Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Hebdon, Skyler D.; Gerritsen, Alida T.; Chen, Yi-Pei; Marcano, Joan G.; Chou, Katherine J.

doi:10.3389/fmicb.2021.695517

Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Journal Article · Tue Sep 07 00:00:00 EDT 2021 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2021.695517· OSTI ID:1819222

Hebdon, Skyler D.; Gerritsen, Alida T.; Chen, Yi-Pei; Marcano, Joan G.; Chou, Katherine J.

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum . Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.

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Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE; USDOE National Renewable Energy Laboratory (NREL), Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC36-08GO28308

OSTI ID:: 1819222

Alternate ID(s):: OSTI ID: 1814598

Report Number(s):: NREL/JA-2700-79716; 695517

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 12; ISSN 1664-302X

Publisher:: Frontiers Media SACopyright Statement

Country of Publication:: Switzerland

Language:: English

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High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints Guo, Yuchun; Mahony, Shaun; Gifford, David K. PLoS Computational Biology, Vol. 8, Issue 8 https://doi.org/10.1371/journal.pcbi.1002638	journal	August 2012
TASmania: A bacterial Toxin-Antitoxin Systems database Akarsu, Hatice; Bordes, Patricia; Mansour, Moise PLOS Computational Biology, Vol. 15, Issue 4 https://doi.org/10.1371/journal.pcbi.1006946	journal	April 2019
The Redox-Sensing Regulator Rex Modulates Central Carbon Metabolism, Stress Tolerance Response and Biofilm Formation by Streptococcus mutans Bitoun, Jacob P.; Liao, Sumei; Yao, Xin PLoS ONE, Vol. 7, Issue 9 https://doi.org/10.1371/journal.pone.0044766	journal	September 2012
Industrial Robustness: Understanding the Mechanism of Tolerance for the Populus Hydrolysate-Tolerant Mutant Strain of Clostridium thermocellum Linville, Jessica L.; Rodriguez, Miguel; Land, Miriam PLoS ONE, Vol. 8, Issue 10 https://doi.org/10.1371/journal.pone.0078829	journal	October 2013
Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design Garcia, Sergio; Thompson, R. Adam; Giannone, Richard J. Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.00772	journal	August 2020
Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq Wei, Hui; Fu, Yan; Magnusson, Lauren Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00142	journal	April 2014

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59 BASIC BIOLOGICAL SCIENCES
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Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

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