Ancient RNA world

Based on the modern concept of multiplicity of RNA functions, certain new mechanisms, which could have played a key role in the origin and evolution of the ancient RNA world, are discussed. In particular, the reaction of spontaneous transesterification of polyribonucleotides, which was discovered by A.B. Chetverin and colleagues, could result in elongation of short initial oligoribonucleotides and produce sequence variants for further natural selection of accidentally arising functionally active molecules. Further, the formation of mixed molecular colonies of RNA on moist solid media, such as clays, could have provided compartmentation of functional RNA ensembles in the absence of envelopes or membranes, which were necessary for further evolution of the RNA world. The systematic exponential enrichment of the RNA population with functionally the best molecules because of alternating dissolution of colonies due to flooding and formation of new colonies due to drying in ancient pools (“primordial natural SELEX”) could be critical for the evolutionary process in the RNA world.     

12 Reconstructing the RNA world

A critical event in the origin of life is thought to have been the emergence of an RNA molecule capable of self-replication as well as mutation, and hence evolution towards ever more efficient replication. As this primordial replicase appears to have been lost in time, we use synthetic biology to build modern-day “Doppelgangers” of the ancestral replicase to reconstruct and study their properties in an effort to learn more about life’s first genetic system. I will discuss our progress in the engineering and evolution of RNA polymerase ribozymes as well as the potential role that structured media such as the eutectic phase of water–ice may have played in the emergence of RNA self-replication.     

Fitting peptides into the RNA world

The structures of several peptide-RNA complexes have been reported in the past year, underscoring the diverse nature of RNA structure and protein interactions. In general, specific peptide conformations are stabilized by the surrounding RNA framework; this is strikingly similar to how peptides are stabilized upon interaction with proteins.     

Expanding the plant non-coding RNA world

Journal of Plant Research - Small nuclear RNA (snRNA) represents a distinct class of non-coding RNA molecules. As these molecules have fundamental roles in RNA metabolism, including pre-mRNA...     

Constructing an RNA world

A popular theory of life’s origins states that the first biocatalysts were not made of protein but were made of RNA or a very similar polymer. Experiments are beginning to confirm that the catalytic abilities of RNA are compatible with this ‘RNA world’ hypothesis. For example, RNA can synthesize short fragments of RNA in a template-directed fashion and promote formation of peptide, ester and glycosidic linkages. However, no known activity fully represents one presumed by the ‘RNA world’ theory, and reactions such as oxidation and reduction have yet to be demonstrated. Filling these gaps would place the hypothesis on much firmer ground and provide components for building minimal forms of RNA-based cellular life.     

Constructing an RNA world

A popular theory of life’s origins states that the first biocatalysts were not made of protein but were made of RNA or a very similar polymer. Experiments are beginning to confirm that the catalytic abilities of RNA are compatible with this ‘RNA world’ hypothesis. For example, RNA can synthesize short fragments of RNA in a template-directed fashion and promote formation of peptide, ester and glycosidic linkages. However, no known activity fully represents one presumed by the ‘RNA world’ theory, and reactions such as oxidation and reduction have yet to be demonstrated. Filling these gaps would place the hypothesis on much firmer ground and provide components for building minimal forms of RNA-based cellular life.     

Exiting an RNA world

The RNA world hypothesis gains support from the in vitro evolution of a bifunctional ribozyme that can recognize an activated glutaminyl ester and subsequently aminoacylate a tRNA molecule.     

Constructing an RNA world

A popular theory of life’s origins states that the first biocatalysts were not made of protein but were made of RNA or a very similar polymer. Experiments are beginning to confirm that the catalytic abilities of RNA are compatible with this ‘RNA world’ hypothesis. For example, RNA can synthesize short fragments of RNA in a template-directed fashion and promote formation of peptide, ester and glycosidic linkages. However, no known activity fully represents one presumed by the ‘RNA world’ theory, and reactions such as oxidation and reduction have yet to be demonstrated. Filling these gaps would place the hypothesis on much firmer ground and provide components for building minimal forms of RNA-based cellular life.     

Coenzymes, viruses and the RNA world

The results of a detailed bioinformatic search for ribonucleotidyl coenzyme biosynthetic sequences in DNA- and RNA viral genomes are presented. No RNA viral genome sequence available as of April 2011 appears to encode for sequences involved in coenzyme biosynthesis. In both single- and double-stranded DNA viruses a diverse array of coenzyme biosynthetic genes has been identified, but none of the viral genomes examined here encodes for a complete pathway. Although our conclusions may be constrained by the unexplored diversity of viral genomes and the biases in the construction of viral genome databases, our results do not support the possibility that RNA viruses are direct holdovers from an ancient RNA/protein world. Extrapolation of our results to evolutionary epochs prior to the emergence of DNA genomes suggest that during those early stages living entities may have depended on discontinuous genetic systems consisting of multiple small-size RNA sequences.     

RNA interference: it's a small RNA world

Short RNAs regulate gene expression in many species. Some are generated from any double-stranded RNA and degrade complementary RNAs; others are encoded by genes and repress specific mRNAs. Both, it turns out, are processed and handled by similar proteins. These pathways offer a glimpse into a world of small RNAs.     

RNA world and its evolution

The early idea of A. N. Belozersky on the precedence of RNA in the origin of life on Earth is developed. Basing on the present knowledge of functional omnipotence of RNA, the author considers three novel mechanisms that could play a critical role in the origin and evolution of the ancient RNA world: (1) the reaction of spontaneous transesterification of polyribonucleotides in aqueous media, discovered by A.B. Chetverin, which could result in elongation of primary short oligoribonucleotides and generation of sequence variants for subsequent selection; (2) compartmentation of functional RNA ensembles in the form of mixed molecular colonies on moist solid surfaces, in the absence of membranes and any other coats; (3) systematic exponential enrichment of RNA population in functionally "the best" molecules by means of alternately dissolving the colonies upon flooding and forming new ones upon drying a pool ("primordial natural SELEX").     

Exploring the post-transcriptional RNA world with DNA microarrays

Genomic approaches are valuable for understanding the complex layer of gene regulation that involves the control of RNA processing, localization and stability. Recent work provides a prime example of the power of unbiased microarray-based methods to discover unexpected functions for proteins in the RNA world. The challenges ahead relate to extending such approaches to larger genomes and to integrating this type of information with that generated by standard expression profiling.