Hairpin structures with conserved sequence motifs determine the 3′ ends of non-polyadenylated invertebrate iridovirus transcripts

•Hairpin-based mRNA 3′end formation appears common in invertebrate iridoviruses.•Specific complementary motifs triggering 3′ end formation were predicted in silico.•Half of the IIV-6 transcripts ended with a CAUUA motif, preceded by UAAUG.•Conservation of xrn1 genes among IIVs hints towards cleavage of pre-mRNAs.•Vertebrate iridoviruses rely on another mechanism for mRNA maturation than IIVs.

Previously, we observed that the transcripts of Invertebrate iridescent virus 6 (IIV6) are not polyadenylated, in line with the absence of canonical poly(A) motifs (AATAAA) downstream of the open reading frames (ORFs) in the genome. Here, we determined the 3′ ends of the transcripts of fifty-four IIV6 virion protein genes in infected Drosophila Schneider 2 (S2) cells. By using ligation-based amplification of cDNA ends (LACE) it was shown that the IIV6 mRNAs often ended with a CAUUA motif. In silico analysis showed that the 3′-untranslated regions of IIV6 genes have the ability to form hairpin structures (22-56 nt in length) and that for about half of all IIV6 genes these 3′ sequences contained complementary TAATG and CATTA motifs. We also show that a hairpin in the 3′ flanking region with conserved sequence motifs is a conserved feature in invertebrate-infecting iridoviruses (genus Iridovirus and Chloriridovirus).

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