Friday, 17 May 2013

poly(A) messages; lost in translation
From a virus' perspective, how do you translate your own messenger RNA (mRNA), whilst not allowing your host cell to continue manufacturing its own proteins, including those that might be detrimental to virus survival? It's a problem viruses have found various ways to overcome, often by manipulating the biology of the mRNAs, which have the following structure:

The classical polyadenylated mRNA ready for translation

Simply, an eIF4F cap-binding complex binds to the cap and a poly(A) binding protein (PABP) interacts with the poly(A) tail. The PABP in turn interacts with eIF4G of the cap binding complex, thus circularising the mRNA for  efficient translation to occur.

The translation complex showing circularisation enabled by PABP linking the poly(A) tail to eIF4G.

A good way in which to specifically translate viral messenger RNAs is to  make the viral mRNAs different in such a way that viral mRNAs are the most efficiently translated mRNAs. Picornaviruses (e.g. polio, foot and mouth disease) and flaviviruses (e.g. West Nile, Hepatitis C), genomes contain an internal ribosome entry site (IRES), which allows ribosome attachment and subsequent translation in the absence of the 5' cap; get rid of the ability of the cell to translate capped mRNAs and suddenly the viral mRNAs are preferentially translated.

Rotaviruses target the other end. Rotavirus mRNAs all end in a specific sequence ....GACC instead of a poly(A) tail. One of the viral non-structural proteins, NSP3, has been shown to act in similar fashion to PABP; NSP3 specifically binds RNAs ending in this sequence (i.e. rotaviral mRNAs), and also binds the cap-binding complex in place of PABP, but with higher affinity than PABP. The overall result is that polyadenylated mRNAs are outcompeted by rotaviral mRNAs. NSP3 also seems to be responsible for PABP accumulating in the nucleus, where it is unable to translate cytoplasmic mRNAs. Even so, there is evidence that rotaviral mRNA translation appears to be independent of NSP3.

A paper has just come out looking into the location of poly(A), i.e. cellular, mRNAs in rotavirus infected cells.
The first question was, where do you find poly(A) mRNAs in infected cells? Using fluorescence in situ hybridisation (FISH) the authors found poly(A) containing mRNAs to accumulate in the nucleus of cells, thus preventing their translation. Removing NSP3 using RNA silencing prevented this from happening, so that poly(A) mRNAs were then found in the cytoplasm, just as in uninfected cells.

Rotavirus (and NSP3) retain polyadenylated mRNA in the nucleus. Oligo (dT) probes detects polyadenylated (i.e. cell-like) mRNA. Normally the mRNA is distributed throughout the cell (top) in infected cells, signal is only observed in the nucleus (middle row) whereas when NSP3 is silenced, the nuclear block is apparently released (bottom).

Next there is an intriguing finding that, perhaps surprisingly, the untranslated regions (UTRs) of rotaviral mRNAs do not influence how well that particular transcript is translated, as luciferase reporter RNAs with host-cell UTRs were not translated any less efficiently than reporter RNAs with rotaviral UTRs. Most strikingly though, was the fact that the overall efficiency of translation appeared to be enhanced in infected cells, implying that the translation machinery is altered upon infection. These mRNAs were directly transfected into the cytoplasm, which isn't how cellular mRNAs originate. To look at this, the authors used two ways of supplying mRNA to the translation machinery, either directly into the cytoplasm, where they again found it to be more efficiently translated in infected cells, or allowed the cell to transcribe it from a plasmid, in which case they observed a decrease in expression as as result of rotavirus infection. Silencing of NSP3 released this apparent inhibition, with the infected cells appearing more like uninfected cells. Together this all leads to the conclusion that, rather than NSP3 affecting the translation of mRNAs directly, the inhibition of poly(A)-dependent translation is due to a lack of export of newly transcribed RNA.

RNA translation in the presence of Rotavirus: (A) when RNA is  transcribed in the nucleus (and needs to be exported for translation), infection suppresses translation, whereas mRNA transfected into cytoplasm implies that rotavirus infection enhances the translation efficiency of the translational machinery. (B) Suppression of rotavirus NSP3 by RNA silencing removes the block imposed upon protein expression from a plasmid.

The authors checked the location of cellular mRNAs too, and found that they too accumulated in the nucleus of infected cells, whereas in mock-infected cells the mRNAs were found in the cytoplasm. Again, when NSP3 was silenced, this block disappeared.
What happens to the polyadenylated mRNAs which accumulate in the nucleus (alongside the normally cytoplasmic PABP which is also retained in the nucleus)? By looking at the length of the RNAs, and using oligos which target the poly(A) tail, they found that the poly(A) tails were increased in length; an observation in line with data showing that PABP accumulation in the nucleus results in hyperadenylation and nuclear retention of RNAs.
Finally, the authors looked to see whether there were more cellular mRNAs in the nucleus compared to the cytoplasm in infected cells. They found that the cytoplasm of infected cells contained 50% less polyadenylated mRNAs. All of this leads to a scenario in which a translationally very active cytoplasm is (comparatively) free of cellular, polyadenylated mRNAs, into which the virus transcribes masses of its own mRNAs; essentially the viral mRNAs now have the cell's translational machinery to themselves, and all of this apparently orchestrated by NSP3.

As a strategy it makes sense; simply get rid of the host's RNAs.

 Rubio, R., Mora, S., Romero, P., Arias, C., & Lopez, S. (2013). Rotavirus Prevents the Expression of Host Responses by Blocking the Nucleocytoplasmic Transport of Polyadenylated mRNAs Journal of Virology, 87 (11), 6336-6345 DOI: 10.1128/​JVI.00361-13
Piron, M. (1998). Rotavirus RNA-binding protein NSP3 interacts with eIF4GI and evicts the poly(A) binding protein from eIF4F The EMBO Journal, 17 (19), 5811-5821 DOI: 10.1093/emboj/17.19.5811

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