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Greenberg A, Simon I. S Phase Duration Is Determined by Local Rate and Global Organization of Replication. BIOLOGY 2022; 11:718. [PMID: 35625446 PMCID: PMC9139170 DOI: 10.3390/biology11050718] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022]
Abstract
The duration of the cell cycle has been extensively studied and a wide degree of variability exists between cells, tissues and organisms. However, the duration of S phase has often been neglected, due to the false assumption that S phase duration is relatively constant. In this paper, we describe the methodologies to measure S phase duration, summarize the existing knowledge about its variability and discuss the key factors that control it. The local rate of replication (LRR), which is a combination of fork rate (FR) and inter-origin distance (IOD), has a limited influence on S phase duration, partially due to the compensation between FR and IOD. On the other hand, the organization of the replication program, specifically the amount of replication domains that fire simultaneously and the degree of overlap between the firing of distinct replication timing domains, is the main determinant of S phase duration. We use these principles to explain the variation in S phase length in different tissues and conditions.
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Affiliation(s)
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel;
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2
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Sequeira-Mendes J, Gutierrez C. Links between genome replication and chromatin landscapes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:38-51. [PMID: 25847096 DOI: 10.1111/tpj.12847] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/27/2015] [Accepted: 04/01/2015] [Indexed: 05/07/2023]
Abstract
Post-embryonic organogenesis in plants requires the continuous production of cells in the organ primordia, their expansion and a coordinated exit to differentiation. Genome replication is one of the most important processes that occur during the cell cycle, as the maintenance of genomic integrity is of primary relevance for development. As it is chromatin that must be duplicated, a strict coordination occurs between DNA replication, the deposition of new histones, and the introduction of histone modifications and variants. In turn, the chromatin landscape affects several stages during genome replication. Thus, chromatin accessibility is crucial for the initial stages and to specify the location of DNA replication origins with different chromatin signatures. The chromatin landscape also determines the timing of activation during the S phase. Genome replication must occur fully, but only once during each cell cycle. The re-replication avoidance mechanisms rely primarily on restricting the availability of certain replication factors; however, the presence of specific histone modifications are also revealed as contributing to the mechanisms that avoid re-replication, in particular for heterochromatin replication. We provide here an update of genome replication mostly focused on data from Arabidopsis, and the advances that genomic approaches are likely to provide in the coming years. The data available, both in plants and animals, point to the relevance of the chromatin landscape in genome replication, and require a critical evaluation of the existing views about the nature of replication origins, the mechanisms of origin specification and the relevance of epigenetic modifications for genome replication.
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Affiliation(s)
- Joana Sequeira-Mendes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain
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3
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Raynaud C, Mallory AC, Latrasse D, Jégu T, Bruggeman Q, Delarue M, Bergounioux C, Benhamed M. Chromatin meets the cell cycle. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2677-89. [PMID: 24497647 DOI: 10.1093/jxb/ert433] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
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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4
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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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5
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Símová I, Herben T. Geometrical constraints in the scaling relationships between genome size, cell size and cell cycle length in herbaceous plants. Proc Biol Sci 2012; 279:867-75. [PMID: 21881135 PMCID: PMC3259922 DOI: 10.1098/rspb.2011.1284] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 08/08/2011] [Indexed: 12/15/2022] Open
Abstract
Plant nuclear genome size (GS) varies over three orders of magnitude and is correlated with cell size and growth rate. We explore whether these relationships can be owing to geometrical scaling constraints. These would produce an isometric GS-cell volume relationship, with the GS-cell diameter relationship with the exponent of 1/3. In the GS-cell division relationship, duration of processes limited by membrane transport would scale at the 1/3 exponent, whereas those limited by metabolism would show no relationship. We tested these predictions by estimating scaling exponents from 11 published datasets on differentiated and meristematic cells in diploid herbaceous plants. We found scaling of GS-cell size to almost perfectly match the prediction. The scaling exponent of the relationship between GS and cell cycle duration did not match the prediction. However, this relationship consists of two components: (i) S phase duration, which depends on GS, and has the predicted 1/3 exponent, and (ii) a GS-independent threshold reflecting the duration of the G1 and G2 phases. The matches we found for the relationships between GS and both cell size and S phase duration are signatures of geometrical scaling. We propose that a similar approach can be used to examine GS effects at tissue and whole plant levels.
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Affiliation(s)
- Irena Símová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Praha 2, Czech Republic.
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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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7
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Abstract
Mutation rates vary significantly within the genome and across species. Recent studies revealed a long suspected replication-timing effect on mutation rate, but the mechanisms that regulate the increase in mutation rate as the genome is replicated remain unclear. Evidence is emerging, however, that DNA repair systems, in general, are less efficient in late replicating heterochromatic regions compared to early replicating euchromatic regions of the genome. At the same time, mutation rates in both vertebrates and invertebrates have been shown to vary with generation time (GT). GT is correlated with genome size, which suggests a possible nucleotypic effect on species-specific mutation rates. These and other observations all converge on a role for DNA replication checkpoints in modulating generation times and mutation rates during the DNA synthetic phase (S phase) of the cell cycle. The following will examine the potential role of the intra-S checkpoint in regulating cell cycle times (GT) and mutation rates in eukaryotes. This article was published online on August 5, 2011. An error was subsequently identified. This notice is included in the online and print versions to indicate that both have been corrected October 4, 2011.
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Affiliation(s)
- John Herrick
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada.
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8
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Bryant JA, Aves SJ. Initiation of DNA replication: functional and evolutionary aspects. ANNALS OF BOTANY 2011; 107:1119-26. [PMID: 21508040 PMCID: PMC3091809 DOI: 10.1093/aob/mcr075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND The initiation of DNA replication is a very important and highly regulated step in the cell division cycle. It is of interest to compare different groups of eukaryotic organisms (a) to identify the essential molecular events that occur in all eukaryotes, (b) to start to identify higher-level regulatory mechanisms that are specific to particular groups and (c) to gain insights into the evolution of initiation mechanisms. SCOPE This review features a wide-ranging literature survey covering replication origins, origin recognition and usage, modification of origin usage (especially in response to plant hormones), assembly of the pre-replication complex, loading of the replisome, genomics, and the likely origin of these mechanisms and proteins in Archaea. CONCLUSIONS In all eukaryotes, chromatin is organized for DNA replication as multiple replicons. In each replicon, replication is initiated at an origin. With the exception of those in budding yeast, replication origins, including the only one to be isolated so far from a plant, do not appear to embody a specific sequence; rather, they are AT-rich, with short tracts of locally bent DNA. The proteins involved in initiation are remarkably similar across the range of eukaryotes. Nevertheless, their activity may be modified by plant-specific mechanisms, including regulation by plant hormones. The molecular features of initiation are seen in a much simpler form in the Archaea. In particular, where eukaryotes possess a number of closely related proteins that form 'hetero-complexes' (such as the origin recognition complex and the MCM complex), archaeans typically possess one type of protein (e.g. one MCM) that forms a homo-complex. This suggests that several eukaryotic initiation proteins have evolved from archaeal ancestors by gene duplication and divergence.
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Affiliation(s)
- John A Bryant
- Biosciences, College of Life and Environmental Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK.
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9
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Lipavská H, Masková P, Vojvodová P. Regulatory dephosphorylation of CDK at G₂/M in plants: yeast mitotic phosphatase cdc25 induces cytokinin-like effects in transgenic tobacco morphogenesis. ANNALS OF BOTANY 2011; 107:1071-86. [PMID: 21339187 PMCID: PMC3091802 DOI: 10.1093/aob/mcr016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/02/2010] [Accepted: 12/03/2010] [Indexed: 05/07/2023]
Abstract
BACKGROUND During the last three decades, the cell cycle and its control by cyclin-dependent kinases (CDKs) have been extensively studied in eukaryotes. This endeavour has produced an overall picture that basic mechanisms seem to be largely conserved among all eukaryotes. The intricate regulation of CDK activities includes, among others, CDK activation by CDC25 phosphatase at G₂/M. In plants, however, studies of this regulation have lagged behind as a plant Cdc25 homologue or other unrelated phosphatase active at G₂/M have not yet been identified. SCOPE Failure to identify a plant mitotic CDK activatory phosphatase led to characterization of the effects of alien cdc25 gene expression in plants. Tobacco, expressing the Schizosaccharomyces pombe mitotic activator gene, Spcdc25, exhibited morphological, developmental and biochemical changes when compared with wild type (WT) and, importantly, increased CDK dephosphorylation at G₂/M. Besides changes in leaf shape, internode length and root development, in day-neutral tobacco there was dramatically earlier onset of flowering with a disturbed acropetal floral capacity gradient typical of WT. In vitro, de novo organ formation revealed substantially earlier and more abundant formation of shoot primordia on Spcdc25 tobacco stem segments grown on shoot-inducing media when compared with WT. Moreover, in contrast to WT, stem segments from transgenic plants formed shoots even without application of exogenous growth regulator. Spcdc25-expressing BY-2 cells exhibited a reduced mitotic cell size due to a shortening of the G₂ phase together with high activity of cyclin-dependent kinase, NtCDKB1, in early S-phase, S/G₂ and early M-phase. Spcdc25-expressing tobacco ('Samsun') cell suspension cultures showed a clustered, more circular, cell phenotype compared with chains of elongated WT cells, and increased content of starch and soluble sugars. Taken together, Spcdc25 expression had cytokinin-like effects on the characteristics studied, although determination of endogenous cytokinin levels revealed a dramatic decrease in Spcdc25 transgenics. CONCLUSIONS The data gained using the plants expressing yeast mitotic activator, Spcdc25, clearly argue for the existence and importance of activatory dephosphorylation at G₂/M transition and its interaction with cytokinin signalling in plants. The observed cytokinin-like effects of Spcdc25 expression are consistent with the concept of interaction between cell cycle regulators and phytohormones during plant development. The G₂/M control of the plant cell cycle, however, remains an elusive issue as doubts persist about the mode of activatory dephosphorylation, which in other eukaryotes is provided by Cdc25 phosphatase serving as a final all-or-nothing mitosis regulator.
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Affiliation(s)
- Helena Lipavská
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Viničná 5, Prague 2, Czech Republic.
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11
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Grant WF, Owens ET. Lycopersicon assays of chemical/radiation genotoxicity for the study of environmental mutagens. Mutat Res 2002; 511:207-37. [PMID: 12088718 DOI: 10.1016/s1383-5742(02)00011-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
From a literature survey, 21 chemicals are tabulated that have been evaluated in 39 assays for their clastogenic effects in Lycopersicon. Nineteen of the 21 chemicals are reported as giving a positive reaction (i.e. causing chromosome aberrations). Of these, five are reported positive with a dose response. In addition, 23 assays have been recorded for six types of radiation, all of which reacted positively. The results of 102 assays with 32 chemicals and seven types of radiation tested for the induction of gene mutations are tabulated, as well as 20 chemicals and/or radiation in combined treatments. The Lycopersicon esculentum (2n=24) assay is a very good plant bioassay for assessing chromosome damage both in mitosis and meiosis and for somatic mutations induced by chemicals and radiations. The Lycopersicon bioassay has been shown to be as sensitive and as specific an assay as other plant genotoxicity assays, such as Hordeum vulgare, Vicia faba, Crepis capillaris, Pisum sativum and Allium cepa and should be considered in further studies in assessing clastogenicity. Tests using L. esculentum can be made for a spectrum of mutant phenotypes of which many are identifiable in young seedlings.
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Affiliation(s)
- William F Grant
- Department of Plant Science, P.O. Box 4000, McGill University, Macdonald Campus, Ste. Anne de Bellevue, Que., Canada H9X 3V9
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12
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Abstract
From a literature survey, 117 chemicals are tabulated that have been assayed in 179 assays for their clastogenic effects in Pisum. Of the 117 chemicals that have been assayed, 65 are reported at giving a positive reaction (i.e. causing chromosome aberrations), 30 positive with a dose response, five borderline positive. Seventeen chemicals gave a negative response. Eighty-one percent of the chemicals gave a definite positive response. A c-mitotic effect was detected from treatment with 17 chemicals. In addition to the above tabulation of chemicals, 39 chemicals have been reported with an antimitotic effect. Thirteen assays have been recorded for five types of radiation, which with the exception of ultrasound reacted positively. The results of assays with 38 chemicals and/or radiations in combined treatments, as well as 15 chemicals and three types of radiations that induce somatic mutations are tabulated. The Pisum sativum (2n=14) bioassay has been shown to be a very good plant bioassay for assessing chromosome damage both in mitosis and meiosis for somatic mutations induced by chemicals, radiations, and environmental pollutants. For some chemicals, the Pisum assay is not as sensitive in assessing clastogenicity as the Allium assay, although this should be considered in relative terms. Pisum fulvum (2n=14) has been used in clastogenic studies also, but to a much lesser extent.
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Affiliation(s)
- W F Grant
- Department of Plant Science, Macdonald Campus of McGill University, P.O. Box 4000, Ste. Anne de Bellevue, Que., Canada H9X 3V9.
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13
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Abstract
The aim of this review is to discuss the molecular controls of the cell cycle in relation to higher plant development. An analysis is made of the current models of the cell cycle based on the biochemistry and genetics of the budding yeast, Saccharomyces cerevisiae and the fission yeast, Schizosaccharomyces pombe. What emerges are universal mechanisms observed in a wide range of taxonomic groups involving a group of protein kinases which regulate the transition from both post-synthetic interphase (G2) to mitosis and from pre-synthetic interphase (G1) to DNA synthetic-(S) phase. The data are consistent in showing the activity of protein kinase complexes operating in conjunction with at least one dephosphorylating enzyme. The natural substrate(s) for the key cell division cycle gene product, p34cdc 2 , has yet to be resolved although the nuclear lamins and microtubular apparatus are strong candidates. These models serve as a basis for assessing the cell cycle in higher plants. Mitosis and various stages of nuclear DNA replication are considered in relation to the presumed initiation and termination factors that regulate these events. In order to make a link between the cell cycle and plant development special consideration has been given to plant meristems. In particular, the activity of the cell cycle in cells that have the capacity to regenerate whole tissue systems ('stem cells') within the meristem is discussed. In the root meristem, the quiescent centre cells conform to a stem cell population; a non-cycling stem cell may be immune to the morphogenetic signals that cause cycling cells to arrest and differentiate. The pericycle may act as a vestigial stem cell population. The shoot apex is also discussed in relation to both vegetative and floral growth. Although gradients of cell division exist in shoot meristems it is far less obvious where 'stem', or founder, cells reside in the apex. The way in which the cell cycle shortens on transition to floral growth is considered critical for identifying when the meristem becomes florally determined. Temperature and toxic metals are given special attention where it is emphasized that G1 phase becomes protracted when plants are stressed. Species that can tolerate stressful environments may have meristems in which a greater number of cells are competent for division. Finally, the cell cycle in vitro is discussed in relation to rapid changes in gene expression which are linked to the transition from G1 to S phase. The latter emerges as a key cell cycle transition for plant meristems both in vivo and in vitro. CONTENTS Summary 1 I. Introduction 2 II. The cell division cycle (cdc) genes 2 III. The plant cell cycle 5 IV. Meristems 9 V. Effects of external stress on the cell cycle in plant meristems 14 VI. The plant cell cycle in vitro 15 VII. Conclusions 15 Acknowledgements 16 References 16.
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Affiliation(s)
- Dennis Francis
- School of Pure and Applied Biology, University of Wales College of Cardiff, P.O. Box 915, Cardiff CF1 3TL, UK
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14
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Ralston E, English J, Dooner HK. Chromosome-breaking structure in maize involving a fractured Ac element. Proc Natl Acad Sci U S A 1989; 86:9451-5. [PMID: 2556713 PMCID: PMC298514 DOI: 10.1073/pnas.86.23.9451] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chromosome breakage in maize can result from an interaction between certain transposable elements. When an Ac (Activator) element and a state I Ds (Dissociation) element are present together in the genome, either linked or unlinked, breaks occur regularly at the locus of the Ds element. We show here that breaks occur with high frequency at or near the locus of a structure consisting of a 2.5-kilobase (kb) terminally deleted or fractured Ac element very tightly linked to a second, intact 4.6-kb Ac element. This structure has the features of a macrotransposon and may behave like one. Loss of the tight linkage abolishes chromosome breakage. A model based on transposition of the macrotransposon is proposed to explain the chromosome-breaking properties of Ac and Ds.
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Affiliation(s)
- E Ralston
- DNA Plant Technology, Oakland, CA 94608
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15
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Kidd AD, Francis D, Bennett MD. Replicon size and rate of DNA replication fork movement are correlated in grasses. Exp Cell Res 1989; 184:262-7. [PMID: 2792227 DOI: 10.1016/0014-4827(89)90385-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In eukaryotes, most nuclear DNA replication proceeds bidirectionally from multiple origins of replication. A unit of DNA, replicated by two replication forks from a single origin, is termed a replicon. Using results from DNA fiber autoradiography we show a novel positive correlation between replicon size and the rate of replication fork movement in root meristem nuclei of 13 grass species. Although there is interspecific variation in replicon size, it is balanced by similar variation in the rate of replication fork progression.
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Affiliation(s)
- A D Kidd
- Department of Biology, University, Southampton, United Kingdom
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16
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Hernández P, Bjerknes CA, Lamm SS, Van't Hof J. Proximity of an ARS consensus sequence to a replication origin of pea (Pisum sativum). PLANT MOLECULAR BIOLOGY 1988; 10:413-422. [PMID: 24277589 DOI: 10.1007/bf00014947] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/1987] [Accepted: 01/12/1988] [Indexed: 06/02/2023]
Abstract
The replication origin (ori-r9) of the 9.0 kb rDNA repeats of pea (Pisum sativum, cv. Alaska) was cloned and found to reside in a 1.5 kb fragment of the non-transcribed spacer region located between the 25 S and 18 S genes. Labeled rDNA rich in replication forks, from cells positioned at the G1/S phase boundary, was used to map ori-r9 by hybridization procedures. Ori-r9 is in a 210-base fragment that is 1.6 kb from the 5' end of the 18 S gene and about 1.5 kb from the 3' end of the 25 S gene. The same procedures, using labeled synthetic ARS consensus sequence as a probe, showed than an ARS consensus sequence is located 3' to ori-r9 in a 710-base fragment. An ARS consensus sequence is, therefore, adjacent to ori-r9 but not coincidental with it.
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Affiliation(s)
- P Hernández
- Centro de Investigaciones Biológicas, C.S.I.C., Madrid, Spain
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17
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Dubey DD, Raman R. Factors influencing replicon organization in tissues having different S-phase durations in the mole rat, Bandicota bengalensis. Chromosoma 1987; 95:285-9. [PMID: 3622082 DOI: 10.1007/bf00294785] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In order to identify factors affecting the length of S-phase in mammals, DNA fibre autoradiograms from different tissues [bone marrow, phytohaemagglutinin (PHA)-stimulated spleen lymphocytes and whole body cells of new-borns] of the mole rat, Bandicota bengalensis, were examined for various parameters of replicon organization. The duration of S-phase in bone marrow and spleen was 12-14 h while that in new-borns was 8-9 h. Fork migration rate was significantly greater in new-borns than in bone marrow, and replicon size was significantly smaller in new-borns than in spleen. Thus it appears that several factors contribute, to varying degrees, in establishing the duration of S-phase in any cell type. In about 20% of the replicon clusters, constituent replicons were found to initiate replication asynchronously. This asynchronous initiation could possibly be due to an effect of transcription on time of initiation since it is likely that neighbouring replicons would be transcribed to different extents.
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18
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Hof JV, Hernandez P, Bjerknes CA, Kraszewska EK, Lamm SS. Replication of the rRNA and legumin genes in synchronized root cells of pea (Pisum sativum): evidence for transient EcoR I sites in replicating rRNA genes. PLANT MOLECULAR BIOLOGY 1987; 8:133-143. [PMID: 24301048 DOI: 10.1007/bf00025324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/1986] [Accepted: 08/29/1986] [Indexed: 06/02/2023]
Abstract
The temporal pattern of replication of the rRNA and legumin genes differs in synchronized pea root cells. The relative number of rRNA genes replicated hourly during the first five hours of S phase ranges between 5 and 10 percent. In late S phase, during hours six through nine, the number of rRNA genes replicated increases reaching a maximum of about 25 percent at the ninth hour. Unlike the rRNA genes, the legumin genes have a wave-like pattern of replication peaking in early S phase at the third hour and again in late S phase at the eighth hour.Replicating rDNA, isolated by benzoylated naphthoylated DEAE-column chromatography, has EcoR I restriction sites that are absent in non-replicating rDNA sequences. The cleavage of these sites is independent of the time of rDNA replication. The transient nature of the EcoR I sites suggests that they exist in a hemimethylated state in parental DNA.The two Hind III repeat-size classes of rDNA of var. Alaska peas are replicated simultaneously as cells progress through S phase. Thus, even if the 9.0 kb and 8.6 kb repeat classes are located on different chromosomes, their temporal order of replication is the same.
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Affiliation(s)
- J V Hof
- Biology Department, Brookhaven National Laboratory, 11973, Upton, NY, U.S.A
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Van't Hof J, Hernández P, Bjerknes CA, Lamm SS. Location of the replication origin in the 9-kb repeat size class of rDNA in pea (Pisum sativum). PLANT MOLECULAR BIOLOGY 1987; 9:87-95. [PMID: 24276898 DOI: 10.1007/bf00015641] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/1987] [Accepted: 04/10/1987] [Indexed: 06/02/2023]
Abstract
The replication origin of the 9-kb rDNA repeat size class of pea (Pisum sativum cv. Alaska) was identified by benzoylated naphthoylated DEAE-cellulose column chromatography and Southern blotting procedures. The origin is located at or near a 0.19-kb EcoR I fragment in the non-transcribed spacer region between the 25S and 18S rRNA genes. Identification of the origin was based on three criteria: (i) an enrichment of the 0.19-kb fragment in replicating rDNA from asynchronously dividing root meristematic cells, (ii) the scarcity of the 0.19-kb fragment in rDNA from non-dividing carbohydrate starved cells, and (iii) a 60-min periodic enrichment of the 0.19-kb fragment in replicating rDNA that temporally coincides with the sequential initiation of replication of replicon families in synchronized pea root cells.
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Affiliation(s)
- J Van't Hof
- Biology Department, Brookhaven National Laboratory, 11973, Upton, New York, USA
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Van't Hof J, Lamm SS, Bjerknes CA. Detection of replication initiation by a replicon family in DNA of synchronized pea (Pisum sativum) root cells using benzoylated naphthoylated DEAE-cellulose chromatography. PLANT MOLECULAR BIOLOGY 1987; 9:77-86. [PMID: 24276897 DOI: 10.1007/bf00015640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/1986] [Revised: 04/08/1987] [Accepted: 04/10/1987] [Indexed: 06/02/2023]
Abstract
Fractionated replicating DNA from pea was obtained from both synchronized cells just starting replication and from carbohydrate-starved cells ending replication. Benzoylated naphthoylated DEAE-cellulose chromatography of pulse-labeled DNA digested with EcoR I gave evidence that a family of replicons initiated replication 45 to 60 min after synchronized cells were released from the G1/S phase boundary. DNA from cells labeled in late S phase, on the other hand, showed no signs of additional replication initiations before entering G2 phase. Results with DNA from both early and late S phase cells comply with a model based on the premise that with short pulses of [(3)H]-thymidine the isotope is localized at replication forks and that longer pulses label both replication forks and recently replicated segments of double-stranded DNA. The model applies only to DNA subjected to fragmentation before chromatography.The results also suggest that benzoylated naphthoylated DEAE-cellulose chromatography is a useful means to isolate origins and replication forks from synchronized plant cells.
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Affiliation(s)
- J Van't Hof
- Biology Department, Brookhaven National Laboratory, 11973, Upton, New York, USA
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Sasaki K, Murakami T, Ogino T, Takahashi M, Kawasaki S. Flow cytometric estimation of cell cycle parameters using a monoclonal antibody to bromodeoxyuridine. CYTOMETRY 1986; 7:391-5. [PMID: 3089742 DOI: 10.1002/cyto.990070415] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
An estimation of cell kinetic parameters was made by simultaneous flow cytometric measurements of DNA and bromodeoxyuridine (BrdUrd) contents of cells. The procedure described in this paper involves the incorporation of BrdUrd by S phase cells, labeling the BrdUrd with an indirect immunofluorescent technique using a monoclonal anti-BrdUrd antibody, and staining DNA with propidium iodide (PI). The amount of incorporated BrdUrd in HeLa cells was proportional to that of synthesized DNA through S phase. For all cell lines examined, the pattern of BrdUrd incorporation was essentially the same and the rate of DNA synthesis during S phase was not constant. The bivariate BrdUrd/DNA distributions showed a horse-shoe pattern, maximum in the mid S phase and minimum in the early and late S phases. Furthermore, the durations of cell cycle (Tc) and S phase (Ts) were estimated from a FLSm (fraction of labeled cells in mid S phase) curve that was generated by plotting the percentage of BrdUrd pulse-labeled cells in a narrow window defined in the mid S phase of the DNA histogram. The values of these parameters in NIH 3T3, HeLa S3, and HL-60 cells were in good accordance with the reported data. This FCM method using the monoclonal anti-BrdUrd antibody allows rapid determination of both cell cycle compartments and also Ts and Tc without the use of radioactive DNA precursors.
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Francis D, Davies ND, Bryant JA, Hughes SG, Sibson DR, Fitchett PN. Effects of psoralen on replicon size and mean rate of DNA synthesis in partially synchronized cells of Pisum sativum L. Exp Cell Res 1985; 158:500-8. [PMID: 4007063 DOI: 10.1016/0014-4827(85)90473-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have examined by fibre autoradiography the spacing of replicons in pea root meristems during synchronized entry into S phase from arrest at the G1/S boundary. Pretreatment with the DNA cross-linking agent, psoralen, produces a marked shortening of replicon spacing, suggesting that premature arrest of the replication fork results in the recruitment of additional initiation points within a given replicon family. This is discussed in relation to models for the control of DNA replication.
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Schvartzman JB, Krimer DB, Van't Hof J. The effects of different thymidine concentrations on DNA replication in pea-root cells synchronized by a protracted 5-fluorodeoxyuridine treatment. Exp Cell Res 1984; 150:379-89. [PMID: 6229414 DOI: 10.1016/0014-4827(84)90581-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Single-cell and DNA fiber autoradiography, cytophotometry and velocity sedimentation in alkaline sucrose gradients were used to analyse DNA replication and nascent replicon maturation in 5-fluorodeoxyuridine (FUdR)-synchronized cells of Pisum sativum. The replicon size was not significantly changed by the protracted FUdR treatment. When the synchronized cells were released from the inhibitor, labeled with [3H]TdR for 30 min, and chased in medium containing 1 X 10(-6) M or lower concentrations of cold thymidine, DNA replication stopped after approx. 25% of the genome had replicated, and the nascent strands failed to grow above 9 - 12 X 10(6) D single-stranded (ss) DNA. When the cells were chased in medium with 1 X 10(-5) M cold thymidine, the DNA content of the labeled cells steadily increased with time and the size of the nascent molecules grew continuously until replicon size was achieved; then they were accumulated at replicon size until the cells arrived in late S or G2. When the FUdR-synchronized cells were chased in medium containing 1 X 10(-4) M cold thymidine, the size of the nascent strands increased continuously with time, indicating that some neighbouring nascent replicons were joined as soon as they completed their replication. These observations led us to postulate that in FUdR-synchronized cells the rates of chain elongation, cell progression through the S phase and nascent replicon maturation are controlled by thymidine availability.
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Abstract
The technique of fiber DNA measurement was used to study the possibility that the lengthening of the DNA "S" phase previously reported for mouse premeiotic spermatogonia was due to a reduced number of initiation sites. The mean replicon size of neonatal mouse preleptotene cells was similar to sizes reported for adult mouse somatic cells. A slow rate of DNA chain growth was observed in all cells from day 1 through days 10-12 of age. It was felt that the meiotic entry in male mouse germ cells may involve a slower replication fork rate and other factors which increased the time between activation and replication of replicon families.
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Replicon size and mean rate of DNA synthesis in rye (Secale cereale L. cv. Petkus Spring). Chromosoma 1982. [DOI: 10.1007/bf00330733] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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