Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus

Abstract

A B S T R A C T Viral noncoding (nc) RNAs have been shown to play important roles in viral life cycle. Many viruses employ different mechanism to produce ncRNAs. Here, we report that coronavirus infectious bronchitis virus (IBV) produces a novel ncRNA in virus-infected cells. This ncRNA consists of 563 nucleotides excluding a poly(A) tail, is mainly derived from the 3′-untranslated region of IBV genome, and contains a 63-nt-long of terminal leader sequence derived from the 5′ end of the viral genome. Using mutagenesis and reverse genetics, we reveal that this ncRNA is a subgenomic RNA generated by discontinuous transcription mechanism.

Multiple novel non-canonically transcribed sub-genomic mRNAs produced by avian coronavirus infectious bronchitis virus

“…1c). This finding supports reports by both An et al (2019), who identified a TRS-B of UAACA [14], and Dinan et al (2019), who identified a putative TRS-B of UAACAU [7]. Sequence alignment of the 3′-UTR for Beau-R and M41-CK identifies that the deletion seen in the latter starts 2 bp into the newly identified TRS-B ( Fig.…”

“…As this paper was in preparation, two further publications have identified this sgmRNA in the Beaudette strain of IBV, transcribed from a TRS-B of UAACA or a putative TRS-B of UAACAU [7,14]. However, this report furthers the findings of both Dinan et al [7] and An et al [14] by (i) confirming the TRS-B of UAACA in the Beaudette strain and (ii) identifying the presence of sgmRNA 7 and associated ORF in several other IBV strains, both vaccine and field isolates, including CR88 and QX, respectively. Interestingly, there is variability in the sequence of the TRS-B between the strains of IBV, with the genome of CR88 containing a 6 nucleotide TRS-B of UUAACA and Italy-02 a 7 nucleotide TRS-B of CUUAACA.…”

“…Whilst this was disappointing, it has provided evidence of the importance of the flanking regions located at the 3′ end of this TRS-B. An et al also demonstrated the importance of the 3′ flanking sequence, particularly the sequence AAUGG at position 27 110-27 114 [14]. Mutations of this motif to UUUCC completely disrupted sgmRNA 7 expression; although it must be noted these mutations also disrupted the start codon.…”

“…Such transcripts are not unique to IBV, and have previously been described in other coronaviruses including SARS-CoV and mouse hepatitis virus (MHV) [12,13]. Two recent publications have described the detection of a non-canonically transcribed sgmRNA in the IBV strain Beaudette, located at the very 3′ terminus of the genome, between the N gene and the poly(A) tail [7,14]. Additionally, Dinan et al identified ribosomes bound to the transcript suggesting protein translation [7].…”

“…The analysis of the full-length genome sequences of several IBV strains has identified a potential ORF at the 3′ end of the genome between the end of N and the poly(A) tail in what is considered as a hypervariable region of the IBV 3′-UTR [7,14]. Britton and Cavanagh (in 2008) had previously considered an ORF in this area due to the presence of an AUG start codon, but discounted the possibility of another gene due to the apparent lack of a TRS-B [44].…”