Publications by authors named "Anne Favel"

15 Publications

  • Page 1 of 1

Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay.

Environ Microbiol 2021 Feb 4. Epub 2021 Feb 4.

INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.

Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.
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http://dx.doi.org/10.1111/1462-2920.15423DOI Listing
February 2021

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus.

DNA Res 2020 Apr;27(2)

INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.
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http://dx.doi.org/10.1093/dnares/dsaa011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7406137PMC
April 2020

Integrative visual omics of the white-rot fungus exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass.

Biotechnol Biofuels 2018 23;11:201. Epub 2018 Jul 23.

1Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.

Background: Plant biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of plant biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a biomass feedstock worldwide.

Results: We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multi-omics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners.

Conclusion: As a peculiar feature of , we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.
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http://dx.doi.org/10.1186/s13068-018-1198-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6055342PMC
July 2018

Trametes polyzona, an emerging filamentous basidiomycete in Réunion Island.

Mycoses 2017 Jun 16;60(6):412-415. Epub 2017 Feb 16.

Service de Microbiologie, CHU Réunion, St Pierre, France.

We describe two serious Trametes polyzona pulmonary infections, which occurred in Réunion Island, in critically ill patients. The identification was performed using sequencing of the internal transcribed spacer region of ribosomal DNA and D1/D2 region of 28S rDNA. In one case, the significance of T. polyzona in the pathological process was certain, proven by histopathological evidence of fungal lung infection. T. polyzona, an emerging filamentous basidiomycete, prevalent in tropical areas, has not been described so far in human infections.
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http://dx.doi.org/10.1111/myc.12609DOI Listing
June 2017

M-CSF improves protection against bacterial and fungal infections after hematopoietic stem/progenitor cell transplantation.

J Exp Med 2016 10 10;213(11):2269-2279. Epub 2016 Oct 10.

Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, 13288 Marseille, France

Myeloablative treatment preceding hematopoietic stem cell (HSC) and progenitor cell (HS/PC) transplantation results in severe myeloid cytopenia and susceptibility to infections in the lag period before hematopoietic recovery. We have previously shown that macrophage colony-stimulating factor (CSF-1; M-CSF) directly instructed myeloid commitment in HSCs. In this study, we tested whether this effect had therapeutic benefit in improving protection against pathogens after HS/PC transplantation. M-CSF treatment resulted in an increased production of mature myeloid donor cells and an increased survival of recipient mice infected with lethal doses of clinically relevant opportunistic pathogens, namely the bacteria Pseudomonas aeruginosa and the fungus Aspergillus fumigatus M-CSF treatment during engraftment or after infection efficiently protected from these pathogens as early as 3 days after transplantation and was effective as a single dose. It was more efficient than granulocyte CSF (G-CSF), a common treatment of severe neutropenia, which showed no protective effect under the tested conditions. M-CSF treatment showed no adverse effect on long-term lineage contribution or stem cell activity and, unlike G-CSF, did not impede recovery of HS/PCs, thrombocyte numbers, or glucose metabolism. These results encourage potential clinical applications of M-CSF to prevent severe infections after HS/PC transplantation.
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http://dx.doi.org/10.1084/jem.20151975DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068229PMC
October 2016

Exploring the natural fungal biodiversity of tropical and temperate forests toward improvement of biomass conversion.

Appl Environ Microbiol 2012 Sep 6;78(18):6483-90. Epub 2012 Jul 6.

INRA, UMR1163 BCF, Marseille, France.

In this study, natural fungal diversity in wood-decaying species was explored for biomass deconstruction. In 2007 and 2008, fungal isolates were collected in temperate forests mainly from metropolitan France and in tropical forests mainly from French Guiana. We recovered and identified 74 monomorph cultures using morphological and molecular identification tools. Following production of fungal secretomes under inductive conditions, we evaluated the capacity of these fungal strains to potentiate a commercial Trichoderma reesei cellulase cocktail for the release of soluble sugars from biomass. The secretome of 19 isolates led to an improvement in biomass conversion of at least 23%. Of the isolates, the Trametes gibbosa BRFM 952 (Banque de Ressources Fongiques de Marseille) secretome performed best, with 60% improved conversion, a feature that was not universal to the Trametes and related genera. Enzymatic characterization of the T. gibbosa BRFM 952 secretome revealed an unexpected high activity on crystalline cellulose, higher than that of the T. reesei cellulase cocktail. This report highlights the interest in a systematic high-throughput assessment of collected fungal biodiversity to improve the enzymatic conversion of lignocellulosic biomass. It enabled the unbiased identification of new fungal strains issued from biodiversity with high biotechnological potential.
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http://dx.doi.org/10.1128/AEM.01651-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426683PMC
September 2012

FunGene-DB: a web-based tool for Polyporales strains authentication.

J Biotechnol 2012 Oct 2;161(3):383-6. Epub 2012 Jul 2.

INRA, UMR 1163 Biotechnologie des Champignons Filamenteux ESIL, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France.

Polyporales are extensively studied wood-decaying fungi with applications in white and green biotechnologies and in medicinal chemistry. We developed an open-access, user-friendly, bioinformatics tool named FunGene-DB (http://www.fungene-db.org). The goal was to facilitate the molecular authentication of Polyporales strains and fruit-bodies, otherwise subjected to morphological studies. This tool includes a curated database that contains ITS1-5.8S-ITS2 rDNA genes screened through a semi-automated pipeline from the International Nucleotide Sequence Database (INSD), and the similarity search BLASTn program. Today, the web-accessible database compiles 2379 accepted sequences, among which 386 were selected as reference sequences (most often fully identified ITS sequences for which a voucher, strain or specimen, has been deposited in a public-access collection). The restriction of the database to one reference sequence per species (or per clade for species complex) allowed most often unequivocal analysis. We conclude that FunGene-DB is a promising tool for molecular authentication of Polyporales. It should be especially useful for scientists who are not expert mycologists but who need to check the identity of strains (e.g. for culture collections, for applied microbiology).
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http://dx.doi.org/10.1016/j.jbiotec.2012.06.023DOI Listing
October 2012

Fusarium verticillioides secretome as a source of auxiliary enzymes to enhance saccharification of wheat straw.

Bioresour Technol 2012 Jun 10;114:589-96. Epub 2012 Mar 10.

INRA, UMR 1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France.

Fusarium verticillioides secretes enzymes (secretome), some of which might be potentially useful for saccharification of lignocellulosic biomass since supplementation of commercial cellulases from Trichoderma reesei with the F. verticillioides secretome improved the enzymatic release of glucose, xylose and arabinose from wheat straw by 24%, 88% and 68%, respectively. Determination of enzymatic activities revealed a broad range of hemicellulases and pectinases poorly represented in commercial cocktails. Proteomics approaches identified 57 proteins potentially involved in lignocellulose breakdown among a total of 166 secreted proteins. This analysis highlighted the presence of carbohydrate-active enzymes (CAZymes) targeting pectin (from glycoside hydrolase families GH5, GH27, GH28, GH43, GH51, GH54, GH62, GH88 and GH93, polysaccharide lyase family PL4 and carbohydrate esterase family CE8) and hemicelluloses (from glycoside hydrolase families GH3, GH10, GH11, GH30, GH39, GH43 and GH67). These data provide a first step towards the identification of candidates to supplement T. reesei enzyme preparations for lignocellulose hydrolysis.
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http://dx.doi.org/10.1016/j.biortech.2012.03.009DOI Listing
June 2012

Post-genomic analyses of fungal lignocellulosic biomass degradation reveal the unexpected potential of the plant pathogen Ustilago maydis.

BMC Genomics 2012 Feb 2;13:57. Epub 2012 Feb 2.

INRA, UMR BCF, Marseille, France.

Background: Filamentous fungi are potent biomass degraders due to their ability to thrive in ligno(hemi)cellulose-rich environments. During the last decade, fungal genome sequencing initiatives have yielded abundant information on the genes that are putatively involved in lignocellulose degradation. At present, additional experimental studies are essential to provide insights into the fungal secreted enzymatic pools involved in lignocellulose degradation.

Results: In this study, we performed a wide analysis of 20 filamentous fungi for which genomic data are available to investigate their biomass-hydrolysis potential. A comparison of fungal genomes and secretomes using enzyme activity profiling revealed discrepancies in carbohydrate active enzymes (CAZymes) sets dedicated to plant cell wall. Investigation of the contribution made by each secretome to the saccharification of wheat straw demonstrated that most of them individually supplemented the industrial Trichoderma reesei CL847 enzymatic cocktail. Unexpectedly, the most striking effect was obtained with the phytopathogen Ustilago maydis that improved the release of total sugars by 57% and of glucose by 22%. Proteomic analyses of the best-performing secretomes indicated a specific enzymatic mechanism of U. maydis that is likely to involve oxido-reductases and hemicellulases.

Conclusion: This study provides insight into the lignocellulose-degradation mechanisms by filamentous fungi and allows for the identification of a number of enzymes that are potentially useful to further improve the industrial lignocellulose bioconversion process.
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http://dx.doi.org/10.1186/1471-2164-13-57DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3298532PMC
February 2012

Phylogeographic relationships in the polypore fungus Pycnoporus inferred from molecular data.

FEMS Microbiol Lett 2011 Dec 3;325(1):37-48. Epub 2011 Oct 3.

INRA, UMR 1163 de Biotechnologie des Champignons Filamenteux, ESIL, Marseille, France.

The genus Pycnoporus forms a group of four species known especially for producing high redox potential laccases suitable for white biotechnology. A sample of 36 Pycnoporus strains originating from different geographical areas was studied to seek informative molecular markers for the typing of new strains in laboratory culture conditions and to analyse the phylogeographic relationships in this cosmopolitan group. ITS1-5.8S-ITS2 ribosomal DNA and partial regions of β-tubulin and laccase lac3-1 gene were sequenced. Phylogenetic trees inferred from these sequences clearly differentiated the group of Pycnoporus cinnabarinus strains from the group of Pycnoporus puniceus strains into strongly supported clades (100% bootstrap value). Molecular clustering based on lac 3-1 sequences enabled the distribution of Pycnoporus sanguineus and Pycnoporus coccineus through four distinct, well supported clades and sub-clades. A neotropical sub-clade, grouping the P. sanguineus strains from French Guiana and Venezuela, corresponded to P. sanguineus sensu stricto. A paleotropical sub-clade, clustering the strains from Madagascar, Vietnam and New Caledonia, was defined as Pycnoporus cf. sanguineus. The Australian clade corresponded to P. coccineus sensu stricto. The Eastern Asian region clade, clustering the strains from China and Japan, formed a P. coccineus-like group. Laccase gene (lac 3-1) analysis within the Pycnoporus species can highlight enzyme functional diversity associated with biogeographical origin.
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http://dx.doi.org/10.1111/j.1574-6968.2011.02412.xDOI Listing
December 2011

Pycnoporus laccase-mediated bioconversion of rutin to oligomers suitable for biotechnology applications.

Appl Microbiol Biotechnol 2011 Apr 6;90(1):97-105. Epub 2011 Jan 6.

UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, ESIL, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France.

The Pycnoporus fungi are white-rot basidiomycetes listed as food- and cosmetic-grade microorganisms. Three high redox potential laccases from Pycnoporus coccineus and Pycnoporus sanguineus were tested and compared, with the commercial Suberase® as reference, for their ability to synthesise natural active oligomers from rutin (quercetin-3-rutinoside, one of the best-known naturally occurring flavonoid glycosides). The aim of this work was to develop a process with technical parameters (solvent, temperature, reaction time and raw materials) that were easy to scale up for industrial production and compatible with cosmetic and pharmaceutical formulation guidelines. The aqueous mixture of glycerol/ethanol/buffer described in this study met this requirement and allowed the solubilisation of rutin and its oxidative bioconversion into oligomers. The four flavonoid oligomer mixtures synthesised using laccases as catalysts were analysed by high performance liquid chromatography-diode array detection-negative electrospray ionisation-multistage mass spectrometry. Their chromatographic elution profiles were compared and 16 compounds were characterised and identified as dimers and trimers of rutin. The oligorutins were different in Suberase® and Pycnoporus laccase reaction mixtures. They were evaluated for their antioxidant, anti-inflammatory and anti-ageing activities on specific enzymatic targets such as cyclooxygenase (COX-2) and human matrix metalloproteinase 3 (MMP-3). Expressed in terms of IC(50), the flavonoid oligomers displayed a 2.5- to 3-fold higher superoxide scavenging activity than monomeric rutin. Pycnoporus laccase and Suberase® oligorutins led to an inhibition of COX-2 of about 35% and 70%, respectively, while monomeric rutin showed a near-negligible inhibition effect, less than about 10%. The best results on MMP-3 activity were obtained with rutin oligomers from P. sanguineus IMB W006-2 laccase and Suberase® with about 70-75% inhibition.
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http://dx.doi.org/10.1007/s00253-010-3075-4DOI Listing
April 2011

Combination of different molecular mechanisms leading to fluconazole resistance in a Candida lusitaniae clinical isolate.

Diagn Microbiol Infect Dis 2009 Feb 12;63(2):188-93. Epub 2008 Dec 12.

Programme Chimiorésistance des Levures Pathogènes, EA209, UFR des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 75006 Paris, France.

We report on the underlying molecular mechanisms likely responsible for the high-level fluconazole resistance in a Candida lusitaniae clinical isolate. Fluconazole resistance correlated with overexpression of ERG11 and of several efflux pump genes, in particular, the orthologs of the Candida albicans MDR1, PDR16, CDR1, CDR2, and YOR1.
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http://dx.doi.org/10.1016/j.diagmicrobio.2008.10.019DOI Listing
February 2009

Differentiation between atypical isolates of Candida lusitaniae and Candida pulcherrima by determination of mating type.

J Clin Microbiol 2005 Mar;43(3):1430-2

Laboratoire des Sciences Végétales, Faculté de Pharmacie, 4 Avenue de l'Observatoire, 75270 Paris Cedex 06, France.

We report on five clinical isolates routinely identified as Candida lusitaniae that the ID 32C system was unable to discriminate from the closely related species Candida pulcherrima. When additional tests did not allow accurate identification, the less usual mating type test identified all of them as Clavispora lusitaniae. Mating type testing appears to be a valuable tool for assessing the true incidence of this emerging non-albicans Candida species.
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http://dx.doi.org/10.1128/JCM.43.3.1430-1432.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1081254PMC
March 2005

Susceptibility of clinical isolates of Candida lusitaniae to five systemic antifungal agents.

J Antimicrob Chemother 2004 Mar 12;53(3):526-9. Epub 2004 Feb 12.

Laboratoire de Botanique, Cryptogamie et Biologie cellulaire, Faculté de Pharmacie, 13385 Marseille, France.

Objectives: The aim of the present study was to expand the MIC database for Candida lusitaniae in order to further determine its antifungal susceptibility pattern.

Methods: The activities of amphotericin B, fluconazole, itraconazole, voriconazole and flucytosine were determined in vitro against 80 clinical isolates of C. lusitaniae. A set of 59 clinical isolates of Candida albicans and of 51 isolates of Candida glabrata was included to compare the susceptibilities to amphotericin B. The MICs were determined by Etest with RPMI 1640 agar, and with both this medium and antibiotic medium 3 (AM3) agar for testing of amphotericin B.

Results: All isolates were highly susceptible to fluconazole. The susceptibility to itraconazole was good; only 4% of isolates had dose-dependent susceptibility (MICs 0.25-0.5 mg/L). Voriconazole was very active in vitro (100% of isolates were inhibited at < or =0.094 mg/L). Flucytosine MICs ranged widely (0.004->32 mg/L). The set included 19% of flucytosine-resistant isolates. For amphotericin B, 100% of isolates were inhibited at < or =0.75 mg/L (MIC(50) 0.047 mg/L; MIC(90) 0.19 mg/L) and at < or =4 mg/L (MIC(50) 0.25 mg/L; MIC(90) 0.75 mg/L) on RPMI and on AM3, respectively. A single isolate was categorized as resistant to amphotericin B (MIC 0.75 and 4 mg/L on RPMI and on AM3, respectively). Amphotericin B thus appeared very active in vitro against C. lusitaniae. Whatever the test medium, the level of susceptibility of C. lusitaniae to amphotericin B did not differ much from those of C. albicans and C. glabrata.

Conclusion: C. lusitaniae appears to be susceptible to amphotericin B, azole antifungal agents, and, to a lesser extent, flucytosine.
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http://dx.doi.org/10.1093/jac/dkh106DOI Listing
March 2004

Colony morphology switching of Candida lusitaniae and acquisition of multidrug resistance during treatment of a renal infection in a newborn: case report and review of the literature.

Diagn Microbiol Infect Dis 2003 Sep;47(1):331-9

Laboratoire de Botanique, Cryptogamie et Biologie cellulaire, Faculté de Pharmacie, 13385 Marseille, France.

Candida lusitaniae is an emerging opportunistic pathogen which exhibits an unusual antifungal susceptibility pattern. We describe a case of fatal renal infection due to C. lusitaniae in a very low birth weight neonate who was treated with short courses of fluconazole given alternately with amphotericin B. A colony morphology switching was detected on the standard primary culture medium by changes in colony size. Switching was shown to affect deeply the susceptibility to amphotericin B. Afterwards, the switched phenotype developed a cross resistance to fluconazole and itraconazole. Several issues raised by this case are discussed in the light of an extensive review of the literature. Our observations point out the importance of both the detection of colony morphology switching and the close monitoring of antifungal susceptibility in the management of infections due to C. lusitaniae. A judicious therapeutic strategy should prevent the acquisition of multidrug resistance during antifungal therapy.
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http://dx.doi.org/10.1016/s0732-8893(03)00094-4DOI Listing
September 2003