Held BW

References (3)

Title : Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii - Floudas_2015_Fungal.Genet.Biol_76_78
Author(s) : Floudas D , Held BW , Riley R , Nagy LG , Koehler G , Ransdell AS , Younus H , Chow J , Chiniquy J , Lipzen A , Tritt A , Sun H , Haridas S , LaButti K , Ohm RA , Kues U , Blanchette RA , Grigoriev IV , Minto RE , Hibbett DS
Ref : Fungal Genet Biol , 76 :78 , 2015
Abstract : Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C. torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C. torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited.
ESTHER : Floudas_2015_Fungal.Genet.Biol_76_78
PubMedSearch : Floudas_2015_Fungal.Genet.Biol_76_78
PubMedID: 25683379
Gene_locus related to this paper: 9agar-a0a0d6zyq5 , 9agar-a0a0d7a2p9 , 9agar-a0a0d7a2v2 , 9agar-a0a0d7abt2 , 9agar-a0a0d7acd3 , 9agar-a0a0d7acx0 , 9agar-a0a0d7acx9 , 9agar-a0a0d7adg2 , 9agar-a0a0d7a6d0 , 9agar-a0a0d7aen7 , 9agar-a0a0d7aez7 , 9agar-a0a0d7ahq5 , 9agar-a0a0d7akr6 , 9agar-a0a0d7al29 , 9agar-a0a0d7an16 , 9agar-a0a0d7ann7 , 9agar-a0a0d7anv1 , 9homo-a0a0d7atv2 , 9homo-a0a0d7ay28 , 9homo-a0a0d7ayz7 , 9homo-a0a0d7b1w8 , 9homo-a0a0d7b2p0 , 9homo-a0a0d7b4n4 , 9homo-a0a0d7b624 , 9homo-a0a0d7b7r3 , 9homo-a0a0d7b7w3 , 9homo-a0a0d7bac5 , 9homo-a0a0d7bav7 , 9homo-a0a0d7bbx7 , 9homo-a0a0d7bdn7 , 9homo-a0a0d7bgj9 , 9homo-a0a0d7biw2 , 9homo-a0a0d7bqi1 , 9homo-a0a0d7bv80 , 9agar-a0a0d7b6f6 , 9agar-a0a0d7b976 , 9agar-a0a0d7aeu9 , 9agar-a0a0d7ag53 , 9agar-a0a0d7b8a5

Title : Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot\/brown-rot paradigm for wood decay fungi - Riley_2014_Proc.Natl.Acad.Sci.U.S.A_111_9923
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
Ref : Proc Natl Acad Sci U S A , 111 :9923 , 2014
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.
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

Title : Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis - Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
Author(s) : Fernandez-Fueyo E , Ruiz-Duenas FJ , Ferreira P , Floudas D , Hibbett DS , Canessa P , Larrondo LF , James TY , Seelenfreund D , Lobos S , Polanco R , Tello M , Honda Y , Watanabe T , Ryu JS , Kubicek CP , Schmoll M , Gaskell J , Hammel KE , St John FJ , Vanden Wymelenberg A , Sabat G , Splinter BonDurant S , Syed K , Yadav JS , Doddapaneni H , Subramanian V , Lavin JL , Oguiza JA , Perez G , Pisabarro AG , Ramirez L , Santoyo F , Master E , Coutinho PM , Henrissat B , Lombard V , Magnuson JK , Kues U , Hori C , Igarashi K , Samejima M , Held BW , Barry KW , LaButti KM , Lapidus A , Lindquist EA , Lucas SM , Riley R , Salamov AA , Hoffmeister D , Schwenk D , Hadar Y , Yarden O , de Vries RP , Wiebenga A , Stenlid J , Eastwood D , Grigoriev IV , Berka RM , Blanchette RA , Kersten P , Martinez AT , Vicuna R , Cullen D
Ref : Proc Natl Acad Sci U S A , 109 :5458 , 2012
Abstract : Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn(2+). Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium.
ESTHER : Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
PubMedSearch : Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
PubMedID: 22434909
Gene_locus related to this paper: cers8-m2r3x2 , cers8-m2qf37 , cers8-m2pcy7 , cers8-m2pcz3 , cers8-m2qn26 , cers8-m2r654 , cers8-m2r8g9 , cers8-m2ps90 , cers8-m2qn44 , cers8-m2q837 , cers8-m2pjy6 , cers8-m2r609 , cers8-m2qy35 , cers8-m2r1n1 , cers8-m2rl22 , cers8-m2qkx5 , cers8-m2qib7 , cers8-m2rgs8 , cers8-m2rlx6 , cers8-m2r4p3 , cers8-m2rf62 , cers8-m2qyx5 , cers8-m2pcz2 , cers8-m2rm22 , cers8-m2qwb7 , cers8-m2r9u3 , cers8-m2pp23 , cers8-m2r613 , cers8-m2rup8 , cers8-m2piv7 , cers8-m2rch3 , cers8-m2qvf7 , cers8-m2qvb7 , cers8-m2qvb2 , cers8-m2pip7 , cers8-m2rb73 , cers8-m2qgd3 , cers8-m2rcg8 , cers8-m2rb68