In silico evolutionary analysis of Helicobacter pylori outer membrane phospholipase A (OMPLA)

Hilde S Vollan,Tone Tannæs,Yoshio Yamaoka,Geir Bukholm

doi:10.1186/1471-2180-12-206

Abstract

BackgroundIn the past decade, researchers have proposed that the pldA gene for outer membrane phospholipase A (OMPLA) is important for bacterial colonization of the human gastric ventricle. Several conserved Helicobacter pylori genes have distinct genotypes in different parts of the world, biogeographic patterns that can be analyzed through phylogenetic trees. The current study will shed light on the importance of the pldA gene in H. pylori. In silico sequence analysis will be used to investigate whether the bacteria are in the process of preserving, optimizing, or rejecting the pldA gene. The pldA gene will be phylogenetically compared to other housekeeping (HK) genes, and a possible origin via horizontal gene transfer (HGT) will be evaluated through both intra- and inter-species evolutionary analyses.ResultsIn this study, pldA gene sequences were phylogenetically analyzed and compared with a large reference set of concatenated HK gene sequences. A total of 246 pldA nucleotide sequences were used; 207 were from Norwegian isolates, 20 were from Korean isolates, and 19 were from the NCBI database. Best-fit evolutionary models were determined with MEGA5 ModelTest for the pldA (K80 + I + G) and HK (GTR + I + G) sequences, and maximum likelihood trees were constructed. Both HK and pldA genes showed biogeographic clustering. Horizontal gene transfer was inferred based on significantly different GC contents, the codon adaptation index, and a phylogenetic conflict between a tree of OMPLA protein sequences representing 171 species and a tree of the AtpA HK protein for 169 species. Although a vast majority of the residues in OMPLA were predicted to be under purifying selection, sites undergoing positive selection were also found.ConclusionsOur findings indicate that the pldA gene could have been more recently acquired than seven of the HK genes found in H. pylori. However, the common biogeographic patterns of both the HK and pldA sequences indicated that the transfer occurred long ago. Our results indicate that the bacterium is preserving the function of OMPLA, although some sites are still being evolutionarily optimized.

Highlights

In the past decade, researchers have proposed that the pldA gene for outer membrane phospholipase A (OMPLA) is important for bacterial colonization of the human gastric ventricle
Bioinformatic analyses of H. pylori pldA and seven core housekeeping genes Gene evolution was assessed by comparing H. pylori pldA gene sequences to concatenated core HK genes
The present study focused on analyzing pldA gene sequences that code for functional OMPLA proteins

Summary

Introduction

Researchers have proposed that the pldA gene for outer membrane phospholipase A (OMPLA) is important for bacterial colonization of the human gastric ventricle. Colonization usually occurs in early childhood and results in disease in about 10% of cases [2]. The human gastric ventricle is the only known natural habitat for H. pylori, and one bacterial strain usually [10,11]. This conservation is reflected in phylogenetic analysis, where HK genes have been used to trace human migration, indicating co-evolution between H. pylori and its host. Linz et al traced H. pylori infection in humans to before their migration from Africa through sequence analysis [11,12]

Objectives

Methods

Results

Discussion

Conclusion