Endogenization

Endogenization leads to vertical transmission of viral DNA.

Endogenization is the evolutionary process by which viral genetic material becomes stably integrated into the germline of a host organism and inherited by offspring through Mendelian inheritance. The integrated sequences become endogenous viral elements, which encompasses all inheritable virus-derived sequences regardless of virus type.

The molecular mechanisms driving this process vary among virus and host types. It can more commonly occur from the direct use of integrases, or through other means such as the incidental hijacking of host DNA repair pathways.

Retroviruses are the most common source of endogenization, as genomic integration is an obligatory step in their replication, and can create endogenous retroviruses. Nevertheless, every category of eukaryotic virus can contribute sequences to host germlines, including RNA viruses with no obligatory DNA stage in their life cycle.

Criteria

Endogenization in multicellar life usually requires that a viral integration occur in a germ cell, such as a sperm or egg cell, or in an early embryo before the somatic and germline lineages separate, so that the viral sequence is transmitted to all cells of the resulting organism and becomes available for vertical transmission. Integration into normal somatic cells, no matter how widespread during an acute infection, will not produce a inheritable endogenous virus in animals, but may in other kingdoms. Because germ cells are a numerically small and often physically isolated target, germline integration is exceedingly rare relative to infection, as such many endogenous viral elements (EVEs) appear to descend from single ancient integration events rather than repeated independent endogenizations.

Once endogenized as a heterozygous insertion in one individual, an EVE is subject to the same forces as any new allele. Neutral or only slightly deleterious EVEs may drift to fixation, while those that are beneficial can spread by selection.

Mechanism

Retroviruses

A reverse transcriptase of HIV-1

Main article: Endogenous retrovirus

Retroviruses encode reverse transcriptase, which converts the RNA genome into double-stranded DNA, and integrase, which inserts that DNA into the host chromosome as a provirus. Because integration is an obligatory step in retroviral replication, occasional germline integration is a normal feature of retroviral biology, making endogenous retroviruses (ERVs) the most abundant class of EVE in vertebrate genomes, including humans where HERVs make up approximately 8% of the human genome.

RNA viruses

LINE-1 retrotransposon

The RNA viruses which encode no reverse transcriptase and whose life cycle is entirely cytoplasmic do not undergo direct or purposeful endogenization of their genes as a retrovirus might, however since the discovery and study of EVEs, it has been demonstrated that they can become endogenized through different means. Bornavirus-like elements from the Bornaviridae family exist in the genomes of humans, other primates, rodents, elephants and others, with some primate integrations dated to over 40 million years ago. Sequences related to Ebolavirus and Marburgvirus (Filoviridae family) were found endogenized in the genomes of rodents, bats and marsupials, indicating that filovirus-like viruses have been contributing germline sequences across mammalian lineages for tens of millions of years.

The endogenization mechanism differs by virus genome type. For ssRNA viruses in animals, the encoded reverse transcriptase of the host genome's LINE-1 elements can act on cytoplasmic viral mRNAs via "target-primed" reverse transcription (TPRT), many resulting EVEs carry poly(A) tails and target-site duplications consistent with this route. However some integration events lack these hallmarks, indicating additional pathways. dsRNA viruses are unsuitable for TPRT, yet totivirus-derived EVEs are widespread across insect genomes, demonstrating that dsRNA endogenization occurs altough the underlying route is uncharacterised.

Integration of a non-retroviral RNA virus sequences or NIRVS into a host cell.

In insects, non-retroviral integrated RNA virus sequences (NIRVS) are particularly enriched in genomic regions populated by LTR and LINE retrotransposons, suggesting this host machinery serves as the primary vehicle for endogenizing viral RNA within the germline. In the Aedes aegypti and Aedes albopictus mosquitoes, NIRVS derived from Flaviviridae and Rhabdoviridae viruses are abundant and produce Piwi-interacting RNA that seem to participate in antiviral defense. These same virus families have a strong presence in insects but have been endogenized across plant species as well.

In single-celled organisms such as dinoflagellates, the frequency of EVEs correlates across genera with host LINE retroelement abundance, and LINE-encoded reverse transcriptase sequences occur in close genomic proximity to insertion sites, attesting to retroelement-driven reverse transcription as the primary endogenization mechanism. DNA repair processes and co-infection with different viruses may also be alternative routes.

DNA viruses

DNA virus families have undergone endogenization by distinct routes. Hepadnaviridae, which replicate through an RNA intermediate using their own reverse transcriptase, have given rise to endogenous elements in birds, snakes, and other vertebrates. A near-complete hepadnaviral genome has been identified at syntenic chromosomal position across multiple bird lineages, dating the endogenization to the Mesozoic. Researchers have used shared hepadnaviral elements these lineages to calibrate a long-term molecular clock for the family. ssDNA viruses Circoviridae and Parvoviridae which lack reverse transcriptase have also been endogenized across mammals, seemingly through DNA repair.

A widespread endogenization of Caulimoviridae and Geminiviridae sequences has been observed in plants genomes. Neither family encodes an integrase, so integration occurs through illegitimate recombination at double-strand breaks. Plants lack a strict germ/soma differentiation as their meristematic cells remain pluripotent and can give rise to gamete-producing tissue, thus an infection in the right developmental context can produce lead to endogenization.

Giant viruses

Giant virus endogenization events correlate with presence of 5-Methylcytosine in eukaryotes.

The giant viruses of nucleocytoviricota can endogenize into eukaryotic host genomes, seemingly an incidental post-infection occurrence, as with other non-retrovial endogenization events. An exception to this is are the viruses of Phycodnaviridae, who encode integrase recombinases and follow a lysogenic life cycle within brown algae.

Epigenetic silencing of endogenized viral DNA can reduce fitness cost to the host, with 5-methylcytosine DNA methylation serving as a primary mechanism in eukaryotic lineages retaining 5mC. Their sequences tend to be hypermethylated, and experimental removal of 5mC is sufficient to reactivate viral gene transcription. Where 5mC is absent, histone methylation can serve an equivalent function, as observed in EsV-1 Ectocarpus provirus. Correspondingly, giant virus endogenizations in eukaryotes are primarily found in lineages with these mechanisms.

On the other hand, giant viruses appear to carry countermeasures against silencing, including viral-encoded DNA methyltransferases and histone demethylases that may protect the endogenized viruses from the host chromatin.

Once endogenized, a viral sequence may undergo progressive genomic erosion. Spliceosomal introns accumulate in viral genes, transposable elements invade the inserted region, and core viral genes may become lost or duplicated through chromosomal rearrangements. Retained genes exhibit high Ka/Ks ratios ratios compared to free-living homologs, whereas introns and protein-coding genes can be shared with flanking genomic regions, and can lead to gradual assimiliton through negative selection

Despite this, the amount of genetic material introduced by the endogenization of giant viruses in eukaryotes (such as Amoebidium) can become a potential source of evolutionary novelty, just as with more commonly endogenized viruses. Giant virus-derived genes have been identified outside their endogenous viral regions while simultaneously exhibiting normal methylation patterns, having presumably been co-opted by their hosts. Study of the endogenization of giant viruses, combined with their unique properties, has helped lend credence the hypothesis of viral eukaryogenesis.

Virophages

Virophages are small dsDNA viruses that parasitize giant viruses. Virophage genomes can undergo endogenization into those of single-celled eukaryotes, and then reactivate upon infection by a giant virus, thereby providing a form of inducible antiviral defense. They encode integrase related to those of Polinton elements, integration is non site-specific and can occur in the nuclear genome of their host in various chromosomal positions, where they produce silent provirophages. Some virophages carry a second integration enzyme, a tyrosine recombinase, suggesting independent acquisitions of integration capacity across lineages.

Effect

Further information: Endogenous viral element and Junk DNA

Endogenization of viral elements typically creates non-functional relics that accumulate mutations and persist by neutral drift, with their original coding capacity eroded. Still, a subset has been exapted for host functions, usually retroviral sequences. endogenous bornavirus-like nucleoproteins have been proposed to interfere with replication of exogenous bornaviruses, representing a form of inheritable antiviral immunity created by past infections. Aberrant reactivation of silenced EVEs has been associated with autoimmune and inflammatory conditions in vertebrates, although establishing certain causality remains a challenge in medical research.

See also

• Koala retrovirus
• Endogenous foamy viruses
• Transposable element
• Long interspersed nuclear element