Archaeological approaches to RNA virus evolution

• Published in: The Journal of physiology 2024-06, Vol.602 (11), p.2469-2478
• Main Authors: Ariza‐Mateos, Ascensión, Briones, Carlos, Perales, Celia, Sobrino, Francisco, Domingo, Esteban, Gómez, Jordi
• Format: Article
• Language: English
• Subjects: Amino acid sequence; Animals; Archaeology; Enzymes; Evolution; Evolution, Molecular; Humans; Information processing; mRNA; palimpsest; Phylogeny; Ribozymes; RNA archaeology; RNA virus; RNA viruses; RNA Viruses - genetics; RNA, Viral - chemistry; RNA, Viral - genetics; RNase P; RNase‐III; Structure-function relationships; UV‐C‐light; viral‐quasispecies
• ISSN: 0022-3751; 1469-7793
• DOI: 10.1113/JP284416

Studies with RNA enzymes (ribozymes) and protein enzymes have identified certain structural elements that are present in some cellular mRNAs and viral RNAs. These elements do not share a primary structure and, thus, are not phylogenetically related. However, they have common (secondary/tertiary) structural folds that, according to some lines of evidence, may have an ancient and common origin. The term ‘mRNA archaeology’ has been coined to refer to the search for such structural/functional relics that may be informative of early evolutionary developments in the cellular and viral worlds and have lasted to the present day. Such identified RNA elements may have developed as biological signals with structural and functional relevance (as if they were buried objects with archaeological value), and coexist with the standard linear information of nucleic acid molecules that is translated into proteins. However, there is a key difference between the methods that extract information from either the primary structure of mRNA or the signals provided by secondary and tertiary structures. The former (sequence comparison and phylogenetic analysis) requires strict continuity of the material vehicle of information during evolution, whereas the archaeological method does not require such continuity. The tools of RNA archaeology (including the use of ribozymes and enzymes to investigate the reactivity of the RNA elements) establish links between the concepts of communication and language theories that have not been incorporated into knowledge of virology, as well as experimental studies on the search for functionally relevant RNA structures. figure legend Molecular tools and concepts from phylosophy of language and archaeology for the search of ancient RNA elements in the current cell.