RNA-based evolution

RNA-based evolution is a theory that posits that RNA is not merely an intermediate between DNA and proteins, but rather a far more dynamic and independent role-player in determining phenotype. By regulating the transcription of DNA sequences, the stability of RNA, and the capability of messenger RNA to be translated, RNA processing events allow for a diverse array of proteins to be synthesized from a single gene. Since RNA processing is heritable, it is subject to natural selection and contributes to the evolution and diversity of most eukaryotic organisms.

Role of RNA in conventional 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]

Variability of RNA processing

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.[7] Processing of RNA influences protein expression by managing the transcription of DNA sequences, the stability of RNA, and the translation of messenger RNA.

Alternative splicing

Splicing is the process by which non-coding regions of RNA are removed. The number and combination of splicing events varies greatly based on differences in transcript sequence and environmental factors. Variation in phenotype caused by alternative splicing is best seen in the sex determination of D. melanogaster. The Tra gene, determinant of sex, in male flies becomes truncated as splicing events fail to remove a stop codon that controls the length of the RNA molecule. In others the stop signal is retained within the final RNA molecule and a functional Tra protein is produced resulting in the female phenotype.[8] Thus, alternative RNA splicing events allow differential phenotypes, regardless of the identity of the coding DNA sequence.

RNA stability

Phenotype may also be determined by the number of RNA molecules, as more RNA transcripts lead to a greater expression of protein. Short tails of repetitive nucleic acids are often added to the ends of RNA molecules in order to prevent degradation, effectively increasing the number of RNA strands able to be translated into protein.[9] During mammalian liver regeneration RNA molecules of growth factors increase in number due to the addition of signaling tails.[10] With more transcripts present the growth factors are produced at a higher rate, aiding the rebuilding process of the organ.

RNA silencing

Silencing of RNA occurs when double stranded RNA molecules are processed by a series of enzymatic reactions, resulting in RNA fragments that degrade complementary RNA sequences.[11][12] By degrading transcripts, a lower amount of protein products are translated and the phenotype is altered by yet another RNA processing event.

Evolutionary mechanism

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.[7] These RNA processing events can also be passed on from generation to generation via reverse transcription into the genome.[7][13] Over time, RNA networks that produce the fittest phenotypes will be more likely to be maintained in a population, contributing to evolution.[14] 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.[15] Human genome searches have also revealed RNA processing events that have provided significant “sequence space for more variability”.[16] On the whole, RNA processing expands the possible phenotypes of a given genotype and contributes to the evolution and diversity of life.

References

  1. ↑ Crick F (1970). "Central dogma of molecular biology". Nature. 227 (5258): 561–563. Bibcode:1970Natur.227..561C. doi:10.1038/227561a0. PMID 4913914.
  2. ↑ Gilbert W (1986). "Origin of life: the RNA world". Nature. 319 (6055): 618–620. Bibcode:1986Natur.319..618G. doi:10.1038/319618a0.
  3. ↑ Jürgen B (2003). "The contribution of RNAs and retroposition to evolutionary novelties". Genetica. 118 (2–3): 99–116. doi:10.1023/A:1024141306559. PMID 12868601.
  4. ↑ Marguet E, Forterre P (1994). "DNA stability at temperatures typical for hyperthermophiles". Nucl. Acids Res. 22 (9): 1681–1686. doi:10.1093/nar/22.9.1681. PMC 308049Freely accessible. PMID 8202372.
  5. ↑ Huang F, Yang Z, Yarus M (1998). "RNA enzymes with two small-molecule substrates". Chem. And Biol. 5 (11): 669–678. doi:10.1016/S1074-5521(98)90294-0.
  6. ↑ Joyce GF (1996). "Ribozymes: building the RNA world". Curr. Biol. 6 (8): 965–967. doi:10.1016/S0960-9822(02)00640-1. PMID 8805318.
  7. 1 2 3 Herbert A, Rich A (1999). "RNA processing in evolution: the logic of soft-wired genomes". Annals of the New York Academy of Sciences. 870: 119–132. Bibcode:1999NYASA.870..119H. doi:10.1111/j.1749-6632.1999.tb08872.x. PMID 10415478.
  8. ↑ Lynch KW, Maniatis T (2009). "Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer". Genes Dev. 10: 2089–2101.
  9. ↑ West S, Gromak N, Norbury CJ, Proudfoot BR (2006). "Adenylation and exosome-mediated degradation of cotranscriptionally cleaved pre-messenger RNA in human cells". Mol. Cell. 21 (3): 437–443. doi:10.1016/j.molcel.2005.12.008. PMID 16455498.
  10. ↑ Kren BT, Steer CJ (1996). "Posttranscriptional regulation of gene expression in liver regeneration: role of mRNA stability". FASEB J. 5 (5): 559–573. PMID 8621056.
  11. ↑ Hannon G (2002). "RNA interference". Nature. 418 (6894): 244–251. Bibcode:2002Natur.418..244H. doi:10.1038/418244a. PMID 12110901.
  12. ↑ Fire A, Xu SQ, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998). "Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans". Nature. 391 (6669): 806–811. Bibcode:1998Natur.391..806F. doi:10.1038/35888. PMID 9486653.
  13. ↑ Jordan IK, Rogozin IB, Glazko GV, Koonin EV (2003). "Origin of a substantial fraction of human regulatory sequences from transposable elements". Trends Genet. 19 (2): 68–72. doi:10.1016/S0168-9525(02)00006-9. PMID 12547512.
  14. ↑ Witzany G (2014). "RNA Sociology: Group Behavioral Motifs of RNA Consortia". Life (Basel). 4: 800–818. doi:10.3390/life4040800. PMID 25426799.
  15. ↑ Hunter P (2008). "The great leap forward: major evolutionary jumps might be caused by changes in gene regulation rather than the emergence of new genes". Sci. And Soc. Anal. 9: 856–867.
  16. ↑ Willemijm M, Gommans SP, Mullen SP, Maas S (2009). "RNA editing: a driving force for adaptive evolution". BioAssays. 9991: 1–9.
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