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

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article number225
JournalBiotechnology for Biofuels
Volume10
Issue number1
DOIs
StatePublished - Sep 21 2017
Externally publishedYes

Keywords

  • Biofuels
  • CLR-2
  • Mannan
  • Network reconstruction
  • Neurospora crassa
  • Plant cell wall degradation network
  • Systems biology
  • Transcriptional regulatory networks

ASJC Scopus subject areas

  • Biotechnology
  • Applied Microbiology and Biotechnology
  • Renewable Energy, Sustainability and the Environment
  • Energy(all)
  • Management, Monitoring, Policy and Law

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