Abstract
BackgroundIt is now believed that in the origin of life, proteins should have been "invented" in an RNA world. However, due to the complexity of a possible RNA-based proto-translation system, this evolving process seems quite complicated and the associated scenario remains very blurry. Considering that RNA can bind amino acids with specificity, it has been reasonably supposed that initial peptides might have been synthesized on "RNA templates" containing multiple amino acid binding sites. This "Direct RNA Template (DRT)" mechanism is attractive because it should be the simplest mechanism for RNA to synthesize peptides, thus very likely to have been adopted initially in the RNA world. Then, how this mechanism could develop into a proto-translation system mechanism is an interesting problem.Presentation of the hypothesisHere an explanation to this problem is shown considering the principle of "replication parsimony" --- genetic information tends to be utilized in a parsimonious way under selection pressure, due to its replication cost (e.g., in the RNA world, nucleotides and ribozymes for RNA replication). Because a DRT would be quite long even for a short peptide, its replication cost would be great. Thus the diversity and the length of functional peptides synthesized by the DRT mechanism would be seriously limited. Adaptors (proto-tRNAs) would arise to allow a DRT's complementary strand (called "C-DRT" here) to direct the synthesis of the same peptide synthesized by the DRT itself. Because the C-DRT is a necessary part in the DRT's replication, fewer turns of the DRT's replication would be needed to synthesize definite copies of the functional peptide, thus saving the replication cost. Acting through adaptors, C-DRTs could transform into much shorter templates (called "proto-mRNAs" here) and substitute the role of DRTs, thus significantly saving the replication cost. A proto-rRNA corresponding to the small subunit rRNA would then emerge to aid the binding of proto-tRNAs and proto-mRNAs, allowing the reduction of base pairs between them (ultimately resulting in the triplet anticodon/codon pair), thus further saving the replication cost. In this context, the replication cost saved would allow the appearance of more and longer functional peptides and, finally, proteins. The hypothesis could be called "DRT-RP" ("RP" for "replication parsimony").Testing the hypothesisThe scenario described here is open for experimental work at some key scenes, including the compact DRT mechanism, the development of adaptors from aa-aptamers, the synthesis of peptides by proto-tRNAs and proto-mRNAs without the participation of proto-rRNAs, etc. Interestingly, a recent computer simulation study has demonstrated the plausibility of one of the evolving processes driven by replication parsimony in the scenario.Implication of the hypothesisAn RNA-based proto-translation system could arise gradually from the DRT mechanism according to the principle of "replication parsimony" --- to save the replication cost of RNA templates for functional peptides. A surprising side deduction along the logic of the hypothesis is that complex, biosynthetic amino acids might have entered the genetic code earlier than simple, prebiotic amino acids, which is opposite to the common sense. Overall, the present discussion clarifies the blurry scenario concerning the origin of translation with a major clue, which shows vividly how life could "manage" to exploit potential chemical resources in nature, eventually in an efficient way over evolution.ReviewersThis article was reviewed by Eugene V. Koonin, Juergen Brosius, and Arcady Mushegian.
Highlights
It is believed that in the origin of life, proteins should have been “invented” in an RNA world
Proteinacious components involved in the modern translation system, including those in the ribosome, aminoacyl-tRNA synthetases (AARSs), and translation factors, have been either evidenced or implied to be absent originally [10,11,12,13]
The present hypothesis (DRTRP), is formulated in such a way, by which I believe would be beneficial both for a comprehensive understanding on its logic and for a detailed design of experiments to test it. Another point that should be noted here is that though the present hypothesis viewpoints are similar or overlapped with some previous hypotheses on the original sources of proto-tRNAs, proto-mRNAs and proto-rRNAs, its viewpoints on the direct advantages of their emergence is unique. All these advantages are believed to be associated with one reason, namely, to save the replication cost for the RNA templates directing the synthesis of functional peptides
Summary
The problem of the origin of protein synthesis in the RNA world As it was stated by Crick et al, “the origin of protein synthesis is a notoriously difficult problem” [1]. Another point that should be noted here is that though the present hypothesis viewpoints are similar or overlapped with some previous hypotheses on the original sources of proto-tRNAs, proto-mRNAs and proto-rRNAs (see the superscript “▲“ in Table 1), its viewpoints on the direct advantages of their emergence is unique Most importantly, all these advantages (except that of proto-lsrRNAs) are believed to be associated with one reason, namely, to save the replication cost for the RNA templates directing the synthesis of functional peptides. All these advantages (except that of proto-lsrRNAs) are believed to be associated with one reason, namely, to save the replication cost for the RNA templates directing the synthesis of functional peptides This “replication parsimony” principle might have figured the major clue within the whole scenario on the origin of translation. We could see the extant genetic code table — complex amino acids and their cognate anticodons were often observed at the RNA-aa (protein) binding interface, but for simple amino acids, this is not the case
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
