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Mol. Biol. Evol. 20(1):38-46. 2003
DOI: 10.1093/molbev/msg011
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

The Esterase and PHD Domains in CR1-Like Non-LTR Retrotransposons

Vladimir V. Kapitonov and Jerzy Jurka

Genetic Information Research Institute, Mountain View, California

Most active non-LTR (long terminal repeat) retrotransposons carry two open reading frames (ORFs) encoding ORF1p and ORF2p proteins. The ORF2p proteins are relatively well studied and are known to contain endonuclease/reverse transcriptase domains. At the same time, the biological function of ORF1p proteins remains poorly understood, except in that they nonspecifically bind single-stranded mRNA/DNA molecules. CR1-like elements form the most widely distributed clade/superfamily of non-LTR retrotransposons. We found that ORF1p proteins encoded by diverse CR1-like elements contain conserved esterase domain (ES) or plant homeodomain (PHD). This indicates that CR1-like ORF1p proteins are either lipolytic enzymes or are involved in protein-protein interactions related to chromatin remodeling. Sequence conservation of ES suggests that interaction with cellular membranes is an important phase in life circles of CR1-like elements. Presumably such interaction helps in penetrating host cells. As a consequence, the presence of multiple young CR1 families characterized by ~10% intrafamily and 40% interfamily identities may be explained by a relatively frequent horizontal transfer of these CR1-like elements. Unexpectedly, ES links together non-LTR retrotransposons and single-stranded RNA viruses like influenza C and coronaviruses, which are known to depend on their own ES.

Key Words: non-LTR retrotransposon • CR1 clade • ORF1p • esterase • PHD homeodomain


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