Qualitative, quantitative and structural analysis of non-coding regions of classical swine fever virus genome

Applications and Uncertainty Estimation of Single Level Standard Addition Method ICP-MS for Elemental Analysis in Various Matrix

The standard addition method (SAM) based on gravimetric sample preparation was investigated as an approach for the removal or cancelling of matrix effects in measurements by inductively coupled plasma mass spectrometry (ICP-MS). Deduction of the equations and experimental confirmation of the method are both given in the present work. After measuring both spiked and non-spiked samples by ICP-MS, the concentration of an element could be calculated based on the signal intensity ratio to an internal standard. A practical example was provided for the measurement of Fe in a certified reference material (CRM), i.e. NMIJ CRM 7512-a (milk powder). The validity of the method had been confirmed by the results of international comparisons with various kinds of matrix, including bioethanol, human serum, biodiesel fuel, drinking water, infant formula milk power, and seafood. The suggested method had been applied to measurements of multiple elements in three CRMs, including tap water, milk powder, and tea leave powder, respectively.

RNA helicase is involved in the expression and replication of classical swine fever virus and interacts with untranslated region

To investigate whether cytoplasmic RNA helicase A (RHA) influences the expression and replication of classical swine fever virus (CSFV), an siRNA molecule targeted to RHA was transfected into PK-15 cells. The siRNA was found to reduce cytoplasmic RHA. In CSFV subgenomic replicon transfected cells, incubation with the siRNAs negatively impacted viral NS3 and RNA production. In the CSFV infected cells, treatment with the siRNA resulted in a significant reduction of viral replication by 65-70%. Furthermore, affinity chromatography and UV-crosslinking assays revealed that RHA can bind the 5' and 3' terminal region of CSFV 3'-untranslated region (UTR), the 5' terminal region and domain III of CSFV 5' UTR. All these regions are important for viral replication and translation. These data showed that RHA is involved in the expression and replication of CSFV and might participate in modulation of RNA synthesis, replication and translation of CSFV by binding these regions.

Classical swine fever virus NS5A protein interacts with 3'-untranslated region and regulates viral RNA synthesis

To investigate the function of classical swine fever virus (CSFV) NS5A protein, the experiments for viral RNA synthesis and viral replication were performed in the co-presence of NS5A and NS5B. Results showed that small concentrations of NS5A stimulated, large concentrations of NS5A inhibited, viral RNA synthesis and viral replication. Affinity chromatography experiments and UV-crosslinking assays revealed that CSFV NS5A and NS5B bound its cognate 3'UTR and that NS5A had higher affinity than NS5B protein in binding to 3'UTR. 200 ng of NS5A inhibited NS5B-3'UTR complex formation by about 95%. CSFV 3'UTR was found to contain two NS5A-binding sites, located in 3'UTRSL-1 (nt 161-231) and 3'UTRSL-2 (nt 90-160), respectively, a NS5B-binding site, also located in 3'UTRSL-1. The 3'UTRSL-1 is the common binding site for NS5A and NS5B. Furthermore, competitive electrophoretic mobility shift assays indicated that binding of CSFV NS5A to 3'UTRSL-1 is more efficiently than to 3'UTRSL-2. These results suggested that the different concentrations of NS5A, the different binding activities of NS5A and NS5B to 3'UTR and binding of NS5A to different regions of 3'UTR might contribute at least partially to modulation of CSFV replication.

Specific interaction between the classical swine fever virus NS5B protein and the viral genome

The NS5B protein of the classical swine fever virus (CSFV) is the RNA-dependent RNA polymerase of the virus and is able to catalyze the viral genome replication. The 3' untranslated region is most likely involved in regulation of the Pestivirus genome replication. However, little is known about the interaction between the CSFV NS5B protein and the viral genome. We used different RNA templates derived from the plus-strand viral genome, or the minus-strand viral genome and the CSFV NS5B protein obtained from the Escherichia coli expression system to address this problem. We first showed that the viral NS5B protein formed a complex with the plus-strand genome through the genomic 3' UTR and that the NS5B protein was also able to bind the minus-strand 3' UTR. Moreover, it was found that viral NS5B protein bound the minus-strand 3' UTR more efficiently than the plus-strand 3' UTR. Further, we observed that the plus-strand 3' UTR with deletion of CCCGG or 21 continuous nucleotides at its 3' terminal had no binding activity and also lost the activity for initiation of minus-strand RNA synthesis, which similarly occurred in the minus-strand 3' UTR with CATATGCTC or the 21 nucleotide fragment deleted from the 3' terminal. Therefore, it is indicated that the 3' CCCGG sequence of the plus-strand 3' UTR, and the 3' CATATGCTC fragment of the minus-strand are essential to in vitro synthesis of the minus-strand RNA and the plus-strand RNA, respectively. The same conclusion is also appropriate for the 3' 21 nucleotide terminal site of both the 3' UTRs.

Influence of a 12-nt insertion present in the 3' untranslated region of classical swine fever virus HCLV strain genome on RNA synthesis

The function of a 12-nt insertion 'CTTTTTTCTTTT' in the 3' untranslated region (3'UTR) of the HCLV strain, a vaccine strain derived from the Shimen strain of classical swine fever virus (CSFV), was examined in vitro. RNA synthesis increased when the 12-nt insertion was deleted from the 3'UTR of the HCLV strain. RNA synthesis also decreased when the 12-nt insertion was introduced into the 3'UTR of the CSFV Shimen, virulent strain. Therefore, the 12-nt insertion present in the 3'UTR of the HCLV strain may be a marker for avirulence. It was also found that the predicted secondary structure of the 3'UTR of the HCLV strain was more stable when the 12-nt insertion was deleted, and that the 3'UTR of Shimen strain was more unstable when the 12-nt insertion was introduced. Replacement of the 12-nt insertion 'CTTTTTTCTTTT' by another 12-nt fragment 'ATTATTATTTAT' in the 3'UTR of HCLV strain facilitated RNA synthesis and stabilized the predicted secondary structure, which was also observed in the 3'UTR of the Shimen strain.