One of the
more fundamental mysteries in the evolution of Life concerns the emergence of
the translation release factors. Release factors are the proteins which severe
the terminal tRNA-aminoacyl bond at the ribosome, enabling the completed
protein chain to diffuse from the ribosome. Release factors accomplish this
task by adopting a structural shape that mimics the tRNA, allowing it to access
and interact with the stop codon in the ribosome. On gaining access to the
ribosome, the release factor catalyzes hydrolysis of the tRNA-aminoacyl bond by
coordinating a water molecule with an absolutely-conserved glumatine residue.
Despite this
crucial and universal function, no single release factor can be traced to the
last universal common ancestor (LUCA) of life: in fact, the principal release
factor proteins of the bacterial and archaeo-eukaryotic lineages belong to two
entirely distinct protein folds. Dueling parsimonious evolutionary scenarios
can account for this observation: 1) one of the two release factor folds was
found in the LUCA, and was later displaced in one of the lineages and 2) the
two versions emerged independently in the lineages, each displacing the
ancestral release factor. In the latter scenario, the release factor could have
been a tRNA or tRNA-related ribozyme, consistent with other RNA-world
hypothesis.
To throw
light on the question of early release factor diversification, we specifically
investigating the evolutionary history of the archaeo-eukaryotic release
factors (aeRF1s) [see Verma et al.]. Through this analysis, we identified a pair of novel clades
in the aeRF1 superfamily, both of which surprisingly had a substantial
bacterial component. One of these clades contained 4 families with an unusually
complicated evolutionary history: the earliest-branching family is found only
in archaea and retains the core architectural features of the classical
archaeal aeRF1s, suggesting it was an ancient duplication of the classical
versions. At some point, representatives from this family were transferred to a
terminally-differentiated bacterial lineage, eventually giving rise to two distinct
families. One of these families, found primarily in Bacteroidetes, was then
acquired early in the evolution of eukaryotes, giving rise to the final family
in the clade. This eukaryotic family is sporadically-distributed across several
lineages, but was fixed early in the crown group eukaryotes
(plants-fungi-amoebozoa-animals) as the central catalytic core of the
Vms1/ANKZF1-like proteins.
Through a collaboration with the Deshaies laboratory, this family was characterized in a recent publication in the Nature magazine as the key missing release factor of the ribosome quality control (RQC) pathway [Verma et al.], the pathway that rescues “jammed” ribosomes which are stalled on mRNA with the growing peptide chain still attached. We suspect, due to shared sequence and domain architectural features, that the prokaryotic families of this clade (named the VLRF1 clade for Vms1-like aeRF1 clade) are also likely to be involved in the clearance of stalled ribosomes.
The second
clade we identified contained a total of 14 previously unrecognized families
found across a diverse assortment of bacterial lineages (named the baeRF1 clade
for bacterial-aeRF1). Despite the monophyly of these families, a wide range of
structural, domain architectural, and sequence diversity is observed,
suggestive of considerable selective pressure being applied to these families.
Perhaps most notably, the characteristic loop region of the aeRF1 superfamily
which typically houses the active site glutamine residue varies tremendously in
length and content both across and within the baeRF1 families, many families
are even predicted to be catalytically inactive due to the lack of a
strongly-conserved glutamine residue. While these families remain functionally
uncharacterized, one strongly-conserved genomic contextual association was
consistently observed across several families: shared genome association with
an HPF-like ribosome hibernation factor. These domains are known to directly
interact with the translational machinery and induce conformational change in
the ribosome to promote the inactivation of ribosomes. The association between
baeRF1 and HPF-like domains could indicate that baeRF1 proteins play a
complementary role in inducing ribosome inactivation, potentially by occupying
the typical tRNA binding sites on the ribosome (consistent with the
inactivation of the enzyme in most families). Alternatively, the association
could act as a regulatory switch, with the baeRF1 displacing HPF and restoring
ribosome function. Given the rapidly-evolving features of the baeRF1 clade, it
seems likely that this function is tied to bacterial conflict. As such, baeRF1
could be activated in response to the detection of invasive elements,
potentially to prevent the element from hijacking the endogenous translation
machinery.
While these
findings speak to a previously poorly-understood complexity in the evolution of
the aeRF1 superfamily and resolves one of the last remaining mysteries of the
RQC pathway, ultimately little is revealed about the state of the release
factor in the LUCA. While it may be tempting to suggest that the VLRF1 and
baeRF1 clades represent the surviving remnants of a potential ancestral
bacterial aeRF1 presence that was displaced early in bacterial lineage by the
bacterial-specific release factor fold, our analysis indicates that both clades
likely emerged from later transfers from a classical archaeal aeRF1 progenitor.
The most
striking evolutionary finding from this analysis is the clear acquisition of
the eukaryotic Vms1/ANKZF1-like release factors from the Bacteroidetes lineage.
This observation adds to an increasing list of key eukaryotic factors which
have their direct antecedents in the Bacteriodetes, suggesting that an
important complement of genetic material in eukaryotes was likely inherited
early in eukaryotic evolution from a Bacteroidetes symbiont, independent of the
α-proteobacterial mitochondrial progenitor.
