A novel class III endogenous retrovirus with a class I envelope gene in African frogs with an intact genome and developmentally regulated transcripts in Xenopus tropicalis

Abstract

Background Retroviruses exist as exogenous infectious agents and as endogenous retroviruses (ERVs) integrated into host chromosomes. Such endogenous retroviruses (ERVs) are grouped into three classes roughly corresponding to the seven genera of infectious retroviruses: class I (gamma-, epsilonretroviruses), class II (alpha-, beta-, delta-, lentiretroviruses) and class III (spumaretroviruses). Some ERVs have counterparts among the known infectious retroviruses, while others represent paleovirological relics of extinct or undiscovered retroviruses. Results Here we identify an intact ERV in the Anuran amphibian, Xenopus tropicalis. XtERV-S has open reading frames (ORFs) for gag, pol (polymerase) and env (envelope) genes, with a small additional ORF in pol and a serine tRNA primer binding site. It has unusual features and domain relationships to known retroviruses. Analyses based on phylogeny and functional motifs establish that XtERV-S gag and pol genes are related to the ancient env-less class III ERV-L family but the surface subunit of env is unrelated to known retroviruses while its transmembrane subunit is class I-like. LTR constructs show transcriptional activity, and XtERV-S transcripts are detected in embryos after the maternal to zygotic mid-blastula transition and before the late tailbud stage. Tagged Gag protein shows typical subcellular localization. The presence of ORFs in all three protein-coding regions along with identical 5’ and 3’ LTRs (long terminal repeats) indicate this is a very recent germline acquisition. There are older, full-length, nonorthologous, defective copies in Xenopus laevis and the distantly related African bullfrog, Pyxicephalus adspersus. Additional older, internally deleted copies in X. tropicalis carry a 300 bp LTR substitution. Conclusions XtERV-S represents a genera-spanning member of the largely env-less class III ERV that has ancient and modern copies in Anurans. This provirus has an env ORF with a surface subunit unrelated to known retroviruses and a transmembrane subunit related to class I gammaretroviruses in sequence and organization, and is expressed in early embryogenesis. Additional XtERV-S-related but defective copies are present in X. tropicalis and other African frog taxa. XtERV-S is an unusual class III ERV variant, and it may represent an important transitional retroviral form that has been spreading in African frogs for tens of millions of years.

Envelope Recombination: A Major Driver in Shaping Retroviral Diversification and Evolution within the Host Genome

“…A very recent example of Env acquisition is the recombination between ERVs of class III spumaretrovirus and class I gammaretrovirus which leads to the emergence of novel XtERV-S. An intact ERV, i.e, Xenopus tropicalis (XtERV-S), was identified in Anuran amphibians by Yedavalli.V et al in 2021 [ 64 ]. This newly reported ERV showed an unusual domain relationship to the known retroviruses, with it having close sequence homology of gag–pol genes with the ancient class III ERVs while the env gene showed major differences.…”

“…This newly reported ERV showed an unusual domain relationship to the known retroviruses, with it having close sequence homology of gag–pol genes with the ancient class III ERVs while the env gene showed major differences. The SU of the env gene did not show a close relationship with any of the known retroviruses and the TM region was observed to be homologous to gammaretroviruses based on its organization and functional motifs [ 64 ]. The CWIC motif present in the TM region of XtERV-S has the potential to establish a covalent bond with its gamma-like TM env .…”

“…As described above, multiple events of env exchange recombination have been observed between class I and class II retroviruses in different species, but XtERV-S is an unusual example of an intact and non-defective ERV genome having the class III ERV backbone with class I env . Therefore, the XtERV-S might represent the ancient evolutionary retroviral form with a combination of viral genes that are not present in modern mammalian retroviruses but are still circulating in African frogs [ 64 ].…”

Exploring the role of endogenous retroviruses in seasonal reproductive cycles: a case study of the ERV-V envelope gene in mink

“…Such transmission events can occur in the form of an endogenous viral (or endogenous retroviral; ERV) element ( Skirmuntt and Katzourakis, 2019 ; Barnes and Price, 2023 ; Liu et al., 2023 ). ERVs are grouped into the following three categories based on the similarities between their reverse transcriptase (RT) sequences and those of other Retroviridae viruses; class I (gamma- and epsilon-RVs) and class II (alpha-, beta-, delta-, and lenti-RVs) are known as ortho-RVs; class III shows a high similarity with spuma-RVs ( Yedavalli et al., 2021 ). Despite originating from viruses that undergo rapid evolution, ERVs undergo genetic drift following integration into the host genome and are influenced by the neutral mutation rate of the host species ( Simpson et al., 2022 ; Kassiotis, 2023 ; Dopkins and Nixon, 2024 ).…”

Unique Structure and Distinctive Properties of the Ancient and Ubiquitous Gamma-Type Envelope Glycoprotein

“…Gammaretrovirus-related ERV loci are abundant in the genomes of a diverse array of vertebrate species, including mammals, birds/reptiles and amphibians [ 28 , 29 , 30 , 31 , 32 ]. Distantly related ERV loci encoding gamma-type Env can also be found in amphibian genomes [ 33 ] and in avian genomes, including recombinant forms [ 34 ] and loci closely related to those of exogenous avian leukemia virus (ALV) [ 29 , 30 ]. Mirroring the situation with exogenous betaretroviruses, ERV related to the betaretroviruses include recombinant forms that appear to have acquired a gamma-type env gene via recombination [ 6 , 34 ].…”