When bacterial cells run out of nutrients, they enter stationary phase and downregulate protein synthesis. Several processes mediate this transition. For instance, in E. coli, 70S ribosomes form 90S dimers upon binding with a small 6.5 kDa protein, ribosome modulation factor RMF. These intermediate ribosome dimers can subsequently bind a hibernation promotion factor (the 10.8 kDa protein, HPF) molecule to form a mature 100S ribosomal particle, in which the dimerization interface is made by the two 30S subunits of the two participating ribosomes. The ribosome dimers represent a hibernation state and are translationally inactive. A third protein that can bind to ribosomes when E. coli cells enter the stationary phase is YfiA (previously known as RaiA). HPF and YfiA are structurally similar, and both proteins can bind to the catalytic A- and P-sites of the ribosome. RMF blocks ribosome binding to mRNA by preventing interaction of the messenger with 16S rRNA. When bound to the ribosomes the C-terminal tail of E. coli YfiA interferes with the binding of RMF, thus preventing dimerization and resulting in the formation of translationally inactive monomeric 70S ribosomes.
In addition to ribosome dimerization, the joining of the two ribosomal subunits can be blocked by RsfS (formerly called RsfA or YbeB). RsfS binds to L14, a protein of the large ribosomal subunit, and thereby blocks joining of the small subunit to form a functional 70S ribosome, slowing down or blocking translation entirely. 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). However, it is not known yet how the expression or activity of RsfS is regulated.
Another ribosome-dissociation factor in Escherichia coli is HflX, previously a GTPase of unknown function. 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.