Secretome Prediction of Two M. tuberculosis Clinical Isolates Reveals Their High Antigenic Density and Potential Drug Targets

Abstract

The Excreted/Secreted (ES) proteins play important roles during Mycobacterium tuberculosis invasion, virulence, and survival inside the host and they are a major source of immunogenic proteins. However, the molecular complexity of the bacillus cell wall has made difficult the experimental isolation of the total bacterial ES proteins. Here, we reported the genomes of two Beijing genotype M. tuberculosis clinical isolates obtained from patients from Vietnam (isolate 46) and South Africa (isolate 48). We developed a bioinformatics pipeline to predict their secretomes and observed that ~12% of the genome-encoded proteins are ES, being PE, PE-PGRS, and PPE the most abundant protein domains. Additionally, the Gene Ontology, KEGG pathways and Enzyme Classes annotations supported the expected functions for the secretomes. The ~70% of an experimental secretome compiled from literature was contained in our predicted secretomes, while only the 34–41% of the experimental secretome was contained in the two previously reported secretomes for H37Rv. These results suggest that our bioinformatics pipeline is better to predict a more complete set of ES proteins in M. tuberculosis genomes. The predicted ES proteins showed a significant higher antigenic density measured by Abundance of Antigenic Regions (AAR) value than the non-ES proteins and also compared to random constructed secretomes. Additionally, we predicted the secretomes for H37Rv, H37Ra, and two M. bovis BCG genomes. The antigenic density for BGG and for isolates 46 and 48 was higher than the observed for H37Rv and H37Ra secretomes. In addition, two sets of immunogenic proteins previously reported in patients with tuberculosis also showed a high antigenic density. Interestingly, mice infected with isolate 46 showed a significant lower survival rate than the ones infected with isolate 48 and both survival rates were lower than the one previously reported for the H37Rv in the same murine model. Finally, after a druggability analysis of the secretomes, we found potential drug targets such as cytochrome P450, thiol peroxidase, the Ag85C, and Ribonucleoside Reductase in the secreted proteins that could be used as drug targets for novel treatments against Tuberculosis.

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

“…Furthermore, the average AAR of the secretome and cell membrane proteins was also found to be significantly lower (p < 0.001) and significantly higher (p < 0.001), respectively, in comparison to the average AAR of randomly chosen, equally sized sets of proteins from the whole proteome (Methods). Note that similar observations on relative AAR of secretome and cell membrane proteins were also recently made in tapeworms, Taenia solium 24 and Echinococcus multilocularis 92 , and in bacterium Mycobacterium tuberculosis 93 . Thus, secreted proteins are likely to be more antigenic than cell membrane proteins, and while choosing candidates for vaccine development, the secretome may provide a more antigenic landscape than cell membrane proteins.…”

Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children

“…Additionally, the abundance of antigenic regions (AAR), which evaluates antigenic density, found differences that were statistically significant between the NW and the O groups. As previous studies by our group have shown, the secretomes of more virulent pathogenic bacteria tend to have a higher antigenic density; this may be an indicator of pathogen activity in the obese subjects that may deserve further study [15,51].…”

“…Proteins can be secreted by bacteria through multiple secretory mechanisms. Thus, we used a bioinformatic strategy [14,15] to predict the secreted proteins encoded in our metatranscriptome. Out of the 115,712 genes that codify for proteins, we predicted 30,024 as potentially secreted, which represented ~ 26% of the total proteins in our metatranscriptome.…”

“…These proteins play a critical role in biological processes important for gut colonization, persistence, interaction with mucosal cells, activating signaling pathways, contributing to probiotic effects, etc. In pathogenic bacteria, the secretome plays a crucial role in parasitism, modulating the host immune response and promoting the proliferation of infection [13][14][15]. Millions of years of co-evolution between the human host and its gut microbial community have resulted in a continuous dialogue of the microbiota with the immune system promoting the gut homeostasis.…”

Proteogenomics in Aid of Host–Pathogen Interaction Studies: A Bacterial Perspective

“…Bacterial secretomes have been studied by different approaches including in silico identification of secretion signals, isolation of the secretomes of in vitro cultured microorganisms under different growth conditions and screening of proteins by phage display. In silico based approaches rely on algorithms to find consensus secretion signals characteristic of secreted proteins [ 95 ]. Secreted proteins are usually targeted to the secretory pathway by a signal either encoded in the N-terminal region of the protein or by the 5′ end of the mRNA sequence [ 96 ].…”