M1 RNA, the catalytic component of Escherichia coli RNase P, is derived from the 3'-end processing of precursor M1 RNA, a major transcript of the rnpB gene. In this study, we investigated the mechanism of 3'-end processing of M1 RNA using the recombinant N-terminal half RNase E. The cleavage site preference of RNase E differed from that of the 40% ammonium sulfate precipitate (ASP-40), a partially purified cell extract containing processing activity. However, the addition of a trace amount of ASP-40 changed the cleavage site preference of RNase E to that of ASP-40 suggesting the involvement of a soluble factor in cleavage site preference. (C) 2002 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.