Abstract
The evolution of release factors catalyzing the hydrolysis of the final peptidyl-tRNA bond and the release of the polypeptide from the ribosome has been a longstanding paradox. While the components of the translation apparatus are generally well-conserved across extant life, structurally unrelated release factor peptidyl hydrolases (RF-PHs) emerged in the stems of the bacterial and archaeo-eukaryotic lineages. We analyze the diversification of RF-PH domains within the broader evolutionary framework of the translation apparatus. Thus, we reconstruct the possible state of translation termination in the Last Universal Common Ancestor with possible tRNA-like terminators. Further, evolutionary trajectories of the several auxiliary release factors in ribosome quality control (RQC) and rescue pathways point to multiple independent solutions to this problem and frequent transfers between superkingdoms including the recently characterized ArfT, which is more widely distributed across life than previously appreciated. The eukaryotic RQC system was pieced together from components with disparate provenance, which include the long-sought-after Vms1/ANKZF1 RF-PH of bacterial origin. We also uncover an under-appreciated evolutionary driver of innovation in rescue pathways: effectors deployed in biological conflicts that target the ribosome. At least three rescue pathways (centered on the prfH/RFH, baeRF-1, and C12orf65 RF-PH domains), were likely innovated in response to such conflicts.
Highlights
The translation apparatus includes the most conserved cellular proteins and RNAs that provide the strongest evidence for the shared ancestry of all life forms (Figure 1)
In the archaeo-eukaryotic lineage the central catalytic aeRF-1 domain is sandwiched between the N-terminal stop-codon-recognition domain of the archaeo-eukaryotic lineage and the C-terminal Pelota domain (which often contains a further zinc-ribbon domain inserted into it [24,25,26] (Figure 2E), a widely-distributed domain which binds
The bRF-PH catalytic domain is inserted into the corbeionfdtshsepbeacciftiecrRiaNl sAtospe-ccoonddoanry-restcrougcntuitrieosn[d27o,m28a]i.nIn[2c0o]n. tTroasgte, tthheerb, tRhFis-PcHomcabtianleydticmdoodmualeinisisfuinsesedrttoedthe N-tifenurtsmoedtihnteaolctoαhre-ehNeolf-itcteharelmGbinaTcaPtleaαrsi-eah-leinsltitcoeaprla-GccotTidnPogansd-ero-eimcnotaegirnnaict[it2oi9nn,g3d0do]om(mFaiaigniun[r2[e2092].,F3T)0.o]Tg(eFhtiehgecuorr,entvh2eFisr)g.cTeonmhcebecintooendvaemcrogomednpucaleertaiosble thraeec-odmompaarianbalercthhirteeec-tduoremianinthaercRhFi-tPecHtusruebiunntihtse oRfFb-PotHh tshuebubnaicttseroifalbaonthd tahrechbaaecote-eriuakl aarnydotaicrclhinaeeaog- es haseubkeaernyoptrioc ploinseeadgetos hhaavs ebreeesnulpterdopforsoemd tthoe hsaevleectrievseupltreedssfuroremtothaedosepltecsttirvuectpurreesssumreimtoickaidnogptthe tRNstAru[c2tu4,r3e1s,m32i]m(Ficikgiunrget2hEe,tFR).NA [24,31,32] (Figure 2E,F)
Summary
The translation apparatus includes the most conserved cellular proteins and RNAs that provide the strongest evidence for the shared ancestry of all life forms (Figure 1). The actual ribosomal decoding of mRNA requires conserved protein factors observed at each of the core steps of translation: initiation, elongation, and release (Figure 1) These factors are primarily GTPases, which act as proofreading switches to ensure accurate decoding of the genetic code. The bacteria initiate recycling via the evolutionarily unrelated ribosome recycling factor (RRF), which instead contains a conserved domain shared with several amino-acyl tRNA synthetases [23] These phyletic patterns of the RF-PHs, the GTPases that load them on to the ribosome, and the recycling factors, are atypical for components of the core apparatus that perform essential functions in translation. We synthesize this information to provide plausible explanations and hypotheses relating to the above questions
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