Characteristics of inteins in invertebrate iridoviruses and factors controlling insertion in their viral hosts

Inteins are self-splicing proteins that occur in-frame within host-coded proteins. DNA elements coding for inteins insert specifically in highly conserved motifs of target genes. These mobile genetic elements have an uneven distribution and thus far have been found only in certain species of bacteria, archaea and fungi, a few viruses of algae and amoebozoa and in the entomopathogen, Chilo iridescent virus (CIV). Here, we report the discovery of seven new inteins parasitizing iridoviruses infecting metazoans: three within their δ DNA polymerase genes and four in genes coding for their large ribonucleotide reductase subunit. Analyses of coding sequences suggest that these inteins were acquired by ancestors shared by viruses currently classified as members of different families of viruses with large double-stranded (ds) DNA genomes and then were maintained by vertical transmission, or lost. Of significant interest is the finding that inteins present in the δ DNA polymerases of iridoviruses insert at a different location into the YGDTDS motif when compared to those found in other viruses and prokaryotes. In addition, our phylogenetic investigations suggest that inteins present in the δ DNA polymerases of these viruses might have an origin different from those found in prokaryotes. Finally, we use the sequence features of the intein insertion sites in host genes to discuss the high polymorphisms of inteins within and among viral species and the immunity of their genetic counterparts in the eukaryotic hosts of these viruses.

Graphical abstractDownload full-size imageHighlights► The first inteins inserting into the DNA polymerase gene of metazoan viruses. ► Iridoviral DpolB inteins would not cleave their DNA insertion target as the other DpolB inteins. ► DpolB inteins are not monophyletic; those in viruses have an archebacterial origin. ► RNR inteins are monophyletic; those in viruses likely have a bacterial ancestor. ► The host range of intein would restricted by the DNA sequence of empty allele.