Tracing gene regulatory networks in the model fungus Neurospora crassa.
A team led by researchers at the University of California, Berkeley used a multi-omics approach to reconstruct and model gene regulatory pathways used by the filamentous fungus Neurospora crassa, and to identify and decide on the order in which this fungus breaks down plant cell wall materials including lignin, cellulose and hemicellulose.
N. crassa is the model organism for filamentous fungi, all of which contain a wide array of plant cell-wall degrading enzymes (PCWDEs) that allow them to efficiently break down the wide array of simple and complex components present in plant biomass. This is of interest for bioenergy researchers looking to improve the industrial production of sustainable biofuels and bioproducts. Filamentous fungi are also being used in the biotechnology industry to produce enzymes, proteins, and other chemicals.
Filamentous fungi are like handymen who show up at a job site for a task that requires a flathead screwdriver with a full toolbox including Phillips and specialty screwdrivers, not to mention Allen wrenches. The fungi are similarly armed with a variety of PCWDEs to first break down the components of plant cell walls, which range from simple to complex carbohydrates, and then convert them into simple sugars. More importantly, when faced with a veritable buffet of carbon sources, these fungi detect which complex chains are available; this information triggers pathways to determine which enzymes should be deployed in what order to most efficiently degrade the plant biomass.
In order to learn more about these regulatory networks in the model fungus N. crassa, a team led by N. Louise Glass at the University of California, Berkeley and her postdoctoral fellow Vincent Wu worked with researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab). The work was enabled in part through JGI’s Community Science Program through a proposal akin to the Encyclopedia of DNA Elements (ENCODE) project, which is aimed at determining the activity, expression and regulation of protein-coding genes.
This first paper integrating multi-omics data from this JGI fungal ENCODE proposal was recently published in the Proceedings of the National Academy of Sciences. Researchers applied multiple omics techniques to reconstruct and model the gene regulatory networks as they responded to available carbon sources, which ranged from simple sugars to plant biomass. One of these techniques was DAP-seq, a high-throughput method for identifying protein binding sites in DNA by DNA Affinity Purification, developed and optimized by Ronan O’Malley, who leads the JGI’s Sequencing Technologies group. DAP-seq allowed the team to identify the direct binding sites of many transcription factors to better understand how nutrients are acquired and carbon is metabolized in filamentous fungi. The work also suggests a new approach to gene annotation, which then can be explored in depth for multiple models and their close relatives across the fungal tree of life,
enriching the work being done as part of the 1000 Fungal Genomes
Funding for the project was also provided by the Energy Biosciences Institute and the Laboratory Directed Research and Development Program of Berkeley Lab, among other organizations.
Ramana Madupu, Ph.D.
Program Manager, DOE Joint Genome Institute
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
N. Louise Glass
University of California, Berkeley
We acknowledge the use of deletion strains generated by Grant P01 GM-068087 “Functional Analysis of a Model Filamentous Fungus” and that are publicly available at the Fungal Genetics Stock Center. This work was supported by an Energy Biosciences Institute Grant, a Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under US Department of Energy Contract DE-AC02-05CH11231, a Joint Genome Institute Community Science Program grant (CSP 982), and funds from the Fred E. Dickinson Chair of Wood Science and Technology to N.L.G.. V.W.W. was partially supported by National Institutes of Health National Research Service Award Trainee Grant 5T32GM007127-39. The work conducted by the US Department of Energy (DOE) Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the US DOE under Contract no. DE-AC02-05CH11231.
- Wu VW et al. The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus. Proc Natl Acad Sci U S A. 2020 Feb 28. pii: 201915611. doi: 10.1073/pnas.1915611117.
- JGI Community Science Program
- JGI CSP 2013 Proposal: The Fungal Nutritional
Encyclopedia of DNA Elements (ENCODE) Project
- JGI 1000 Fungal Genomes Project
- Neurospora crassa on the JGI Fungal Portal MycoCosm
By: Massie S. Ballon