The central goal of the three interdependent efforts in this Program Project builds upon successful functional genomics, annotation, and expression analyses of Neurospora crassa, a premier filamentous fungus model for over 250,000 species of non-yeast fungi. A primary goal, targeted through molecular, cell biological, genomic and computational approaches, will be to understand how N. crassa transitions from mycelial growth to complete asexual spore development. We will focus on two key triggers of asexual development: light and desiccation. In addition, we will leverage our prior successes to expand systematic knockouts to an additional prominent model system, Aspergillus nidulans. Neurospora is a salient model for basic research in eukaryotes, as is Aspergillus, and fungi allied to these species include most animal and plant pathogens as well as industrial strains yielding antibiotics, chemicals, enzymes, and Pharmaceuticals. Gene predictions among the 9846 genes encoded by the fully sequenced 43 Mb Neurospora genome are supported by over 250,000 ESTs derived from this P01. During the past 4 years, we revolutionized the tools and techniques for gene knockouts in filamentous fungi and exceeded our initial goal by over 40%. Project #1 will complete the Neurospora gene knockouts and extend the systematic disruption of genes to Aspergillus. We will develop strains, tools, and background information in support of Projects #2 and #3, and of the overarching goal of understanding regulatory pathways governing filamentous fungal development. Projects #2 and #3 will aim to describe and reconstruct the cascading regulatory programs that underlie N. crassa's developmental response to light and air, from the level of chromatin structure through the gene regulatory network. Project #3 will use ChIP-seq mapping of histone modifications, transcription factor binding sites, sites of DNA methylation and nucleosome occupancy with corresponding transcriptome measurements to generate a deep description of genome and epigenome dynamics. Project #2, in an informatic-intensive systems biology approach, will integrate these data and use computational modeling to develop predictive models of the interconnected light and asexual development gene regulatory networks. These models will be fleshed out tested through incorporation of new data arising from Project #3 and refined via perturbation analyses facilitated through the use of strains developed in Project #1 and characterized using the tools employed in Project #3. This effort will anchor, promote, and exploit genomic exploration within model systems that provide gateways to the Kingdom of the Fungi.

Public Health Relevance

Filamentous fungi, typically known as molds, are common animal and plant pathogens, but they are also widely used as industrial strains to provide antibiotics, chemicals, enzymes, and Pharmaceuticals. We'd be dead without them but they can kill us. We seek to understand how genes and proteins work together to regulate fungal growth and development, so as to enhance the good things and control the bad things produced by fungi.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Program Projects (P01)
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Special Emphasis Panel (ZRG1-GGG-M)
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Dartmouth College
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Fuller, Kevin K; Loros, Jennifer J; Dunlap, Jay C (2015) Fungal photobiology: visible light as a signal for stress, space and time. Curr Genet 61:275-88
De Souza, Colin P; Hashmi, Shahr B; Osmani, Aysha H et al. (2014) Application of a new dual localization-affinity purification tag reveals novel aspects of protein kinase biology in Aspergillus nidulans. PLoS One 9:e90911
Gooch, Van D; Johnson, Alicia E; Bourne, Brian J et al. (2014) A kinetic study of the effects of light on circadian rhythmicity of the frq promoter of Neurospora crassa. J Biol Rhythms 29:38-48
Benz, J Philipp; Chau, Bryant H; Zheng, Diana et al. (2014) A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations. Mol Microbiol 91:275-99
Dettmann, Anne; Heilig, Yvonne; Valerius, Oliver et al. (2014) Fungal communication requires the MAK-2 pathway elements STE-20 and RAS-2, the NRC-1 adapter STE-50 and the MAP kinase scaffold HAM-5. PLoS Genet 10:e1004762
Wu, Cheng; Yang, Fei; Smith, Kristina M et al. (2014) Genome-wide characterization of light-regulated genes in Neurospora crassa. G3 (Bethesda) 4:1731-45
Samarajeewa, Dilini A; Sauls, Pegan A; Sharp, Kevin J et al. (2014) Efficient detection of unpaired DNA requires a member of the rad54-like family of homologous recombination proteins. Genetics 198:895-904
Fu, Ci; Tanaka, Asuma; Free, Stephen J (2014) Neurospora crassa 1,3-?-glucan synthase, AGS-1, is required for cell wall biosynthesis during macroconidia development. Microbiology 160:1618-27
Gooch, Van D; Johnson, Alicia E; Larrondo, Luis F et al. (2014) Bright to dim oscillatory response of the Neurospora circadian oscillator. J Biol Rhythms 29:49-59
Chinnici, Jennifer L; Fu, Ci; Caccamise, Lauren M et al. (2014) Neurospora crassa female development requires the PACC and other signal transduction pathways, transcription factors, chromatin remodeling, cell-to-cell fusion, and autophagy. PLoS One 9:e110603

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