Polymorphisms of the acid sensing histidine kinase gene arsS in Helicobacter pylori populations from anatomically distinct gastric sites

Abstract

Phase variation is frequently utilized by bacterial species to affect gene expression such that phenotypic variants are maintained within populations, ensuring survival as environmental or host conditions change. Unusual among Helicobacter pylori phase variable or contingency genes is arsS, encoding a sensory histidine kinase involved in the acid acclimation of the organism. The presence of a 3' homopolymeric cytosine tract of variable length in arsS among Helicobacter pylori strains allows for the expression of various functional ArsS isoforms, differing in carboxy-terminal protein domains. In this study, we analyzed this 3'arsS region via amplified fragment length polymorphism (AFLP) and sequencing analyses for H. pylori populations from 3 different gastric sites of 12 patients. Our data indicate the presence of multiple arsS alleles within each population of H. pylori derived from the gastric antrum, cardia, or corpus of these patients. We also show that H. pylori, derived from the same anatomical site and patient, are predicted to express multiple ArsS isoforms in each population investigated. Furthermore, we identify a polymorphic deletion within arsS that generates another alternate ArsS C-terminal end. These findings suggest that four C-terminal variations of ArsS adds to the complexity of the ArsRS acid adaptation mechanism as a whole and may influence the ability of H. pylori to persist in the gastric niche for decades.

Figure 1. arsS polymorphisms and the arsRS operon

The arsRS operon consists of arsR, arsS, hemB, and hp0162, a gene encoding a hypothetical protein. DNA sequence of the 3′ terminus of arsS and the 5′ region of hemB is shown. The arsS homopolymeric cytosine tract and associated stop codons of the different arsS ORFs are indicated. As the homopolymeric cytosine tract varies in length (C_n), different C-terminal regions of ArsS (PKI*, LWG*, EKQ*, and SND*) are encoded due to different ORFs. Many of the H. pylori populations in this study possessed a thymine deletion in the third stop codon (in italics), allowing for the alternate SND* C-terminal region to be predicted. The predicted stop codon of this C-terminal end is located within hemB gene.

Figure 2. Variable ArsS C-terminal regions

Sequence logos were generated based on the 360 cloned 3′ arsS region sequences and depict the 4 variable ArsS C-terminal regions past the homopolymeric cytosine tract. Amino acid sequence differences and similarities are apparent. The x-axis represents the amino acid sequence distal to the final proline (P) encoded by the homopolymeric cytosine tract. The y-axis represents the probability of the amino acid present. Amino acids are also colored due to their hydropathy index values, where hydrophobic amino acids are black, hydrophilic are blue, and neutral are green. (A) Sequence logo for PKI* was generated with 93 cloned 3′ arsS region sequences from 31 H. pylori populations. (B) Sequence logo for LWG* was derived from 158 sequences from 36 H. pylori populations. (C) Sequence logo EKQ* was generated with 30 sequences from 11 populations. (D) Sequence logo for SND* was derived from 76 3′ arsS region sequences from 24 populations.