| Title: |
Identification and Characterization of Preferred DNA-Binding Sites for the Thermus thermophilus HB8 Transcriptional Regulator TTHA0973 |
| Authors: |
James Shell Cox; Kristi Moncja; Mykala Mckinnes; Michael W. Van Dyke |
| Source: |
International Journal of Molecular Sciences, Vol 20, Iss 13, p 3336 (2019) |
| Publisher Information: |
MDPI AG |
| Publication Year: |
2019 |
| Collection: |
Directory of Open Access Journals: DOAJ Articles |
| Subject Terms: |
bioinformatics; biolayer interferometry (BLI); electrophoretic mobility shift assay (EMSA); extremophile; type IIS restriction endonuclease; Biology (General); QH301-705.5; Chemistry; QD1-999 |
| Description: |
Advances in genomic sequencing have allowed the identification of a multitude of genes encoding putative transcriptional regulatory proteins. Lacking, often, is a fuller understanding of the biological roles played by these proteins, the genes they regulate or regulon. Conventionally this is achieved through a genetic approach involving putative transcription factor gene manipulation and observations of changes in an organism’s transcriptome. However, such an approach is not always feasible or can yield misleading findings. Here, we describe a biochemistry-centric approach, involving identification of preferred DNA-binding sequences for the Thermus thermophilus HB8 transcriptional repressor TTHA0973 using the selection method Restriction Endonuclease Protection, Selection and Amplification (REPSA), massively parallel sequencing, and bioinformatic analyses. We identified a consensus TTHA0973 recognition sequence of 5′−AACnAACGTTnGTT−3′ that exhibited nanomolar binding affinity. This sequence was mapped to several sites within the T. thermophilus HB8 genome, a subset of which corresponded to promoter regions regulating genes involved in phenylacetic acid degradation. These studies further demonstrate the utility of a biochemistry-centric approach for the facile identification of potential biological functions for orphan transcription factors in a variety of organisms. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
https://www.mdpi.com/1422-0067/20/13/3336; https://doaj.org/toc/1422-0067; https://doaj.org/article/af1dfab495424ecb8569179f6eae28b3 |
| DOI: |
10.3390/ijms20133336 |
| Availability: |
https://doi.org/10.3390/ijms20133336; https://doaj.org/article/af1dfab495424ecb8569179f6eae28b3 |
| Accession Number: |
edsbas.79DF0CE1 |
| Database: |
BASE |