Recent findings in the modern RNA world

Abstract

It is assumed that modern life forms arose from a molecular ancestor in which RNA molecules both stored genetic information and catalyzed biochemical reactions. In modern cells, these functions are carried out, respectively, by DNA and proteins, but diverse cellular RNAs are also involved in key cellular functions. In this paper, we review the cellular RNAs that are ubiquitous and/or that perform essential biological functions, and we discuss the evolutionary relationships of such RNAs with a prebiotic RNA world. This unexpected biological diversity of cellular RNAs and the crucial functions they perform in cellular metabolism demonstrate the complexity of an RNA-driven metabolism in an ancient RNA world and in modern life. Cellular RNAs are involved in translation (tRNA and rRNA) but also in ribosome maturation (snoRNA) and more generally in RNA processing (snRNA and snoRNA), replication (telomerase RNA), editing, protein translocation (SRP RNA), cellular transport (vRNA) and translation quality control (tmRNA). In addition, the function of many other cellular RNAs has not yet been determined. Future investigations of RNA function will allow us to better understand not only early evolutionary biological processes but also the central metabolism of modern cells.

When transfer‐messenger RNA scars reveal its ancient origins

“…As a proof of their links to the ancient times, such molecules would need to be catalytic, ubiquitous, and/or central to some aspect of metabolism. 38,39 Among the numerous modern RNA molecules that fulfill these criteria, tmRNA stands out. It is a powerful and central component, and able to play the two main roles (tRNA and mRNA) indispensable to the emergence of ribosome-driven protein synthesis.…”

Genome-wide identification and evolutionary analysis of long non-coding RNAs in cereals

“…In addition, considering that their ubiquity and central place in cellular metabolism, these "relics from the RNA world" (Jeffares, Poole et al 1998) are great models of RNA evolution. The fact that small ncRNAs derived from a common ancestry may share short conserved sequence domains and also well-conserved secondary structure elements, rather than strong sequence homologies (Meli, Albert-Fournier et al 2001), stresses the importance of RNA secondary structure in functional continuity during evolution.…”

“…Given "the RNA world" assumption and structural conservation shared by central small ncRNAs (Jeffares, Poole et al 1998;Meli, Albert-Fournier et al 2001), we expect that the natural selection pressure has been reflected on lncRNAs as conserved elements and structures.…”

“…An RNA sequence is malleable to fold into a number of combinations of thermodynamiccally stable helices; vice versa, a similar structure may adopt quite distinct genotypes (Wan, Kertesz et al 2011). For example, AT-AC and GT-AG snRNAs share well-conserved secondary structure elements critical for activity even if there is no strong homology shown at the sequence level (Meli, Albert-Fournier et al 2001). As mentioned before, in contrast to the iconic tRNA cloverleaf structure, its nucleotide sequence may vary up to over 90% (Meli, Albert-Fournier et al 2001;Mercer and Mattick 2013).…”

The Dual Life of RNA

“…RNA directs protein synthesis and some RNA molecules, the ribozymes, can, like proteins, have catalytic activity. RNA is involved in many key cellular functions in all living cells and it has been argued that RNA played a predominant role in early life (Meli et al 2001). There are several lines of evidence in support of this.…”