Abstract
Immunity conferred by antigen-specific CD4+ T cells is critical for controlling infection with Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. However, despite research that spans more than a century, many of the characteristics of protective immune responses to Mtb remain elusive. Defining the repertoire of antigenic targets is central to understanding the immune response against this pathogen. Although traditional methods of antigen discovery have identified many immunodominant antigens, they afford limited proteome coverage. Recent advances in proteomic techniques that are based on peptide library and protein microarray technology have enabled interrogation of the entire proteome of Mtb for antigens. Though these techniques have limitations and are still evolving, early studies using these techniques provide an unbiased view of the immune response to Mtb. Here we review proteome-wide approaches to antigen discovery and summarize what these have revealed so far on the composition of the Mtb immunoproteome.
Introduction
Decades of research on T cell responses to Mycobacterium tuberculosis (Mtb) have identified many immunodominant antigens, some of which provide significant protection as immunogens in animal models (). A major focus has been to identify antigens recognized by CD4+ T cells, since these cells are believed to play a dominant role in controlling Mtb infection (). However, robust immune responses induced by immunodominant antigens do not necessarily translate into protective immunity (), which reflects the complex and incompletely understood role of host immunity in the natural history of tuberculosis. On the one hand, antigen-specific CD4+ T cell responses are critical for protection against tuberculosis, and Mtb has evolved many strategies that subvert and evade the host adaptive immune response (). On the other hand, Mtb exploits immune responses for its own benefit, and evidence suggests that immune-mediated tissue destruction facilitates the spread of Mtb among hosts. In agreement with this, recent studies have found that T cell epitopes of known immunodominant antigens of Mtb are hyperconserved, implying that immune responses against them may be in some cases more beneficial to the bacilli than to the host ().
Given this complex relationship between host and pathogen, a full definition of the antigenic repertoire or “immunoproteome” of Mtb is an important step toward understanding how to effectively vaccinate against this infection. Until recently, most approaches to antigen discovery were based on traditional methods for separation and identification of antigens from complex mycobacterial protein mixtures (). Alternative methods have employed screening of Mtb expression libraries in Escherichia coli with T cell clones derived from latently infected individuals (). Although these methods have been successful in identifying immunodominant antigens, they provide restricted coverage of the Mtb proteome which has over 4,000 proteins. Advances in proteome-wide screening methods now enable a more extensive and unbiased survey of antigenic targets on complex pathogens like Mtb. Here, we review results from recently published proteome-wide antigen screens, and discuss how this powerful new approach may improve our understanding of the CD4+ T cell response to Mtb.
Defining the Immunoproteome of Mtb
With the development of technologies that allow high-throughput peptide and protein synthesis, it is now possible to interrogate the entire Mtb proteome for antigens. So far, three proteome-wide and relatively unbiased approaches to identify candidate antigens for CD4+ T cell responses from the Mtb proteome have been described (Figure 1). One approach was based on the use of a peptide library designed to screen potential targets of CD4+ T cell responses in latently infected individuals (). In contrast to previous studies which typically involved in vitro expansion of Mtb-specific T cells, circulating T cells from Mtb infected donors were directly tested against the synthetic peptide library using IFNγ ELISPOT assay. This screen involved predicting Mtb peptides that bind with high affinity to commonly expressed MHC class II alleles using a consensus approach based on results from three prediction methods (). Two other studies used analysis of serum antibody responses as a surrogate for CD4+ T cell responses, relying on the assumption that a strong linkage exists between the targets of antibodies and of the CD4+ helper T cells involved in their generation (). In one case, protein microarrays printed with products of all expressed open reading frames of Mtb were used to screen sera from TB patients and controls for antibody reactivity (). In the other study, a similar screen for serum antibody responses against the Mtb proteome in TB patients was performed using traditional methods of recombinant protein expression and ELISA ().
Figure 1
Despite major differences in their goals and methodology, all studies concluded that human immune responses target a subset of the Mtb proteome during infection (Figure 1). In the direct screen for CD4+ T cell responses to synthetic peptides, ∼2% of the proteome accounted for 80% of the total responses (
PE/PPE Proteins as Targets of CD4+ T Cells
PE/PPE proteins are unique proteins found exclusively in pathogenic mycobacteria. There are genes for 99 PE proteins and 68 PPE proteins in the genome of Mtb, constituting ∼10% of its coding capacity (
Figure 2

PE/PPE and ESX proteins. (A) Classification of PE/PPE proteins. PE/PPE proteins are broadly divided into PE and PPE proteins based on their characteristic N-terminal proline-glutamic acid (PE) and proline-proline-glutamic acid (PPE) sequences. These motifs occur within a span of ∼110 aminoacids in PE proteins and ∼180 aminoacids in PPE proteins. The PE family is further subdivided into two groups based on the presence or absence of a C-terminal domain with multiple tandem repeats of Gly-Gly-Ala or Gly-Gly -Asn sequences (PGRS, polymorphic GC-rich repetitive sequences). The PPE family is subdivided into three groups based on characteristic motifs in their C-termini, as indicated. (B) General features of ESX secretion systems. Organization of genes in the ESX-3 cluster, which induced maximal responses in the CD4+ T cell screen, are shown along with a schematic of a typical ESX or type VII secretion system. All ESX clusters contain a pair of Esx genes, the products of which form 1:1 complexes that are secreted. ESX clusters can exist as either complete (designated ESX-1 through ESX-5 systems) or partial clusters. In addition to the two Esx genes, complete ESX clusters encode four core components (ESX core component, Ecc) which are EccA (an ATPase), EccB (a membrane protein), EccC (an ATPase), EccD (a transmembrane protein), EccE (a transmembrane protein), and EccF (MycP, a subtilisin-like serine protease). Based on the current model of type VII secretion system, Esx heterodimers are recognized by EccC which then form an active ATPase providing energy for transport. EccC then propels these substrates through EccD, the transmembrane protein forming the export channel. MycP might be involved in processing certain substrates. The channel that transports the substrates thought the mycolate layer is yet to be identified. ESX clusters contain additional genes that code for other proteins called ESX secretion-associated proteins (Esp). In most of the complete and incomplete ESX systems, a pair of genes that code for PE/PPE proteins also exists in close proximity to the Esx genes.
All three published proteome-wide antigen screens showed that PE/PPE proteins are major targets of human immune responses. Among the antigens identified by peptide library screening for CD4+ T cell responses, ∼45% were PE/PPE proteins though they constitute <5% of the open reading frames of Mtb. In addition, PE/PPE proteins represented approximately half of the novel antigens identified, suggesting that immune responses to these proteins remain mostly unexplored. Proteome-wide antibody screening also revealed an enrichment of PE/PPE proteins among the antigens though the enrichment was less than that observed for CD4 responses (an average of ∼5–6% of the total targets recognized). It is possible that the relatively lower enrichment found for these proteins for antibody responses compared to cellular responses could in part reflect difficulties in expressing these proteins by recombinant techniques that were used to generate antigens for the antibody-based screening. The identification of PE/PPE proteins as prominent antigenic targets of CD4+ T cells in these studies of the immunoproteome is consistent with other more targeted analyses showing that these proteins are highly immunogenic in mycobacteria-infected humans and cattle (
Components of ESX Secretion System as Targets of CD4+ T Cells
ESX secretion systems are specialized protein export systems originally identified in mycobacteria and constitute a distinct mechanism for protein secretion known as the type VII secretion system. The system is named after two proteins, EsxA (also known as Early Secretory Antigenic Target-6, or ESAT-6) and EsxB (Culture Filtrate Protein-10, or CFP-10). There are five complete (ESX-1–5) and five to six incomplete ESX secretion systems in Mtb, and all carry a pair of genes that encode homologs of EsxA and EsxB (Figure 2). Most of the complete and incomplete ESX systems also contain or are closely linked to a pair of genes that code for PE/PPE proteins. These secretion systems export small proteins that contain a WXG amino acid motif (tryptophan and glycine separated by one amino acid). Secretion of EsxA and EsxB or their homologs, as well as many PE/PPE proteins, is dependent on ESX systems. Despite similarities, ESX systems do not complement each other and each one is likely to play distinct roles in Mtb virulence and physiology. For example, ESX-1 is required for survival of mycobacteria in mice, for granuloma formation, and for escape of Mtb from phagosome into cytosol (
ESX proteins are among the well known immunodominant antigens of Mtb. Commercial tests for Mtb infection (QuantiFERON® and T-SPOT.TB) use EsxA and EsxB as antigens since circulating T cells from most infected individuals respond strongly to these proteins. However, the proteome-wide screens reveal for the first time the extent of immunodominance of ESX proteins. For example, Lindestam Arlehamn et al. showed that 42% of the cellular responses they detected were directed against a set of proteins that represented 0.55% of the Mtb genome. These proteins were encoded by genes located in three distinct regions of the Mtb genome, which the authors called antigenic islands. All three islands include Esx protein pairs (i.e., EsxA/EsxB or homologs) and two contain the complete type VII secretion systems ESX-1 and ESX-3. Immunoproteome analysis using antibody screening also revealed that components of ESX systems induce strong immune responses in humans. Pathway analysis of the data from probing of microarrays with sera from active TB patients showed a significant enrichment in reactivity to proteins controlled by Zur, a regulator of Zinc uptake. Zur regulates a set of 56 genes which includes genes that code for three ESX systems. Interestingly, two of these three systems (ESX-3 and a partial ESX cluster containing genes for EsxQ, EsxR, and EsxS) were included in the three antigenic islands identified in the proteome-wide screen for CD4+ T cell responses. In addition, two proteins of the ESX-1 system were among the top five antigens associated with active TB. Collectively, these data underscore the immunodominance of ESX systems.
Surprisingly, it appears that both secreted and non-secreted components of the ESX systems induce strong immune responses. For example, previous studies have shown that eight different T cell antigens are encoded by genes in and around the ESX-1 region. Since the antigens tend to cluster in the genome, ESX systems had been called immunogenicity islands (
Limitations of Current Methods for Proteome-Wide Screening
Although uniquely powerful, high-throughput approaches of antigen discovery do not necessarily capture responses to all immunodominant antigens. For example, in the screen for cellular responses, only 20–25% of the latently infected donors responded to EsxA or EsxB (
Conservation Versus Variation of Epitope Sequences
The question of whether certain immune responses induced by Mtb antigens could actually be more beneficial to the bacteria than to the host remains open. According to classical models that portray the host-pathogen interaction as an “evolutionary arms race,” immunodominant epitopes are likely to be less conserved due to high selection pressure from the immune response. Recent studies suggest that this model may not consistently apply to mycobacteria. By analyzing genome sequences of a diverse collection of Mtb strains, Comas et al. showed that the great majority of known T cell epitopes display little sequence variation, with lower ratios of non-synonymous to synonymous changes than seen in other coding regions of essential and non-essential genes (
For antigens that derive from multigene families such as the PE/PPE and ESX proteins, another potentially important feature that may contribute to immunodominance is the presence of cross-reactive epitopes that are shared by multiple homologous family members. Indeed, PE/PPE proteins are known to carry highly conserved sequences. The relevance of this point was suggested by a study showing that both magnitude and frequency of T cell responses to PE/PPE proteins were greater to peptide pools representing the more conserved N-terminal regions than to pools representing other regions of the proteins (
Conclusion
New methods enabling proteome-wide antigen screens provide for the first time a general view of the immune responses induced by Mtb. The data obtained so far using these methods indicate that during Mtb infection, immune responses target a small subset of the proteome enriched for membrane-associated and secreted proteins. Among these antigens, members of the families of PE/PPE and ESX proteins are major targets of immune responses. These results should encourage future efforts to characterize the role of these protein families in pathogenesis, and stimulate interest in developing them as components of novel vaccines. While these two protein families comprise important potential components of novel vaccines, it remains to be determined whether the most prominent antigens in natural infection are also among the most effective antigens in the context of vaccination. Since most of the data obtained so far have come from analyses of immune responses in chronically infected individuals, it will be important to extend these studies to subjects with acute infection who may target a different antigenic repertoire.
Statements
Acknowledgments
The authors were supported by grants from NIH/NIAID (RO1 AI093649 and PO1 AI063537).
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Summary
Keywords
peptide library, protein microarray, antigen discovery, type VII secretion system, ESX proteins, PE/PPE proteins
Citation
Kunnath-Velayudhan S and Porcelli SA (2013) Recent Advances in Defining the Immunoproteome of Mycobacterium tuberculosis. Front. Immunol. 4:335. doi: 10.3389/fimmu.2013.00335
Received
30 July 2013
Accepted
29 August 2013
Published
11 October 2013
Volume
4 - 2013
Edited by
Lawrence J. Stern, Albert Einstein College of Medicine of Yeshiva University, USA
Reviewed by
Laurence C. Eisenlohr, Thomas Jefferson University, USA; Marianne Boes, University Medical Centre Utrecht, Netherlands
Copyright
© 2013 Kunnath-Velayudhan and Porcelli.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Steven Anthony Porcelli, Department of Microbiology and Immunology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA e-mail: steven.porcelli@einstein.yu.edu
This article was submitted to Antigen Presenting Cell Biology, a section of the journal Frontiers in Immunology.
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