title: Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes.
abstract: Many non-long terminal repeat (non-LTR) retrotransposons lack internal promoters and are co-transcribed with their host genes. These transcripts need to be liberated before inserting into new loci. Using structure-based bioinformatics, we show that several classes of retrotransposons in phyla-spanning arthropods, nematodes, and chordates utilize self-cleaving ribozymes of the hepatitis delta virus (HDV) family for processing their 5' termini. Ribozyme-terminated retrotransposons include rDNA-specific R2, R4, and R6, telomere-specific SART, and Baggins and RTE. The self-scission of the R2 ribozyme is strongly modulated by the insertion site sequence in the rDNA, with the most common insertion sequences promoting faster processing. The ribozymes also promote translation initiation of downstream open reading frames in vitro and in vivo. In some organisms HDV-like and hammerhead ribozymes appear to be dedicated to processing long and short interspersed elements, respectively. HDV-like ribozymes serve several distinct functions in non-LTR retrotransposition, including 5' processing, translation initiation, and potentially trans-templating.
authors: Departments of Molecular Biology and Biochemistry, University of California, Irvine, California 92697.
authors: Dana J
authors: DJ
authors: Ruminski
authors: Departments of Molecular Biology and Biochemistry, University of California, Irvine, California 92697.
authors: Chiu-Ho T
authors: CT
authors: Webb
authors: Department of Chemistry, University of California, Irvine, California 92697.
authors: Nathan J
authors: NJ
authors: Riccitelli
authors: Departments of Molecular Biology and Biochemistry, University of California, Irvine, California 92697; Department of Chemistry, University of California, Irvine, California 92697; Department of Pharmaceutical Sciences, University of California, Irvine, California 92697. Electronic address: aluptak@uci.edu.
authors: Andrej
authors: A
authors: Lupták
mesh_terms: D000818:Animals; D002460:Cell Line; D004331:Drosophila melanogaster; D003698:Hepatitis Delta Virus / Q000235:genetics / Q000378:metabolism*; D016366:Open Reading Frames; D010442:Peptide Chain Initiation, Translational; D016337:RNA, Catalytic / Q000235:genetics / Q000378:metabolism*; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D018626:Retroelements; D020079:Terminal Repeat Sequences
chemical_list: D016337:RNA, Catalytic; D012367:RNA, Viral; D018626:Retroelements