MRC PhD student

Level of study: PhD

Title: Host Induced Microevolution of ESX Secretion Systems of M. tuberculosis

Despite the relative lack of genetic diversity in contemporary populations of M. tuberculosis compared to other organisms, there is mounting evidence that strains of M. tuberculosis differ in the way they handle host immunity. Recent studies show that mutations in genes, such as Rv1519 or a polyketide synthase required for PGL production, can alter the interaction between the tubercle bacilli and human hosts.

The hypothesis to be explored is that ESX systems, through their wide range of effector molecules, that influence immunogenicity and pathogenicity, could also be important in generating phenotypic diversity in clinical isolates of M. tuberculosis. Characterizing such diversity also has important implications for diagnostics and vaccine design as the ESX effector molecules ESAT-6 and CFP10 have been used as the basis of diagnostic tests as well as subunit vaccines.  Thus, the aim is to specifically establish whether differences in sequence, expression profiles and protein patterns related to ESX secreted proteins exist between different clinical isolates, and if differences evolve over time.

To do this, a vast collection of clinical isolates will be used. This includes a family of closely related strains circulating in the South African Province of KwaZulu-Natal (KZN) that have been collected over an 11-year period and have become drug resistant and some extensively drug resistant. The genome sequences of four of these strains is available through projects at the Broad Institute, Boston and an ongoing project with the LIFElab supported South African Genomics Platform in Durban that has recently commissioned a Roche Genome Sequencer FLX system.

Specific aims of the project
The main objectives of this research are to use highly innovative approaches of molecular biology, cell biology and animal models to elucidate the function and role of the ESX, PE and PPE families of proteins in the M. tuberculosis infection process.

The overall aim of the research is to evaluate potential genetic variation in ESX secretion systems of clinical isolates of M. tuberculosis. This will be achieved by:

1. Characterization of DNA sequence diversity of the ESX 1-3-5 systems and associated PE, and PPE genes.
2. Comparative expression analysis of the ESX 1-3-5 systems, effectors and associated regulators in clinical isolates of M. tuberculosis.
3. Determining secretion profiles of clinical isolates of M. tuberculosis