Identification of a restriction fragment length polymorphism associated with a deletion that maps in a transcriptionally active open-reading frame, orfX, in Mycobacterium tuberculosis Erdman.

A two-component system of Mycobacterium tuberculosis H37Rv, designated as devR-devS, was identified in our laboratory, that encodes a response regulator and a histidine sensor-kinase respectively. Southern analysis of the devR-devS locus in the genomes of M. tuberculosis H37Rv, H37Ra and Erdman indicated the presence of an EcoRI restriction fragment length polymorphism (RFLP) in the Erdman strain. Studies employing polymerase chain reaction (PCR), suggested that the RFLP is associated with a deletion in M. tuberculosis Erdman. Deoxyribonucleic acid sequence analysis of this region in the Erdman strain confirmed a deletion of 330 bp. The deletion maps in an open reading frame (ORF) designated as orfX (which maps upstream of the devR-devS locus) that is present in M. tuberculosis H37Rv and H37Ra, and in all five isolates of M. tuberculosis examined in this study. OrfX is transcriptionally active in M. tuberculosis H37Rv and H37Ra but not in the Erdman strain. These observations point towards variations in genomic organization and in transcriptional activity of virulent strains of M. tuberculosis. OrfX gene deletion can be utilized in a rapid PCR-based assay to differentiate between H37Rv and Erdman strains.