Figures and data
NLSs are required for the nuclear translocation of MmpE.
(A) qRT-PCR analysis of mmpE mRNA expression in HEK293T cells over 48 hpt. (B) Western blot analysis of nuclear fractions showing time-dependent accumulation of MmpE-EGFP (top), and corresponding quantification of nuclear MmpE-EGFP levels (bottom). Histone H3 and β-actin were used as nuclear and cytoplasmic markers, respectively. (C) Domain architecture of MmpE, including a Tat signal peptide (1-54 amino acids, with a twin-arginine translocation motif) and two nuclear localization signals (NLS1: 20-22 aa; NLS2: 460-462 aa). The structure of the MmpE protein was predicted using AlphaFold 2.2.0, with NLS1 and NLS2 highlighted in red and green, respectively. (D) Subcellular localization of EGFP-tagged wild-type and NLS-deleted MmpE. (left) Schematic representation of EGFP-tagged constructs. (right) Confocal microscopy images of HEK293T cells transfected with the indicated constructs for 36 hpt. EGFP fluorescence (green) and nuclear staining with DAPI (blue) were visualized using an FLUOVIEW software (v5.0). Scale bar, 10 µm. Images were acquired with a ×100 oil immersion objective (NA = 1.4). (E) Quantification of nuclear EGFP intensity of wild-type and mutant MmpE in (Figure 1D). Data are shown as mean ± SD, n = 12 cells. (F) Western blot analysis of nuclear and cytoplasmic fractions from HEK293T cells transfected with wild-type and mutant MmpE-EGFP confirmed their subcellular localization. MmpE-EGFP was detected using an anti-GFP antibody, and histone H3 and β-actin served as nuclear and cytoplasmic markers, respectively. (G) Quantitative analysis of MmpE-EGFP levels in the cytoplasmic and nuclear compartments of (Figure 1F). Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-tailed unpaired Student’s t-tests, *P < 0.05, **P < 0.01, ***P < 0.001.
Deletion of NLSs does not alter the phosphatase activity of MmpE.
(A) Domain architecture of MmpE. Schematic representation of MmpE with the annotated functional domains, including a Tat signal peptide (1-41 aa, twin-arginine translocation motif), a purple acid phosphatase domain (68-149 aa), a calcineurin-like phosphoesterase domain (211-389 aa) and two nuclear localization signals (NLS1: 20-22 aa; NLS2: 460-462 aa). (B) Phylogenetic and structural conservation of MmpE. Neighbor-joining phylogenetic tree of MmpE homologs across Mycobacterium species (1,000 bootstrap replicates; values ≥50% shown). Species abbreviations: M. tuberculosis (Mtu), M. bovis BCG (Mbb), M. orygis (Mory), M. kubicae (Mku), M. paraterrae (Mpa), M. farcinogenes (Mfg), M. mucogenicum (Mmuc), M. vicinigordonae (Mgor), M. lentiflavum (Mlf), M. avium (Mav), M. manitobense (Mman). (C) Phosphatase activity of MmpEΔTat (lacking the N-terminal Tat signal peptide) was measured using p-NPP as the substrate in the presence of increasing concentrations (0-500 μM) of Fe³⁺ and Zn²⁺. (D) Prediction of metal ion-binding residues in MmpE. Structural modeling and visualization were performed using PyMOL. Conserved residues in the putative metal-binding pocket are shown as sticks, colored by atom type. The predicted metal coordination site is highlighted, with key binding residues labeled. Surface representation depicts the spatial accessibility of the pocket. (E) Phosphatase activity of increasing concentrations of MmpEΔTat and the mutant MmpEΔTat-H348AN359A was measured in the absence or presence of 50 μM Fe³⁺. (F) Phosphatase activity of increasing concentrations of MmpEΔTat and MmpEΔTat/ΔNLS1-2 was measured under standard conditions. Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-way ANOVA, *P < 0.05, **P < 0.01, ***P < 0.001.
The nuclear translocation and phosphatase activity of MmpE are essential for M. bovis BCG survival in macrophage cells.
(A-B) Intracellular survival of BCG strains in human THP-1 macrophages (A) and RAW264.7 macrophages (B). Strains include BCG WT, ΔMmpE, Comp-MmpE, and Comp-MmpEΔNLS2. (C-D) Intracellular survival of strains in THP-1 (C) and RAW264.7 macrophages (D). Strains include BCG WT, ΔMmpE, Comp-MmpE, Comp-MmpEΔNLS1and Comp-MmpEΔNLS1-2. (E) Intracellular survival of Comp-MmpE-H348AN359H mutant in THP-1 cells. (F-H) Inflammatory cytokine expression in infected THP-1 cells. mRNA levels of IL-1A (F), IL-1B (G), and IL-6 (H) were quantified by qRT-PCR 24 hpi with the indicated BCG strains. Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-way ANOVA or two-tailed unpaired Student’s t-tests, *P < 0.05, **P < 0.01, ***P < 0.001.
MmpE regulates host transcription network involved in inflammation response and lysosomal maturation.
(A) Volcano plot showing DEGs in THP-1 cells infected with ΔMmpE versus WT strains. DEGs were defined as | log2(fold change) | ≥ 1 and P < 0.05. (B) Enrichment analysis of DEGs shown in (A). The circular plot shows enriched biological process and molecular function terms. Outer rings represent GO terms (red) and downregulated (green) genes; inner rings reflect z-scores (blue to pink). Selected terms are listed with GO IDs and descriptions. (C) KEGG enrichment analysis of DEGs shown in (A). Bar length denotes the number of associated DEGs, and color represents statistical significance (-log10 (P-value)). (D) Protein-protein interaction network of immune-related DEGs, constructed using STRING v12.0 and visualized in Cytoscape. (E) Heatmap of immune-related DEGs in ΔMmpE-infected and WT-infected THP-1 cells. Log2(fold change) values are shown across three biological replicates. Red and blue indicate upregulation and downregulation, respectively. (F-G) qRT-PCR validation of representative DEGs in THP-1 cells infected with WT or ΔMmpE for 24 hpi. Cytokine-related genes (F); lysosomal acidification and V-ATPase subunits genes (G). Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-way ANOVA, *P < 0.05, **P < 0.01, ***P < 0.001.
MmpE regulates the PI3K-Akt-mTOR signaling pathway during macrophage infection.
(A-D) Cut&Tag analysis of MmpE-binding regions in HEK293T cells. (A) Genomic distribution of potential MmpE-binding regions in HEK293T cells. (B) Chromosomal localization of MmpE-enriched peaks (fold enrichment > 9). (C) Biotype distribution of potential MmpE-binding regions in HEK293T cells. (D) Distribution of binding sites relative to the nearest transcription start sites (TSS) within ±20 kb of protein-coding genes. (E) Immunoblot analysis of pathway activation in THP-1 macrophages infected with WT, ΔMmpE, Comp-MmpE, Comp-MmpEΔNLS1, Comp-MmpEΔNLS2, Comp-MmpEΔNLS1-2, or Comp-MmpE-H348A/N359A. Phosphorylation of Akt, mTOR, and p70S6K was evaluated at 8 hpi. (F) Quantification of phosphorylation levels across time points. (G) (left) Confocal microscopy analysis of phagosome acidification in infected THP-1 macrophages at 24 hpi. Cells were stained with LysoTracker Red and BCG strains were stained with DiD. (right) Co-localization between mycobacteria and LysoTracker was assessed. Representative images showing co-localization of intracellular bacterial with LysoTracker signal. Scale bar, 10 μm. Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-way ANOVA or two-tailed unpaired Student’s t-tests, *P < 0.05, **P < 0.01, ***P < 0.001.
MmpE suppresses the expression of VDR during BCG infection
(A) Heatmap of transcription factors associated with MmpE ChIP-seq peaks in HEK293T cells. Color scale indicates expression changes (red: upregulated; blue: downregulated). (B) De novo motif analysis of MmpE-bound sequences using HOMER. Enrichment P-values were calculated with TOMTOM. “% of targets” indicates the proportion of peaks containing each motif; letter height reflects nucleotide frequency. (C) Quantitative RT-PCR analysis of VDR expression in THP-1 cells infected with WT or ΔMmpE strains for 24 h. (D-G) ChIP-PCR and qPCR analysis of the VDR promoter region. HEK293T cells were transfected with EGFP, MmpE-EGFP, or MmpE- H348A/N359A-EGFP. Chromatin was immunoprecipitated using anti-GFP antibody. PCR was performed with primers targeting the VDR promoter and GAPDH (negative control), and products were analyzed by agarose electrophoresis (D, F). Enrichment was quantified by qPCR using the 2-ΔCt method (E, G). (H-I) EMSA using purified MmpE protein and a DNA probe corresponding to the VDR promoter. Samples were resolved by native PAGE. Arrows indicate the positions of free DNA and slower-migrating species (H); signal intensities were quantified by densitometry (I). Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-way ANOVA or two-tailed unpaired Student’s t-tests, ***P < 0.001.
Nuclear translocation of MmpE is essential for mycobacterial survival in mice.
(A) Bacterial burden in lungs of infected mice. Specific pathogen-free (SPF) C57BL/6 mice (n = 6 per group) were intranasally infected with 1.0 × 107 CFUs of BCG strains, including WT, ΔMmpE, Comp-MmpE, or Comp-MmpEΔNLS1-2. Bacterial titers in lung homogenates were quantified by CFU assays at 0, 14, 28, and 56 dpi. (B) Histopathology of infected lung tissues. Hematoxylin and eosin (H&E)-stained lung sections from mice infected as in (A) show granulomatous inflammation, Scale bars: 200 μm. (C-D) Pro-inflammatory cytokine expression in the spleen of infected mice. qRT-PCR analysis of cytokine mRNA levels of Il1a (C), Il1b (D)and Il6 (E) in spleen tissues from infected mice (n = 6/group) at 2 to 28 dpi. Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-way ANOVA, *P < 0.05, **P < 0.01, ***P < 0.001.
Schematic diagram of nucleomodulin MmpE-mediated immune suppression and enhanced mycobacterial survival.
During infection, the nucleomodulin MmpE translocates into the host nucleus via its C-terminal NLS2 motif (RRK⁴⁶⁰-⁴⁶²), where it binds to the VDR promoter and suppresses transcription of inflammatory genes. Simultaneously, MmpE regulates the PI3K-Akt-mTOR signaling pathway, thereby inhibiting lysosome maturation. These dual mechanisms contribute to immune evasion and promote intracellular survival of mycobacteria.
Identification of MmpE as a nucleomodulin in Mycobacterium.
(A) Subnuclear distribution of MmpE-EGFP in transfected cells. Confocal microscopy was performed at indicated time points post-transfection. Nuclei were stained with DAPI (blue); MmpE-EGFP is shown in green. Scale bar, 10 μm. (B) Structural modeling of MmpE and NLS mutants. Predicted structures of wild type MmpE, NLS-deletion construct, and mutants lacking NLS1, NLS2, or both were generated using AlphaFold2. Models were visualized with UCSF ChimeraX, and prediction confidence was evaluated using pLDDT scores. (C) Immunoblot analysis of MmpE-Flag expression in bacterial lysates and culture supernatants from recombinant BCG strains. Ag85B and GlpX served as positive and negative controls for secretion, respectively. MmpE-Flag was detected with anti-Flag antibody. (D) Subcellular distribution of MmpE during infection. THP-1 macrophages were infected for 24 h with recombinant BCG strains expressing Flag-tagged wild-type MgdE or NLS-deletion mutants (MmpEΔNLS1, MmpEΔNLS2, and MmpEΔNLS1-2). Cytoplasmic and nuclear fractions were prepared and analyzed by immunoblotting using anti-Flag antibody. Histone H3 and β-actin were included as nuclear and cytoplasmic markers, respectively.
Identification of MmpE as a conserved Fe3+/Zn2+- metallophosphatase in Mycobacteria.
(A) Sequence and structure-based analyses of MmpE. UCSF Chimera was used to analyze conserved domains and structural features. Structural similarity was evaluated by comparison with known metallophosphatases. Alignments with Z-scores >10 and RMSD <4 were considered high-confidence matches. (B) Clustal Omega sequence alignment of MmpE from various mycobacterial species, highlighting conserved residues (≥90% identity, shown in red). Blue stars indicate the predicted NLSs, and red triangles mark characteristic sequences found in metallophosphatases. Species abbreviations: M. tuberculosis (Mtu), M. bovis BCG (Mbb), M. orygis (Mory), M. kubicae (Mku), M. paraterrae (Mpa), M. farcinogenes (Mfg), M. mucogenicum (Mmuc), M. vicinigordonae (Mgor), M. lentiflavum (Mlf), M. avium (Mav), M. manitobense (Mman).
The nuclear translocation and phosphatase activity of MmpE are essential for M. bovis BCG survival in macrophage cells.
(A) Construction and validation of the MmpE-deleted strain of BCG. (left) Schematic diagram of the homologous recombination strategy used to delete mmpE from the BCG genome. (right) Wild-type and ΔMmpE strains were used as templates to amplify the mmpE gene (600 bp upstream-600 bp downstream) by PCR. Lanes 1 and 3: wild-type genomic DNA; lanes 2 and 4: ΔMmpE genomic DNA. (B) qRT-PCR detected the mmpE expression level in WT and ΔMmpE strains. (C) Sequencing results of ΔMmpE genomic DNA. The forward primer amplified a 300 bp upstream fragment, and the reverse primer a 300 bp downstream fragment. (D-E) Growth curve analysis of BCG strains. Strains including WT, ΔMmpE, Comp-MmpE, Comp-MmpEΔNLS1, Comp- MmpEΔNLS2, Comp-MmpEΔNLS1-2 strains(C), or Comp-MmpE-H348AN359H (D), were measured in 7H9 medium. Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-way ANOVA, *P < 0.05, **P < 0.01, ***P < 0.001.
MmpE modulates host transcription network involved in inflammation response and lysosomal maturation
(A) Biotype distribution of potential MmpE-regulating DEGs in THP-1 cells. (B-D) Quantitative RT-PCR analysis of gene expression in infected THP-1 cells. Cells were infected with WT, ΔMmpE, Comp-MmpE, Comp-MmpEΔNLS1, Comp-MmpEΔNLS2, Comp-MmpEΔNLS1-2 and Comp-MmpE-H348AN359H strains for 24 hpi. Cytokine-related genes (IL23A, CSF2, CD69, IDO1, IL12B, CEACAM1) (B); genes associated with lysosomal maturation (TFEB, LAMP1, LAMP2) (C); genes encoding V-ATPase subunits (ATP6V0A1, ATP6V0C, ATP6V1A, ATP6V1B2, and ATP6V1E1) (D). Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-way ANOVA, *P < 0.05, **P < 0.01, ***P < 0.001.
MmpE regulates the PI3K-Akt-mTOR signaling pathway during macrophage infection.
(A) Interaction network of DEGs associated with MmpE-binding sites. The network was constructed using STRING v12.0 and visualized with Cytoscape. (B) KEGG pathway enrichment analysis of MmpE-binding sites identified in MmpE-EGFP-transfected HEK293T cells. Selected significantly enriched pathways are shown. Bar length indicates the number of associated genes; color represents -log10(P-value). Enriched pathways include aldosterone-regulated sodium reabsorption (hsa04925), mTOR signaling (hsa04150), axon guidance (hsa04360), serotonergic synapse (hsa04726), circadian entrainment (hsa04713), inflammatory mediator regulation of TRP channels (hsa04750), cAMP signaling (hsa04024), calcium signaling (hsa04020), glutamatergic synapse (hsa04724), and cGMP-PKG signaling (hsa04022). (C) (left) Immunoblot analysis of PI3K-Akt-mTOR pathway activation in THP-1 macrophages infected with either wild-type (WT) or ΔMmpE strains. Phosphorylation of Akt (Ser473), mTOR (Ser2448), and p70S6K (Thr389) was assessed at 0, 2, 4, and 8 hpi. (right) Quantification of phosphorylation levels across time points. Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-tailed unpaired Student’s t-tests, *P < 0.05, **P < 0.01.
MmpE promotes pathogen intracellular survival via the PI3K-Akt-mTOR signaling pathway.
(A-C) Effects of BEZ235 on the growth and intracellular survival of BCG strains. Bacterial growth in 7H9 medium with or without BEZ235 (0-200 nM) (A). Intracellular survival of WT and ΔMmpE strains in THP-1 macrophages treated with or without BEZ235 (0-200 nM); CFUs were quantified at 48 hpi (B). Intracellular survival of WT, ΔMmpE, Comp-MmpE, Comp-MmpEΔNLS1, Comp-MmpEΔNLS2, Comp-MmpEΔNLS1-2, Comp-MmpE-H348AN359H in THP-1 macrophages treated with or without 100 nM BEZ235; CFUs were determined at 4, 48 hpi (C). Data represent mean ± SD of three independent biological replicates. Statistical significance determined using two-way ANOVA, *P < 0.05, **P < 0.01, ***P < 0.001.
MmpE modulates the transcription of immune-associated genes.
(A) Venn diagram showing the overlap between DEGs identified by RNA-seq and differential peak-associated genes identified by CUT&Tag-seq. (B) Four-quadrant scatter plot comparing CUT&Tag-seq and RNA-seq data. Log2(fold change) values of peak-associated genes from CUT&Tag-seq are plotted against log₂(fold change) of FPKM values from RNA-seq. (C) KEGG enrichment analysis of the DEGs shown in (A). (D) Chord diagram illustrating DEGs to enriched GO Biological Process terms.
MmpE facilitates bacterial colonization in the spleens of infected mice.
(A) Bacterial colonization was assessed in splenic homogenates from infected mice (as described in Figure 7A) by quantifying bacterial DNA using quantitative PCR at 2, 14, 21, 28, and 56 dpi. (B-I) mRNA expression in mice spleen at 14 and 28 dpi in lung and spleen tissues of infected animals. Vdr expression (B); Cytokine-related genes (C and D); lysosomal acidification (E and F) and V-ATPase subunits genes (G and H). Data represent mean ± SD of six independent biological replicates. Statistical significance determined using two-way ANOVA, *P < 0.05, **P < 0.01, ***P < 0.001.
