A Bacterial Pathogen Targets a Host Rab-Family GTPase Defense Pathway with a GAP

Abstract

Cell-autonomous defense mechanisms are potent strategies that protect individual cells against intracellular pathogens. The Rab-family GTPase Rab32 was previously shown to restrict the intracellular human pathogen Salmonella Typhi, but its potential broader role in antimicrobial defense remains unknown. We show that Rab32 represents a general cell-autonomous, antimicrobial defense that is counteracted by two Salmonella effectors. Mice lacking Rab-32 or its nucleotide exchange factor BLOC-3 are permissive to S. Typhi infection and exhibit increased susceptibility to S. Typhimurium. S. Typhimurium counters this defense pathway by delivering two type III secretion effectors, SopD2, a Rab32 GAP, and GtgE, a specific Rab32 protease. An S. Typhimurium mutant strain lacking these two effectors exhibits markedly reduced virulence, which is fully restored in BLOC-3-deficient mice. These results demonstrate that a cell-autonomous, Rab32-dependent host defense pathway plays a central role in the defense against vacuolar pathogens and describe a mechanism evolved by a bacterial pathogen to counter it.

Keywords: Rab GTPases; Rab32; Salmonella Typhi; Salmonella pathogenesis; bacterial pathogenesis; cell-autonomous defense; innate immunity; lysosome-related organelles; lysosomes; macrophages; membrane traffic; type III secretion; typhoid fever.

Figure 1. The Rab32-BLOC-3-Dependent Pathogen-Restriction Pathway Limits the Growth of S. Typhimurium and S. Typhi in a Mouse Model of Infection

(A and B) C57BL/6 (WT), C57B6.C3-Pde6b^rd1 Hps4^le/J (BLOC-3 deficient), or Rab32-deficient mice were intraperitoneally infected with 10² CFU of wild-type S. Typhimurium, and 5 days after infection the levels of the CFU in the spleens were enumerated. Each triangle represents the bacterial load for an individual animal, and horizontal bars indicate medians of the CFU. The p values of the differences in bacterial loads between the indicated animals determined by the Wilcoxon-Mann-Whitney test are shown. (C) C57BL/6 (WT) or C57B6.C3-Pde6b^rd1 Hps4^le/J (BLOC-3 deficient) mice were infected intraperitoneally with 10⁵ CFU of wild-type S. Typhi, and bacterial loads in the spleens were enumerated at the indicated days after infection. Each triangle represents the bacterial load for an individual animal, and horizontal bars indicate the medians of the CFU. The p values of the difference sin bacterial loads between the indicated animals determined by the Wilcoxon-Mann-Whitney test are shown. (D) C57BL/6 mice were intraperitoneally infected with equal numbers (10³ CFU each) of the wild-type, ΔgtgE, or gtgE^E151A (encoding a GtgE catalytic mutant) strains (in the indicated combinations), and 5 days after infection, the levels of the different strains in the spleen of infected mice were enumerated. Each triangle represents the competitive index for the indicated strains in an individual mouse, and the horizontal bars are the medians of the competitive indices.

Figure 2. The S. Typhimurium Effector Proteins SopD2 and GtgE Prevent the Recruitment of Rab32 to the S. Typhimurium-Containing Vacuole

(A and B) COS-1 cells expressing CFP-Rab32 (green) were infected with the indicated strains of S. Typhi or S. Typhimurium expressing mCherry (red), and 3 hr after infection, the infected cells were visualized by fluorescence microscopy. Images show maximum-intensity projections of confocal z stacks (scale bars, 5 μm) (A). The mean ± SEM of the percentage of Salmonella-containing vacuoles that were positive for Rab32 in three independent experiments are shown (B). At least 100 bacteria were counted in each experimental condition. *p < 0.01 (Student's t test) for the difference with the values obtained in cells infected with wild-type S. Typhi or S. Typhimurium. The strain indicated as S. Typhimurium Δ11 psopB lacks 11 type III secretion effector proteins and carries a plasmid encoding sopB (see Experimental Procedures and text for details). See also Figure S1.

Figure 3. SopD2 Is a GAP for Rab-Family GTPases

(A) HeLa cells were transiently cotransfected with plasmids expressing FLAG-epitope-tagged SopD2 along with plasmids expressing GFP-tagged wild-type (WT), dominant-negative (T22N or T23N), or constitutively active (Q67L or Q68L) forms of Rab8A, Rab8B, or Rab10. Sixteen hours after transfection, cell lysates were analyzed by immunoprecipitation with anti-FLAG and western immunoblotting with anti-GFP, FLAG, and tubulin (as loading control) antibodies. Dotted lines indicate places where the experimentally relevant lanes were spliced together (all lanes originate from a single gel). (B and C) The indicated purified GTPases were incubated alone or in the presence of purified SopD2 or the irrelevant protein PltB (as a negative control). The intrinsic GTPase activity of the different GTPases was then measured as indicated in Experimental Procedures. Values represent the ratio of GTPase activities observed in the presence or absence of SopD2 (or the indicated control protein) and are the mean ± SD of three independent determinations. *p < 0.001 (Student's t test) relative to incubation in the absence of SopD2. See also Figures S2–S4 and Table S1.

Figure 4. SopD2 Catalytic Activity Mimics Eukaryotic GAPs

(A) Size-exclusion chromatography profiles of purified proteins used in these experiments. (B and C) The indicated purified Rab GTPases were incubated with purified SopD2 or the indicated mutants, and the intrinsic GTPase activity of the different GTPases was then measured as indicated in Experimental Procedures. Values represent the ratio of GTPase activities observed in the presence or absence of the different SopD2 preparations and are the mean ± DS of three independent determinations. *p < 0.001 (Student's t test) relative to incubation with wild-type SopD2. (D) HeLa cells expressing YFP-Rab32 were infected with S. Typhimurium ΔgtgE ΔsopD2 strains carrying a plasmid encoding sopD2, sopD2^R315A, or the plasmid vector alone, and 4 hr after infection the infected cells were fixed, stained with an antibody against S. Typhimurium LPS, and visualized by fluorescence microscopy. Values represent the mean ± SD of the percentage of Salmonella-containing vacuoles that are positive for Rab32 and have been normalized according to the values observed in cells infected with the S. Typhimurium ΔgtgE ΔsopD2 strain carrying the vector control, which was considered to be 100% (the actual value for the control was 59% ± 3%). The values were obtained from three independent experiments in which at least 100 cells for each experimental condition were examined. *p < 0.01 (Student's t test) for the difference with the values obtained in cells infected with S. Typhimurium ΔgtgE ΔsopD2 complemented with a wild-type copy of SopD2. (E) Crystal structure of SopD2 depicting the location of the catalytic arginine. The visualization of the atomic structure (PDB No. 5CQ9) was carried using PyMol. See also Figures S5–S7.

Figure 5. Functional Redundancy of SopD2 and GtgE in S. Typhimurium Virulence

(A) C57BL/6 mice were intraperitoneally infected with 10³ CFU of the indicated S. Typhimurium strains, and 5 days after infection, the levels of the different strains in the spleen of the infected mice were enumerated. Each triangle represents the bacterial load for an individual animal, and horizontal bars indicate the geometric median of the CFU. The significant p values of the differences in bacterial loads between the indicated strains determined by the Wilcoxon-Mann-Whitney test are shown. (B) Survival of C57BL/6 mice orally infected with 10⁷ CFU of the S. Typhimurium ΔgtgE (n = 3) or ΔgtgE ΔsopD2 (n = 4) mutant strains. (C) C57BL/6 mice were intraperitoneally infected with 10³ CFU of the indicated strains of S. Typhimurium, and 5 days after infection, the levels of the different strains in the spleen of infected mice were enumerated. The significant p values of the differences in bacterial loads between the indicated conditions determined by the Wilcoxon-Mann-Whitney test are shown. (D) Survival of C57BL/6 mice orally infected with 10⁷ CFU of S. Typhimurium ΔgtgE ΔsopD2 mutant strain carrying a plasmid encoding wild-type SopD2 or its catalytic mutant SopD2^R315A (n = 5 for each strain). (E) C57BL/6 mice were intraperitoneally infected with equal numbers (10³ CFU each) of the S. Typhimurium ΔspiA and ΔsopD ΔgtgE mutant strains, and 5 days after infection, the levels of the different strains in the spleen of infected mice were enumerated. Each triangle represents the competitive index for the indicated strains in an individual mouse, and the horizontal bars are the medians of the competitive indices.

Figure 6. SopD2 and GtgE Redundantly Target the Rab32/BLOC-3 Pathogen-Restriction Pathway

C57BL/6- or BLOC-3-deficient mice were intraperitoneally infected with 10² CFU of the indicated strains of S. Typhimurium, and 5 days after infection, the levels of the different strains in the spleen of infected mice were enumerated. Each triangle represents the bacterial load for an individual animal, and horizontal bars indicate medians of the CFU. The significant p values of the differences in bacterial loads between the indicated conditions determined by the Wilcoxon-Mann-Whitney test are shown.

Figure 7. Model for the Rab32/BLOC-3-Dependent, Cell-Autonomous Defense Pathway and the Mechanisms Evolved by the Broad-Host S. Typhimuriumto Counter It

Asterisk represents an antimicrobial factor delivered to the Salmonella-containing vacuole.