Abstract
A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells.
Highlights
IntroductionIt has become customary to refer as “RNA relics” or “molecular fossils” to the several kinds of RNA (or more generally XNAs with X for the D of DNA, the R of RNA, or the P of PNA, the peptide nucleotidic acids potential precursors of the RNAs in the primordial forms of life) sequences that perform highly preserved functions and appear almost everywhere in the tree of life
It has become customary to refer as “RNA relics” or “molecular fossils” to the several kinds of RNA sequences that perform highly preserved functions and appear almost everywhere in the tree of life
The calculated ring AL would be a good candidate of plausible primitive transfer RNAs (tRNAs) (Figure 2), and along with the other similar circular RNAs found through stability criteria, it might have been the raw material for the first biological systems
Summary
It has become customary to refer as “RNA relics” or “molecular fossils” to the several kinds of RNA (or more generally XNAs with X for the D of DNA, the R of RNA, or the P of PNA, the peptide nucleotidic acids potential precursors of the RNAs in the primordial forms of life) sequences that perform highly preserved functions and appear almost everywhere in the tree of life. By base-pairing with mRNAs, miRs (and more generally small RNAs) inhibit their related functions (e.g., translation for mRNAs) during a lapse of time, depending on the force of hybridization This is what is called the 'silencing' process. These small RNAs act by base-pairing with target mRNAs, resulting in changes in the translation and stability of these mRNAs. miRs themselves can be down-regulated, increasing the complexity of the regulatory loops in which the are implied. This stereochemical mechanism furnishes an understanding for a coupled emergence of the genetic–triplet–code and peptide synthesis
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