Function of the Plant DNA Polymerase Epsilon in Replicative Stress Sensing, a Genetic Analysis

Pedroza-García, José-Antonio; Mazubert, Christelle; Olmo, Iván del; Bourge, Mickaël; Domenichini, Séverine; Bounon, Rémi; Tariq, Zakia; Delannoy, Étienne; Piñeiro, Manuel; Jarillo, José A.; Bergounioux, Catherine; Benhamed, Moussa; Raynaud, Cécile

doi:10.1104/pp.17.00031

Cited by 29 publications

(72 citation statements)

References 60 publications

(93 reference statements)

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“…In addition, lines deficient for the replicative DNA Pol ε showed the constitutive activation of DDR genes, including TK1a . In this context, TK1a activation was dependent upon SOG1 but not upon ATM (Pedroza‐Garcia et al ., ; Pedroza‐García et al ., ), indicating that both the ATR and the ATM branches of the DDR can trigger TK1a expression. In agreement with the previous findings, we found that TK1a expression was strongly induced when plants were exposed to genotoxic stress (Pedroza‐García et al ., ), whereas expression of TK1b did not seem to vary much in response to genotoxic stress.…”

Section: Discussionmentioning

confidence: 98%

Role of pyrimidine salvage pathway in the maintenance of organellar and nuclear genome integrity

et al. 2018

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Summary Nucleotide biosynthesis proceeds through a de novo pathway and a salvage route. In the salvage route, free bases and/or nucleosides are recycled to generate the corresponding nucleotides. Thymidine kinase (TK) is the first enzyme in the salvage pathway to recycle thymidine nucleosides as it phosphorylates thymidine to yield thymidine monophosphate. The Arabidopsis genome contains two TK genes −TK1a and TK1b− that show similar expression patterns during development. In this work, we studied the respective roles of the two genes during early development and in response to genotoxic agents targeting the organellar or the nuclear genome. We found that the pyrimidine salvage pathway is crucial for chloroplast development and genome replication, as well as for the maintenance of its integrity, and is thus likely to play a crucial role during the transition from heterotrophy to autotrophy after germination. Interestingly, defects in TK activity could be partially compensated by supplementation of the medium with sugar, and this effect resulted from both the availability of a carbon source and the activation of the nucleotide de novo synthesis pathway, providing evidence for a compensation mechanism between two routes of nucleotide biosynthesis that depend on nutrient availability. Finally, we found differential roles of the TK1a and TK1b genes during the plant response to genotoxic stress, suggesting that different pools of nucleotides exist within the cells and are required to respond to different types of DNA damage. Altogether, our results highlight the importance of the pyrimidine salvage pathway, both during plant development and in response to genotoxic stress.

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Section: Discussionmentioning

confidence: 98%

Role of pyrimidine salvage pathway in the maintenance of organellar and nuclear genome integrity

et al. 2018

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“…A last class of pol2a-12 upregulated PCGs (174), neither marked by H3K27me3 nor upregulated in atxr5/6, was enriched for genes involved in biological processes related to cell proliferation, cell cycle and homologous recombination (tab S2). Elevated rates of homologous recombination and increased S-phase length were reported in pol2a-8 mutants (15,40). We conclude that PCG upregulation in pol2a-12 mostly results from decreased H3K27me3 levels, constitutive replicative stress and disturbed cell cycle progression.…”

Section: H3k27me3 and Disturbed Dna Replicationmentioning

confidence: 61%

“…This extends previous observations at the SOC1 and FT genes (24) and suggests that about half of PCG upregulation in pol2a-12 likely results from impaired PRC2-mediated H3K27me3 deposition at these loci. The pol2a-8 mutants show increased expression of DNA repair genes, which results from a state of constitutive replication stress (15,39,40). We found that DNA repair genes are also upregulated in pol2a-12, and noticeably, they are not marked by H3K27me3 in the WT (fig S2D), suggesting that these genes are not controlled by H3K27me3 and that their upregulation in pol2a-12 is likely triggered by constitutive replicative stress.…”

Section: H3k27me3 and Disturbed Dna Replicationmentioning

confidence: 68%

“…We also detected hypermethylation of CHG sites in plants treated with HU, which causes replication stress by depleting cellular dNTP pools. HU-induced replication stress activates the S-phase checkpoint, resembling pol2a mutants where it is constitutively activated (40,54). The replication-stress response is mediated by the ATM-and Rad3-related (ATR) kinase, while ATAXIA TELANGIECTASIA MUTATED (ATM) is required for the response to double-strand breaks (DSBs) (55).…”

Section: Discussionmentioning

confidence: 99%

“…Both ATXR5/6 and POL2A function at DNA replication, and their mutations are associated with constitutive activation of the DNA damage response (10,15,40,41). We determined the atxr5/6 methylome in young (13-day-old) seedlings as we did for pol2a and found that atxr5/6 mutants also exhibited increased methylation at CHG sites, although to a lesser extent than in pol2a (fig 6A), a conclusion that was supported by re-analyzing previously published atxr5/6 methylome data generated from different tissues (3-week-old rosette leaves) ( fig S9A).…”

Section: Impairing Dna Replication Generally Triggers Chg Dna Hypermementioning

confidence: 99%

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DNA polymerase epsilon is a central coordinator of heterochromatin structure and function in Arabidopsis

Bourguet

López-González

Gómez-Zambrano

et al. 2020

Preprint

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BackgroundChromatin organizes the DNA molecule and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications must be faithfully passed on to daughter strands. There is evidence that DNA polymerases play a role in transcriptional silencing, but the extent of their contribution and how it relates to heterochromatin maintenance is unclear.ResultsWe isolate a strong hypomorphic Arabidopsis thaliana mutant of the POL2A catalytic subunit of DNA polymerase epsilon and show that POL2A is required to stabilize heterochromatin silencing genome wide, likely by preventing replicative stress. We reveal that POL2A inhibits DNA methylation and histone H3 lysine 9 methylation. Hence, release of heterochromatin silencing in POL2A deficient mutants paradoxically occurs in a chromatin context of increased level of these two repressive epigenetic marks. At the nuclear level, POL2A defect is associated with fragmentation of heterochromatin.ConclusionThese results indicate that POL2A is critical to secure both heterochromatin structure and function. We also reveal that unhindered replisome progression is required for the faithful propagation of DNA methylation through the cell cycle.

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Comprehensive Transcriptome Analysis of Arabidopsis thaliana DNA Polymerase Epsilon Catalytic Subunit A and B Mutants

Wickramasuriya¹,

Hewavithana²,

Silva³

et al. 2023

Tropical Plant Biol.

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In Arabidopsis, the catalytic subunit of DNA polymerase ε (POLE) is encoded by two genes: DNA polymerase epsilon catalytic subunit A (AtPOL2A) and B (AtPOL2B). Although studies have shown AtPOL2A to be involved in various biological processes, the role of AtPOL2B remains to be determined.In the present study, leaf cDNA libraries of one AtPOL2A mutant (atpol2a-1) and three AtPOL2B mutants (atpol2b-1, -2 and -3) were sequenced using the Illumina platform. Analysis of gene expression profiles identified a total of 198, 76, 141 and 67 differentially expressed genes (DEGs) in atpol2a-1, atpol2b-1, atpol2b-2 and atpol2b-3, respectively. It was noted that the majority of pericentromeric transposable elements were transcriptionally active in atpol2a-1 as compared to atpol2b mutants and wild-type plants. Computational analysis of the proteins encoded by the DEGs identified CER1, Replication Protein A 1E (RPA1E) and AT5G60250 as potential interactors of AtPOL2A, and Pathogenesis-related gene 1 (PR1) and AT5G48490 as potential interactors of AtPOL2B. Interestingly, all these proteins showed a significant interaction with the POLE catalytic subunit of Saccharomyces cerevisiae. Furthermore, the in silico promoter analysis showed that the AtPOL2A promoter sequence is overrepresented with cis-acting regulatory elements associated with cell cycle regulation, meristematic/reproductive tissue-specific pattern of expression and MYB protein recognition, whereas the AtPOL2B promoter sequence was mainly enriched with stress-responsive elements; defense--2 -responsive elements were only detected in the AtPOL2B promoter. Our data support the idea that AtPOL2B may coexpress with stress-responsive genes. The findings of the present study begin to unravel the potential molecular interactors of AtPOL2 genes at the molecular level and suggest new avenues for future studies.

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Function of the Plant DNA Polymerase Epsilon in Replicative Stress Sensing, a Genetic Analysis

Cited by 29 publications

References 60 publications

Role of pyrimidine salvage pathway in the maintenance of organellar and nuclear genome integrity

Role of pyrimidine salvage pathway in the maintenance of organellar and nuclear genome integrity

DNA polymerase epsilon is a central coordinator of heterochromatin structure and function in Arabidopsis

Comprehensive Transcriptome Analysis of Arabidopsis thaliana DNA Polymerase Epsilon Catalytic Subunit A and B Mutants

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