Evidence for the location of bicyclomycin binding to the Escherichia coli transcription termination factor Rho

The commercial antibiotic bicyclomycin (Bcm) has been shown to target the e ssential transcription termination factor Rho in Escherichia coil, Little i s known about the Bcm binding domain in Rho, A recent structure-activity re lationship study led us to evaluate the reductive amination probe, 5a-(3-fo rmylanilino)dihydrobicyclomycin (FD-Bcm), Biochemical studies showed that F D-Bcm possessed inhibitory activities comparable to Bcm in Rho-dependent AT Pase and transcription termination assays, Incubation of Rho with FD-Bcm, A TP, and poly(C) followed by NaBH4 reduction and dialysis led to an apprecia ble loss of ATPase activity. Inclusion of Bcm with FD-Bcm in the reductive amination reaction protected Rho, indicating that Bcm and FD-Bcm competed f or the same binding site in Rho, Incubation of Rho with FD-Bcm and poly(C) followed by NaBH4 reduction provided a sample with residual ATPase activity (12%). Mass spectrometric analysis indicated the presence of two proteins in an approximate 1.2:1 ratio, whose masses corresponded to wild-type Rho ( 47,010 Dal and lysine-modified Rho (47,417 Dal, respectively. Trypsin diges tion of the Rho sample followed by high performance liquid chromatography s eparation and tandem mass spectrometry analysis identified the site of modi fication as Lys(181) within the combined tryptic fragment, Gly-Leu-Ile-Val- Ala-Pro-Pro-Lys-Ala-Gly-Lys (residues 174-184), Similar analysis of a lesse r modified sample (following incubation with inclusion of ATP) showed that addition had again occurred at Lys(181) These findings provide the first st ructural information concerning the site of Bcm binding in Rho.