title: Characterization of DNA binding sites of the ComE response regulator from Streptococcus mutans.
abstract: In Streptococcus mutans, both competence and bacteriocin production are controlled by ComC and the ComED two-component signal transduction system. Recent studies of S. mutans suggested that purified ComE binds to two 11-bp direct repeats in the nlmC-comC promoter region, where ComE activates nlmC and represses comC. In this work, quantitative binding studies and DNase I footprinting analysis were performed to calculate the equilibrium dissociation constant and further characterize the binding site of ComE. We found that ComE protects sequences inclusive of both direct repeats, has an equilibrium dissociation constant in the nanomolar range, and binds to these two direct repeats cooperatively. Furthermore, similar direct repeats were found upstream of cslAB, comED, comX, ftf, vicRKX, gtfD, gtfB, gtfC, and gbpB. Quantitative binding studies were performed on each of these sequences and showed that only cslAB has a similar specificity and high affinity for ComE as that seen with the upstream region of comC. A mutational analysis of the binding sequences showed that ComE does not require both repeats to bind DNA with high affinity, suggesting that single site sequences in the genome may be targets for ComE-mediated regulation. Based on the mutational analysis and DNase I footprinting analysis, we propose a consensus ComE binding site, TCBTAAAYSGT.
authors: Department of Molecular and Computational Biology, Division of Biomedical Science, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089-0641, USA.
authors: David C I
authors: DC
authors: Hung
authors: Jennifer S
authors: JS
authors: Downey
authors: Eduardo A
authors: EA
authors: Ayala
authors: Jens
authors: J
authors: Kreth
authors: Richard
authors: R
authors: Mair
authors: Dilani B
authors: DB
authors: Senadheera
authors: Fengxia
authors: F
authors: Qi
authors: Dennis G
authors: DG
authors: Cvitkovitch
authors: Wenyuan
authors: W
authors: Shi
authors: Steven D
authors: SD
authors: Goodman
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