Secreted Effectors Encoded within and outside of the Francisella Pathogenicity Island Promote Intramacrophage Growth

Abstract

The intracellular bacterial pathogen Francisella tularensis causes tularemia, a zoonosis that can be fatal. The type VI secretion system (T6SS) encoded by the Francisella pathogenicity island (FPI) is critical for the virulence of this organism. Existing studies suggest that the complete repertoire of T6SS effectors delivered to host cells is encoded by the FPI. Using a proteome-wide approach, we discovered that the FPI-encoded T6SS exports at least three effectors encoded outside of the island. These proteins share features with virulence determinants of other pathogens, and we provide evidence that they can contribute to intramacrophage growth. The remaining proteins that we identified are encoded within the FPI. Two of these FPI-encoded proteins constitute effectors, whereas the others form a unique complex required for core function of the T6SS apparatus. The discovery of secreted effectors mediating interactions between Francisella and its host significantly advances our understanding of the pathogenesis of this organism.

Figure 1. The T6SSⁱⁱ System Facilitates the Export of at Least Eight Proteins, Including Three Encoded Outside of the FPI

(A) Quantitative mass spectrometric-based comparison of the extracellular proteomes of F. novicida wild-type and ΔdotU. Proteins highlighted in red and blue are absent or detected in significantly lower abundance in ΔdotU relative to the wild-type, respectively. (B–D) Regions of the F. novicida genome encoding T6SSⁱⁱ substrates: the FPI (B) and two distant genomic loci (C and D). Functions assigned in this study are indicated by fill color; secreted structural components are green and effectors are purple. Grey shading denotes the region of duplication overlapping opiB loci. (E–G) Western blot analysis probing candidate T6SSⁱⁱ substrate levels in the supernatant (Sup) and cell fractions of F. novicida wild-type and ΔdotU. Genetic backgrounds are denoted below the western blots. Substrates were detected by antibodies against N- (V–) or C-terminal (–V) vesicular stomatitis virus glycoprotein (VSV-G) epitope fusions encoded at native chromosomal loci (E), protein-specific antibodies (F), or via VSV-G fusions produced ectopically (G).

Figure 2. T6SSⁱⁱ Substrates Distribute into Two Phenotypic Classes

(A–E) Analysis of supernatant and cell fractions from the indicated F. novicida strains. (A) Core function of the T6SSⁱⁱ apparatus as determined by IglC secretion in strains lacking substrate-encoding genes. Sequence duplication within the opiB loci prohibited their individual manipulation, thus ΔopiB corresponds to a deletion of opiB-1-opiB-3. (BE) Western blot analysis of supernatant (Sup) and cell fractions of wild-type F. novicida (C) or strains expressing chromosomally-encoded VSV-G fusions to pdpC (V–pdpC) (B), vgrG (vgrG–V) (D), pdpA (V–pdpA) (E).

Figure 3. VgrG Interacts with PdpA Independent of the Predicted PAAR-like Protein IglG

(A, C and D) Western blot analysis of samples derived from the indicated F. novicida strains prior to (Total) or following (IP) anti-VSV-G immunoprecipitation. The band denoted IglF in (D) was identified via mass spectrometry. (B) anti-IglC western blot analysis of supernatant and cell fractions from the indicated strains.

Figure 4. PdpA Interacts Directly with VgrG and Limits Filament Length

(A, B, D, G) Negatively stained electron micrographs of (A) VgrG-V immunoprecipitated from F. novicida (FN) or (B) PdpA, (D) VgrG, or (G) VrgG and PdpA heterologously expressed and purified from E. coli (EC). Arrowheads indicate particle regions corresponding PdpA (red) and VgrG (green). Scale bar represents 50 nm. Representative negative stain electron micrographs are presented in Figure S2. (C) Class averages of PdpA–VgrG-VSV-G complexes immunoprecipitated from F. novicida (top), or PdpA (middle) or PdpA–VgrG (bottom) expressed and purified from E. coli. Scale bar represents 10nm. (E) Filament lengths of VgrG purified from F. novicida, or E. coli (EC) heterologously expressing VgrG or co-expressing PdpA and VgrG (n=100/group). Horizontal lines represent mean and standard deviation for each group. Asterisks denote statistically significant differences (** p ≤ 0.001). (F) Structural model of F. novicida VgrG (VgrG^FN) adjacent to the crystal structure of VgrG1 from P. aeruginosa (VgrG^PA; PDB ID, 4MTK) (Spinola-Amilibia et al., 2016). Regions bearing structural similarity to gp5 and gp27 from T4 bacteriophage are colored blue and orange, respectively.

Figure 5. T6SSⁱⁱ effectors act in concert to facilitate phagosomal escape and intramacrophage growth

(A) Core T6SSⁱⁱ function is maintained in a strain lacking all effectors identified in this study. Western blot analysis of secreted structural proteins in the cell and supernatant fractions of the indicated strains. (B) Phagosomal escape of wild type and mutant F. novicida strains in human macrophage-like THP-1 cells. THP-1 cells were infected as described in Materials & Methods, processed for immunofluorescence staining of bacteria (red), LAMP1 (green) and nuclei (blue) and localization of bacteria in LAMP1-positive phagosomes was scored over a 4h time course. Data represent mean ± stdev of three independent experiments. (C) Representative confocal micrographs of 60 and 240 min time points of experiment described in (B). Arrows indicate areas magnified in insets. Scale bars, 5 and 1 μm. (D) Growth of the indicated F. novicida strains in PMA-differentiated THP-1 cells 24 hours post infection. Data from each technical replicate was normalized to the number of intracellular bacteria immediately post infection and data from each of three biological replicates was normalized to ΔdotU. Asterisks denote statistically significant differences cited in the text (* p ≤ 0.05, ** P ≤ 0.001).

Figure 6. OpiA and OpiB are Virulence-associated Proteins

(A) Phylogenetic tree of Francisella and closely related organisms that possess the FPI (see methods) indicating the presence (filled) or absence (open) of secreted F. novicida T6SSⁱⁱ effectors and structural proteins identified in this study. If present, the degree of conservation with the F. novicida ortholog is indicated (fill color). The tree is adapted from Sjodin et al.; branch lengths do not represent evolutionary distance (Sjodin et al., 2012). Vertical lines within boxes indicate multiple copies of a given element and background colors denote host-specificities as indicated. (B) Overview of OpiB domain organization and conservation of its predicted N-terminal protease domain among diverse effector proteins. All proteins are shown to scale. The location of predicted or experimentally determined catalytic residues are indicated by colored lines, and box fill denotes protease domain (grey) and ankyrin motifs (green). Conserved catalytic motifs based on the alignment of a broader group of representative orthologs are shown as sequence logos. Amino acid composition at each position is shown according to (Aasland et al., 2002). The experimentally determined or predicted export pathway of each protein is provided at right. Proteins shown are: OpiB-1 A0Q6U1, OpiB-2 A0Q6U2, OpiB-3 A0Q6U3, OpiB^FT Q5NH59, OpiB^LVS Q2A3V2, LspA2 Q9ZHL3, LegA7 Q5ZYG9, AvrPhpB Q9F3T4, YopT O68703.