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Aminoglycosides

Kanamycin and its close relatives neomycin and gentamicin are members of a larger group of antibiotics, the aminoglycoside antibiotics, which also includes streptomycin. They seem to affect translocation by binding to the A site of the ribosome. Aminoglycosides have a very broad spectrum of action, and some of them inhibit translation in plant and animal cells, as well as in bacteria. However, their toxicity, especially during sustained use, and high rates of resistance somewhat limit their usefulness as therapeutic agents.

Bacterial mutants resistant to aminoglycosides arise primarily due to genes exchanged on transposons and plasmids. The products of some of these genes inactivate the aminoglycosides by phosphorylating, acetylating, or adenylating (adding adenosine to) them. For example, the neo gene for kanamycin and neomycin resistance, from transposon Tn5, phosphorylates these antibiotics.

Fusidic Acid

Fusidic acid specifically inhibits EF-G (called EF-2 in eukaryotes), probably by preventing its dissociation from the ribosome after GTP cleavage. It has been very useful in studies of the function of ribosomes. In E. coli, mutations that confer resistance to fusidic acid are in the fusA gene, which encodes EF-G. Unexpectedly, some acetyltransferases that confer resistance to chloramphenicol also bind to and inactivate fusidic acid.

A variety of physical techniques, combined with much indirect information accumulated over the years from genetics and biochemistry, have revealed many details of the overall structure of the ribosome. The crystal structures of the individual subunits and the entire 70S ribosome have been determined and correlated with the earlier indirect information. Many laboratories participated in this project, and this awesome achievement will go down in history as one of the major milestones in molecular biology, recognized by the Nobel Prize. We can review only a few of the most salient features here.

Figure 2.21 The composition of a bacterial ribosome containing one copy each of the 16S, 23S, and 5S rRNAs, as well as many proteins. The proteins of the large 50S subunit are designated L1 to L31. The proteins of the small 30S subunit are designated S1 to S21. The 30S and 50S subunits combine to form the 70S ribosome, which carries out protein synthesis.

The two subunits of the ribosome are frequently represented as ovals, with a flat side that binds to the other subunit, leaving a small gap between them. It is through this gap that the mRNA moves, and the aa-tRNAs enter, interact with the mRNA, and pass through the ribosome, contributing their amino acids to the growing polypeptide chain. The newly synthesized polypeptide chain exits through a channel running through the 50S subunit. This channel is long enough to hold a chain of about 70 amino acids, so a polypeptide of this length must be synthesized before the N-terminal end of a protein first emerges from the ribosome.

The rRNAs play many of the most important roles in the ribosome, and the ribosomal proteins seem to be present mostly to give rigidity to the structure, helping to hold the rRNAs in place. This has contributed to speculation that RNAs were the primordial enzymes and that proteins came along later in the earliest stages of life on

Earth. The 23S rRNA, rather than a ribosomal protein, acts as the peptidyltransferase enzyme that performs the enzymatic function that forms the peptide bonds between the carboxyl end of the growing polypeptide and the amino group of the incoming amino acid. Thus, 23S rRNA is an RNA enzyme, or ribozyme. The 23S rRNA also forms most of the channel in the 50S subunit through which the growing polypeptide passes. The 16S RNA plays crucial roles in translation initiation and in matching each incoming aa-tRNA with the mRNA. A structure of the ribosome is shown in Figure 2.22.