Ribozymes: Flexible molecular devices at work

• Published in: Biochimie 2011-11, Vol.93 (11), p.1998-2005
• Main Authors: Talini, Giulia, Branciamore, Sergio, Gallori, Enzo
• Format: Article
• Language: English
• Subjects: Bifunctional ribozymes; Catalysis; DNA; Evolution; Evolution, Molecular; Gene expression; Gene Expression Regulation; Gene regulation; Humans; Inverted Repeat Sequences - genetics; Molecular Structure; Nucleic Acid Conformation; Nucleotide sequence; Plasticity; Riboswitch - genetics; Riboswitches; Ribozymes; RNA; RNA plasticity; RNA World; RNA, Catalytic - chemistry; RNA, Catalytic - genetics; RNA, Catalytic - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA-Binding Proteins - genetics; Structure-function relationships
• ISSN: 0300-9084; 1638-6183
• DOI: 10.1016/j.biochi.2011.06.026

The discovery of ribozymes, RNAs with catalytic activity, revealed the extraordinary characteristic of this molecule, and corroborated the idea that RNA was the first informative polymer. The “RNA world” hypothesis asserts that the DNA/RNA/PROTEIN world arose from an earlier RNA world in which were present only RNA molecules able to perform both of the two functions performed separately by DNA and proteins in the present-day cells: the ability to transfer genetic information and to carry out catalytic activity. The catalytic properties of ribozymes are exclusively due to the capacity of RNA molecules to assume particular structures. Moreover, the structural versatility of RNA can allow to a single RNA sequence to fold in more than one structure, able to perform more than one function. In the first part of this work we will discuss the RNA plasticity, focusing on “bifunctional” ribozymes isolated by in vitro selection experiments, and on the consequences of this plasticity in the prospective of the emergence of new specific functions. The possibility that one sequence could have more than one structure/function, greatly increase the evolutionary potential of RNA, and the capacity of RNA to switch from a structure/function to another is probably one of the reasons of the evolutionary success also in modern-day cells. Naturally occurring ribozymes discovered in contemporary cells, demonstrate the crucial role that ribozymes still have in the modern protein world. In the second part of this paper we will discuss the capacity of natural ribozymes to modulate gene expression making use of their exclusive catalytic properties. Moreover, we will consider the possibility of their ancient origin. ► We reviewed “bifunctional” ribozymes isolated by in vitro selection experiments. ► RNA plasticity in the prospective of the emergence of new specific functions. ► Capacity of natural occurring ribozymes to modulate gene expression in present-day cells. ► Present day ribozymes as relics of RNA World.