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Article

Discovering the DNA-Binding Consensus of the Thermus thermophilus HB8 Transcriptional Regulator TTHA1359

Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA 30144, USA
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Author to whom correspondence should be addressed.
Academic Editor: Sarath Chandra Janga
Int. J. Mol. Sci. 2021, 22(18), 10042; https://doi.org/10.3390/ijms221810042
Received: 26 August 2021 / Revised: 14 September 2021 / Accepted: 15 September 2021 / Published: 17 September 2021
(This article belongs to the Section Molecular Genetics and Genomics)
Transcription regulatory proteins, also known as transcription factors, function as molecular switches modulating the first step in gene expression, transcription initiation. Cyclic-AMP receptor proteins (CRPs) and fumarate and nitrate reduction regulators (FNRs) compose the CRP/FNR superfamily of transcription factors, regulating gene expression in response to a spectrum of stimuli. In the present work, a reverse-genetic methodology was applied to the study of TTHA1359, one of four CRP/FNR superfamily transcription factors in the model organism Thermus thermophilus HB8. Restriction Endonuclease Protection, Selection, and Amplification (REPSA) followed by next-generation sequencing techniques and bioinformatic motif discovery allowed identification of a DNA-binding consensus for TTHA1359, 5′–AWTGTRA(N)6TYACAWT–3′, which TTHA1359 binds to with high affinity. By bioinformatically mapping the consensus to the T. thermophilus HB8 genome, several potential regulatory TTHA1359-binding sites were identified and validated in vitro. The findings contribute to the knowledge of TTHA1359 regulatory activity within T. thermophilus HB8 and demonstrate the effectiveness of a reverse-genetic methodology in the study of putative transcription factors. View Full-Text
Keywords: bioinformatics; biolayer interferometry (BLI); electrophoretic mobility shift assay (EMSA); extremophile; protein-DNA binding; type IIS restriction endonuclease bioinformatics; biolayer interferometry (BLI); electrophoretic mobility shift assay (EMSA); extremophile; protein-DNA binding; type IIS restriction endonuclease
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MDPI and ACS Style

Teague, J.L.; Barrows, J.K.; Baafi, C.A.; Van Dyke, M.W. Discovering the DNA-Binding Consensus of the Thermus thermophilus HB8 Transcriptional Regulator TTHA1359. Int. J. Mol. Sci. 2021, 22, 10042. https://doi.org/10.3390/ijms221810042

AMA Style

Teague JL, Barrows JK, Baafi CA, Van Dyke MW. Discovering the DNA-Binding Consensus of the Thermus thermophilus HB8 Transcriptional Regulator TTHA1359. International Journal of Molecular Sciences. 2021; 22(18):10042. https://doi.org/10.3390/ijms221810042

Chicago/Turabian Style

Teague, Josiah L., John K. Barrows, Cynthia A. Baafi, and Michael W. Van Dyke 2021. "Discovering the DNA-Binding Consensus of the Thermus thermophilus HB8 Transcriptional Regulator TTHA1359" International Journal of Molecular Sciences 22, no. 18: 10042. https://doi.org/10.3390/ijms221810042

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