Determination and Dissection of DNA-Binding Specificity for the Thermus thermophilus HB8 Transcriptional Regulator TTHB099
Open Access
- 26 October 2020
- journal article
- research article
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 21 (21), 7929
- https://doi.org/10.3390/ijms21217929
Abstract
Transcription factors (TFs) have been extensively researched in certain well-studied organisms, but far less so in others. Following the whole-genome sequencing of a new organism, TFs are typically identified through their homology with related proteins in other organisms. However, recent findings demonstrate that structurally similar TFs from distantly related bacteria are not usually evolutionary orthologs. Here we explore TTHB099, a cAMP receptor protein (CRP)-family TF from the extremophile Thermus thermophilus HB8. Using the in vitro iterative selection method Restriction Endonuclease Protection, Selection and Amplification (REPSA), we identified the preferred DNA-binding motif for TTHB099, 5′–TGT(A/g)NBSYRSVN(T/c)ACA–3′, and mapped potential binding sites and regulated genes within the T. thermophilus HB8 genome. Comparisons with expression profile data in TTHB099-deficient and wild type strains suggested that, unlike E. coli CRP (CRPEc), TTHB099 does not have a simple regulatory mechanism. However, we hypothesize that TTHB099 can be a dual-regulator similar to CRPEc.This publication has 39 references indexed in Scilit:
- NCBI GEO: archive for functional genomics data sets—updateNucleic Acids Research, 2012
- Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcAGene Regulation and Systems Biology, 2012
- Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon SourcesPLOS ONE, 2011
- Involvement of CarA/LitR and CRP/FNR Family Transcriptional Regulators in Light-Induced Carotenoid Production in Thermus thermophilusJournal of Bacteriology, 2011
- FIMO: scanning for occurrences of a given motifBioinformatics, 2011
- Structural basis for cAMP-mediated allosteric control of the catabolite activator proteinProceedings of the National Academy of Sciences of the United States of America, 2009
- Regulation by transcription factors in bacteria: beyond descriptionFEMS Microbiology Reviews, 2008
- DOOR: a database for prokaryotic operonsNucleic Acids Research, 2008
- Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different GenesPLoS Computational Biology, 2007
- Autoregulation of the Escherichia coli crp gene: CRP is a transcriptional repressor for its own geneCell, 1983