Browsing by Subject "RNA virus"

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  • Untiveros, Milton; Olspert, Allan; Artola, Katrin; Firth, Andrew E.; Kreuze, Jan F.; Valkonen, Jari P. T. (2016)
    The single-stranded, positive-sense RNA genome of viruses in the genus Potyvirus encodes a large polyprotein that is cleaved to yield 10 mature proteins. The first three cleavage products are P1, HCpro and P3. An additional short open reading frame (ORF), called pipo, overlaps the P3 region of the polyprotein ORF. Four related potyviruses infecting sweet potato (Ipomoea batatas) are predicted to contain a third ORF, called pispo, which overlaps the 3 third of the P1 region. Recently, pipo has been shown to be expressed via polymerase slippage at a conserved GA(6) sequence. Here, we show that pispo is also expressed via polymerase slippage at a GA(6) sequence, with higher slippage efficiency (approximate to 5%) than at the pipo site (approximate to 1%). Transient expression of recombinant P1 or the transframe' product, P1N-PISPO, in Nicotiana benthamiana suppressed local RNA silencing (RNAi), but only P1N-PISPO inhibited short-distance movement of the silencing signal. These results reveal that polymerase slippage in potyviruses is not limited to pipo expression, but can be co-opted for the evolution and expression of further novel gene products.
  • Dhaygude, Kishor Uttam; Johansson, Helena; Kulmuni, Jonna Katharina; Sundström, Liselotte (2019)
    We present the genome organization and molecular characterization of the three Formica exsecta viruses, along with ORF predictions, and functional annotation of genes. The Formica exsecta virus-4 (FeV4; GenBank ID: MF287670) is a newly discovered negative-sense single-stranded RNA virus representing the first identified member of order Mononegavirales in ants, whereas the Formica exsecta virus-1 (FeV1; GenBank ID: KF500001), and the Formica exsecta virus-2 (FeV2; GenBank ID: KF500002) are positive single-stranded RNA viruses initially identified (but not characterized) in our earlier study. The new virus FeV4 was found by re-analyzing data from a study published earlier. The Formica exsecta virus-4 genome is 9,866 bp in size, with an overall G + C content of 44.92%, and containing five predicted open reading frames (ORFs). Our bioinformatics analysis indicates that gaps are absent and the ORFs are complete, which based on our comparative genomics analysis suggests that the genomes are complete. Following the characterization, we validate virus infection for FeV1, FeV2 and FeV4 for the first time in field-collected worker ants. Some colonies were infected by multiple viruses, and the viruses were observed to infect all castes, and multiple life stages of workers and queens. Finally, highly similar viruses were expressed in adult workers and queens of six other Formica species: F. fusca, F. pressilabris, F. pratensis, F. aquilonia, F. truncorum and F. cinerea. This research indicates that viruses can be shared between ant species, but further studies on viral transmission are needed to understand viral infection pathways.
  • Mönttinen, Heli; Ravantti, Janne; Poranen, Minna (2021)
    RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.
  • Dutta, Pinky (Helsingin yliopisto, 2018)
    The trans-replication system of a virus deals with the idea where the viral RNA involved in the translation of replicase protein is separate from the one involved in the replication of the virus. This system has been successfully used to study virus replication complexes and numerous viral and host factors involved in the replication and infection process of Semliki Forest virus, Chikungunya virus and Sindbis virus. We attempted to test for the feasibility of this system with Potato virus X (PVX), an alpha-like virus, in planta. A viral RNA template was designed to produce a non-functional replicase protein, with the coat protein sequence deleted to prevent formation of virions. All other RNA features of the template sequence had been left unaltered, possibly making it recognizable by the replicase. The replicase construct encodes for the replicase protein and its RNA lacks other virus-specific recognition sequences. Both of the constructs were delivered into the mesophyll cells of the Nicotiana benthamiana leaves via Agrobacterium-mediated infiltration. Templates of various lengths, ranging from 2569 to 7562 nucleotides were tested. The longer templates did not replicate at 4 and 6 days post inoculation, when the replicase protein was provided in trans. Further optimization of the system with shorter templates and addition of helper component proteinase (HCPro), a potyviral silencing suppressor, led to effective trans-replication of the templates in plant cells. However, the replication sites were observed to be scattered across the leaf lamina suggesting that further optimization is required for increased efficiency of the trans-replication system. All in all, it has been established that PVX is capable of trans-replicating and the experimental freedom offered by this system can be utilized to delve deeper into understanding the replication mechanism of the virus.