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  1. Article ; Online: Chromatin dynamics and RNA metabolism are double-edged swords for the maintenance of plant genome integrity.

    Bergis-Ser, Clara / Reji, Meega / Latrasse, David / Bergounioux, Catherine / Benhamed, Moussa / Raynaud, Cécile

    Nature plants

    2024  

    Abstract: Maintenance of genome integrity is an essential process in all organisms. Mechanisms avoiding the formation of DNA lesions or mutations are well described in animals because of their relevance to human health and cancer. In plants, they are of growing ... ...

    Abstract Maintenance of genome integrity is an essential process in all organisms. Mechanisms avoiding the formation of DNA lesions or mutations are well described in animals because of their relevance to human health and cancer. In plants, they are of growing interest because DNA damage accumulation is increasingly recognized as one of the consequences of stress. Although the cellular response to DNA damage is mostly studied in response to genotoxic treatments, the main source of DNA lesions is cellular activity itself. This can occur through the production of reactive oxygen species as well as DNA processing mechanisms such as DNA replication or transcription and chromatin dynamics. In addition, how lesions are formed and repaired is greatly influenced by chromatin features and dynamics and by DNA and RNA metabolism. Notably, actively transcribed regions or replicating DNA, because they are less condensed and are sites of DNA processing, are more exposed to DNA damage. However, at the same time, a wealth of cellular mechanisms cooperate to favour DNA repair at these genomic loci. These intricate relationships that shape the distribution of mutations along the genome have been studied extensively in animals but much less in plants. In this Review, we summarize how chromatin dynamics influence lesion formation and DNA repair in plants, providing a comprehensive view of current knowledge and highlighting open questions with regard to what is known in other organisms.
    Language English
    Publishing date 2024-04-24
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2055-0278
    ISSN (online) 2055-0278
    DOI 10.1038/s41477-024-01678-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A conserved role for γ-tubulin as a regulator of E2F transcription factors.

    Raynaud, Cécile / Nisa, Maherun

    Journal of experimental botany

    2020  Volume 71, Issue 4, Page(s) 1199–1202

    MeSH term(s) Cell Cycle ; Cell Cycle Proteins ; E2F Transcription Factors ; Transcription Factors/genetics ; Tubulin
    Chemical Substances Cell Cycle Proteins ; E2F Transcription Factors ; Transcription Factors ; Tubulin
    Language English
    Publishing date 2020-02-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2976-2
    ISSN 1460-2431 ; 0022-0957
    ISSN (online) 1460-2431
    ISSN 0022-0957
    DOI 10.1093/jxb/erz557
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: CRUMPLED LEAF supports plastid OUTER ENVELOPE PROTEIN OF 80 KDA complex formation in Arabidopsis.

    Yoshimura, Ryo / Minamikawa, Syun / Suzuki, Takamasa / Goto, Kotaro / Latrasse, David / Sicar, Sanchari / Raynaud, Cécile / Benhamed, Moussa / Yoshioka, Yasushi

    Plant physiology

    2024  Volume 194, Issue 4, Page(s) 2422–2433

    Abstract: Embedded β-barrel proteins in the outer envelope membrane mediate most cellular trafficking between the cytoplasm and plastids. Although the TRANSLOCON AT THE OUTER ENVELOPE MEMBRANE OF CHLOROPLASTS 75-V (TOC75-V)/OUTER ENVELOPE PROTEIN OF 80 KDA (OEP80) ...

    Abstract Embedded β-barrel proteins in the outer envelope membrane mediate most cellular trafficking between the cytoplasm and plastids. Although the TRANSLOCON AT THE OUTER ENVELOPE MEMBRANE OF CHLOROPLASTS 75-V (TOC75-V)/OUTER ENVELOPE PROTEIN OF 80 KDA (OEP80) complex has been implicated in the insertion and assembly of β-barrel proteins in the outer envelope membrane of Arabidopsis (Arabidopsis thaliana) chloroplasts, relatively little is known about this process. CRUMPLED LEAF (CRL) encodes a chloroplast outer envelope membrane-localized protein, and its loss-of-function mutation results in pleiotropic defects, including altered plant morphogenesis, growth retardation, suppression of plastid division, and spontaneous light intensity-dependent localized cell death. A suppressor screen conducted on mutagenized crl mutants revealed that a missense mutation in OEP80 suppresses the pleiotropic defects of crl. Furthermore, we found that OEP80 complex formation is compromised in crl. Additionally, we demonstrated that CRL interacts with OEP80 in vivo and that a portion of CRL is present at the same molecular weight as the OEP80 complex. Our results suggest that CRL interacts with OEP80 to facilitate its complex formation. CRL is involved in plastid protein import; therefore, the pleiotropic defects in crl are likely due to the combined effects of decreased plastid protein import and altered membrane integration of β-barrel proteins in the outer envelope membrane. This study sheds light on the mechanisms that allow β-barrel protein integration into the plastid outer envelope membrane and the importance of this finding for plant cellular processes.
    MeSH term(s) Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Chloroplast Proteins/metabolism ; Chloroplasts/metabolism ; Membrane Proteins/metabolism ; Plastids/genetics ; Plastids/metabolism ; Protein Transport
    Chemical Substances Arabidopsis Proteins ; Chloroplast Proteins ; CRUMPLED LEAF protein, Arabidopsis ; Membrane Proteins ; OEP80 protein, Arabidopsis
    Language English
    Publishing date 2024-01-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 208914-2
    ISSN 1532-2548 ; 0032-0889
    ISSN (online) 1532-2548
    ISSN 0032-0889
    DOI 10.1093/plphys/kiae005
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  4. Article: DNA-Damaging Effectors: New Players in the Effector Arena

    Camborde, Laurent / Dumas, Bernard / Gaulin, Elodie / Raynaud, Cécile

    Trends in plant science. 2019 Dec., v. 24, no. 12

    2019  

    Abstract: In animal cells, nuclear DNA is the target of genotoxins produced by bacterial pathogens that cause genomic mutations eventually leading to apoptosis, senescence, and carcinogenic development. In response to the insult, the DNA damage response (DDR) is ... ...

    Abstract In animal cells, nuclear DNA is the target of genotoxins produced by bacterial pathogens that cause genomic mutations eventually leading to apoptosis, senescence, and carcinogenic development. In response to the insult, the DNA damage response (DDR) is activated to ensure lesion repair. Accumulation of DNA breaks is also detected in plants during microbial infection. In this opinion article we propose that phytopathogens can produce DNA-damaging effectors. The recent identification of a functional genotoxin in devastating eukaryotic plant pathogens, such as oomycetes, supports the concept that DNA-damaging effectors may contribute to pathogenicity. Additionally, this raises the question of how plants can perceive these damages and whether this perception can be connected to the plant immune system.
    Keywords apoptosis ; carcinogenicity ; DNA damage ; genomics ; immune system ; mutagens ; mutation ; nuclear genome ; Oomycetes ; pathogenicity ; plant pathogens
    Language English
    Dates of publication 2019-12
    Size p. 1094-1101.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1305448-x
    ISSN 1878-4372 ; 1360-1385
    ISSN (online) 1878-4372
    ISSN 1360-1385
    DOI 10.1016/j.tplants.2019.09.012
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: DNA-Damaging Effectors: New Players in the Effector Arena.

    Camborde, Laurent / Raynaud, Cécile / Dumas, Bernard / Gaulin, Elodie

    Trends in plant science

    2019  Volume 24, Issue 12, Page(s) 1094–1101

    Abstract: In animal cells, nuclear DNA is the target of genotoxins produced by bacterial pathogens that cause genomic mutations eventually leading to apoptosis, senescence, and carcinogenic development. In response to the insult, the DNA damage response (DDR) is ... ...

    Abstract In animal cells, nuclear DNA is the target of genotoxins produced by bacterial pathogens that cause genomic mutations eventually leading to apoptosis, senescence, and carcinogenic development. In response to the insult, the DNA damage response (DDR) is activated to ensure lesion repair. Accumulation of DNA breaks is also detected in plants during microbial infection. In this opinion article we propose that phytopathogens can produce DNA-damaging effectors. The recent identification of a functional genotoxin in devastating eukaryotic plant pathogens, such as oomycetes, supports the concept that DNA-damaging effectors may contribute to pathogenicity. Additionally, this raises the question of how plants can perceive these damages and whether this perception can be connected to the plant immune system.
    MeSH term(s) Animals ; Bacteria ; DNA ; Oomycetes ; Plant Diseases ; Plants ; Virulence
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2019-11-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1305448-x
    ISSN 1878-4372 ; 1360-1385
    ISSN (online) 1878-4372
    ISSN 1360-1385
    DOI 10.1016/j.tplants.2019.09.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions.

    Nisa, Maher-Un / Huang, Ying / Benhamed, Moussa / Raynaud, Cécile

    Frontiers in plant science

    2019  Volume 10, Page(s) 653

    Abstract: Maintenance of genome integrity is a key issue for all living organisms. Cells are constantly exposed to DNA damage due to replication or transcription, cellular metabolic activities leading to the production of Reactive Oxygen Species (ROS) or even ... ...

    Abstract Maintenance of genome integrity is a key issue for all living organisms. Cells are constantly exposed to DNA damage due to replication or transcription, cellular metabolic activities leading to the production of Reactive Oxygen Species (ROS) or even exposure to DNA damaging agents such as UV light. However, genomes remain extremely stable, thanks to the permanent repair of DNA lesions. One key mechanism contributing to genome stability is the DNA Damage Response (DDR) that activates DNA repair pathways, and in the case of proliferating cells, stops cell division until DNA repair is complete. The signaling mechanisms of the DDR are quite well conserved between organisms including in plants where they have been investigated into detail over the past 20 years. In this review we summarize the acquired knowledge and recent advances regarding the DDR control of cell cycle progression. Studying the plant DDR is particularly interesting because of their mode of development and lifestyle. Indeed, plants develop largely post-embryonically, and form new organs through the activity of meristems in which cells retain the ability to proliferate. In addition, they are sessile organisms that are permanently exposed to adverse conditions that could potentially induce DNA damage in all cell types including meristems. In the second part of the review we discuss the recent findings connecting the plant DDR to responses to biotic and abiotic stresses.
    Language English
    Publishing date 2019-05-17
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2019.00653
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Plant DNA Polymerases.

    Pedroza-Garcia, Jose-Antonio / De Veylder, Lieven / Raynaud, Cécile

    International journal of molecular sciences

    2019  Volume 20, Issue 19

    Abstract: Maintenance of genome integrity is a key process in all organisms. DNA polymerases (Pols) are central players in this process as they are in charge of the faithful reproduction of the genetic information, as well as of DNA repair. Interestingly, all ... ...

    Abstract Maintenance of genome integrity is a key process in all organisms. DNA polymerases (Pols) are central players in this process as they are in charge of the faithful reproduction of the genetic information, as well as of DNA repair. Interestingly, all eukaryotes possess a large repertoire of polymerases. Three protein complexes, DNA Pol α, δ, and ε, are in charge of nuclear DNA replication. These enzymes have the fidelity and processivity required to replicate long DNA sequences, but DNA lesions can block their progression. Consequently, eukaryotic genomes also encode a variable number of specialized polymerases (between five and 16 depending on the organism) that are involved in the replication of damaged DNA, DNA repair, and organellar DNA replication. This diversity of enzymes likely stems from their ability to bypass specific types of lesions. In the past 10-15 years, our knowledge regarding plant DNA polymerases dramatically increased. In this review, we discuss these recent findings and compare acquired knowledge in plants to data obtained in other eukaryotes. We also discuss the emerging links between genome and epigenome replication.
    MeSH term(s) DNA Damage ; DNA Repair ; DNA Replication ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/metabolism ; Epigenomics/methods ; Genome, Plant ; Meiosis ; Plants/enzymology ; Plants/genetics ; Protein Subunits ; Replication Origin ; Signal Transduction ; Stress, Physiological
    Chemical Substances Protein Subunits ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
    Language English
    Publishing date 2019-09-27
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms20194814
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  8. Article ; Online: The plant DNA polymerase theta is essential for the repair of replication-associated DNA damage.

    Nisa, Maherun / Bergis, Clara / Pedroza-Garcia, Jose-Antonio / Drouin-Wahbi, Jeannine / Mazubert, Christelle / Bergounioux, Catherine / Benhamed, Moussa / Raynaud, Cécile

    The Plant journal : for cell and molecular biology

    2021  Volume 106, Issue 5, Page(s) 1197–1207

    Abstract: Safeguarding of genome integrity is a key process in all living organisms. Due to their sessile lifestyle, plants are particularly exposed to all kinds of stress conditions that could induce DNA damage. However, very few genes involved in the maintenance ...

    Abstract Safeguarding of genome integrity is a key process in all living organisms. Due to their sessile lifestyle, plants are particularly exposed to all kinds of stress conditions that could induce DNA damage. However, very few genes involved in the maintenance of genome integrity are indispensable to plants' viability. One remarkable exception is the POLQ gene, which encodes DNA polymerase theta (Pol θ), a non-replicative polymerase involved in trans-lesion synthesis during DNA replication and double-strand break (DSB) repair. The Arabidopsis tebichi (teb) mutants, deficient in Pol θ, have been reported to display severe developmental defects, leading to the conclusion that Pol θ is required for normal plant development. However, this essential role of Pol θ in plants is challenged by contradictory reports regarding the phenotypic defects of teb mutants and the recent finding that rice (Oryza sativa) null mutants develop normally. Here we show that the phenotype of teb mutants is highly variable. Taking advantage of hypomorphic mutants for the replicative DNA polymerase epsilon, which display constitutive replicative stress, we show that Pol θ allows maintenance of meristem activity when DNA replication is partially compromised. Furthermore, we found that the phenotype of Pol θ mutants can be aggravated by modifying their growth conditions, suggesting that environmental conditions impact the basal level of replicative stress and providing evidence for a link between plants' responses to adverse conditions and mechanisms involved in the maintenance of genome integrity.
    MeSH term(s) Arabidopsis/genetics ; Arabidopsis/physiology ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; DNA Breaks, Double-Stranded ; DNA Damage ; DNA Polymerase II/genetics ; DNA Polymerase II/metabolism ; DNA Repair ; DNA Replication ; DNA, Plant/genetics ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Genomic Instability ; Genotype ; Meristem/genetics ; Meristem/physiology ; Models, Biological ; Mutation ; Phenotype ; Plant Roots/genetics ; Plant Roots/physiology ; Stress, Physiological ; DNA Polymerase theta
    Chemical Substances Arabidopsis Proteins ; DNA, Plant ; POL2a protein, Arabidopsis (EC 2.7.7.-) ; TEBICHI protein, Arabidopsis (EC 2.7.7.-) ; DNA Polymerase II (EC 2.7.7.7) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
    Language English
    Publishing date 2021-05-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1088037-9
    ISSN 1365-313X ; 0960-7412
    ISSN (online) 1365-313X
    ISSN 0960-7412
    DOI 10.1111/tpj.15295
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  9. Article: The plant DNA polymerase theta is essential for the repair of replication‐associated DNA damage

    Nisa, Maherun / Bergis, Clara / Pedroza‐Garcia, Jose‐Antonio / Drouin‐Wahbi, Jeannine / Mazubert, Christelle / Bergounioux, Catherine / Benhamed, Moussa / Raynaud, Cécile

    plant journal. 2021 June, v. 106, no. 5

    2021  

    Abstract: Safeguarding of genome integrity is a key process in all living organisms. Due to their sessile lifestyle, plants are particularly exposed to all kinds of stress conditions that could induce DNA damage. However, very few genes involved in the maintenance ...

    Abstract Safeguarding of genome integrity is a key process in all living organisms. Due to their sessile lifestyle, plants are particularly exposed to all kinds of stress conditions that could induce DNA damage. However, very few genes involved in the maintenance of genome integrity are indispensable to plants’ viability. One remarkable exception is the POLQ gene, which encodes DNA polymerase theta (Pol θ), a non‐replicative polymerase involved in trans‐lesion synthesis during DNA replication and double‐strand break (DSB) repair. The Arabidopsis tebichi (teb) mutants, deficient in Pol θ, have been reported to display severe developmental defects, leading to the conclusion that Pol θ is required for normal plant development. However, this essential role of Pol θ in plants is challenged by contradictory reports regarding the phenotypic defects of teb mutants and the recent finding that rice (Oryza sativa) null mutants develop normally. Here we show that the phenotype of teb mutants is highly variable. Taking advantage of hypomorphic mutants for the replicative DNA polymerase epsilon, which display constitutive replicative stress, we show that Pol θ allows maintenance of meristem activity when DNA replication is partially compromised. Furthermore, we found that the phenotype of Pol θ mutants can be aggravated by modifying their growth conditions, suggesting that environmental conditions impact the basal level of replicative stress and providing evidence for a link between plants’ responses to adverse conditions and mechanisms involved in the maintenance of genome integrity.
    Keywords Arabidopsis ; DNA damage ; DNA replication ; DNA-directed DNA polymerase ; Oryza sativa ; genes ; lifestyle ; meristems ; phenotype ; plant development ; rice ; viability
    Language English
    Dates of publication 2021-06
    Size p. 1197-1207.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 1088037-9
    ISSN 1365-313X ; 0960-7412
    ISSN (online) 1365-313X
    ISSN 0960-7412
    DOI 10.1111/tpj.15295
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  10. Article ; Online: Distinctive and complementary roles of E2F transcription factors during plant replication stress responses.

    Nisa, Maherun / Eekhout, Thomas / Bergis, Clara / Pedroza-Garcia, Jose-Antonio / He, Xiaoning / Mazubert, Christelle / Vercauteren, Ilse / Cools, Toon / Brik-Chaouche, Rim / Drouin-Wahbi, Jeannine / Chmaiss, Layla / Latrasse, David / Bergounioux, Catherine / Vandepoele, Klaas / Benhamed, Moussa / De Veylder, Lieven / Raynaud, Cécile

    Molecular plant

    2023  Volume 16, Issue 8, Page(s) 1269–1282

    Abstract: Survival of living organisms is fully dependent on their maintenance of genome integrity, being permanently threatened by replication stress in proliferating cells. Although the plant DNA damage response (DDR) regulator SOG1 has been demonstrated to cope ...

    Abstract Survival of living organisms is fully dependent on their maintenance of genome integrity, being permanently threatened by replication stress in proliferating cells. Although the plant DNA damage response (DDR) regulator SOG1 has been demonstrated to cope with replication defects, accumulating evidence points to other pathways functioning independent of SOG1. Here, we report the roles of the Arabidopsis E2FA and EF2B transcription factors, two well-characterized regulators of DNA replication, in plant response to replication stress. Through a combination of reverse genetics and chromatin immunoprecipitation approaches, we show that E2FA and E2FB share many target genes with SOG1, providing evidence for their involvement in the DDR. Analysis of double- and triple-mutant combinations revealed that E2FB, rather than E2FA, plays the most prominent role in sustaining plant growth in the presence of replication defects, either operating antagonistically or synergistically with SOG1. Conversely, SOG1 aids in overcoming the replication defects of E2FA/E2FB-deficient plants. Collectively, our data reveal a complex transcriptional network controlling the replication stress response in which E2Fs and SOG1 act as key regulatory factors.
    MeSH term(s) Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Arabidopsis/metabolism ; Transcription Factors/metabolism ; E2F Transcription Factors/genetics ; E2F Transcription Factors/metabolism ; Gene Expression Regulation, Plant/genetics
    Chemical Substances Arabidopsis Proteins ; Transcription Factors ; E2F Transcription Factors ; SOG1 protein, Arabidopsis
    Language English
    Publishing date 2023-07-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2393618-6
    ISSN 1752-9867 ; 1674-2052
    ISSN (online) 1752-9867
    ISSN 1674-2052
    DOI 10.1016/j.molp.2023.07.002
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