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.
Citation Formats
TY - DATA
AB - 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.
AU - Chou
A2 - Hebdon
A3 - Gerritsen
DB - Open Energy Data Initiative (OEDI)
DP - Open EI | National Renewable Energy Laboratory
DO -
KW - transcriptional regulatory networks
KW - Clostridium thermocellum
KW - regulon
KW - transcription factor
KW - DNA binding site
KW - bioinformatics
KW - DAP-seq
LA - English
DA - 2021/04/19
PY - 2021
PB - National Renewable Energy Laboratory
T1 - Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum
UR - https://data.openei.org/submissions/8222
ER -
Chou, et al. Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum. National Renewable Energy Laboratory, 19 April, 2021, NREL. https://data.nrel.gov/submissions/161.
Chou, Hebdon, & Gerritsen. (2021). Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum. [Data set]. NREL. National Renewable Energy Laboratory. https://data.nrel.gov/submissions/161
Chou, Hebdon, and Gerritsen. Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum. National Renewable Energy Laboratory, April, 19, 2021. Distributed by NREL. https://data.nrel.gov/submissions/161
@misc{OEDI_Dataset_8222,
title = {Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum},
author = {Chou and Hebdon and Gerritsen},
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.},
url = {https://data.nrel.gov/submissions/161},
year = {2021},
howpublished = {NREL, National Renewable Energy Laboratory, https://data.nrel.gov/submissions/161},
note = {Accessed: 2025-05-03}
}
Details
Data from Apr 19, 2021
Last updated Jan 21, 2025
Submitted Apr 19, 2021
Organization
National Renewable Energy Laboratory
Contact
Katherine Chou
Authors
Original Source
https://data.nrel.gov/submissions/161Research Areas
Keywords
transcriptional regulatory networks, Clostridium thermocellum, regulon, transcription factor, DNA binding site, bioinformatics, DAP-seqDOE Project Details
Project Name Center for Bioenergy Innovation (CBI)
Project Number DE-AC05-00OR22725