Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses

Polavarapu, Nalini; Bowen, Nathan J.; McDonald, John F.

doi:10.1186/gb-2006-7-6-r51

Cited by 49 publications

(51 citation statements)

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“…Genome-wide screening for all genera of retroviruses has been performed in many species of mammals and birds (11)(12)(13), revealing a rich diversity of gammaretroviruses, a genus closely related to epsilonretroviruses. However, epsilon-like ERVs have not been identified in most mammals.…”

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confidence: 99%

Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates

Brown

Emes

Tarlinton

2014

J Virol

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Several types of cancer in fish are caused by retroviruses, including those responsible for major outbreaks of disease, such as walleye dermal sarcoma virus and salmon swim bladder sarcoma virus. These viruses form a phylogenetic group often described as the epsilonretrovirus genus. Epsilon-like retroviruses have become endogenous retroviruses (ERVs) on several occasions, integrating into germ line cells to become part of the host genome, and sections of fish and amphibian genomes are derived from epsilon-like retroviruses. However, epsilon-like ERVs have been identified in very few mammals. We have developed a pipeline to screen full genomes for ERVs, and using this pipeline, we have located over 800 endogenous epsilon-like ERV fragments in primate genomes. Genomes from 32 species of mammals and birds were screened, and epsilon-like ERV fragments were found in all primate and tree shrew genomes but no others. These viruses appear to have entered the genome of a common ancestor of Old and New World monkeys between 42 million and 65 million years ago. Based on these results, there is an ancient evolutionary relationship between epsilon-like retroviruses and primates. Clearly, these viruses had the potential to infect the ancestors of primates and were at some point a common pathogen in these hosts. Therefore, this result raises questions about the potential of epsilonretroviruses to infect humans and other primates and about the evolutionary history of these retroviruses. IMPORTANCEEpsilonretroviruses are a group of retroviruses that cause several important diseases in fish. Retroviruses have the ability to become a permanent part of the DNA of their host by entering the germ line as endogenous retroviruses (ERVs), where they lose their infectivity over time but can be recognized as retroviruses for millions of years. Very few mammals are known to have epsilon-like ERVs; however, we have identified over 800 fragments of endogenous epsilon-like ERVs in the genomes of all major groups of primates, including humans. These viruses seem to have circulated and infected primate ancestors 42 to 65 million years ago. We are now interested in how these viruses have evolved and whether they have the potential to infect modern humans or other primates.

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Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates

Brown

Emes

Tarlinton

2014

J Virol

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“…This route of transmission results in an organism-wide presence of provirus in the genomes of progeny. Such endogenization events have occurred numerous times during primate evolution and many proviruses have become fixed in host populations (2)(3)(4)(5). Endogenous retroviruses thus represent a record of ancient infections and these "paleoviruses" can provide information about the evolution of host-virus interactions (6,7).…”

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“…Endogenous γ-retroviruses are abundant in primate genomes and among them, chimpanzee endogenous retroviruses-1 and -2 (CERV1 and CERV2) and their relatives are the groups most closely related to the modern prototype γ-retrovirus, MLV (3,4). CERV1 and -2 are assumed to be extinct, although without exhaustive sampling, it is nearly impossible to definitively demonstrate that intact exogenous relatives are not currently replicating in some modern primate species.…”

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Identification of a receptor for an extinct virus

Soll

Neil

Bieniasz

2010

Proc. Natl. Acad. Sci. U.S.A.

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The resurrection of endogenous retroviruses from inactive molecular fossils has allowed the investigation of interactions between extinct pathogens and their hosts that occurred millions of years ago. Two such paleoviruses, chimpanzee endogenous retrovirus-1 and -2 (CERV1 and CERV2), are relatives of modern MLVs and are found in the genomes of a variety of Old World primates, but are absent from the human genome. No extant CERV1 and -2 proviruses are known to encode functional proteins. To investigate the host range restriction of these viruses, we attempted to reconstruct functional envelopes by generating consensus genes and proteins. CERV1 and -2 enveloped MLV particles infected cell lines from a range of mammalian species. Using CERV2 Env-pseudotyped MLV reporters, we identified copper transport protein 1 (CTR1) as a receptor that was presumably used by CERV2 during its ancient exogenous replication in primates. Expression of human CTR1 was sufficient to confer CERV2 permissiveness on otherwise resistant hamster cells, and CTR1 knockdown or CuCl 2 treatment specifically inhibited CERV2 infection of human cells. Mutations in highly conserved CTR1 residues that have rendered hamster cells resistant to CERV2 include a unique deletion in a copper-binding motif. These CERV2 receptor-inactivating mutations in hamster CTR1 are accompanied by apparently compensating changes, including an increased number of extracellular coppercoordinating residues, and this may represent an evolutionary barrier to the acquisition of CERV2 resistance in primates.endogenous retrovirus | copper transport T he ability of retroviruses to integrate into the genomes of target cells allows for the possibility of Mendelian inheritance of proviruses if integration into the host germ line occurs (1). This route of transmission results in an organism-wide presence of provirus in the genomes of progeny. Such endogenization events have occurred numerous times during primate evolution and many proviruses have become fixed in host populations (2-5). Endogenous retroviruses thus represent a record of ancient infections and these "paleoviruses" can provide information about the evolution of host-virus interactions (6, 7).Endogenous γ-retroviruses are abundant in primate genomes and among them, chimpanzee endogenous retroviruses-1 and -2 (CERV1 and CERV2) and their relatives are the groups most closely related to the modern prototype γ-retrovirus, MLV (3, 4). CERV1 and -2 are assumed to be extinct, although without exhaustive sampling, it is nearly impossible to definitively demonstrate that intact exogenous relatives are not currently replicating in some modern primate species. They are of particular interest because of their peculiar absence from the human genome, although homologs exist in the genomes of chimpanzee, bonobo, gorilla, and Old World monkeys. Thus, both viruses apparently replicated after the divergence of the human and chimpanzee lineages approximately 6 million years ago, with zoonoses ultimately resulting in endogenization in diver...

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“…Rodrigo Ramalho deu início a procura de ERV da família K nos genomas humano e de chimpanzé, utilizando as ferramentas Blastn e Fastacmd (Polavarapu et al, 2006a;Polavarapu et al, 2006b Se-Al (Rambaut, 1996). Para as análises filogenéticas, os alinhamentos foram exportados em formato nexus e utilizados como entrada para os programas de reconstrução.…”

Section: Busca E Mapeamento In Silico De Genomas Completos De Erv-k Eunclassified

Caracterização e dinâmica evolutiva de retrovírus endógenos da família K (ERV-K) em genomas de primatas.

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Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses

Cited by 49 publications

References 50 publications

Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates

Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates

Identification of a receptor for an extinct virus

Caracterização e dinâmica evolutiva de retrovírus endógenos da família K (ERV-K) em genomas de primatas.

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