Epigenetic engineering to increase expression of novel feedstocks and lignocellulolytic enzymes
EMSL Project ID
47802
Abstract
Responses to environmental stimuli, e.g. changes in nutritional status, require space- and time-dependent transcription of genes in the context of chromatin, the assembly of DNA and proteins that compacts chromosomes in most eukaryotes. Post-translational histone modifications are essential to coordinate eukaryotic transcriptional networks. "Trithorax group" (TrxG) and "polycomb group" (PcG) proteins are key for gene activity by catalyzing histone H3 lysine 4 methylation (H3K4me) and for gene silencing by H3K27me, respectively. We use filamentous soil fungi (mostly Fusarium and Trichoderma) as models to understand PcG-dependent gene silencing. Fungi are genetically, biochemically and cytologically tractable and contain a PcG complex called "Polycomb Repressive Complex 2"? (PRC2), which catalyzes H3K27 trimethylation. Mutation of three Fusarium PRC2 subunits results in severe defects during development, altered morphology and fertility. We found that >1,500 genes are expressed under conditions when they are silent in the wild type, resulting in de-repression of dozens of novel metabolic pathways that remain to be studied in detail. Major working hypotheses for this proposal are that (1) Fusarium has one PRC2 core complex that makes use of several interacting proteins to deliver PRC2 to CAZyme and secondary metabolite cluster genes, that (2) PRC2-interacting proteins bind specific DNA sequence motifs, and (3) that PRC2 and H3K27me3 generate large silent chromatin territories ("polycomb bodies"). Three specific aims address our hypotheses, as we wish to (1) understand how H3K27me3 controls expression of CAZyme and other gene clusters, (2) determine distribution and function of gene clusters in "polycomb bodies"?, and (3) discover novel secreted proteins and metabolites produced in PRC2 mutants. Our project is designed as a broad-based collaboration between our team and several scientists at EMSL. We combine several state-of-the-art capabilities at EMSL to (1) improve our yield of high-throughput sequencing in ChIP- and RNA-seq experiments (by SOLiD sequencing), (2) identify novel PRC2-associated proteins (by "bottom up" mass spectrometry; MS), (3) map discrete silent and active nuclear territories (by STORM and SIM), (4) identify and characterize novel metabolites or enzymes produced in PRC2 mutants (by MS, GC-MS and NMR), and (5) identify combinatorial histone modifications within H3K27me3-enriched chromatin (by "top down"? MS), perhaps the most innovative approach. This combination of capabilities is not available at Oregon State University. Our experiments will provide key knowledge on gene silencing of gene clusters in industrially important fungi and improve strategies to overexpress enzymes or novel compounds. Taken together, we will gain insights into the nature of silencing complexes and associated proteins, the composition of H3K27me3 chromatin, the specificity of DNA-based signals for H3K27me3 targeting, and the interplay between epigenetic modifications and chromatin proteins that are required for gene silencing in secondary metabolite gene clusters, important regions that produce lignocelluloytic enzymes, novel metabolites and other bioactive compounds. We will push the boundaries of what is currently known in other eukaryotic systems. Innovation lies in our combination of established methods, promising immediate discovery of new metabolites, with novel experimental approaches to identify modification states of intact histones from homogeneous chromatin in vivo, a major hurdle in other systems.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2013-10-01
End Date
2016-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members