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Nucleic Acids Research, 1995, Vol. 23, No. 13 2371-2380
© 1995

RNA

Mapping the path of the nascent peptide chain through the 23S in the 50S ribosomal subunit

Katrin Stade, Nicole Jünke and Richard Brimacombe*

Max-Planck-Institut Für Molekulare Genetik (AG Ribosomen) Ihnestrasse 73,D-14195 Berlin (Dahlem), Germany

*To whom corespondence should be addressed

Received April 21, 1995. Accepted May 19, 1995.

peptides of different lengths encoded by suitable mRNA fragments were biosyntheslzed in situ on Escherichia coll rlbosomes. The peptides carried a diazirine derivative bound to their N-terminal methlonlne residue, which was photoactivated whilst the peptides were still attached to the ribosome. Subsequently, the sites of photo-cross-linking to 23S RNA were analyzed by our standard procedures. The N-termini of peptides of increasing length became progressively cross-linked to nucleotlde 750 (peptides of 6, 9 or 13–15 amino acids), to nucleotide 1614 and concomltantly to a second site between nucleotides 1305 and 1350 (a peptide of 25–26 amino acids), and to nucleotide 91 (a peptide of 29–33 amino acids). reviously we had shown that peptides of 1 or 2 amino acids were cross-linked to nucleotides 2062,2506 and 2585 within the peptidyl transferase ring, whereas triand tetrapeptides were additionally cross-linked to nucleotides 2609 and 1781. Taken together, the data demonstrate that the path of the nascent peptide chain moves from the peptidyl transferase ring in domain V of the 23S RNA to domain IV, then to domain II, then to domain III, and finally to domain I. These cross-linking results are correlated with other types of topographical data relating to the 50S subunit


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