FLEXIBILITY OF THE NASCENT POLYPEPTIDE-CHAIN WITHIN THE RIBOSOME - CONTACTS FROM THE PEPTIDE N-TERMINUS TO A SPECIFIC REGION OF THE 30S SUBUNIT

The ribosomal environment of the N-terminus of the nascent polypeptide chain has been investigated using peptides of different lengths, synt hesized in situ on Escherichia coli ribosomes: the peptides each carry a photoreactive diazirine moiety at their N-terminus, so as to genera te cross-links to neighbouring ribosomal components. Our previous stud ies [Choi, K. M, & Brimacombe, R. (1998) Nucleic Acids Res. 26, 887-89 5] with three independent families of peptides. derived from the E. to il ompA protein gene, the tetracycline-resistance gene and the bacteri ophage T4 gene 60, identified a series of sites within the 23S rRNA to which the peptides became cross-linked. The distribution of these cro ss-links indicated that the nascent peptide is very flexible within th e 50S subunit. Here, we demonstrate that the N-termini of the ompA and gene-60 peptides can, in addition, even become concomitantly cross-li nked to the 30S subunit. The cross-linking is predominantly to 30S rib osomal proteins S1, S2, 4 and (to a lesser extent) S3, which form a cl uster near to the decoding region. This result is discussed in terms o f the flexibility of the nascent peptide during the co-translational f olding process. and in terms of the 'ribosomal bypass' phenomenon whic h is known to occur during translation of the gene 60 mRNA,