Doctoral defence: Liubov Cherkashchenko “New insights into alphaviral nsP2 functions”

On 10 February at 13:15 Liubov Cherkashchenko will defend her doctoral thesis “New insights into alphaviral nsP2 functions” for obtaining the degree of Doctor of Philosophy (in Biomedical Technology).

Supervisor:
Professor Andres Merits, University of Tartu

Opponent:
Associate Professor Jelke Fros, Wageningen University (Netherlands)

Summary
Over the last decades, the intensive studies of factors/activities responsible for multiple aspects of alphavirus infection have been performed. In particular, our understanding about structures and functions of viral RNA replicase and its components has significantly increased. Novel findings emphasize that one of the first and most essential event in alphavirus infection is processing of the ns polyprotein carried out by its nsP2 region and an individual nsP2; this process not only ensures the release of functional replicase subunits but also determines would these proteins form the active RCs or not. Thus, it is increasingly evident that nsP2 is one of the “main driving forces” of successful RNA replication. Furthermore, due to its versatile functions and various activities nsP2 is involved in other aspects of infection. It is one of the key determinants associated with activation as well as counteracting of antiviral response in infected cells. Therefore, different modifications of the protein, including point mutations, often have drastic impact on alphavirus infection. However, much of the precise mechanisms of P2 action remain enigmatic. What is clear is that nsP2 does not act alone, its activities are modulated by other components of viral replicase.

The current study allowed us to identify and confirm new functions and properties of nsP2 and alphavirus RNA replicase. The general conclusions of this study can be presented as follows:

1. Alphavirus trans-replicase systems can be applied as a tool for studies of functions of nsP2 associated with inhibition of RC formation/activity. These functions are essential for SIE and are likely related to these used to regulate RNA replication in the alphavirus infected cells. Using trans-replicase systems of CHIKV and SINV, it was found that the key event in SIE is targeting of replicase precursor (P1234) by an individual nsP2 protein and that this ability of nsP2 can be altered by mutations present in its functionally important regions. 
2. It was found that synthesis of an individual (free) nsP2 in mosquito cells has an inhibitory effect on the alphavirus RC formation/functionality. This is not, however, a result of a single mechanism but results from combination of nsP2 protease-activity dependent mechanism and protease-activity independent mechanisms. The level and dominant mode of inhibition of alphavirus RNA replication depends form the virus, source of free nsP2 and substitutions present in this protein. The protease-activity mediated mechanism is important for suppression of replication of matching virus and relies mostly on ability of nsP2 to cleave 2/3 site in ns polyprotein. For some viruses such as SINV it is also dominant mechanism used to suppress formation of RNA replicases of heterologous alphaviruses.
3. nsP2 of SINV and CHIKV can inhibit formation/activity of RNA replicase of heterologous alphavirus using protease-activity independent mechanisms; for nsP2 of CHIKV this is the dominant mechanism to suppress activity of RNA replicases of heterologous alphaviruses. The precise details of protease-activity independent mode of action of nsP2 remain unknown; however, it is clear that this property can be enhanced by introduction of certain mutations into nsP2. It is likely that the protease-activity independent inhibitory effect originates not from a single mechanism but from several mechanisms. 
4. Trans-replicase of highly pathogenic EEEV was found to be highly active in human and mosquito cells. Splitting of construct of EEEV P1234 expression into two (P123 and nsP4) or three (nsP1, P23 and nsP4) expression construct allowed analysis of requirements of active RC formation. It was found that activity of EEEV RNA replicase depends from correct ratio of P123 (or nsP1+P23) component to nsP4 component and that in contrast to previously studied alphaviruses an excess of nsP4 reduced activity of EEEV RNA replicase. The reduction was due to the decrease of a number of cells were RNA replication was initiated as well as to the reduced RNA replicase activity in such cells. It remains unclear, is this property unique for EEEV RNA replicase.
5. Natural isolate RRV 2528 was found to be a prominent inducer of type-I IFN expression. This property was associated with specific amino acid substitutions in the nsP2 encoded by this isolate. None of these substitutions or their combination affected ability of RRV to induce shutdown of cellular protein synthesis or level of viral structural proteins expression. Similarly, no effect on the processing of P1234 was detected. Combined, these findings indicate that the excessive type-I IFN induction was not due to the lack of the ability to induce general shutdown of cellular gene expression or due to the defects in RC formation.

Defence can be also followed in Zoom: https://ut-ee.zoom.us/j/94804633358?pwd=dEZ0c0MxMkM5T0VhY3BSMWdna2ZUQT09 (Meeting ID: 948 0463 3358, Passcode: 352223).