferreira PCG, Hemerly AS. ABAP1 Plays a Role in the Differentiation of Male and Female Gametes in Arabidopsis thaliana. Front Plant Sci 2021; 12:642758. [PMID: 33643370 PMCID: PMC7903899 DOI: 10.3389/fpls.2021.642758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/22/2021] [Indexed: 05/07/2023]
Abstract
The correct development of a diploid sporophyte body and a haploid gametophyte relies on a strict coordination between cell divisions in space and time. During plant reproduction, these divisions have to be temporally and spatially coordinated with cell differentiation processes, to ensure a successful fertilization. Armadillo BTB Arabidopsis protein 1 (ABAP1) is a plant exclusive protein that has been previously reported to control proliferative cell divisions during leaf growth in Arabidopsis. Here, we show that ABAP1 binds to different transcription factors that regulate male and female gametophyte differentiation, repressing their target genes expression. During male gametogenesis, the ABAP1-TCP16 complex represses CDT1b transcription, and consequently regulates microspore first asymmetric mitosis. In the female gametogenesis, the ABAP1-ADAP complex represses EDA24-like transcription, regulating polar nuclei fusion to form the central cell. Therefore, besides its function during vegetative development, this work shows that ABAP1 is also involved in differentiation processes during plant reproduction, by having a dual role in regulating both the first asymmetric cell division of male gametophyte and the cell differentiation (or cell fusion) of female gametophyte.
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Affiliation(s)
- Luiz M. Cabral
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Biologia Celular e Molecular, Instituto de Biologia, Universidade Federal Fluminense, Niterói, Brazil
| | - Hana P. Masuda
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, Brazil
| | - Helkin F. Ballesteros
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Janice de Almeida-Engler
- Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Institut Sophia Agrobiotech, Université Côte d’Azur, Sophia Antipolis, France
| | - Márcio Alves-Ferreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Karen L. G. De Toni
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda M. Bizotto
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, Brazil
| | - Paulo C. G. Ferreira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adriana S. Hemerly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- *Correspondence: Adriana S. Hemerly, ;
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Abstract
An increasing number of eukaryotic proteins have been shown to have a dual localization in the DNA-containing organelles, mitochondria and plastids, and/or the nucleus. Regulation of dual targeting and relocation of proteins from organelles to the nucleus offer the most direct means for communication between organelles as well as organelles and nucleus. Most of the mitochondrial proteins of animals have functions in DNA repair and gene expression by modelling of nucleoid architecture and/or chromatin. In plants, such proteins can affect replication and early development. Most plastid proteins with a confirmed or predicted second location in the nucleus are associated with the prokaryotic core RNA polymerase and are required for chloroplast development and light responses. Few plastid–nucleus-located proteins are involved in pathogen defence and cell cycle control. For three proteins, it has been clearly shown that they are first targeted to the organelle and then relocated to the nucleus, i.e. the nucleoid-associated proteins HEMERA and Whirly1 and the stroma-located defence protein NRIP1. Relocation to the nucleus can be experimentally demonstrated by plastid transformation leading to the synthesis of proteins with a tag that enables their detection in the nucleus or by fusions with fluoroproteins in different experimental set-ups. This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
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Affiliation(s)
- Karin Krupinska
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Nicolás E Blanco
- Centre of Photosynthetic and Biochemical Studies, Faculty of Biochemical Science and Pharmacy, National University of Rosario (CEFOBI/UNR-CONICET), Rosario, Argentina
| | - Svenja Oetke
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Michela Zottini
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131 Padova, Italy
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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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Qian J, Chen Y, Xu Y, Zhang X, Kang Z, Jiao J, Zhao J. Interactional similarities and differences in the protein complex of PCNA and DNA replication factor C between rice and Arabidopsis. BMC Plant Biol 2019; 19:257. [PMID: 31200645 PMCID: PMC6570896 DOI: 10.1186/s12870-019-1874-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 06/06/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Proliferating cell nuclear antigen (PCNA), a conserved trimeric ring complex, is loaded onto replication fork through a hetero-pentameric AAA+ ATPase complex termed replication factor C (RFC) to maintain genome stability. Although architectures of PCNA-RFC complex in yeast have been revealed, the functions of PCNA and protein-protein interactions of PCNA-RFC complex in higher plants are not very clear. Here, essential regions mediating interactions between PCNA and RFC subunits in Arabidopsis and rice were investigated via yeast-two-hybrid method and bimolecular fluorescence complementation techniques. RESULTS We observed that OsPCNA could interact with all OsRFC subunits, while protein-protein interactions only exist between Arabidopsis RFC2/3/4/5 and AtPCNA1/2. The truncated analyses indicated that the C-terminal of Arabidopsis RFC2/3/4/5 and rice RFC1/2 is essential for binding PCNA while the region of rice RFC3/4/5 mediating interaction with PCNA distributed both at the N- and C-terminal. On the other hand, we found that the C- and N-terminal of Arabidopsis and rice PCNA contribute equally to PCNA-PCNA interaction, and the interdomain connecting loop (IDCL) domain and C-terminal of PCNAs are indispensable for interacting RFC subunits. CONCLUSIONS These results indicated that Arabidopsis and rice PCNAs are highly conserved in sequence, structure and pattern of interacting with other PCNA monomer. Nevertheless, there are also significant differences between the Arabidopsis and rice RFC subunits in binding PCNA. Taken together, our results could be helpful for revealing the biological functions of plant RFC-PCNA complex.
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Affiliation(s)
- Jie Qian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yueyue Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yaxing Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiufeng Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhuang Kang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jinxia Jiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
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12
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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. Plant J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Glab N, Oury C, Guérinier T, Domenichini S, Crozet P, Thomas M, Vidal J, Hodges M. The impact of Arabidopsis thaliana SNF1-related-kinase 1 (SnRK1)-activating kinase 1 (SnAK1) and SnAK2 on SnRK1 phosphorylation status: characterization of a SnAK double mutant. Plant J 2017; 89:1031-1041. [PMID: 27943466 DOI: 10.1111/tpj.13445] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/14/2016] [Indexed: 05/20/2023]
Abstract
Arabidopsis thaliana SNF1-related-kinase 1 (SnRK1)-activating kinase 1 (AtSnAK1) and AtSnAK2 have been shown to phosphorylate in vitro and activate the energy signalling integrator, SnRK1. To clarify this signalling cascade in planta, a genetic- and molecular-based approach was developed. Homozygous single AtSnAK1 and AtSnAK2 T-DNA insertional mutants did not display an apparent phenotype. Crossing of the single mutants did not allow the isolation of double-mutant plants, whereas self-pollinating the S1-/- S2+/- sesquimutant specifically gave approximatively 22% individuals in their offspring that, when rescued on sugar-supplemented media in vitro, were shown to be AtSnAK1 AtSnAK2 double mutants. Interestingly, this was not obtained in the case of the other sesquimutant, S1+/- S2-/-. Although reduced in size, the double mutant had the capacity to produce flowers, but not seeds. Immunological characterization established the T-loop of the SnRK1 catalytic subunit to be non-phosphorylated in the absence of both SnAKs. When the double mutant was complemented with a DNA construct containing an AtSnAK2 open reading frame driven by its own promoter, a normal phenotype was restored. Therefore, wild-type plant growth and development is dependent on the presence of SnAK in vivo, and this is correlated with SnRK1 phosphorylation. These data show that both SnAKs are kinases phosphorylating SnRK1, and thereby they contribute to energy signalling in planta.
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Affiliation(s)
- Nathalie Glab
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Sud, INRA, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay Cedex, France
| | - Céline Oury
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Sud, INRA, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay Cedex, France
| | - Thomas Guérinier
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Sud, INRA, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay Cedex, France
| | - Séverine Domenichini
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Sud, INRA, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay Cedex, France
| | - Pierre Crozet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Sud, INRA, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay Cedex, France
| | - Martine Thomas
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Sud, INRA, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay Cedex, France
| | - Jean Vidal
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Sud, INRA, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay Cedex, France
| | - Michael Hodges
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Sud, INRA, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay Cedex, France
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15
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Pedroza-Garcia JA, Domenichini S, Bergounioux C, Benhamed M, Raynaud C. Chloroplasts around the plant cell cycle. Curr Opin Plant Biol 2016; 34:107-113. [PMID: 27816816 DOI: 10.1016/j.pbi.2016.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 10/19/2016] [Accepted: 10/23/2016] [Indexed: 06/06/2023]
Abstract
Plastids arose from an endosymbiosis between a host cell and free-living bacteria. One key step during this evolutionary process has been the establishment of coordinated cell and symbiont division to allow the maintenance of organelles during proliferation of the host. However, surprisingly little is known about the underlying mechanisms. In addition, due to their central role in the cell's energetic metabolism and to their sensitivity to various environmental cues such as light or temperature, plastids are ideally fitted to be the source of signals allowing plants to adapt their development according to external conditions. Consistently, there is accumulating evidence that plastid-derived signals can impinge on cell cycle regulation. In this review, we summarize current knowledge of the dialogue between chloroplasts and the nucleus in the context of the cell cycle.
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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, Batiment 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, Batiment 630, 91405 Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Li Z, Defoort J, Tasdighian S, Maere S, Van de Peer Y, De Smet R. Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms. Plant Cell 2016; 28:326-44. [PMID: 26744215 PMCID: PMC4790876 DOI: 10.1105/tpc.15.00877] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/04/2016] [Indexed: 05/02/2023]
Abstract
Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes.
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Affiliation(s)
- Zhen Li
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Jonas Defoort
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Setareh Tasdighian
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Steven Maere
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Riet De Smet
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
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18
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Van Leene J, Eeckhout D, Cannoot B, De Winne N, Persiau G, Van De Slijke E, Vercruysse L, Dedecker M, Verkest A, Vandepoele K, Martens L, Witters E, Gevaert K, De Jaeger G. An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes. Nat Protoc 2015; 10:169-87. [DOI: 10.1038/nprot.2014.199] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Chu P, Liu H, Yang Q, Wang Y, Yan G, Guan R. An RNA-seq transcriptome analysis of floral buds of an interspecific Brassica hybrid between B. carinata and B. napus. Plant Reprod 2014; 27:225-237. [PMID: 25398253 DOI: 10.1007/s00497-014-0253-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/03/2014] [Indexed: 06/04/2023]
Abstract
Interspecific hybridizations promote gene transfer between species and play an important role in plant speciation and crop improvement. However, hybrid sterility that commonly found in the first generation of hybrids hinders the utilization of interspecific hybridization. The combination of divergent parental genomes can create extensive transcriptome variations, and to determine these gene expression alterations and their effects on hybrids, an interspecific Brassica hybrid of B. carinata × B. napus was generated. Scanning electron microscopy analysis indicated that some of the hybrid pollen grains were irregular in shape and exhibited abnormal exine patterns compared with those from the parents. Using the Illumina HiSeq 2000 platform, 39,598, 32,403 and 42,208 genes were identified in flower buds of B. carinata cv. W29, B. napus cv. Zhongshuang 11 and their hybrids, respectively. The differentially expressed genes were significantly enriched in pollen wall assembly, pollen exine formation, pollen development, pollen tube growth, pollination, gene transcription, macromolecule methylation and translation, which might be associated with impaired fertility in the F1 hybrid. These results will shed light on the mechanisms underlying the low fertility of the interspecific hybrids and expand our knowledge of interspecific hybridization.
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Affiliation(s)
- Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Yin K, Ueda M, Takagi H, Kajihara T, Sugamata Aki S, Nobusawa T, Umeda-Hara C, Umeda M. A dual-color marker system for in vivo visualization of cell cycle progression in Arabidopsis. Plant J 2014; 80:541-52. [PMID: 25158977 DOI: 10.1111/tpj.12652] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 08/18/2014] [Accepted: 08/20/2014] [Indexed: 05/08/2023]
Abstract
Visualization of the spatiotemporal pattern of cell division is crucial to understand how multicellular organisms develop and how they modify their growth in response to varying environmental conditions. The mitotic cell cycle consists of four phases: S (DNA replication), M (mitosis and cytokinesis), and the intervening G1 and G2 phases; however, only G2/M-specific markers are currently available in plants, making it difficult to measure cell cycle duration and to analyze changes in cell cycle progression in living tissues. Here, we developed another cell cycle marker that labels S-phase cells by manipulating Arabidopsis CDT1a, which functions in DNA replication origin licensing. Truncations of the CDT1a coding sequence revealed that its carboxy-terminal region is responsible for proteasome-mediated degradation at late G2 or in early mitosis. We therefore expressed this region as a red fluorescent protein fusion protein under the S-specific promoter of a histone 3.1-type gene, HISTONE THREE RELATED2 (HTR2), to generate an S/G2 marker. Combining this marker with the G2/M-specific CYCB1-GFP marker enabled us to visualize both S to G2 and G2 to M cell cycle stages, and thus yielded an essential tool for time-lapse imaging of cell cycle progression. The resultant dual-color marker system, Cell Cycle Tracking in Plant Cells (Cytrap), also allowed us to identify root cells in the last mitotic cell cycle before they entered the endocycle. Our results demonstrate that Cytrap is a powerful tool for in vivo monitoring of the plant cell cycle, and thus for deepening our understanding of cell cycle regulation in particular cell types during organ development.
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Affiliation(s)
- Ke Yin
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara, 630-0192, Japan
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Abstract
The cell cycle is one of the most comprehensively studied biological processes, due primarily to its significance in growth and development, and its deregulation in many human disorders. Studies using a diverse set of model organisms, including yeast, worms, flies, frogs, mammals, and plants, have greatly expanded our knowledge of the cell cycle and have contributed to the universally accepted view of how the basic cell cycle machinery is regulated. In addition to the oscillating activity of various cyclin-dependent kinase (CDK)-cyclin complexes, a plethora of proteins affecting various aspects of chromatin dynamics has been shown to be essential for cell proliferation during plant development. Furthermore, it was reported recently that core cell cycle regulators control gene expression by modifying histone patterns. This review focuses on the intimate relationship between the cell cycle and chromatin. It describes the dynamics and functions of chromatin structures throughout cell cycle progression and discusses the role of heterochromatin as a barrier against re-replication and endoreduplication. It also proposes that core plant cell cycle regulators control gene expression in a manner similar to that described in mammals. At present, our challenge in plants is to define the complete set of effectors and actors that coordinate cell cycle progression and chromatin structure and to understand better the functional interplay between these two processes.
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Affiliation(s)
- Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Allison C Mallory
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - David Latrasse
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Teddy Jégu
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Quentin Bruggeman
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Marianne Delarue
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
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