OMICS Techniques and Identification of Pathogen Virulence Genes Application to the Analysis of Respiratory Pathogens

Sergio H

doi:10.4172/jcsb.1000024

Abstract

The advent of genomics should have facilitated the identification of microbial virulence factors, a key objective for vaccine design, especially for live attenuated vaccines. It is generally assumed than when the bacterial pathogen infects the host it expresses a set of genes, a number of them being virulence factors. However, up to now, although several Omics methods have been applied to identify virulence genes, i.e., DNA microarrays, In Vivo Expression Technology (IVET), Signature-Tagged Mutagenesis (STM), Differential Fluorescence Induction (DFI), etc., the results are quite meager. Among the genes identified by these techniques there are many related to cellular stress, basal metabolism, etc., which cannot be directly involved in virulence, or at least cannot be considered useful candidates to be deleted for designing a vaccine. Among the genes disclosed by these methodologies there are a number annotated as being hypothetical or unknown proteins. As these ORFs can hide some true virulence factors, we have selected all of these hypothetical proteins from several respiratory diseases and predicted their biological functions by a careful and in-depth analysis of each one. Although some of the re-annotations match with functions that can be related to microbial virulence, it can be concluded that identification of virulence factors remains elusive.

Highlights

Vaccination is the method of choice to fight microbial pathogens and presents the best cost/benefit ratio among current clinical and pharmaceutical practices
For bacterial pathogens related to respiratory diseases, with a significant number of sequenced pathogen genomes.) A number of genes found in the experiments by In Vivo Expression Technology (IVET), Signature-Tagged Mutagenesis (STM), Differential Fluorescence Induction (DFI), SCOTS and DNA microarrays correspond to hypothetical or unknown proteins
Some respiratory microbial pathogens computationally predict, from the protein sequences, the have been chosen of which IVET, STM, DFI, SCOTS and actual main protective antigens among the hundreds of DNA microarrays assays have been reported elsewhere

Summary

Introduction

Vaccination is the method of choice to fight microbial pathogens and presents the best cost/benefit ratio among current clinical and pharmaceutical practices. Sometimes the gene/protein may be a true virulence factor, but its deletion does not lead to an effective vaccine strain because the microorganism has alternative pathways or proteins to perform the function. For bacterial pathogens related to respiratory diseases, with a significant number of sequenced pathogen genomes.) A number of genes found in the experiments by IVET, STM, DFI, SCOTS and DNA microarrays correspond to hypothetical or unknown proteins. Some respiratory microbial pathogens computationally predict, from the protein sequences, the have been chosen of which IVET, STM, DFI, SCOTS and actual main protective antigens among the hundreds of DNA microarrays assays have been reported elsewhere.

Table in Supplementary Material shows the list of the

Results and Discussion

GroEL htrA Lon FbpA