The PE-PPE Family of Mycobacterium tuberculosis: Proteins in Disguise

Mycobacterium tuberculosis has thrived in parallel with humans for millennia, and despite our efforts, M. tuberculosis continues to plague us, currently infecting a third of the world's population. The success of M. tuberculosis has recently been attributed, in part, to the PE-PPE family; a unique collection of 168 proteins fundamentally involved in the pathogenesis of M. tuberculosis. The PE-PPE family proteins have been at the forefront of intense research efforts since their discovery in 1998 and whilst our knowledge and understanding has significantly advanced over the last two decades, many important questions remain to be elucidated. This review consolidates and examines the vast body of existing literature regarding the PE-PPE family proteins, with respect to the latest developments in elucidating their evolution, structure, subcellular localisation, function, and immunogenicity. This review also highlights significant inconsistencies and contradictions within the field. Additionally, possible explanations for these knowledge gaps are explored. Lastly, this review poses many important questions, which need to be addressed to complete our understanding of the PE-PPE family, as well as highlighting the challenges associated with studying this enigmatic family of proteins. Further research into the PE-PPE family, together with technological advancements in genomics and proteomics, will undoubtedly improve our understanding of the pathogenesis of M. tuberculosis, as well as identify key targets/candidates for the development of novel drugs, diagnostics, and vaccines.

PE_PGRS33, an Important Virulence Factor of Mycobacterium tuberculosis and Potential Target of Host Humoral Immune Response

PE_PGRS proteins are surface antigens of Mycobacterium tuberculosis (Mtb) and a few other pathogenic mycobacteria. The PE_PGRS33 protein is among the most studied PE_PGRSs. It is known that the PE domain of PE_PGRS33 is required for the protein translocation through the mycobacterial cell wall, where the PGRS domain remains available for interaction with host receptors. Interaction with Toll like receptor 2 (TLR2) promotes secretion of inflammatory chemokines and cytokines, which are key in the immunopathogenesis of tuberculosis (TB). In this review, we briefly address some key challenges in the development of a TB vaccine and attempt to provide a rationale for the development of new vaccines aimed at fostering a humoral response against Mtb. Using PE_PGRS33 as a model for a surface-exposed antigen, we exploit the availability of current structural data using homology modeling to gather insights on the PGRS domain features. Our study suggests that the PGRS domain of PE_PGRS33 exposes four PGII sandwiches on the outer surface, which, we propose, are directly involved through their loops in the interactions with the host receptors and, as such, are promising targets for a vaccination strategy aimed at inducing a humoral response.

PE_PGRS: Vital proteins in promoting mycobacterial survival and modulating host immunity and metabolism

Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is the leading infectious cause of mortality worldwide. One of the key reasons for M. tb pathogenesis is the capability of M. tb to evade immune elimination and survive in macrophage, eventually causing chronic infection. However the pathogenicity mechanism of M. tb is not unclear yet, and thus diagnosis and therapy for TB remains a challenge. The genome of M. tb, encodes a unique protein family known as the PGRS family, with largely unexplored functions. Recently, an increasing number of reports have shown that the PE_PGRS proteins play critical roles in bacterial pathogenesis and immune evasion. The PE_PGRS protein family, characterized by a special N-terminal PE (Pro (P)-Glu (E) motif) domain and a C-terminal PGRS (Polymorphic GC-rich Repetitive Sequences) domain, is restricted mainly to pathogenic mycobacteria. Here we summarize current literature on the PE_PGRS as vital proteins in promoting bacterial survival and modulating host immunity, cell death and metabolism. We also highlight the potential of PE_PGRS as novel targets of anti-mycobacterial interventions for TB control.

The role of immunoinformatics in the development of T-cell peptide-based vaccines against Mycobacterium tuberculosis

INTRODUCTION

Tuberculosis (TB) is a major health problem worldwide. The BCG, the only authorized vaccine to fight TB, shows a variable protection in the adult population highlighting the need of a new vaccine. Immunoinformatics offers a variety of tools that can predict immunogenic T-cell peptides of Mycobacterium tuberculosis (Mtb) that can be used to create a new vaccine. Immunoinformatics has made possible the identification of immunogenic T-cell peptides of Mtb that have been tested in vitro showing a potential for using these molecules as part of a new TB vaccine.

AREAS COVERED

This review summarizes the most common immunoinformatics tools to identify immunogenic T-cell peptides and presents a compilation about research studies that have identified T-cell peptides of Mtb by using immunoinformatics. Also, it is provided a summary of the TB vaccines undergoing clinical trials.

EXPERT OPINION

In the next few years, the field of peptide-based vaccines will keep growing along with the development of more efficient and sophisticated immunoinformatic tools to identify immunogenic peptides with a greater accuracy.

Mycobacterium tuberculosis PE31 (Rv3477) Attenuates Host Cell Apoptosis and Promotes Recombinant M. smegmatis Intracellular Survival via Up-regulating GTPase Guanylate Binding Protein-1

The Mycobacterium (M.) tuberculosis comprising proline–glutamic acid (PE) subfamily proteins associate with virulence, pathogenesis, and host-immune modulations. While the functions of most of this family members are not yet explored. Here, we explore the functions of “PE only” subfamily member PE31 (Rv3477) in virulence and host-pathogen interactions. We have expressed the M. tuberculosis PE31 in non-pathogenic Mycobacterium smegmatis strain (Ms_PE31) and demonstrated that PE31 significantly altered the cell facet features including colony morphology and biofilm formation. PE31 expressing M. smegmatis showed more resistant to the low pH, diamide, H₂O₂ and surface stress. Moreover, Ms_PE31 showed higher intracellular survival in macrophage THP-1 cells. Ms_PE31 significantly down-regulated the production of IL-12p40 and IL-6, while up-regulates the production of IL-10 in macrophages. Ms_PE31 also induced the expression of guanylate-binding protein-1 (GBP-1) in macrophages. Further analysis demonstrates that Ms_PE31 inhibits the caspase-3 activation and reduces the macrophages apoptosis. Besides, the NF-κB signaling pathway involves the interplay between Ms_PE31 and macrophages. Collectively, our finding identified that PE31 act as a functionally relevant virulence factor of M. tuberculosis.

Molecular Basis Underlying Host Immunity Subversion by Mycobacterium tuberculosis PE/PPE Family Molecules

Mycobacterium tuberculosis proline-glutamic acid (PE)/proline-proline-glutamic acid (PPE) family proteins, with >160 members, are crucial for virulence, cell wall, host cell fate, host Th1/Th2 balance, and CD8⁺ T cell recognition. Ca²⁺ signaling is involved in PE/PPE protein-mediated host-pathogen interaction. PE/PPE proteins also function in heme utilization and nitric oxide production. PE/PPE family proteins are intensively pursued as diagnosis biomarkers and vaccine components.

Expression and regulatory networks of Mycobacterium tuberculosis PE/PPE family antigens

PE/PPE family antigens are distributed mainly in pathogenic mycobacteria and serve as potential antituberculosis (TB) vaccine components. Some PE/PPE family antigens can regulate the host innate immune response, interfere with macrophage activation and phagolysosome fusion, and serve as major sources of antigenic variation. PE/PPE antigens have been associated with mycobacteria pathogenesis; pe/ppe genes are mainly found in pathogenic mycobacteria and are differentially expressed between Mtb and Mycobacterium bovis. PE/PPE proteins were essential for the growth of Mtb, and PE/PPE proteins were differentially expressed under a variety of conditions. Multiple mycobacterial-virulence-related transcription factors, sigma factors, the global transcriptional regulation factor Lsr2, MprAB, and PhoPR two-component regulatory systems, and cyclic adenine monophosphate-dependent regulators, regulate the expression of PE/PPE family antigens. Multiple-scale integrative analysis revealed the expression and regulatory networks of PE/PPE family antigens underlying the virulence and pathogenesis of Mtb, providing important clues for the discovery of new anti-TB measures.

Cell death at the cross roads of host-pathogen interaction in Mycobacterium tuberculosis infection

Tuberculosis (TB) continues to be the leading cause of death by any single infectious agent, accounting for around 1.7 million annual deaths globally, despite several interventions and support programs by national and international agencies. With the development of drug resistance in Mycobacterium tuberculosis (M. tb), there has been a paradigm shift in TB research towards host-directed therapy. The potential targets include the interactions between host and bacterial proteins that are crucial for pathogenesis. Hence, collective efforts are being made to understand the molecular details of host-pathogen interaction for possible translation into host-directed therapy. The present review focuses on 'host cell death modalities' of host-pathogen interaction, which play a crucial role in determining the outcome of TB disease progression. Several cell death modalities that occur in response to mycobacterial infection have been identified in human macrophages either as host defences for bacterial clearance or as pathogen strategies for multiplication and dissemination. These cell death modalities include apoptosis, necrosis, pyroptosis, necroptosis, pyronecrosis, NETosis, and autophagy. These processes are highly overlapping with several mycobacterial proteins participating in more than one cell death pathway. Until now, reviews in M. tb and host cell death have discussed either focusing on host evasion strategies, apoptosis, autophagy, and necrosis or describing all these forms with limited discussions of their role in host-pathogen interactions. Here, we present a comprehensive review of various mycobacterial factors modulating host cell death pathways and the cross-talk between them. Besides this, we have discussed the networking of host cell death pathways including the interference of host miRNA during M. tb infection with their respective targets. Through this review, we present the host targets that overlap across several cell death modalities and the technical limitations of methodology in cell death research. Given the compelling need to discover alternative drug target(s), this review identifies these overlapping cell death factors as potential targets for host-directed therapy.

Charge clusters signatures in prokaryotic proteomes: Temperature-dependence and distribution

The identification and the screening of Charged Clusters (CCs) residues in proteins is a key analysis to assess any quantitative structure-function correlation in proteins. Here, we present a proteome wide scan for the occurrence of (CCs) in 99292 proteins using a new tool. Finding Clusters Charge in Protein Sequences Program (FCCP). The FCCP has been employed to search CCs in 35 prokaryotic proteomes (7 Psychrophiles, 10 Mesophiles, 9 thermophiles and for 9 hyperthermophiles). A new repository of 855 CC has been created. Results showed that the mapped proteins containing positive and negative charge clusters are mostly transmembrane proteins while the conserved CCs within the same proteome are transposases or involved in DNA binding and integration. Interestingly, the negative charged cluster was associated to bacteria growth's temperature (p=0.002) acting as proteins' core signature. Taken together the various results provide a consistent picture of these screened CCs in terms of its potentials functional roles.

The BCGΔBCG1419c strain, which produces more pellicle in vitro, improves control of chronic tuberculosis in vivo

Mycobacterium tuberculosis (Mtb) has been a threat to humans since ancient times, and it is the main causative agent of tuberculosis (TB). Until today, the only licensed vaccine against Mtb is the live attenuated M. bovis Bacillus Calmette-Guérin (BCG), which has variable levels of protection against the pulmonary form of infection. The quest for a new vaccine is a priority given the rise of multidrug-resistant Mtb around the world, as well as the tremendous burden imposed by latent TB. The objective of this study was to evaluate the immunogenicity and capacity of protection of a modified BCG strain (BCGΔBCG1419c) lacking the c-di-GMP phosphodiesterase gene BCG1419c, in diverse mice models. In a previous report, we have shown that BCGΔBCG1419c was capable of increasing biofilm production and after intravenous infection of immunocompetent mice; this strain persisted longer in lungs than parental BCG Pasteur. This led us to hypothesize that BCGΔBCG1419c might therefore possess some advantage as vaccine candidate. Our results in this report indicate that compared to conventional BCG, vaccination with BCGΔBCG1419c induced a better activation of specific T-lymphocytes population, was equally effective in preventing weight loss despite being used at lower dose, reduced tissue damage (pneumonic scores), increased local IFNγ(+) T cells, and diminished bacterial burden in lungs of BALB/c mice infected intratracheally with high dose Mtb H37Rv to induce progressive TB. Moreover, vaccination with BCGΔBCG1419c improved resistance to reactivation after immunosuppression induced by corticosterone in a murine model of chronic infection similar to latent TB. Furthermore, despite showing increased persistence in immunocompetent mice, BCGΔBCG1419c was as attenuated as parental BCG in nude mice. To our knowledge, this is the first demonstration that a modified BCG vaccine candidate with increased pellicle/biofilm production has the capacity to protect against Mtb challenge in chronic and reactivation models of infection.