Evidence for apparent gene instability in the rifamycin-producing oligoketide synthase. Implications for combinatorial biosynthesis and heterologous gene expression.

The oligoketide ('polyketide') synthase leading to the formation of proansamycin X in Amycolatopsis mediterranei also prematurely releases a range of acyclic intermediates from the enzyme complex. We intended to study the chemical biology of this ectopic chain release using RifA as a model protein system; however, we were unable to clone the rifA gene in its entirety. Restriction analysis of cosmid clones revealed that rifA is subject to random deletions at high frequency, especially in central regions of the locus. Examination of the gene sequence in this region reveals a high concentration of inverted repeats; we suggest that these sequences are subject to alteration in secondary structure when cloned outside the environment of the A. mediterranei genome, leading to recombination and deletion.