Introduction

Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, has posed a persistent global health burden for centuries. Despite significant advances in elucidating the molecular mechanisms of its pathogenesis, current research has largely focused on effector proteins that modulate host cell membrane and cytoplasmic processes (Nisa et al., 2022; Nasiri and Venketaraman, 2025). In contrast, investigations into effector proteins that target the host cell nucleus, the central hub for gene regulation and cellular control, remain comparatively limited.

Nucleomodulins are a class of bacterial effector proteins that can translocate into the host nucleus, where they modulate nuclear processes to promote pathogen survival (Chai et al., 2020; Bierne and Cossart, 2021). These proteins affect host gene expression by directly interacting with chromatin or by mimicking transcription factors, chromatin modifiers, or other nuclear regulators (Li et al., 2013; Rolando et al., 2013; Mitra et al., 2018; Hanford et al., 2021). For instance, LntA from Listeria monocytogenes directly binds the chromatin repressor BAHD1, disrupting its function and derepressing interferon-stimulated genes in a type III interferon-dependent manner, ultimately promoting bacterial persistence (Lebreton et al., 2011; Lebreton et al., 2014). Similarly, Ank1 and Ank6 from Orientia tsutsugamushi localize to the host nucleus and facilitate the export of the NF-κB p65 subunit via exportin 1, thereby suppressing the transcription of pro-inflammatory genes (Evans et al., 2018; Steiert and Weber, 2025). Although bacterial nucleomodulins utilize diverse strategies to manipulate host nuclear functions, the identity and functional characterization of M. tuberculosis nucleomodulins remain poorly defined.

Nucleomodulins employ various strategies to enter access to the host cell nucleus, including passive diffusion, hijacking host proteins that contain nuclear localization signals (NLSs), or using of their own NLSs to interact with the nuclear pore complex (Hanford et al., 2021). Among these mechanisms, NLSs play a particularly important role. Based on their amino acid composition, NLSs are broadly classified into classical (cNLS), non-classical (ncNLS), and other types (Lange et al., 2008; Lu et al., 2021). Classical NLSs are further divided into monopartite (MP) and bipartite (BP) forms. Monopartite NLSs consist of a single cluster of 4–8 basic residues, primarily lysine (K) or arginine (R), with a typical consensus motif of K-K/R-X-K/R (Fontes et al., 2000; Kosugi et al., 2009; Cautain et al., 2015). Nuclear localization enables these effectors to manipulate host gene expression, disrupt immune signaling, and reprogram cellular processes to promote pathogen survival. For example, EspF from enteropathogenic Escherichia coli contains an N-terminal NLS that directs it to the nucleolus, where it interferes with ribosome biogenesis (Dean et al., 2010; Singh et al., 2018). NUE, a SET domain-containing nucleomodulin secreted by Chlamydia trachomatis, also possesses an NLS that mediates its nuclear localization, where it functions as a histone lysine methyltransferase (HKMTase) targeting host histones H2B, H3, and H4 (Pennini et al., 2010; Jermy, 2010).

Beyond their nuclear localization capabilities, some nucleomodulins directly affect host immunity through intrinsic enzymatic activities (Agarwal et al., 2012). For example, the nucleomodulin PtpA promotes Mtb survival within macrophages by dephosphorylating host cytoplasmic proteins (Wang et al., 2017). NleC from E. coli, a Zn-dependent metalloprotease, suppresses host immune responses by cleaving the p65 subunit of NF-κB in the cytoplasm, thereby inhibiting its nuclear translocation, and can enter the nucleus to reduce nuclear p65 levels, blocking NF-κB-dependent transcription of pro-inflammatory genes (Baruch et al., 2011; Hodgson et al., 2015). Among these enzymatically active nucleomodulins, purple acid phosphatases (PAPs) represent a distinct and functionally significant, yet underexplored, subclass within the metallophosphatase superfamily. PAPs are characterized by a conserved β-α-β-α-β fold and five signature motifs (DxG, GDXXY, GNH[D/E], VXXH, GHXH), which coordinate seven metal-ligating residues at a binuclear metal center (Rodriguez et al., 2014; Bhadouria et al., 2017; Bhadouria and Giri, 2022). These enzymes have been extensively studied in plants and mammals, where they are involved in key biological processes such as phosphorus metabolism and the generation of reactive oxygen species (Comba et al., 2013; Feder et al., 2020; Liu et al., 2025). In contrast, only a few bacterial PAPs have been identified, such as BcPAP from Burkholderia cenocepacia, and their functions remain largely unknown (Yeung et al., 2009). Notably, in Mtb, MmpE is the only identified PAP protein (Schenk et al., 2000), but its specific contribution to infection and pathogenesis remain elusive.

In this study, we characterized MmpE as a conserved nucleomodulin in mycobacteria and demonstrated its nuclear translocation mediated by two NLSs, RRR^20–22 and RRK^460–462. Upon entering the nuclear, MmpE binds to the promoter region of the VDR gene, a key regulator of antimicrobial responses, resulting in transcriptional repression of pro-inflammatory genes. In addition, MmpE inhibits phagosome maturation by suppressing the expression of genes in the PI3K–Akt–mTOR signaling pathway. These actions collectively facilitate increased intracellular survival in both macrophage and mouse. Beyond its nuclear function, MmpE functions as a Fe³⁺/Zn²⁺ metallophosphatase, with enzymatic activity reliant on the conserved residues His³⁴⁸ and Asp³⁵⁹, and partially contributes to intracellular survival. Taken together, our findings identify MmpE as a bifunctional effector that integrates immune modulation and enzymatic catalysis, underscoring its role in mycobacterial pathogenesis and its potential as a therapeutic target.

Results

NLSs are required for the nuclear translocation of MmpE

In the prior study, we systematically identified some conserved nucleomodulins in mycobacterium. Among them, the hypothetical protein Rv2577 (MmpE) was identified as a candidate exhibiting strong nuclear localization in mammalian cells (Chen et al., 2025). Based on these findings, we transfected HEK293T cells with a C-terminal EGFP-tagged MmpE (MmpE-EGFP) and monitored its transcriptional level and nuclear localization at different time points. As a result, a time-dependent increase in the MmpE-EGFP content was observed in the host nucleus (Figure 1A, upper panel; Figure S1A). Nuclear–cytoplasmic fractionation assays further confirmed these results, showing a progressive enrichment of MmpE in the nuclear compartment over the course of transfection (Figure 1A, bottom panel). Collectively, these results indicate that MmpE possesses intrinsic nuclear translocation ability.

Figure 1.

MmpE contains two putative NLSs, N-terminus (RRR^20–22, NLS1) and C-terminus (RRK^460-462, NLS2) (Figure 1B). To evaluate the structural contribution of these motifs, we utilized AlphaFold to model the impact of NLS truncations on the overall conformation of MmpE. The predicted structures indicated that deletion of either NLS1, NLS2, or both did not obviously alter the the protein fold (Figure S1B). Based on this analysis, we generated a series of NLS-deleted mutants, including MmpE^ΔNLS1, MmpE^ΔNLS2, and MmpE^ΔNLS1-2, to assess the functional relevance of each motif in nuclear localization. Subcellular localization of wild-type MmpE-EGFP and NLS deletion mutants was examined in HEK293T cells by fluorescence microscopy at 36 hpt (hours post-transfection). Deletion of either NLS1 or NLS2 alone significantly reduced the nuclear accumulation of MmpE-EGFP, with the effect of NLS2 deletion being more pronounced than that of NLS1. Simultaneous deletion of both NLS motifs (MmpE^ΔNLS1-2) completely abolished nuclear localization, resulting in exclusive cytoplasmic distribution (Figure 1C and D). These findings were further validated by immunoblotting of nuclear and cytoplasmic fractions. Under the similar transfection conditions, wild-type MmpE-EGFP was detected in both compartments, whereas MmpE^ΔNLS1 and MmpE^ΔNLS2 exhibited substantially reduced nuclear abundance. By contrast, MmpE^ΔNLS1-2 was exclusively localized to the cytoplasmic fraction, suggesting that both NLS motifs are required for efficient nuclear import (Figure 1E). Taken together, our findings identify MmpE as a nucleomodulin, with nuclear import mediated by the N- and C-terminal NLS motifs.

Deletion of NLSs does not alter the phosphatase activity of MmpE

Bioinformatic analyses identified MmpE as a Fe³⁺/Zn²⁺-metallophosphatase containing a purple acid phosphatase (PAP) motif (Figure 2A; Figure S2A). Multiple sequence alignment and phylogenetic reconstruction revealed that MmpE is highly conserved among mycobacterial species and harbors canonical motifs characteristic of metallophosphatases, including GD, GNHX, and GHXH (Figure 2B, Figure S2B). These motifs are typically associated with enzymes that catalyze phosphate hydrolysis via a binuclear metal ion-dependent mechanism, wherein residues such as Asp, His, and Asn coordinate essential metal cofactors, commonly Fe³⁺, Mn²⁺, or Zn²⁺, at the active site.

Figure 2.

To identify key amino acid residues of MmpE involved in metal coordination, AlphaFold was used to predict the structure of MmpE, followed by the molecular docking using PyMOL. As shown in Figure 2C, H³⁴⁸ and N³⁵⁹ were identified as candidate residues likely involved in metal ion coordination within the predicted active site. Subsequently, recombinant MBP-tagged MmpE deleting the Tat signal peptide (MmpE^ΔTat) was subjected to in vitro phosphatase assays using p-nitrophenyl phosphate (p-NPP) as the substrate. Reactions were supplemented with varying concentrations of Fe³⁺ and Zn²⁺ to evaluate their individual effects on MmpE enzymatic activity. The results demonstrated that, at equivalent concentrations, Fe³⁺ significantly enhanced MmpE activity compared to Zn²⁺, with maximal enzymatic activity was observed at 50 μM Fe³⁺ (Figure 2D). Next, a double mutant (MmpE^ΔTat-H³⁴⁸AN³⁵⁹A) was generated via site-directed mutagenesis to validate the functional importance of these residues. As shown in Figure 2E, the addition of 50 μM Fe³⁺ significantly increased the in vitro phosphatase activity of MmpE^ΔTat compared to reactions without metal ions. However, the enzymatic activity of the MmpE^ΔTat-H³⁴⁸AN³⁵⁹A in the presence of 50 μM Fe³⁺ was markedly reduced and nearly indistinguishable from that of MmpE^ΔTat under metal-free conditions. These results confirm that residues H³⁴⁸ and N³⁵⁹ are essential for Fe³⁺ binding and catalytic activity.

Given that MmpE relies on NLSs to enter the host nucleus, we examined whether deletion of NLS affects its phosphatase activity. Compared to wild-type MmpE, the NLS-deleted mutant showed no significant change in enzymatic activity (Figure 2F), which is consistent with the structural comparison results (Figure S1B). Collectively, these results suggest that MmpE is a highly conserved Fe³⁺/Zn²⁺-dependent metallophosphatase in mycobacteria, and its enzymatic activity is independent of NLS.

The nuclear translocation and phosphatase activity of MmpE are essential for M. bovis BCG survival in macrophage cells

To investigate the role of MmpE during infection, we first generated recombinant M. bovis BCG strains expressing C-terminally Flag-tagged Ag85B (positive control) and MmpE. Immunoblot analysis confirmed high levels of Ag85B-2×Flag and MmpE-2×Flag in bacterial lysates, and both proteins were also detected in the culture supernatants (Figure S3A), indicating that MmpE is indeed a secreted protein.

Furthermore, a series of recombinant BCG strains were constructed, including wild-type (WT), mmpE-deleted mutant (ΔMmpE) (Figure S3B), ΔMmpE complemented with wild-type mmpE (Comp-MmpE), and ΔMmpE complemented with NLS-deleted mutant (Comp-MmpE^ΔNLS1, Comp-MmpE^ΔNLS2, and Comp-MmpE^ΔNLS1-2). Deletion of NLS1 may reduce or abolish MmpE secretion (Stanley et al., 2000; Buchanan et al., 2001), while deletion of NLS2 impaired its nuclear localization. All strains exhibited similar growth rate under the normal culture conditions (Figure S3C). Subsequently, these strains were used to infect THP-1 macrophages. As shown in Figure 3A and B, the bacterial load of the ΔMmpE strain exhibited significantly reduced relative to the WT strain, and bacterial clearance was accelerated over time. The phenotype of ΔMmpE was rescued by complementation with wild-type gene mmpE. Meanwhile, the load of the Comp-MmpE^ΔNLS2 strain displayed significantly lower compared to Comp-MmpE in both THP-1 and RAW264.7 macrophages, indicating that nuclear localization mediated by NLS2 is critical for MmpE function. Notably, the Comp-MmpE^ΔNLS1 and Comp-MmpE^ΔNLS1-2 strains demonstrated obvious higher load than those of the ΔMmpE strain, yet lower than those of the Comp-MmpE strain (Figure 3C and D). These results suggest that MmpE contributes to virulence not only through nuclear modulation but also through additional mechanisms.

Figure 3.

Next, we investigated the role of the Fe³⁺/Zn²⁺-dependent metallophosphatase of MmpE on intracellular survival. As shown in Figure S3D, a double mutant strain (Comp-MmpE-H³⁴⁸AN³⁵⁹A) was constructed and used to infect macrophage cells. The results showed that this mutant exhibited significantly reduced intracellular load compared with the Comp-MmpE strain (Figure 3E), indicating that the phosphatase activity also plays an essential role in MmpE-mediated bacterial survival. To reveal the underlying mechanism, cytokine expression assays were conducted in infected macrophages. Compared with the WT and Comp-MmpE strains, cells infected with the ΔMmpE and Comp-MmpE^ΔNLS1-2 strains showed markedly elevated levels of pro-inflammatory cytokines, including IL1Α, IL1Β, and IL6 (Figure 3F).

Collectively, these results suggest that MmpE functions as a bifunctional effector, possessing both nuclear import capability and phosphatase activity, promoting immune evasion and enhancing intracellular survival during infection.

MmpE modulates host transcription network involved in inflammation response and lysosomal maturation

To investigate the role of the nucleomodulin MmpE on host gene expression, we performed RNA-seq assays on THP-1 macrophages infected with either wild-type (BCG/wt) or MmpE-deleted (KommpE) strains at 20 hpi (hours post-infection). As a result, a total of 175 differentially expressed genes (DEGs) were identified, with 142 genes upregulated and 33 genes downregulated in KommpE-infected macrophages compared to those infected with BCG/wt (Figure 4A, Table S1). These DEGs were significantly enriched in immune-related biological processes, particularly those associated with apoptosis and cell death, as well as molecular functions related to immune activation and cellular stress responses, such as pyrophosphatase activity and nucleoside-triphosphatase activity (Figure 4B). Further analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that the DEGs were primarily involved in immune and inflammatory signaling pathways, including cytokine–cytokine receptor interaction, TNF signaling, Toll-like receptor signaling, chemokine signaling, NF-κB signaling, JAK–STAT signaling, and the PI3K−Akt signaling pathway. Additionally, several DEGs were enriched in pathways related to cell survival and apoptosis. Another group of DEGs was associated with host defense mechanisms, as evidenced by their enrichment in the lysosome pathway (Figure 4C). Together, these data highlight MmpE as a critical modulator of host transcriptional responses that facilitate mycobacterial immune evasion and intracellular survival.

Figure 4.

To gain further insight into the functional relevance of the 175 differentially expressed genes, we performed protein–protein interaction (PPI) network analysis, focusing on protein-coding genes, which accounted for 38% of the total (Figure S4A). A tightly connected network centered around key immune regulatory, including IL23A, IL12B, CSF2, CD69, IDO1, and CEACAM1, which are critically involved in inflammatory cytokine production (Figure 4D). Consistently, these genes expression was upregulation in KommpE-infected macrophages (Figure 4E). Given that inflammatory signaling and lysosomal function are both essential for macrophage-mediated host defense against mycobacterial infection, we further examined the expression of representative inflammatory cytokines and key lysosomal maturation markers under the same experimental conditions, such as TFEB, LAMP1, LAMP2, and several V-ATPase subunit genes (ATP6V0A1, ATP6V0C, ATP6V1A, ATP6V1B2, and ATP6V1E1). Consistent with transcriptomic findings, the KommpE strain induced significantly higher expression of both inflammatory cytokines and lysosomal maturation-related genes compared to the WT strain (Figure 4F and G). Both the Comp-MmpE^ΔNLS2 and Comp-MmpE^ΔNLS1-2 strains showed significantly higher expression of these cytokine genes compared to the Comp-MmpE strain (Figure S4B and C). Taken together, these results suggest that MmpE manipulates host transcriptional networks governing inflammation and lysosomal function, thereby subverting antimicrobial immunity.

MmpE suppresses the expression of VDR and inhibits activation of the PI3K– Akt–mTOR signaling pathway

To elucidate the mechanism by which MmpE modulates host gene expression, we performed ChIP-seq in HEK293T cells transfected with EGFP-MmpE. 2,903 potential MmpE-binding sites (Table S2) were identified, with 18.49% (537) in intergenic regions and 39.44% (1145) in intragenic regions (Figure 5A). Chromosomal distribution revealed significant enrichment on chromosomes 1 and 2 (Figure 5B). Notably, 99.7% (2894) of these binding sites were associated with protein-coding regions. Among these, 1013 sites were located within 3 kb of transcription start sites (TSS), including promoter (≤1 kb, 63.18%), promoter (1–2 kb, 22.9%), and promoter (2–3 kb, 13.92%) (Figure 5C and D), suggesting that MmpE primarily targets promoter regions to regulate transcription. PPI analysis of the 1013 potential target genes revealed significant enrichment in protein kinase-related genes, such as PRKCB, PLCG2 and PIK3CB, involved in regulating immune activation and inflammatory responses via the PI3K–Akt and mTOR signaling pathways, suggesting that MmpE may influence cell immune responses through a coordinated network of signaling pathways (Figure S5A and B). In parallel, we examined the expression of key components in this signaling axis in THP-1 macrophages infected with either BCG/wt or the KommpE strains. Notably, KommpE infection led to a significant upregulation of genes associated with the pathway, including PIK3CA, PIK3CB, PIK3R1, mTOR, AKT1–3, and FOXO1/3 (Figure S5C). These genes encode critical regulators of cell survival and immune activation within the PI3K–Akt–mTOR axis.

Figure 5.

To identify the direct target gene of MmpE in macrophages, we focused on analysis of the promoter regions (≤1 kb upstream of the transcription start site) of significantly upregulated genes with | Log₂FC > 1| and P < 0.05. Four transcription factors were identified, including CREBBP, VDR, GREB1, and FOXP4 (Figure 5E). Integrative analysis using HOMER de novo motif prediction revealed that only the promoter region of VDR, a key anti-inflammatory gene (Aggeletopoulou et al., 2022), harbored a potential MmpE-binding motif (Figure 5F). These findings suggest that MmpE may directly bind to the VDR promoter. To validate the hypothesis, we examined VDR expression in macrophages infected with recombinant strains. Compared to the BCG/wt, VDR expression was significantly downregulated in THP-1 cells infected with the KommpE strain (Figure S5D). To further test whether MmpE directly binds the VDR promoter, we cloned the VDR promoter region (−100 bp to +50 bp) and performed chromatin immunoprecipitation (ChIP) assays in HEK293T cells. While both VDR and GAPDH (control) sequences were present in input samples, VDR promoter DNA was detected exclusively in ChIP samples from EGFP-MmpE transfected cells (Figure 5G and H). Furthermore, the DNA-binding capacity of MmpE was unaffected by its phosphatase activity (Figure S5E and F). To confirm these results, we performed electrophoretic mobility shift assays (EMSA) using the same VDR promoter fragment. As shown in Figure 5I and 5J, the shift bands corresponding to MmpE and VDR promoter complex were observed, and a corresponding increase was observed in the percentage of protein/DNA complexes. Collectively, these results provide strong evidence that MmpE directly interacts with the VDR promoter both in vivo and in vitro to repress host inflammatory signaling pathways and facilitating immune evasion during mycobacterial infection.

To further characterize the transcriptional programs regulated by MmpE, we performed an integrative analysis of CUT&Tag and RNA-seq datasets. This analysis identified 298 DEGs with direct or proximal MmpE binding sites (Table S3; Figure S6A and B). Notably, genes such as RHEX, PLXDC1, and GAS6 exhibited significant expression changes and were enriched in pathways associated with cell differentiation and small GTPase-mediated signaling (Figure S6C and D). These pathways play critical roles in shaping immune cell function, trafficking, and inflammatory responses during host– pathogen interactions (Li et al., 2023; Ma et al., 2024). Taken together, these data establish MmpE as a nucleomodulin that directly alters host transcriptional networks involved in immune regulation and cellular defense, thereby supporting mycobacterial survival within host cells.

Nuclear translocation of MmpE is essential for mycobacterial survival in mice

Next, C57BL/6 mice were intranasally infected with M. bovis BCG strains, including wild-type (WT), ΔMmpE, Comp-MmpE, and Comp-MmpE^ΔNLS1-2, and systematically assessed bacterial persistence, pulmonary inflammation, and cytokine dynamics. Our results show that mice infected with the ΔMmpE strain exhibited significantly lower bacterial loads in the infected mice lung compared to those infected with the WT or Comp-MmpE strains. Remarkably, mice infected with the Comp-MmpE^ΔNLS1-2 strain showed significantly lower than those in the Comp-MmpE strains but higher than those in the ΔMmpE strains (Figure 6A). A similar trend was observed in splenic bacterial colonization (Figure S7). Hematoxylin and eosin (H&E) staining revealed extensive inflammatory infiltrates in the lungs of mice infected with WT or Comp-MmpE, whereas mice infected with ΔMmpE or Comp-MmpE^ΔNLS1-2 exhibited markedly reduced inflammation (Figure 6B). Mice infected with ΔMmpE and Comp-MmpE^ΔNLS1-2 strains exhibited significantly elevated levels of Il1α, Il1β, and Il6 compared to those infected with WT or Comp-MmpE strains, despite lower bacterial burdens (Figure 6C and E).

Figure 6.

Collectively, these results demonstrate that MmpE indeed contributes to M. bovis BCG survival in vivo, with its nuclear translocation being essential for mycobacterial intracellular survival.

Discussion

MmpE Functions as a Bifunctional Protein with Nuclear Localization and Phosphatase Activity

In this study, we identified two independent NLSs within the MmpE protein, RRR²⁰⁻²² (NLS1) and RRK⁴⁶⁰⁻⁴⁶² (NLS2), which together form a bipartite NLS motif that is rarely observed in bacterial effector proteins. Loss of a single NLS significantly reduced the nuclear accumulation of MmpE, with NLS2 deletion causing a more pronounced effect than that of NLS1. Simultaneous deletion of both motifs completely abolished nuclear localization (Figure 1C-E). These findings indicate that NLS1 and NLS2 function in a synergistic manner, with NLS2 likely playing a dominant role in nuclear import. Further sequence analysis revealed that NLS1 (RRR²⁰⁻²²) is embedded within the conserved twin-arginine translocation (Tat) signal motif (S/TRR-X-FLK), a well-characterized determinant of Tat-dependent secretion (Gimenez et al., 2018). The adjacent twin-arginine residues are critical for recognition by the Tat translocase, and mutations in this motif have been shown to significantly impair or abolish secretion (Ulfig et al., 2017). Accordingly, the Comp-MmpE^ΔNLS1 strain likely exhibits impaired secretion, and the Comp-MmpE^ΔNLS2 strain is deficient in nuclear localization. Consistent with this, both the Comp-MmpE^ΔNLS1 and Comp-MmpE^ΔNLS2 strains exhibited lower intracellular survival than the Comp-MmpE strain and higher than that of the ΔMmpE strain (Figure 3A-D), suggesting that the nuclear localization ability of MmpE indeed contributes to bacterial survival. Interestingly, MmpE also functions as a Fe³⁺/Zn²⁺-dependent metallophosphatase, with residues H³⁴⁸ and N³⁵⁹ being essential for its catalytic activity (Figure 2D and E). The mutant strain (Comp-MmpE-H³⁴⁸AN³⁵⁹A) showed markedly reduced intracellular survival Compared to Comp-MmpE (Figure 3E), indicating that the phosphatase activity of MmpE is also required for intracellular survival. This explains why the intracellular survival of the Comp-MmpE^ΔNLS1-2 strain is significantly lower than that of the Comp-MmpE strain, yet obviously higher than that of the ΔMmpE strain (Figure 3C and D, Figure 6A).

Taken together, these findings suggest that MmpE is a dual-function effector protein that promotes intracellular survival during infection through the coordinated action of its nuclear localization signal and phosphatase activity.

MmpE’s direct targeting of the host gene VDR represents a unique immune evasion strategy

VDR is a critical nuclear receptor that controls the expression of numerous genes involved in host immune defense, including antimicrobial peptides and cytokines (Usategui-Martín et al., 2022). For example, Mtb suppresses the expression of the host gene CYP27B1 to reduce active vitamin D synthesis, thereby limiting VDR activation and downstream antimicrobial responses (Liu et al., 2006). Similarly, Salmonella downregulates VDR through miRNA-mediated mechanisms, weakening mucosal immunity (Chen et al., 2014). In this study, we found that MmpE directly binds to the promoter of the VDR gene (Figure 5F–J) and attenuates the expression of VDR-regulated inflammatory genes (Figure 3F; Figure 6C-E), ultimately promoting bacterial intracellular survival (Figure 6A). This mode of action represents a novel strategy employed by bacterial pathogens to evade host defenses through the direct manipulation of host gene promoters by nucleomodulins. Although previous studies have reported that bacterial nucleomodulins interfere with the host transcriptional machinery, these effects have typically occurred indirectly, such as through epigenetic modifications or inhibition of signaling pathways (Jose et al., 2016; Singh et al., 2023). Direct promoter binding by a nucleomodulin, however, remains relatively uncommon and represents a distinct mechanism of host gene regulation.

MmpE regulates the expression of host genes involved in phagosome maturation

As an intracellular pathogen, Mtb employs multiple strategies to evade phagolysosomal degradation, a process essential for bacterial clearance (Chandra et al., 2022; Zhang et al., 2023; Singh and Nagaraja, 2025). Improtantly, approximately 70% of phagosomes harboring Mtb fail to fuse with lysosomes, in part due to the activity of secreted phosphatases such as PtpA, PknG, and SapM, which disrupt vesicular trafficking (Wong et al., 2011; Ge et al., 2022; Zhang et al., 2024; Alsayed and Gunosewoyo, 2024). MmpE has also been shown to contribute to the arrest of phagosome maturation in human cells, although the underlying mechanisms remain unclear (Forrellad et al., 2020). In this study, we identify a potential mechanism by which MmpE inhibits phagosome maturation. Deletion of mmpE led to significant upregulation of lysosome-associated genes, including TFEB, LAMP1, LAMP2, and V-ATPase subunit genes (Figure 4C and G). Among these, TFEB is a master transcriptional regulator of lysosomal biogenesis and function (Jeong et al., 2021; Wang et al., 2024). Furthermore, ChIP-seq analysis revealed that MmpE directly binds to promoter regions of host genes within the PI3K–Akt–mTOR signaling pathway (Figure S5A), a key upstream regulator of TFEB activity (Fang et al., 2021; Gounis et al., 2025). Collectively, these results indicate that MmpE may act as a transcriptional regulator that targets the PI3K–Akt–mTOR–TFEB axis, thereby inhibiting lysosomal maturation.

MmpE is a Fe³⁺/Zn²⁺-dependent metallophosphatase that is essential for mycobacterial intracellular survival

Previous studies have shown that phosphatases play critical roles in host–pathogen interactions by modulating phosphorylation-dependent signaling pathways (Sajid et al., 2015; Bonne Køhler et al., 2020). In bacterial pathogens, these enzymes frequently contribute to immune evasion and intracellular survival. For example, the tyrosine phosphatase YopH from Yersinia enterocolitica disrupts phagocytic signaling in host macrophages, thereby impairing oxidative burst responses and promoting bacterial persistence (Davicino et al., 2017; Shaban et al., 2020). Similarly, PpzA, a phosphatase from Aspergillus fumigatus, has been implicated in fungal adaptation to immune pressure under iron-replete conditions (Manfiolli et al., 2017; Kurucz et al., 2018). In this study, we found that MmpE contains a predicted purple acid phosphatase (PAP)-like domain and exhibits phosphatase activity that requires Fe³⁺ and Zn²⁺ ions as cofactors (Figure 2A and D). Through site-directed mutagenesis, we identified His³⁴⁸ and Asn³⁵⁹ as critical residues for Fe³⁺ coordination. Substitution of these residues (H³⁴⁸AN³⁵⁹A) significantly impaired phosphatase function in the presence of Fe³⁺, leading to a marked reduction in bacterial intracellular load (Figure 2E; Figure 3E). However, the precise molecular mechanism by which MmpE interacts with Fe³⁺ remains to be elucidated in future studies.

In conclusion, our study identifies MmpE as a novel bifunctional virulence factor of mycobacteria, combining Fe³⁺/Zn²⁺-dependent phosphatase activity with nuclear translocation capability. MmpE translocates into the host nucleus and directly binds to the promoters of some key host genes, such as VDR, thereby inhibiting the expression of the downstream targets implicated with the inflammation responses and lysosomal maturation, thereby promoting mycobacterial survival in macrophages and in mice (Figure 7). These findings reveal a sophisticated mechanism by which bacterial pathogen manipulates host gene transcription and signaling pathway to promote intracellular persistence.

Figure 7.

Materials and methods

Key resources used in this study

Bacterial strains and culture conditions

The bacterial strains used in this study are detailed in Table S5. E. coli DH5α and BL21 were cultured in Luria-Bertani (LB) medium under standard conditions. M. bovis BCG strains were grown in Middlebrook 7H9 broth supplemented with 10% (v/v) OADC (oleic acid, albumin, dextrose, catalase), 0.05% (v/v) Tween-80, and 2% (v/v) glycerol. Antibiotics were added as required at the following final concentrations: 50 µg/mL hygromycin (for mycobacteria) and 50 µg/mL kanamycin (for both mycobacteria and E. coli).

Cell culture

THP-1 cells were cultured in Roswell Park memorial institute 1640 (RPMI 1640) medium supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), 1 mM sodium pyruvate, 2 mM L-glutamine, 10 mM HEPES buffer (pH 7.2–7.5), and 50 µM 2-mercaptoethanol. For differentiation into macrophages, THP-1 cells were treated with 200 nM phorbol 12-myristate 13-acetate (PMA) for 24 h, followed by an additional 48 h incubation in fresh PMA-free medium to allow complete differentiation prior to experimental use.

HEK293T and RAW264.7 monocytes were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% (v/v) FBS and 50 µg/mL penicillin-streptomycin. All cells were maintained at 37 °C in a humidified atmosphere with 5% CO₂.

Recombinant expression and secretion of MmpE

Recombinant M. bovis BCG strains expressing C-terminally 2×Flag-tagged Ag85B (positive control) and MmpE were constructed to assess protein expression and secretion under standard in vitro culture conditions. The strains were cultured in 200 mL of Middlebrook 7H9 broth supplemented with 10% (v/v) OADC, 2% (v/v) glycerol, and 0.05% Tween-80 at 37 °C until mid-log phase (OD₆₀₀ = 0.6). Cultures were centrifuged at 4,000 × g for 60 min to separate bacterial pellets from supernatants. Pellets were washed and lysed by bead beating in phosphate-buffered saline (PBS) supplemented with protease inhibitors. Culture supernatants were filtered through 0.22 μm sterile filters to remove residual bacteria and concentrated to a final volume of 2 mL using Amicon Ultra centrifugal filters (10 kDa molecular weight cutoff). Both bacterial lysates and concentrated supernatants were analyzed by SDS–PAGE followed by immunoblotting using anti-Flag antibodies to detect the expression and secretion of 2×Flag-tagged proteins.

Phylogenetic and sequence analysis

To investigate the evolutionary conservation and sequence features of MmpE homologs, phylogenetic reconstruction was performed using MEGA version 12.0 and iTOL platform with a neighbor-joining algorithm. Parameters included pairwise deletion for gap treatment, a poisson substitution model (selected for its suitability in analyzing closely related bacterial sequences), and 1,000 bootstrap replicates to assess node support. Only nodes with bootstrap values ≥50% were retained, and no additional tree pruning was applied.

The analysis combined metallophosphatase MmpE homologs from 11 Mycobacterium strains, including M. tuberculosis (Mtu), M. bovis BCG (Mbb), M. orygis (Mory), M. kubicae (Mku), M. paraterrae (Mpaa), M. farcinogenes (Mfg), M. mucogenicum (Mmuc),

M. vicinigordonae (Mgor), M. lentiflavum (Mlw), M. avium (Mav), M. manitobense (Mman). Genomic sequences were retrieved from the NCBI RefSeq database, filtered for completeness, and aligned using Clustal Omega v1.2.4 with default parameters (gap opening penalty = 10, gap extension = 0.2, and iterative refinement enabled). Sequence conservation was visualized using ESPript 3.0, with residues exhibiting ≥90% identity across all homologs highlighted in red.

Cell transfection and confocal microscopy

HEK293T cells were seeded at 70% confluency in poly-L-lysine-coated 35-mm glass-bottom dishes and maintained in DMEM supplemented with 10% (v/v) FBS at 37 °C under 5% CO₂. Transfection was performed using the Hieff Trans™ Liposomal Transfection Reagent according to the manufacturer’s protocol. Briefly, 0.5 μg of plasmid DNA and 1.5 μL of transfection reagent were diluted in 50 μL of Opti-MEM, incubated at room temperature for 20 minutes, and then added dropwise to each well of 35-mm six-chamber glass-bottom dishes.

At 24–48 hpt, cells were washed with PBS, fixed in 4% paraformaldehyde for 15 min, and permeabilized with 0.1% Triton X-100 for 10 min. Nuclei were counterstained with 1 μg/mL DAPI (4′,6-diamidino-2-phenylindole) for 10 min. Confocal imaging was performed using an Olympus FV1000 Confocal Laser Scanning Microscope equipped with a 100×/1.40 NA oil immersion objective. EGFP and DAPI signals were detected with 488 nm and 405 nm lasers, respectively. Spectral unmixing was carried out using the Olympus FV10-ASW software (v4.2) to minimize signal cross-talk. Z-stack images were acquired in sequential mode with a 0.5 μm step size across all samples to ensure imaging consistency.

Immunoblot analysis

For immunoblotting, the cells were lysed in radioimmunoprecipitation assay (RIPA) buffer supplemented with 1.5% (v/v) protease inhibitor cocktail. Protein concentrations were quantified using the bicinchoninic acid (BCA) assay. Equal amounts of protein (20–40 µg) were resolved by SDS-PAGE and transferred onto PVDF membranes. Membranes were blocked for 1 h at room temperature with 5% (w/v) non-fat milk in TBST (25 mM Tris, 150 mM NaCl, 2 mM KCl, and 0.2% Tween-20, pH 7.4) and incubated overnight at 4 °C with primary antibodies. After three washes with TBST (10 min each), membranes were incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies for 1 hour at room temperature. Protein bands were visualized using an enhanced chemiluminescence (ECL) substrate and imaged using the ChemiDoc™ MP Imaging System (Bio-Rad). β-actin, GAPDH, or histone H3 was used as an internal control for normalization. Antibody details are provided in the Key resources table.

For subcellular fractionation, cytoplasmic and nuclear proteins were isolated using a Nuclear and Cytoplasmic Protein Extraction Kit (manufacturer’s protocol). Briefly, after treatment, cells were washed and harvested in cold PBS. Cytoplasmic and nuclear fractions were separated according to the manufacturer’s instructions. Protein concentrations were measured using the BCA assay, and equal amounts of protein were analyzed by immunoblotting as described above.

AlphaFold Predicted Structural Modeling of MmpE with NLS Truncations

The structural models of MmpE with NLS truncations were generated using AlphaFold version 2.2.0. The full-length MmpE sequence was used as the input to predict the reference structure. To assess the impact of NLS deletions, modified sequences were prepared by removing the residues corresponding to NLS1 (RRR^20–22), NLS2 (RRK^{460– 462}), or both motifs. Structural prediction was performed for each sequence using the default AlphaFold parameters, which include the application of the pre-trained model and multiple sequence alignment (MSA) generation using the UniRef90 and MGnify databases. The confidence of the predictions was evaluated using the predicted local distance difference test (pLDDT) scores provided by AlphaFold. The resulting models were visualized and analyzed using UCSF ChimeraX to compare the overall protein conformations and assess structural changes due to NLS deletions.

Prediction of metal ion-binding residues in MmpE

The structure of MmpE was predicted using AlphaFold version 2.2.0 to investigate its potential metal ion dependence and identify key residues involved in metal coordination. The predicted structure was analyzed using PyMOL to identify residues within the putative active site. Residues were selected based on their spatial arrangement in the active site, and their proximity to regions likely involved in metal ion binding was annotated. Visualization and annotation of the predicted active site were performed using PyMOL to determine the potential roles of these residues in metal ion coordination.

Protein Expression and Purification

N-terminal maltose-binding protein (MBP)-tagged and C-terminal His₆-tagged wild-type MmpE, as well as mutant variants lacking the Tat signal peptide were expressed in E. coli BL21 (DE3). Protein expression was performed in 1 L of LB medium. Cultures were grown at 37 °C until the optical density at 600 nm (OD₆₀₀) reached approximately 0.8, after which protein expression was induced with 0.2 mM isopropyl-β-D-thiogalactopyranoside (IPTG) at 18 °C for 24 h. Following induction, cells were harvested by centrifugation and lysed by sonication in ice-cold lysis buffer containing 150 mM NaCl, 30 mM Tris-HCl (pH 7.5), and 1 mM phenylmethylsulfonyl fluoride (PMSF). The lysate was clarified by centrifugation, and the supernatant was subjected to affinity purification using an MBP affinity column.

Phosphatase activity assay

Phosphatase activity was measured using p-nitrophenyl phosphate (p-NPP) as the substrate in a final reaction volume of 200 μL. Reactions were initiated by incubating 0–80 μg of purified protein with p-NPP at 37 °C for 60 min. The release of p-nitrophenol (p-NP), the dephosphorylated product, was quantified by measuring absorbance at 405 nm using a microplate spectrophotometer.

Kinetic parameters were determined under initial velocity (V₀) conditions using substrate concentrations ranging from 0.1 to 10 mM p-NPP. The kinetic constants Km and Vmax were calculated by fitting the data to the Michaelis-Menten equation using nonlinear regression analysis in GraphPad Prism 8.0. The catalytic turnover rate (Kcat) was calculated using the equation Kcat = Vmax/E₀, where Vmax was expressed as ηM p-NP min⁻¹ and E₀ represents the active enzyme concentration in ηM. Control reactions were carried out in the absence of either the substrate or the enzyme to measure background absorbance. All assays were performed in triplicate to ensure the reproducibility of results.

Quantitative real-time PCR

THP-1 cells were infected with the M. bovis BCG strain and harvested 20 h post-infection for total RNA isolation. RNA was extracted using 1 mL of TRIzol^® reagent following the manufacturer’s protocol. To eliminate genomic DNA contamination, RNA samples were treated with DNase I for 30 min at 37 °C, followed by heat inactivation at 65 °C for 10 min. RNA concentration and purity were assessed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific).

For cDNA synthesis, 1 µg of total RNA was reverse transcribed using the HiScript^® III cDNA Reverse Transcription Kit with random hexamers primers, according to the manufacturer’s protocol. qRT-PCR was performed using ChamQ SYBR^® Green RT-PCR Master Mix. Relative mRNA expression levels were calculated using the 2^−ΔΔCt method, normalizing Ct values to the housekeeping gene HPRT. All qRT-PCR experiments were conducted in triplicate, with at least three independent biological replicates and two technical replicates per condition. Primer sequences are listed in Table S6.

RNA-seq analysis

THP-1 cells were seeded at a density of 1 × 10⁶ cells well in 6-well plates and differentiated into macrophages by treatment with 100 nM PMA for 48 h. After differentiation, cells were washed with PBS and infected with M. bovis BCG WT or KommpE strains at a multiplicity of infection (MOI) of 10:1. Following 20 h of infection, total RNA was extracted using TRIzol^® reagent according to the manufacturer’s protocol.

High-quality sequencing reads were then aligned to the human reference genome (GRCh38) using HISAT2 (v2.2.1). Transcript quantification was performed using FeatureCounts (v2.0.3), and differential gene expression analysis was conducted using DESeq2 (v1.38.3) in R. Genes with an adjusted P-value < 0.05 and an absolute |log₂ fold change ≥ 1| were considered significantly differentially expressed. RNA-seq data were visualized using GraphPad Prism version 8.0, as well as volcano plots, heatmaps, and other graphical outputs generated via the SRplot platform (Tang et al., 2023).

CUT&Tag analysis

HEK293T cells were cultured in 10 cm² flat dish at a density of 1 × 10⁷ cells per well and transfected with 10 μg of the MmpE-pEGFP expression plasmid using Hieff Trans™ Liposomal Transfection Reagent, following the manufacturer’s protocol. Cells transfected with the empty vector pEGFP-N1 served as controls. After 36 h of transfection, cells were harvested for CUT&Tag analysis.

For the CUT&Tag, cells were cross-linked with 1% formaldehyde at room temperature for 10 minutes, and the reaction was quenched with 0.125 M glycine. Cells were collected by centrifugation and permeabilized using ice-cold wash buffer containing 0.05% digitonin. Primary antibody incubation was performed overnight at 4 °C using mouse anti-GFP antibody (1:500 dilution), followed by a 2-hour incubation at room temperature with a Protein A/G-conjugated secondary antibody (1:100 dilution). The cells were then incubated at 37 °C for 1 hour with a Protein A–Tn5 transposase complex (1:100 dilution) preloaded with Illumina sequencing adapters, enabling site-specific cleavage and adapter insertion near MmpE binding sites.

The reaction was terminated using lysis buffer containing 10% SDS, followed by proteinase K digestion. DNA was purified and amplified by PCR (12 cycles) using the NEBNext Ultra II DNA Library Preparation Kit. Fragment size distribution (150–300 bp) was confirmed using the Agilent 2100 Bioanalyzer.

Sequencing was performed on the Illumina NovaSeq 6000 platform, producing 150 bp paired-end reads. Raw reads were quality-checked using FastQC and aligned to the human reference genome (hg38). Peak calling was conducted using MACS2 (v2.2.7) with the parameters --nomodel --qvalue 0.05, identifying 2,903 high-confidence MmpE binding sites with >9-fold enrichment. Genomic annotation, including promoter analysis and gene ontology (GO) enrichment, was performed using HOMER (v4.11). De novo motif discovery was also conducted with HOMER, and motifs were statistically validated using TOMTOM with a significance threshold of P < 0.001.

Chromatin Immunoprecipitation (ChIP) assays

ChIP assays were performed to validate the direct binding of MmpE to the promoter regions of target genes. HEK293T cells were transfected with either an empty control vector, EGFP, or MmpE–EGFP expression plasmids. Cross-linking, chromatin isolation, fragmentation, and immunoprecipitation were carried out following the same procedure described for the CUT&Tag experiments.

DNA was purified from both input and immunoprecipitated (IP) samples and subjected to PCR using primers specific to the promoter regions of the target genes (–100 bp to +50 bp relative to the transcription start site). GAPDH promoter primers were used as a negative control. PCR products were analyzed by agarose gel electrophoresis to assess the presence of enriched promoter fragments.

For quantitative analysis, ChIP–qPCR was performed to measure the enrichment of specific promoter regions in IP samples. All reactions were carried out in triplicate. Relative enrichment was calculated using the 2^−ΔCt method, normalized to input DNA.

Electrophoretic mobility shift assays (EMSA)

DNA substrates were amplified by PCR from the genomic DNA of Mycobacterium tuberculosis H37Rv. The sequences of the oligonucleotide fragments used in the assay are listed in Table S6. EMSA was carried out using a modified protocol as previously described (Li et al., 2020). Each 20 μL reaction contained PCR-amplified DNA fragments, purified MmpE protein at varying concentrations, and binding buffer composed of 50 mM Tris–HCl (pH 7.5), 50 mM NaCl, 50 mM FeCl₃, 0.05 mg/mL bovine serum albumin (BSA), and 10% (v/v) glycerol. Reaction mixtures were incubated on ice for 30 minutes to allow protein–DNA complex formation. Samples were then resolved on a 4.8% native polyacrylamide gel using a running buffer containing 15 mM Tris-HCl (pH 7.5) and 0.1 M glycine at 80 V. Following electrophoresis, gels were stained with ethidium bromide and visualized using a Gel Imaging Analysis System (JIAPENG, China).

Colony-Forming Unit (CFU) assay

For bacterial preparation, mid-log phase cultures of M. bovis BCG (OD₆₀₀ = 0.8) were harvested, washed with PBS, and resuspended in fresh medium. THP-1 cells were seeded in 24-well plates at a density of 5 × 10⁵ cells per well and infected at a MOI of 1:10. After 4 hours of infection, extracellular bacteria were removed by treatment with penicillin–streptomycin (100 μg/mL) for 2 hours. Cells were then washed three times with PBS and maintained in antibiotic-free medium until harvest. To count intracellular bacteria, macrophages were lysed with 0.25% SDS for 10 minutes at room temperature. Lysates were serially diluted in PBS, and 100 μL aliquots of each dilution were plated on Middlebrook 7H10 agar supplemented with 10% OADC and kanamycin (50 μg/mL). Plates were incubated at 37 °C for 14 days. CFUs were enumerated, and final counts were calculated by applying the corresponding dilution factors. M. bovis BCG strains used in this study are listed in Table S5.

Animal experiments

Specific pathogen-free (SPF) female C57BL/6 mice (6–8 weeks old, 16–18 g) were obtained from Chang-sheng Bio (Liaoning, China). All animals were maintained under SPF conditions in individually ventilated cages with controlled temperature and humidity, on a 12-hour light/dark cycle. Mice had ad libitum access to sterilized food and water.

Mice infection

Mice were infected as described previously (Chen et al., 2022), with minor modifications. Mid-log phase M. bovis BCG cultures were washed twice in PBS containing 0.05% Tween 80 and briefly sonicated to disrupt bacterial clumps. Female C57BL/6 mice were anesthetized with isoflurane and intranasally inoculated with 1 × 10⁷ CFUs of M. bovis BCG in 40 μL of PBS. To confirm the inoculation dose, six mice were euthanized at 48 hours post-infection. Lungs were harvested, homogenized in 1 mL of PBS using a tissue homogenizer, and serial dilutions of the homogenates were plated on Middlebrook 7H10 agar supplemented with 10% OADC. Plates were incubated at 37 °C with 5% CO₂ for 14 days, after which CFUs were enumerated.

Histological analysis

Lung tissues from M. bovis BCG-infected mice were fixed in 4% phosphate-buffered formalin at room temperature for 24 h, followed by paraffin embedding. Paraffin-embedded tissue samples were sectioned into 2–3 µm thick slices using a microtome. Sections were deparaffinized, rehydrated through a graded ethanol series, and stained with hematoxylin and eosin (H&E). Stained tissue sections were examined using an Olympus BX53 light microscope. For digital analysis and annotation, scanned slides were visualized using CaseViewer software (version 2.0; 3DHISTECH).

Ethics approval

All animal experiments were conducted in accordance with the protocols approved by the Animal Ethics Committee of the Huazhong Agricultural University.

Statistical analyses

Data are presented as mean ± standard deviation (SD). Statistical comparisons between two groups were performed using two-tailed unpaired Student’s t-tests, following verification of normal distribution. A P-value less than 0.05 was considered statistically significant. Significance levels are indicated in figures as follows: P > 0.05 (ns, not significant), P < 0.05 (*), P < 0.01 (**), and P < 0.001 (***). All statistical analyses were performed using GraphPad Prism (version 8.0). Data were obtained from at least three independent biological replicates, each including two or more technical replicates.

Supplementary Figures

Supplementary Figure 1.

Supplementary Figure 2.

Supplementary Figure 3.

Supplementary Figure 4.

Supplementary Figure 5.

Supplementary Figure 6.

Supplementary Figure 7.

Acknowledgements

This work was supported by the Fundamental Research Funds for the Central Universities (#2662023DKQD001), Talent Start-up Funds of Huazhong Agricultural University (#11042310008), National Natural Science Foundation of China (#32473123), China Agriculture Research System of MOF and MARA (#CARS-37), and National Key Research and Development Program of China (#2021YFD1800403).

Additional information

Author contributions

Conceptualization: L. C., A. G., and L. Z.; Methodology: L. C.; Validation: L. C., B. D., and Q. J.; Formal analysis: L. C., Y. W.; Investigation: L. C., B. D., Q. J., and Y. W.; Resources: A. G., L. Z., and Y. C.; Data curation: L. C., Q. J., and Y. W.; Writing - original draft: L. C., L. Z., and A. G.; Writing - review & editing: L. C., L. Z., and A. G.; Visualization: L. C., Q. J., Y. C., L. Z., and A. G.; Supervision: A. G., and L. Z.; Project administration: A. G., and L. Z.; Funding acquisition: A. G., L. Z., and Y. C.

Additional files

Table S1. 175 genes were differentially expressed genes in RNA-seq.

Table S2. 2903 candidate MmpE-specific ChIP-seq signals.

Table S3. 298 genes were differentially expressed in both CUT&Tag and RNA-seq.

Table S4. Plasmids used in this study.

Table S5. Bacterial strains used in this study.

Table S6. Primers used in this study.