Review of Literature
- Introduction the viral relics in the human genome. What they are and where they came from-
- 8% of the human genome is composed of retroviral relics.
- It has been estimated that the human genome contained roughly 31 different families of virus.
- Retroviruses replicate a DNA intermediate, called a provirus, that becomes integrated in the host organism’s genome. If such integration occurs in a cell that gives rise to gametes, the retroviral insert DNA can be inherited.
- Some groups have been able to analyze retroviral insertions, such as those originating from the Hepadnaviridae family and determine the time at which the insertion occurred. In their paper, Gilbert and Feschotte examined Hepadnaviridae insertions within the zebra finch genome.
- The determined that the Hepadnaviridae insertion was at least 19 million years old.
- The Hepadnaviridae family is composed of small viruses with genomes that are partially double stranded DNA. Hepatitis B virus is within the Hepadnaviridae family.
- Additionally, some viruses that contain DNA genomes and replicate within the host cell nucleus also have been known to leave “fossil” relics.
- The pararetroviruses have left numerous copies of viral DNA segments within plant genomes
- Similar activities have also been reported in flaviviruses with the mosquito host, totovirus-like and M2-killer-like viruses in fungi, and gemini-like viruses in tobacco. “Conservation of integrated sequences in plant genomes might indicate benefits for the host during evolution.” (Staginnus, 2006).
- “The recent discovery of multiple endogenous bornaviruses and filoviruses in diverse mammals showed that these single-stranded RNA viruses were able to infiltrate repeatedly the germline of distant mammalian species over at least the past 40 My” (Gilbert, 2010),
- Introduce the study of paleovirology. What it is and why it is useful and problems within the field-
- Paleovirology is an emerging field which examines exogenous ‘fossil’ virus insertions within the host genome. It allows researchers to examine the evolutionary history of such viruses, as well as further the understanding between the selective pressures behind the evolution of host immune systems. In a study regarding foamy viruses within sloth species, “our analysis highlights the role of evolutionary constraint in maintaining viral genome structure and indicates that accessory genes and mammalian mechanisms of innate immunity are the products of macroevolutionary conflict played out over a geological time scale.” (Katzourakis, 2009).
- It is also useful for understanding the long-terms evolutionary tendencies of extant viruses.
- Though the field is new, its potential is multifaceted and could have many implications in the study of evolution. Currently researchers are working to answer several questions, such as the role of prehistoric viruses in evolutionary transition events, the role of mutation rates on population dynamics, as well as determining whether correlated positive selection for specific antiviral genes within the primate phylogeny depicts responses to the same viral pathogen.
- It is often difficult to estimate the age of different viral lineages, due to their absence in the fossil record. The fossil record refers to DNA samples taken from prehistoric human specimens, as well as the viral fossil relics within the modern human genome. Natural selection plays a definite role in cleansing potentially problematic exogenous DNA insertions.
- It has also proved difficult to study viruses that have left relatively no trace of their existence within the human genome. However, researchers have recently discovered traces of a bornavirus gene that inserted itself into mammalian hosts several times throughout evolutionary history.
- One of the prevailing questions within the field of paleovirology is how prehistoric viruses shaped modern life. The proposed project will investigate the potential relation between viral pressures and immune system development, as well as potential viral influence over evolutionary transitional events.
- Different groupings of species will be chosen based upon commonalities between immune systems.
- Such commonalities will be assessed by sequence and functional similarity of specific cytokines, cytokine receptors, MHC I receptors, antimicrobial peptides secreted within the mucus and lymphocytes.
- The genomes of such organisms will then be examined in attempt to detect similarities between retroviral elements as well as any other viral relics maintained within the DNA.
- Studies such as the one conducted by Gilbert and Feschotte utilize an array of techniques to determine the point in evolutionary history in which the viral insert emerged. They utilized “cross-species analysis of orthologous insertions, molecular dating, and phylogenetic analyses to demonstrate that hepadnaviruses infiltrated repeatedly the germline genome of passerine birds” (Gilbert 2010). Such techniques could be similarly applied to the proposed project.
- The admission of such elements will then be dated, so as to estimate at which point the insertion originated. This will then be compared to known evolutionary history as well as the known development of immune system characteristics.
The expected results could vary. It would not be unreasonable to assume that certain pathogenic pressures helped shape immunity. However, whether or not this will be depicted through the retroviral elements present within host genomes is uncertain.
It would be interesting if such pressures also helped trigger the development of specific morphological features that protect against infection, such as mucus membranes, and impermeable barriers such as skin.
For more information on the conflict between species definitions, please refer to: Hey, J., 2001. The mind of the species problem. Trends in Ecology and Evolution. 16 (7 ): 326-329.
“Paleovirology Expanded: Non-Retroviral Virus Fragments Found in Animal Genomes.”ScienceDaily. ScienceDaily, 18 Nov. 2010. Web. 02 Apr. 2012.
Katzourakis, A., Gifford, R., 2010. Endogenous Viral Elements in Animal Genomes. PLoS Genetics. 6(11): e1001191.
Gilbert, C., Feschotte, C., 2010. Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses. PLoS Biology. 8(9): e1000495.
Duffy S, Shackelton L. A, Holmes E. C, 2008. Rates of evolutionary change in viruses: patterns and determinants. National Review Genetics. 9: 267–276.
Holmes E. C, 2003. Molecular clocks and the puzzle of RNA virus origins. J Virol 77: 3893–3897.
Bannert N, Kurth R, 2006. The evolutionary dynamics of human endogenous retroviral families. Annu Rev Genomics Hum Genet 7: 149–173.
Staginnus C, Richert-Pöggeler K. R., 2006. Endogenous pararetroviruses: two-faced travelers in the plant genome. Trends Plant Sci 11: 485–491
Katzourakis A, Gifford R. J, Tristem M, Gilbert M. T. P, Pybus O. G, 2009. Macroevolution of complex retroviruses. Science 325: 1512.