Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis
Elena Fernández-Fueyo,Francisco J. Ruiz-Dueñas,Patricia Ferreira,Dimitrios Floudas,David S. Hibbett,Paulo Canessa,Luis F. Larrondo,Timothy Y. James,Daniela Seelenfreund,Sergio Lobos,Rubén Polanco,Mario Tello,Yoichi Honda,Takahito Watanabe,Takashi Watanabe,Ryu Jae San,Christian P. Kubicek,Monika Schmoll,Jill Gaskell,Kenneth E. Hammel,Franz J. St John,Amber Vanden Wymelenberg,Grzegorz Sabat,Sandra Splinter BonDurant,Khajamohiddin Syed,Jagjit S. Yadav,Harshavardhan Doddapaneni,Venkataramanan Subramanian,José Luis Lavín,José A. Oguiza,Gúmer Pérez,Antonio G. Pisabarro,Lucía Ramírez,Francisco Santoyo,Emma R. Master,Pedro M. Coutinho,Bernard Henrissat,Vincent Lombard,Jon K. Magnuson,Ursula Kües,Chiaki Hori,Kiyohiko Igarashi,Masahiro Samejima,Benjamin W. Held,Kerrie Barry,Kurt LaButti,Alla Lapidus,Erika Lindquist,Susan Lucas,Robert Riley,Asaf Salamov,Dirk Hoffmeister,Daniel Schwenk,Yitzhak Hadar,Oded Yarden,Ronald P. de Vries,Ad Wiebenga,Jan Stenlid,Daniel C. Eastwood,Igor V. Grigoriev,Randy M. Berka,Robert A. Blanchette,Phil Kersten,Ángel T. Martínez,Rafael Vicuña,Dan Cullen +65 more
TLDR
In this paper, a comparative genome analysis of C. subvermispora and P. chrysosporium was conducted to investigate the basis for selective ligninolysis.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 Mn2+. 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.read more
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Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
TL;DR: A new class introduced in the CAZy database is named “Auxiliary Activities” in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion and provides a better coverage of the full extent of the lignin degradation machinery.
Journal ArticleDOI
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
Robert Riley,Asaf Salamov,Daren W. Brown,László Nagy,Dimitrios Floudas,Benjamin W. Held,Anthony Levasseur,Vincent Lombard,Emmanuelle Morin,Robert Otillar,Erika Lindquist,Hui Sun,Kurt LaButti,Jeremy Schmutz,Dina Jabbour,Hong Luo,Scott E. Baker,Antonio G. Pisabarro,Jonathan D. Walton,Robert A. Blanchette,Bernard Henrissat,Francis Martin,Daniel Cullen,David S. Hibbett,Igor V. Grigoriev +24 more
TL;DR: The results indicate that the prevailing paradigm of white rot vs. brown rot does not capture the diversity of fungal wood decay mechanisms, and suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay.
Journal ArticleDOI
Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution.
Grzegorz Janusz,Anna Pawlik,Justyna Sulej,Urszula Świderska-Burek,Anna Jarosz-Wilkołazka,Andrzej Paszczynski +5 more
TL;DR: A detailed description of low molecular weight compounds is presented, which gives these organisms not only an advantage in wood degradation processes, but seems rather to be a new evolutionatory alternative to enzymatic combustion.
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Genome sequence of the model medicinal mushroom Ganoderma lucidum
Shilin Chen,Jiang Xu,Chang Liu,Yingjie Zhu,David R. Nelson,Shiguo Zhou,Chunfang Li,Lizhi Wang,Xu Guo,Yongzhen Sun,Hongmei Luo,Ying Li,Jingyuan Song,Bernard Henrissat,Anthony Levasseur,Jun Qian,Jianqin Li,Xiang Luo,Linchun Shi,Liu He,Li Xiang,Xiaolan Xu,Yunyun Niu,Qiushi Li,Mira V. Han,Haixia Yan,Jin Zhang,Haimei Chen,Aiping Lv,Zhen Wang,Mingzhu Liu,David C. Schwartz,Chao Sun +32 more
TL;DR: The sequence analysis reveals an impressive array of genes encoding cytochrome P450s (CYPs), transporters and regulatory proteins that cooperate in secondary metabolism, making this organism a potential model system for the study of secondary metabolic pathways and their regulation in medicinal fungi.
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Exploring bacterial lignin degradation.
TL;DR: Recent advances in studying bacterial lignin degradation as an approach to exploring greater diversity in the environment are discussed.
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