The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods

W D Burke; H S Malik; J P Jones; T H Eickbush

doi:10.1093/oxfordjournals.molbev.a026132

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The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods

Journal article

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Peer reviewed

The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods

W D Burke, H S Malik, J P Jones and T H Eickbush

Molecular biology and evolution, Vol.16(4), pp.502-511

04/1999

DOI: https://doi.org/10.1093/oxfordjournals.molbev.a026132

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https://hdl.handle.net/2376/112465

PMID: 10331276

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Abstract

Amino Acid Sequence

Endonucleases - genetics

Arthropods - genetics

Species Specificity

Retroelements

Models, Molecular

Molecular Sequence Data

DNA Primers - genetics

DNA - genetics

Proteins - genetics

Sequence Homology, Amino Acid

Animals

Base Sequence

RNA-Directed DNA Polymerase - genetics

Conserved Sequence

Protein Conformation

Proteins - chemistry

RNA, Ribosomal, 28S - genetics

Evolution, Molecular

R2 elements are non-LTR retrotransposons that insert in the 28S rRNA genes of arthropods. Partial sequence data from many species have previously suggested that these elements have been vertically inherited since the origin of this phylum. Here, we compare the complete sequences of nine R2 elements selected to represent the diversity of arthropods. All of the elements exhibited a uniform structure. Identification of their conserved sequence features, combined with our biochemical studies, allows us to make the following inferences concerning the retrotransposition mechanism of R2. While all R2 elements insert into the identical sequence of the 28S gene, it is only the location of the initial nick in the target DNA that is rigidly conserved across arthropods. Variation at the R2 5' junctions suggests that cleavage of the second strand of the target site is not conserved within or between species. The extreme 5' and 3' ends of the elements themselves are also poorly conserved, consistent with a target primed reverse transcription mechanism for attachment of the 3' end and a template switch model for the attachment of the 5' end. Comparison of the approximately 1,000-aa R2 ORF reveals that it can be divided into three domains. The central 450-aa domain can be folded by homology modeling into a tertiary structure resembling the fingers, palm, and thumb subdomains of retroviral reverse transcriptases. The carboxyl terminal end of the R2 protein appears to be the endonuclease domain, while the amino-terminal end contains zinc finger and c-myb-like DNA-binding motifs.

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Title: The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods
Creators: W D Burke - Department of Biology, University of Rochester, New York 14627-0211, USA
H S Malik
J P Jones
T H Eickbush
Publication Details: Molecular biology and evolution, Vol.16(4), pp.502-511
Academic Unit: Chemistry, Department of
Publisher: United States
Grant note: GM42790 / NIGMS NIH HHS
Identifiers: 99900547993201842
Language: English
Resource Type: Journal article