Identification of a conserved baculoviral microRNA coded by Spodoptera frugiperda Multiple Nucleopolyhedrovirus

GÓMEZ BERGNA SANTIAGO MANUEL; PIDRE MATIAS LUIS; FERRELLI MARÍA LETICIA

Congreso; 2nd Women in Bioinformatics & Data Science LA Conference; 2021

Spodoptera frugiperda Multiple Nucleopolyhedrovirus (SfMNPV) belongs to theAlphabaculovirus genus, Baculoviridae. Its natural host is Spodoptera frugiperda, anagronomically important pest. MicroRNAs (miRNA) are endogenous eukaryotic smallnoncoding RNAs that regulate gene expression by kidnapping or cleaving mRNAs in asequence specific manner. Several miRNAs were found and well characterized inviruses, including baculoviruses. The aim of this work was to identify a miRNA encodedin the SfMNPV genome, ortholog to the previously described and experimentallyvalidated BmNPV-miR-2 encoded in Bombyx mori nucleopolyhedrovirus (BmNPV)genome. BmNPV-miR-2 is coded in the complement strand of the chi-a gene, whichencodes the chitinase protein. Initially, we used the Matcher algorithm to perform alocal alignment between BmNPV-miR-2 sequence and the complement strand of thechitinase gene of SfMNPV. It generated an alignment with 81 % identity, matching asequence similar in location to the site where BmNPV-miR-2 is encoded in BmNPV.Next, using the miRNAFold webserver, we looked for putative sequences that couldacquire the characteristic stem-loop structure and that included the sequence found inthe alignment. We found a sequence of 81 nucleotides that generated a secondarystructure with a minimum free energy (MFE) of -23,24 kcal/mol. In order to validatethe conservation, we performed a blastn search with the pre-miRNA sequenceobtained from miRNAFold as a query. We found highly conserved sequences in morethan 25 different baculovirus species, including BmNPV. Finally, we looked for putativeviral targets using the miRanda algorithm, in the galaxy webserver. It predicted 34possible targets, expressed mostly in late and very late stages of the infection. Inconclusion, we found a novel miRNA in SfMNPV, ortholog to BmNPV-miR-2 andpotentially capable of regulating gene expression of multiple putative targets.