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Huang T, Chamberlain A, Zhu J, Harris ME. A minimal RNA substrate with dual fluorescent probes enables rapid kinetics and provides insight into bacterial RNase P active site interactions. RSC Chem Biol 2024; 5:652-668. [PMID: 38966670 PMCID: PMC11221534 DOI: 10.1039/d4cb00049h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/17/2024] [Indexed: 07/06/2024] Open
Abstract
Bacterial ribonuclease P (RNase P) is a tRNA processing endonuclease that occurs primarily as a ribonucleoprotein with a catalytic RNA subunit (P RNA). As one of the first ribozymes discovered, P RNA is a well-studied model system for understanding RNA catalysis and substrate recognition. Extensive structural and biochemical studies have revealed the structure of RNase P bound to precursor tRNA (ptRNA) and product tRNA. These studies also helped to define active site residues and propose the molecular interactions that are involved in substrate binding and catalysis. However, a detailed quantitative model of the reaction cycle that includes the structures of intermediates and the process of positioning active site metal ions for catalysis is lacking. To further this goal, we used a chemically modified minimal RNA duplex substrate (MD1) to establish a kinetic framework for measuring the functional effects of P RNA active site mutations. Substitution of U69, a critical nucleotide involved in active site Mg2+ binding, was found to reduce catalysis >500-fold as expected, but had no measurable effect on ptRNA binding kinetics. In contrast, the same U69 mutations had little effect on catalysis in Ca2+ compared to reactions containing native Mg2+ ions. CryoEM structures and SHAPE mapping suggested increased flexibility of U69 and adjacent nucleotides in Ca2+ compared to Mg2+. These results support a model in which slow catalysis in Ca2+ is due to inability to engage U69. These studies establish a set of experimental tools to analyze RNase P kinetics and mechanism and can be expanded to gain new insights into the assembly of the active RNase P-ptRNA complex.
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Affiliation(s)
- Tong Huang
- Department of Chemistry, University of Florida Gainesville FL 32608 USA
| | | | - Jiaqiang Zhu
- Department of Chemistry, University of Florida Gainesville FL 32608 USA
| | - Michael E Harris
- Department of Chemistry, University of Florida Gainesville FL 32608 USA
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2
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Wang P, Lin J, Zheng X, Xu X. RNase P: Beyond Precursor tRNA Processing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae016. [PMID: 38862431 DOI: 10.1093/gpbjnl/qzae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/18/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
Ribonuclease P (RNase P) was first described in the 1970's as an endoribonuclease acting in the maturation of precursor transfer RNAs (tRNAs). More recent studies, however, have uncovered non-canonical roles for RNase P and its components. Here, we review the recent progress of its involvement in chromatin assembly, DNA damage response, and maintenance of genome stability with implications in tumorigenesis. The possibility of RNase P as a therapeutic target in cancer is also discussed.
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Affiliation(s)
- Peipei Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China
| | - Juntao Lin
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Xiangyang Zheng
- Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine, Dehua Hospital, Dehua 362500, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China
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3
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Mao G, Srivastava AS, Wu S, Kosek D, Kirsebom LA. Importance of residue 248 in Escherichia coli RNase P RNA mediated cleavage. Sci Rep 2023; 13:14140. [PMID: 37644068 PMCID: PMC10465520 DOI: 10.1038/s41598-023-41203-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023] Open
Abstract
tRNA genes are transcribed as precursors and RNase P generates the matured 5' end of tRNAs. It has been suggested that residue - 1 (the residue immediately 5' of the scissile bond) in the pre-tRNA interacts with the well-conserved bacterial RNase P RNA (RPR) residue A248 (Escherichia coli numbering). The way A248 interacts with residue - 1 is not clear. To gain insight into the role of A248, we analyzed cleavage as a function of A248 substitutions and N-1 nucleobase identity by using pre-tRNA and three model substrates. Our findings are consistent with a model where the structural topology of the active site varies and depends on the identity of the nucleobases at, and in proximity to, the cleavage site and their potential to interact. This leads to positioning of Mg2+ that activates the water that acts as the nucleophile resulting in efficient and correct cleavage. We propose that in addition to be involved in anchoring the substrate the role of A248 is to exclude bulk water from access to the amino acid acceptor stem, thereby preventing non-specific hydrolysis of the pre-tRNA. Finally, base stacking is discussed as a way to protect functionally important base-pairing interactions from non-specific hydrolysis, thereby ensuring high fidelity during RNA processing and the decoding of mRNA.
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Affiliation(s)
- Guanzhong Mao
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, 751 24, Uppsala, Sweden
| | - Abhishek S Srivastava
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, 751 24, Uppsala, Sweden
| | - Shiying Wu
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, 751 24, Uppsala, Sweden
| | - David Kosek
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, 751 24, Uppsala, Sweden
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, 751 24, Uppsala, Sweden.
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4
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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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5
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Ender A, Grafl N, Kolberg T, Findeiß S, Stadler PF, Mörl M. Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes. RNA (NEW YORK, N.Y.) 2022; 28:551-567. [PMID: 35022261 PMCID: PMC8925977 DOI: 10.1261/rna.078814.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Removal of the 5'-leader region is an essential step in the maturation of tRNA molecules in all domains of life. This reaction is catalyzed by various RNase P activities, ranging from ribonucleoproteins with ribozyme activity to protein-only forms. In Escherichia coli, the efficiency of RNase P-mediated cleavage can be controlled by computationally designed riboswitch elements in a ligand-dependent way, where the 5'-leader sequence of a tRNA precursor is either sequestered in a hairpin structure or presented as a single-stranded region accessible for maturation. In the presented work, the regulatory potential of such artificial constructs is tested on different forms of eukaryotic RNase P enzymes-two protein-only RNase P enzymes (PRORP1 and PRORP2) from Arabidopsis thaliana and the ribonucleoprotein of Homo sapiens The PRORP enzymes were analyzed in vitro as well as in vivo in a bacterial RNase P complementation system. We also tested in HEK293T cells whether the riboswitches remain functional with human nuclear RNase P. While the regulatory principle of the synthetic riboswitches applies for all tested RNase P enzymes, the results also show differences in the substrate requirements of the individual enzyme versions. Hence, such designed RNase P riboswitches represent a novel tool to investigate the impact of the structural composition of the 5'-leader on substrate recognition by different types of RNase P enzymes.
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Affiliation(s)
- Anna Ender
- Institute for Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Nadine Grafl
- Institute for Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Tim Kolberg
- Institute for Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Science, 04103 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria
- Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, 04103 Leipzig, Germany
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Bouchoucha A, Waltz F, Bonnard G, Arrivé M, Hammann P, Kuhn L, Schelcher C, Zuber H, Gobert A, Giegé P. Determination of protein-only RNase P interactome in Arabidopsis mitochondria and chloroplasts identifies a complex between PRORP1 and another NYN domain nuclease. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:549-561. [PMID: 31319441 DOI: 10.1111/tpj.14458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/03/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
The essential type of endonuclease that removes 5' leader sequences from transfer RNA precursors is called RNase P. While ribonucleoprotein RNase P enzymes containing a ribozyme are found in all domains of life, another type of RNase P called 'PRORP', for 'PROtein-only RNase P', is composed of protein that occurs only in a wide variety of eukaryotes, in organelles and in the nucleus. Here, to find how PRORP functions integrate with other cell processes, we explored the protein interaction network of PRORP1 in Arabidopsis mitochondria and chloroplasts. Although PRORP proteins function as single subunit enzymes in vitro, we found that PRORP1 occurs in protein complexes and is present in high-molecular-weight fractions that contain mitochondrial ribosomes. The analysis of immunoprecipitated protein complexes identified proteins involved in organellar gene expression processes. In particular, direct interaction was established between PRORP1 and MNU2 a mitochondrial nuclease. A specific domain of MNU2 and a conserved signature of PRORP1 were found to be directly accountable for this protein interaction. Altogether, results revealed the existence of an RNA maturation complex in Arabidopsis mitochondria and suggested that PRORP proteins cooperated with other gene expression factors for RNA maturation in vivo.
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Affiliation(s)
- Ayoub Bouchoucha
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Florent Waltz
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Géraldine Bonnard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Mathilde Arrivé
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg-Esplanade, CNRS, Université de Strasbourg, 15 rue René Descartes, Strasbourg, F-67084, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg-Esplanade, CNRS, Université de Strasbourg, 15 rue René Descartes, Strasbourg, F-67084, France
| | - Cédric Schelcher
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Anthony Gobert
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Giegé
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
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7
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Klemm BP, Karasik A, Kaitany KJ, Shanmuganathan A, Henley MJ, Thelen AZ, Dewar AJL, Jackson ND, Koutmos M, Fierke CA. Molecular recognition of pre-tRNA by Arabidopsis protein-only Ribonuclease P. RNA (NEW YORK, N.Y.) 2017; 23:1860-1873. [PMID: 28874505 PMCID: PMC5689006 DOI: 10.1261/rna.061457.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/31/2017] [Indexed: 05/06/2023]
Abstract
Protein-only ribonuclease P (PRORP) is an enzyme responsible for catalyzing the 5' end maturation of precursor transfer ribonucleic acids (pre-tRNAs) encoded by various cellular compartments in many eukaryotes. PRORPs from plants act as single-subunit enzymes and have been used as a model system for analyzing the function of the metazoan PRORP nuclease subunit, which requires two additional proteins for efficient catalysis. There are currently few molecular details known about the PRORP-pre-tRNA complex. Here, we characterize the determinants of substrate recognition by the single subunit Arabidopsis thaliana PRORP1 and PRORP2 using kinetic and thermodynamic experiments. The salt dependence of binding affinity suggests 4-5 contacts with backbone phosphodiester bonds on substrates, including a single phosphodiester contact with the pre-tRNA 5' leader, consistent with prior reports of short leader requirements. PRORPs contain an N-terminal pentatricopeptide repeat (PPR) domain, truncation of which results in a >30-fold decrease in substrate affinity. While most PPR-containing proteins have been implicated in single-stranded sequence-specific RNA recognition, we find that the PPR motifs of PRORPs recognize pre-tRNA substrates differently. Notably, the PPR domain residues most important for substrate binding in PRORPs do not correspond to positions involved in base recognition in other PPR proteins. Several of these residues are highly conserved in PRORPs from algae, plants, and metazoans, suggesting a conserved strategy for substrate recognition by the PRORP PPR domain. Furthermore, there is no evidence for sequence-specific interactions. This work clarifies molecular determinants of PRORP-substrate recognition and provides a new predictive model for the PRORP-substrate complex.
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Affiliation(s)
- Bradley P Klemm
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Agnes Karasik
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Kipchumba J Kaitany
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Aranganathan Shanmuganathan
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Matthew J Henley
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Z Thelen
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Allison J L Dewar
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nathaniel D Jackson
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Markos Koutmos
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Carol A Fierke
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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8
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Gößringer M, Lechner M, Brillante N, Weber C, Rossmanith W, Hartmann RK. Protein-only RNase P function in Escherichia coli: viability, processing defects and differences between PRORP isoenzymes. Nucleic Acids Res 2017; 45:7441-7454. [PMID: 28499021 PMCID: PMC5499578 DOI: 10.1093/nar/gkx405] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/02/2017] [Indexed: 11/12/2022] Open
Abstract
The RNase P family comprises structurally diverse endoribonucleases ranging from complex ribonucleoproteins to single polypeptides. We show that the organellar (AtPRORP1) and the two nuclear (AtPRORP2,3) single-polypeptide RNase P isoenzymes from Arabidopsis thaliana confer viability to Escherichia coli cells with a lethal knockdown of its endogenous RNA-based RNase P. RNA-Seq revealed that AtPRORP1, compared with bacterial RNase P or AtPRORP3, cleaves several precursor tRNAs (pre-tRNAs) aberrantly in E. coli. Aberrant cleavage by AtPRORP1 was mainly observed for pre-tRNAs that can form short acceptor-stem extensions involving G:C base pairs, including tRNAAsp(GUC), tRNASer(CGA) and tRNAHis. However, both AtPRORP1 and 3 were defective in processing of E. coli pre-tRNASec carrying an acceptor stem expanded by three G:C base pairs. Instead, pre-tRNASec was degraded, suggesting that tRNASec is dispensable for E. coli under laboratory conditions. AtPRORP1, 2 and 3 are also essentially unable to process the primary transcript of 4.5S RNA, a hairpin-like non-tRNA substrate processed by E. coli RNase P, indicating that PRORP enzymes have a narrower, more tRNA-centric substrate spectrum than bacterial RNA-based RNase P enzymes. The cells' viability also suggests that the essential function of the signal recognition particle can be maintained with a 5΄-extended 4.5S RNA.
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Affiliation(s)
- Markus Gößringer
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Marcus Lechner
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Nadia Brillante
- Center for Anatomy & Cell Biology, Medical University of Vienna, Währinger Straße 13, 1090 Vienna, Austria
| | - Christoph Weber
- Center for Anatomy & Cell Biology, Medical University of Vienna, Währinger Straße 13, 1090 Vienna, Austria
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Währinger Straße 13, 1090 Vienna, Austria
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35037 Marburg, Germany
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