The chromosomal integration site of the Streptomyces element pSAM2 overlaps a putative tRNA gene conserved among actinomycetes.

The pSAM2 element of Streptomyces ambofaciens integrates site-specifically in the genome of different Streptomyces species by recombination between a 58 bp sequence common to the plasmid (attP) and the chromosome (attB). Southern hybridization analysis showed that sequences similar to the pSAM2 attB site were found in other actinomycetes (Mycobacterium, Nocardia, Micromonospora) as well as unrelated bacteria (Bacillus circulans, Escherichia coli, Clostridium botulinum, Bordetella pertussis, and Legionella pneumophila). Hybridizing fragments from B. circulans and Mycobacterium tuberculosis were cloned and sequenced. Comparison of these sequences with the sequence of the integration zone of S. ambofaciens revealed a conserved region of 76 bp which overlapped with the attB site. This conserved sequence was similar to the Salmonella typhimurium and E. coli tRNA(pro1) genes as well as a number of eucaryotic tRNA genes and had a proline-tRNA-like cloverleaf structure. Furthermore, the Streptomyces lividans attB site of the Streptomyces glaucescens element pIJ408 was also found to overlap a potential tRNA gene (tRNA(thr)). We note here that these two putative tRNA genes as well as those which overlap the attB site of the elements SLP1 of Streptomyces coelicolor and pMEA100 of Nocardia mediterranei all contain the site where integrative recombination takes place. These presumptive actinomycete tRNA genes lack the 3' terminal CCA sequence found in most procaryotic tRNA genes.