Filipe Pereira, Roman Biek, Alberto Alberti, Kreg Leymaster, Ya-ping Zhang, Manuela Mura, Matthew C. Golder, Massimo Palmarini, Li Yu, Bernardo Chessa, Mariana Varela, Frederick Arnaud, Marco Caporale, James C. DeMartini, Thomas E. Spencer, Unité mixte de recherche retrovirus et pathologie comparée, Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA), Institute of Comparative Medicine, Veterinary School, University of Glasgow, Sezione di Malattie Infettive del Dipartimento di Patologia e Clinica Veterinaria, University of Sassari, Physics, King‘s College London, State Key Laboratory of Genetic Resources, Kunming Institute of Zoology, Chinese Academy of Agricultural Sciences (CAAS), Modélisation, Information et Systèmes - UR UPJV 4290 (MIS), Université de Picardie Jules Verne (UPJV), Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Colorado State University [Fort Collins] (CSU), US Meat Animal Research Center, Institut du Développement Durable et des Relations Internationales (IDDRI), Institut d'Études Politiques [IEP] - Paris, Centre for Virus Research, MRC - University of Glasgow Centre for Virus Research, Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Faculdade de Ciências, Department of Microbiology, Immunology and Pathology, Center for Animal Biotechnology and Genomics, Department of Animal Science, and Texas A&M University System
Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of the host germline transmitted vertically from generation to generation. It is hypothesized that some ERVs are used by the host as restriction factors to block the infection of pathogenic retroviruses. Indeed, some ERVs efficiently interfere with the replication of related exogenous retroviruses. However, data suggesting that these mechanisms have influenced the coevolution of endogenous and/or exogenous retroviruses and their hosts have been more difficult to obtain. Sheep are an interesting model system to study retrovirus-host coevolution because of the coexistence in this animal species of two exogenous (i.e., horizontally transmitted) oncogenic retroviruses, Jaagsiekte sheep retrovirus and Enzootic nasal tumor virus, with highly related and biologically active endogenous retroviruses (enJSRVs). Here, we isolated and characterized the evolutionary history and molecular virology of 27 enJSRV proviruses. enJSRVs have been integrating in the host genome for the last 5–7 million y. Two enJSRV proviruses (enJS56A1 and enJSRV-20), which entered the host genome within the last 3 million y (before and during speciation within the genus Ovis), acquired in two temporally distinct events a defective Gag polyprotein resulting in a transdominant phenotype able to block late replication steps of related exogenous retroviruses. Both transdominant proviruses became fixed in the host genome before or around sheep domestication (∼ 9,000 y ago). Interestingly, a provirus escaping the transdominant enJSRVs has emerged very recently, most likely within the last 200 y. Thus, we determined sequentially distinct events during evolution that are indicative of an evolutionary antagonism between endogenous and exogenous retroviruses. This study strongly suggests that endogenization and selection of ERVs acting as restriction factors is a mechanism used by the host to fight retroviral infections., Author Summary The genome of all vertebrates is heavily colonized by “endogenous” retroviruses (ERVs). ERVs derive from retrovirus infections of the germ cells of the host during evolution, leading to permanent integration of the viral genome into the host DNA. Because ERVs are integrated in the host genome, they are transmitted to subsequent generations like any other host gene. The function of endogenous retroviruses is not completely clear, but some ERVs can block the replication cycle of horizontally transmitted “exogenous” pathogenic retroviruses. These observations lead to the hypothesis that ERVs have protected the host during evolution against incoming pathogenic retroviruses. Here, by characterizing the evolutionary history and molecular virology of a particular group of endogenous betaretroviruses of sheep (enJSRVs) we show a fascinating series of events unveiling the endless struggle between host and retroviruses. In particular, we discovered that: (i) two enJSRV loci that entered the host genome before speciation within the genus Ovis (∼ 3 million y ago) acquired, after their integration, a mutated defective viral protein capable of blocking exogenous related retroviruses; (ii) both these transdominant enJSRV loci became fixed in the host genome before or around sheep domestication (∼ 10,000 y ago); (iii) the invasion of the sheep genome by ERVs of the JSRV/enJSRVs group is still in progress; and (iv) new viruses have recently emerged (less than 200 y ago) that can escape the transdominant enJSRV loci. This study strongly suggests that endogenization and selection of ERVs acting as restriction factors is a mechanism used by the host to fight retroviral infections.