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Full-length HERV-H elements with env SU open reading frames in the human genome.
Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Sciences. (klinisk virologi)
Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Sciences. (klinisk virologi)
Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Sciences. (klinisk virologi)
Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Sciences. (klinisk virologi)
2002 (English)In: AIDS Res Hum Retroviruses, ISSN 0889-2229, Vol. 18, no 9, 671-6 p.Article in journal (Refereed) Published
Place, publisher, year, edition, pages
2002. Vol. 18, no 9, 671-6 p.
Keyword [en]
Amino Acid Sequence, Chromosomes; Human; Pair 1, Chromosomes; Human; Pair 2, Endogenous Retroviruses/*genetics, Gene Products; env/*genetics, Genome; Human, Humans, Molecular Sequence Data, Multigene Family, Mutation, Open Reading Frames/genetics, Retroviridae Proteins/*genetics, Sequence Homology; Amino Acid
Identifiers
URN: urn:nbn:se:uu:diva-74374PubMedID: 12079564OAI: oai:DiVA.org:uu-74374DiVA: diva2:102284
Available from: 2005-09-22 Created: 2005-09-22 Last updated: 2011-01-13
In thesis
1. Genomic Variation and Evolution of HERV-H and other Endogenous Retroviruses (ERVs)
Open this publication in new window or tab >>Genomic Variation and Evolution of HERV-H and other Endogenous Retroviruses (ERVs)
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

An exogenous retrovirus (XRV) that integrates into a germ cell may be inherited as a Mendelian gene; it becomes an endogenous retrovirus (ERV). The human genome consists of up to 8% HERVs.

The gammaretroviral (ERV class I) HERV-H, with 926 members, is the largest ERV group. Despite millions of years since integration, it has polymorphic envelope open reading frames in at least three loci. Selections for functional envelopes are indicated on chromosomes 1 and 2. However, envelopes were present only in a fraction of the total HERV-H. Mutated polymerases, indicating old ERVs, contradicted relatively intact long terminal repeats. To explain this, we formulated a “Midwife” element theory where proteins are complemented in trans.

A phylogenetic analysis did not support separate HERV-H and -F groups. The new taxonomy included HERV-H like (RGH2-like and RTVLH2-like subgroups) and Adjacent HERV-H like. A bioinformatic reconstruction of a putative ancestral HERV-H exposed novel traits. Two nucleocapsid zinc fingers and a pronounced nucleotide bias for C in the HERV-H like were unique among the gammaretroviruses.

Two recently integrated gammaretroviral groups (PtNeo-I[PTERV1] and -II) were found in chimpanzees but not in humans. The PtNeo groups were most similar to baboon ERVs and a macaque sequence, but neither to other chimpanzee nor to any human gammaretroviruses. The pattern was consistent with cross-species transfer via predation.

To advance the retroviral taxonomy, we projected structural markers over sequence phylogenetic trees. A number of markers were useful to distinguish between genera and to delineate groups.

Basic retroviral knowledge is vital to understand emerging infections. Phylogenetic analyses of taxonomically improved sequences, facilitates the search for common retroviral denominators to target. This thesis provided new insights in retroviral evolution and taxonomy using the ERVs, with special focus on the large gammaretroviral HERV-H group, as an additional source of information next to that of XRVs.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2005. 77 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 62
Keyword
Microbiology, Endogenous Retrovirus (ERV), HERV-H, Phylogeny, Evolution, Sequence Variation, Polymorphism, Recent Integrations, Horizontal Transfer, Master Elements, Taxonomy, Mikrobiologi
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-5906 (URN)91-554-6319-3 (ISBN)
Public defence
2005-10-01, Föreläsningssalen, Klinisk virologi, Akademiska Sjukhuset, ing. D1, Dag Hammarkjölds väg 17, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2005-09-09 Created: 2005-09-09 Last updated: 2011-09-06Bibliographically approved

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Jern, PatricLindeskog, MatsBlomberg, Jonas

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