U.S. Department of EnergyOffice of Scientific and Technical Information
Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum
Abstract
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 shedmore »
- Authors:
-
- National Renewable Energy Lab; National Renewable Energy Laboratory
- National Renewable Energy Lab
- Computational Sciences Center
- Publication Date:
- Other Number(s):
- DE-AC05-00OR22725
- DOE Contract Number:
- AC05-00OR22725
- Research Org.:
- National Renewable Energy Laboratory - Data (NREL-DATA), Golden, CO (United States); National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Sponsoring Org.:
- National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Subject:
- 09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; Clostridium thermocellum; DAP-seq; DNA binding site; bioinformatics; regulon; transcription factor; transcriptional regulatory networks
- OSTI Identifier:
- 1778964
- DOI:
- https://doi.org/10.7799/1778964
Citation Formats
Chou, Katherine, Hebdon, Skyler, and Gerritsen, Alida. Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum. United States: N. p., 2021.
Web. doi:10.7799/1778964.
Chou, Katherine, Hebdon, Skyler, & Gerritsen, Alida. Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum. United States. doi:https://doi.org/10.7799/1778964
Chou, Katherine, Hebdon, Skyler, and Gerritsen, Alida. 2021.
"Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum". United States. doi:https://doi.org/10.7799/1778964. https://www.osti.gov/servlets/purl/1778964. Pub date:Mon Apr 19 00:00:00 EDT 2021
@article{osti_1778964,
title = {Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum},
author = {Chou, Katherine and Hebdon, Skyler and Gerritsen, Alida},
abstractNote = {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.},
doi = {10.7799/1778964},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Apr 19 00:00:00 EDT 2021},
month = {Mon Apr 19 00:00:00 EDT 2021}
}