Genetic Aspects Of Viral Oncogenesis In Inbred Strains and Wild Mouse Species

National Institute Of Allergy And Infectious Diseases

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Abstract

Our work has long focused on mouse leukemia viruses (MLVs), some of which are pathogenic, the various host factors that restrict the replication of these viruses, and the adaptive co-evolution of interactive host/pathogen pairings. This work examines laboratory mouse strains as well as wild mice for a broad sampling of the genetic diversity in Mus and to examine survival strategies in natural populations that harbor virus and in geographically separated species. The wild mice additionally provide a source of novel resistance genes and virus variants. In FY23, we expanded these studies to describe unusual and functionally important ERVs (endogenous retroviruses) found in other mammalian species and initiated a project to examine MMTVs (mouse mammary tumor viruses) in inbred and wild mice. In FY23, we identified two ancient related non-orthologous ERV env (envelope) genes, ARTenvV and CARenvV, that are preserved with large open reading frames (ORFs) in the mammalian orders Artiodactyla and Carnivora, respectively, but are not found in other mammals. These Env proteins lack a transmembrane motif, but phylogenetic analyses show strong sequence preservation and positive selection of the env surface domsin in their respective orders. Transcriptomic analyses showed a broad tissue expression pattern for both ARTenvV and CARenvV, suggesting that these genes may be exapted for a host function. Multiple lines of evidence indicate that ARTenvV and CARenvV were derived from an ancient ancestral exogenous gamma-like retrovirus that was independently endogenized in two mammalian orders more than 60 million years ago, which roughly coincides with the K-Pg mass extinction event and subsequent mammalian diversification. Thus, these findings identify the oldest known retroviral cross-ordinal transmission of a gamma-like retrovirus with no known extant infectious counterpart in mammals, and the first discovery of the convergent co-option of an ERV gene derived from the same ancestral retrovirus in two different mammalian orders. In Fy23, we expanded on our previous identification of a co-opted gag gene discovered in simian primates that is placenta specific in its expression. This is noteworthy because most studies on co-opted ERVs have focused on envelope genes, including the syncytins that function in placentation. In a search for other intact gag genes in non-primate mammalian lineages, we began by searching for intact ERV gag genes in the genomes of extant camel species which is a basal lineage in the order Artiodactyla. We found a gagpol gene with a large open reading frame (ORF) (>3500 bp) in the same orthologous location in Artiodactyla species but that is absent in other mammals. Thus, this ERV was fixed in the common ancestor of all Artiodactyla at least 64 million years ago. The amino acid sequence of this gene, termed ARTgagpol, contains recognizable matrix, capsid, nucleocapsid, reverse transcriptase domains in ruminants, with an RNase H domain in camels and pigs. Phylogenetic analysis and structural prediction of its reverse transcriptase and RNase H domains groups ARTgagpol with gammaretroviruses. Transcriptomic analysis shows ARTgagpol expression in multiple tissues suggestive of a co-opted host function. These findings identify the oldest and largest ERV-derived gagpol gene with an intact ORF in mammals, an intriguing milestone in the co-evolution of mammals and retroviruses. In FY22, we concentrated on the different susceptibilities of mice to infection by MLVs (mouse leukemia viruses) and to virus-induced diseases, documenting the adaptive spatial and temporal co-evolutionary trajectories at the critical interfaces of MLVs and the host factors that restrict their replication. In FY23 we directed this interest to an examination of mouse mammary tumor viruses (MMTVs). Analysis of the sequenced genomes of 17 Mus musculus strains and species identified 29 distinct MMTV ERVs (termed Mtvs). Sequence variations representing functional variants mark the C-terminal ends of the pol (polymerase) and sag (superantigen) genes while mutational changes result from often major editing by the antiviral cytidine deaminase Apobec3. Most laboratory mouse Mtvs predate the development of inbred strains except the intact and expressed Mtv1 which endogenized more recently. Mtv ERVs are found in all Mus musculus subspecies and in Mus spretus, but none are orthologs of inbred strain Mtvs and the only shared wild mouse Mtv is a variant found in SE Asia. Most Mtvs are intact with multiple open reading frames (ORFs), but many wild mouse Mtvs have an unusual deletion in envelope (env). This deletion corresponds to an intron of the MMTV Rem accessory factor suggesting its derivation from spliced MMTV cDNAs. These deleted ERV envs show subspecies specific sequence variation and are found in geographically separated M. musculus subspecies consistent with their recurrent generation. The highly variable Sag gene, responsible for resistance to exogenous infection, shows evidence of recombination and positive selection, but the spread of Mtvs in Mus is not marked by an active arms race pitting the MMTV env against its cellular receptor. Thus, acquisition of potentially disease-inducing Mtvs is a recent and ongoing process in Mus accompanied by recombination, positive selection and recurrent env deletions.