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 RNA, rescues stalled ribosomes and clears the cell of incomplete polypeptides. We report that native Escherichia coli tmRNA interacts specifically with native or synthetic E.coli tRNA alanine (tRNA Ala ) in vitro , alanine being the first codon of the tmRNA internal open reading frame. Aminoacylatable RNA microhelices also bind tmRNA. Complex formation was monitored by gel retardation assays combined with structural probes. Nucleotides from the acceptor stem of tRNA Ala are essential for complex formation with tmRNA. tRNA Ala isoacceptors recognize tmRNA with different affinities, with an important contribution from tRNA Ala post‐transcriptional modifications. The most abundant tRNA Ala isoacceptor in vivo binds tmRNA with the highest affinity. 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 interacts with the tRNA that decodes the resume codon prior to entering the ribosome. Biological implications of promoting specific complexes between tmRNA and aminoacylatable RNAs are discussed, with emphasis on primitive versions of the translation apparatus.