PHYSIOLOGICALLY DEPENDENT APPEARANCE OF A LOW-DENSITY REGION THAT CORRESPONDS TO THE TUNNEL THROUGH THE 50S PART OF THE 70S RIBOSOME

Ribosomes have different conformations in cells that are starved for a required amino acid (giving amino-acyl.tRNA starvation), or treated w ith kirromycin (blocking EF-Tu.GDP release), or are in exponential gro wth. A tunnel spans the 50S ribosome from a location facing the 70S ri bosomal intersubunit space to the back side of the subunit in Escheric hia coli cells. Here we have analyzed the internal low density region that corresponds to this tunnel in ribosomes in vivo. The data suggest that the tunnel is opened in connection with spatial separation of th e subunits in ribosomes that have an empty A-site due to starvation fo r amino-acyl.tRNA. A region that corresponds to this tunnel can be fou nd in the more compact structure of ribosomes in kirromycin-treated ce lls only after a substantial removal of low density material. This reg ion is even less prominent in ribosomes in undefined working modes in growing bacteria. The data suggest that appearance of the tunnel throu gh the 50S ribosomal subunit is working-mode dependent and it is not a characteristic feature of the major fraction of the ribosomal populat ion in growing cells. (C) 1998 Academic Press.