Extracellular M. tuberculosis DNA targets bacteria for autophagy by activating the host DNA-sensing pathway

Abstract

Eukaryotic cells sterilize the cytosol by using autophagy to route invading bacterial pathogens to the lysosome. During macrophage infection with Mycobacterium tuberculosis, a vacuolar pathogen, exogenous induction of autophagy can limit replication, but the mechanism of autophagy targeting and its role in natural infection remain unclear. Here we show that phagosomal permeabilization mediated by the bacterial ESX-1 secretion system allows cytosolic components of the ubiquitin-mediated autophagy pathway access to phagosomal M. tuberculosis. Recognition of extracelluar bacterial DNA by the STING-dependent cytosolic pathway is required for marking bacteria with ubiquitin, and delivery of bacilli to autophagosomes requires the ubiquitin-autophagy receptors p62 and NDP52 and the DNA-responsive kinase TBK1. Remarkably, mice with monocytes incapable of delivering bacilli to the autophagy pathway are extremely susceptible to infection. Our results reveal an unexpected link between DNA sensing, innate immunity, and autophagy and indicate a major role for this autophagy pathway in resistance to M. tuberculosis infection.

Figure 1. M. tuberculosis Targeting to Autophagosomes Requires Phagosomal Permeabilization via ESX-1

(A) Fluorescence images of GFP-LC3 BMDMs (green) infected for 4 hr with mCherry-expressing WT or Δesat-6 M. tuberculosis (red). (B) Quantitative analysis of GFP-LC3 colocalization with WT and Δesat-6 M. tuberculosis at indicated times after infection. Results are the means ± SEM of three independent experiments. (C) Fluorescence images of BMDMs infected for 4 hr with mCherry-expressing WT or Δesat-6 M. tuberculosis (red) and immunostained with anti-ATG12 (green). (D) Quantitative analysis of colocalization with ATG12 at 4 hr post-infection. Results are the means ± SEM of three independent experiments. (E) Western blot analysis of LC3 and actin (loading control) of BMDMs infected for 4 hr with WT M. tuberculosis. (F) Fluorescence images of RAW 264.7 cells stably expressing GFP-LC3 (green) infected for 6 hr with either mCherry-expressing BCG or BCG complemented with RD1 (red). (G) Quantitative analysis of GFP-LC3 colocalization with WT M. tuberculosis, BCG, or BCG complemented with RD1 at 6 hr post-infection. Results are the means ± SEM of three independent experiments (n = 3 per group, *p < 0.005). (H) Fluorescence images of GFP-LC3 RAW 264.7 cells (green) infected with the Δesat-6 M. tuberculosis (red) or Δesat-6 M. tuberculosis expressing listeriolysin-O (LLO) (red) (n = 3 per group, *p < 0.005). (I) Quantitative analysis of GFP-LC3 colocalization with WT M. tuberculosis, Δesat-6 M. tuberculosis, and Δesat-6 M. tuberculosis expressing LLO. Results are the means ± SEM of three independent experiments (n = 3 per group, *p < 0.005). (J) Quantitative analysis of GFP-LC3 colocalization with WT M. marinum, ΔRD1 M. marinum, and ΔRD1 M. marinum expressing LLO. Results are the means ± SEM of three independent experiments (n = 3 per group, *p < 0.005). (K) Fluorescence images of GFP-LC3 RAW 264.7 cells (green) infected for 6 hr with Rv1596::Tn, moaB::Tn and Δesat-6 M. tuberculosis (red). (L) Quantitative analysis of GFP-LC3 colocalization with WT, Δesat-6 Rv1596::Tn, and moaB::Tn M. tuberculosis. Results are the means ± SEM of three independent experiments. See also Figure S1 and Movie S1.

Figure 2. The Autophagy Receptors p62 and NDP52 and the Kinase TBK1 Are Required for Efficient Delivery of M. tuberculosis to Autophagosomes

(A) Fluorescence images of BMDMs infected for 4 hr with mCherry-expressing WT or Δesat-6 M. tuberculosis (red) and immunostained with anti-p62 (green). (B) Quantitative analysis of colocalization with p62 at 4 hr post-infection. Results are the means ± SEM of three independent experiments. (C) Fluorescence images of BMDMs infected for 4 hr with mCherry-expressing WT or Δesat-6 M. tuberculosis (red) and immunostained with anti-NDP52 (green). (D) Quantitative analysis of colocalization with NDP52 at 4 hr post-infection. Results are the means ± SEM of three independent experiments. (E) Fluorescence images of BMDMs infected with WT M. tuberculosis (blue) for 4 hr and immunostained with anti-LC3 (green), anti-p62 (red), or anti-NDP52 (red). (F) Quantitative analysis of M. tuberculosis colocalization with p62, NDP52 and LC3 at 4 hr post-infection. Results are the means ± SEM of three independent experiments. (G) Quantitative analysis of GFP-LC3 colocalization with WT M. tuberculosis after shRNA knockdown of p62 or NDP52 in GFP-LC3 RAW 264.7 cells. Results are the means ± SEM of three independent experiments. Data are expressed as a percentage relative to control (scrambled shRNA) knockdown cells (n = 3 per group, *p < 0.006). See also Figure S3. (H) Fluorescence images of BMDMs infected with either mCherry-expressing WT or Δesat-6 M. tuberculosis (red) for 4 hr and immunostained with anti-phospho- TBK1 (red). (I) Quantitative analysis of M. tuberculosis colocalization with phospho-TBK1 and LC3 at 4 hr post-infection. Results are the means ± SEM of three independent experiments. (J) Fluorescence images of BMDMs infected for 4 hr with mCherry-expressing WT M. tuberculosis (blue) and immunostained with anti-LC3 (green) and antiphospho-TBK1 (red) (n = 3 per group, *p < 0.01). (K) Quantitative analysis of M. tuberculosis colocalization with TBK1 and LC3 at 4 hr post-infection. Results are the means ± SEM of three independent experiments. (L) Quantitative analysis of BMDMs from Tbk1^+/+ and Tbk1^−/− mice infected with WT M. tuberculosis for 4 hr and immunostained with anti-LC3 antibodies. Results are the means ± SEM of three independent experiments.

Figure 3. Mycobacterial ESX-1 System Is Required for Ubquitin Colocalization

(A) Fluorescence images of BMDMs infected for 4 hr with mCherry-expressing WT or Δesat-6 M. tuberculosis (red) and immunostained with antiubiquitin antibodies (green). (B) Quantitative analysis of ubiquitin and LC3 colocalization with WT or Δesat-6 M. tuberculosis at indicated times post-infection. Results are the means ± SEM of three independent experiments. (C) Fluorescence images of BMDMs infected for 4 hr with mCherry-expressing WT M. tuberculosis (blue) and immunostained with anti-LC3 (green) and anti-ubiquitin antibodies (red). (D) Quantitative analysis of M. tuberculosis colocalization with ubiquitin and LC3 at 4 hr postinfection. Results are the means ± SEM of three independent experiments. (E) Fluorescence images of BMDMs infected with mCherry-expressing WT M. tuberculosis and immunostained with anti-K63 and anti-K48 ubiquitin antibodies (green). (F) Quantitative analysis of K63 and K48 ubiquitin colocalization in BMDMs infected with WT M. tuberculosis at 4 hr post-infection. Results are the means ± SEM of three independent experiments. See also Figure S2.

Figure 4. Cytosolic DNA Is Targeted by Ubiquitin-Mediated Selective Autophagy and Requires NDP52 and STING

(A) Fluorescence images of GFP-LC3 RAW 264.7 cells (green) at 4 hr post-transfection with lipofectamine alone (control), plasmid DNA, cyclic di-AMP, or cyclic di-GMP or treated with rapamycin. (B) Western blot analysis of LC3 in Atg5⁺ and Atg5⁻ BMDMs transfected with DNA for 3 hr. (C) Fluorescence images of GFP-LC3 RAW 264.7 cells at 4 hr post-transfection with Cy3-labeled nucleic acid. Plasmid DNA was introduced by either lipofection (plasmid-lipo) or electroporation (plasmid-electro), and all the other nucleic acid species were introduced by lipofection. Cells were also treated with lipofectamine reagent alone (lipo) or DNA without transfection reagent (DNA only). (D) Quantitative analysis of Cy3-labeled plasmid DNA with GFP-LC3 RAW 264.7 cells at 4 hr post-transfection. Results are the means ± SEM of three independent experiments. (E) Western blot analysis of LC3 after streptavidin immunoprecipitation of cell lysates 4 hr post-transfection of dsDNA or biotintylated dsDNA. (F) Fluorescence images of BMDMs transfected with Cy3-labeled plasmid DNA (red) and immunostained with anti-ATG12, anti-ubiquitin, anti-LAMP-1, anti-NDP52, or anti-phospho-TBK1 antibodies (green). (G) Quantitative analysis of GFP-LC3 colocalization with Cy3-labeled plasmid DNA at 4 hr post-transfection after shRNA knockdown of NDP52 in GFP-LC3 RAW 264.7 cells. Results are the means ± SEM of three independent experiments. Data are expressed as a percentage relative to control knockdown cells (n = 3 per group, *p < 0.005). (H) Fluorescence images of WT and Sting^−/− BMDMs at 4 hr post-transfection with Cy3-labeled plasmid DNA (red) and immunostained with anti-ubiquitin or anti-LC3 antibodies. (I) Quantitative analysis of ubiquitin, NDP52, and LC3 colocalization with Cy3-labeled plasmid DNA at 4 hr post-transfection in WT and Sting^−/−BMDMs. Results are the means ± SEM of three independent experiments. Data are expressed as a percentage relative to control knockdown cells (n = 3 per group, *p < 0.005). See also Figure S4.

Figure 5. STING and Cytosolic DNases Modulate Autophagic Targeting ofM. tuberculosis

(A) Quantitative analysis of ubiquitin colocalization with WT M. tuberculosis at 4 hr post-infection in WT or Sting^−/− BMDMs. Results are the means ± SEM of three independent experiments. Data are expressed as the percentage of ubiquitin-positive cells relative to WT BMDMs (n = 3 per group, *p < 0.003). (B) Quantitative analysis of LC3 colocalization with WT M. tuberculosis at 4 hr post-infection in WT or Sting^−/− BMDMs. Results are the means ± SEM of three independent experiments. Data are expressed as the percentage of LC3-positive cells relative to WT BMDMs (n = 3 per group, *p < 0.003). (C) Quantitative analysis of phospho-TBK1 and -NDP52 colocalization with WT M. tuberculosis at 4 hr post-infection in WT or Sting^−/− BMDMs. Results are the means ± SEM of three independent experiments. Data are expressed as the percentage of marker-positive cells relative to WT BMDMs. (D) Quantitative analysis of ubiquitin colocalization with WT M. tuberculosis at 4 hr post-infection in RAW cells stably overexpressing TREX1 or DNASE IIa. Results are the means ± SEM of three independent experiments. Data are expressed as the percentage of ubiquitin-positive cells relative to control (vector only) cells (n = 3 per group, *p < 0.019). (E) Quantitative analysis of GFP-LC3 colocalization with WT M. tuberculosis at 4 hr post-infection in GFP-LC3 RAW 264.7 cells stably overexpressing TREX1 and DNASE IIa. Results are the means ± SEM of three independent experiments. Data are expressed as the percentage of GFP-LC3-positive cells relative to control (vector only) cells (n = 3 per group, *p < 0.003). (F) Quantitative analysis of ubiquitin colocalization with WT M. tuberculosis at 4 hr post-infection in WT or Trex1^−/−. Results are the means ± SEM of three independent experiments. Data are expressed as the percentage of ubiquitin-positive cells relative to WT BMDMs (n = 3 per group, *p < 0.005). (G) Quantitative analysis of LC3 colocalization with WT M. tuberculosis at 4 hr post-infection in WT or Trex1^−/− BMDMs. Results are the means ± SEM of three independent experiments. Data are expressed as the percentage of GFP-LC3-positive cells relative to WT BMDMs (n = 3 per group, *p < 0.02). See also Figure S5.

Figure 6. STING-, TBK1-, and ATG5-Dependent Delivery of M. tuberculosis to Lysosomes Limits Bacterial Replication

(A) Fluorescence images of indicated BMDM genotypes infected for 4 hr with mCherry-expressing WT M. tuberculosis (red) and immunostained with anti-LAMP-1 (green) antibodies. (B) Quantitative analysis of LAMP-1 colocalization with WT M. tuberculosis at 4 hr post-infection in indicated BMDM genotypes. Results are the means ± SEM of three independent experiments. Data are expressed as the percentage of Lamp-1-positive cells relative to control BMDMs (n = 3 per group, *p < 0.012). (C) BMDMs of the indicated genoytpes were infected with WT M. tuberculosis (multiplicity of infection [moi] 1) for 0, 6, and 24 hr. Bacterial viability was assessed by CFUs. Results are the means ± SEM of three independent experiments. Data are expressed as the percentage of bacterial survival compared to time zero relative to control macrophages (n = 3 per group, *p < 0.025). (D) RAW 264.7 cells were infected with WT M. tuberculosis (moi 1) for 0, 6, and 24 hr after shRNA knockdown of NDP52. Bacterial viability was assessed by CFUs. Results are the means ± SEM of three independent experiments. Data are expressed as the percentage of bacterial survival compared to time zero relative to scrambled shRNA (control) (n = 3 per group, *p < 0.046).

Figure 7. ATG5 Is Required In Vivo for Control ofM. tuberculosis

Atg5^fl/fl (Atg5⁺) and Lyz-Cre-Atg5^fl/fl (Atg5⁻) from a single cohort were infected with 200 CFUs of WT M. tuberculosis via the aerosol route (n = 30 per group). (A) Atg5⁺ mice showed significantly improved survival compared to Atg5⁻ mice as calculated by log-rank test (**p < 0.001). (B and C) Bacterial burdens as measured by CFUs in the lungs 0, 7, and 21 days post-infection (B) and the spleen and liver 21 days post-infection (C) (n = 5 per time point, *p < 0.005, **p < 0.001). (D) Lungs from Atg5⁺ and Atg5⁻ mice 21 days post-infection. (E) H&E staining of lung sections from Atg5⁺ and Atg5⁻ mice 21 days post-infection. Arrows indicate large pulmonary abscesses not observed in WT mice. (F) Multiplex ELISA analysis of cytokines from lungs of control and Atg5⁻ mice 21 days postinfection (n = 4 per group).