Comparative genomics of
Ceriporiopsis subvermispora
and
Phanerochaete chrysosporium
provide insight into selective ligninolysis
Authors: Fernandez-Fueyo Elena , Ruiz-Dueñas Francisco J. , Ferreira Patricia , Floudas Dimitrios , Hibbett David S. , Canessa Paulo , Larrondo Luis F. , James Tim Y. , Seelenfreund Daniela , Lobos Sergio , Polanco Rubén , Tello Mario , Honda Yoichi , Watanabe Takahito , Watanabe Takashi , Ryu Jae San , Kubicek Christian P. , Schmoll Monika , Gaskell Jill , Hammel Kenneth E. , St. John Franz J. , Vanden Wymelenberg Amber , Sabat Grzegorz , Splinter BonDurant Sandra , Syed Khajamohiddin , Yadav Jagjit S. , Doddapaneni Harshavardhan , Subramanian Venkataramanan , Lavín José L. , Oguiza José A. , Perez Gumer , Pisabarro Antonio G. , Ramirez Lucia , Santoyo Francisco , Master Emma , Coutinho Pedro M. , Henrissat Bernard , Lombard Vincent , Magnuson Jon Karl , Kües Ursula , Hori Chiaki , Igarashi Kiyohiko , Samejima Masahiro , Held Benjamin W. , Barry Kerrie W. , LaButti Kurt M. , Lapidus Alla , Lindquist Erika A. , Lucas Susan M. , Riley Robert , Salamov Asaf A. , Hoffmeister Dirk , Schwenk Daniel , Hadar Yitzhak , Yarden Oded , de Vries Ronald P. , Wiebenga Ad , Stenlid Jan , Eastwood Daniel , Grigoriev Igor V. , Berka Randy M. , Blanchette Robert A. , Kersten Phil , Martinez Angel T. , Vicuna Rafael , Cullen Dan 
Published: March 2012

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
.