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Lecture 8

BIO240 Lecture 8

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Jennifer Harris

Lecture 8: Viruses, RNA & Gene Expression - Today we’re going to take a look at the interplay b/w RNA and the organization of DNA. - Start first of all with the novel aspect of the regulation of RNA done by organisms that invade eucaryotes & procaryotes & that’s viruses - Incidences of viral infection of animals such as the Avian flu – starting with fowl-like poultry but then migrating to humans. - Such flu viruses can have profound impact on populations of individuals. Perhaps most profoundly in human population is the 1918 flu epidemic that killed 40 million people – more than both world wars combined – wiped out almost a whole generation of people – sometimes called the Spanish flu epidemic. - Viruses don’t only infect animals but they infect everything from procaryotes to eucaryotes. - Here we see an example of viral infection of bacteria – we’ve got a lawn of bacteria growing on surface of petri plate – all bacteria growing right here in different titers or concentrations of viruses that have been grown simultaneously with these bacteria. What we see as a consequence are cleared areas and blacks where the viruses have affected bacteria & lyse the cells & now infected bacteria, lyse the cells-3 so on – see almost complete lyses at a high titer of the bacteria at 10 . - Such bacteria that infect microbes are known as bacteriophage. - See it is infecting a bacterial cell – it’ll inject its genome into the cell where it’ll be replicated, burst open & begin the replication cycle again & we can see a bunch of T4 bacteriophage – very simple virus. Missing Slide - There are others where we can see the exterior of the virus. The capsid, a protein coat that surrounds - Poliovirus infects humans. viruses - Tomato bushy stunt virus when it’s particularly difficult or causes significant disease symptoms on tomato & related nightshades so even Poliovirus tobacco, for example. Tomato Bushy Stunt Virus - Tobacco mosaic virus – plant virus, creating symptoms on tobacco. Tobacco Mosaic Virus - Looking at all of these viruses brings the attention that there is a significant diversity in viruses that are out there. - These viruses can be identified on the basis of their protein coat, the capsid that surrounds the outside of the virus. - Viruses can also be defined on the basis of the genome that they use, that is RNA or DNA. DNA RNA DNA RNA Single Double Host’s - The way in which viruses replicate: viruses are so effective at what it is they do b/c they’ve got an entirely paired down genome, very small genome. What they do is they hijack or pirate the host’s gene regulatory machinery (can see this in the figure). - Figure: we’ve got a DNA virus with its protein coat, enters the cell, releases its DNA, the DNA is transcribed by host’s transcriptional apparatus, the DNA is replicated normally by enzymes provided by the virus itself. The RNA is then translated using the host’s translational machinery & the DNA & protein get together to assemble new viruses that are then released from the cell and the cycle begins again. - Worked with a virus that has the capacity to infect tobacco. - Virus infected tobacco (seen on the right) is all wrinkly & is less efficient at what it does. - Single-stranded RNA genome that encodes a # of different proteins. - Encodes a replicase: RNA-dependent RNA polymerase (RdRp) – must use RNA template to generate other RNA – this is what needs to happen for an RNA virus – it needs to replicate its own RNA/genome and that’s the enzyme that does it. - In plants, the virus also needs to move from cell to cell through plasmodesmata – small circular pore-like structures that are b/w plant cells – movement proteins allow the virus to move from cell to cell through plasmodesmata, at least in plants. - Coat protein – makes up the capsid that protects the genome so when it’s outside of the cell, that’s what’s going to be transmitted from one plant to another – one host to another. - RNA-binding protein – function not perfectly characterized today but it’s thought that it may sequester the RNA to one part of cell in order to ensure that it is translated. RNA-dependent RNA polymerase (RdRp) - 2 different plant cells and there plasmodesmata in b/w them from one cell to the other. Let’s start with our RNA molecule. RNA 5’ to 3’ - Binds to it & synthesize new RNA strand in the 5’ to 3’ direction starting from the 3’ end of the template – so it functions just like a normal polymerase. - Note this important step: What’s happened is we’ve created a double-stranded RNA molecule – this is very important (we will come back to the importance of this in the future). - Now it turns out that RdRp will now go back to synthesize a complementary strand, but in the meantime, we’re going to talk about what happens to that transcript? Where is it going to go? Movement proteins - Movement proteins binding to the plasmodesmata & we end up with passage through the plasmodesmata so that they are now in another cell. - Just going to show the events occurring in the next cell but of course they will be occurring everywhere that the movement proteins has moved the RNA and of course in the original cell as well. - Finally the virus will assemble, the co-protein will associate & transmission, at least in plants, will occur by insect vector. Self Assembly - Identical coat proteins associate with each other without any outside mechanism – it’s a form known as self assembly. - Ask question that will be dealt with in the next lecture: you’ve got such a cunning system that is got inside the host & has captured the host’s mechanisms – how is it that hosts defending themselves against such insidious invaders? **Lecture 8 finishes here ** **Lecture 9 starts here ** - In the past lecture he talked about viruses and how viruses captured or pirated components of the central dogma as we see above, how they take advantage of the fact that the host effectively allows them to transcribe and translate their own genomes so they can propagate from one generation to the next. - What he promised to talked about was the interplay between this and the regulation of chromatin. Viruses themselves don’t have chromatin so it must be something that happens to the chromatin of the host that’s related to the virus.  Virus induced gene silencing  RNA interference - He finished with the question: how do hosts defend themselves against such insidious invaders? Ones that are taking advantage of their own gene regulatory system and you can’t shut that down since you have to regulate your own genes. How does an organism defend itself against something that acts so stealthily? There are a number of host defenses that can be invoked to protect the host against viral pathogens, sometimes there are none. We know examples of this, for example the acquired immune deficiency virus or the human immunodeficiency virus HIV, there aren’t really effective host defense mechanisms. - In other instances there is the adaptive immune response – the ability to make antibodies that recognize the viral co-protein normally or the replicase and thereby silence the virus through recognition of the virus and shutting it down through the immune response. - In addition there is something that is known as the innate immune response, this isn’t derived from antibodies but are a series of mechanisms inside the cell, and there is another form of immunity (covered next lecture) which is not adaptive, that resides inside cells to protect them. - We will touch on an innate immune response today; virus induced gene silencing AKA RNA interference, it is one of the coolest recent discoveries ever, it tells us how hosts protects themselves from viruses highlighting a mechanism we end up using in just normal growth & development to regulate gene expression. - Back to hypothetical plant cells. - Plant cells do not make antibodies, they don’t have the capacity to make antibodies to protect themselves from viruses. Instead they invoke virus induced gene silencing (VIGS) if they are able to. - We have single stranded RNA in the plant cell, the RNA dependent RNA polymerase comes along and synthesizes a new RNA strand. - There is an important implication b/c in lecture what he said has been done is that the RNA dependent RNA polymerase has created double stranded RNA. This double stranded RNA is unusual for the cell, we know there are instances of double stranded RNA & indeed we know now that there are many instances of double stranded RNA. Ex: that tRNA has regions of double strandedness as the tRNA molecule loops back on itself and bonds then by Watson-crick base pairing through complementary bases to make that T-like structure. - Normally eucaryotic cell shouldn’t see double stranded RNA unless invaded by a virus. Cells possess a surveillance system that detects these double stranded RNAs and chops it up into 21-23 nucleotide length fragments.  The enzyme that does it is called DICER (RNase) which cuts inside the RNA to create fragments of 21-23 nucleotide length fragments. - This makes it effectively an endonuclease because it's cutting within the RNA to give rise to the fragments.  RNA induced silencing complex (RISC) - Multi-protein system is known as the RNA induced silencing complex. This complex binds the 21-23 nucleotide fragments, evidence suggests that it probably binds only one strand and this forms a complex which contained within, is a small RNA segment that corresponds to the original double stranded molecule. It will be complementary to one or the other of those double strands so that’s important. - What happens is that the RISC goes back and silences those molecules that have sequence homology to these fragments – so it goes back and recognizes portions of RNA and silences it. It prevents it from being replicated and translated. It does this through two mechanisms: one is to block translation and also it functions to degrade the RNA (to say target this RNA specifically for degradation – don’t use it because it's double stranded, it's bad most likely a virus). - This silencing occurs throughout the plant body, the silencing system travels through plasmodesmata (the tiny pores between cells) and allows the defense mechanism to travel through the plant body. This is said to be systemic silencing b/c it runs throughout the whole system. - Here is everything. Now onto something that’s based on this. Hopefully you’re thinking hey this is pretty cool, this system of the recognition of double stranded RNA and silencing any RNA that is homologous to what’s been recognized as being double stranded. - Imagine that there is a mRNA that is synthesized from the host genome (this is shown in the right cell, no nucleus in both cells to save space bu
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