The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus

Wu, Vincent W.; Thieme, Nils; Huberman, Lori B.; Dietschmann, Axel; Kowbel, David J.; Lee, Juna; Calhoun, Sara; Singan, Vasanth R.; Lipzen, Anna; Xiong, Yi; Monti, Remo; Blow, Matthew J.; O’Malley, Ronan C.; Grigoriev, Igor V.; Benz, J. Philipp; Glass, N. Louise

doi:10.1073/pnas.1915611117

Title: The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus

Journal Article · Fri Feb 28 00:00:00 EST 2020 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1915611117· OSTI ID:1602098

Wu, Vincent W.; Thieme, Nils; Huberman, Lori B.; Dietschmann, Axel; Kowbel, David J.; Lee, Juna; Calhoun, Sara; Singan, Vasanth R.; Lipzen, Anna; Xiong, Yi; Monti, Remo; Blow, Matthew J.; O’Malley, Ronan C.; Grigoriev, Igor V.;

;

Filamentous fungi, such as Neurospora crassa , are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading enzymes, by remodeling metabolism to accommodate production of secreted enzymes, and by enabling transport and intracellular utilization of plant biomass components. Although a number of enzymes and transcriptional regulators involved in plant biomass utilization have been identified, how filamentous fungi sense and integrate nutritional information encoded in the plant cell wall into a regulatory hierarchy for optimal utilization of complex carbon sources is not understood. Here, we performed transcriptional profiling of N. crassa on 40 different carbon sources, including plant biomass, to provide data on how fungi sense simple to complex carbohydrates. From these data, we identified regulatory factors in N. crassa and characterized one (PDR-2) associated with pectin utilization and one with pectin/hemicellulose utilization (ARA-1). Using in vitro DNA affinity purification sequencing (DAP-seq), we identified direct targets of transcription factors involved in regulating genes encoding plant cell wall-degrading enzymes. In particular, our data clarified the role of the transcription factor VIB-1 in the regulation of genes encoding plant cell wall-degrading enzymes and nutrient scavenging and revealed a major role of the carbon catabolite repressor CRE-1 in regulating the expression of major facilitator transporter genes. These data contribute to a more complete understanding of cross talk between transcription factors and their target genes, which are involved in regulating nutrient sensing and plant biomass utilization on a global level.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); Fred E. Dickinson Chair of Wood Science and Technology; National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231; P01 GM-068087; CSP 982; 5T32GM007127-39

OSTI ID:: 1602098

Alternate ID(s):: OSTI ID: 1609116

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Vol. 117 Journal Issue: 11; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 42 works

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59 BASIC BIOLOGICAL SCIENCES
transcriptional networks
plant biomass deconstruction
nutrient sensing
DAP-seq
RNA-seq

Title: The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus

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