Domain-architecture aware phylogenetic profiling indicates a functional diversification of type IVa pili in the nosocomial pathogen Acinetobacter baumannii

Abstract

The Gram-negative bacterial pathogen Acinetobacter baumannii is a major cause of hospital-acquired opportunistic infections. The increasing spread of pan-drug resistant strains, paired with a surge in virulence, makes A. baumannii top-ranking among the ESKAPE pathogens for which novel routes of treatment are urgently needed. Comparative genomics approaches have successfully identified genetic changes that coincide with the emergence of pathogenicity in Acinetobacter. Genes that are prevalent both in pathogenic and a-pathogenic Acinetobacter species were not considered ignoring that virulence factors may emerge by the modification of evolutionarily old and widespread proteins. Here, we increased the resolution of comparative genomics analyses to also include lineage-specific changes in protein domain architectures. Using type IVa pili (T4aP) as an example, we show that two pilus components, FimU and the pilus tip adhesin ComC, exist with markedly differing domain architectures in pathogenic Acinetobacter species. ComC, has gained a von Willebrand Factor type A domain displaying a finger-like protrusion, and we provide experimental evidence that this finger conveys virulence-related functions in A. baumannii. Both genes together form an evolutionary cassette, which has been replaced at least twice during A. baumannii diversification. The resulting strain-specific differences in T4aP layout suggests differences in the way how individual strains interact with their host. Our study underpins the hypothesis that A. baumannii uses T4aP for host infection as it was shown previously for other pathogens. It also indicates that many more functional complexes may exist whose precise function can be rapidly adjusted by changing the domain architecture of individual proteins. Author SummaryType IVa pili (T4aP) are hair-like, extendable, and retractable appendages that many bacteria use for interacting with their environment. Several human pathogens have independently recruited these pili for processes related to host infection, but the modifications necessary to turn T4aP into virulence factors are largely unknown. Here, we studied if and how T4aP components have changed in the nosocomial pathogen A. baumannii compared to its largely a-pathogenic relatives in the Acinetobacter genus. Most A. baumannii isolates have T4aP with a pilus tip adhesin containing a protein domain not seen outside the pathogenic clade. This domain is essential for bacterial motility and contributes to host cell adhesion and natural competence. However, some isolates have T4aP resembling those of largely a-pathogenic species in this genus. This indicates that the way these pili are used during infection processes differs between A. baumannii isolates probably as a result of niche adaptation. In a broader perspective, our findings highlight that many relevant genetic differences between pathogens and their a-pathogenic relatives emerge only on the domain- and sub-domain level. This suggests that comparative genomics studies have only uncovered the tip of the iceberg of genetic determinants that contribute to A. baumannii virulence.