It has previously been shown that the P promoter from can be used as a DNA probe to identify an RFLP between wild-type and the vaccine strain BCG. To investigate the genetic basis of this phenomenon, DNA fragments from a New Zealand cattle strain and BCG Pasteur, containing the P-binding region, were isolated from gene libraries, sequenced and characterized. Sequence analysis and comparison with database sequences showed that the P region in BCG and is identical and shares 70% similarity to the P sequence from The Shine-Dalgarno sequence and the −10 and −35 promoter regions are conserved between the different species. Analysis of the flanking sequences of the P region revealed that less than 1 kb downstream of P is a 2405 bp fragment that is present in BCG but absent in the wild-type strain. The distribution of the 2405 bp fragment in members of the complex was investigated and found to be present in 70 out of 70 M. strains, and 7 out of 7 BCG daughter strains, 2 out of 2 strains, 2 out of 2 strains and 7 out of 25 strains. This is the first report of a genetic region of BCG that is not universally present in strains. The fragment does not appear to be present in any mycobacterial species outside the complex. It does not possess any characteristics of known transposable elements and the flanking sequences do not have any obvious features to suggest a deletion mechanism. The genetic location of this region is close to the 3′ end of the RD1 region of and The polymorphic nature of this locus in will provide an additional genetic marker for strain differentiation.


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