Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.
Identifieur interne : 000440 ( Main/Corpus ); précédent : 000439; suivant : 000441Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.
Auteurs : Elena Fernandez-Fueyo ; Francisco J. Ruiz-Due As ; Patricia Ferreira ; Dimitrios Floudas ; David S. Hibbett ; Paulo Canessa ; Luis F. Larrondo ; Tim Y. James ; Daniela Seelenfreund ; Sergio Lobos ; Rubén Polanco ; Mario Tello ; Yoichi Honda ; Takahito Watanabe ; Takashi Watanabe ; Jae San Ryu ; 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 L. Lavín ; José A. Oguiza ; Gumer Perez ; Antonio G. Pisabarro ; Lucia Ramirez ; Francisco Santoyo ; Emma Master ; Pedro M. Coutinho ; Bernard Henrissat ; Vincent Lombard ; Jon Karl Magnuson ; Ursula Kües ; Chiaki Hori ; Kiyohiko Igarashi ; Masahiro Samejima ; Benjamin W. Held ; Kerrie W. Barry ; Kurt M. Labutti ; Alla Lapidus ; Erika A. Lindquist ; Susan M. Lucas ; Robert Riley ; Asaf A. Salamov ; Dirk Hoffmeister ; Daniel Schwenk ; Yitzhak Hadar ; Oded Yarden ; Ronald P. De Vries ; Ad Wiebenga ; Jan Stenlid ; Daniel Eastwood ; Igor V. Grigoriev ; Randy M. Berka ; Robert A. Blanchette ; Phil Kersten ; Angel T. Martinez ; Rafael Vicuna ; Dan CullenSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 1091-6490 ] ; 2012.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Lignin.
- classification : Basidiomycota.
- genetics : Basidiomycota.
- Genomics, Hydrolysis, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Species Specificity.
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.
DOI: 10.1073/pnas.1119912109
PubMed: 22434909
PubMed Central: PMC3325662
Links to Exploration step
pubmed:22434909Le document en format XML
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<affiliation><nlm:affiliation>Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, E-28040 Madrid, Spain.</nlm:affiliation>
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<date when="2012">2012</date>
<idno type="RBID">pubmed:22434909</idno>
<idno type="pmid">22434909</idno>
<idno type="doi">10.1073/pnas.1119912109</idno>
<idno type="pmc">PMC3325662</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.</title>
<author><name sortKey="Fernandez Fueyo, Elena" sort="Fernandez Fueyo, Elena" uniqKey="Fernandez Fueyo E" first="Elena" last="Fernandez-Fueyo">Elena Fernandez-Fueyo</name>
<affiliation><nlm:affiliation>Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, E-28040 Madrid, Spain.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Ruiz Due As, Francisco J" sort="Ruiz Due As, Francisco J" uniqKey="Ruiz Due As F" first="Francisco J" last="Ruiz-Due As">Francisco J. Ruiz-Due As</name>
</author>
<author><name sortKey="Ferreira, Patricia" sort="Ferreira, Patricia" uniqKey="Ferreira P" first="Patricia" last="Ferreira">Patricia Ferreira</name>
</author>
<author><name sortKey="Floudas, Dimitrios" sort="Floudas, Dimitrios" uniqKey="Floudas D" first="Dimitrios" last="Floudas">Dimitrios Floudas</name>
</author>
<author><name sortKey="Hibbett, David S" sort="Hibbett, David S" uniqKey="Hibbett D" first="David S" last="Hibbett">David S. Hibbett</name>
</author>
<author><name sortKey="Canessa, Paulo" sort="Canessa, Paulo" uniqKey="Canessa P" first="Paulo" last="Canessa">Paulo Canessa</name>
</author>
<author><name sortKey="Larrondo, Luis F" sort="Larrondo, Luis F" uniqKey="Larrondo L" first="Luis F" last="Larrondo">Luis F. Larrondo</name>
</author>
<author><name sortKey="James, Tim Y" sort="James, Tim Y" uniqKey="James T" first="Tim Y" last="James">Tim Y. James</name>
</author>
<author><name sortKey="Seelenfreund, Daniela" sort="Seelenfreund, Daniela" uniqKey="Seelenfreund D" first="Daniela" last="Seelenfreund">Daniela Seelenfreund</name>
</author>
<author><name sortKey="Lobos, Sergio" sort="Lobos, Sergio" uniqKey="Lobos S" first="Sergio" last="Lobos">Sergio Lobos</name>
</author>
<author><name sortKey="Polanco, Ruben" sort="Polanco, Ruben" uniqKey="Polanco R" first="Rubén" last="Polanco">Rubén Polanco</name>
</author>
<author><name sortKey="Tello, Mario" sort="Tello, Mario" uniqKey="Tello M" first="Mario" last="Tello">Mario Tello</name>
</author>
<author><name sortKey="Honda, Yoichi" sort="Honda, Yoichi" uniqKey="Honda Y" first="Yoichi" last="Honda">Yoichi Honda</name>
</author>
<author><name sortKey="Watanabe, Takahito" sort="Watanabe, Takahito" uniqKey="Watanabe T" first="Takahito" last="Watanabe">Takahito Watanabe</name>
</author>
<author><name sortKey="Watanabe, Takashi" sort="Watanabe, Takashi" uniqKey="Watanabe T" first="Takashi" last="Watanabe">Takashi Watanabe</name>
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<author><name sortKey="Ryu, Jae San" sort="Ryu, Jae San" uniqKey="Ryu J" first="Jae San" last="Ryu">Jae San Ryu</name>
</author>
<author><name sortKey="San, Ryu Jae" sort="San, Ryu Jae" uniqKey="San R" first="Ryu Jae" last="San">Ryu Jae San</name>
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<author><name sortKey="Kubicek, Christian P" sort="Kubicek, Christian P" uniqKey="Kubicek C" first="Christian P" last="Kubicek">Christian P. Kubicek</name>
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<author><name sortKey="Schmoll, Monika" sort="Schmoll, Monika" uniqKey="Schmoll M" first="Monika" last="Schmoll">Monika Schmoll</name>
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<author><name sortKey="Gaskell, Jill" sort="Gaskell, Jill" uniqKey="Gaskell J" first="Jill" last="Gaskell">Jill Gaskell</name>
</author>
<author><name sortKey="Hammel, Kenneth E" sort="Hammel, Kenneth E" uniqKey="Hammel K" first="Kenneth E" last="Hammel">Kenneth E. Hammel</name>
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<author><name sortKey="St John, Franz J" sort="St John, Franz J" uniqKey="St John F" first="Franz J" last="St John">Franz J. St John</name>
</author>
<author><name sortKey="Vanden Wymelenberg, Amber" sort="Vanden Wymelenberg, Amber" uniqKey="Vanden Wymelenberg A" first="Amber" last="Vanden Wymelenberg">Amber Vanden Wymelenberg</name>
</author>
<author><name sortKey="Sabat, Grzegorz" sort="Sabat, Grzegorz" uniqKey="Sabat G" first="Grzegorz" last="Sabat">Grzegorz Sabat</name>
</author>
<author><name sortKey="Splinter Bondurant, Sandra" sort="Splinter Bondurant, Sandra" uniqKey="Splinter Bondurant S" first="Sandra" last="Splinter Bondurant">Sandra Splinter Bondurant</name>
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<author><name sortKey="Syed, Khajamohiddin" sort="Syed, Khajamohiddin" uniqKey="Syed K" first="Khajamohiddin" last="Syed">Khajamohiddin Syed</name>
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<author><name sortKey="Yadav, Jagjit S" sort="Yadav, Jagjit S" uniqKey="Yadav J" first="Jagjit S" last="Yadav">Jagjit S. Yadav</name>
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<author><name sortKey="Doddapaneni, Harshavardhan" sort="Doddapaneni, Harshavardhan" uniqKey="Doddapaneni H" first="Harshavardhan" last="Doddapaneni">Harshavardhan Doddapaneni</name>
</author>
<author><name sortKey="Subramanian, Venkataramanan" sort="Subramanian, Venkataramanan" uniqKey="Subramanian V" first="Venkataramanan" last="Subramanian">Venkataramanan Subramanian</name>
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<author><name sortKey="Lavin, Jose L" sort="Lavin, Jose L" uniqKey="Lavin J" first="José L" last="Lavín">José L. Lavín</name>
</author>
<author><name sortKey="Oguiza, Jose A" sort="Oguiza, Jose A" uniqKey="Oguiza J" first="José A" last="Oguiza">José A. Oguiza</name>
</author>
<author><name sortKey="Perez, Gumer" sort="Perez, Gumer" uniqKey="Perez G" first="Gumer" last="Perez">Gumer Perez</name>
</author>
<author><name sortKey="Pisabarro, Antonio G" sort="Pisabarro, Antonio G" uniqKey="Pisabarro A" first="Antonio G" last="Pisabarro">Antonio G. Pisabarro</name>
</author>
<author><name sortKey="Ramirez, Lucia" sort="Ramirez, Lucia" uniqKey="Ramirez L" first="Lucia" last="Ramirez">Lucia Ramirez</name>
</author>
<author><name sortKey="Santoyo, Francisco" sort="Santoyo, Francisco" uniqKey="Santoyo F" first="Francisco" last="Santoyo">Francisco Santoyo</name>
</author>
<author><name sortKey="Master, Emma" sort="Master, Emma" uniqKey="Master E" first="Emma" last="Master">Emma Master</name>
</author>
<author><name sortKey="Coutinho, Pedro M" sort="Coutinho, Pedro M" uniqKey="Coutinho P" first="Pedro M" last="Coutinho">Pedro M. Coutinho</name>
</author>
<author><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name>
</author>
<author><name sortKey="Lombard, Vincent" sort="Lombard, Vincent" uniqKey="Lombard V" first="Vincent" last="Lombard">Vincent Lombard</name>
</author>
<author><name sortKey="Magnuson, Jon Karl" sort="Magnuson, Jon Karl" uniqKey="Magnuson J" first="Jon Karl" last="Magnuson">Jon Karl Magnuson</name>
</author>
<author><name sortKey="Kues, Ursula" sort="Kues, Ursula" uniqKey="Kues U" first="Ursula" last="Kües">Ursula Kües</name>
</author>
<author><name sortKey="Hori, Chiaki" sort="Hori, Chiaki" uniqKey="Hori C" first="Chiaki" last="Hori">Chiaki Hori</name>
</author>
<author><name sortKey="Igarashi, Kiyohiko" sort="Igarashi, Kiyohiko" uniqKey="Igarashi K" first="Kiyohiko" last="Igarashi">Kiyohiko Igarashi</name>
</author>
<author><name sortKey="Samejima, Masahiro" sort="Samejima, Masahiro" uniqKey="Samejima M" first="Masahiro" last="Samejima">Masahiro Samejima</name>
</author>
<author><name sortKey="Held, Benjamin W" sort="Held, Benjamin W" uniqKey="Held B" first="Benjamin W" last="Held">Benjamin W. Held</name>
</author>
<author><name sortKey="Barry, Kerrie W" sort="Barry, Kerrie W" uniqKey="Barry K" first="Kerrie W" last="Barry">Kerrie W. Barry</name>
</author>
<author><name sortKey="Labutti, Kurt M" sort="Labutti, Kurt M" uniqKey="Labutti K" first="Kurt M" last="Labutti">Kurt M. Labutti</name>
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<author><name sortKey="Lapidus, Alla" sort="Lapidus, Alla" uniqKey="Lapidus A" first="Alla" last="Lapidus">Alla Lapidus</name>
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<author><name sortKey="Lindquist, Erika A" sort="Lindquist, Erika A" uniqKey="Lindquist E" first="Erika A" last="Lindquist">Erika A. Lindquist</name>
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<author><name sortKey="Lucas, Susan M" sort="Lucas, Susan M" uniqKey="Lucas S" first="Susan M" last="Lucas">Susan M. Lucas</name>
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<author><name sortKey="Riley, Robert" sort="Riley, Robert" uniqKey="Riley R" first="Robert" last="Riley">Robert Riley</name>
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<author><name sortKey="Salamov, Asaf A" sort="Salamov, Asaf A" uniqKey="Salamov A" first="Asaf A" last="Salamov">Asaf A. Salamov</name>
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<author><name sortKey="Hoffmeister, Dirk" sort="Hoffmeister, Dirk" uniqKey="Hoffmeister D" first="Dirk" last="Hoffmeister">Dirk Hoffmeister</name>
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<author><name sortKey="Schwenk, Daniel" sort="Schwenk, Daniel" uniqKey="Schwenk D" first="Daniel" last="Schwenk">Daniel Schwenk</name>
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<author><name sortKey="Hadar, Yitzhak" sort="Hadar, Yitzhak" uniqKey="Hadar Y" first="Yitzhak" last="Hadar">Yitzhak Hadar</name>
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<author><name sortKey="Yarden, Oded" sort="Yarden, Oded" uniqKey="Yarden O" first="Oded" last="Yarden">Oded Yarden</name>
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</author>
<author><name sortKey="Grigoriev, Igor V" sort="Grigoriev, Igor V" uniqKey="Grigoriev I" first="Igor V" last="Grigoriev">Igor V. Grigoriev</name>
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<author><name sortKey="Berka, Randy M" sort="Berka, Randy M" uniqKey="Berka R" first="Randy M" last="Berka">Randy M. Berka</name>
</author>
<author><name sortKey="Blanchette, Robert A" sort="Blanchette, Robert A" uniqKey="Blanchette R" first="Robert A" last="Blanchette">Robert A. Blanchette</name>
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<author><name sortKey="Kersten, Phil" sort="Kersten, Phil" uniqKey="Kersten P" first="Phil" last="Kersten">Phil Kersten</name>
</author>
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<author><name sortKey="Vicuna, Rafael" sort="Vicuna, Rafael" uniqKey="Vicuna R" first="Rafael" last="Vicuna">Rafael Vicuna</name>
</author>
<author><name sortKey="Cullen, Dan" sort="Cullen, Dan" uniqKey="Cullen D" first="Dan" last="Cullen">Dan Cullen</name>
</author>
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<series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title>
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<imprint><date when="2012" type="published">2012</date>
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<term>Basidiomycota (genetics)</term>
<term>Genomics (MeSH)</term>
<term>Hydrolysis (MeSH)</term>
<term>Lignin (metabolism)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Oxidation-Reduction (MeSH)</term>
<term>Phylogeny (MeSH)</term>
<term>Species Specificity (MeSH)</term>
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<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Lignin</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Basidiomycota</term>
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<keywords scheme="MESH" xml:lang="en"><term>Genomics</term>
<term>Hydrolysis</term>
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<front><div type="abstract" xml:lang="en">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.</div>
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<Month>05</Month>
<Day>21</Day>
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<Title>Proceedings of the National Academy of Sciences of the United States of America</Title>
<ISOAbbreviation>Proc Natl Acad Sci U S A</ISOAbbreviation>
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<ArticleTitle>Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.</ArticleTitle>
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<Abstract><AbstractText>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.</AbstractText>
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<Note>San, Ryu Jae [corrected to Ryu, Jae San]</Note>
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