A novel 4-base-recognizing RNA cutter that can remove the single 3' terminal nucleotides from RNA molecules

Nucleic Acids Research
Hiroaki TakakuM Nashimoto

Abstract

Mammalian tRNase ZL shows versatility in substrate recognition. This enzyme can not only process pre-tRNAs by cleaving off their 3' trailer sequences, but also recognize and cleave pre-tRNA-like complexes and micro-pre-tRNAs. Here we demonstrate that 24-27 nt hairpin RNAs (hook RNAs) can guide cleavages of separate target RNAs by tRNase ZL through the micro-pre-tRNA-like complexes between the targets and the hook RNAs and that tRNase ZL together with hook RNA works as 4-7-base-recognizing RNA cutters. The cleavage sites were located only after the nucleotide corresponding to the discriminator nucleotide. Cleavage assays for various substrate/hooker complexes showed that the cleavage efficiency changes depending on the maximum number of substrate/hooker recognition base pairings and the stem length of hook RNA and that a 5 nt recognition sequence and a hook RNA containing a 6 or 7 bp stem are the best combination for the optimal target cleavage. We also show that a 4-base RNA cutter can remove the single 3' terminal nucleotides from RNA molecules. These results indicate that this new type of RNA cutter can be utilized to homogenize at their 3' termini RNA transcripts synthesized in vitro with a bacteriophage RNA polymerase.

References

May 15, 1991·Biochemical and Biophysical Research Communications·M NashimotoY Mishima
Apr 7, 1999·Journal of Molecular Biology·M NashimotoR L Kaspar
Feb 15, 2001·Nature Genetics·S V TavtigianL A Cannon-Albright
May 29, 2002·The EMBO Journal·Steffen SchifferAnita Marchfelder
Jun 13, 2002·Nucleic Acids Research·Heike SchürerMario Mörl
Apr 25, 2003·Nucleic Acids Research·Hiroaki TakakuMasayuki Nashimoto
Jul 31, 2003·Nucleic Acids Research·Masato TamuraMasayuki Nashimoto
Jul 31, 2003·Nucleic Acids Research·Scott C WalkerGraeme L Conn
Jan 13, 2004·Nucleic Acids Research·Edward B DubrovskyAnita Marchfelder
Jan 30, 2004·The Journal of Biological Chemistry·Asako MinagawaMasayuki Nashimoto
Feb 20, 2004·Nucleic Acids Research·Agnieszka WichlaczJerzy Ciesiołka

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Citations

Jul 15, 2006·Nucleosides, Nucleotides & Nucleic Acids·Masahiro IkedaHiroshi Takaku
Apr 12, 2007·Nucleic Acids Research·Lisa J SchererJohn J Rossi
Jun 16, 2009·PloS One·Reyad A ElbarbaryMasayuki Nashimoto
Jun 8, 2012·PloS One·Masayuki TakahashiMasayuki Nashimoto
Sep 16, 2009·FEBS Letters·Reyad A ElbarbaryMasayuki Nashimoto
Aug 5, 2015·Molecular Medicine Reports·Masato TamuraMasayuki Nashimoto
Oct 25, 2012·Cancer Letters·Masayuki TakahashiMasayuki Nashimoto
Jan 13, 2009·Biochemical and Biophysical Research Communications·Reyad A ElbarbaryMasayuki Nashimoto
Dec 7, 2011·Biochemical and Biophysical Research Communications·Takako SanoMasayuki Nashimoto
May 14, 2011·Macromolecular Rapid Communications·Stefano TurriMarinella Levi
Feb 11, 2005·The Journal of Biological Chemistry·Ryohei IshiiShigeyuki Yokoyama
Apr 13, 2005·The Journal of Biological Chemistry·Hirotaka S ShibataMasayuki Nashimoto
May 11, 2018·Journal of Experimental & Clinical Cancer Research : CR·Shi-Qiong HuangQing Li
Feb 11, 2021·Briefings in Functional Genomics·Valentina MianoIsaia Barbieri
Feb 9, 2021·Biochemistry and Biophysics Reports·Tadasuke NozakiMasayuki Nashimoto
Aug 20, 2021·Biochemical and Biophysical Research Communications·Masayuki TakahashiMasayuki Nashimoto
Dec 23, 2021·Cell Death & Disease·Bowen LiuTianjiao Wang

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