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Network reconstruction and systems analysis of plant cell wall deconstruction by neurospora crassa

Areejit Samal, James P. Craig, Samuel T. Coradetti, J. Philipp Benz, James A. Eddy, Nathan D. Price, N. Louise Glass
doi: https://doi.org/10.1101/133165
Areejit Samal
1Institute for Systems Biology, Seattle, WA 98109, USA
2Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704, USA
3The Institute of Mathematical Sciences, Chennai 600113, India
4The Abdus Salam International Centre for Theoretical Physics, Trieste 34151, Italy
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James P. Craig
2Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704, USA
5Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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Samuel T. Coradetti
2Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704, USA
5Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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J. Philipp Benz
2Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704, USA
6Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising 85354, Germany
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James A. Eddy
1Institute for Systems Biology, Seattle, WA 98109, USA
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Nathan D. Price
1Institute for Systems Biology, Seattle, WA 98109, USA
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  • For correspondence: Lglass@berkeley.edu nprice@systemsbiology.org
N. Louise Glass
2Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704, USA
5Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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  • For correspondence: Lglass@berkeley.edu nprice@systemsbiology.org
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Abstract

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. 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 weighed 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 (PCWDN), 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 Neurospora crassa. Our network serves as a scaffold for integration of diverse experimental data, leading to elucidation of regulatory design principles for plant cell wall deconstruction by filamentous fungi, and guiding efforts to rationally engineer industrially relevant hyper-production strains.

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Posted May 02, 2017.
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Network reconstruction and systems analysis of plant cell wall deconstruction by neurospora crassa
Areejit Samal, James P. Craig, Samuel T. Coradetti, J. Philipp Benz, James A. Eddy, Nathan D. Price, N. Louise Glass
bioRxiv 133165; doi: https://doi.org/10.1101/133165
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Network reconstruction and systems analysis of plant cell wall deconstruction by neurospora crassa
Areejit Samal, James P. Craig, Samuel T. Coradetti, J. Philipp Benz, James A. Eddy, Nathan D. Price, N. Louise Glass
bioRxiv 133165; doi: https://doi.org/10.1101/133165

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