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Title: Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing

Abstract

Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. Using a combination of RNA sequencing and DNA affinity purification sequencing, we performed a global survey of the N. crassa sulfur starvation response and the role of CYS-3 in regulating sulfur-responsive genes. The CYS-3 transcription factor bound the promoters and regulated genes involved in sulfur metabolism. Additionally, CYS-3 directly activated the expression of a number of uncharacterized transporter genes, suggesting that regulation of sulfur import is an important aspect of regulation by CYS-3. CYS-3 also directly regulated the expression of genes involved in mitochondrial electron transfer. During sulfur starvation, genes involved in nitrogen metabolism, such as amino acid and nucleic acid metabolic pathways, along with genes encoding proteases and nucleases that are necessary for scavenging nitrogen, were activated. Sulfur starvation also caused changes in the expression of genesmore » involved in carbohydrate metabolism, such as those encoding glycosyl hydrolases. Thus, our data suggest a connection between sulfur metabolism and other aspects of cellular metabolism.« less

Authors:
ORCiD logo [1];  [2];  [3];  [3];  [4]; ORCiD logo [5];
  1. Plant and Microbial Biology Department, University of California, Berkeley, California, USA, Energy Biosciences Institute, University of California, Berkeley, California, USA, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
  2. Plant and Microbial Biology Department, University of California, Berkeley, California, USA, Energy Biosciences Institute, University of California, Berkeley, California, USA
  3. U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  4. U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
  5. Plant and Microbial Biology Department, University of California, Berkeley, California, USA, Energy Biosciences Institute, University of California, Berkeley, California, USA, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); USDOE Laboratory Directed Research and Development (LDRD) Program; National Institutes of Health (NIH)
OSTI Identifier:
1820496
Alternate Identifier(s):
OSTI ID: 1855186
Grant/Contract Number:  
AC02-05CH11231; ST32GM007127-39; CSP 982
Resource Type:
Published Article
Journal Name:
mSphere
Additional Journal Information:
Journal Name: mSphere Journal Volume: 6 Journal Issue: 5; Journal ID: ISSN 2379-5042
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DAP-seq; nutrient sensing; sulfur starvation response; transcriptional profiling

Citation Formats

Huberman, Lori B., Wu, Vincent W., Lee, Juna, Daum, Chris, O’Malley, Ronan C., Glass, N. Louise, and Mitchell, ed., Aaron P. Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing. United States: N. p., 2021. Web. doi:10.1128/mSphere.00564-21.
Huberman, Lori B., Wu, Vincent W., Lee, Juna, Daum, Chris, O’Malley, Ronan C., Glass, N. Louise, & Mitchell, ed., Aaron P. Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing. United States. https://doi.org/10.1128/mSphere.00564-21
Huberman, Lori B., Wu, Vincent W., Lee, Juna, Daum, Chris, O’Malley, Ronan C., Glass, N. Louise, and Mitchell, ed., Aaron P. Wed . "Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing". United States. https://doi.org/10.1128/mSphere.00564-21.
@article{osti_1820496,
title = {Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing},
author = {Huberman, Lori B. and Wu, Vincent W. and Lee, Juna and Daum, Chris and O’Malley, Ronan C. and Glass, N. Louise and Mitchell, ed., Aaron P.},
abstractNote = {Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. Using a combination of RNA sequencing and DNA affinity purification sequencing, we performed a global survey of the N. crassa sulfur starvation response and the role of CYS-3 in regulating sulfur-responsive genes. The CYS-3 transcription factor bound the promoters and regulated genes involved in sulfur metabolism. Additionally, CYS-3 directly activated the expression of a number of uncharacterized transporter genes, suggesting that regulation of sulfur import is an important aspect of regulation by CYS-3. CYS-3 also directly regulated the expression of genes involved in mitochondrial electron transfer. During sulfur starvation, genes involved in nitrogen metabolism, such as amino acid and nucleic acid metabolic pathways, along with genes encoding proteases and nucleases that are necessary for scavenging nitrogen, were activated. Sulfur starvation also caused changes in the expression of genes involved in carbohydrate metabolism, such as those encoding glycosyl hydrolases. Thus, our data suggest a connection between sulfur metabolism and other aspects of cellular metabolism.},
doi = {10.1128/mSphere.00564-21},
journal = {mSphere},
number = 5,
volume = 6,
place = {United States},
year = {2021},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1128/mSphere.00564-21

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