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2. Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

Author

Suzuki Hitoshi, MacDonald Jacqueline, Syed Khajamohiddin, Salamov Asaf, Hori Chiaki, Aerts Andrea, Henrissat Bernard, Wiebenga Ad, vanKuyk Patricia A, Barry Kerrie, Lindquist Erika, LaButti Kurt, Lapidus Alla, Lucas Susan, Coutinho Pedro, Gong Yunchen, Samejima Masahiro, Mahadevan Radhakrishnan, Abou-Zaid Mamdouh, de Vries Ronald P, Igarashi Kiyohiko, Yadav Jagjit S, Grigoriev Igor V, and Master Emma R

Subjects
Phanerochaete carnosa, Comparative genomics, Phanerochaete chrysosporium, Softwood degradation, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome. Results P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood. Conclusions The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.

Published
2012
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6. Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

Author

Hori, Chiaki, Ishida, Takuya, Igarashi, Kiyohiko, Samejima, Masahiro, Suzuki, Hitoshi, Master, Emma, Ferreira, Patricia, Ruiz-Dueñas, Francisco J., Held, Benjamin, Canessa, Paulo, Larrondo, Luis F., Schmoll, Monika, Druzhinina, Irina S., Kubicek, Christian P., Gaskell, Jill A., Kersten, Phil, St. John, Franz, Glasner, Jeremy, Sabat, Grzegorz, Splinter BonDurant, Sandra, Syed, Khajamohiddin, Yadav, Jagjit, Mgbeahuruike, Anthony C., Kovalchuk, Andriy, Asiegbu, Fred O., Lackner, Gerald, Hoffmeister, Dirk, Rencoret, Jorge, Gutiérrez, Ana, Sun, Hui, Lindquist, Erika, Barry, Kerrie, Riley, Robert, Grigoriev, Igor V., Henrissat, Bernard, Kües, Ursula, Berka, Randy M., Martínez, Angel T., Covert, Sarah F., Blanchette, Robert A., and Cullen, Daniel

Published
2014

8. Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

Author

Suzuki, Hitoshi, MacDonald, Jacqueline, Syed, Khajamohiddin, Salamov, Asaf, Hori, Chiaki, Aerts, Andrea, Henrissat, Bernard, Wiebenga, Ad, vanKuyk, Patricia A., Barry, Kerrie, Lindquist, Erika, LaButti, Kurt, Lapidus, Alla, Lucas, Susan, Coutinho, Pedro, Gong, Yunchen, Samejima, Masahiro, Mahadevan, Radhakrishnan, Abou-Zaid, Mamdouh, Vries, Ronald P. de, Igarashi, Kiyohiko, Yadav, Jagit S., Grigoriev, Igor V., and Master, Emma R.

Subjects
Phanerochaete carnosa, Comparative genomics, Phanerochaete chrysosporium, softwood degradation
Abstract

BackgroundSoftwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome.ResultsP. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood.ConclusionsThe P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.

Published
2012

9. The Paleozoic origin of enzymatic mechanisms for lignin degradation reconstructed using 31 fungal genomes

Author

Floudas, Dimitrios, Binder, Manfred, Riley, Robert, Barry, Kerrie, Blanchette, Robert A, Henrissat, Bernard, Martinez, Angel T., Otillar, Robert, Spatafora, Joseph W., Yadav, Jagit S., Aerts, Andrea, Benoit, Isabelle, Boyd, Alex, Carlson, Alexis, Copeland, Alex, Coutinho, Pedro M., Vries, Ronald P. de, Ferreira, Patricia, Findley, Keisha, Foster, Brian, Gaskell, Jill, Glotzer, Dylan, Gorecki, Pawel, Heitman, Joseph, Hesse, Cedar, Hori, Chiaki, Igarashi, Kiyohiko, Jurgens, Joel A., Kallen, Nathan, Kersten, Phil, Kohler, Annegret, Kues, Ursula, Kumar, T. K. Arun, Kuo, Alan, LaButti, Kurt, Larrondo, Luis F., Lindquist, Erika, Ling, Albee, Lombard, Vincent, Lucas, Susan, Lundell, Taina, Martin, Rachael, McLaughlin, David J., Morgenstern, Ingo, Morin, Emanuelle, Murat, Claude, Nagy, Laszlo G., Nolan, Matt, Ohm, Robin A., Patyshakuliyeva, Aleksandrina, Rokas, Antonis, Ruiz-Duenas, Francisco J., Sabat, Grzegorz, Salamov, Asaf, Samejima, Masahiro, Schmutz, Jeremy, Slot, Jason C., John, Franz St., Stenlid, Jan, Sun, Hui, Sun, Sheng, Syed, Khajamohiddin, Tsang, Adrian, Wiebenga, Ad, Young, Darcy, Pisabarro, Antonio, Eastwood, Daniel C., Martin, Francis, Cullen, Dan, Grigoriev, Igor V., and Hibbett, David S.

Abstract

Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non?lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.

Published
2012

10. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis

Author

Fernandez-Fueyo, Elena, Ruiz-Duenas, Francisco J., Ferreira, Patrica, Floudas, Dimitrios, HIbbett, David S., Canessa, Paulo, Larrondo, Luis F., James, Tim Y., Seelenfreund, Daniela, Lobos, Sergio, Polanco, Ruben, Tello, Mario, Honda, Yoichi, Watanabe, Takahito, Watanabe, Takashi, Ryu, Jae San, Kubicek, Christian P., Schmoll, Monika, Gaskell, Jill, Hammel, Kenneth E., John, Franz J. St., Wymelenberg, Amber Vanden, Sabat, Grzegorz, BonDurant, Sandra Splinter, Syed, Khajamohiddin, Yadav, Jagjit S., Doddapaneni, Harshavardhan, Subramanian, Venkataramanan, Lavin, Jose L., Oguiza, Jose A., Perez, Gumer, Pisabarro, Antonio G., Ramirez, Lucia, Santoyo, Francisco, Master, Emma, Coutinho, Pedro M., Henrissat, Bernard, Lombard, Vincent, Magnuson, Jon Karl, Kues, 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, Vries, Ronald P. de, Wiebenga, Ad, Stenlid, Jan, Eastwood, Daniel, Grigoriev, Igor V., Berka, Randy M., Blanchette, Robert A., Kersten, Phil, Martinez, Angel T., Vicuna, Rafael, and Cullen, Dan

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.

Published
2012

23. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

Author

Flundas, Dimitrios, Binder, Manfred, Riley, Robert, Barry, Kerrie, Blanchette, Robert A., Henrissat, Bernard, Martínez, Angel T., Otillar, Robert, Spatafora, Joseph W., Yadav, Jagjit S., Aerts, Andrea, Benoit, Isabelle, Boyd, Alex, Carlson, Alexis, Copeland, Alex, Coutinho, Pedro M., de Vries, Ronald P., Ferreira, Patricia, Findley, Keisha, Foster, Brian, Gaskell, Jill, Glotzer, Dylan, Górecki, Paweł, Heitman, Joseph, Hesse, Cedar, Hori, Chiaki, Igarashi, Kiyohiko, Jurgens, Joel A., Kallen, Nathan, Kersten, Phil, Kohler, Annegret, Kües, Ursula, Kumar, T. K. Arun, Kuo, Alan, LaButti, Kurt, Larrondo, Luis F., Lindquist, Erika, Ling, Albee, Lombard, Vincent, Lucas, Susan, Lundell, Taina, Martin, Rachael, McLaughlin, David J., Morgenstern, Ingo, Morin, Emanuelle, Murat, Claude, Nagy, Laszlo G., Nolan, Matt, Ohm, Robin A., Patyshakuliyeva, Aleksandrina, Rokas, Antonis, Ruiz-Dueñas, Francisco J., Sabat, Grzegorz, Salamov, Asaf, Samejima, Masahiro, Schmutz, Jeremy, Slot, Jason C., St. John, Franz, Stenlid, Jan, Sun, Hui, Sun, Sheng, Syed, Khajamohiddin, Tsang, Adrian, Wiebenga, Ad, Young, Darcy, Pisabarro, Antonio, Eastwood, Daniel C., Martin, Francis, Cullen, Dan, Grigoriev, Igor V., and Hibbett, David S.

Published
2012
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30. Acetylated Xylan Degradation by Glycoside Hydrolase Family 10 and 11 Xylanases from the White-rot Fungus Phanerochaete chrysosporium

Author

Kojima, Keisuke, Sunagawa, Naoki, Yoshimi, Yoshihisa, Tryfona, Theodora, Samejima, Masahiro, Dupree, Paul, Igarashi, Kiyohiko, Igarashi, Kiyohiko [0000-0001-5152-7177], and Apollo - University of Cambridge Repository

Subjects
Phanerochaete chrysosporium, xylanase, acetylated xylan, glycoside hydrolase, biomass utilization
Abstract

Endo-type xylanases are key enzymes in microbial xylanolytic systems, and xylanases belonging to glycoside hydrolase (GH) families 10 or 11 are the major enzymes degrading xylan in nature. These enzymes have typically been characterized using xylan prepared by alkaline extraction, which removes acetyl sidechains from the substrate, and thus the effect of acetyl groups on xylan degradation remains unclear. Here, we compare the ability of GH10 and 11 xylanases, PcXyn10A and PcXyn11B, from the white-rot basidiomycete Phanerochaete chrysosporium to degrade acetylated and deacetylated xylan from various plants. Product quantification revealed that PcXyn10A effectively degraded both acetylated xylan extracted from Arabidopsis thaliana and the deacetylated xylan obtained by alkaline treatment, generating xylooligosaccharides. In contrast, PcXyn11B showed limited activity towards acetyl xylan, but showed significantly increased activity after deacetylation of the xylan. Polysaccharide analysis using carbohydrate gel electrophoresis showed that PcXyn11B generated a broad range of products from native acetylated xylans extracted from birch wood and rice straw, including large residual xylooligosaccharides, while non-acetylated xylan from Japanese cedar was readily degraded into xylooligosaccharides. These results suggest that the degradability of native xylan by GH11 xylanases is highly dependent on the extent of acetyl group substitution. Analysis of 31 fungal genomes in the Carbohydrate-Active enZymes database indicated that the presence of GH11 xylanases is correlated to that of carbohydrate esterase (CE) family 1 acetyl xylan esterases (AXEs), while this is not the case for GH10 xylanases. These findings may imply co-evolution of GH11 xylanases and CE1 AXEs.

Published
2022

40. Role of Tryptophan 38 in Loading Substrate Chain into the Active-site Tunnel of Cellobiohydrolase I from Trichoderma reesei

Author

Nakamura, Akihiko, Kanazawa, Takashi, Furuta, Tadaomi, Sakurai, Minoru, Saloheimo, Markku, Samejima, Masahiro, Koivula, Anu, and Igarashi, Kiyohiko

Subjects
cellobiohydrolase, steady-state kinetics, Trichoderma reesei, Regular Paper, processive reaction
Abstract

Cellobiohydrolase I from Trichoderma reesei ( Tr Cel7A) is one of the best-studied cellulases, exhibiting high activity towards crystalline cellulose. Tryptophan residues at subsites -7 and -4 (Trp40 and Trp38 respectively) are located at the entrance and middle of the tunnel-like active site of Tr Cel7A, and are conserved among the GH family 7 cellobiohydrolases. Trp40 of Tr Cel7A is important for the recruitment of cellulose chain ends on the substrate surface, but the role of Trp38 is less clear. Comparison of the effects of W38A and W40A mutations on the binding energies of sugar units at the two subsites indicated that the contribution of Trp38 to the binding was greater than that of Trp40. In addition, the smooth gradient of binding energy was broken in W38A mutant. To clarify the importance of Trp38, the activities of Tr Cel7A WT and W38A towards crystalline cellulose and amorphous cellulose were compared. W38A was more active than WT towards amorphous cellulose, whereas its activity towards crystalline cellulose was only one-tenth of that of WT. To quantify the effect of mutation at subsite -4, we measured kinetic parameters of Tr Cel7A WT, W40A and W38A towards cello-oligosaccharides. All combinations of enzymes and substrates showed substrate inhibition, and comparison of the inhibition constants showed that the Trp38 residue increases the velocity of substrate intake ( k on for forming productive complex) from the minus side of the subsites. These results indicate a key role of Trp38 residue in processively loading the reducing-end of cellulose chain into the catalytic tunnel.

Published
2021
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48. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

Author

Floudas, Dimitrios, Binder, Manfred, Riley, Robert, Barry, Kerrie, Blanchette, Robert A., Henrissat, Bernard, Martínez, Angel T., Otillar, Robert, Spatafora, Joseph W., Yadav, Jagjit S., Aerts, Andrea, Benoit, Isabelle, Boyd, Alex, Carlson, Alexis, Copeland, Alex, Coutinho, Pedro M., de Vries, Ronald P., Ferreira, Patricia, Findley, Keisha, Foster, Brian, Gaskell, Jill, Glotzer, Dylan, Górecki, Paweł, Heitman, Joseph, Hesse, Cedar, Hori, Chiaki, Igarashi, Kiyohiko, Jurgens, Joel A., Kallen, Nathan, Kersten, Phil, Kohler, Annegret, Kües, Ursula, Kumar, Arun T. K., Kuo, Alan, LaButti, Kurt, Larrondo, Luis F., Lindquist, Erika, Ling, Albee, Lombard, Vincent, Lucas, Susan, Lundell, Taina, Martin, Rachael, McLaughlin, David J., Morgenstern, Ingo, Morin, Emanuelle, Murat, Claude, Nagy, Laszlo G., Nolan, Matt, Ohm, Robin A., Patyshakuliyeva, Aleksandrina, Rokas, Antonis, Ruiz-Dueñas, Francisco J., Sabat, Grzegorz, Salamov, Asaf, Samejima, Masahiro, Schmutz, Jeremy, Slot, Jason C., John, Franz St., Stenlid, Jan, Sun, Hui, Sun, Sheng, Syed, Khajamohiddin, Tsang, Adrian, Wiebenga, Ad, Young, Darcy, Pisabarro, Antonio, Eastwood, Daniel C., Martin, Francis, Cullen, Dan, Grigoriev, Igor V., and Hibbett, David S.

Published
2012
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