RNA heptamers that direct RNA cleavage by mammalian tRNA 3' processing endoribonuclease.
Mammalian tRNA 3' processing endoribonuclease (3' tRNase) can recognize and cleave any target RNA that forms a precursor tRNA-like complex with another RNA. Various sets of RNA molecules were tested to identify the smallest RNA that can direct target RNA cleavage by 3' tRNase. A 3' half tRNAArgwas cleaved efficiently by 3' tRNase in the presence of small 5' half tRNAArgvariants, the D stem-loop region of which was partially deleted. Remarkably, 3' tRNase also cleaved the 3' half tRNAArgin the presence of a 7 nt 5' tRNAArg composed only of the acceptor stem region with a catalytic efficiency comparable with that of cleavage directed by an intact 5' half tRNAArg. The catalytic efficiency of cleavage directed by the heptamer decreased as the stability of the T stem-loop structures of 3' half tRNAArg variants decreased. No heptamer-directed cleavage of a 3' half tRNAArg without T stem base pairs was detected. A heptamer also directed cleavage of an HIV-1 RNA containing a stable hairpin structure. These findings suggest that in the presence of an RNA heptamer, 3' tRNase can discriminate and eliminate target RNAs that possess a stable hairpin adjacent to the heptamer binding sequence from a large complex RNA pool.
Nashimoto
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M
Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA. mnashimoto@chemgate.byu.edu
Geary
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Tamura
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Kaspar
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D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D004722:Endoribonucleases / Q000378:metabolism* / Q000502:physiology; D015752:Genes, env; D015750:Genes, gag; D015497:HIV-1 / Q000235:genetics; D051379:Mice; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012347:RNA, Transfer, Arg / Q000378:metabolism*; D012367:RNA, Viral / Q000378:metabolism; D013379:Substrate Specificity
D012347:RNA, Transfer, Arg; D012367:RNA, Viral; D004722:Endoribonucleases; C072389:tRNA 3'-processing endonuclease