LINE-1 retrotransposons facilitate horizontal gene transfer into poxviruses

Abstract

There is ample phylogenetic evidence that many critical virus functions, like immune evasion, evolved by the acquisition of genes from their hosts through horizontal gene transfer (HGT). However, the lack of an experimental system has prevented a mechanistic understanding of this process. We developed a model to elucidate the mechanisms of HGT into vaccinia virus, the prototypic poxvirus. All identified gene capture events showed signatures of long interspersed nuclear element-1 (LINE-1)-mediated retrotransposition, including spliced-out introns, polyadenylated tails, and target site duplications. In one case, the acquired gene integrated together with a polyadenylated host U2 small nuclear RNA. Integrations occurred across the genome, in some cases knocking out essential viral genes. These essential gene knockouts were rescued through a process of complementation by the parent virus followed by non-homologous recombination during serial passaging to generate a single, replication-competent virus. This work links multiple evolutionary mechanisms into one adaptive cascade and identifies host retrotransposons as major drivers for virus evolution.

Molecular Mechanisms of Poxvirus Evolution

“…For example, the human-restricted variola virus encodes relatively short ITRs, generally less than 1 kb, that do not contain any genes ( 5 , 82 ). Mutations or gene insertions in one ITR region are usually also reflected in the other ITR region, probably through recombination ( 83 – 85 ).…”

“…Furthermore, some orthopoxviruses encode homologs of the Golgi anti-apoptotic protein (GAAP), which shows about 76% protein identity with mammalian homologs, indicating relatively recent HGT ( 116 ). These viral genes are flanked by adjacent target site duplications and a putative poly(A) tail remnant, implicating LINE-1 in the capture of a GAAP host gene ( 84 , 85 ).…”

“…Two recent experimental studies address the mechanism(s) of HGT in poxviruses ( 84 , 85 ). In each study, the authors used a replication-deficient vaccinia virus, which lacks PKR inhibitors E3L and K3L and can only replicate in PKR-deficient cells or in the presence of PKR inhibitors provided in trans .…”

“…These genetic signatures are characteristic of LINE-1-mediated transposition of host RNA into the viral genome. In one study, the captured genes primarily integrated outside the central region ( 84 ), while in the other study, captured genes were distributed throughout the genome, including the central conserved region ( 85 ). In some cases, integration was found in essential genes, which presumably inactivated these genes.…”

A life LINE for large viruses

“…Yet virtually no specific evidence has been available to corroborate this conjecture so far. Now, in eLife, two teams based in the United States – one led by Nels Elde, with Sarah Fixsen as first author, and one led by Stefan Rothenburg with M Julhasur Rahman as first author – finally report such evidence ( Fixsen et al, 2022 ; Rahman et al, 2022 ).…”