Do viroids and RNA viruses derive from a system that exchanges genetic information between eukaryotic cells?

The simple emergence of complex molecular function

At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge de novo with relative ease. At early times of molecular evolution, random polymers could have sufficed for the appearance of incipient chemical activity, while the cellular environment harbours a myriad of proto-functional molecules. The emergence of function is facilitated by several mechanisms intrinsic to molecular organization, such as redundant mapping of sequences into structures, phenotypic plasticity, modularity or cooperative associations between genomic sequences. It is the availability of niches in the molecular ecology that filters new potentially functional proposals. New phenotypes and subsequent levels of molecular complexity could be attained through combinatorial explorations of currently available molecular variants. Natural selection does the rest. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Virus-associated small satellite RNAs and viroids display similarities in their replication strategies

Since the discovery of non-coding, small, highly structured, satellite RNAs (satRNAs) and viroids as subviral pathogens of plants , have been of great interest to molecular biologists as possible living fossils of pre-cellular evolution in an RNA world. Despite extensive studies performed in the last four decades, there is still mystery surrounding the origin and evolutionary relationship between these subviral pathogens. Recent technical advances revealed some commonly shared replication features between these two subviral pathogens. In this review, we discuss our current perception of replication and evolutionary origin of these petite RNA pathogens.

Intercellular and systemic movement of RNA silencing signals

In most eukaryotes, double-stranded RNA is processed into small RNAs that are potent regulators of gene expression. This gene silencing process is known as RNA silencing or RNA interference (RNAi) and, in plants and nematodes, it is associated with the production of a mobile signal that can travel from cell-to-cell and over long distances. The sequence-specific nature of systemic RNA silencing indicates that a nucleic acid is a component of the signalling complex. Recent work has shed light on the mobile RNA species, the genes involved in the production and transport of the signal. This review discusses the advances in systemic RNAi and presents the current challenges and questions in this rapidly evolving field.

Avsunviroidae family: viroids containing hammerhead ribozymes

This chapter focuses on the second viroid family, whose members are also referred to as hammerhead viroids, taking into account their most outstanding feature. If the word “small” is the first to come to mind when considering viroids, perhaps the second word is “hammerhead,” because this class of ribozymes, which because of its structural simplicity has an enormous biotechnological potential, is described in avocado sunblotch viroid (ASBVd) as well as in a viroid-like satellite RNA. The most outstanding feature of the Avsunviroidae members is their potential to adopt hammerhead structures in both polarity strands and to self-cleave in vitro accordingly. Viroids differ from viruses not only in their genome size but also in other fundamental aspects, prominent among which is the lack of messenger activity of both viroid RNAs and their complementary strands.

Entropic DNA

The presence of mobile genetic elements without apparent biological function within genomes requires explanation. It is argued that consideration of DNA as an open thermodynamic system leads to the simple hypothesis that mobile genetic material increases the internal entropy thereby lowering the free energy of the DNA relative to DNA of the same size. This phenomenon enhances the survival of such sequences by simple structural stabilization. The consequences of this idea are discussed in terms of the proposed Bekenstein limit to the entropy to energy ratio of thermodynamic systems and biological entropy/information flow.

Identification of a small RNA containing the trypanosome spliced leader: a donor of shared 5' sequences of trypanosomatid mRNAs?

The 35 nucleotide spliced leader (SL) sequence is found on the 5' end of numerous trypanosome mRNAs, yet the tandemly organized reiteration units encoding this leader are not detectably linked to any of these structural genes. Here we report the presence of a class of discrete small SL RNA molecules that are derived from the genomic SL reiteration units of Trypanosoma brucei, Trypanosoma cruzi, and Leptomonas collosoma. These small SL RNAs are 135, 105, and 95 nucleotides, respectively, and contain a 5'-terminal SL or SL-like sequence. S1 nuclease analyses demonstrate that these small SL RNAs are transcribed from continuous sequence within the respective SL reiteration units. With the exception of the SL sequence and a concensus donor splice site immediately following it, these small RNAs are not well conserved. We suggest that the small SL RNAs may function as a donor of the SL sequence in an intermolecular process that places the SL at the 5' terminus of many trypanosomatid mRNAs.

Homologous proteins encoded by yeast mitochondrial introns and by a group of RNA viruses from plants

Hensgens et al. (1983a) have demonstrated the existence of distant homology (averaging 19.6%) between the central sections of seven proteins encoded by introns (and one product of an apparently independent gene) in yeast mitochondrial DNA. The homologous regions are typically segments of about 115 amino acids within open reading frames of about 10(3) bases. Genetic studies indicate that at least two of these proteins are required for the splicing of mitochondrial transcripts. This paper reports that two distantly related proteins of Mr 30,000 that are encoded by different strains of tobacco mosaic virus both contain central sections whose amino acid sequences are 15% to 23% identical in a single alignment to those of one group of four intron-encoded proteins, and possess certain groups of conserved residues also characteristic of the mitochondrial proteins. Genetic studies implicate these proteins in the spreading of viral lesions. While this level of identity cannot establish conclusively that the proteins are related, it suggests the possibility of a functional and/or evolutionary connection that would, if borne out, have important implications.