In silico identification of conserved cis-acting RNA elements in the SARS-CoV-2 genome

Aim: The aim of this study was to computationally predict conserved RNA sequences and structures known as cis-acting RNA elements (CREs) in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Materials & methods: Bioinformatics tools were used to analyze and predict CREs by obtaining viral sequences from available databases. Results: Computational analysis revealed the presence of RNA stem-loop structures within the 3′ end of the ORF1ab region analogous to previously identified SARS-CoV genomic packaging signals. Alignment-based RNA secondary structure predictions of the 5′ end of the SARS-CoV-2 genome also identified conserved CREs. Conclusion: These CREs may be potential vaccine and/or antiviral therapeutic targets; however, further studies are warranted to confirm their roles in the SARS-CoV-2 life cycle.

In silico identification of conserved cis-acting RNA elements in the SARS-CoV-2 genome

AimThe aim of this study was to computationally predict conserved RNA sequences and structures known as cis-acting RNA elements (CREs) located within the SARS-CoV-2 genome.Materials & methodsBioinformatics tools were used to analyse and predict cis-acting regulatory elements by obtaining viral sequences from available databases.ResultsComputational analysis prediction revealed the presence of RNA stem-loop structures within the 3’ end of the ORF1ab region that are analogous to the previously identified SARS-CoV genomic packaging signals. Alignment-based RNA secondary structures prediction of the 5’ end of the SARS-CoV-2 genome identified also conserved CREs.ConclusionThese CREs could be used as potential targets for a vaccine and/or antiviral therapeutics developments; however, further studies would be required to confirm their roles in the SARS-CoV-2 life cycle.

Unspliced Rous Sarcoma Virus Genomic RNAs Are Translated and Subjected to Nonsense-Mediated mRNA Decay before Packaging

ABSTRACT Retroviruses package full-length, unspliced RNAs into progeny virions as dimerized RNA genomes. They also use unspliced RNAs as mRNAs to produce the gag and pol gene products. We asked whether a single Rous sarcoma virus (RSV) RNA can be translated and subsequently packaged or whether genomic packaging requires a nontranslated population of RNAs. We addressed this issue by utilizing the translation-dependent nonsense-mediated mRNA decay (NMD) pathway. NMD is the selective destruction of mRNAs bearing premature termination codons (PTCs). The pathway has been shown to be associated with splicing in higher eukaryotes. Here, we demonstrate that both translation and the cellular factor Upf1 are required for the decay of unspliced, PTC-bearing RSV RNA by the NMD pathway. To address the relationship between RNA translation and packaging, we examined virus produced in cells cotransfected with PTC-bearing retroviral clones and wild-type viral clones. We observed that PTC-bearing transcripts are packaged into viral particles at levels three- to fivefold less than those of control RNAs. Since PTC-mediated degradation requires translation, we conclude that RSV can package progeny virion particles using previously translated RNAs.

Analysis of Specific Binding Involved in Genomic Packaging of the Double-Stranded-RNA Bacteriophage φ6

ABSTRACT The genomes of bacteriophage φ6 and its relatives are packaged through a mechanism that involves the recognition and translocation of the three different plus-strand transcripts of the segmented double-stranded-RNA genomes into preformed polyhedral structures called procapsids or inner cores. The packaging requires the hydrolysis of nucleoside triphosphates and takes place in the order segment S-segment M, segment L. Packaging is dependent upon unique sequences of about 200 nucleotides near the 5′ ends of plus-strand transcripts of the three genomic segments. It appears that P1 is the determinant of the RNA binding sites. Directed mutation of P1 was used to locate regions that are important for genomic packaging. Specific binding of RNA to the exterior of the procapsid was dependent upon ATP, and a region that showed a high level of cross-linking to phage-specific RNA was located. Antibodies to peptide sequences were prepared, and their abilities to bind to the exterior of procapsids were determined. Sites sensitive to trypsin and to factor Xa were determined as well.