Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

Nigel J Saunders,Prawit Boonmee,John F Peden,Stephen A Jarvis

doi:10.1186/1471-2164-6-9

Nigel J Saunders, Prawit Boonmee + Show 2 more

Open Access

https://doi.org/10.1186/1471-2164-6-9

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Abstract

BackgroundHorizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of established signature analysis with textual analysis approaches. This approach has been used to analyze the two available genome sequences of H. pylori.ResultsThis gene-by-gene analysis reveals a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds. These frequently involve single genes or small numbers of genes that are not associated with transposases or bacteriophage genes, nor with inverted repeats typically used as markers for horizontal transfer. In addition, clear examples of horizontal exchange in genes associated with 'core' metabolic functions were identified, supported by differences between the sequenced strains, including: ftsK, xerD and polA. In some cases it was possible to determine which strain represented the 'parent' and 'altered' states for insertion-deletion events. Different signature component lengths showed different sensitivities for the detection of some horizontally transferred genes, which may reflect different amelioration rates of sequence components.ConclusionNew implementations of signature analysis that can be applied on a gene-by-gene basis for the identification of horizontally acquired sequences are described. These findings highlight the central role of the availability of homologous substrates in evolution mediated by horizontal exchange, and suggest that some components of the supposedly stable 'core genome' may actually be favoured targets for integration of foreign sequences because of their degree of conservation.

Highlights

Horizontal gene transfer is central to evolution in most bacterial species
On the basis of the similarities determined in the H. pylori strain J99 sequence annotation, 7 of the most divergent genes as determined by dinucleotide signatures (DNS)
We describe the use of a linear implementation of signature analysis that can efficiently address a range of walking window sizes using dinucleotide signatures (DNS) and longer signatures

Summary

Introduction

Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. The acquisition of genes from other strains and species is by far the most rapid evolutionary process This occurs frequently without loss of existing functions, is central to the evolution of (page number not for citation purposes) niche-adaptive and pathogenic characteristics of bacteria, and greatly influences inter-strain differences in gene complement [3,4,5]. In this context, it is notable that none of the traits typically used to differentiate E. coli from Salmonella can be attributed to point mutation genes but are broadly attributable to horizontal exchange [6]. H. pylori is relatively unusual in that it is a naturally transformable

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