Spatial partitioning and differential expression by wood-degrading fungi
EMSL Project ID
48607
Abstract
Certain filamentous fungi are uniquely able to deconstruct lignocellulose, and their poorly understood mechanisms have potential biofuels applications. A key hindrance to harnessing these fungal mechanisms has been their spatial complexity. Our past work has shown that differentiated networks of hyphae that penetrate wood are not metabolically uniform, with critical reactions occurring near the hyphal front. Standard omics analyses of these fungi from artificial media or from colonized wood ground en masse fail to distinguish expression of key gene products occurring in localized regions along growing hyphae.This spatially-motivated research in collaboration with EMSL (within the Quiet Wing) is focused on brown rot fungi, a more recently evolved decay fungal group (relative to white rot) that circumvents the lignin barrier to extract sugars from lignocellulose. Current theory holds that this is accomplished by staggering an oxidative pretreatment from cellulolytic lysis of carbohydrates. The genetic basis for how this capacity evolved away from white rot multiple times remains unknown, despite the modern options to align the compare brown rot and white rot fungal genomes. The spatial mechanisms employed to control these staggered oxidative and enzymatic reactions is also poorly defined, largely due to resolution limitations.
Our motivation for working with EMSL aims to couple Helium Ion Microscopy (HIM) with fluorescence in-situ hybridization (FISH) to deeply probe two aspects potentially contributing to the partitioning of these incompatible reactions. 1) The HIM system will be used specifically to probe the inner surface of the secondary cell walls in gamma sterilized pine, with the goal of elucidating structural changes at high resolution. 2) The FISH approach will specifically be a single-molcecule effort, using two oligo probe sets to amplify mRNA transcripts in planta at high resolution. Combined, our goal is better resolution of fungal differential expression and its context across wood cell walls that may be deconstructed heterogeneously.
Project Details
Project type
Special Science
Start Date
2014-10-15
End Date
2015-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Zhang J, GN Presley, KE Hammel, JS Ryu, J Menke, M Figueroa, D Hu, G Orr, and JS Schilling. 2016. "Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta." Proceedings of the National Academy of Sciences of the United States of America 113(39):10968-10973. doi:10.1073/pnas.1608454113