Transfer RNA(Ala) recognizes transfer-messenger RNA with specificity; a functional complex prior to entering the ribosome?

tmRNA (SsrA or 10Sa RNA) functions as both a transfer RNA and a messenger R NA, rescues stalled ribosomes and clears the cell of incomplete polypeptide s. We report that native Escherichia coil tmRNA interacts specifically with native or synthetic E,coli tRNA alanine (tRNA(Ala)) in vitro, alanine bein g the first codon of the tmRNA internal open reading frame. Aminoacylatable RNA microhelices also bind tmRNA. Complex formation was monitored by gel r etardation assays combined with structural probes. Nucleotides from the acc eptor stem of tRNA(Ala) are essential for complex formation with tmRNA, tRN A(Ala) isoacceptors recognize tmRNA with different affinities, with an impo rtant contribution from tRNA(Ala) post-transcriptional modifications. The m ost abundant tRNA(Ala) isoacceptor in vivo binds tmRNA with the highest aff inity. A complex between tRNA(Ala) and tmRNA might involve up to 140 tmRNA molecules out of 500 present per E.coli cell. Our data suggest that tmRNA i nteracts with the tRNA that decodes the resume codon prior to entering the ribosome, Biological implications of promoting specific complexes between t mRNA and aminoacylatable RNAs are discussed, with emphasis on primitive ver sions of the translation apparatus.