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Accueil > Départements > Biologie des Génomes > Fabienne MALAGNAC : Epigénétique et Développement chez les Champignons

Publications de l’équipe


  • P. Grognet, H. Timpano, F. Carlier, J. Aït-Benkhali, V. Berteaux-Lecellier, R. Debuchy, F. Bidard, et F. Malagnac, « A RID-like putative cytosine methyltransferase homologue controls sexual development in the fungus Podospora anserina », PLoS genetics, vol. 15, nᵒ 8, p. e1008086, août 2019.
    Résumé : DNA methyltransferases are ubiquitous enzymes conserved in bacteria, plants and opisthokonta. These enzymes, which methylate cytosines, are involved in numerous biological processes, notably development. In mammals and higher plants, methylation patterns established and maintained by the cytosine DNA methyltransferases (DMTs) are essential to zygotic development. In fungi, some members of an extensively conserved fungal-specific DNA methyltransferase class are both mediators of the Repeat Induced Point mutation (RIP) genome defense system and key players of sexual reproduction. Yet, no DNA methyltransferase activity of these purified RID (RIP deficient) proteins could be detected in vitro. These observations led us to explore how RID-like DNA methyltransferase encoding genes would play a role during sexual development of fungi showing very little genomic DNA methylation, if any. To do so, we used the model ascomycete fungus Podospora anserina. We identified the PaRid gene, encoding a RID-like DNA methyltransferase and constructed knocked-out ΔPaRid defective mutants. Crosses involving P. anserina ΔPaRid mutants are sterile. Our results show that, although gametes are readily formed and fertilization occurs in a ΔPaRid background, sexual development is blocked just before the individualization of the dikaryotic cells leading to meiocytes. Complementation of ΔPaRid mutants with ectopic alleles of PaRid, including GFP-tagged, point-mutated and chimeric alleles, demonstrated that the catalytic motif of the putative PaRid methyltransferase is essential to ensure proper sexual development and that the expression of PaRid is spatially and temporally restricted. A transcriptomic analysis performed on mutant crosses revealed an overlap of the PaRid-controlled genetic network with the well-known mating-types gene developmental pathway common to an important group of fungi, the Pezizomycotina.
    Mots-clés : DBG, EDC, MRP.
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  • G. Lelandais, T. Denecker, C. Garcia, N. Danila, T. Léger, et J. - M. Camadro, « Label-free quantitative proteomics in Candida yeast species: technical and biological replicates to assess data reproducibility », BMC research notes, vol. 12, nᵒ 1, p. 470, août 2019.
    Résumé : OBJECTIVE: Label-free quantitative proteomics has emerged as a powerful strategy to obtain high quality quantitative measures of the proteome with only a very small quantity of total protein extract. Because our research projects were requiring the application of bottom-up shotgun mass spectrometry proteomics in the pathogenic yeasts Candida glabrata and Candida albicans, we performed preliminary experiments to (i) obtain a precise list of all the proteins for which measures of abundance could be obtained and (ii) assess the reproducibility of the results arising respectively from biological and technical replicates. DATA DESCRIPTION: Three time-courses were performed in each Candida species, and an alkaline pH stress was induced for two of them. Cells were collected 10 and 60 min after stress induction and proteins were extracted. Samples were analysed two times by mass spectrometry. Our final dataset thus comprises label-free quantitative proteomics results for 24 samples (two species, three time-courses, two time points and two runs of mass spectrometry). Statistical procedures were applied to identify proteins with differential abundances between stressed and unstressed situations. Considering that C. glabrata and C. albicans are human pathogens, which face important pH fluctuations during a human host infection, this dataset has a potential value to other researchers in the field.
    Mots-clés : Alkaline pH, Candida albicans, Candida glabrata, DBG, EDC, Label-free quantitative proteomics, Mass spectrometry.
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  • P. Silar, J. - M. Dauget, V. Gautier, P. Grognet, M. Chablat, S. Hermann-Le Denmat, A. Couloux, P. Wincker, et R. Debuchy, « A gene graveyard in the genome of the fungus Podospora comata », Molecular Genetics and Genomics, vol. 294, nᵒ 1, p. 177-190, févr. 2019.
    Résumé : Mechanisms involved in fine adaptation of fungi to their environment include differential gene regulation associated with single nucleotide polymorphisms and indels (including transposons), horizontal gene transfer, gene copy amplification, as well as pseudogenization and gene loss. The two Podospora genome sequences examined here emphasize the role of pseudogenization and gene loss, which have rarely been documented in fungi. Podospora comata is a species closely related to Podospora anserina, a fungus used as model in several laboratories. Comparison of the genome of P. comata with that of P. anserina, whose genome is available for over 10 years, should yield interesting data related to the modalities of genome evolution between these two closely related fungal species that thrive in the same types of biotopes, i.e., herbivore dung. Here, we present the genome sequence of the mat+isolate of the P. comata reference strain T. Comparison with the genome of the mat+isolate of P. anserina strain S confirms that P. anserina and P. comata are likely two different species that rarely interbreed in nature. Despite having a 94-99% of nucleotide identity in the syntenic regions of their genomes, the two species differ by nearly 10% of their gene contents. Comparison of the species-specific gene sets uncovered genes that could be responsible for the known physiological differences between the two species. Finally, we identified 428 and 811 pseudogenes (3.8 and 7.2% of the genes) in P. anserina and P. comata, respectively. Presence of high numbers of pseudogenes supports the notion that difference in gene contents is due to gene loss rather than horizontal gene transfers. We propose that the high frequency of pseudogenization leading to gene loss in P. anserina and P. comata accompanies specialization of these two fungi. Gene loss may be more prevalent during the evolution of other fungi than usually thought.
    Mots-clés : anserina, BIOCELL, biodiversity, DBG, DSMC, EDC, FDMITO, Lasiosphaeriaceae, MRP, neanderthal, Podospora anserina, Podospora comata, Pseudogene, pseudogenes, sequence, Sordariales, Speciation.


  • R. Ferrari, I. Lacaze, P. Le Faouder, J. Bertrand-Michel, C. Oger, J. - M. Galano, T. Durand, S. Moularat, L. C. H. Tong, C. Boucher, J. Kilani, Y. Petit, O. Vanparis, C. Trannoy, S. Brun, H. Lalucque, F. Malagnac, et P. Silar, « Cyclooxygenases and lipoxygenases are used by the fungus Podospora anserina to repel nematodes », Biochimica Et Biophysica Acta-General Subjects, vol. 1862, nᵒ 10, p. 2174-2182, oct. 2018.
    Résumé : Oxylipins are secondary messengers used universally in the living world for communication and defense. The paradigm is that they are produced enzymatically for the eicosanoids and non-enzymatically for the isoprostanoids. They are supposed to be degraded into volatile organic compounds (VOCs) and to participate in aroma production. Some such chemicals composed of eight carbons are also envisoned as alternatives to fossil fuels. In fungi, oxylipins have been mostly studied in Aspergilli and shown to be involved in signalling asexual versus sexual development, mycotoxin production and interaction with the host for pathogenic species. Through targeted gene deletions of genes encoding oxylipin-producing enzymes and chemical analysis of oxylipins and volatile organic compounds, we show that in the distantly-related ascomycete Podospora anserina, isoprostanoids are likely produced enzymatically. We show the disappearance in the mutants lacking lipoxygenases and cyclooxygenases of the production of 10-hydroxy-octadecadienoic acid and that of 1-octen-3-ol, a common volatile compound. Importantly, this was correlated with the inability of the mutants to repel nematodes as efficiently as the wild type. Overall, our data show that in this fungus, oxylipins are not involved in signalling development but may rather be used directly or as precursors in the production of odors against potential agressors. Significance: We analyzse the role in inter-kingdom communication of lipoxygenase (lox) and cyclooxygenase (cox) genes in the model fungus Podospora anserina. Through chemical analysis we define the oxylipins and volatile organic compounds (VOCs)produce by wild type and mutants for cox and lox genes, We show that the COX and LOX genes are required for the production of some eight carbon VOCs. We show that COX and LOX genes are involved in the production of chemicals repelling nematodes. This role is very different from the ones previously evidenced in other fungi.
    Mots-clés : aspergillus-fumigatus, chromatography, Cyclooxygenase, DBG, EDC, endophytic fungus, Fungi, lc-ms/ms, Lipoxygenase, metabolites, Oxylipins, Podospora anserina, Volatile organic compounds.

  • C. Murat, T. Payen, B. Noel, A. Kuo, E. Morin, J. Chen, A. Kohler, K. Krizsan, R. Balestrini, C. Da Silva, B. Montanini, M. Hainaut, E. Levati, K. W. Barry, B. Belfiori, N. Cichocki, A. Clum, R. B. Dockter, L. Fauchery, J. Guy, M. Iotti, F. Le Tacon, E. A. Lindquist, A. Lipzen, F. Malagnac, A. Mello, V. Molinier, S. Miyauchi, J. Poulain, C. Riccioni, A. Rubini, Y. Sitrit, R. Splivallo, S. Traeger, M. Wang, L. Zifcakova, D. Wipf, A. Zambonelli, F. Paolocci, M. Nowrousian, S. Ottonello, P. Baldrian, J. W. Spatafora, B. Henrissat, L. G. Nagy, J. - M. Aury, P. Wincker, I. Grigoriev, P. Bonfante, et F. M. Martin, « Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle », Nature Ecology & Evolution, vol. 2, nᵒ 12, p. 1956-1965, déc. 2018.
    Résumé : Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Perigord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged -100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries.
    Mots-clés : DBG, ecology, EDC, mechanisms, microbiome, mycorrhizal.


  • H. Lalucque, F. Malagnac, K. Green, V. Gautier, P. Grognet, L. Chan Ho Tong, B. Scott, et P. Silar, « IDC2 and IDC3, two genes involved in cell non-autonomous signaling of fruiting body development in the model fungus Podospora anserina », Developmental Biology, vol. 421, nᵒ 2, p. 126-138, janv. 2017.
    Résumé : Filamentous ascomycetes produce complex multicellular structures during sexual reproduction. Little is known about the genetic pathways enabling the construction of such structures. Here, with a combination of classical and reverse genetic methods, as well as genetic mosaic and graft analyses, we identify and provide evidence for key roles for two genes during the formation of perithecia, the sexual fruiting bodies, of the filamentous fungus Podospora anserina. Data indicate that the proteins coded by these two genes function cell-non-autonomously and that their activity depends upon conserved cysteines, making them good candidate for being involved in the transmission of a reactive oxygen species (ROS) signal generated by the PaNox1 NADPH oxidase inside the maturing fruiting body towards the PaMpk1 MAP kinase, which is located inside the underlying mycelium, in which nutrients are stored. These data provide important new insights to our understanding of how fungi build multicellular structures.
    Mots-clés : DBG, Developmental mutants, DSMC, EDC, Fungal development, Multicellular fruiting bodies, Perithecium, Podospora anserina.

  • T. - S. Nguyen, H. Lalucque, F. Malagnac, et P. Silar, « Chapter 5 - Prions and Prion-Like Phenomena in Epigenetic Inheritance », in Handbook of Epigenetics (Second Edition), T. O. Tollefsbol, Éd. Academic Press, 2017, p. 61-72.
    Résumé : At the time that the concept of gene as a stretch of DNA encoding a function was not fully established, several models proposed that regulatory networks or macromolecular structures could also generate hereditary traits. Long forgotten, this kind of epigenetic inheritance has been revived by the discovery that some non-mendelian inheritance in the yeast Saccharomyces cerevisiae is due to proteins able to switch their structure in an autocatalytic manner, now called prion. We review here what we know about these cellular prions; and also about additional phenomena, which in their genetic determinism resemble prions, however, based on alternative states of macromolecular complexes or regulatory networks.
    Mots-clés : cytotaxis, DBG, DSMC, EDC, emergent properties, hysteresis, prions, regulatory inheritance, structural inheritance.



  • A. Goarin, P. Silar, et F. Malagnac, « Gene replacement in Penicillium roqueforti », Current Genetics, vol. 61, nᵒ 2, p. 203-210, mai 2015.
    Résumé : Most cheese-making filamentous fungi lack suitable molecular tools to improve their biotechnology potential. Penicillium roqueforti, a species of high industrial importance, would benefit from functional data yielded by molecular genetic approaches. This work provides the first example of gene replacement by homologous recombination in P. roqueforti, demonstrating that knockout experiments can be performed in this fungus. To do so, we improved the existing transformation method to integrate transgenes into P. roqueforti genome. In the meantime, we cloned the PrNiaD gene, which encodes a NADPH-dependent nitrate reductase that reduces nitrate to nitrite. Then, we performed a deletion of the PrNiaD gene from P. roqueforti strain AGO. The ΔPrNiaD mutant strain is more resistant to chlorate-containing medium than the wild-type strain, but did not grow on nitrate-containing medium. Because genomic data are now available, we believe that generating selective deletions of candidate genes will be a key step to open the way for a comprehensive exploration of gene function in P. roqueforti.
    Mots-clés : Cheese, DBG, DSMC, EDC, Gene Knockout Techniques, Genetic Engineering, Homologous Recombination, Humans, Nitrate Reductase (NADPH), Penicillium.
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Publications Principales avant 2015

- Grognet P, Lalucque H, Malagnac F, Silar P. (2014) Genes that bias mendelian segregation.
PLoS Genet May 15 ;10(5):e1004387. doi : 10.1371/journal.pgen.1004387. eCollection 2014 May.

- Grognet P, Bidard F, Kuchly C, Chan Ho Tong L, Coppin E, Benkhal, JA, Couloux A, Wincker P, Debuchy R, Silar P. (2014). Maintaining Two Mating Types : Structure of the Mating Type Locus and Its Role in Heterokaryosis in Podospora anserina.
Genetics 197, 421–432.

- Cheeseman K, Ropars J, Renault P, Dupont J, Gouzy J, Branca A, Abraham AL, Ceppi M, Conseiller E, Debuchy R, Malagnac F, Goarin A, Silar P, Lacoste S, Sallet E, Bensimon A, Giraud T, Brygoo Y. (2014) Multiple recent horizontal transfers of a large genomic region in cheese making fungi.
Nat Commun. Jan 10 ;5:2876. doi : 10.1038/ncomms3876.

- Philippe Silar & Fabienne Malagnac
Les champignons redécouverts
Belin, DL 2013, cop. 2013
ISBN 978-2-7011-5902-7
EAN 9782701159027

- Malagnac F, Fabret C, Prigent M, Rousset JP, Namy O, Silar P. (2013) Rab-GDI Complex Dissociation Factor Expressed through Translational Frameshifting in Filamentous Ascomycetes.
PLoS One Sep 19 ;8(9):e73772. doi : 10.1371/journal.pone.0073772.

- Ropars J, Dupont J, Fontanillas E, Rodriguez de la Vega RC, Malagnac F, Coton M, Giraud T, Lopez-Villavicencio M. (2012) Sex in Cheese : Evidence for Sexuality in the Fungus Penicillium roqueforti.
PLoS ONE 7(11) : e49665. doi:10.1371/journal.pone.0049665

- Déquard-Chablat M, Nguyen T-T, Contamine V, Hermann-Le Denmat S, Malagnac F. (2012) Efficient tools to target DNA to Podospora anserina.
Fungal Genetics Reports 59 : 21-25.

- Lalucque H, Malagnac F, Brun S, Kicka S, Silar P. (2012) A Non-Mendelian MAPK-Generated Hereditary Unit Controlled by a Second MAPK Pathway in Podospora anserina.
Genetics. Jun 191(2):419-33.

- Espagne E, Vasnier C, Storlazzi A, Kleckner NE, Silar P, Zickler D, Malagnac F. (2011) Sme4 coiled-coil protein mediates synaptonemal complex assembly, recombinosome relocalization, and spindle pole body morphogenesis.
Proc Natl Acad Sci U S A. 108(26):10614-9.

- Malagnac F. and Silar P.
Epigenetics of Eukaryotic Microbes.
“Handbook of Epigenetics : The New Molecular and Medical Genetics”.
Academic Press. SEP-2010. ISBN 13 : 978-0-12-375709-8.

- Lalucque H., Malagnac F. and Silar P.
Prions and prion-like phenomena in epigenetic inheritance.
“Handbook of Epigenetics : The New Molecular and Medical Genetics”.
Academic Press. SEP-2010. ISBN 13 : 978-0-12-375709-8.

- Brun S., Malagnac F., Bidard F., Lalucque H. and Silar P. (2009) Functions and regulation of the Nox family in the filamentous fungus Podospora anserina : a new role in cellulose degradation.
Mol Microbiol. 74(2):480-96.

- Martins M, Rodrigues-Lima F, Dairou J, Lamouri A, Malagnac F, Silar P, Dupret JM.
An acetyltransferase conferring tolerance to toxic aromatic amine chemicals : molecular and functional studies.
J Biol Chem. (2009) 284(28):18726-33.

- Malagnac F., Bidard F., Lalucque H., Brun S., Lambou K., Lebrun M-H. and Silar P. (2008) Convergent evolution of morphogenetic processes in fungi : Role of tetraspanins and NADPH oxidases 2 in plant pathogens and saprobes.
Commun & Integr Biol. 2:180-181.

- Lambou K, Malagnac F, Barbisan C, Tharreau D, Marc-Henri Lebrun, and Silar P. (2008) The crucial role during ascospore germination of the Pls1 tetraspanin in Podospora anserina provides an example of the convergent evolution of morphogenetic processes in fungal plant pathogens and saprobes.
Eukaryot Cell. 7(10):1809-18

- Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, Porcel BM, Couloux A, Aury JM, Ségurens B, Poulain J, Anthouard V, Grossetete S, Khalili H, Coppin E, Déquard-Chablat M, Picard M, Contamine V, Arnaise S, Bourdais A, Berteaux-Lecellier V, Gautheret D, de Vries RP, Battaglia E, Coutinho PM, Danchin EG, Henrissat B, Khoury RE, Sainsard-Chanet A, Boivin A, Pinan-Lucarré B, Sellem CH, Debuchy R, Wincker P, Weissenbach J, Silar P. (2008) The genome sequence of the model ascomycete fungus Podospora anserina.
Genome Biol. May 6 ;9(5):R77.

- Malagnac F, Klapholz B, Silar P. (2007)
PaTrx1 and PaTrx3, two cytosolic thioredoxins of the filamentous ascomycete Podospora anserina involved in sexual development and cell degeneration.
Eukaryot Cell. 6(12):2323-31.

- Martins M, Silar P, Dairou J, Malagnac F, Rodrigues-Lima F and Dupret JM. (2007) Cloning and functional characterization of two NAT enzymes in the soil fungus Podospora anserina.
FEBS J. 274:226.

- Malagnac F and Silar P. (2006) Regulation, Cell Differentiation and Protein-Based Inheritance.
Cell Cycle. 5(22):2584-2587

- Haedens V, Malagnac F, Silar P. (2005) Genetic control of an epigenetic cell degeneration syndrome in Podospora anserina.
Fungal Genet Biol. 42(6):564-77.

- Malagnac F, Lalucque H, Lepere G, Silar P. (2004) Two NADPH oxidase isoforms are required for sexual reproduction and ascospore germination in the filamentous fungus Podospora anserina.
Fungal Genet Biol. 41(11):982-97.

- Malagnac F and Silar P. (2003) Non-Mendelian determinants of morphology in fungi.
Curr Opin Microbiol. 6(6):641-5.

- Malagnac F, Bartee L, Bender J. (2002) An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation.
EMBO J. 21(24):6842-52.

- Bartee L, Malagnac F, Bender J. (2001) Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene.
Genes Dev. 15(14):1753-8.

- Malagnac F, Gregoire A, Goyon C, Rossignol JL, Faugeron G. (1999) Masc2, a gene from Ascobolus encoding a protein with a DNA-methyltransferase activity in vitro, is dispensable for in vivo methylation.
Mol Microbiol 31(1):331-8.

- Malagnac F, Wendel B, Goyon C, Faugeron G, Zickler D, Rossignol JL, Noyer-Weidner M, Vollmayr P, Trautner TA, Walter J. (1997) A gene essential for de novo methylation and development in Ascobolus reveals a novel type of eukaryotic DNA methyltransferase structure.
Cell 91(2):281-90.

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