Discovering the DNA-Binding Consensus of the <i>Thermus thermophilus</i> HB8 Transcriptional Regulator TTHA1359
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 t...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/18/10042 |
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| author | Josiah L. Teague John K. Barrows Cynthia A. Baafi Michael W. Van Dyke |
| author_facet | Josiah L. Teague John K. Barrows Cynthia A. Baafi Michael W. Van Dyke |
| author_sort | Josiah L. Teague |
| collection | DOAJ |
| description | 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 <i>Thermus thermophilus</i> 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)<sub>6</sub>TYACAWT–3′, which TTHA1359 binds to with high affinity. By bioinformatically mapping the consensus to the <i>T. thermophilus</i> 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 <i>T. thermophilus</i> HB8 and demonstrate the effectiveness of a reverse-genetic methodology in the study of putative transcription factors. |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T07:35:07Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-ac9d58bec8834d63bd5c34f913f86d2a2023-11-22T13:31:38ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-09-0122181004210.3390/ijms221810042Discovering the DNA-Binding Consensus of the <i>Thermus thermophilus</i> HB8 Transcriptional Regulator TTHA1359Josiah L. Teague0John K. Barrows1Cynthia A. Baafi2Michael W. Van Dyke3Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA 30144, USADepartment of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA 30144, USADepartment of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA 30144, USADepartment of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA 30144, USATranscription 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 <i>Thermus thermophilus</i> 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)<sub>6</sub>TYACAWT–3′, which TTHA1359 binds to with high affinity. By bioinformatically mapping the consensus to the <i>T. thermophilus</i> 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 <i>T. thermophilus</i> HB8 and demonstrate the effectiveness of a reverse-genetic methodology in the study of putative transcription factors.https://www.mdpi.com/1422-0067/22/18/10042bioinformaticsbiolayer interferometry (BLI)electrophoretic mobility shift assay (EMSA)extremophileprotein-DNA bindingtype IIS restriction endonuclease |
| spellingShingle | Josiah L. Teague John K. Barrows Cynthia A. Baafi Michael W. Van Dyke Discovering the DNA-Binding Consensus of the <i>Thermus thermophilus</i> HB8 Transcriptional Regulator TTHA1359 International Journal of Molecular Sciences bioinformatics biolayer interferometry (BLI) electrophoretic mobility shift assay (EMSA) extremophile protein-DNA binding type IIS restriction endonuclease |
| title | Discovering the DNA-Binding Consensus of the <i>Thermus thermophilus</i> HB8 Transcriptional Regulator TTHA1359 |
| title_full | Discovering the DNA-Binding Consensus of the <i>Thermus thermophilus</i> HB8 Transcriptional Regulator TTHA1359 |
| title_fullStr | Discovering the DNA-Binding Consensus of the <i>Thermus thermophilus</i> HB8 Transcriptional Regulator TTHA1359 |
| title_full_unstemmed | Discovering the DNA-Binding Consensus of the <i>Thermus thermophilus</i> HB8 Transcriptional Regulator TTHA1359 |
| title_short | Discovering the DNA-Binding Consensus of the <i>Thermus thermophilus</i> HB8 Transcriptional Regulator TTHA1359 |
| title_sort | discovering the dna binding consensus of the i thermus thermophilus i hb8 transcriptional regulator ttha1359 |
| topic | bioinformatics biolayer interferometry (BLI) electrophoretic mobility shift assay (EMSA) extremophile protein-DNA binding type IIS restriction endonuclease |
| url | https://www.mdpi.com/1422-0067/22/18/10042 |
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