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 reg...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-09-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.695517/full |
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| author | Skyler D. Hebdon Alida T. Gerritsen Yi-Pei Chen Joan G. Marcano Katherine J. Chou |
| author_facet | Skyler D. Hebdon Alida T. Gerritsen Yi-Pei Chen Joan G. Marcano Katherine J. Chou |
| author_sort | Skyler D. Hebdon |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T20:29:26Z |
| format | Article |
| id | doaj.art-2b86fa8d42894f8d8c0de27fbe801111 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-13T20:29:26Z |
| publishDate | 2021-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-2b86fa8d42894f8d8c0de27fbe8011112022-12-21T23:32:27ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-09-011210.3389/fmicb.2021.695517695517Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellumSkyler D. Hebdon0Alida T. Gerritsen1Yi-Pei Chen2Joan G. Marcano3Katherine J. Chou4Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United StatesComputational Sciences Center, National Renewable Energy Laboratory, Golden, CO, United StatesBiosciences Center, National Renewable Energy Laboratory, Golden, CO, United StatesBiosciences Center, National Renewable Energy Laboratory, Golden, CO, United StatesBiosciences Center, National Renewable Energy Laboratory, Golden, CO, United StatesClostridium 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.https://www.frontiersin.org/articles/10.3389/fmicb.2021.695517/fulltranscriptional regulatory networksClostridium thermocellum DSM 1313regulontranscription factorDNA binding sitebioinformatics |
| spellingShingle | Skyler D. Hebdon Alida T. Gerritsen Yi-Pei Chen Joan G. Marcano Katherine J. Chou Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum Frontiers in Microbiology transcriptional regulatory networks Clostridium thermocellum DSM 1313 regulon transcription factor DNA binding site bioinformatics |
| title | Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum |
| title_full | Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum |
| title_fullStr | Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum |
| title_full_unstemmed | Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum |
| title_short | Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum |
| title_sort | genome wide transcription factor dna binding sites and gene regulatory networks in clostridium thermocellum |
| topic | transcriptional regulatory networks Clostridium thermocellum DSM 1313 regulon transcription factor DNA binding site bioinformatics |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.695517/full |
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