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

Skyler Hebdon, Alida Gerritsen, Yi-Pei Chen, Joan Marvano, Katherine Chou

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3 Scopus Citations


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.

Original languageAmerican English
Article number695517
Number of pages21
JournalFrontiers in Microbiology
StatePublished - 2021

Bibliographical note

Publisher Copyright:
© Copyright © 2021 Hebdon, Gerritsen, Chen, Marcano and Chou.

NREL Publication Number

  • NREL/JA-2700-79716


  • bioinformatics
  • Clostridium thermocellum DSM 1313
  • DNA binding site
  • regulon
  • transcription factor
  • transcriptional regulatory networks


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