Abstract
Pararetroviruses, taxon Caulimoviridae, are typical of retroelements with reverse transcriptase and share a common origin with retroviruses and LTR retrotransposons, presumably dating back 1.6 billion years and illustrating the transition from an RNA to a DNA world. After transcription of the viral genome in the host nucleus, viral DNA synthesis occurs in the cytoplasm on the generated terminally redundant RNA including inter- and intra-molecule recombination steps rather than relying on nuclear DNA replication. RNA recombination events between an ancestral genomic retroelement with exogenous RNA viruses were seminal in pararetrovirus evolution resulting in horizontal transmission and episomal replication. Instead of active integration, pararetroviruses use the host DNA repair machinery to prevail in genomes of angiosperms, gymnosperms and ferns. Pararetrovirus integration – leading to Endogenous ParaRetroViruses, EPRVs – by illegitimate recombination can happen if their sequences instead of homologous host genomic sequences on the sister chromatid (during mitosis) or homologous chromosome (during meiosis) are used as template. Multiple layers of RNA interference exist regulating episomal and chromosomal forms of the pararetrovirus. Pararetroviruses have evolved suppressors against this plant defense in the arms race during co-evolution which can result in deregulation of plant genes. Small RNAs serve as signaling molecules for Transcriptional and Post-Transcriptional Gene Silencing (TGS, PTGS) pathways. Different populations of small RNAs comprising 21–24 nt and 18–30 nt in length have been reported for Citrus, Fritillaria, Musa, Petunia, Solanum and Beta. Recombination and RNA interference are driving forces for evolution and regulation of EPRVs.
Highlights
Retroelements can be considered to lie at the transition from an RNA to a DNA world
Special focus will be given to mechanisms related to recombination, dsDNA break repair, and RNA interference, explaining the endogenous PRVs (EPRVs) virosphere, the space in which EPRVs occur and which is influenced by them
Ancient recombination events between proliferating Long Terminal Repeat (LTR) retrotransposons and co-infecting RNA viruses may have occurred in the ancestral plant cell
Summary
Retroelements (class I transposable elements) can be considered to lie at the transition from an RNA to a DNA world. Besides intracellular forms, e.g., Long Terminal Repeat (LTR) retrotransposons, virionforming elements exist that can leave the cell These infectious retroelements developed two distinct strategies during adaptation and co-evolution with their respective hosts. True retroviruses are lacking but plants have infective pararetroviruses (PRV), family Caulimoviridae They encapsidate circular dsDNA that, after release and transport to the nucleus, forms a minichromosome allowing synthesis of terminal redundant viral RNA (Gronenborn, 1987; Hohn and Rothnie, 2013). Sequence and structural analysis of the capsid proteins support the hypotheses that retroviruses, pararetroviruses and LTR retrotransposons share the same origin dating back 1.6 billion years (Krupovic and Koonin, 2017) They most likely evolved from a common ancestor that encoded the genes for a capsid protein, protease and reverse transcriptase including the RNase H domain. Special focus will be given to mechanisms related to recombination, dsDNA break repair, and RNA interference, explaining the EPRV virosphere, the space in which EPRVs occur and which is influenced by them
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