Identification of murine T-cell epitopes on low-molecular-mass secretory proteins (CFP11, CFP17, and TB18.5) of Mycobacterium tuberculosis

Modulating mycobacterial envelope integrity for antibiotic synergy with benzothiazoles

Developing effective tuberculosis drugs is hindered by mycobacteria's intrinsic antibiotic resistance because of their impermeable cell envelope. Using benzothiazole compounds, we aimed to increase mycobacterial cell envelope permeability and weaken the defenses of Mycobacterium marinum, serving as a model for Mycobacterium tuberculosis Initial hit, BT-08, significantly boosted ethidium bromide uptake, indicating enhanced membrane permeability. It also demonstrated efficacy in the M. marinum-zebrafish embryo infection model and M. tuberculosis-infected macrophages. Notably, BT-08 synergized with established antibiotics, including vancomycin and rifampicin. Subsequent medicinal chemistry optimization led to BT-37, a non-toxic and more potent derivative, also enhancing ethidium bromide uptake and maintaining synergy with rifampicin in infected zebrafish embryos. Mutants of M. marinum resistant to BT-37 revealed that MMAR_0407 (Rv0164) is the molecular target and that this target plays a role in the observed synergy and permeability. This study introduces novel compounds targeting a new mycobacterial vulnerability and highlights their cooperative and synergistic interactions with existing antibiotics.

Mycobacterium smegmatis MSMEG_0129 is a nutrition-associated regulator that interacts with CarD and ClpP2

Mycobacterium smegmatis MSMEG_0129 and Rv0164, its homologue in Mycobacterium tuberculosis, are single START-domain proteins essential for bacterial growth and survival, but their biochemical activities and biological roles remain undetermined. Here, we probed the possible functions of MSMEG_0129 and its underlying mechanisms by determining its cellular location, searching for its interaction partners and monitoring its transcription profile. MSMEG_0129, and Rv0164 by extension, were found to be cytosolic proteins rather than secreted components as previously understood. Increases in MSMEG_0129 expression at physiological levels accelerated bacterial growth in a proportional manner, but additional growth acceleration was not observed when MSMEG_0129 was overexpressed up to 20 fold. MSMEG_0129 is a short-lived protein, unstable at both the mRNA and protein levels. Co-IP and GST pull-down assays showed that MSMEG_0129 interacts with the ClpP2 protease and a global transcription factor, CarD, their expression being correlated with that of MSMEG_0129. Nutrient deficiency led to the downregulation of MSMEG_0129 but upregulation of CarD. However, in the context of constitutive MSMEG_0129 overexpression under nutrient-rich or starvation conditions, the mRNA level of CarD was reduced 3 fold. Conversely, expression of ClpP2 decreased with MSMEG_0129 downregulation under starvation conditions, but increased 4-8 fold when MSMEG_0129 was overexpressed. Our data suggest that MSMEG_0129, and Rv0164 by analogy, are likely to be nutrition sensing factors that regulate mycobacterial growth and may be involved in signal transfer under nutrient deficiency, possibly via physical and regulatory interactions with CarD and ClpP2.

Structural and genetic analysis of START superfamily protein MSMEG_0129 from Mycobacterium smegmatis

Mycobacterium tuberculosis is a notorious pathogen that continues to threaten human health. Rv0164, an antigen of both T- and B cells conserved across mycobacteria, and MSMEG_0129, its close homolog in Mycobacterium smegmatis, are predicted members of the START domain superfamily, but their molecular function is unknown. Here, gene knockout studies demonstrate MSMEG_0129 is essential for bacterial growth, suggesting Rv0164 may be a potential drug target. The MSMEG_0129 crystal structure determined at 1.95 Å reveals a fold similar to that in polyketide aromatase/cyclases ZhuI and TcmN from Streptomyces sp. Structural comparisons and docking simulations, however, infer that MSMEG_0129 and Rv0164 are unlikely to catalyze polyketide aromatization/cyclization, but probably play an irreplaceable role during mycobacterial growth, for example, in lipid transfer during cell envelope synthesis.

The putative polyketide cyclase MSMEG_0129 from Mycobacterium smegmatis: purification, crystallization and X-ray crystallographic analysis

Mycobacterium tuberculosis Rv0164 has previously been identified as a human T-cell antigen that induces significant production of IFN-γ in human peripheral blood mononuclear cells. M. smegmatis MSMEG_0129 shares 59% sequence identity with Rv0164. Based on sequence alignment, both proteins are predicted to be members of the cyclase/dehydrase family, which is part of a large group of enzymes referred to as type II polyketide synthases (PKSs). In biosynthetic pathways mediated by type II PKSs, cyclases catalyze the conversion of linear poly-β-ketones to cyclized intermediates. To date, no mycobacterial type II PKSs have been reported. Here, the goal is to determine whether these proteins adopt similar folds to reported cyclase structures, and to this end MSMEG_0129 was cloned, expressed, purified and crystallized. An X-ray diffraction data set was collected to 1.95 Å resolution from a crystal belonging to space group P6₂, with unit-cell parameters a = 109.76, b = 109.76, c = 56.5 Å, α = 90, β = 90, γ = 120°. Further crystallographic analysis should establish a basis for investigating the structure and function of this putative mycobacterial type II PKS enzyme.

Evaluation of 5 Novel protein biomarkers for the rapid diagnosis of pulmonary and extra-pulmonary tuberculosis: preliminary results

Improved methods are required for the early and accurate diagnosis of tuberculosis, especially in the patients with smear-negative disease. Several biomarkers have been tried but most have shown poor sensitivity or specificity. In present study we aimed to evaluate the diagnostic utility of five novel antigens identified earlier by us. This is an initial study conducted on 250 subjects. The five recombinant antigens, named as rSS1 (Rv2145c), rSS2 (Rv0164), rSS3 (Rv1437), rSS4 (Rv1827) and rSS5 (Rv2970c), were expressed in pQE-30 expression vector, purified and their sero-diagnostic efficacy was evaluated in an unblinded manner using dot-blot and ELISA methods. The sensitivity and specificity of these novel antigens were compared with commercially available standard esat6 and 38 kDa antigens. Bacteriologically confirmed TB patients, non-TB disease controls and healthy individuals were included. which are based on novel antigen or novel technology, Area under curve (AUC) of the selected antigens were 0.98 (0.98-0.99) for rSS1, 0.88 (0.84-0.92) for rSS2, 0.88 (0.84-0.92) for rSS3, 0.95 (0.93-0.98) for rSS4 and 0.99 (0.98-1.0) for rSS5. Receiver operative characteristic (ROC) curve showed highly significant difference between TB and healthy subjects (p = <0.001). These initial findings, show that the recombinant antigens rSS1, rSS4 and rSS5 could be used as highly potential biomarkers for the serological diagnosis of active TB.

T-cell antigens of Mycobacterium immunogenum, an etiological agent of occupational hypersensitivity pneumonitis

The T lymphocyte-mediated immune lung disease hypersensitivity pneumonitis (HP) in machinists is poorly understood for disease mechanisms and diagnosis due in part to lack of information on causative T-cell antigens of the etiological agent Mycobacterium immunogenum (MI). Therefore, overall objective of the current study was to identify T-cell reactive antigens of this recently recognized pathogen. In this direction, purified recombinant form of five of the seroreactive proteins (reported in our initial study), including three cell wall-associated (arbitrarily designated as antigens A through C) and two secretory (AgD & AgE), were examined for their potential to activate antigen-presenting cells (APCs) viz. alveolar macrophages and human monocyte-derived dendritic cells (DCs) and for T-cell reactivity. All five proteins strongly activated APCs by inducing inflammatory cytokines (TNF-α, IL-6 & IL-1α) and nitric oxide (NO), albeit to a varying extent (AgE≥AgD>AgB≥AgA≥AgC), implying their differential potential for activation of APCs. However, only two of the five proteins (AgA, AgD) showed significant T-cell response (T lymphocyte proliferation and IFN-γ secretion) when tested using sensitized T-cells from MI-induced HP mouse model. These antigens also activated the human naïve CD4(+) T cells in presence of autologous DCs as measured using ELISPOT for IFN-γ. Immuno-informatic analysis predicted that the identified T-cell antigens (AgA and AgD) bind more number of class I and class II HLA alleles as compared with the reference immuno-dominant antigens ESAT-6 and CFP-10 from the tuberculous mycobacterial species M. tuberculosis. Predicted human population coverage for the epitopes of AgA (90.87%) and AgD (88.09%) was also higher as compared to those for the reference antigens ESAT-6 (82.42%) and CFP-10 (80.21%). These two antigens were further predicted to be highly immunogenic for class I peptide MHC (pMHC) complex as compared to the reference antigens. Collectively, our results imply that AgA and AgD are T-cell antigens with a high HLA binding frequency as well as population coverage for HLA alleles. This first report on T-cell antigens and epitopes of M. immunogenum is significant as it is expected to open up avenues for understanding pathogenesis mechanisms and developing T-cell-based immunodiagnostic tools for this poorly investigated occupational lung disease.

Analysis of the secretome and identification of novel constituents from culture filtrate of bacillus Calmette-Guerin using high-resolution mass spectrometry

Tuberculosis (TB) is an infectious bacterial disease that causes morbidity and mortality, especially in developing countries. Although its efficacy against TB has displayed a high degree of variability (0%-80%) in different trials, Mycobacterium bovis bacillus Calmette-Guérin (BCG) has been recognized as an important weapon for preventing TB worldwide for over 80 years. Because secreted proteins often play vital roles in the interaction between bacteria and host cells, the secretome of mycobacteria is considered to be an attractive reservoir of potential candidate antigens for the development of novel vaccines and diagnostic reagents. In this study, we performed a proteomic analysis of BCG culture filtrate proteins using SDS-PAGE and high-resolution Fourier transform mass spectrometry. In total, 239 proteins (1555 unique peptides) were identified, including 185 secreted proteins or lipoproteins. Furthermore, 17 novel protein products not annotated in the BCG database were detected and validated by means of RT-PCR at the transcriptional level. Additionally, the translational start sites of 52 proteins were confirmed, and 22 proteins were validated through extension of the translational start sites based on N-terminus-derived peptides. There are 103 secreted proteins that have not been reported in previous studies on BCG [corrected] secretome and are unique to our study. The physicochemical characteristics of the secreted proteins were determined. Major components from the culture supernatant, including low-molecular-weight antigens, lipoproteins, Pro-Glu and Pro-Pro-Glu family proteins, and Mce family proteins, are discussed; some components represent potential predominant antigens in the humoral and cellular immune responses.

Identification of T cell epitopes of Mycobacterium tuberculosis with biolistic DNA vaccination

Tuberculosis (TB) has been listed as one of the most prevalent and serious infectious diseases worldwide. The etiological pathogen of TB is Mycobacterium tuberculosis (Mtb), a facultative intracellular bacterium. Mycobacterium bovis bacillus Calmette-Guérin (BCG) is the only approved vaccine against TB to date. BCG has been widely used, but the efficacy is questionable, especially in adult pulmonary TB. Therefore, more effective, safe and reliable TB vaccines have been urgently needed. T cell-mediated cellular immune response is a key immune response for effective protective immunity against TB. DNA vaccines using Mtb antigens have been studied as promising future TB vaccines. Most TB DNA vaccine studies so far reported used intramuscular or intradermal injection with needles, as these methods tend to induce a type 1 helper T lymphocyte (Th1)-type immune response that is critical for the protective immunity. We have been using DNA vaccines with gene gun bombardment for T cell epitope identification of various Mtb antigens. We show here our strategy to identify precise Mtb T cell epitopes using DNA vaccines with gene gun bombardment.