Structure elucidation of the daptomycin products generated upon heterologous expression of the daptomycin resistance gene cluster drcAB

Recently, a high-level daptomycin (DAP) resistant Mammaliicoccus sciuri strain (TS92) was identified which mediates a 33 percent decline of DAP when incubated in Mueller-Hinton (MH) medium. The genetic background of the DAP resistance in TS92 is a newly discovered two-gene operon, named drcAB, whose expression was reported to impair the structural integrity of DAP, eventually leading to its inactivation. Here we set out to elucidate the chemical nature of drcAB-mediated DAP modification by applying a general unknown comparative screening (GUCS) approach in high-resolution mass spectrometry. DAP in MH medium was incubated with Staphylococcus aureus strain RN4220_Pxyl/tet-drcAB, which carries the drcAB operon under control of an inducible promotor on a plasmid, and GUCS test and reference samples were obtained upon and without drcAB expression. A two-step process catalyzed by DrcAB was discovered, comprising a structural alteration of DAP. The mass spectrometric data indicate an N-substitution at the aniline moiety of kynurenine with dehydroalanine, and subsequently, a cleavage of the ester bond of the DAP core between kynurenine and threonine by means of water. The structures postulated were confirmed by comparison of in silico versus measured fragmentation patterns.