More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells

Abstract

The genusLegionellacomprises 65 species, among whichLegionella pneumophilais a human pathogen causing severe pneumonia. To understand the evolution of an environmental to an accidental human pathogen, we have functionally analyzed 80Legionellagenomes spanning 58 species. Uniquely, an immense repository of 18,000 secreted proteins encoding 137 different eukaryotic-like domains and over 200 eukaryotic-like proteins is paired with a highly conserved type IV secretion system (T4SS). Specifically, we show that eukaryotic Rho- and Rab-GTPase domains are found nearly exclusively in eukaryotes andLegionella. Translocation assays for selected Rab-GTPase proteins revealed that they are indeed T4SS secreted substrates. Furthermore, F-box, U-box, and SET domains were present in >70% of all species, suggesting that manipulation of host signal transduction, protein turnover, and chromatin modification pathways are fundamental intracellular replication strategies for legionellae. In contrast, the Sec-7 domain was restricted toL. pneumophilaand seven other species, indicating effector repertoire tailoring within different amoebae. Functional screening of 47 species revealed 60% were competent for intracellular replication in THP-1 cells, but interestingly, this phenotype was associated with diverse effector assemblages. These data, combined with evolutionary analysis, indicate that the capacity to infect eukaryotic cells has been acquired independently many times within the genus and that a highly conserved yet versatile T4SS secretes an exceptional number of different proteins shaped by interdomain gene transfer. Furthermore, we revealed the surprising extent to which legionellae have coopted genes and thus cellular functions from their eukaryotic hosts, providing an understanding of how dynamic reshuffling and gene acquisition have led to the emergence of major human pathogens.

A Novel Legionella Genomic Island Encodes a Copper-Responsive Regulatory System and a Single Icm/Dot Effector Protein Transcriptionally Activated by Copper

“…In addition, these regulatory systems have been shown to assemble into an interconnected regulatory network using accessory components, such as modulators (AckA-Pta and PTS Ntr [22,38]) and connectors (LetE and LerC [22,39,40]). All the direct regulators of EEGs described above (PmrA, CpxR, CsrA, Fis1, Fis3, and Fur) were found to be present in all the Legionella species examined (41,42), and they function as global regulators that regulate the expression of a large number of genes, including EEGs, scattered throughout the L. pneumophila genome (18)(19)(20)22). Besides global regulators, local regulators that regulate the expression of a small number of adjacent genes are also common in many bacterial systems (43,44), including pathogenesis-related genes in Vibrio cholerae and Salmonella enterica (45).…”

Study of Legionella Effector Domains Revealed Novel and Prevalent Phosphatidylinositol 3-Phosphate Binding Domains

“…It is well established that Legionella effectors harbor domains typically found in eukaryotic proteins, such as ankyrin, F-box, and U-box domains and more (36,37,48,49). The analysis performed here indicates that the three novel PI3P-binding domains identified, even though not homologous to eukaryotic PI-binding domains, share the same amino acids critical for PI binding (22).…”

“…Previous studies have shown that the Legionella genus contains thousands of effectors (35,36). These effectors are expected to function inside host cells during infection and to modulate host cell processes to the benefit of the bacteria.…”

“…The temporal localization of these two PIs is likely to dictate the time postinfection in which specific effectors are localized to the LCV. The Legionella genus includes more than 50 species, most of which are pathogenic, and they all contain the conserved Icm/Dot type IV secretion system (35,36). In a previous study, we predicted thousands of effectors in 41 Legionella species, and this high number of effectors made it possible to identify conserved effector domains in these Legionella species (35).…”

Bacterial Factors Targeting the Nucleus: The Growing Family of Nucleomodulins

“…It is remarkable that some of them have evolved as mimics of eukaryotic nuclear proteins, either through sequence homologies (e.g., ANK, LRR, MYND, SET, F-box, U-box) or through true structural innovations (e.g., NEL domain). Interestingly, computational biology approaches suggest the presence of many uncharacterized proteins with potential nucleomodulin domains in the genomes of intracellular bacteria, such as Anaplasma [113], Legionella [114], and other species [115,116]. This opens up an important field of research into their functional roles.…”