A Repetitive DNA Element Regulates Expression of the Helicobacter pylori Sialic Acid Binding Adhesin by a Rheostat-like Mechanism

Abstract

During persistent infection, optimal expression of bacterial factors is required to match the ever-changing host environment. The gastric pathogen Helicobacter pylori has a large set of simple sequence repeats (SSR), which constitute contingency loci. Through a slipped strand mispairing mechanism, the SSRs generate heterogeneous populations that facilitate adaptation. Here, we present a model that explains, in molecular terms, how an intergenically located T-tract, via slipped strand mispairing, operates with a rheostat-like function, to fine-tune activity of the promoter that drives expression of the sialic acid binding adhesin, SabA. Using T-tract variants, in an isogenic strain background, we show that the length of the T-tract generates multiphasic output from the sabA promoter. Consequently, this alters the H. pylori binding to sialyl-Lewis x receptors on gastric mucosa. Fragment length analysis of post-infection isolated clones shows that the T-tract length is a highly variable feature in H. pylori. This mirrors the host-pathogen interplay, where the bacterium generates a set of clones from which the best-fit phenotypes are selected in the host. In silico and functional in vitro analyzes revealed that the length of the T-tract affects the local DNA structure and thereby binding of the RNA polymerase, through shifting of the axial alignment between the core promoter and UP-like elements. We identified additional genes in H. pylori, with T- or A-tracts positioned similar to that of sabA, and show that variations in the tract length likewise acted as rheostats to modulate cognate promoter output. Thus, we propose that this generally applicable mechanism, mediated by promoter-proximal SSRs, provides an alternative mechanism for transcriptional regulation in bacteria, such as H. pylori, which possesses a limited repertoire of classical trans-acting regulatory factors.

Helicobacter pylori chronic infection and mucosal inflammation switches the human gastric glycosylation pathways

“…5A), which is in accordance with the SabA expression frequency described on European populations [11,31,49]. Importantly, SabA expression has been demonstrated to be subject to a dynamic on–off switching regulated by different genetic mechanisms, including slipped-strand mispairing (SSM) [11], a repetitive DNA element regulation by a rheostat-like mechanism [60], gene duplication by gene conversion [61], and by the acid-responsive signal (ArsRS) two component signal transduction regulatory system [62]. This rapid switch of SabA expression may explain the lack of association between SabA protein expression and sialyl-Le a and sialyl-Le x tissue levels (Fig.…”

Dynamic Expression of the BabA Adhesin and Its BabB Paralog during Helicobacter pylori Infection in Rhesus Macaques

“…Recent structural analysis has demonstrated that the basis for this functional diversity lies in two "diversity loops" within the carbohydrate binding site that represent areas of strong positive selection among babA sequences (13). Similarly, SabA shows polymorphism among clinical isolates in binding affinity to sialyl Lewis x (sLex) (31) and can be modulated by phase variation (32), gene conversion (33), and even variation in the length of a poly-T tract in the promoter region that serves as a rheostat-like mechanism to alter gene expression (34).…”

Lactobacilli Reduce Helicobacter pylori Attachment to Host Gastric Epithelial Cells by Inhibiting Adhesion Gene Expression

“…A dinucleotide cytosine-thymidine repeat in the 5= coding region allows for phase variation, which turns the expression of SabA on and off (18). A T-tract, located at the promoter region, controls sabA transcription initiation because the T-tract length influences binding of the RNA polymerase (45,46). Finally, the two-component signal transduction system ArsRS mediates the regulation of gene transcription by environmental changes.…”