Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori

Chaille T Webb,Rebecca J Gorrell,Rhys D Grinter,Rebecca S Bamert,Terry Kwok,Jiangning Song,Rhys A Dunstan,Richard A Strugnell,Dilini Chandrapala,Siti Nurbaya Oslan,Trevor Lithgow

doi:10.1002/mbo3.513

Abstract

Helicobacter pylori is a gram‐negative bacterial pathogen that chronically inhabits the human stomach. To survive and maintain advantage, it has evolved unique host–pathogen interactions mediated by Helicobacter‐specific proteins in the bacterial outer membrane. These outer membrane proteins (OMPs) are anchored to the cell surface via a C‐terminal β‐barrel domain, which requires their assembly by the β‐barrel assembly machinery (BAM). Here we have assessed the complexity of the OMP C‐terminal β‐barrel domains employed by H. pylori, and characterized the H. pylori BAM complex. Around 50 Helicobacter‐specific OMPs were assessed with predictive structural algorithms. The data suggest that H. pylori utilizes a unique β‐barrel architecture that might constitute H. pylori‐specific Type V secretions system. The structural and functional diversity in these proteins is encompassed by their extramembrane domains. Bioinformatic and biochemical characterization suggests that the low β‐barrel‐complexity requires only minimalist assembly machinery. The H. pylori proteins BamA and BamD associate to form a BAM complex, with features of BamA enabling an oligomerization that might represent a mechanism by which a minimalist BAM complex forms a larger, sophisticated machinery capable of servicing the outer membrane proteome of H. pylori.

Highlights

In the model of Darwinian evolution, bacterial pathogens compete vigorously with normal flora, other pathogens, and host defenses to establish themselves within specific host niches
These distinct stages in the pathogenic lifecycle generally require remodeling of transcriptional programs, the bacterial surface proteome and metabolic capacity. In many pathogens, such as the various pathovars of Escherichia coli, the outer membrane proteome complexity is well characterized and shown to be expanded through variable surface carbohydrates (LPS and capsules) and the acquisition of protein secretion systems, fimbriae, and other cell surface structures through horizontal gene transfer (Diaz-Mejia, Babu, & Emili, 2009; Hacker & Kaper, 2000; Needham & Trent, 2013). These diverse cell surface structures are topologically intricate, but the majority of protein components are efficiently assembled into the E. coli outer membrane by multicomponent molecular machines (Grijpstra, Bos, & Tommassen, 2013; O’Neil, Rollauer, Noinaj, & Buchanan, 2015; Selkrig, Leyton, Webb, & Lithgow, 2014)
We found that the barrel assembly machinery (BAM) complex, far from being more sophisticated, contains just two of the five characteristic components: BamA and BamD

Summary

| INTRODUCTION

In the model of Darwinian evolution, bacterial pathogens compete vigorously with normal flora, other pathogens, and host defenses to establish themselves within specific host niches. The VacA toxin that promotes vacuole formation and disruption of mitochondria, has been confirmed as a Type 5 secretion system (Palframan, Kwok, & Gabriel, 2012) and three additional proteins ImaA, FaaA, and VlpC are considered to be “VacA-like” (Alm et al, 2000; Celik et al, 2012; Tomb et al, 1997), as they appear to remain tethered onto the surface of the bacterial outer membrane after secretion (Radin et al, 2013) In keeping with this limited protein secretion capability, H. pylori has dispensed with components involved in OMP assembly, such as the translocation assembly module (TAM) (Heinz, Selkrig, Belousoff, & Lithgow, 2015). We discuss the analogies between the Hp_OMP family and Type 5 secretion systems, significant in that this would be the first bacterial protein secretion system known to be species-specific

| EXPERIMENTAL PROCEDURES

Findings

| DISCUSSION