G. D. Brown, D. W. Denning, N. A. Gow, S. M. Levitz, M. G. Netea et al., Hidden killers: human fungal infections, Sci Transl Med, vol.4, pp.165-178, 2012.

T. F. Patterson, G. R. Thompson, . Iii, D. W. Denning, J. A. Fishman et al., Practice guidelines for the diagnosis and management of aspergillosis: 2016 update by the Infectious Diseases Society of America, Clin Infect Dis, vol.63, pp.1-60, 2016.

A. J. Ullmann, J. M. Aguado, S. Arikan-akdagli, D. W. Denning, A. H. Groll et al., Diagnosis and management of Aspergillus diseases: executive summary of the 2017 ESCMID-ECMM-ERS guideline, Clin Microbiol Infect, vol.24, issue.1, pp.1-38, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01953645

J. E. Nett and D. R. Andes, Antifungal agents: spectrum of activity, pharmacology, and clinical indications, Infect Dis Clin North Am, vol.30, pp.51-83, 2016.

A. Chowdhary, C. Sharma, and J. F. Meis, Azole-resistant aspergillosis: epidemiology, molecular mechanisms, and treatment, J Infect Dis, vol.216, pp.436-444, 2017.

J. F. Meis, A. Chowdhary, J. L. Rhodes, M. C. Fisher, and P. E. Verweij, Clinical implications of globally emerging azole resistance in Aspergillus fumigatus, Philos Trans R Soc B, vol.371, 2016.

W. J. Steinbach, Are we there yet? Recent progress in the molecular diagnosis and novel antifungal targeting of Aspergillus fumigatus and invasive aspergillosis, PLoS Pathog, vol.9, 2013.

J. Onishi, M. Meinz, J. Thompson, J. Curotto, S. Dreikorn et al., Discovery of novel antifungal (1,3)-beta-D-glucan synthase inhibitors, Antimicrob Agents Chemother, vol.44, pp.368-377, 2000.

J. C. Bowman, P. S. Hicks, M. B. Kurtz, H. Rosen, D. M. Schmatz et al., The antifungal echinocandin caspofungin acetate kills growing cells of Aspergillus fumigatus in vitro, Antimicrob Agents Chemother, vol.46, pp.3001-3012, 2002.

D. S. Perlin, Mechanisms of echinocandin antifungal drug resistance, 2015.

, Ann N Y Acad Sci, vol.1354, pp.1-11

M. Aruanno, E. Glampedakis, and F. Lamoth, Echinocandins for the treatment of invasive aspergillosis: from laboratory to bedside, Antimicrob Agents Chemother, vol.63, pp.399-418, 2019.

C. Jimenez-ortigosa, C. Moore, D. W. Denning, and D. S. Perlin, Emergence of Echinocandin resistance due to a point mutation in the fks1 gene of Aspergillus fumigatus in a patient with chronic pulmonary aspergillosis, Antimicrob Agents Chemother, vol.61, pp.1277-1294, 2017.

L. A. Walker, N. A. Gow, and C. A. Munro, Fungal echinocandin resistance, Fungal Genet Biol, vol.47, pp.117-126, 2010.

J. R. Fortwendel, P. R. Juvvadi, B. Z. Perfect, L. E. Rogg, J. R. Perfect et al., Transcriptional regulation of chitin synthases by calcineurin controls paradoxical growth of Aspergillus fumigatus in response to caspofungin, Antimicrob Agents Chemother, vol.54, pp.1555-1563, 2010.

S. Satish, C. Jimenez-ortigosa, Y. Zhao, M. H. Lee, E. Dolgov et al., Stress-induced changes in the lipid microenvironment of beta-(1,3)-d-glucan synthase cause clinically important echinocandin resistance in Aspergillus fumigatus, mBio, vol.10, pp.779-798, 2019.

W. J. Steinbach, F. Lamoth, and P. R. Juvvadi, Potential microbiological effects of higher dosing of echinocandins, Clin Infect Dis, vol.61, issue.6, pp.669-677, 2015.

R. Altwasser, C. Baldin, J. Weber, R. Guthke, O. Kniemeyer et al., Network modeling reveals cross talk of map kinases during adaptation to caspofungin stress in Aspergillus fumigatus, PLoS One, vol.10, 2015.

P. R. Juvvadi, A. Munoz, F. Lamoth, E. J. Soderblom, M. A. Moseley et al., Calcium-mediated induction of paradoxical growth following caspofungin treatment is associated with calcineurin activation and phosphorylation in Aspergillus fumigatus, Antimicrob Agents Chemother, vol.59, pp.4946-4955, 2015.

F. Lamoth, P. R. Juvvadi, C. Gehrke, Y. G. Asfaw, and W. J. Steinbach, Transcriptional activation of heat shock protein 90 mediated via a proximal promoter region as trigger of caspofungin resistance in Aspergillus fumigatus, J Infect Dis, vol.209, pp.473-481, 2014.

S. Suwunnakorn, H. Wakabayashi, and E. Rustchenko, Chromosome 5 of human pathogen Candida albicans carries multiple genes for negative control of caspofungin and anidulafungin susceptibility, Antimicrob Agents Chemother, vol.60, pp.7457-7467, 2016.

F. Yang, L. Zhang, H. Wakabayashi, J. Myers, Y. Jiang et al., , 2017.

, Candida albicans is associated with at least three distinctive mechanisms that govern expression of FKS genes and cell wall remodeling, Antimicrob Agents Chemother, vol.61

P. A. De-castro, A. C. Colabardini, A. O. Manfiolli, J. Chiaratto, L. P. Silva et al., Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance, PLoS Genet, vol.15, p.1008551, 2019.

L. Ries, M. C. Rocha, P. A. De-castro, R. Silva-rocha, R. N. Silva et al., The Aspergillus fumigatus CrzA transcription factor activates chitin synthase gene expression during the caspofungin paradoxical effect, vol.8, pp.705-722, 2017.

V. Loiko and J. Wagener, The paradoxical effect of echinocandins in Aspergillus fumigatus relies on recovery of the beta-1,3-glucan synthase Fks1, Antimicrob Agents Chemother, vol.61, pp.1690-1706, 2017.

T. Furukawa, N. Van-rhijn, M. Fraczek, F. Gsaller, E. Davies et al., The negative cofactor 2 complex is a key regulator of drug resistance in Aspergillus fumigatus, Nat Commun, vol.11, p.427, 2020.

P. Hortschansky, H. Haas, E. M. Huber, M. Groll, and A. A. Brakhage, The CCAAT-binding complex (CBC) in Aspergillus species, Biochim Biophys Acta Gene Regul Mech, vol.1860, pp.560-570, 2017.

D. Hagiwara, S. Suzuki, K. Kamei, T. Gonoi, and S. Kawamoto, The role of AtfA and HOG MAPK pathway in stress tolerance in conidia of Aspergillus fumigatus, Fungal Genet Biol, vol.73, pp.138-149, 2014.

P. Silva, L. , A. De-castro, P. , D. Reis et al., Genome-wide transcriptome analysis of Aspergillus fumigatus exposed to osmotic stress reveals regulators of osmotic and cell wall stresses that are SakA(HOG1) and MpkC dependent, Cell Microbiol, vol.19, 2017.

M. C. Rocha, J. H. Fabri, K. Franco-de-godoy, A. De-castro, P. Hori et al., Aspergillus fumigatus MADS-box transcription factor rlmA is required for regulation of the cell wall integrity and virulence, Bethesda), vol.3, pp.2983-3002, 2016.

V. Valiante, C. Baldin, P. Hortschansky, R. Jain, A. Thywißen et al., The Aspergillus fumigatus conidial melanin production is regulated by the bifunctional bHLH DevR and MADS-box RlmA transcription factors, Mol Microbiol, vol.102, pp.321-335, 2016.

M. E. Da-silva-ferreira, I. Malavazi, M. Savoldi, A. A. Brakhage, M. H. Goldman et al., Transcriptome analysis of Aspergillus fumigatus exposed to voriconazole, Curr Genet, vol.50, pp.32-44, 2006.

F. M. Soriani, I. Malavazi, M. Savoldi, E. Espeso, T. M. Dinamarco et al., Identification of possible targets of the Aspergillus fumigatus CRZ1 homologue, CrzA. BMC Microbiol, vol.10, p.12, 2010.

M. Schrettl, N. Beckmann, J. Varga, T. Heinekamp, I. D. Jacobsen et al., HapX-mediated adaption to iron starvation is crucial for virulence of Aspergillus fumigatus, PLoS Pathog, vol.6, 2010.

M. Schrettl, E. Bignell, C. Kragl, C. Joechl, T. Rogers et al., Siderophore biosynthesis but not reductive iron assimilation is essential for Aspergillus fumigatus virulence, J Exp Med, vol.200, pp.1213-1219, 2004.

M. Grundlinger, Y. S. Lechner, B. E. Geley, S. Schrettl, M. Hynes et al., Fungal siderophore biosynthesis is partially localized in peroxisomes, Mol Microbiol, vol.88, pp.862-875, 2013.

L. Schafferer, N. Beckmann, U. Binder, G. Brosch, and H. Haas, AmcA-a putative mitochondrial ornithine transporter supporting fungal siderophore biosynthesis, Front Microbiol, vol.6, p.252, 2015.

N. Long, X. Xu, H. Qian, S. Zhang, and L. Lu, A putative mitochondrial iron transporter mrsa in Aspergillus fumigatus plays important roles in azole-, oxidative stress responses and virulence, Front Microbiol, vol.7, 2016.

T. Magnani, F. M. Soriani, V. P. Martins, A. M. Nascimento, V. G. Tudella et al., Cloning and functional expression of the mitochondrial alternative oxidase of Aspergillus fumigatus and its induction by oxidative stress, FEMS Microbiol Lett, vol.271, pp.230-238, 2007.

G. Chamilos, R. E. Lewis, and D. P. Kontoyiannis, Inhibition of Candida parapsilosis mitochondrial respiratory pathways enhances susceptibility to caspofungin, Antimicrob Agents Chemother, vol.50, pp.744-747, 2006.

T. Tatsuta and T. Langer, Quality control of mitochondria: protection against neurodegeneration and ageing, EMBO J, vol.27, pp.306-314, 2008.

L. A. Walker, K. K. Lee, C. A. Munro, and N. A. Gow, Caspofungin treatment of Aspergillus fumigatus results in chsg-dependent upregulation of chitin synthesis and the formation of chitin-rich microcolonies, Antimicrob Agents Chemother, vol.59, pp.5932-5941, 2015.

E. C. Mattos, L. P. Silva, C. Valero, P. A. De-castro, D. Reis et al., The Aspergillus fumigatus phosphoproteome reveals roles of high-osmolarity glycerol mitogen-activated protein kinases in promoting cell wall damage and caspofungin tolerance, mBio, vol.11, pp.2962-2981, 2020.

T. Ohya, S. Maki, Y. Kawasaki, and A. Sugino, Structure and function of the fourth subunit (Dpb4p) of DNA polymerase epsilon in Saccharomyces cerevisiae, Nucleic Acids Res, vol.28, pp.3846-3852, 2000.

A. Bambach, M. P. Fernandes, A. Ghosh, M. Kruppa, A. D. Li et al., Goa1p of Candida albicans localizes to the mitochondria during stress and is required for mitochondrial function and virulence, Eukaryot Cell, vol.8, pp.1706-1720, 2009.

K. Khamooshi, P. Sikorski, N. Sun, R. Calderone, and D. Li, The Rbf1, Hfl1 and Dbp4 of Candida albicans regulate common as well as transcription factor-specific mitochondrial and other cell activities, BMC Genomics, vol.15, p.56, 2014.

J. A. Inostroza, F. H. Mermelstein, I. Ha, W. S. Lane, and D. Reinberg, Dr1, a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription, Cell, vol.70, issue.92, pp.90172-90181, 1992.

M. Meisterernst and R. G. Roeder, Family of proteins that interact with TFIID and regulate promoter activity, Cell, vol.67, issue.91, p.90530, 1991.

T. K. Albert, K. Grote, S. Boeing, G. Stelzer, A. Schepers et al., Global distribution of negative cofactor 2 subunit-alpha on human promoters, Proc Natl Acad Sci U S A, vol.104, pp.10000-10005, 2007.

N. Gómez-navarro, A. Jordán-pla, F. Estruch, and J. Pérez-ortín, Defects in the NC2 repressor affect both canonical and non-coding RNA polymerase II transcription initiation in yeast, BMC Genomics, vol.17, p.183, 2016.

M. Shariq, S. Dhamgaye, R. Nair, N. Goyal, V. Jain et al., The global regulator Ncb2 escapes from the core promoter and impacts transcription in response to drug stress in Candida albicans, Sci Rep, vol.7, 2017.

F. J. Van-werven, H. Van-bakel, H. A. Van-teeffelen, A. F. Altelaar, M. G. Koerkamp et al., Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome, Genes Dev, vol.22, pp.2359-2369, 2008.

S. Shukla, V. Yadav, G. Mukhopadhyay, and R. Prasad, Ncb2 is involved in activated transcription of CDR1 in azole-resistant clinical isolates of Candida albicans, Eukaryot Cell, vol.10, pp.1357-1366, 2011.

F. M. Soriani, I. Malavazi, M. E. Da-silva-ferreira, M. Savoldi, V. Z. Kress et al., Functional characterization of the Aspergillus fumigatus CRZ1 homologue, CrzA. Mol Microbiol, vol.67, pp.1274-1291, 2008.

M. J. Dagley, I. E. Gentle, T. H. Beilharz, F. A. Pettolino, J. T. Djordjevic et al., Cell wall integrity is linked to mitochondria and phospholipid homeostasis in Candida albicans through the activity of the post-transcriptional regulator Ccr4-Pop2, Mol Microbiol, vol.79, pp.968-989, 2011.

M. Sarinová, E. Tichá, M. Obernauerová, and Y. Gbelská, Impact of mitochondrial function on yeast susceptibility to antifungal compounds, Folia Microbiol (Praha), vol.52, pp.223-229, 2007.

K. Shirey, K. R. Stover, J. Cleary, N. Hoang, and J. Hosler, Membraneanchored cyclic peptides as effectors of mitochondrial oxidative phosphorylation, Biochemistry, vol.55, pp.2100-2111, 2016.

Q. Yu, B. Zhang, J. Li, B. Zhang, H. Wang et al., Endoplasmic reticulumderived reactive oxygen species (ROS) is involved in toxicity of cell wall stress to Candida albicans, Free Radic Biol Med, vol.99, pp.572-583, 2016.

M. Aruanno, D. Bachmann, D. Sanglard, and F. Lamoth, Link between heat shock protein 90 and the mitochondrial respiratory chain in the caspofungin stress response of Aspergillus fumigatus, Antimicrob Agents Chemother, vol.63, pp.208-227, 2019.

R. W. Bastos, L. Rossato, C. Valero, K. Lagrou, A. L. Colombo et al., Potential of gallium as an antifungal agent, Front Cell Infect Microbiol, vol.9, p.414, 2019.

Y. W. Lai, L. T. Campbell, M. R. Wilkins, C. N. Pang, S. Chen et al., Synergy and antagonism between iron chelators and antifungal drugs in Cryptococcus, Int J Antimicrob Agents, vol.48, pp.388-394, 2016.

J. Wagener and V. Loiko, Recent insights into the paradoxical effect of echinocandins, J Fungi (Basel), vol.4, p.5, 2017.

E. Käfer, Meiotic and mitotic recombination in Aspergillus and its chromosomal aberrations, Adv Genet, vol.19, issue.08, p.60245, 1977.

C. Zhao, M. G. Fraczek, L. Dineen, R. Lebedinec, J. Macheleidt et al., High-throughput gene replacement in Aspergillus fumigatus, Curr Protoc Microbiol, vol.54, 2019.

H. V. Colot, G. Park, G. E. Turner, C. Ringelberg, C. M. Crew et al., A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors, Proc Natl Acad Sci U S A, vol.103, pp.10352-10357, 2006.

I. Malavazi and G. H. Goldman, Gene disruption in Aspergillus fumigatus using a PCR-based strategy and in vivo recombination in yeast, Methods Mol Biol, vol.845, pp.99-118, 2012.

M. K. Chaveroche, J. M. Ghigo, and C. Enfert, A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans, Nucleic Acids Res, vol.28, 2000.

C. P. Semighini, M. Marins, M. H. Goldman, and G. H. Goldman, Quantitative analysis of the relative transcript levels of ABC transporter Atr genes in Aspergillus nidulans by real-time reverse transcription-PCR assay, Appl Environ Microbiol, vol.68, pp.1351-1357, 2002.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014.

E. Kopylova, L. Noe, and H. Touzet, SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinformatics, vol.28, pp.3211-3217, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00748990

Y. Liao, G. K. Smyth, and W. Shi, The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote, Nucleic Acids Res, vol.41, 2013.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

Y. Benjamini, D. Drai, G. Elmer, N. Kafkafi, and I. Golani, Controlling the false discovery rate in behavior genetics research, Behav Brain Res, vol.125, pp.279-284, 2001.

J. Smedsgaard, Micro-scale extraction procedure for standardized screening of fungal metabolite production in cultures, J Chromatogr A, vol.760, pp.264-270, 1997.

M. Vodisch, D. Albrecht, F. Lessing, A. D. Schmidt, R. Winkler et al., Two-dimensional proteome reference maps for the human pathogenic filamentous fungus Aspergillus fumigatus, Proteomics, vol.9, pp.1407-1415, 2009.

E. F. Hartree, Determination of protein: a modification of the Lowry method that gives a linear photometric response, Anal Biochem, vol.48, pp.422-427, 1972.

L. Franco, B. S. Moda, M. Soares, and M. H. Barros, Msc6p is required for mitochondrial translation initiation in the absence of formylated Met-tRNA(fMet), FEBS J, vol.286, pp.1407-1419, 2019.

S. Kumar, G. Stecher, and K. Tamura, MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets, Mol Biol Evol, vol.33, pp.1870-1874, 2016.

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, vol.4, pp.406-425, 1987.

J. Felsenstein, Confidence limits on phylogenies: an approach using the bootstrap, Evolution, vol.39, pp.783-791, 1985.