RIBOSOME REGULATION BY THE NASCENT PEPTIDE

Studies of bacterial and eukaryotic systems have identified two-gene o perons in which the translation product of the upstream gene influence s translation of the downstream gene. The upstream gene, referred to a s a leader (gene) in bacterial systems or an upstream open reading fra me (uORF) in eukaryotes, encodes a peptide that interferes with a func tion(s) of its translating ribosome. The peptides are therefore cis-ac ting negative regulators of translation. The inhibitory peptides typic ally consist of fewer than 25 residues and function prior to emergence from the ribosome. A biological role for this class of translation in hibitor is demonstrated in translation attenuation, a form of regulati on that controls the inducible translation of the chloramphenicol resi stance genes cat and cmlA in bacteria. Induction of cat or cmlA requit es ribosome stalling nt a particular codon in the leader region of the mRNA. Stalling destabilizes an adjacent downstream mRNA secondary str ucture that normally sequesters the ribosome-binding site for the cat or cmlA coding regions. Genetic studies indicate that the nascent, lea der-encoded peptide is the selector of the site of ribosome stalling i n leader mRNA by cis interference with translation. Synthetic lender p eptides inhibit ribosomal peptidyltransferase in vitro, leading to the prediction that this activity is the basis for stall site selection. Recent studies have shown that the leader peptides are rRNA-binding pe ptides with targets at the peptidyl transferase center of 23S rRNA. uO RFs associated with several eukaryotic genes inhibit downstream transl ation. When inhibition depends on the specific codon sequence of the u ORF, it has been proposed that the uORF-encoded nascent peptide preven ts ribosome release from the mRNA at the uORF stop codon. This sets up a blockade to ribosome scanning which minimizes downstream translatio n. Segments within large proteins also appear to regulate ribosome act ivity in cis, although in most of the known examples the active amino acid sequences function after their emergence fr om the ribosome. cis control of translation by the nascent peptide is gene specific; nearly all such regulatory peptides exert no obvious trans effects in cells. The in vitro biochemical activities of the cat/cmla leader peptides o n ribosomes and rRNA suggest a mechanism through which the nascent pep tide can modify ribosome behavior: Other cis-acting regulatory peptide s may involve more complex ribosomal interactions.