Peptidyl-tRNA

Prokaryotic translation is the process by which messenger RNA is translated into proteins in prokaryotes.

Initiation of translation in prokaryotes involves the assembly of the components of the translation system, which are: the two ribosomal subunits (50S and 30S subunits); the mature mRNA to be translated; the tRNA charged with N-formylmethionine (the first amino acid in the nascent peptide); guanosine triphosphate (GTP) as a source of energy; the prokaryotic elongation factor EF-P and the three prokaryotic initiation factors IF1, IF2, and IF3, which help the assembly of the initiation complex. Variations in the mechanism can be anticipated.

The ribosome has three active sites: the A site, the P site, and the E site. The A site is the point of entry for the aminoacyl tRNA (except for the first aminoacyl tRNA, which enters at the P site). The P site is where the peptidyl tRNA is formed in the ribosome. And the E site which is the exit site of the now uncharged tRNA after it gives its amino acid to the growing peptide chain.

The selection of an initiation site (usually an AUG codon) depends on the interaction between the 30S subunit and the mRNA template. The 30S subunit binds to the mRNA template at a purine-rich region (the Shine-Dalgarno sequence) upstream of the AUG initiation codon. The Shine-Dalgarno sequence is complementary to a pyrimidine rich region on the 16S rRNA component of the 30S subunit. This sequence has been evolutionarily conserved and plays a major role in the microbial world we know today. During the formation of the initiation complex, these complementary nucleotide sequences pair to form a double stranded RNA structure that binds the mRNA to the ribosome in such a way that the initiation codon is placed at the P site.

Well-known coding regions that do not have AUG initiation codons are those of lacI (GUG) and lacA (UUG) in the E. coli lac operon. Two more recent studies have independently shown that 17 or more non-AUG start codons may initiate translation in E. coli .

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