Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
Abstract Background Plant biomass degradation by fungal-derived enzymes is rapidly expanding in economic importance as a clean and efficient source for biofuels. The ability to rationally engineer filamentous fungi would facilitate biotechnological applications for degradation of plant cell wall pol...
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| Format: | Article |
| Language: | English |
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BMC
2017-09-01
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| Series: | Biotechnology for Biofuels |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13068-017-0901-2 |
| _version_ | 1828338657851867136 |
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| author | Areejit Samal James P. Craig Samuel T. Coradetti J. Philipp Benz James A. Eddy Nathan D. Price N. Louise Glass |
| author_facet | Areejit Samal James P. Craig Samuel T. Coradetti J. Philipp Benz James A. Eddy Nathan D. Price N. Louise Glass |
| author_sort | Areejit Samal |
| collection | DOAJ |
| description | Abstract Background Plant biomass degradation by fungal-derived enzymes is rapidly expanding in economic importance as a clean and efficient source for biofuels. The ability to rationally engineer filamentous fungi would facilitate biotechnological applications for degradation of plant cell wall polysaccharides. However, incomplete knowledge of biomolecular networks responsible for plant cell wall deconstruction impedes experimental efforts in this direction. Results To expand this knowledge base, a detailed network of reactions important for deconstruction of plant cell wall polysaccharides into simple sugars was constructed for the filamentous fungus Neurospora crassa. To reconstruct this network, information was integrated from five heterogeneous data types: functional genomics, transcriptomics, proteomics, genetics, and biochemical characterizations. The combined information was encapsulated into a feature matrix and the evidence weighted to assign annotation confidence scores for each gene within the network. Comparative analyses of RNA-seq and ChIP-seq data shed light on the regulation of the plant cell wall degradation network, leading to a novel hypothesis for degradation of the hemicellulose mannan. The transcription factor CLR-2 was subsequently experimentally shown to play a key role in the mannan degradation pathway of N. crassa. Conclusions Here we built a network that serves as a scaffold for integration of diverse experimental datasets. This approach led to the elucidation of regulatory design principles for plant cell wall deconstruction by filamentous fungi and a novel function for the transcription factor CLR-2. This expanding network will aid in efforts to rationally engineer industrially relevant hyper-production strains. |
| first_indexed | 2024-04-13T22:31:52Z |
| format | Article |
| id | doaj.art-bf0b1babf0494295a47e7a498a987898 |
| institution | Directory Open Access Journal |
| issn | 1754-6834 |
| language | English |
| last_indexed | 2024-04-13T22:31:52Z |
| publishDate | 2017-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Biotechnology for Biofuels |
| spelling | doaj.art-bf0b1babf0494295a47e7a498a9878982022-12-22T02:26:55ZengBMCBiotechnology for Biofuels1754-68342017-09-0110112110.1186/s13068-017-0901-2Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassaAreejit Samal0James P. Craig1Samuel T. Coradetti2J. Philipp Benz3James A. Eddy4Nathan D. Price5N. Louise Glass6Institute for Systems BiologyEnergy Biosciences Institute, University of California BerkeleyEnergy Biosciences Institute, University of California BerkeleyEnergy Biosciences Institute, University of California BerkeleyInstitute for Systems BiologyInstitute for Systems BiologyEnergy Biosciences Institute, University of California BerkeleyAbstract Background Plant biomass degradation by fungal-derived enzymes is rapidly expanding in economic importance as a clean and efficient source for biofuels. The ability to rationally engineer filamentous fungi would facilitate biotechnological applications for degradation of plant cell wall polysaccharides. However, incomplete knowledge of biomolecular networks responsible for plant cell wall deconstruction impedes experimental efforts in this direction. Results To expand this knowledge base, a detailed network of reactions important for deconstruction of plant cell wall polysaccharides into simple sugars was constructed for the filamentous fungus Neurospora crassa. To reconstruct this network, information was integrated from five heterogeneous data types: functional genomics, transcriptomics, proteomics, genetics, and biochemical characterizations. The combined information was encapsulated into a feature matrix and the evidence weighted to assign annotation confidence scores for each gene within the network. Comparative analyses of RNA-seq and ChIP-seq data shed light on the regulation of the plant cell wall degradation network, leading to a novel hypothesis for degradation of the hemicellulose mannan. The transcription factor CLR-2 was subsequently experimentally shown to play a key role in the mannan degradation pathway of N. crassa. Conclusions Here we built a network that serves as a scaffold for integration of diverse experimental datasets. This approach led to the elucidation of regulatory design principles for plant cell wall deconstruction by filamentous fungi and a novel function for the transcription factor CLR-2. This expanding network will aid in efforts to rationally engineer industrially relevant hyper-production strains.http://link.springer.com/article/10.1186/s13068-017-0901-2BiofuelsSystems biologyNeurospora crassaNetwork reconstructionPlant cell wall degradation networkTranscriptional regulatory networks |
| spellingShingle | Areejit Samal James P. Craig Samuel T. Coradetti J. Philipp Benz James A. Eddy Nathan D. Price N. Louise Glass Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Biotechnology for Biofuels Biofuels Systems biology Neurospora crassa Network reconstruction Plant cell wall degradation network Transcriptional regulatory networks |
| title | Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa |
| title_full | Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa |
| title_fullStr | Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa |
| title_full_unstemmed | Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa |
| title_short | Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa |
| title_sort | network reconstruction and systems analysis of plant cell wall deconstruction by neurospora crassa |
| topic | Biofuels Systems biology Neurospora crassa Network reconstruction Plant cell wall degradation network Transcriptional regulatory networks |
| url | http://link.springer.com/article/10.1186/s13068-017-0901-2 |
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