RNA-based evolution

In accordance with the central dogma of molecular biology, RNA passes information between the DNA of a genome and the proteins expressed within an organism.[1] Therefore, from an evolutionary standpoint, a mutation within the DNA bases results in an alteration of the RNA transcripts, which in turn leads to a direct difference in phenotype. RNA is also believed to have been the genetic material of the first life on Earth. The role of RNA in the origin of life is best supported by the ease of forming RNA from basic chemical building blocks (such as amino acids, sugars, and hydroxyl acids) that were likely present 4 billion years ago.[2][3] Molecules of RNA have also been shown to effectively self-replicate, catalyze basic reactions, and store heritable information.[4][5] As life progressed and evolved over time only DNA, which is much more chemically stable than RNA, could support large genomes and eventually took over the role as the major carrier of genetic information.[6]

Single-stranded RNA molecules can single handedly fold into complex structures. The molecules fold into secondary and tertiary structures by intramolecular base pairing.[7] There is a fine dynamic of disorder and order that facilitate an efficient structure formation. RNA strands form complementary base pairs. These complementary strands of RNA base pair with another strand, which results in a three-dimensional shape from the paired strands folding in on itself. The formation of the secondary structure results from base pairing by hydrogen bonds between the strands, while tertiary structure results from folding of the RNA. The three-dimensional structure consists of grooves and helices.[8] The formation of these complex structure gives reason to suspect that early life could have formed by RNA.

Research within the past decade has shown that strands of RNA are not merely transcribed from regions of DNA and translated into proteins. Rather RNA has retained some of its former independence from DNA and is subject to a network of processing events that alter the protein expression from that bounded by just the genomic DNA.[9] Processing of RNA influences protein expression by managing the transcription of DNA sequences, the stability of RNA, and the translation of messenger RNA.

In Earth's early developmental history RNA was the primary substance of life. RNA served as a blueprint for genetic material and was the catalyst to multiply said blueprint. Currently RNA acts by forming proteins. protein enzymes carry out catalytic reactions. RNAs are critical in gene expression and that gene expression depends on mRNA, rRNA, and tRNA.[15] There is a relationship between protein and RNAs. This relationship could suggest that there is a mutual transfer of energy or information.[16] In vitro RNA selection experiments have produced RNA that bind tightly to amino acids. It has been shown that the amino acids recognized by the RNA nucleotide sequences had a disproportionately high frequency of codons for said amino acids. There is a possibility that the direct association of amino acids containing specific RNA sequences yielded a limited genetic code.[17]

Most RNA processing events work in concert with one another and produce networks of regulating processes that allow a greater variety of proteins to be expressed than those strictly directed by the genome.[9] These RNA processing events can also be passed on from generation to generation via reverse transcription into the genome.[9][18] Over time, RNA networks that produce the fittest phenotypes will be more likely to be maintained in a population, contributing to evolution. Studies have shown that RNA processing events have especially been critical with the fast phenotypic evolution of vertebrates—large jumps in phenotype explained by changes in RNA processing events.[19] Human genome searches have also revealed RNA processing events that have provided significant “sequence space for more variability”.[20] On the whole, RNA processing expands the possible phenotypes of a given genotype and contributes to the evolution and diversity of life.

RNA virus evolution appears to be facilitated by a high mutation rate caused by the lack of a proofreading mechanism during viral genome replication.[21] In addition to mutation, RNA virus evolution is also facilitated by genetic recombination.[21] Genetic recombination can occur when at least two RNA viral genomes are present in the same host cell and has been studies in numerous RNA viruses.[22] RNA recombination appears to be a major driving force in viral evolution among Picornaviridae ((+)ssRNA) (e.g. poliovirus).[23] In the Retroviridae ((+)ssRNA)(e.g. HIV), damage in the RNA genome appears to be avoided during reverse transcription by strand switching, a form of genetic recombination.[24][25][26] Recombination also occurs in the Coronaviridae ((+)ssRNA) (e.g. SARS).[27] Recombination in RNA viruses appears to be an adaptation for coping with genome damage.[22] Recombination can occur infrequently between animal viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans.[27]

• RNA world