A Distinct and Divergent Lineage of Genomic Island-Associated Type IV Secretion Systems in Legionella

Bryan A Wee,Megan Woolfit,Scott A Beatson,Nicola K Petty

doi:10.1371/journal.pone.0082221

Abstract

Legionella encodes multiple classes of Type IV Secretion Systems (T4SSs), including the Dot/Icm protein secretion system that is essential for intracellular multiplication in amoebal and human hosts. Other T4SSs not essential for virulence are thought to facilitate the acquisition of niche-specific adaptation genes including the numerous effector genes that are a hallmark of this genus. Previously, we identified two novel gene clusters in the draft genome of Legionella pneumophila strain 130b that encode homologues of a subtype of T4SS, the genomic island-associated T4SS (GI-T4SS), usually associated with integrative and conjugative elements (ICE). In this study, we performed genomic analyses of 14 homologous GI-T4SS clusters found in eight publicly available Legionella genomes and show that this cluster is unusually well conserved in a region of high plasticity. Phylogenetic analyses show that Legionella GI-T4SSs are substantially divergent from other members of this subtype of T4SS and represent a novel clade of GI-T4SSs only found in this genus. The GI-T4SS was found to be under purifying selection, suggesting it is functional and may play an important role in the evolution and adaptation of Legionella. Like other GI-T4SSs, the Legionella clusters are also associated with ICEs, but lack the typical integration and replication modules of related ICEs. The absence of complete replication and DNA pre-processing modules, together with the presence of Legionella-specific regulatory elements, suggest the Legionella GI-T4SS-associated ICE is unique and may employ novel mechanisms of regulation, maintenance and excision. The Legionella GI-T4SS cluster was found to be associated with several cargo genes, including numerous antibiotic resistance and virulence factors, which may confer a fitness benefit to the organism. The in-silico characterisation of this new T4SS furthers our understanding of the diversity of secretion systems involved in the frequent horizontal gene transfers that allow Legionella to adapt to and exploit diverse environmental niches.

Highlights

Type IV secretion systems (T4SSs) are a highly diverse family of complex macromolecular structures involved in a variety of functions, including conjugation, protein translocation and DNA uptake and release
No Legionella Genomic Islands (LGI)-T4SS cluster was identified in the genome sequence of L. longbeachae NSW150, the other eight genomes were each found to encode between one and four distinct LGI-T4SSs
The association of the lvrRABC genes with multiple T4SSs in Legionella suggests a role in coordinating the expression of the T4SS, and these genes were recently shown to regulate the excision of the genomic island encoding the T4ASS Trb-1 in strain Corby [28]

Summary

Introduction

Type IV secretion systems (T4SSs) are a highly diverse family of complex macromolecular structures involved in a variety of functions, including conjugation, protein translocation and DNA uptake and release (for a review, see [1]). Attempts to classify T4SSs into subtypes have been based on function and the type of substrate (DNA or protein) translocated, or phylogenetic relationships between shared representative genes [1,2]. These classification schemes are hampered by the diversity of functions and structures of the T4SS family as well as the mosaic nature of the genomic loci that encode them, which have evolved though extensive recombination and modular exchange. A third distinct class of T4SSs was found to be associated exclusively with genomic islands and called GI type or genomic island-associated T4SS (GI-T4SS) [6]

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Conclusion