#18 Nucleic acid activated viral defence pathways Flashcards
why are RNAs complex?
- they have a lot of self complementarity
- can form mismatched pairs
- they can form complex structures that are dynamic
what two forms of information does RNA have
structure and sequence
non-coding regions of RNA code for this
what do virus sequence components of RNA contain?
- contain information to counteract the immune system, immune regulation, to control viral replication and host defences
what type of result does PRRs give
a non-specific response and produce generic antiviral mediators
what RNA in plants is used in specific nucleic acid antiviral activity? ‘the genetic immune system’
- small non-coding RNAs are used as effectors
-
explain the genetic immunity process in ringspot infection of plants
- virus produced dsRNA
- the DICER enzyme that is a RNAse will cleave the RNA into short fragments called siRNAs
- the siRNA will load onto RISC enzyme
- The RISC/siRNA will bind to the complementary ss strand of the RNA virus
- RISC will cleave the RNA strand / it can cleave multiple strands
what invertebrate was genetic immunity shown in?
c.elegans
they were fed bacteria with GFP
the GFP was switched off
how is mRNA silencing mediated by invertebrates and plants?
- they all use viral dsRNA as a PAMP
- they will generate siRNAs with the RNA and will target and silence that viral mRNA
what is the bacterial genetic defence system?
crRNAs
what are the properties of siRNA generated by invertebrates and plants
- short perfectly duplexed 19 base pair double helix of RNA with 2-nucleotide 3’ single stranded tails
- both plants and invertebrates produce this
- perfectly duplexed siRNAs will cause CLEAVAGE of the target RNA
what are the two argonaut proteins in the RISC complex and what do they do?
Argo1: RNA endonuclease (slicer protein)
Argo2: RNA transcription inhibitor (silencer protein)
explain how siRNA is made in plants and invertebrates?
- long dsRNA is processed by dicer to make siRNA
- there is sequence and structure selection where the strand with the less tightly base paired 5’ end is incorporated into RISC and becomes the guide strand
- the guide strand determines the target for viral mRNA
what is the outcome for viral RNA when targeted by siRNA?
- the mRNA will be cleaved from siRNA targeting
- uses Argo1
what is the outcome for viral RNA when targeted by miRNA or shRNA (hairpin rna)?
- the mRNA being targeted will not be cleaved, it will be silenced !
how do you distinguish siRNA from miRNA?
siRNA is perfectly duplexed
miRNA has mismatches
do humans have miRNAs?
yes
describe the RITS process?
what uses it?
what is it used for?
- identified in plants and invertebrates
- siRNAs load onto RITS instead of RISC
- this makes epigenetic modicfications rather than cleavage of the target mRNA
- it is used to control gene transcription in plants and invertebrates
- it will methylate the RNA which will shut down expression of the gene
what does long dsRNA in human cells activate?
- dsRNA longer than 30nucleotides will activate PRRs in cell
- PKR
- cause apoptosis
what does dsRNA the size of 21-27 nucleotides trigger in human cells?
- the RNA silencing pathway will be triggered for this size
how does RNA silencing pathway work in humans
what is it used for
- in human cells ssRNA of the right size will produce hairpins or stem loops
- the RNA will engage with the DROSHA in the nucleus
- DROSHA will cleave the RNA to make pre-miRNA
- the pre-miRNA will then export to the cytoplasm where it DICER will cleave the loop off of it to make miRNA
- a miRNA strand will be chaperoned by TRBP protein and loaded onto RISC
- miRNA will bind to the 3’ end of the target complimentary mRNA and repress mRNA translation so it cannot produce protein
it is used to control gene expression in our cells! a control system
how do human cells control gene transcription?
using miRNAs!
- we have many miRNAs that are produced. mostly from introns
what do miRNAs achieve in human cells? how is the outcome different to invertebrates and plants?
- miRNA in human cells does not act to cleave target mRNA!
- it will bind to the target and stop its translation
- they act as translational repressors
- cleavage or silencing can occur in plants and invertebrates
do viruses have miRNAs?
yes
how many mRNAs so HSV and CMV code?
they can splice their mRNA and produce 11 different miRNAs!`
what do viruses use miRNA for?
- many ways
- used to inhibit viral mRNA expression (control gene expression of virus)
- can inhibit host cell mRNA expression!! (control gene expression of host)
how does human miRNA silence Primate foamy virus
- human miRNA called miR-32 will target the ORF2 region on PFV
- this inhibits PFV-1 replication
- how human cell defends itself from virus
how can PFV-1 get around the miRNA silencing from the host cell?
it produces a Tas protein that can inhibit the cellular RISC protein so miRNAs cannot work in the cell!
how is cellular miRNA a positive factor for Hep.C?
- there is a miRNA present in just hepatocytes called miR-22
- miR-22 will bind to the 5’ UTR of Hep. C virus and enhance its expression
why do we only get Hep. C in the liver?
- due to the presence of miR-22
- this binds to Hep. C and increases its expression
how does Adenovirus use RNA polymerise III?
- Adenovirus has a promoter for the cellular RNA polymerase III
- Pol III will bind to adenovirus and short RNAs will be made called VA1’s
- VA1 has lots of self complementarity, it will bind to cellular PKR proteins and inactivate them!
- this stops PKR from phosphorylating and activating
what does the VA1 protein of adenovirus do?
it will bind to cellular PKR proteins and inactivate them!
- this stops PKR from phosphorylating and activating
- it will also block exportin-5 protein and block miRNAs from exporting to the cytosol
- it will also inhibit the dicer enzyme
(inhibits PKR and RNAi)
how does SV40 utilise miRNAs?
- SV40 uses 2 promoter regions
- when early genes are produced T anitgen will also be produced
- eventually late structural genes will be produced
- when late genes are made, a late structured RNA within an intron will be processed through DROSHER to produce pre-miRNAs - then into SV-miRNAs
- Sv-miRNAs will target early genes including t-antigen for degradation
this is how the SV40 virus switches from early gene expression to late gene expression- USED FOR GENE EXPRESSION
it will also cause less production of T antigen to make the cell less susceptible to CTL killing
what do HSV miRNAs do
- HSV LAT proteins encode miRNAs
- these miRNAs target TGF-b and SMAD3 proteins in human cells
- makes cell resistant to CTL killing and apoptosis cannot occur!
how does HIV tat protein suppress RNA silencing?
- TAT protein interferes with the biogenesis of miRNA
- has a TRBP that inhibits PKR, drives miRNA biogenesis and enhances translation of HIV transcripts
what does HIV produce miRNAs for ?
- produces a bunch of miRNAs for latency in CD4s
what are APOBEC3, SAMHD1 and tetherin?
they are cellular restriction factors
they are produced in response to IFNs
what is tetherin and how does it act
it is a cellular restriction factor
will be turned on in response to IFN in a cell
tetherin stops the release of vesicles from a cell
what do HIV proteins: VPU VPX VIF act on?
VPU: acts on tetherin
VPX: acts on SAMHD1
VIF: acts on APOBEC3 - will degrade it!
what is APOBEC3 and how does it work?
cellular restriction factor
it is a cytidine deaminase
it changes cytosine into uracil
it will be incorporated into viral HIV RNA
it will induce a G to A hypermutation and mutate the virus - it will not survive
