Abstract
BackgroundThe microRNA-based gene-silencing machinery has been recognized as a promising approach to control viral replication and used for improving safety for the live attenuated virus vaccines. The effective host microRNA response elements (MREs) have been incorporated into a virus sequence mainly based on the experimental trials for identifying both microRNA binding sites and effective mutations. The design of MREs for viral genomes or with multiple host microRNAs of interest, then, will be time and cost consuming.ResultsIn this paper, we introduced a computational flow that could be used to design MREs of human microRNAs within Influenza A H1N1 virus gene segments. The main steps of the flow includes locating possible binding sites; MREs, of human microRNAs within the viral sequences using a miRNA target prediction tool (miranda), performing various mutations among mismatched binding positions, calculating the binding energy, score, identity, and the effects of changed physical properties of amino acids according to the changed bases in RNA level, and prioritizing the mutated binding sites. The top ranked MREs of human microRNA hsa-miR-93 is consistent with previous literature while other results waited to be experimentally verified. To make the computational flow easily accessible by virologists, we also developed MicroLive, a web server version of the MRE design flow together with the database of miranda-predicted MREs within gene sequences of seven RNA viruses including Influenza A, dengue, hepatitis C, measles, mumps, poliovirus, and rabies. Users may design MREs of specific human microRNAs for their input viral sequences using MRE design tool or optimize the miranda-predicted MREs of seven viruses available on the system. Also, users could design varied number of MREs for multiple human microRNAs to modulate the degree of live vaccine attenuation and reduce the likelihood of escape mutants.ConclusionsThe computational design of MREs helps reduce time and cost for experimental trials. While the flow was demonstrated using human microRNAs and Influenza A H1N1 virus, it could be flexibly applied to other hosts (e.g., animals) and viruses of interest for constructing host-specific live attenuated vaccines. Also, it could be deployed for engineering tissue-specific oncolytic viruses in cancer virotherapeutics. The MicroLive web server is freely accessible at http://www.biotec.or.th/isl/microlive.
Highlights
The microRNA-based gene-silencing machinery has been recognized as a promising approach to control viral replication and used for improving safety for the live attenuated virus vaccines
Cellular miRNAs miR-24 and miR-93 were reported to target viral large protein (L protein) and phosphoprotein (P protein) genes and their decreased expression increased vesicular stomatitis virus (VSV) replication [7]. These findings strongly suggest that binding cellular miRNAs to its target sequences in the viral messenger RNA (mRNA) could be another mechanism by which invading viruses could be counteracted by the host
To ease the design of microRNA response elements (MREs) and to reduce time for wet-lab experiments, here, we proposed a computational flow and a web server for designing MREs of human miRNAs that could be incorporated into the open reading frames (ORFs) of a viral genome with efficacy, and having no or least effects on physical properties of amino acids due to mutated bases in RNA level
Summary
The microRNA-based gene-silencing machinery has been recognized as a promising approach to control viral replication and used for improving safety for the live attenuated virus vaccines. It has been shown that miRNAs are, to some extent, complementary to messenger RNA (mRNA) molecules in most, if not all, eukaryotic cells and that their main function is to inhibit gene expression via a number of mechanisms, such as direct mRNA cleavage, translational repression, and deadenylation [1]. Cellular miRNAs miR-24 and miR-93 were reported to target viral large protein (L protein) and phosphoprotein (P protein) genes and their decreased expression increased vesicular stomatitis virus (VSV) replication [7]. Taken together, these findings strongly suggest that binding cellular miRNAs to its target sequences in the viral mRNA could be another mechanism by which invading viruses could be counteracted by the host
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