Individual subunits of ATP synthase, encoded by the eight genes of the atp operon (atpA through atpH), have been found to be synthesized at a 10-fold range in molar amounts (D.L. Foster and R.H. Fillingame, J. Biol. Chem. 257:2009-2015, 1982; K. von Meyenburg, B.B. Jorgensen, J. Nielsen, F.G. Hansen, and O. Michelsen. Tokai J. Exp. Clin. Med. 7:23-31, 1982). We have determined the functional half-lives at 30 degrees C of mRNAs transcribed from these genes either during constitutive expression in a partial diploid strain or after induced expression from a plasmid. Accurate decay kinetics of the relative mRNA levels were determined by monitoring the rates of synthesis of the individual ATP synthase subunits by radioactive pulse labeling at different times after blocking transcription initiation with rifampin. The mRNA transcribed from the atp operon was found to be inactivated about twice as fast as the bulk mRNA in E. coli. Exceptions are the mRNA from the promoter-proximal atpB gene, which was inactivated about three times as fast as the bulk mRNA, and atpC mRNA, the inactivation rate of which was comparable to that of the bulk mRNA. These moderate differences in the kinetics of functional decay explain only a minor part of the differences in expression levels of the atp genes. We conclude, therefore, that the individual atp mRNAs must be translated with widely different efficiencies. The present analysis further revealed that mRNA degradation is sensitive to heat shock; i.e., after incubation at 39 degrees C for 5 min followed by a shift back to 30 degrees C, the decay rate of the bulk mRNA was decreased by 30%.