Identification and Characterization of Two Closely Related Unclassifiable Endogenous Retroviruses in Pythons (<i>Python molurus</i>and<i>Python curtus</i>)

The structure of the transmembrane subunit (TM) of the retroviral envelope glycoprotein (Env) is highly conserved among most retrovirus genera and includes a pair of cysteines that forms an intramolecular disulfide loop within the ectodomain. Alpha-, gamma-, and deltaretroviruses have a third cysteine, adjacent to the loop, which forms a disulfide bond between TM and the surface subunit (SU) of Env, while lentiviruses, which have noncovalently associated subunits, lack this third cysteine. The Betaretrovirus genus includes Jaagsiekte sheep retrovirus (JSRV) and mouse mammary tumor virus (MMTV), as well as many endogenous retroviruses. Envelope subunit association had not been characterized in the betaretroviruses, but lack of a third cysteine in the TM ectodomain suggested noncovalently associated subunits. We tested the Env proteins of JSRV and MMTV, as well as human endogenous retrovirus K (HERV-K)108 -a betaretrovirus-like human endogenous retrovirus-for intersubunit bonding and found that, as in the lentiviruses, the Env subunits lack an intersubunit disulfide bond. Since these results suggest that the number of cysteines in the TM loop region readily distinguishes between covalent and noncovalent structure, we surveyed endogenous retroviral TM sequences in the genomes of vertebrates represented in public databases and found that (i) retroviruses with noncovalently associated subunits have been present during all of anthropoid evolution and (ii) the noncovalent env motif is limited to mammals, while the covalent type is found among five vertebrate classes. We discuss implications of these findings for retroviral evolution, cross-species transmissions, and recombination events involving the env gene. R etrovirus infection is mediated by the envelope (Env) glycoprotein, which is a class I viral fusion protein (VFP) in all of the orthoretroviral genera except the epsilonretroviruses. Class I VFPs are synthesized as precursors that trimerize in the endoplasmic reticulum and are cleaved by cellular furin in the late Golgi apparatus to generate two subunits: a surface subunit (SU), which interacts with the receptor on target cells, and a transmembrane subunit (TM), which mediates fusion and is anchored in the viral envelope near its C terminus. After cleavage, SU and TM remain associated either noncovalently or via an intersubunit disulfide bond (1-3, 82, 83), resulting in trimers of heterodimers that traffic to the cell's plasma membrane to become part of the viral envelope when newly synthesized particles bud from the cell (4).During infection, the fusion subunits of class I VFPs go through a series of conformational changes that lead from a metastable to a stable state. The first conformational change, which occurs upon binding of SU to the receptor, exposes a hydrophobic region at the N terminus of TM-the fusion peptide-which inserts into the plasma membrane of the target cell. This step then triggers the formation by TM of a highly stable six-helix bundle, a trimeric hairpin structure built around alpha-helic...

Section: Discussionmentioning

confidence: 99%

Betaretroviral Envelope Subunits Are Noncovalently Associated and Restricted to the Mammalian Class

Henzy

Coffin

2013

“…All procedures relating to this work are described in detail elsewhere (11). In short, milk plasma from seropositive goats was tested for reverse transcriptase (RT) activity by the product-enhanced RT (PERT) assay (20), and 1.0 ml of the sample with the highest activity was fractionated on a 7.5 to 60% sucrose density gradient.…”

Section: Methodsmentioning

confidence: 99%

“…In short, milk plasma from seropositive goats was tested for reverse transcriptase (RT) activity by the product-enhanced RT (PERT) assay (20), and 1.0 ml of the sample with the highest activity was fractionated on a 7.5 to 60% sucrose density gradient. The fraction with peak RT activity and a density of 1.15 g/ml was used for amplification of the full-length viral RNA sequence by particle-associated retroviral RNA amplification (PARRA), restricting the initial cDNA synthesis in the 5Ј rapid amplification of cDNA ends (RACE) step of PARRA to priming by primer pK1 (11). DNA sequence information obtained from PARRA was used to design specific primers for nested PCR.…”

Section: Methodsmentioning

confidence: 99%

Direct Evidence for Natural Transmission of Small-Ruminant Lentiviruses of Subtype A4 from Goats to Sheep and Vice Versa

Shah

Huder

Böni

et al. 2004

Self Cite

113

Small-ruminant lentiviruses (SRLV), which include the caprine arthritis-encephalitis and the maedi-visna virus, cause persistent inflammatory infections in goats and sheep. SRLV are mainly transmitted from mother to offspring through milk. Transmission after prolonged contact between adult animals has also been observed. The observation that certain SRLV subtypes are found in both goats and sheep suggests that interspecies transmission has occurred on several occasions in the past. We investigated seropositive goats and sheep that were kept together in small mixed herds. Phylogenetic analysis of long proviral sequences in gag and pol, combined with epidemiologic information, demonstrated natural sheep-to-goat transmission of the recently identified SRLV subtype A4 in two instances and goat-to-sheep transmission of the same subtype in one instance. In a further mixed cluster, the direction of the interspecies transmission could not be determined. These findings present for the first time direct evidence that natural interspecies transmission of SRLV is ongoing in both directions. The findings are of relevance to virus eradication programs in both species. (14,17,18,28). Earlier phylogenetic analysis, mostly based on short sequences, has suggested that these very diverse viruses can be divided into six different sequence clades, I to VI (12,21,22,32). Recent work based on long sequences in gag and pol of more than 100 new isolates from Switzerland and all available database sequences has, however, demonstrated that the SRLV should rather be divided into four principal sequence groups A to D, which differ by 25 to 37% in gag and pol sequences. Sequence groups A and B are further divided into different subtypes that differ from each other by 15 to 27%. Group A contains at least 7 subtypes, A1 to A7, and group B contains two subtypes, B1 and B2 (26). To date, subtypes A1 and A2 have been isolated only from sheep, and subtypes A5, A7, and B1 and groups C and D have been isolated only from goats. In contrast, subtypes A3, A4, A6, and B2 have been isolated from both sheep and goats. Caprine arthritis-encephalitis virus (CAEV) and maedivisna virus (MVV) are small-ruminant lentiviruses (SRLV) that infect goats and sheep

“…Other such recombinants have been described in mammals, including the exogenous and endogenous primate type D betaretroviruses (e.g., MPMV) (12, 29, 34), a recently described bat ERV (35), and endogenous intracisternal A particles (IAPs), which have recombined with gammaretroviral env, in the genomes of the shrew and guinea pig (36). The only previously characterized class II/gammaretroviral recombinants found outside mammals are two related ERVs of pythons (PyERV) (37). Second, TgERV-F demonstrates a unique mix of alpha-, beta-, and gammaretroviral features.…”

Section: Figmentioning

confidence: 99%

A Novel Recombinant Retrovirus in the Genomes of Modern Birds Combines Features of Avian and Mammalian Retroviruses

Henzy

Gifford

Johnson

et al. 2014

Endogenous retroviruses (ERVs) represent ancestral sequences of modern retroviruses or their extinct relatives. The majority of ERVs cluster alongside exogenous retroviruses into two main groups based on phylogenetic analyses of the reverse transcriptase (RT) enzyme. Class I includes gammaretroviruses, and class II includes lentiviruses and alpha-, beta-, and deltaretroviruses. However, analyses of the transmembrane subunit (TM) of the envelope glycoprotein (env) gene result in a different topology for some retroviruses, suggesting recombination events in which heterologous env sequences have been acquired. We previously demonstrated that the TM sequences of five of the six genera of orthoretroviruses can be divided into three types, each of which infects a distinct set of vertebrate classes. Moreover, these classes do not always overlap the host range of the associated RT classes. Thus, recombination resulting in acquisition of a heterologous env gene could in theory facilitate cross-species transmissions across vertebrate classes, for example, from mammals to reptiles. Here we characterized a family of class II avian ERVs, "TgERV-F," that acquired a mammalian gammaretroviral env sequence. Although TgERV-F clusters near a sister clade to alpharetroviruses, its genome also has some features of betaretroviruses. We offer evidence that this unusual recombinant has circulated among several avian orders and may still have infectious members. In addition to documenting the infection of a nongalliform avian species by a mammalian retrovirus, TgERV-F also underscores the importance of env sequences in reconstructing phylogenies and supports a possible role for env swapping in allowing cross-species transmissions across wide taxonomic distances. IMPORTANCERetroviruses can sometimes acquire an envelope gene (env) from a distantly related retrovirus. Since env is a key determinant of host range, such an event affects the host range of the recombinant virus and can lead to the creation of novel retroviral lineages. Retroviruses insert viral DNA into the host DNA during infection, and therefore vertebrate genomes contain a "fossil record" of endogenous retroviral sequences thought to represent past infections of germ cells. We examined endogenous retroviral sequences in avian genomes for evidence of recombination events involving env. Although cross-species transmissions of retroviruses between vertebrate classes (from mammals to birds, for example) are thought to be rare, we here characterized a group of avian retroviruses that acquired an env sequence from a mammalian retrovirus. We offer evidence that this unusual recombinant circulated among songbirds 2 to 4 million years ago and has remained active into the recent past.