When viruses infect our cells they take over the cellular machinery and hijack our genetic repertoire that is responsible for transcription and translation. This causes the host cell to produce viral genes and proteins at the expense of its own proteins – a process called host shut-off. As a result, the viruses rapidly replicate and viral proteins take over the host cell and the infection accelerates.
Virus. Image Credit: Jezper/Shutterstock.com
Over the past few decades, several mechanisms were suggested by which the virus infection leads to the observed host shut-off. These include 1) cap-snatching of host cell mRNAs, 2) inhibition of polyadenylation of cellular pre-mRNAs, 3) Degradation of RNA Polymerase II, 4) Retention of cellular mRNAs in the nucleus, 5) Degradation of cellular mRNAs, and 6) Enhanced translation of viral mRNAs over host mRNAs.
What is cap snatching?
Cap snatching is a mechanism by which some viruses steal or “snatch” the 5’-cap sequence from the host messenger RNAs (mRNAs) to make their own viral proteins.
In eukaryotic cells, the 5′ termini of mRNAs, contain a co-transcriptionally attached 7-methylguanosine (m7G) cap. This 5′- cap is crucial for the process of translation, as it serves as a recognition site for translation initiation factors.
Except for some viruses that have developed translation strategies independent from a 5′-cap structure, viruses also need to cap their own mRNAs. Most viruses add the 5′- cap via a viral methyltransferase (MT) which is encoded within their polymerases.
However, some segmented negative-sense RNA viruses (sNSVs) like those belonging to the order Bunyavirales and the families Orthomyxoviridae (Influenza virus), Hanta viridae (Hantavirus), Phenuiviridae (rift valley fever virus), and Arenaviridae (Lassa virus), do not possess the methyltransferase activity within their polymerases. These sNSVs have evolved a rather brilliant and unique genetic mechanism where-in they snatch the 5′- cap sequence from the host to cap their own mRNAs. This process is called cap snatching.
Cap snatching in sNSVs involves the cleavage of short 5’-capped RNA leaders derived from the host mRNAs by the endonuclease activity of the viral RNA-dependent RNA polymerase (RdRp). The polymerase domain of the viral RdRp then uses the 5’ leader sequence to prime its own mRNA synthesis, leading to chimeric host–viral mRNAs. The host-derived 5’-cap is usually 10–20 long except in some members of Nairoviridae and Arenaviridae which utilize a shorter host-derived cap.
Cap snatching in influenza viruses
Cap snatching strategy is best described in influenza A virus (IAV)(De Vlugt et al., 2018). In the IAV cap snatching occurs in the nucleus, while in other viruses like Bunyavirales and Arenaviridae it occurs in the cytoplasm. In IAV the RdRp has 3 subunits-PA, PB1, and PB2.
The PB1 subunit of RdRP first binds the 5’ end of the IAV RNA (vRNA), which then activates PB2 resulting in the 3’ end of the viral RNA to form a double-stranded zone with the 5’ end. The PB2 proceeds to bind cellular mRNA at the (m7G) 5’cap. The PA subunit has an endonuclease activity at its N terminus. The PA subunit then cleaves the viral RNA, 10-13 nucleotides from the cap structure. The PB1 subunit which has the polymerase activity, initially adds on two new nucleotides. Then the cap-snatched primer moves through the product exit tunnel in the PB1 domain to serve as the primer for transcription.
The UCGUUUU nucleotides at the 3’ end of the viral RNA are free and unbound by the polymerase allowing for complementary binding with the capped RNA primer. Transcription is initiated with G or C residue at the 3’ end of the capped primer. Chain elongation is completed by the PB1 subunit in the 5’ to 3’ direction and then releasing the cap.
Polyadenylation of the viral RNA occurs at the end of transcription, by polymerase stuttering from the steric hindrance of the vRNA loop. Following all of these steps, the viral mRNA ultimately looks identical to the host mRNA, which makes it conducive for the host cellular machinery to recognize it as its own and carry out processing and nuclear export.
The cap snatched host mRNAs are targeted for degradation, leading to the downregulation of cellular mRNA. Interestingly, the Influenza RdRp undergoes a conformational change by interacting with the C-terminal domain of cellular Polymerase II (Pol II) potentially promoting viral transcription.
What is start snatching?
Viruses can’t make their own proteins in the host. Therefore, they hijack the hosts’ translational machinery to make many new previously unknown chimeric proteins called Upstream Frankenstein Open reading frame (UFO) proteins, which are encoded by stitching together the host and viral genes. This process is called start snatching by which the sNSVs hijack the hosts’ genetic signals to make their own proteins.
Start-snatching allows translation of “untranslated regions” (UTRs) in the host and viral genes to create N-terminally extended viral proteins or entirely new chimeric proteins depending on the start codon.
It has been shown that both types of chimeric proteins are made in IAV-infected cells, generating T cell responses, and contributing to virulence.
These hybrid genes could be potential targets for vaccines against IAV and eventually other viruses. The phenomenon of hijacking the host genetic material is only recently being established in IAV and viruses like Bunyaviruses. Further research in this area will not only enhance our understanding of the genetic mechanism of how viruses steal our genetic material but we can now use this knowledge to eradicate diseases and prevent global epidemics and pandemics.
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