Assistant Professor, School of Integrative Plant Science Plant Pathology and Plant-Microbe Biology Section
Lori's lab is interested in understanding how fungi sense and respond to their environment. The lab uses genetic and genomic techniques spanning from classical molecular biology to high-throughput functional genomics. Specifically, the lab is pursuing projects focusing on nutrient sensing in filamentous fungi and developing barcoded mutant libraries that will enable massively parallel screens to get from phenotype to genotype.
How fungi interact with the environment
Nutrient sensing in filamentous fungi
High-throughput functional genomics
Filamentous fungi at the buffet: Understanding the regulatory and transcriptional landscape of nutrient sensing
Sensing available nutrients and efficiently utilizing them is a challenge common to all organisms. Saprophytic and plant pathogenic fungi catabolize a variety of carbohydrates: from simple sugars to the complex carbohydrates found in plant cell walls. Additionally, filamentous fungi utilize a variety of organic and inorganic nitrogen sources. The transcriptional network regulating these interconnected metabolic pathways is an interplay of transcriptional activators and repressors that ensure expression of only the genes required to utilize the most preferred nutrients available. We use classical genetics and systems biology tools to explore this transcriptional network.
Developing a high-throughput functional genomics platform for filamentous fungi
Advances in sequencing technology that allow for rapid and inexpensive whole-genome sequencing highlight how few genes have been functionally characterized. This problem is particularly acute in fungal biology, where even in the best studied organisms upwards of half of genes are annotated as hypothetical. High-throughput tools to identify gene function exist for single-celled organisms, such as yeast and bacteria. However, filamentous fungi present a number of challenges to high-throughput gene characterization, including multinucleate cells and asexual fusion. We are currently working to overcome these challenges and develop high-throughput functional genomics for filamentous fungi using the model fungus Neurospora crassa and expanding to plant pathogens, such as Aspergillus flavus. To assign roles to novel genes, we are making libraries with hundreds of thousands of uniquely barcoded insertional mutants and mapping the locations of these barcoded insertions using high-throughput sequencing. We are now working to develop massively parallel screens to get from phenotype to genotype. Quantifying relative barcode abundance will allow us to determine the relative importance of disrupted genes in experimental conditions and assign functions to hypothetical genes. Generating barcoded insertional mutagenesis libraries in a number of fungal systems will enable the rapid characterization of gene function and allow us to expand our understanding of fungal biology.
Wu, V.W., Thieme, N., Huberman, L.B., Dietschmann, A., Kowbel, D.J., Lee, J., Calhoun, S., Singan, V., Lipzen, A., Xiong, Y., Monti, R., Blow, M.J., O’Malley, R.C., Grigoriev, I.V., Benz, J.P., and Glass, N.L. (2020) The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus. Proc Natl Acad Sci U S A 117(11): 6003-3014. doi: 10.1073/pnas.1915611117.
Huberman, L.B., Coradetti, S.T., and Glass, N.L. (2017) Network of nutrient-sensing pathways and a conserved kinase cascade integrate osmolarity and carbon sensing in Neurospora crassa. Proc Natl Acad Sci U S A 114(41): E8665-E8674. doi: 10.1073/pnas.1707713114.
Huberman, L.B., Liu, J., Qin, L., and Glass, N.L. (2016) Regulation of the lignocellulolytic response in filamentous fungi. Fungal Biology Reviews 30: 101-111. doi: 10.1016/j.fbr.2016.06.001.
Huberman, L.B. and Murray, A.W. (2014) A model for cell wall dissolution in mating yeast cells: polarized secretion and restricted diffusion of cell wall remodeling enzymes induces local dissolution. PLoS ONE 9(10): e109780. doi: 10.1371/journal.pone.0109780.
Huberman, L.B. and Murray, A.W. (2013) Genetically engineered transvestites reveal novel mating genes in budding yeast. Genetics 195: 1277-1290. doi: 10.1534/genetics.113.155846. Faculty of 1000 Recommended Paper
307 Plant Science Building
Ithaca, NY 14853
huberman [at] cornell.edu
Lori in the news
Fungal biologist Lori Huberman will use a $1.9 million grant from the National Institutes of Health to study how fungi sense and use nutrients, basic research with potential applications for treatment of cancer, obesity, Type 2 diabetes and...
- School of Integrative Plant Science
- Plant Pathology and Plant-Microbe Biology Section
- Center of Excellence in Food and Agriculture
- Cornell AgriTech
- School of Integrative Plant Science