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

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 high-throughput application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a thermophile. 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 towards a desired phenotype.
2 Data Resources
Name Size Type Resource Description History
Cytoscape network file representing the predicted regulon for each TF and a global network encompassing all predicted regulons controlled by the TFs 275.39 KB Document Cytoscape network file representing the predicted regulon for each TF and a global network encompassing all predicted regulons controlled by the TFs
Supplementary File S1 157.81 KB Document Figures of reconstructed Clostridium thermocellum transcriptional regulatory networks showing the predicted regulon for each transcription factor (TF) and a global network encompassing all predicted regulons controlled by the TFs.
Author Information
Katherine Chou, National Renewable Energy Lab
Skyler Hebdon, National Renewable Energy Lab
Alida Gerritsen, Computational Sciences Center
Cite This Dataset
Chou, Katherine; Hebdon, Skyler ; Gerritsen, Alida (2021): Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum. National Renewable Energy Laboratory. https://data.nrel.gov/submissions/161
About This Dataset
161
10.7799/1778964
Public
04/22/2021
DOE Project
Center for Bioenergy Innovation (CBI)
Facilities
Biomass & Biosciences Research (BBR)
Funding Organization
Department of Energy (DOE)
Sponsoring Organization
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division
Research Areas
Bioenergy
License
View License
Digital Object Identifier
10.7799/1778964