ToxR activates the
            <i>Vibrio cholerae</i>
            virulence genes by tethering DNA to the membrane through versatile binding to multiple sites

Transcriptional factors (TFs) in bacteria play a crucial role in gene regulation by binding to specific DNA sequences, thereby assisting in the activation or repression of genes. Despite their central role, deciphering shape recognition of bacterial TFs-DNA interactions remains an intricate challenge. A deeper understanding of DNA secondary structures could greatly enhance our knowledge of how TFs recognize and interact with DNA, thereby elucidating their biological function. In this study, we employed machine learning algorithms to predict transcription factor binding sites (TFBS) and classify them as directed-repeat (DR) or inverted-repeat (IR). To accomplish this, we divided the set of TFBS nucleotide sequences by size, ranging from 8 to 20 base pairs, and converted them into thermodynamic data known as DNA duplex stability (DDS). Our results demonstrate that the Random Forest algorithm accurately predicts TFBS with an average accuracy of over 82% and effectively distinguishes between IR and DR with an accuracy of 89%. Interestingly, upon converting the base pairs of several TFBS-IR into DDS values, we observed a symmetric profile typical of the palindromic structure associated with these architectures. This study presents a novel TFBS prediction model based on a DDS characteristic that may indicate how respective proteins interact with base pairs, thus providing insights into molecular mechanisms underlying bacterial TFs-DNA interaction.

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Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation inVibrio cholerae

Hullinger,

Green,

Klancher

et al. 2024

Preprint

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Transcriptional regulators are a broad class of proteins that alter gene expression in response to environmental stimuli. Transmembrane transcriptional regulators (TTRs) are a subset of transcriptional regulators in bacteria that can directly regulate gene expression while remaining anchored in the membrane. Whether this constraint impacts the ability of TTRs to bind their DNA targets remains unclear. Vibrio cholerae uses two TTRs, ChiS and TfoS, to activate horizontal gene transfer by natural transformation in response to chitin by inducing the tfoR promoter (PtfoR). While TfoS was previously shown to bind and regulate PtfoR directly, the role of ChiS in PtfoR activation remains unclear. Here, we show that ChiS directly binds PtfoR upstream of TfoS, and that ChiS directly interacts with TfoS. By independently disrupting ChiS-PtfoR and ChiS-TfoS interactions, we show that ChiS-PtfoR interactions play the dominant role in PtfoR activation. Correspondingly, we show that in the absence of ChiS, recruitment of the PtfoR locus to the membrane is sufficient for PtfoR activation when TfoS is expressed at native levels. Finally, we show that the overexpression of TfoS can bypass the need for ChiS for PtfoR activation. All together, these data suggest a model whereby ChiS both (1) recruits the PtfoR DNA locus to the membrane for TfoS and (2) directly interacts with TfoS to increase its local concentration near the membrane-proximal promoter. This work furthers our understanding of the molecular mechanisms that drive chitin-induced responses in V. cholerae and more broadly highlights how the membrane-embedded localization of TTRs can impact their activity.

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ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites

Cited by 4 publications

References 56 publications

Wastewater-based surveillance of Vibrio cholerae: Molecular insights on biofilm regulatory diguanylate cyclases, virulence factors and antibiotic resistance patterns

Wastewater-based surveillance of Vibrio cholerae: Molecular insights on biofilm regulatory diguanylate cyclases, virulence factors and antibiotic resistance patterns

Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability

Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation inVibrio cholerae

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