In silico proteomic and phylogenetic analysis of the outer membrane protein repertoire of gastric Helicobacter species

Abstract

Helicobacter (H.) pylori is an important risk factor for gastric malignancies worldwide. Its outer membrane proteome takes an important role in colonization of the human gastric mucosa. However, in zoonotic non-H. pylori helicobacters (NHPHs) also associated with human gastric disease, the composition of the outer membrane (OM) proteome and its relative contribution to disease remain largely unknown. By means of a comprehensive survey of the diversity and distribution of predicted outer membrane proteins (OMPs) identified in all known gastric Helicobacter species with fully annotated genome sequences, we found genus- and species-specific families known or thought to be implicated in virulence. Hop adhesins, part of the Helicobacter-specific family 13 (Hop, Hor and Hom) were restricted to the gastric species H. pylori, H. cetorum and H. acinonychis. Hof proteins (family 33) were putative adhesins with predicted Occ- or MOMP-family like 18-stranded β-barrels. They were found to be widespread amongst all gastric Helicobacter species only sporadically detected in enterohepatic Helicobacter species. These latter are other members within the genus Helicobacter, although ecologically and genetically distinct. LpxR, a lipopolysaccharide remodeling factor, was also detected in all gastric Helicobacter species but lacking as well from the enterohepatic species H. cinaedi, H. equorum and H. hepaticus. In conclusion, our systemic survey of Helicobacter OMPs points to species and infection-site specific members that are interesting candidates for future virulence and colonization studies.

N6‐methyladenosine regulatory machinery in plants: composition, function and evolution

“…Such orthologous proteins are generally known to perform analogous biological functions and are widely distributed in diverse species (Schlicker et al, 2006). Phylogenetic analysis is a rapid and relatively accurate method to identify orthologous proteins (Bauwens et al, 2018;Jensen et al, 2018). Consequently, we constructed a phylogenetic tree for AlkBH proteins based on sequence similarity using MEGA6.0 and the neighbourjoining (NJ) method was adopted with 1000 bootstrap replications (Kumar et al, 2008).…”

Distinct transcriptome signatures of Helicobacter suis and Helicobacter heilmannii strains upon adherence to human gastric epithelial cells

“…Bacterial OMPs are directly involved in the interactions of pathogenic bacteria with their environment. However, the role of the different H. suis and H. heilmannii OMPs in gastric colonization and pathogenesis remains largely unknown [43]. While H. suis and H. heilmannii lack all known H. pylori adhesins described so far [24,46,56], H. heilmannii HofE and HofF OMPs have been shown to be important for adhesion to the mouse gastric mucosa, with a higher affinity for gastric epithelial cells than for mucins [57].…”

“…Helicobacter species contain a large set of outer membrane proteins (OMPs) as an adaptation to the hostile environment of the stomach [43]. Their outer membrane proteome takes an important role in the colonization of the gastric mucosa.…”

Review: Other Helicobacter species

“…As no signs of admixture events were found between H. pylori (and its two closest relatives) and the porcine, canine, and feline NHPH, it was concluded that these two groups did not evolve together but rather in parallel following a very distinctive evolutionary path. 66 The genome of the proposed "Helicobacter apodemus" strain SCJK1 isolated from the gastrointestinal tract of the striped field mouse has also been sequenced. They concluded that gastric and enterohepatic Helicobacters evolved for survival in a nutrient-rich stomach versus a nutrient-devoid intestinal tract, respectively, and that they utilize different pathogenic mechanisms to chronically infect and cause inflammation and tissue damage in their hosts.…”

“…65 A further study focused specifically on the outer membrane protein (OMP) repertoire of gastric Helicobacters as compared to the enterohepatic members within the Helicobacter genus and other genera residing in the intestinal tract which identified species and infection-site-specific OMPs as interesting candidates for future studies. 66 The genome of the proposed "Helicobacter apodemus" strain SCJK1 isolated from the gastrointestinal tract of the striped field mouse has also been sequenced. 67 The complete genome of "H. apodemus" has been shown to be composed of two circular contigs, one chromosome 2 034 706 bp long and one plasmid 33,248 bp long, and to have an average G+C content of 33.14% (chromosome, 33.2%; plasmid, 29.4%).…”