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Karasik A, Fierke CA, Koutmos M. Interplay between substrate recognition, 5' end tRNA processing and methylation activity of human mitochondrial RNase P. RNA (NEW YORK, N.Y.) 2019; 25:1646-1660. [PMID: 31455609 PMCID: PMC6859853 DOI: 10.1261/rna.069310.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 08/16/2019] [Indexed: 05/07/2023]
Abstract
Human mitochondrial ribonuclease P (mtRNase P) is an essential three-protein complex that catalyzes the 5' end maturation of mitochondrial precursor tRNAs (pre-tRNAs). Mitochondrial RNase P Protein 3 (MRPP3), a protein-only RNase P (PRORP), is the nuclease component of the mtRNase P complex and requires a two-protein S-adenosyl-methionine (SAM)-dependent methyltransferase MRPP1/2 subcomplex to function. Dysfunction of mtRNase P is linked to several human mitochondrial diseases, such as mitochondrial myopathies. Despite its central role in mitochondrial RNA processing, little is known about how the protein subunits of mtRNase P function synergistically. Here, we use purified mtRNase P to demonstrate that mtRNase P recognizes, cleaves, and methylates some, but not all, mitochondrial pre-tRNAs in vitro. Additionally, mtRNase P does not process all mitochondrial pre-tRNAs uniformly, suggesting the possibility that some pre-tRNAs require additional factors to be cleaved in vivo. Consistent with this, we found that addition of the TRMT10C (MRPP1) cofactor SAM enhances the ability of mtRNase P to bind and cleave some mitochondrial pre-tRNAs. Furthermore, the presence of MRPP3 can enhance the methylation activity of MRPP1/2. Taken together, our data demonstrate that the subunits of mtRNase P work together to efficiently recognize, process, and methylate human mitochondrial pre-tRNAs.
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Affiliation(s)
- Agnes Karasik
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Carol A Fierke
- Department of Chemistry, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Markos Koutmos
- Department of Chemistry, Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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Zylicz-Stachula A, Zebrowska J, Czajkowska E, Wrese W, Sulecka E, Skowron PM. Engineering TaqII bifunctional endonuclease DNA recognition fidelity: the effect of a single amino acid substitution within the methyltransferase catalytic site. Mol Biol Rep 2016; 43:269-82. [PMID: 26886214 DOI: 10.1007/s11033-016-3949-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 02/08/2016] [Indexed: 01/04/2023]
Abstract
The aim of this study was to improve a useful molecular tool-TaqII restriction endonuclease-methyltransferase-by rational protein engineering, as well as to show an application of our novel method of restriction endonuclease activity modulation through a single amino acid change in the NPPY motif of methyltransferase. An amino acid change was introduced using site-directed mutagenesis into the taqIIRM gene. The mutated gene was expressed in Escherichia coli. The protein variant was purified and characterized. Previously, we described a TspGWI variant with an amino acid change in the methyltransferase motif IV. Here, we investigate a complex, pleiotropic effect of an analogous amino acid change on its homologue-TaqII. The methyltransferase activity is reduced, but not abolished, while TaqII restriction endonuclease can be reactivated by sinefungin, with an increased DNA recognition fidelity. The general method for engineering of the IIS/IIC/IIG restriction endonuclease activity/fidelity is developed along with the generation of an improved TaqII enzyme for biotechnological applications. A successful application of our novel strategy for restriction endonuclease activity/fidelity alteration, based on bioinformatics analyses, mutagenesis and the use of cofactor-analogue activity modulation, is presented.
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Affiliation(s)
- Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Joanna Zebrowska
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Edyta Czajkowska
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Weronika Wrese
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Ewa Sulecka
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
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Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014; 42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022] Open
Abstract
This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
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Affiliation(s)
- Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Geoffrey G Wilson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Wolfgang Wende
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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Zhu Z, Guan S, Robinson D, El Fezzazi H, Quimby A, Xu SY. Characterization of cleavage intermediate and star sites of RM.Tth111II. Sci Rep 2014; 4:3838. [PMID: 24452415 PMCID: PMC3899748 DOI: 10.1038/srep03838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/03/2014] [Indexed: 11/09/2022] Open
Abstract
Tth111II is a thermostable Type IIGS restriction enzyme that recognizes DNA sites CAARCA (R = A or G) and cleaves downstream at N11/N9. Here, the tth111IIRM gene was cloned and expressed in E. coli, and Tth111II was purified. The purified enzyme contains internally-bound S-adenosylmethionine (SAM). When the internal SAM was removed, the endonuclease activity was stimulated by adding SAM or its analog sinefungin. The cleavage intermediate is mostly top-strand nicked DNA on a single-site plasmid. Addition of duplex oligos with a cognate site stimulates cleavage activity of the one-site substrate. Tth111II cleaves a two-site plasmid DNA with equal efficiency regardless of site orientation. We propose the top-strand nicking is carried out by a Tth111II monomer and bottom-strand cleavage is carried out by a transient dimer. Tth111II methylates cleavage product-like duplex oligos CAAACAN9, but the modification rate is estimated to be much slower than the top-strand nicking rate. We cloned and sequenced a number of Tth111II star sites which are 1-bp different from the cognate sites. A biochemical pathway is proposed for the restriction and methylation activities of Tth111II.
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Affiliation(s)
- Zhenyu Zhu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Derek Robinson
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Hanna El Fezzazi
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Aine Quimby
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shuang-yong Xu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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