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2. Long 5' leaders inhibit removal of a 3' trailer from a precursor tRNA by mammalian tRNA 3' processing endoribonuclease

Author

Duane R. Wesemann, Susanna Geary, Masayuki Nashimoto, Masato Tamura, and Roger L. Kaspar

Subjects
Genetics, Base Sequence, Stereochemistry, Nucleotides, Trailer, Endoribonuclease, Molecular Sequence Data, Processing efficiency, Biology, TRNA 3' processing endoribonuclease, Enzyme Activation, Transfer RNA, Endoribonucleases, RNA Precursors, Animals, RNA Processing, Post-Transcriptional, Research Article
Abstract

Mammalian tRNA 3' processing endoribonuclease (3' tRNase) can remove a 3' trailer from various pre-tRNAs without 5' leader nucleotides. To examine how 5[prime] leader sequences affect 3' processing efficiency, we performed in vitro 3' processing reactions with purified pig 3' tRNase and pre-tRNAArgs containing a 13-nt 3' trailer and a 5[prime] leader of various lengths. The 3' processing was slightly stimulated by 5[prime] leaders containing up to 7 nt, whereas leaders of 9 nt or longer severely inhibited the reaction. Structure probing indicated that the 5' leader sequences had little effect on pre-tRNA folding. Similar results were obtained using pre-tRNA(Val)s containing a 5' leader of various lengths. We also investigated whether 3'tRNase can remove 3' trailers that are stably base-paired with 5' leaders to form an extended acceptor stem. Even such small 5' leaders as 3 and 6 nt, when base-paired with a 3' trailer, severely hindered removal of the 3' trailer by 3' tRNase.

Published
1999

3. RNA heptamers that direct RNA cleavage by mammalian tRNA 3' processing endoribonuclease

Author

Masayuki Nashimoto, Roger L. Kaspar, Susanna Geary, and Masato Tamura

Subjects
Base pair, Stereochemistry, Endoribonuclease, Molecular Sequence Data, RNA, Transfer, Arg, Biology, Cleavage (embryo), Genes, env, Cell Line, Substrate Specificity, Mice, Endoribonucleases, Genetics, Animals, Gene, Base Sequence, RNA, Molecular biology, Genes, gag, Transfer RNA, HIV-1, Nucleic Acid Conformation, RNA, Viral, RNA Cleavage, Research Article
Abstract

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.

Published
1998

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