Writing Assignment – Dr. Henderson

1.When an organism is transfected with a virus, it triggers several mechanisms to protect itself from the viral genes affecting it. Such mechanisms involve the innate immune response of the D. Melanogaster against the virus. Another mechanism that has been discovered not too long ago is the ability of silencing viral genes using an RNA interference pathway. The Argonaute paper has focused on the RNAi pathway of D. Melanogaster. The pathway involves a RISC complex composed of Argonaute 2 , viral siRNA and other proteins that act as a “strike and search” antagonist against viral genes and silencing them. In counter-defense, Viruses try to protect themselves by encoding viral suppressors of RNAi VSR to suppress the RNAi pathway. This leads to an “arms race” of adaptation and counter-adaptation by the host and virus. An important aspect of viral genome is its ability to undergo mutations to protect its self. Viral RNA is capable of antigenic shift and antigenic drift to cause mutations in its own genome and remain adaptable in host environment. The RNA Polymerase of the virus is phage-induced, so it is going to replicate the mutated genome and is different than eukaryotic Polymerase in that manner. In turn, host will evolve according to the viral genome to silence the “new” mutated genes. The evolutionary significance of VSRs in the Argonaute paper has enabled to understand how a conserved protein VP1 from Nora Virus is able to suppress viral siRNA in D. Melanogaster. The same function is carried by another VSR, the CrPV1 from a different virus the Cricket Paralysis Virus to suppress the RNAi pathway in its effector phase. Although the proteins have the same function, their protein analysis shows differential amino acid sequence, giving proof for convergent evolution. The evolutionary significance of viral siRNAs in this paper is the ability of AGO2 Slicer activity to be triggered upon transfection irrespective of the different viruses that attack the host. The RNAi pathways is therefore are going to be shaped according to the virus that infects it. Examples of other viruses that involve this evolutionary mechanism are the P1 VSR from Potyvirus and P22 VSR from the family of Closteroviridae. P1 VSR of Potyviruses is highly variable both in length and sequence, and shows evidence of recombination between potyviral ancestors. Potyviruses typically have a second VSR called Hc-Pro, but in cucumber vein yellowing virus from the related genus Ipomovirus, Hc-Pro has been lost and its function appears to have been taken on by a highly duplicated copy of P1. Similarly, in the Closteroviridae there is a lot of diversity if the sequence of VSR P22, and in one species, the Sweet Potato Chlorotic Stunt Virus, some viral isolates have lost this suppressor function. Evolutionary significance of the RNAi pathway includes the counter-defense mechanism of RNAi pathway to the viral genome by mutating its key components; Dicer, Argonaute 2 and R2D2. A study involving DNA sequences from different species of Drosophila shows the rate of amino acid evolution is substantially elevated in genes related to antiviral RNAi function (Dcr2, R2D2, and Ago2). They are among the fastest evolving 3% of all Drosophila genes; they evolve significantly faster than other components of innate immunity and faster than many comparative housekeeping proteins.

2. A defense mechanism used by higher vertebrates involves the induction of apoptosis of infected host cells upon viral infection. This affect has also been observed in mosquito species. However, with the evolution of viral genome, the infected host has able to change this apoptosis mechanism to adapt to the presence of the viral infection in itself. In the Dengue paper, apoptosis is inhibited by IAP (inhibitor of apoptosis) a novel find, that synergistically works with the viral phage, making the host a vector. When a phage invades an organism, the infected cell senses the unscheduled activation of the cell cycle by viral proteins. To be determined, cell cycle activation shown by these viral proteins is recognized as inappropriate and the cell kills itself through apoptosis. This process is however reversed in this paper by the expression of IAP in infected host cells that suppresses the apoptosis, and therefore the infected host cells remain intact. Infected by Adenovirus, the E1A-induced, p53-mediatedApoptosis of the host can be blocked by either of the two main gene products of the E1B transcription unit, i.e. E1B 19K protein or the E1B 55K protein and both proteins can co-operate with E1A for complete cell transformation. E1B 55K protein interferes with p53-mediated apoptosis by directly binding p53 but does not prevent p53 attachment to cognate DNA sequences. Human cytomegalovirus encodes two early proteins in the host which independently can block apoptosis
These two gene products, IE1 and IE2 are transcription factors. IE2 binds to the TATA box binding protein, pRb and IE2 has been shown to repress p53 transcriptional activity and this is why it could be able to inhibit apoptosis in host cells.

References Alvarado, Veria, and Herman Scholthof. "AGO2: A New Argonaute Compromising Plant Virus Accumulation." Frontiers in Plant Science 2 (2012): n. pag. Print. Apoptosis in viral pathogenesis, J M Hardwick, Nature, February 2001, Volume 8, Number 2, Pages 109-110 The evolution of RNAi as a defence against viruses and transposable elements Phil. Trans. R. Soc. B 12 January 2009 vol. 364 no. 1513 99-115 Viruses and Apoptosis, Journal of General Virology (1998), 79, 1833–1845. Printed in Great Britain Convergent Evolution of Argonaute-2 Slicer Antagonism in Two Distinct Insect RNA Virusesvan Mierlo JT, Bronkhorst AW, Overheul GJ, Sadanandan SA, Ekström J-O, et al. (2012) Convergent Evolution of Argonaute-2 Slicer Antagonism in Two Distinct Insect RNA Viruses. PLoS Pathog 8(8): e1002872. doi:10.1371/journal.ppat.100287

Additive Protection by Antioxidant and Apoptosis-Inhibiting Effects on Mosquito Cells with Dengue 2 Virus Infection Chen T-H, Lo Y-P, Yang C-F, Chen W-J (2012) Additive Protection by Antioxidant and Apoptosis-Inhibiting Effects on Mosquito Cells with Dengue 2 Virus Infection. PLoS Negl Trop Dis 6(4): e1613. doi:10.1371/journal.pntd.0001613