Abstract
We have isolated and sequenced a genomic clone from Saccharomyces cerevisiae that shows structural features of a novel retrotransposon, designated Ty4. The element is 6.2 kilobases in length, and its genetic organization of the deduced functional domains is similar to Ty1 and Ty2 and thus different from Ty3. In contrast to hitherto known Ty elements from yeast, Ty4 is flanked by long terminal tau-element repeats instead of delta or sigma sequences. Ty4 contains two overlapping open reading frames. The first open reading frame, TYA4, is 1230 base pairs long and encodes a protein with a motif found in the nucleic acid-binding gag-protein of retroviruses. The second 4395-base pair open reading frame, TYB4, encodes a polyprotein that has domains with significant homology to retroviral protease, integrase, reverse transcriptase, and RNase H, structurally arranged in that order. The deduced amino acid sequence shows the greatest similarity with Ty2 and Ty1. The overall identity of the deduced functional protein domains is 28% with Ty2, 25% with Ty1, 19% with copia from Drosophila, and 18% with Ty3. Examination of genomic DNA from several laboratory strains indicates that Ty4 is present in two to four copies. Ty4 mRNA is of low abundance as compared to other Ty retrotransposons. At the 3' end of Ty4, two "solo" delta-elements, a full length and an overlapping, truncated one, are associated.
Highlights
Isolation and Sequence Analysisof Ty4-In search of a quite from amino acids 44-164 may code for a different yeast gene (Gunther et al, 1991) using oligonucleo- protease activity required for processing the polyprotein to tide probes, we have isolated a further,cross-hybridizing thematureproteins(VonderHelm, 1977; Yoshinakaand genomic clone, whose analysis led us to the identification of Luftig, 1977; Youngren et al, 1988)
A comparison of the predicted aminoacid sequence compiled is found at the active site of aspartyl proteases (Pearl and in data basesrevealed that Ty4 has homology with Tyl and Taylor, 1987)
Proteins is not highly conserved among retroviruses except Ty3 is differentwhere the organizationof the polyprotein for a small carboxyl-terminalmotif consisting of cysteine and isconcernedinthistransposonthe reverse transcriptase histidinearrangedasC-X2-C-X4-H-X4-C(Copeland et al, precedes the endonuclease domain (Clarekt al., 1988; Hansen 1984; Covey, 1986)
Summary
Isolation and Sequence Analysisof Ty4-In search of a quite from amino acids 44-164 (bases 1776-2139) may code for a different yeast gene (Gunther et al, 1991) using oligonucleo- protease activity required for processing the polyprotein to tide probes, we have isolated a further,cross-hybridizing thematureproteins(VonderHelm, 1977; Yoshinakaand genomic clone, whose analysis led us to the identification of Luftig, 1977; Youngren et al, 1988). L T R sequences contains twoverlapping openreading amino acids downstream by a pair of cysteines. Isreminiscent of themetal finger of some DNAbinding It may code for a 414-amino acid-long protein. Be- about 550 amino acids withnosignificant homology, the cause of its arrangement within the elementw, e have desig- presumptive domainsfor a reversetranscriptase (aminoacids nated ORFl asTYA (to be consistent with the yeast nomen- 965-1252; bases 4539-5402) and RNaseH The predicted domains structural proteinsof the nucleocapsid. The sequence of these have high identity withTyl andTy2, but muchless with Ty3. Proteins is not highly conserved among retroviruses except Ty3 is differentwhere the organizationof the polyprotein for a small carboxyl-terminalmotif consisting of cysteine and isconcernedinthistransposonthe reverse transcriptase histidinearrangedasC-X2-C-X4-H-X4-C(Copeland et al, precedes the endonuclease domain
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