Author Report for: Levasseur ANo contact information in database for Levasseur A
de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M and Grigoriev IV <107 more author(s)> de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram O, Benocci T, Braus-Stromeyer SA, Caldana C, Canovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damasio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hilden KS, Hope R, Hossain A, Karabika E, Karaffa L, Karanyi Z, Krasevec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, Maccabe A, Makela MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnar AP, Mule G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramon A, Rauscher S, Record E, Riano-Pachon DM, Robert V, Rohrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sandor E, Sanguinetti M, Schutze T, Sepcic K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pocsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV (- 107) Ref: Genome Biol, 18:28, 2017 : PubMed ESTHER: de Vries_2017_Genome.Biol_18_28 PubMedSearch: de Vries 2017 Genome.Biol 18 28 PubMedID: 28196534 Gene_locus related to this paper: asptu-a0a1l9nhd0, aspve-a0a1l9pxx8, aspve-a0a1l9q4m3, aspwe-a0a1l9s133, 9euro-a0a1l9t3v9, aspwe-a0a1l9rcx6, aspna-g3y5a6, aspgl-a0a1l9v4d3, 9euro-a0a1l9sa36, aspsb-a0a319eji6, aspve-a0a1l9px96, 9euro-a0a1l9tay1, aspgl-a0a1l9vbc0, aspc5-a0a1r3rh65, 9euro-a0a2v5i956, aspwe-a0a1l9rpp6, aspna-g3xpw9, aspve-a0a1l9plv1, 9euro-a0a1l9tk47, aspve-a0a1l9pde9, aspve-a0a1l9pz72, aspwe-a0a1l9rde6, 9euro-a0a1l9tdb5, aspkw-g7xq95, aspbc-a0a1l9u6h4, aspbc-a0a1l9u2l4, asptc-a0a1l9mx83, aspgl-a0a1l9ve90, aspve-a0a1l9pvz9, 9euro-a0a1l9tdh3, aspc5-a0a1r3rmn9, aspwe-a0a1l9rlq2, asptc-a0a1l9nby7, aspng-a0a100i8t9, aspc5-a0a1r3rem6, aspbc-a0a1l9uy89, aspa1-anee, aspa1-aneh, aspa1-acrc, aspbc-alba, aspa1-acui Abstract BACKGROUND: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi. Title: Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E and Grigoriev IV <15 more author(s)> Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R, Lindquist EA, Sun H, LaButti KM, Schmutz J, Jabbour D, Luo H, Baker SE, Pisabarro AG, Walton JD, Blanchette RA, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV (- 15) Ref: Proc Natl Acad Sci U S A, 111:9923, 2014 : PubMed ESTHER: Riley_2014_Proc.Natl.Acad.Sci.U.S.A_111_9923 PubMedSearch: Riley 2014 Proc.Natl.Acad.Sci.U.S.A 111 9923 PubMedID: 24958869 Gene_locus related to this paper: pleos-a0a067nlj6, 9agar-a0a067t0n0, 9agar-a0a067sha0, 9homo-a0a067pav0, pleos-a0a067n337, 9homo-a0a067pz82, 9homo-a0a067m7p7, pleos-a0a067p245, 9homo-a0a067lrz6, 9homo-a0a067m4r5, 9homo-a0a067mr63, 9homo-a0a067mrq8, 9agar-a0a067t4j6, 9homo-a0a067pdz2, 9homo-a0a067q2n9, 9agar-a0a067tsx5, 9homo-a0a067mfq5, 9homo-a0a067qc90, pleos-a0a067p113, 9homo-a0a067pwi6, 9agar-a0a067s6d7, 9agar-a0a067tie7, pleos-a0a067ngc3, 9agar-a0a067st69, 9agar-a0a067t6h9, 9agar-a0a067tj80, pleos-a0a067npl2, 9agar-a0a067sm07, 9agar-a0a067tar9, 9agar-a0a067tid6, 9agar-a0a067u335, pleos-a0a067ndv5, pleos-a0a067nqw6, 9homo-a0a067pkj2, 9agar-a0a067t683, 9homo-a0a067mgl1, 9agar-a0a067sg35, 9homo-a0a067q7g6, 9agar-a0a067tub0, 9agar-a0a067t8f5, 9agar-a0a067tj19, 9homo-a0a067pyu9, 9agar-a0a067tjp8, 9agar-a0a067sjg9, 9agar-a0a067u0h4, pleos-a0a067nxe9, 9agar-a0a067sqt2, 9agar-a0a067tgx3, 9homo-a0a067psv8, 9agar-a0a067sq58, 9homo-a0a067m4m0, 9agar-a0a067tqz5, pleos-a0a067new9, 9homo-a0a067m9v3, 9agar-a0a067tlx5, 9agar-a0a067tfq4, pleos-a0a067nln4, pleos-a0a067ndf5, pleos-a0a067nn26, pleos-a0a067nfv2, 9homo-a0a067pnd3, 9agar-a0a067sw48, pleos-a0a067neg3, pleos-a0a067nz51, pleos-a0a067naf9, pleos-a0a067nad7, 9agar-a0a067sxe2, 9agar-a0a067slu3, pleos-a0a067n7p8, pleos-a0a067nl60, pleos-a0a067ncd0, 9agar-a0a067th99, 9agar-a0a067sp22, pleos-a0a067pbw7, 9homo-a0a067q916, 9homo-a0a067pwe5, galm3-a0a067scb0, galm3-popa Abstract Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay. Title: The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry de Wit PJ, van der Burgt A, Okmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P and Bradshaw RE <29 more author(s)> de Wit PJ, van der Burgt A, Okmen B, Stergiopoulos I, Abd-Elsalam KA, Aerts AL, Bahkali AH, Beenen HG, Chettri P, Cox MP, Datema E, de Vries RP, Dhillon B, Ganley AR, Griffiths SA, Guo Y, Hamelin RC, Henrissat B, Kabir MS, Jashni MK, Kema G, Klaubauf S, Lapidus A, Levasseur A, Lindquist E, Mehrabi R, Ohm RA, Owen TJ, Salamov A, Schwelm A, Schijlen E, Sun H, van den Burg HA, van Ham RC, Zhang S, Goodwin SB, Grigoriev IV, Collemare J, Bradshaw RE (- 29) Ref: PLoS Genet, 8:e1003088, 2012 : PubMed ESTHER: de Wit_2012_PLoS.Genet_8_E1003088 PubMedSearch: de Wit 2012 PLoS.Genet 8 E1003088 PubMedID: 23209441 Gene_locus related to this paper: mycpj-q30dw8, mycp1-n1pnd6, mycp1-n1per0, mycp1-n1pg49, mycp1-n1pwj1, mycp1-n1pcl8, mycp1-m2y2b1, mycp1-n1pwu7, mycp1-n1ppa8, mycp1-m2yk59, mycp1-n1pps5, mycp1-n1pw13, mycp1-n1pe19, mycp1-m2xhl1, mycp1-n1pnh6, mycp1-n1psn5, mycp1-n1puh9, mycp1-n1phf7, mycp1-m2y2h4, mycp1-n1q523, dotsn-n1q1b1, dotsn-n1q415, dotsn-est1 Abstract We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an alpha-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation. Title: Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U and Breuil C <13 more author(s)> DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U, Alamouti SM, Tsui CK, Docking RT, Levasseur A, Haridas S, Robertson G, Birol I, Holt RA, Marra MA, Hamelin RC, Hirst M, Jones SJ, Bohlmann J, Breuil C (- 13) Ref: Proc Natl Acad Sci U S A, 108:2504, 2011 : PubMed ESTHER: Diguistini_2011_Proc.Natl.Acad.Sci.U.S.A_108_2504 PubMedSearch: Diguistini 2011 Proc.Natl.Acad.Sci.U.S.A 108 2504 PubMedID: 21262841 Gene_locus related to this paper: grocl-dapb, grocl-f0x6y5, grocl-f0x7n2, grocl-f0x8u4, grocl-f0x9c7, grocl-f0x9d5, grocl-f0x966, grocl-f0xbs9, grocl-f0xc51, grocl-f0xcj4, grocl-f0xee9, grocl-f0xh50, grocl-f0xip5, grocl-f0xjv7, grocl-f0xk48, grocl-f0xke2, grocl-f0xkp2, grocl-f0xl11, grocl-f0xl25, grocl-f0xlh9, grocl-f0xm76, grocl-f0xnw8, grocl-f0xsu8, grocl-f0xtk0, grocl-f0xtm0, grocl-f0xv04, grocl-f0x8s2, grocl-f0xa18, grocl-f0xm17, grocl-f0x801, grocl-f0xfy2 Abstract In western North America, the current outbreak of the mountain pine beetle (MPB) and its microbial associates has destroyed wide areas of lodgepole pine forest, including more than 16 million hectares in British Columbia. Grosmannia clavigera (Gc), a critical component of the outbreak, is a symbiont of the MPB and a pathogen of pine trees. To better understand the interactions between Gc, MPB, and lodgepole pine hosts, we sequenced the approximately 30-Mb Gc genome and assembled it into 18 supercontigs. We predict 8,314 protein-coding genes, and support the gene models with proteome, expressed sequence tag, and RNA-seq data. We establish that Gc is heterothallic, and report evidence for repeat-induced point mutation. We report insights, from genome and transcriptome analyses, into how Gc tolerates conifer-defense chemicals, including oleoresin terpenoids, as they colonize a host tree. RNA-seq data indicate that terpenoids induce a substantial antimicrobial stress in Gc, and suggest that the fungus may detoxify these chemicals by using them as a carbon source. Terpenoid treatment strongly activated a approximately 100-kb region of the Gc genome that contains a set of genes that may be important for detoxification of these host-defense chemicals. This work is a major step toward understanding the biological interactions between the tripartite MPB/fungus/forest system. Title: Genome sequence of the model mushroom Schizophyllum commune Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A and Wosten HA <22 more author(s)> Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kues U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, vanKuyk PA, Horton JS, Grigoriev IV, Wosten HA (- 22) Ref: Nat Biotechnol, 28:957, 2010 : PubMed ESTHER: Ohm_2010_Nat.Biotechnol_28_957 PubMedSearch: Ohm 2010 Nat.Biotechnol 28 957 PubMedID: 20622885 Gene_locus related to this paper: schcm-d8pqz6, schcm-d8prj2, schcm-d8pug6, schcm-d8pxe8, schcm-d8pxe9, schcm-d8pxz1, schcm-d8q1c7, schcm-d8q2b4, schcm-d8q3j1, schcm-d8q5m5, schcm-d8q7x7.1, schcm-d8q7x7.2, schcm-d8q8y8, schcm-d8q9n6, schcm-d8q697, schcm-d8qip8, schcm-d8q5s5, schcm-d8ppb3, schcm-d8ppb6, schcm-d8pv73, schcm-d8pzm1, schcm-d8q5a7, schcm-d8qif0 Abstract Much remains to be learned about the biology of mushroom-forming fungi, which are an important source of food, secondary metabolites and industrial enzymes. The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass. Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune. Whereas inactivation of one of these, fst4, prevented mushroom formation, inactivation of another, fst3, resulted in more, albeit smaller, mushrooms than in the wild-type fungus. Antisense transcripts may also have a role in the formation of fruiting bodies. Better insight into the mechanisms underlying mushroom formation should affect commercial production of mushrooms and their industrial use for producing enzymes and pharmaceuticals. Title: Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family Levasseur A, Gouret P, Lesage-Meessen L, Asther M, Record E, Pontarotti P Ref: BMC Evol Biol, 6:92, 2006 : PubMed ESTHER: Levasseur_2006_BMC.Evol.Biol_6_92 PubMedSearch: Levasseur 2006 BMC.Evol.Biol 6 92 PubMedID: 17092334 Abstract BACKGROUND: There have been many claims of adaptive molecular evolution, but what role does positive selection play in functional divergence? The aim of this study was to test the relationship between evolutionary and functional shifts with special emphasis on the role of the environment. For this purpose, we studied the fungal lipase/feruloyl esterase A family, whose functional diversification makes it a very promising candidate. Title: Homologous expression of the feruloyl esterase B gene from Aspergillus niger and characterization of the recombinant enzyme Levasseur A, Benoit I, Asther M, Record E Ref: Protein Expr Purif, 37:126, 2004 : PubMed ESTHER: Levasseur_2004_Protein.Expr.Purif_37_126 PubMedSearch: Levasseur 2004 Protein.Expr.Purif 37 126 PubMedID: 15294290 Gene_locus related to this paper: aspng-faeb Abstract The faeB gene encoding the feruloyl esterase B (FAEB) was isolated from Aspergillus niger BRFM131 genomic DNA. The faeB gene, with additional sequence coding for a C-terminal histidine tag, was inserted into an expression vector under the control of the gpd promoter and trpC terminator and expressed in a protease deficient A. niger strain. Homologous overproduction allows to reach an esterase activity of 18 nkat mL(-1) against MCA as substrate. The improvement factor was 16-fold higher as compared to the production level obtained with non-transformed A. niger strain induced by sugar beet pulp. The corresponding secretion yield was estimated to be around 100 mg L(-1). Recombinant FAEB was purified 14.6-fold to homogeneity from an 8-day-old culture by a single affinity chromatographic step with a recovery of 64%. SDS-PAGE revealed a single band with a molecular mass of 75 kDa, while under non-denatured conditions, native enzyme has a molecular mass of around 150 kDa confirming that the recombinant FAEB is a homodimer. The recombinant and native FAEB have the same characteristics concerning temperature and pH optima, i.e., 50 degrees C and 6, respectively. In addition, the recombinant FAEB was determined to be quite stable up to 50 degrees C for 120 min. Kinetic constants for MCA, MpCA, and chlorogenic acid (5-O-caffeoyl quinic acid) were as follows: Km: 0.13, 0.029, and 0.16 mM and Vmax: 1101, 527.6, and 28.3 nkat mg(-1), respectively. This is the first report on the homologous overproduction of feruloyl esterase B in A. niger. | |||||||
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