Identification of gene fusion events in Mycobacterium tuberculosis that encode chimeric proteins.

James Gallant,Samantha L Sampson,Jomien Mouton,Wilbert Bitter,Arnab Pain,Nastassja Kriel,Roy Ummels,Tiaan Heunis,Corinne Ten Hagen-Jongman,Robin M Warren

doi:10.1093/nargab/lqaa033

Abstract

Mycobacterium tuberculosis is a facultative intracellular pathogen responsible for causing tuberculosis. The harsh environment in which M. tuberculosis survives requires this pathogen to continuously adapt in order to maintain an evolutionary advantage. However, the apparent absence of horizontal gene transfer in M. tuberculosis imposes restrictions in the ways by which evolution can occur. Large-scale changes in the genome can be introduced through genome reduction, recombination events and structural variation. Here, we identify a functional chimeric protein in the ppe38–71 locus, the absence of which is known to have an impact on protein secretion and virulence. To examine whether this approach was used more often by this pathogen, we further develop software that detects potential gene fusion events from multigene deletions using whole genome sequencing data. With this software we could identify a number of other putative gene fusion events within the genomes of M. tuberculosis isolates. We were able to demonstrate the expression of one of these gene fusions at the protein level using mass spectrometry. Therefore, gene fusions may provide an additional means of evolution for M. tuberculosis in its natural environment whereby novel chimeric proteins and functions can arise.

Highlights

Mycobacterium tuberculosis, the causative agent of the disease tuberculosis, is a facultative intracellular pathogen
It was recently reported that a multi-operon deletion in the ppe38–71 operon of M. tuberculosis had a major effect on the surface characteristics of this pathogen, as it resulted in the loss of all secreted proline–glutamic acid polymorphic GC-rich sequence (PE-PGRS) and PPE major polymorphic tandem repeat proteins [13]
By using unique features found in individual genomes in a proteogenomics approach, structures such as chimeric proteins can be identified in the proteomes of clinical M. tuberculosis isolates

Summary

INTRODUCTION

Mycobacterium tuberculosis, the causative agent of the disease tuberculosis, is a facultative intracellular pathogen. It was recently reported that a multi-operon deletion in the ppe operon of M. tuberculosis had a major effect on the surface characteristics of this pathogen, as it resulted in the loss of all secreted proline–glutamic acid polymorphic GC-rich sequence (PE-PGRS) and PPE major polymorphic tandem repeat proteins [13] This was especially striking due to the deletion occurring naturally within members of the highly successful Beijing strain family of M. tuberculosis [13]. This process will only produce a functional chimeric protein if the frame is maintained when creating gene fusions This phenomenon has garnered much attention in the cancer research field, where cells are prone to large-scale rearrangements in the genome [14,15,16], and similar mechanisms have recently been demonstrated in bacteria [17,18]. We demonstrate an additional means for M. tuberculosis evolution, which is likely applicable to the adaptation of other intracellular pathogens as well

MATERIALS AND METHODS

RESULTS

Findings

DISCUSSION