The present study focused on analyzing pldA gene sequences that c

The present study focused on analyzing pldA gene sequences that code for functional OMPLA proteins. In previous studies, we showed that most clinical isolates contain these

coding pldAON sequences [13]. In this study, we included 155 isolates from a Norwegian population used in the Sørreisa study [24]. Most (97.5%) of these ubiquitin-Proteasome degradation isolates showed an ON phase variant, indicating that the gene encodes a functional OMPLA protein in most individuals. The homopolymeric tract induces a shift between a functional and a truncated protein by enabling a frameshift mutation. Wernegreen et al. postulated that selection will purge nucleotide changes that could interrupt the slippery tract, to maintain otherwise volatile sequences [25]. Why the pldA gene in H. pylori contains a homopolymeric tract is an enigma, and we explored whether its existence could be part of a gene deletion process or perhaps a mechanism needed to prevent activation in certain environments. The homopolymeric tract corresponded to residues 226–228 in the translated OMPLA protein. Residue 278 was the most downstream site that was predicted to be under positive selection in this protein. The remaining twenty percent of the protein (after residue ITF2357 number 279) is under purifying selection,

indicating functional constraints and implying that the protein is important to bacterial survival. Genes under purifying selection are often involved in host-pathogen interactions. For example, purifying selection in orthopoxvirus is probably caused by host defense mechanisms [26]. However, pathogens must also much evolve novel residues to evade the host immune system, resulting in positive selection on some residues [27]. Such positive selection has been shown in the flagellum-coding gene flA, which is involved in adhesion in Aeromonas; nearly the entire protein was under purifying selection, while

17 residues were subject to positive selection [28]. Our analyses demonstrated purifying selection in most of the pldA sequence, while the remaining residues were predicted to be under positive selection. The positively-selected sites were scattered throughout the OMPLA protein. Petersen et al. concluded that positively-selected sites are exclusively located in the loops of outer membrane this website proteins [27]. In Rickettsiaceae, positively-selected sites were important for host-parasite interactions and were located at the exterior of the proteins [29]. The E. coli OMPLA structure had a beta-barrel transmembrane conformation [30]. Thus, one might reasonably assume that its positively-selected sites are also within surface-exposed regions. The N-terminal end of the protein contained four positively-selected sites (two with p ≥ 99), but they are most likely a signal sequence and not part of the mature protein. Bacterial survival and persistence in the gastric mucosa requires adapting to an environment with constant fluctuating pH.

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