Bacterial translation
The SD sequence is recognized by an complementary "anti-SD" region on the 16S rRNA component of the 30S subunit.
In the canonical model, the 30S ribosome is first joined up with the three initiation factors, forming an unstable "pre-initiation complex".
The mRNA then pairs up with this anti-SD region, causing it to form a double-stranded RNA structure, roughly positioning the start codon at the P site.
Well-known coding regions that do not have AUG initiation codons are those of lacI (GUG)[2] and lacA (UUG) in the E. coli lac operon.
The deacylated tRNA at the E site is released from the ribosome during the next A-site occupation by an aminoacyl-tRNA again facilitated by EF-Tu.
The translation machinery works relatively slowly compared to the enzyme systems that catalyze DNA replication.
Testing and rejecting incorrect aminoacyl-tRNA molecules takes time and slows protein synthesis.
This is not possible in eukaryotes because transcription and translation are carried out in separate compartments of the cell (the nucleus and cytoplasm).
These factors trigger the hydrolysis of the ester bond in peptidyl-tRNA and the release of the newly synthesized protein from the ribosome.
[16] When bacterial cells run out of nutrients, they enter stationary phase and downregulate protein synthesis.
[21] A third protein that can bind to ribosomes when E. coli cells enter the stationary phase is YfiA (previously known as RaiA).
[22] HPF and YfiA are structurally similar, and both proteins can bind to the catalytic A- and P-sites of the ribosome.
RsfS proteins are found in almost all eubacteria (but not archaea) and homologs are present in mitochondria and chloroplasts (where they are called C7orf30 and iojap, respectively).
Zhang et al. (2015) showed that HflX is a heat shock–induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes.
The N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation.
Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock and possibly other stress conditions.
They exploit the differences between prokaryotic and eukaryotic translation mechanisms to selectively inhibit protein synthesis in bacteria without affecting the host.
