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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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Li X, Wu J, Yi F, Lai J, Chen J. High temporal-resolution transcriptome landscapes of maize embryo sac and ovule during early seed development. PLANT MOLECULAR BIOLOGY 2023; 111:233-248. [PMID: 36508138 DOI: 10.1007/s11103-022-01318-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/07/2022] [Indexed: 06/18/2023]
Abstract
Here we provided a high temporal-resolution transcriptome atlas of maize embryo sac and ovule to reveal the gene activity dynamic during early seed development. The early maize (Zea mays) seed development is initiated from double fertilization in the embryo sac and needs to undergo a highly dynamic and complex development process to form the differentiated embryo and endosperm. Despite the importance of maize seed for food, feed, and biofuel, many regulators responsible for controlling its early development are not known yet. Here, we reported a high temporal-resolution transcriptome atlas of embryo sac and ovule based on 44 time point samples collected within the first four days of seed development. A total of 25,187 genes including 1598 transcription factors (TFs) involved in early seed development were detected. Global comparisons of the expressions of these genes revealed five distinct development stages of early seed, which are mainly related to double fertilization, asymmetric cell division of the zygote, as well as coenocyte formation, cellularization and differentiation in endosperm. We identified 3327 seed-specific genes, which more than one thousand seed-specific genes with main expressions during early seed development were newly identified here, including 859 and 186 genes predominantly expressed in the embryo sac and ovule, respectively. Combined with the published transcriptome data of seed, we uncovered the dominant auxin biosynthesis, transport and signaling related genes at different development stages and subregions of seed. These results are helpful for understanding the genetic control of early seed development.
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Affiliation(s)
- Xinchen Li
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, People's Republic of China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Jian Wu
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Fei Yi
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, People's Republic of China
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, People's Republic of China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, People's Republic of China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Jian Chen
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, People's Republic of China.
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, People's Republic of China.
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Cabral D, Forero Ballesteros H, de Melo BP, Lourenço-Tessutti IT, Simões de Siqueira KM, Obicci L, Grossi-de-Sa MF, Hemerly AS, de Almeida Engler J. The Armadillo BTB Protein ABAP1 Is a Crucial Player in DNA Replication and Transcription of Nematode-Induced Galls. FRONTIERS IN PLANT SCIENCE 2021; 12:636663. [PMID: 33995437 PMCID: PMC8121025 DOI: 10.3389/fpls.2021.636663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
The biogenesis of root-knot nematode (Meloidogyne spp.)-induced galls requires the hyperactivation of the cell cycle with controlled balance of mitotic and endocycle programs to keep its homeostasis. To better understand gall functioning and to develop new control strategies for this pest, it is essential to find out how the plant host cell cycle programs are responding and integrated during the nematode-induced gall formation. This work investigated the spatial localization of a number of gene transcripts involved in the pre-replication complex during DNA replication in galls and report their akin colocation with the cell cycle S-phase regulator Armadillo BTB Arabidopsis Protein 1 (ABAP1). ABAP1 is a negative regulator of pre-replication complex controlling DNA replication of genes involved in control of cell division and proliferation; therefore, its function has been investigated during gall ontogenesis. Functional analysis was performed upon ABAP1 knockdown and overexpression in Arabidopsis thaliana. We detected ABAP1 promoter activity and localized ABAP1 protein in galls during development, and its overexpression displayed significantly reduced gall sizes containing atypical giant cells. Profuse ABAP1 expression also impaired gall induction and hindered nematode reproduction. Remarkably, ABAP1 knockdown likewise negatively affected gall and nematode development, suggesting its involvement in the feeding site homeostasis. Microscopy analysis of cleared and nuclei-stained whole galls revealed that ABAP1 accumulation resulted in aberrant giant cells displaying interconnected nuclei filled with enlarged heterochromatic regions. Also, imbalanced ABAP1 expression caused changes in expression patterns of genes involved in the cell division control as demonstrated by qRT-PCR. CDT1a, CDT1b, CDKA;1, and CYCB1;1 mRNA levels were significantly increased in galls upon ABAP1 overexpression, possibly contributing to the structural changes in galls during nematode infection. Overall, data obtained in galls reinforced the role of ABAP1 controlling DNA replication and mitosis and, consequently, cell proliferation. ABAP1 expression might likely take part of a highly ordered mechanism balancing of cell cycle control to prevent gall expansion. ABAP1 expression might prevent galls to further expand, limiting excessive mitotic activity. Our data strongly suggest that ABAP1 as a unique plant gene is an essential component for cell cycle regulation throughout gall development during nematode infection and is required for feeding site homeostasis.
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Affiliation(s)
- Danila Cabral
- INRAE, Université Côte d’Azur, CNRS, ISA, Sophia Antipolis, France
| | - Helkin Forero Ballesteros
- INRAE, Université Côte d’Azur, CNRS, ISA, Sophia Antipolis, France
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Paes de Melo
- INRAE, Université Côte d’Azur, CNRS, ISA, Sophia Antipolis, France
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Isabela Tristan Lourenço-Tessutti
- INRAE, Université Côte d’Azur, CNRS, ISA, Sophia Antipolis, France
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | | | - Luciana Obicci
- INRAE, Université Côte d’Azur, CNRS, ISA, Sophia Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Adriana S. Hemerly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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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] [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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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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Long YP, Xie DJ, Zhao YY, Shi DQ, Yang WC. BICELLULAR POLLEN 1 is a modulator of DNA replication and pollen development in Arabidopsis. THE NEW PHYTOLOGIST 2019; 222:588-603. [PMID: 30484867 DOI: 10.1111/nph.15610] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
During male gametogenesis in Arabidopsis, the haploid microspore undergoes an asymmetric division to produce a vegetative and a generative cell, the latter of which continues to divide symmetrically to form two sperms. This simple system couples cell cycle with cell fate specification. Here we addressed the role of DNA replication in male gametogenesis using a mutant bicellular pollen 1 (bice1), which produces bicellular, rather than tricellular, pollen grains as in the wild-type plant at anthesis. The mutation prolonged DNA synthesis of the generative cell, which resulted in c. 40% of pollen grains arrested at the two-nucleate stage. The extended S phase did not impact the cell fate of the generative cell as shown by cell-specific markers. BICE1 encodes a plant homolog of human D123 protein that is required for G1 progression, but the underlying mechanism is unknown. Here we showed that BICE1 interacts with MCM4 and MCM7 of the pre-replication complex. Consistently, double mutations in BICE1 and MCM4, or MCM7, also led to bicellular pollen and condensed chromosomes. These suggest that BICE1 plays a role in modulating DNA replication via interaction with MCM4 and MCM7.
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Affiliation(s)
- Yan-Ping Long
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, East Lincui Road, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China
| | - Dong-Jiang Xie
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, East Lincui Road, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China
| | - Yan-Yan Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, East Lincui Road, Beijing, 100101, China
| | - Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, East Lincui Road, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China
| | - Wei-Cai Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, East Lincui Road, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Yuquan Road, Beijing, 100049, China
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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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Chen J, Strieder N, Krohn NG, Cyprys P, Sprunck S, Engelmann JC, Dresselhaus T. Zygotic Genome Activation Occurs Shortly after Fertilization in Maize. THE PLANT CELL 2017; 29:2106-2125. [PMID: 28814645 PMCID: PMC5635985 DOI: 10.1105/tpc.17.00099] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/19/2017] [Accepted: 08/15/2017] [Indexed: 05/18/2023]
Abstract
The formation of a zygote via the fusion of an egg and sperm cell and its subsequent asymmetric division herald the start of the plant's life cycle. Zygotic genome activation (ZGA) is thought to occur gradually, with the initial steps of zygote and embryo development being primarily maternally controlled, and subsequent steps being governed by the zygotic genome. Here, using maize (Zea mays) as a model plant system, we determined the timing of zygote development and generated RNA-seq transcriptome profiles of gametes, zygotes, and apical and basal daughter cells. ZGA occurs shortly after fertilization and involves ∼10% of the genome being activated in a highly dynamic pattern. In particular, genes encoding transcriptional regulators of various families are activated shortly after fertilization. Further analyses suggested that chromatin assembly is strongly modified after fertilization, that the egg cell is primed to activate the translational machinery, and that hormones likely play a minor role in the initial steps of early embryo development in maize. Our findings provide important insights into gamete and zygote activity in plants, and our RNA-seq transcriptome profiles represent a comprehensive, unique RNA-seq data set that can be used by the research community.
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Affiliation(s)
- Junyi Chen
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Nicholas Strieder
- Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany
| | - Nadia G Krohn
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Philipp Cyprys
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Julia C Engelmann
- Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
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Grimplet J, Tello J, Laguna N, Ibáñez J. Differences in Flower Transcriptome between Grapevine Clones Are Related to Their Cluster Compactness, Fruitfulness, and Berry Size. FRONTIERS IN PLANT SCIENCE 2017; 8:632. [PMID: 28496449 PMCID: PMC5406470 DOI: 10.3389/fpls.2017.00632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/07/2017] [Indexed: 05/21/2023]
Abstract
Grapevine cluster compactness has a clear impact on fruit quality and health status, as clusters with greater compactness are more susceptible to pests and diseases and ripen more asynchronously. Different parameters related to inflorescence and cluster architecture (length, width, branching, etc.), fruitfulness (number of berries, number of seeds) and berry size (length, width) contribute to the final level of compactness. From a collection of 501 clones of cultivar Garnacha Tinta, two compact and two loose clones with stable differences for cluster compactness-related traits were selected and phenotyped. Key organs and developmental stages were selected for sampling and transcriptomic analyses. Comparison of global gene expression patterns in flowers at the end of bloom allowed identification of potential gene networks with a role in determining the final berry number, berry size and ultimately cluster compactness. A large portion of the differentially expressed genes were found in networks related to cell division (carbohydrates uptake, cell wall metabolism, cell cycle, nucleic acids metabolism, cell division, DNA repair). Their greater expression level in flowers of compact clones indicated that the number of berries and the berry size at ripening appear related to the rate of cell replication in flowers during the early growth stages after pollination. In addition, fluctuations in auxin and gibberellin signaling and transport related gene expression support that they play a central role in fruit set and impact berry number and size. Other hormones, such as ethylene and jasmonate may differentially regulate indirect effects, such as defense mechanisms activation or polyphenols production. This is the first transcriptomic based analysis focused on the discovery of the underlying gene networks involved in grapevine traits of grapevine cluster compactness, berry number and berry size.
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Affiliation(s)
- Jérôme Grimplet
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Gobierno de La Rioja)Logroño, Spain
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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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Zhao P, Begcy K, Dresselhaus T, Sun MX. Does Early Embryogenesis in Eudicots and Monocots Involve the Same Mechanism and Molecular Players? PLANT PHYSIOLOGY 2017; 173:130-142. [PMID: 27909044 PMCID: PMC5210740 DOI: 10.1104/pp.16.01406] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/30/2016] [Indexed: 05/18/2023]
Abstract
A comparison of eudicot and monocot model plants explores recent advances and open questions on gene regulatory networks during zygote development, parental influences on early embryogenesis, zygotic genome activation, and cell fate determination.
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Affiliation(s)
- Peng Zhao
- College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China (P.Z., M.-X.S.); and
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany (K.B., T.D.)
| | - Kevin Begcy
- College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China (P.Z., M.-X.S.); and
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany (K.B., T.D.)
| | - Thomas Dresselhaus
- College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China (P.Z., M.-X.S.); and
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany (K.B., T.D.)
| | - Meng-Xiang Sun
- College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China (P.Z., M.-X.S.); and
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany (K.B., T.D.)
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Gene Expression Differences between High-Growth Populus Allotriploids and Their Diploid Parents. FORESTS 2015. [DOI: 10.3390/f6030839] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Lesur I, Le Provost G, Bento P, Da Silva C, Leplé JC, Murat F, Ueno S, Bartholomé J, Lalanne C, Ehrenmann F, Noirot C, Burban C, Léger V, Amselem J, Belser C, Quesneville H, Stierschneider M, Fluch S, Feldhahn L, Tarkka M, Herrmann S, Buscot F, Klopp C, Kremer A, Salse J, Aury JM, Plomion C. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics 2015; 16:112. [PMID: 25765701 PMCID: PMC4350297 DOI: 10.1186/s12864-015-1331-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 02/09/2015] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. RESULTS The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. CONCLUSION In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.
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Affiliation(s)
- Isabelle Lesur
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- HelixVenture, F-33700, Mérignac, France.
| | - Grégoire Le Provost
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Pascal Bento
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Corinne Da Silva
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Jean-Charles Leplé
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075, Orléans, France.
| | - Florent Murat
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, F-63039, Clermont-Ferrand, France.
| | - Saneyoshi Ueno
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tree Genetics Laboratory, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Jerôme Bartholomé
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- CIRAD, UMR AGAP, F-34398, Montpellier, France.
| | - Céline Lalanne
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - François Ehrenmann
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Céline Noirot
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, F-31326, Auzeville Castanet-Tolosan, France.
| | - Christian Burban
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Valérie Léger
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Joelle Amselem
- INRA, Unité de Recherche Génomique Info (URGI), F78026, Versailles, France.
| | - Caroline Belser
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Hadi Quesneville
- INRA, Unité de Recherche Génomique Info (URGI), F78026, Versailles, France.
| | | | - Silvia Fluch
- AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Str 24, 3430, Tulln, Austria.
| | - Lasse Feldhahn
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany.
| | - Mika Tarkka
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany.
- iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany.
| | - Sylvie Herrmann
- iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany.
- Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, 06120, Halle/Saale, Germany.
| | - François Buscot
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany.
- iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany.
| | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, F-31326, Auzeville Castanet-Tolosan, France.
| | - Antoine Kremer
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Jérôme Salse
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, F-63039, Clermont-Ferrand, France.
| | - Jean-Marc Aury
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Christophe Plomion
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
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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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15
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Juranić M, Srilunchang KO, Krohn NG, Leljak-Levanić D, Sprunck S, Dresselhaus T. Germline-specific MATH-BTB substrate adaptor MAB1 regulates spindle length and nuclei identity in maize. THE PLANT CELL 2012; 24:4974-91. [PMID: 23250449 PMCID: PMC3556970 DOI: 10.1105/tpc.112.107169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 11/05/2012] [Accepted: 11/28/2012] [Indexed: 05/03/2023]
Abstract
Germline and early embryo development constitute ideal model systems to study the establishment of polarity, cell identity, and asymmetric cell divisions (ACDs) in plants. We describe here the function of the MATH-BTB domain protein MAB1 that is exclusively expressed in the germ lineages and the zygote of maize (Zea mays). mab1 (RNA interference [RNAi]) mutant plants display chromosome segregation defects and short spindles during meiosis that cause insufficient separation and migration of nuclei. After the meiosis-to-mitosis transition, two attached nuclei of similar identity are formed in mab1 (RNAi) mutants leading to an arrest of further germline development. Transient expression studies of MAB1 in tobacco (Nicotiana tabacum) Bright Yellow-2 cells revealed a cell cycle-dependent nuclear localization pattern but no direct colocalization with the spindle apparatus. MAB1 is able to form homodimers and interacts with the E3 ubiquitin ligase component Cullin 3a (CUL3a) in the cytoplasm, likely as a substrate-specific adapter protein. The microtubule-severing subunit p60 of katanin was identified as a candidate substrate for MAB1, suggesting that MAB1 resembles the animal key ACD regulator Maternal Effect Lethal 26 (MEL-26). In summary, our findings provide further evidence for the importance of posttranslational regulation for asymmetric divisions and germline progression in plants and identified an unstable key protein that seems to be involved in regulating the stability of a spindle apparatus regulator(s).
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Affiliation(s)
- Martina Juranić
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
- Department of Molecular Biology, Faculty of Science and Mathematics, University of Zagreb, 10000 Zagreb, Croatia
| | | | - Nádia Graciele Krohn
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirao Preto 14040-903, Brazil
| | - Dunja Leljak-Levanić
- Department of Molecular Biology, Faculty of Science and Mathematics, University of Zagreb, 10000 Zagreb, Croatia
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
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Sanchez MDLP, Costas C, Sequeira-Mendes J, Gutierrez C. Regulating DNA replication in plants. Cold Spring Harb Perspect Biol 2012; 4:a010140. [PMID: 23209151 PMCID: PMC3504439 DOI: 10.1101/cshperspect.a010140] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chromosomal DNA replication in plants has requirements and constraints similar to those in other eukaryotes. However, some aspects are plant-specific. Studies of DNA replication control in plants, which have unique developmental strategies, can offer unparalleled opportunities of comparing regulatory processes with yeast and, particularly, metazoa to identify common trends and basic rules. In addition to the comparative molecular and biochemical studies, genomic studies in plants that started with Arabidopsis thaliana in the year 2000 have now expanded to several dozens of species. This, together with the applicability of genomic approaches and the availability of a large collection of mutants, underscores the enormous potential to study DNA replication control in a whole developing organism. Recent advances in this field with particular focus on the DNA replication proteins, the nature of replication origins and their epigenetic landscape, and the control of endoreplication will be reviewed.
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Affiliation(s)
- Maria de la Paz Sanchez
- Centro de Biologia Molecular "Severo Ochoa," CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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17
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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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18
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Costas C, Sanchez MDLP, Sequeira-Mendes J, Gutierrez C. Progress in understanding DNA replication control. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:203-9. [PMID: 21763530 DOI: 10.1016/j.plantsci.2011.04.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/07/2011] [Accepted: 04/24/2011] [Indexed: 05/19/2023]
Abstract
Completion of genome duplication during the S-phase of the cell cycle is crucial for the maintenance of genomic integrity. In eukaryotes, chromosomal DNA replication is accomplished by the activity of multiple origins of DNA replication scattered across the genome. Origin specification, selection and activity as well as the availability of replication factors and the regulation of DNA replication licensing, have unique and common features among eukaryotes. Although the initial studies on the semiconservative nature of chromosome duplication were carried out in the mid 1950s in Vicia faba, since then plant DNA replication studies have been scarce. However, they have received an unprecedented drive in the last decade after the completion of sequencing the Arabidopsis thaliana genome, and more recently of other plant genomes. In particular, the past year has witnessed major advances with the use of genomic approaches to study chromosomal replication timing, DNA replication origins and licensing control mechanisms. In this minireview article we discuss these recent discoveries in plants in the context of what is known at the genomic level in other eukaryotes. These studies constitute the basis for addressing in the future key questions about replication origin specification and function that will be of relevance not only for plants but also for the rest of multicellular organisms.
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Affiliation(s)
- Celina Costas
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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19
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Dang HQ, Tran NQ, Gill SS, Tuteja R, Tuteja N. A single subunit MCM6 from pea promotes salinity stress tolerance without affecting yield. PLANT MOLECULAR BIOLOGY 2011; 76:19-34. [PMID: 21365356 DOI: 10.1007/s11103-011-9758-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 02/17/2011] [Indexed: 05/18/2023]
Abstract
The eukaryotic pre-replicative complex (Pre-RC), including heterohexameric minichromosome maintenance (MCM2-7) proteins, ensures that the DNA in genome is replicated only once per cell division cycle. The MCMs provide DNA unwinding function during the DNA replication. Since MCM proteins play essential role in cell division and most likely are affected during stress conditions therefore their overexpression in plants may help in stress tolerance. But the role of MCMs in abiotic stress tolerance in plants has not been reported so far. In this study we report that: a) the MCM6 transcript is upregulated in pea plant in response to high salinity and cold stress and not with ABA, drought and heat stress; b) MCM6 overexpression driven by a constitutive cauliflower mosaic virus-35S promoter in tobacco plants confers salinity tolerance. The T(1) transgenics plants were able to grow to maturity and set normal viable seeds under continuous salinity stress, without yield penalty. It was observed that in salt-grown T(1) transgenic plants the Na(+) ions is mostly accumulated in mature leaves and not in seeds of T(1) transgenic lines as compared with the wild-type (WT) plants. T(1) transgenic plants exhibited better growth status under salinity stress conditions in comparison to WT plants. Furthermore, the T(1) transgenic plants maintained significantly higher levels of leaf chlorophyll content, net photosynthetic rate and therefore higher dry matter accumulation and yield with 200 mM NaCl as compared to the WT plants. Tolerance index data showed better salt tolerance potential of T(1) transgenic plants in comparison to WT. These findings provide first direct evidence that overexpression of single subunit MCM6 confers salinity stress tolerance without yield loss. The possible mechanism of salinity tolerance is discussed. These findings suggest that DNA replication machinery can be exploited for promoting stress tolerance in crop plants.
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Affiliation(s)
- Hung Quang Dang
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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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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22
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Ni DA, Sozzani R, Blanchet S, Domenichini S, Reuzeau C, Cella R, Bergounioux C, Raynaud C. The Arabidopsis MCM2 gene is essential to embryo development and its over-expression alters root meristem function. THE NEW PHYTOLOGIST 2009; 184:311-322. [PMID: 19650778 DOI: 10.1111/j.1469-8137.2009.02961.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
* Minichromosome maintenance (MCM) proteins are subunits of the pre-replication complex that probably function as DNA helicases during the S phase of the cell cycle. Here, we investigated the function of AtMCM2 in Arabidopsis. * To gain an insight into the function of AtMCM2, we combined loss- and gain-of-function approaches. To this end, we analysed two null alleles of AtMCM2, and generated transgenic plants expressing AtMCM2 downstream of the constitutive 35S promoter. * Disruption of AtMCM2 is lethal at a very early stage of embryogenesis, whereas its over-expression results in reduced growth and inhibition of endoreduplication. In addition, over-expression of AtMCM2 induces the formation of additional initials in the columella root cap. In the plt1,2 mutant, defective for root apical meristem maintenance, over-expression of AtMCM2 induces lateral root initiation close to the root tip, a phenotype not reported in the wild-type or in plt1,2 mutants, even when cell cycle regulators, such as AtCYCD3;1, were over-expressed. * Taken together, our results provide evidence for the involvement of AtMCM2 in DNA replication, and suggest that it plays a crucial role in root meristem function.
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Affiliation(s)
- Di An Ni
- Institut de Biotechnologie des Plantes (UMR8618), Université Paris-XI, 91405 Orsay, France
| | - Rosangela Sozzani
- Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Sophie Blanchet
- Institut de Biotechnologie des Plantes (UMR8618), Université Paris-XI, 91405 Orsay, France
| | - Séverine Domenichini
- Institut de Biotechnologie des Plantes (UMR8618), Université Paris-XI, 91405 Orsay, France
| | - Christophe Reuzeau
- CropDesign N.V.-a BASF Plant Science Company, Technologiepark 3, B-9052 Gent, Belgium
| | - Rino Cella
- Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Catherine Bergounioux
- Institut de Biotechnologie des Plantes (UMR8618), Université Paris-XI, 91405 Orsay, France
| | - Cécile Raynaud
- Institut de Biotechnologie des Plantes (UMR8618), Université Paris-XI, 91405 Orsay, France
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Shultz RW, Lee TJ, Allen GC, Thompson WF, Hanley-Bowdoin L. Dynamic localization of the DNA replication proteins MCM5 and MCM7 in plants. PLANT PHYSIOLOGY 2009; 150:658-69. [PMID: 19357199 PMCID: PMC2689970 DOI: 10.1104/pp.109.136614] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 04/02/2009] [Indexed: 05/21/2023]
Abstract
Genome integrity in eukaryotes depends on licensing mechanisms that prevent loading of the minichromosome maintenance complex (MCM2-7) onto replicated DNA during S phase. Although the principle of licensing appears to be conserved across all eukaryotes, the mechanisms that control it vary, and it is not clear how licensing is regulated in plants. In this work, we demonstrate that subunits of the MCM2-7 complex are coordinately expressed during Arabidopsis (Arabidopsis thaliana) development and are abundant in proliferating and endocycling tissues, indicative of a role in DNA replication. We show that endogenous MCM5 and MCM7 proteins are localized in the nucleus during G1, S, and G2 phases of the cell cycle and are released into the cytoplasmic compartment during mitosis. We also show that MCM5 and MCM7 are topologically constrained on DNA and that the MCM complex is stable under high-salt conditions. Our results are consistent with a conserved replicative helicase function for the MCM complex in plants but not with the idea that plants resemble budding yeast by actively exporting the MCM complex from the nucleus to prevent unauthorized origin licensing and rereplication during S phase. Instead, our data show that, like other higher eukaryotes, the MCM complex in plants remains in the nucleus throughout most of the cell cycle and is only dispersed in mitotic cells.
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Affiliation(s)
- Randall W Shultz
- Department of Molecular and Structural Biochemistry , North Carolina State University, Raleigh, North Carolina 27695-7651, USA.
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Positive regulation of minichromosome maintenance gene expression, DNA replication, and cell transformation by a plant retinoblastoma gene. Proc Natl Acad Sci U S A 2009; 106:4042-7. [PMID: 19234120 DOI: 10.1073/pnas.0813329106] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Retinoblastoma-related (RBR) genes inhibit the cell cycle primarily by repressing adenovirus E2 promoter binding factor (E2F) transcription factors, which drive the expression of numerous genes required for DNA synthesis and cell cycle progression. The RBR-E2F pathway is conserved in plants, but cereals such as maize are characterized by having a complex RBR gene family with at least 2 functionally distinct members, RBR1 and RBR3. Although RBR1 has a clear cell cycle inhibitory function, it is not known whether RBR3 has a positive or negative role. By uncoupling RBR3 from the negative regulation of RBR1 in cultured maize embryos through a combination of approaches, we demonstrate that RBR3 has a positive and critical role in the expression of E2F targets required for the initiation of DNA synthesis, DNA replication, and the efficiency with which transformed plants can be obtained. Titration of endogenous RBR3 activity through expression of a dominant-negative allele with a compromised pocket domain suggests that these RBR3 functions require an activity distinct from its pocket domain. Our results indicate a cell cycle pathway in maize, in which 2 RBR genes have specific and opposing functions. Thus, the paradigm that RBR genes are negative cell cycle regulators cannot be considered universal.
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Cho JH, Kim HB, Kim HS, Choi SB. Identification and characterization of a rice MCM2 homologue required for DNA replication. BMB Rep 2008; 41:581-6. [PMID: 18755073 DOI: 10.5483/bmbrep.2008.41.8.581] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The pre-replication complex (pre-RC), including the core hexameric MCM2-7 complex, ensures that the eukaryotic genome is replicated only once per cell division cycle. In this study, we identified a rice minichromosome maintenance (MCM) homologue (OsMCM2) that functionally complemented fission yeast MCM2 (CDC19) mutants. We found OsMCM2 transcript expression in roots, leaves, and seeds, although expression levels differed slightly among the organs. Likewise, the OsMCM2 protein was ubiquitously expressed, but it was downregulated when nutritients were limiting, indicating that MCM2 expression (and therefore cell cycle progression) requires adequate nutrition. Yeast two-hybrid and GST pull-down assays demonstrated that OsMCM2 interacted with the COP9 signalosome 5 (CSN5). Taken as a whole, our results indicated that OsMCM2 functions as a subunit of the rice MCM complex and interacts with CSN5 during developmental regulation.
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Affiliation(s)
- Jae Han Cho
- Department of Biological Sciences, Myongji University, Yongin, Korea
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Masuda HP, Cabral LM, De Veylder L, Tanurdzic M, de Almeida Engler J, Geelen D, Inzé D, Martienssen RA, Ferreira PCG, Hemerly AS. ABAP1 is a novel plant Armadillo BTB protein involved in DNA replication and transcription. EMBO J 2008; 27:2746-56. [PMID: 18818695 DOI: 10.1038/emboj.2008.191] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2008] [Accepted: 09/01/2008] [Indexed: 12/20/2022] Open
Abstract
In multicellular organisms, organogenesis requires a tight control of the balance between cell division and cell differentiation. Distinct signalling pathways that connect both cellular processes with developmental cues might have evolved to suit different developmental plans. Here, we identified and characterized a novel protein that interacts with pre-replication complex (pre-RC) subunits, designated Armadillo BTB Arabidopsis protein 1 (ABAP1). Overexpression of ABAP1 in plants limited mitotic DNA replication and decreased cell proliferation in leaves, whereas ABAP1 downregulation increased cell division rates. Activity of ABAP1 in transcription was supported by its association with the transcription factor AtTCP24. The ABAP1-AtTCP24 complex bound specifically to the promoters of AtCDT1a and AtCDT1b in vitro and in vivo. Moreover, expression levels of AtCDT1a and AtCDT1b were reduced in ABAP1-overexpressing plants and they were increased in plants with reduced levels of ABAP1. We propose that ABAP1 participates in a negative feedback loop regulating mitotic DNA replication during leaf development, either by repressing transcription of pre-RC genes and possibly by regulating pre-RC utilization through direct association with pre-RC components.
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Affiliation(s)
- Hana Paula Masuda
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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In vitro fertilization: analysis of early post-fertilization development using cytological and molecular techniques. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s00497-007-0060-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Shultz RW, Tatineni VM, Hanley-Bowdoin L, Thompson WF. Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice. PLANT PHYSIOLOGY 2007; 144:1697-714. [PMID: 17556508 PMCID: PMC1949880 DOI: 10.1104/pp.107.101105] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 05/29/2007] [Indexed: 05/15/2023]
Abstract
Core DNA replication proteins mediate the initiation, elongation, and Okazaki fragment maturation functions of DNA replication. Although this process is generally conserved in eukaryotes, important differences in the molecular architecture of the DNA replication machine and the function of individual subunits have been reported in various model systems. We have combined genome-wide bioinformatic analyses of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) with published experimental data to provide a comprehensive view of the core DNA replication machinery in plants. Many components identified in this analysis have not been studied previously in plant systems, including the GINS (go ichi ni san) complex (PSF1, PSF2, PSF3, and SLD5), MCM8, MCM9, MCM10, NOC3, POLA2, POLA3, POLA4, POLD3, POLD4, and RNASEH2. Our results indicate that the core DNA replication machinery from plants is more similar to vertebrates than single-celled yeasts (Saccharomyces cerevisiae), suggesting that animal models may be more relevant to plant systems. However, we also uncovered some important differences between plants and vertebrate machinery. For example, we did not identify geminin or RNASEH1 genes in plants. Our analyses also indicate that plants may be unique among eukaryotes in that they have multiple copies of numerous core DNA replication genes. This finding raises the question of whether specialized functions have evolved in some cases. This analysis establishes that the core DNA replication machinery is highly conserved across plant species and displays many features in common with other eukaryotes and some characteristics that are unique to plants.
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Affiliation(s)
- Randall W Shultz
- Department of Plant Biology , North Carolina State University, Raleigh, North Carolina 27695, USA
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