Thursday, March 21, 2013

RNA Polymerase ||| and the RIG-I pathway

A little story about immune responses in cells.

Type-I interferons (IFNs) are important for antiviral and autoimmune responses.  They interfere with viruses as the viruses try to borrow the cell's replication mechanism to reproduce themselves.

The cell will produce interferons due to a couple of proteins: the retinoic acid induced gene I (RIG-I) and mitochondrial antiviral signaling (MAVS) proteins.

These, in turn, start the production process when cytosolic double-stranded RNA or single-stranded RNA containing 5′-triphosphate (5′-ppp) are nearby.

Here's a surprising thing: Cytosolic B-form double-stranded DNA can also induce IFN-β. For example, a DNA sequence of repeating AT can induce it (It’s known as poly(dA-dT). But no one knew how. Until a paper came out in 2009 by Yu-Hsin Chiu and a couple of other people. It turned out that inside the cell, the poly(dA-DT) was actually being converted into 5′-ppp. 

But how? It turns out that an enzyme uses the poly(dA-dT) as a template to synthesizes 5′-ppp RNA. The enzyme is DNA-dependent RNA polymerase III (Pol-III). This was interesting because it was known that the Pol-III had a role in the nucleus of the cell, but not that it had to do with the immune system.

If you inhibit the working of Pol-III in a cell, and then introduce a bacteria like Legionella pneumophil, the bacteria grows in the cell. The implication is that Pol-III senses the DNA of the bacteria and triggers the IFN process.

How did they do it? 

In a cell, they attached a luciferase reporter to the IFN-β promoter, so if the cell creates IFN-β, it would bioluminesce.

Then, they put different things in the cell. Of all the things tested, only poly(dA-dT) activated the IRF3.

To ensure that there wasn’t something going on at another step in the path, some other things were tried: A silencing RNA strand was introduced into the cell that would stop the production of RIG-I and MAVS. No IFN-β was produced. DNASE-I is an enzyme that breaks down DNA. When that was introduced, no IFN-β was produced. On the other hand, IFN-β was produced in the presence of RNASE-I, so breaking down RNA had no effect.

Nucleic acids from the poly(dA-dT) cells were able to induce IFN- β, even in the presence of DNase I, so it wasn’t DNA that was causing it. Production stopped in the presence of RNase I though, so it must have been RNA that was being produced.

Similar tests were done to determine the exact length of the poly. As few as 30 base pairs were able to trigger the IFN. But, longer sequences with G’s and C have failed to trigger anything.

RNA Characteristics

 Two enzymes, polynucleotide kinase (PNK) and shrimp alkaline phosphatase (SAP) are used by chemists: the former adds a phosphate group to a DNA or RNA molecule, the latter removes one. A third enzyme, Terminator Exonuclease, or Ter Ex, breaks apart RNA with exactly one phosphate at the 5’ end.

When the SAP was used to remove the phosphate, the RNA no longer induced IFN- β (the PNK had no effect). Even when the PNK was used to add back the phosphate that was removed, there was still no induction, implying that a single phosphate was inadequate. Similarly, treating the RNA with Ter Ex also made no difference.

Another pair of RNase enzymes break apart specifically single stranded RNA (ssRNA) or double stranded RNA (dsRNA). RNase III breaks apart dsRNA, while RNase T1 breaks apart ssRNA. RNase III turned out to inhibit the IFN- β, indicating that dsRNA was required.

Put all these together and it seems that the trigger is dsRNA with multiple phosphate groups attached.

So the chain takes you from the poly(dA-dT) to a 5′-ppp.


Other tests bring you to the conclusion that Pol-III is the enzyme that triggers this conversion. Thus, Poly-III, in the cytoplasm of a cell, actually acts as a DNA sensor that will trigger an immune response. An entirely different function from the one it has inside the cell nucleus. Quite a surprise!