Protein Synthesis: A brief overview of ribosome function and a new regulatory mechanism
Ribosomes are complexes that catalyze the synthesis of all proteins in all organisms. The ribosome is composed of messenger RNA (mRNA) that carries the code for the protein, the small subunit, the large subunit, and a variety of other cofactors and molecules. On both the large subunit and small subunit, there are three corresponding translation sites – the aminoacylated (A), peptidyl (P), and exit (E) sites. tRNA molecules are adaptors that, within the ribosomal complex, translate the mRNA code into a specific sequence of amino acids. Cytosolic aminoacyl tRNAs are delivered to the presented mRNA codon in the A site. The peptidyl tRNA in the P site is deacylated by peptidyl transfer to the aminoacyl tRNA in the A site. The deacylated tRNA then moves to the E site and is released into the cytoplasm. The ribosome then moves down the mRNA, in the 5’ to 3’ direction, to the next codon and the cycle repeats to add on to the peptide chain. During protein synthesis, this peptide elongation cycle happens 10-20 times per second.
One of the mechanisms regulating the elongation cycle is the hinging movement of the L1 stalk, a protein complex found on the large ribosomal subunit. In the last ten years, studies have conclusively found that the L1 stalk undergoes conformational changes associated with the release of deacylated tRNA from the E site, which contributes to the regulation of protein synthesis.
As such, the L1 stalk is vital for proper ribosome function and so for cell viability. The hinging of the L1 stalk contributes to the mechanism by which tRNAs are released from the ribosome during elongation. Thus, in combination with the ratchet-like rotation of the small ribosomal subunit (SSU), L1 stalk movement is a significant regulatory point in protein synthesis. The fact that the L1 stalk and SSU ratcheting rotation are both regulated by Elongation Factor-G (EF-G) binding suggests that the two movements are permissive to the function of the other. With the assistance of EF-G, the combination of these movements drives translation of mRNA forward. The EF-G regulatory mechanism is dependent on the state of the tRNA molecules present in the ribosomal E, P, and A sites. Thus, in addition to adapting the mRNA into an amino acid sequence, tRNA is also a co-factor in ribosomal protein synthesis. In effect, the substrate is a cofactor, a competitive inhibitor, and an allosteric inhibitor of mRNA translation.
This complex regulation surrounding the flexibility of the L1 stalk may be the foundation for the success of RNA from an evolutionary perspective. RNA is used in combination with ribosomal subunits in all living organisms to synthesize the proteins necessary for life. The structure and function of the L1 stalk is similar in bacterial, archaeal, and mammalian ribosomes, strongly suggesting convergent evolution for a highly successful translation mechanism. No better method is known to have been evolutionarily selected for in nature. It is, perhaps, so favoured because the L1 hinging movement allows the cell to accommodate its metabolic pathways to varying environmental conditions. Furthermore, the similarities in the L1 mechanism in all living organisms is significant from a research perspective, in that studies conducted on bacterial specimen, which tends to be much more efficient and economical, may be applied to all organisms, including humans. For example, drugs that very specifically target ribosomal function in humans may first be tested on bacteria for effectiveness, consistency, and side effects, among other parameters. Thus, the recent studies uncovering the details of L1 function and regulation are a vital step forward academically.