1
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Vučković A, Freyer C, Wredenberg A, Hillen HS. The molecular machinery for maturation of primary mtDNA transcripts. Hum Mol Genet 2024; 33:R19-R25. [PMID: 38779769 PMCID: PMC11112384 DOI: 10.1093/hmg/ddae023] [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: 01/31/2024] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 05/25/2024] Open
Abstract
Human mitochondria harbour a circular, polyploid genome (mtDNA) encoding 11 messenger RNAs (mRNAs), two ribosomal RNAs (rRNAs) and 22 transfer RNAs (tRNAs). Mitochondrial transcription produces long, polycistronic transcripts that span almost the entire length of the genome, and hence contain all three types of RNAs. The primary transcripts then undergo a number of processing and maturation steps, which constitute key regulatory points of mitochondrial gene expression. The first step of mitochondrial RNA processing consists of the separation of primary transcripts into individual, functional RNA molecules and can occur by two distinct pathways. Both are carried out by dedicated molecular machineries that substantially differ from RNA processing enzymes found elsewhere. As a result, the underlying molecular mechanisms remain poorly understood. Over the last years, genetic, biochemical and structural studies have identified key players involved in both RNA processing pathways and provided the first insights into the underlying mechanisms. Here, we review our current understanding of RNA processing in mammalian mitochondria and provide an outlook on open questions in the field.
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MESH Headings
- Humans
- DNA, Mitochondrial/genetics
- RNA Processing, Post-Transcriptional
- Mitochondria/genetics
- Mitochondria/metabolism
- RNA, Mitochondrial/genetics
- RNA, Mitochondrial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Animals
- Transcription, Genetic
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Ana Vučković
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Anna Steckséns gata 47, 171 64 Solna, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Anna Steckséns gata 47, 171 64 Solna, Sweden
| | - Hauke S Hillen
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Robert-Koch-Straße 40, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
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2
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Rossmanith W, Giegé P, Hartmann RK. Discovery, structure, mechanisms, and evolution of protein-only RNase P enzymes. J Biol Chem 2024; 300:105731. [PMID: 38336295 PMCID: PMC10941002 DOI: 10.1016/j.jbc.2024.105731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
The endoribonuclease RNase P is responsible for tRNA 5' maturation in all domains of life. A unique feature of RNase P is the variety of enzyme architectures, ranging from dual- to multi-subunit ribonucleoprotein forms with catalytic RNA subunits to protein-only enzymes, the latter occurring as single- or multi-subunit forms or homo-oligomeric assemblies. The protein-only enzymes evolved twice: a eukaryal protein-only RNase P termed PRORP and a bacterial/archaeal variant termed homolog of Aquifex RNase P (HARP); the latter replaced the RNA-based enzyme in a small group of thermophilic bacteria but otherwise coexists with the ribonucleoprotein enzyme in a few other bacteria as well as in those archaea that also encode a HARP. Here we summarize the history of the discovery of protein-only RNase P enzymes and review the state of knowledge on structure and function of bacterial HARPs and eukaryal PRORPs, including human mitochondrial RNase P as a paradigm of multi-subunit PRORPs. We also describe the phylogenetic distribution and evolution of PRORPs, as well as possible reasons for the spread of PRORPs in the eukaryal tree and for the recruitment of two additional protein subunits to metazoan mitochondrial PRORP. We outline potential applications of PRORPs in plant biotechnology and address diseases associated with mutations in human mitochondrial RNase P genes. Finally, we consider possible causes underlying the displacement of the ancient RNA enzyme by a protein-only enzyme in a small group of bacteria.
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Affiliation(s)
- Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, Austria.
| | - Philippe Giegé
- Institute for Plant Molecular Biology, IBMP-CNRS, University of Strasbourg, Strasbourg, France.
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany.
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3
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Wilhelm CA, Kaitany K, Kelly A, Yacoub M, Koutmos M. The protein-only RNase Ps, endonucleases that cleave pre-tRNA: Biological relevance, molecular architectures, substrate recognition and specificity, and protein interactomes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1836. [PMID: 38453211 DOI: 10.1002/wrna.1836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/27/2024] [Accepted: 02/06/2024] [Indexed: 03/09/2024]
Abstract
Protein-only RNase P (PRORP) is an essential enzyme responsible for the 5' maturation of precursor tRNAs (pre-tRNAs). PRORPs are classified into three categories with unique molecular architectures, although all three classes of PRORPs share a mechanism and have similar active sites. Single subunit PRORPs, like those found in plants, have multiple isoforms with different localizations, substrate specificities, and temperature sensitivities. Most recently, Arabidopsis thaliana PRORP2 was shown to interact with TRM1A and B, highlighting a new potential role between these enzymes. Work with At PRORPs led to the development of a ribonuclease that is being used to protect against plant viruses. The mitochondrial RNase P complex, found in metazoans, consists of PRORP, TRMT10C, and SDR5C1, and has also been shown to have substrate specificity, although the cause is unknown. Mutations in mitochondrial tRNA and mitochondrial RNase P have been linked to human disease, highlighting the need to continue understanding this complex. The last class of PRORPs, homologs of Aquifex RNase P (HARPs), is found in thermophilic archaea and bacteria. This most recently discovered type of PRORP forms a large homo-oligomer complex. Although numerous structures of HARPs have been published, it is still unclear how HARPs bind pre-tRNAs and in what ratio. There is also little investigation into the substrate specificity and ideal conditions for HARPs. Moving forward, further work is required to fully characterize each of the three classes of PRORP, the pre-tRNA binding recognition mechanism, the rules of substrate specificity, and how these three distinct classes of PRORP evolved. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
| | - Kipchumba Kaitany
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Abigail Kelly
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew Yacoub
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
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4
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Sridhara S. Multiple structural flavors of RNase P in precursor tRNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1835. [PMID: 38479802 DOI: 10.1002/wrna.1835] [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: 08/28/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 06/06/2024]
Abstract
The precursor transfer RNAs (pre-tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5'-processing, 3'-processing, modifications at specific sites, if any, and 3'-CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre-tRNA sequences at the 5' end by the removal of phosphodiester linkages between nucleotides at position -1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless-position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion-mediated conserved catalytic reaction. While the canonical RNA-based ribonucleoprotein RNase P has been well-known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA-free protein-only RNase P in eukaryotes and RNA-free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA-based and RNA-free RNase P holoenzymes towards harnessing critical RNA-protein and protein-protein interactions in achieving conserved pre-tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications. This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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5
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Arrivé M, Bruggeman M, Skaltsogiannis V, Coudray L, Quan YF, Schelcher C, Cognat V, Hammann P, Chicher J, Wolff P, Gobert A, Giegé P. A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei. NATURE PLANTS 2023; 9:2031-2041. [PMID: 37945696 DOI: 10.1038/s41477-023-01564-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023]
Abstract
RNase P is the essential activity that performs the 5' maturation of transfer RNA (tRNA) precursors. Beyond the ancestral form of RNase P containing a ribozyme, protein-only RNase P enzymes termed PRORP were identified in eukaryotes. In human mitochondria, PRORP forms a complex with two protein partners to become functional. In plants, although PRORP enzymes are active alone, we investigate their interaction network to identify potential tRNA maturation complexes. Here we investigate functional interactions involving the Arabidopsis nuclear RNase P PRORP2. We show, using an immuno-affinity strategy, that PRORP2 occurs in a complex with the tRNA methyl transferases TRM1A and TRM1B in vivo. Beyond RNase P, these enzymes can also interact with RNase Z. We show that TRM1A/TRM1B localize in the nucleus and find that their double knockout mutation results in a severe macroscopic phenotype. Using a combination of immuno-detections, mass spectrometry and a transcriptome-wide tRNA sequencing approach, we observe that TRM1A/TRM1B are responsible for the m22G26 modification of 70% of cytosolic tRNAs in vivo. We use the transcriptome wide tRNAseq approach as well as RNA blot hybridizations to show that RNase P activity is impaired in TRM1A/TRM1B mutants for specific tRNAs, in particular, tRNAs containing a m22G modification at position 26 that are strongly downregulated in TRM1A/TRM1B mutants. Altogether, results indicate that the m22G-adding enzymes TRM1A/TRM1B functionally cooperate with nuclear RNase P in vivo for the early steps of cytosolic tRNA biogenesis.
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Affiliation(s)
- Mathilde Arrivé
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Mathieu Bruggeman
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Vasileios Skaltsogiannis
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Léna Coudray
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Yi-Fat Quan
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Cédric Schelcher
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
| | - Philippe Wolff
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Anthony Gobert
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Giegé
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France.
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6
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Wilhelm CA, Mallik L, Kelly AL, Brotzman S, Mendoza J, Anders AG, Leskaj S, Castillo C, Ruotolo BT, Cianfrocco MA, Koutmos M. Bacterial RNA-free RNase P: Structural and functional characterization of multiple oligomeric forms of a minimal protein-only ribonuclease P. J Biol Chem 2023; 299:105327. [PMID: 37806495 PMCID: PMC10652100 DOI: 10.1016/j.jbc.2023.105327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
tRNAs are typically transcribed with extended 5' and 3' ends that must be removed before they attain their active form. One of the first steps of tRNA processing in nearly every organism is the removal of the 5' leader sequence by ribonuclease P (RNase P). Here, we investigate a recently discovered class of RNase P enzymes, Homologs of Aquifex RNase P (HARPs). In contrast to other RNase Ps, HARPs consist only of a metallonuclease domain and lack the canonical substrate recognition domain essential in other classes of proteinaceous RNase P. We determined the cryo-EM structure of Aquifex aeolicus HARP (Aq880) and two crystal structures of Hydrogenobacter thermophilus HARP (Hth1307) to reveal that both enzymes form large ring-like assemblies: a dodecamer in Aq880 and a tetradecamer in Hth1307. In both oligomers, the enzyme active site is 42 Å away from a positively charged helical region, as seen in other protein-only RNase P enzymes, which likely serves to recognize and bind the elbow region of the pre-tRNA substrate. In addition, we use native mass spectrometry to confirm and characterize the previously unreported tetradecamer state. Notably, we find that multiple oligomeric states of Hth1307 are able to cleave pre-tRNAs. Furthermore, our single-turnover kinetic studies indicate that Hth1307 cleaves pre-tRNAs from multiple species with a preference for native substrates. These data provide a closer look at the nuanced similarities and differences in tRNA processing across disparate classes of RNase P.
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Affiliation(s)
| | - Leena Mallik
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Abigail L Kelly
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Shayna Brotzman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Johnny Mendoza
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Anna G Anders
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Suada Leskaj
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Carmen Castillo
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Cianfrocco
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA.
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7
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Vilardo E, Toth U, Hazisllari E, Hartmann R, Rossmanith W. Cleavage kinetics of human mitochondrial RNase P and contribution of its non-nuclease subunits. Nucleic Acids Res 2023; 51:10536-10550. [PMID: 37779095 PMCID: PMC10602865 DOI: 10.1093/nar/gkad713] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 10/03/2023] Open
Abstract
RNase P is the endonuclease responsible for the 5' processing of precursor tRNAs (pre-tRNAs). Unlike the single-subunit protein-only RNase P (PRORP) found in plants or protists, human mitochondrial RNase P is a multi-enzyme assembly that in addition to the homologous PRORP subunit comprises a methyltransferase (TRMT10C) and a dehydrogenase (SDR5C1) subunit; these proteins, but not their enzymatic activities, are required for efficient pre-tRNA cleavage. Here we report a kinetic analysis of the cleavage reaction by human PRORP and its interplay with TRMT10C-SDR5C1 including 12 different mitochondrial pre-tRNAs. Surprisingly, we found that PRORP alone binds pre-tRNAs with nanomolar affinity and can even cleave some of them at reduced efficiency without the other subunits. Thus, the ancient binding mode, involving the tRNA elbow and PRORP's PPR domain, appears basically retained by human PRORP, and its metallonuclease domain is in principle correctly folded and functional. Our findings support a model according to which the main function of TRMT10C-SDR5C1 is to direct PRORP's nuclease domain to the cleavage site, thereby increasing the rate and accuracy of cleavage. This functional dependence of human PRORP on an extra tRNA-binding protein complex likely reflects an evolutionary adaptation to the erosion of canonical structural features in mitochondrial tRNAs.
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Affiliation(s)
- Elisa Vilardo
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Ursula Toth
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Enxhi Hazisllari
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, 35037 Marburg, Germany
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
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8
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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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9
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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10
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Gößringer M, Wäber NB, Wiegard JC, Hartmann RK. Characterization of RNA-based and protein-only RNases P from bacteria encoding both enzyme types. RNA (NEW YORK, N.Y.) 2023; 29:376-391. [PMID: 36604113 PMCID: PMC9945441 DOI: 10.1261/rna.079459.122] [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: 09/21/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
A small group of bacteria encode two types of RNase P, the classical ribonucleoprotein (RNP) RNase P as well as the protein-only RNase P HARP (homolog of Aquifex RNase P). We characterized the dual RNase P activities of five bacteria that belong to three different phyla. All five bacterial species encode functional RNA (gene rnpB) and protein (gene rnpA) subunits of RNP RNase P, but only the HARP of the thermophile Thermodesulfatator indicus (phylum Thermodesulfobacteria) was found to have robust tRNA 5'-end maturation activity in vitro and in vivo in an Escherichia coli RNase P depletion strain. These findings suggest that both types of RNase P are able to contribute to the essential tRNA 5'-end maturation activity in T. indicus, thus resembling the predicted evolutionary transition state in the progenitor of the Aquificaceae before the loss of rnpA and rnpB genes in this family of bacteria. Remarkably, T. indicus RNase P RNA is transcribed with a P12 expansion segment that is posttranscriptionally excised in vivo, such that the major fraction of the RNA is fragmented and thereby truncated by ∼70 nt in the native T. indicus host as well as in the E. coli complementation strain. Replacing the native P12 element of T. indicus RNase P RNA with the short P12 helix of Thermotoga maritima RNase P RNA abolished fragmentation, but simultaneously impaired complementation efficiency in E. coli cells, suggesting that intracellular fragmentation and truncation of T. indicus RNase P RNA may be beneficial to RNA folding and/or enzymatic activity.
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Affiliation(s)
- Markus Gößringer
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Nadine B Wäber
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Jana C Wiegard
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
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11
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Bhatta A, Hillen HS. Structural and mechanistic basis of RNA processing by protein-only ribonuclease P enzymes. Trends Biochem Sci 2022; 47:965-977. [PMID: 35725940 DOI: 10.1016/j.tibs.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022]
Abstract
Ribonuclease P (RNase P) enzymes are responsible for the 5' processing of tRNA precursors. In addition to the well-characterised ribozyme-based RNase P enzymes, an evolutionarily distinct group of protein-only RNase Ps exists. These proteinaceous RNase Ps (PRORPs) can be found in all three domains of life and can be divided into two structurally different types: eukaryotic and prokaryotic. Recent structural studies on members of both families reveal a surprising diversity of molecular architectures, but also highlight conceptual and mechanistic similarities. Here, we provide a comparison between the different types of PRORP enzymes and review how the combination of structural, biochemical, and biophysical studies has led to a molecular picture of protein-mediated tRNA processing.
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Affiliation(s)
- Arjun Bhatta
- Department of Cellular Biochemistry, University Medical Center Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany; Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Goettingen, Germany
| | - Hauke S Hillen
- Department of Cellular Biochemistry, University Medical Center Goettingen, Humboldtallee 23, D-37073 Goettingen, Germany; Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Goettingen, Germany; Cluster of Excellence Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Goettingen, D-37075 Goettingen, Germany.
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12
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Crystal structures and insights into precursor tRNA 5'-end processing by prokaryotic minimal protein-only RNase P. Nat Commun 2022; 13:2290. [PMID: 35484139 PMCID: PMC9051087 DOI: 10.1038/s41467-022-30072-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 03/30/2022] [Indexed: 11/08/2022] Open
Abstract
Besides the canonical RNA-based RNase P, pre-tRNA 5’-end processing can also be catalyzed by protein-only RNase P (PRORP). To date, various PRORPs have been discovered, but the basis underlying substrate binding and cleavage by HARPs (homolog of Aquifex RNase P) remains elusive. Here, we report structural and biochemical studies of HARPs. Comparison of the apo- and pre-tRNA-complexed structures showed that HARP is able to undergo large conformational changes that facilitate pre-tRNA binding and catalytic site formation. Planctomycetes bacterium HARP exists as dimer in vitro, but gel filtration and electron microscopy analysis confirmed that HARPs from Thermococcus celer, Thermocrinis minervae and Thermocrinis ruber can assemble into larger oligomers. Structural analysis, mutagenesis and in vitro biochemical studies all supported one cooperative pre-tRNA processing mode, in which one HARP dimer binds pre-tRNA at the elbow region whereas 5’-end removal is catalyzed by the partner dimer. Our studies significantly advance our understanding on pre-tRNA processing by PRORPs. HARP are member of protein-only RNase P, which catalyzes pre-tRNA 5’-end processing and maturation. Here, the authors present crystal structure and provide mechanistic insights into pre-tRNA binding and cleavage by HARP proteins.
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13
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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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14
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Structural and Functional Insight into the Mechanism of Bacillus subtilis 6S-1 RNA Release from RNA Polymerase. Noncoding RNA 2022; 8:ncrna8010020. [PMID: 35202093 PMCID: PMC8876501 DOI: 10.3390/ncrna8010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022] Open
Abstract
Here we investigated the refolding of Bacillus subtilis 6S-1 RNA and its release from σA-RNA polymerase (σA-RNAP) in vitro using truncated and mutated 6S-1 RNA variants. Truncated 6S-1 RNAs, only consisting of the central bubble (CB) flanked by two short helical arms, can still traverse the mechanistic 6S RNA cycle in vitro despite ~10-fold reduced σA-RNAP affinity. This indicates that the RNA’s extended helical arms including the ‘−35′-like region are not required for basic 6S-1 RNA functionality. The role of the ‘central bubble collapse helix’ (CBCH) in pRNA-induced refolding and release of 6S-1 RNA from σA-RNAP was studied by stabilizing mutations. This also revealed base identities in the 5’-part of the CB (5’-CB), upstream of the pRNA transcription start site (nt 40), that impact ground state binding of 6S-1 RNA to σA-RNAP. Stabilization of the CBCH by the C44/45 double mutation shifted the pRNA length pattern to shorter pRNAs and, combined with a weakened P2 helix, resulted in more effective release from RNAP. We conclude that formation of the CBCH supports pRNA-induced 6S-1 RNA refolding and release. Our mutational analysis also unveiled that formation of a second short hairpin in the 3′-CB is detrimental to 6S-1 RNA release. Furthermore, an LNA mimic of a pRNA as short as 6 nt, when annealed to 6S-1 RNA, retarded the RNA’s gel mobility and interfered with σA-RNAP binding. This effect incrementally increased with pLNA 7- and 8-mers, suggesting that restricted conformational flexibility introduced into the 5’-CB by base pairing with pRNAs prevents 6S-1 RNA from adopting an elongated shape. Accordingly, atomic force microscopy of free 6S-1 RNA versus 6S-1:pLNA 8- and 14-mer complexes revealed that 6S-1:pRNA hybrid structures, on average, adopt a more compact structure than 6S-1 RNA alone. Overall, our findings also illustrate that the wild-type 6S-1 RNA sequence and structure ensures an optimal balance of the different functional aspects involved in the mechanistic cycle of 6S-1 RNA.
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15
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Di Giulio M. The RNase P, LUCA, the ancestors of the life domains, the progenote, and the tree of life. Biosystems 2021; 212:104604. [PMID: 34979158 DOI: 10.1016/j.biosystems.2021.104604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 11/15/2022]
Abstract
I have tried to interpret the phylogenetic distribution of the RNase P with the aim of helping to clarify the stage reached by the evolution of cellularity in the Last Universal Common Ancestor (LUCA); that is to say, if the evolutionary stage of the LUCA was represented by a protocell (progenote) or by a complete cell (genote). Since there are several arguments that lead one to believe that only the RNA moiety of the RNase P was present in the LUCA, this might imply that this evolutionary stage was actually the RNA world. If true this would imply that the LUCA was a progenote because the RNA world being a world subject to multiple evolutionary transitions that would involve a high noise at many its levels, which would fall within the definition of the progenote. Furthermore, since RNA-mediated catalysis is much less efficient than protein-mediated catalysis, then the only RNA moiety that was present in the LUCA could imply - by per se, without invoking the existence of the RNA world - that the LUCA was a progenote because an inefficient catalysis might have characterized this evolutionary stage. This evolutionary stage would still fall under the definition of the progenote. In addition, the observation that the protein moieties of the RNase P of bacteria and archaea are not-homologs would imply that these originated independently in the two main phyletic lineages. In turn, this would imply the progenotic nature of the ancestors of both archaea and bacteria. Indeed, it is admissible that such a late origin - in the main phyletic lineages - of the protein moieties of the RNase P is witness to an evolutionary transition towards a more efficient catalysis, evidently made clear precisely by the evolution of the protein moieties of the RNase P which would have helped the RNA of the RNase P to a more efficient catalysis. Hence, this would date that evolutionary moment as a transition to a much more efficient catalysis and consequently would imply which in that evolutionary stage there was the actual transition from the progenotic to genotic status. Finally, this late origin of the RNase P protein moieties in the bacterial and archaeal domains per se could imply the presence of a progenotic stage for their ancestors, or at least that a cell stage would have been much less likely. In fact, it is true that genes can originate both in a cellular and in a progenotic stage, but they mainly typify the latter because they are, by definition, in formation. Then it is expected that in the evolutionary stage of the formation of the main phyletic lineages - that is to say, in an evolutionary time in which the formation of genes might be expected - that the origin of proteins is to be related to a rapid and progressive evolution typical of the progenote precisely because in such an evolutionary stage the origin of genes is more easily and simply explained as reflecting a progenotic rather than a genotic stage. Indeed, if instead the evolutionary stage of the ancestors of bacteria and archaea had been the cellular one, then observing the origin of the protein moieties of the RNase P would have been, to some extent, anomalous because this completion should have already occurred, simply because the transformation of a ribozyme into an enzyme should have already taken place precisely because it falls within the very definition of the cellular status. The conclusion is that both the LUCA and the ancestor of archaea and that of bacteria may have been progenotes. If these arguments were true then either the tree of life as commonly understood would not exist and therefore the main phyletic lineages would have originated directly from the LUCA, or there would have been at least two different populations of progenotes that would have finally defined the domain of bacteria and that of archaea.
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Affiliation(s)
- Massimo Di Giulio
- The Ionian School, Genetic Code and tRNA Origin Laboratory, Via Roma 19, 67030, Alfedena (L'Aquila), Italy.
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16
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Shaukat AN, Kaliatsi EG, Skeparnias I, Stathopoulos C. The Dynamic Network of RNP RNase P Subunits. Int J Mol Sci 2021; 22:ijms221910307. [PMID: 34638646 PMCID: PMC8509007 DOI: 10.3390/ijms221910307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Ribonuclease P (RNase P) is an important ribonucleoprotein (RNP), responsible for the maturation of the 5′ end of precursor tRNAs (pre-tRNAs). In all organisms, the cleavage activity of a single phosphodiester bond adjacent to the first nucleotide of the acceptor stem is indispensable for cell viability and lies within an essential catalytic RNA subunit. Although RNase P is a ribozyme, its kinetic efficiency in vivo, as well as its structural variability and complexity throughout evolution, requires the presence of one protein subunit in bacteria to several protein partners in archaea and eukaryotes. Moreover, the existence of protein-only RNase P (PRORP) enzymes in several organisms and organelles suggests a more complex evolutionary timeline than previously thought. Recent detailed structures of bacterial, archaeal, human and mitochondrial RNase P complexes suggest that, although apparently dissimilar enzymes, they all recognize pre-tRNAs through conserved interactions. Interestingly, individual protein subunits of the human nuclear and mitochondrial holoenzymes have additional functions and contribute to a dynamic network of elaborate interactions and cellular processes. Herein, we summarize the role of each RNase P subunit with a focus on the human nuclear RNP and its putative role in flawless gene expression in light of recent structural studies.
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17
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Use of tandem affinity-buffer exchange chromatography online with native mass spectrometry for optimizing overexpression and purification of recombinant proteins. Methods Enzymol 2021; 659:37-70. [PMID: 34752295 DOI: 10.1016/bs.mie.2021.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Purification of recombinant proteins typically entails overexpression in heterologous systems and subsequent chromatography-based isolation. While denaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis is routinely used to screen a variety of overexpression conditions (e.g., host, medium, inducer concentration, post-induction temperature and/or incubation time) and to assess the purity of the final product, its limitations, including aberrant protein migration due to compositional eccentricities or incomplete denaturation, often preclude firm conclusions regarding the extent of overexpression and/or purification. Therefore, we recently reported an automated liquid chromatography-mass spectrometry-based strategy that couples immobilized metal affinity chromatography (IMAC) with size exclusion-based online buffer exchange (OBE) and native mass spectrometry (nMS) to directly analyze cell lysates for the presence of target proteins. IMAC-OBE-nMS can be used to assess whether target proteins (1) are overexpressed in soluble form, (2) bind and elute from an IMAC resin, (3) oligomerize, and (4) have the expected mass. Here, we use four poly-His-tagged proteins to demonstrate the potential of IMAC-OBE-nMS for expedient optimization of overexpression and purification conditions for recombinant protein production.
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18
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Phan HD, Lai LB, Zahurancik WJ, Gopalan V. The many faces of RNA-based RNase P, an RNA-world relic. Trends Biochem Sci 2021; 46:976-991. [PMID: 34511335 DOI: 10.1016/j.tibs.2021.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/11/2021] [Accepted: 07/28/2021] [Indexed: 12/24/2022]
Abstract
RNase P is an essential enzyme that catalyzes removal of the 5' leader from precursor transfer RNAs. The ribonucleoprotein (RNP) form of RNase P is present in all domains of life and comprises a single catalytic RNA (ribozyme) and a variable number of protein cofactors. Recent cryo-electron microscopy structures of representative archaeal and eukaryotic (nuclear) RNase P holoenzymes bound to tRNA substrate/product provide high-resolution detail on subunit organization, topology, and substrate recognition in these large, multisubunit catalytic RNPs. These structures point to the challenges in understanding how proteins modulate the RNA functional repertoire and how the structure of an ancient RNA-based catalyst was reshaped during evolution by new macromolecular associations that were likely necessitated by functional/regulatory coupling.
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Affiliation(s)
- Hong-Duc Phan
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Lien B Lai
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Walter J Zahurancik
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
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19
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Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis. J Biol Chem 2021; 297:101028. [PMID: 34339732 PMCID: PMC8405995 DOI: 10.1016/j.jbc.2021.101028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/20/2021] [Accepted: 07/29/2021] [Indexed: 11/22/2022] Open
Abstract
Ribonuclease P (RNase P) is an endoribonuclease that catalyzes the processing of the 5' leader sequence of precursor tRNA (pre-tRNA). Ribonucleoprotein RNase P and protein-only RNase P (PRORP) in eukaryotes have been extensively studied, but the mechanism by which a prokaryotic nuclease recognizes and cleaves pre-tRNA is unclear. To gain insights into this mechanism, we studied homologs of Aquifex RNase P (HARPs), thought to be enzymes of approximately 23 kDa comprising only this nuclease domain. We determined the cryo-EM structure of Aq880, the first identified HARP enzyme. The structure unexpectedly revealed that Aq880 consists of both the nuclease and protruding helical (PrH) domains. Aq880 monomers assemble into a dimer via the PrH domain. Six dimers form a dodecamer with a left-handed one-turn superhelical structure. The structure also revealed that the active site of Aq880 is analogous to that of eukaryotic PRORPs. The pre-tRNA docking model demonstrated that 5' processing of pre-tRNAs is achieved by two adjacent dimers within the dodecamer. One dimer is responsible for catalysis, and the PrH domains of the other dimer are responsible for pre-tRNA elbow recognition. Our study suggests that HARPs measure an invariant distance from the pre-tRNA elbow to cleave the 5' leader sequence, which is analogous to the mechanism of eukaryotic PRORPs and the ribonucleoprotein RNase P. Collectively, these findings shed light on how different types of RNase P enzymes utilize the same pre-tRNA processing.
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20
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RNase P Inhibitors Identified as Aggregators. Antimicrob Agents Chemother 2021; 65:e0030021. [PMID: 33972249 DOI: 10.1128/aac.00300-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNase P is an essential enzyme responsible for tRNA 5'-end maturation. In most bacteria, the enzyme is a ribonucleoprotein consisting of a catalytic RNA subunit and a small protein cofactor termed RnpA. Several studies have reported small-molecule inhibitors directed against bacterial RNase P that were identified by high-throughput screenings. Using the bacterial RNase P enzymes from Thermotoga maritima, Bacillus subtilis, and Staphylococcus aureus as model systems, we found that such compounds, including RNPA2000 (and its derivatives), iriginol hexaacetate, and purpurin, induce the formation of insoluble aggregates of RnpA rather than acting as specific inhibitors. In the case of RNPA2000, aggregation was induced by Mg2+ ions. These findings were deduced from solubility analyses by microscopy and high-performance liquid chromatography (HPLC), RnpA-inhibitor co-pulldown experiments, detergent addition, and RnpA titrations in enzyme activity assays. Finally, we used a B. subtilis RNase P depletion strain, whose lethal phenotype could be rescued by a protein-only RNase P of plant origin, for inhibition zone analyses on agar plates. These cell-based experiments argued against RNase P-specific inhibition of bacterial growth by RNPA2000. We were also unable to confirm the previously reported nonspecific RNase activity of S. aureus RnpA itself. Our results indicate that high-throughput screenings searching for bacterial RNase P inhibitors are prone to the identification of "false positives" that are also termed pan-assay interference compounds (PAINS).
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21
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Feyh R, Waeber NB, Prinz S, Giammarinaro PI, Bange G, Hochberg G, Hartmann RK, Altegoer F. Structure and mechanistic features of the prokaryotic minimal RNase P. eLife 2021; 10:70160. [PMID: 34180399 PMCID: PMC8266387 DOI: 10.7554/elife.70160] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022] Open
Abstract
Endonucleolytic removal of 5'-leader sequences from tRNA precursor transcripts (pre-tRNAs) by ribonuclease P (RNase P) is essential for protein synthesis. Beyond RNA-based RNase P enzymes, protein-only versions of the enzyme exert this function in various eukarya (there termed PRORPs) and in some bacteria (Aquifex aeolicus and close relatives); both enzyme types belong to distinct subgroups of the PIN domain metallonuclease superfamily. Homologs of Aquifex RNase P (HARPs) are also expressed in some other bacteria and many archaea, where they coexist with RNA-based RNase P and do not represent the main RNase P activity. Here, we solved the structure of the bacterial HARP from Halorhodospira halophila by cryo-electron microscopy, revealing a novel screw-like dodecameric assembly. Biochemical experiments demonstrate that oligomerization is required for RNase P activity of HARPs. We propose that the tRNA substrate binds to an extended spike-helix (SH) domain that protrudes from the screw-like assembly to position the 5'-end in close proximity to the active site of the neighboring dimer. The structure suggests that eukaryotic PRORPs and prokaryotic HARPs recognize the same structural elements of pre-tRNAs (tRNA elbow region and cleavage site). Our analysis thus delivers the structural and mechanistic basis for pre-tRNA processing by the prokaryotic HARP system.
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Affiliation(s)
- Rebecca Feyh
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Nadine B Waeber
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Simone Prinz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Pietro Ivan Giammarinaro
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg Hochberg
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
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22
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Lui LM, Nielsen TN, Arkin AP. A method for achieving complete microbial genomes and improving bins from metagenomics data. PLoS Comput Biol 2021; 17:e1008972. [PMID: 33961626 PMCID: PMC8172020 DOI: 10.1371/journal.pcbi.1008972] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 06/02/2021] [Accepted: 04/16/2021] [Indexed: 11/19/2022] Open
Abstract
Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.
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Affiliation(s)
- Lauren M. Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Torben N. Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, CA, United States of America
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23
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Teramoto T, Kaitany KJ, Kakuta Y, Kimura M, Fierke CA, Hall TMT. Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA. Nucleic Acids Res 2020; 48:11815-11826. [PMID: 32719843 DOI: 10.1093/nar/gkaa627] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
Pentatricopeptide repeat (PPR) motifs are α-helical structures known for their modular recognition of single-stranded RNA sequences with each motif in a tandem array binding to a single nucleotide. Protein-only RNase P 1 (PRORP1) in Arabidopsis thaliana is an endoribonuclease that uses its PPR domain to recognize precursor tRNAs (pre-tRNAs) as it catalyzes removal of the 5'-leader sequence from pre-tRNAs with its NYN metallonuclease domain. To gain insight into the mechanism by which PRORP1 recognizes tRNA, we determined a crystal structure of the PPR domain in complex with yeast tRNAPhe at 2.85 Å resolution. The PPR domain of PRORP1 bound to the structurally conserved elbow of tRNA and recognized conserved structural features of tRNAs using mechanisms that are different from the established single-stranded RNA recognition mode of PPR motifs. The PRORP1 PPR domain-tRNAPhe structure revealed a conformational change of the PPR domain upon tRNA binding and moreover demonstrated the need for pronounced overall flexibility in the PRORP1 enzyme conformation for substrate recognition and catalysis. The PRORP1 PPR motifs have evolved strategies for protein-tRNA interaction analogous to tRNA recognition by the RNA component of ribonucleoprotein RNase P and other catalytic RNAs, indicating convergence on a common solution for tRNA substrate recognition.
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Affiliation(s)
- Takamasa Teramoto
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.,Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Kipchumba J Kaitany
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yoshimitsu Kakuta
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Makoto Kimura
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Carol A Fierke
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.,Departments of Chemistry and Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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24
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Thüring M, Ganapathy S, Schlüter MAC, Lechner M, Hartmann RK. 6S-2 RNA deletion in the undomesticated B. subtilis strain NCIB 3610 causes a biofilm derepression phenotype. RNA Biol 2020; 18:79-92. [PMID: 32862759 DOI: 10.1080/15476286.2020.1795408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Bacterial 6S RNA regulates transcription via binding to the active site of RNA polymerase holoenzymes. 6S RNA has been identified in the majority of bacteria, in most cases encoded by a single gene. Firmicutes including Bacillus subtilis encode two 6S RNA paralogs, 6S-1 and 6S-2 RNA. Hypothesizing that the regulatory role of 6S RNAs may be particularly important under natural, constantly changing environmental conditions, we constructed 6S RNA deletion mutants of the undomesticated B. subtilis wild-type strain NCIB 3610. We observed a strong phenotype for the ∆6S-2 RNA strain that showed increased biofilm formation on solid media and the ability to form surface-attached biofilms in liquid culture. This phenotype remained undetected in derived laboratory strains (168, PY79) that are defective in biofilm formation. Quantitative RT-PCR data revealed transcriptional upregulation of biofilm marker genes such as tasA, epsA and bslA in the ∆6S-2 RNA strain, particularly during transition from exponential to stationary growth phase. Salt stress, which blocks sporulation at a very early stage, was found to override the derepressed biofilm phenotype of the ∆6S-2 RNA strain. Furthermore, the ∆6S-2 RNA strain showed retarded swarming activity and earlier spore formation. Finally, the ∆6S-1&2 RNA double deletion strain showed a prolonged lag phase of growth under oxidative, high salt and alkaline stress conditions, suggesting that the interplay of both 6S RNAs in B. subtilis optimizes and fine-tunes transcriptomic adaptations, thereby contributing to the fitness of B. subtilis under the unsteady and temporarily harsh conditions encountered in natural habitats.
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Affiliation(s)
- Marietta Thüring
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - Sweetha Ganapathy
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - M Amri C Schlüter
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology, Bioinformatics Core Facility , Marburg, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
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25
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Ellis JC. P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB). BMC Genomics 2020; 21:334. [PMID: 32349659 PMCID: PMC7191817 DOI: 10.1186/s12864-020-6615-z] [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: 10/17/2019] [Accepted: 02/24/2020] [Indexed: 11/23/2022] Open
Abstract
Background The rnpB gene encodes for an essential catalytic RNA (RNase P). Like other essential RNAs, RNase P’s sequence is highly variable. However, unlike other essential RNAs (i.e. tRNA, 16 S, 6 S,...) its structure is also variable with at least 5 distinct structure types observed in prokaryotes. This structural variability makes it labor intensive and challenging to create and maintain covariance models for the detection of RNase P RNA in genomic and metagenomic sequences. The lack of a facile and rapid annotation algorithm has led to the rnpB gene being the most grossly under annotated essential gene in completed prokaryotic genomes with only a 24% annotation rate. Here we describe the coupling of the largest RNase P RNA database with the local alignment scoring algorithm to create the most sensitive and rapid prokaryote rnpB gene identification and annotation algorithm to date. Results Of the 2772 completed microbial genomes downloaded from GenBank only 665 genomes had an annotated rnpB gene. We applied P Finder to these genomes and were able to identify 2733 or nearly 99% of the 2772 microbial genomes examined. From these results four new rnpB genes that encode the minimal T-type P RNase P RNAs were identified computationally for the first time. In addition, only the second C-type RNase P RNA was identified in Sphaerobacter thermophilus. Of special note, no RNase P RNAs were detected in several obligate endosymbionts of sap sucking insects suggesting a novel evolutionary adaptation. Conclusions The coupling of the largest RNase P RNA database and associated structure class identification with the P Finder algorithm is both sensitive and rapid, yielding high quality results to aid researchers annotating either genomic or metagenomic data. It is the only algorithm to date that can identify challenging RNAse P classes such as C-type and the minimal T-type RNase P RNAs. P Finder is written in C# and has a user-friendly GUI that can run on multiple 64-bit windows platforms (Windows Vista/7/8/10). P Finder is free available for download at https://github.com/JChristopherEllis/P-Finder as well as a small sample RNase P RNA file for testing.
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Affiliation(s)
- J Christopher Ellis
- Computational Biology and Bioinformatics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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26
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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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27
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Schwarz TS, Wäber NB, Feyh R, Weidenbach K, Schmitz RA, Marchfelder A, Hartmann RK. Homologs of aquifex aeolicus protein-only RNase P are not the major RNase P activities in the archaea haloferax volcanii and methanosarcina mazei. IUBMB Life 2019; 71:1109-1116. [PMID: 31283101 DOI: 10.1002/iub.2122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/07/2019] [Accepted: 06/09/2019] [Indexed: 01/20/2023]
Abstract
The mature 5'-ends of tRNAs are generated by RNase P in all domains of life. The ancient form of the enzyme is a ribonucleoprotein consisting of a catalytic RNA and one or more protein subunits. However, in the hyperthermophilic bacterium Aquifex aeolicus and close relatives, RNase P is a protein-only enzyme consisting of a single type of polypeptide (Aq_880, ~23 kDa). In many archaea, homologs of Aq_880 were identified (termed HARPs for Homologs of Aquifex RNase P) in addition to the RNA-based RNase P, raising the question about the functions of HARP and the classical RNase P in these archaea. Here we investigated HARPs from two euryarchaeotes, Haloferax volcanii and Methanosarcina mazei. Archaeal strains with HARP gene knockouts showed no growth phenotypes under standard conditions, temperature and salt stress (H. volcanii) or nitrogen deficiency (M. mazei). Recombinant H. volcanii and M. mazei HARPs were basically able to catalyse specific tRNA 5'-end maturation in vitro. Furthermore, M. mazei HARP was able to rescue growth of an Escherichia coli RNase P depletion strain with comparable efficiency as Aq_880, while H. volcanii HARP was unable to do so. In conclusion, both archaeal HARPs showed the capacity (in at least one functional assay) to act as RNases P. However, the ease to obtain knockouts of the singular HARP genes and the lack of growth phenotypes upon HARP gene deletion contrasts with the findings that the canonical RNase P RNA gene cannot be deleted in H. volcanii, and a knockdown of RNase P RNA in H. volcanii results in severe tRNA processing defects. We conclude that archaeal HARPs do not make a major contribution to global tRNA 5'-end maturation in archaea, but may well exert a specialised, yet unknown function in (t)RNA metabolism. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1109-1116, 2019.
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Affiliation(s)
| | - Nadine B Wäber
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Rebecca Feyh
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Katrin Weidenbach
- Institute of General Microbiology, Christian-Albrechts-Universität, Kiel, Germany
| | - Ruth A Schmitz
- Institute of General Microbiology, Christian-Albrechts-Universität, Kiel, Germany
| | | | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
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28
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Bechhofer DH, Deutscher MP. Bacterial ribonucleases and their roles in RNA metabolism. Crit Rev Biochem Mol Biol 2019; 54:242-300. [PMID: 31464530 PMCID: PMC6776250 DOI: 10.1080/10409238.2019.1651816] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.
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Affiliation(s)
- David H. Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Murray P. Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
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29
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Gobert A, Bruggeman M, Giegé P. Involvement of PIN-like domain nucleases in tRNA processing and translation regulation. IUBMB Life 2019; 71:1117-1125. [PMID: 31066520 DOI: 10.1002/iub.2062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/24/2019] [Indexed: 12/29/2022]
Abstract
Transfer RNAs require essential maturation steps to become functional. Among them, RNase P removes 5' leader sequences of pre-tRNAs. Although RNase P was long thought to occur universally as ribonucleoproteins, different types of protein-only RNase P enzymes were discovered in both eukaryotes and prokaryotes. Interestingly, all these enzymes belong to the super-group of PilT N-terminal-like nucleases (PIN)-like ribonucleases. This wide family of enzymes can be subdivided into major subgroups. Here, we review recent studies at both functional and mechanistic levels on three PIN-like ribonucleases groups containing enzymes connected to tRNA maturation and/or translation regulation. The evolutive distribution of these proteins containing PIN-like domains as well as their organization and fusion with various functional domains is discussed and put in perspective with the diversity of functions they acquired during evolution, for the maturation and homeostasis of tRNA and a wider array of RNA substrates. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1117-1125, 2019.
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Affiliation(s)
- Anthony Gobert
- Institut de Biologie de Moléculaire des Plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Mathieu Bruggeman
- Institut de Biologie de Moléculaire des Plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Giegé
- Institut de Biologie de Moléculaire des Plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
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30
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Import of Non-Coding RNAs into Human Mitochondria: A Critical Review and Emerging Approaches. Cells 2019; 8:cells8030286. [PMID: 30917553 PMCID: PMC6468882 DOI: 10.3390/cells8030286] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/19/2019] [Accepted: 03/23/2019] [Indexed: 01/26/2023] Open
Abstract
Mitochondria harbor their own genetic system, yet critically depend on the import of a number of nuclear-encoded macromolecules to ensure their expression. In all eukaryotes, selected non-coding RNAs produced from the nuclear genome are partially redirected into the mitochondria, where they participate in gene expression. Therefore, the mitochondrial RNome represents an intricate mixture of the intrinsic transcriptome and the extrinsic RNA importome. In this review, we summarize and critically analyze data on the nuclear-encoded transcripts detected in human mitochondria and outline the proposed molecular mechanisms of their mitochondrial import. Special attention is given to the various experimental approaches used to study the mitochondrial RNome, including some recently developed genome-wide and in situ techniques.
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31
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Boivin V, Faucher-Giguère L, Scott M, Abou-Elela S. The cellular landscape of mid-size noncoding RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1530. [PMID: 30843375 PMCID: PMC6619189 DOI: 10.1002/wrna.1530] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/06/2023]
Abstract
Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid-size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes. Many are found in multiple copies in genomes. mncRNAs are highly structured and carry many posttranscriptional modifications. Both of these facets dictate their RNA-binding protein partners and ultimately their function. mncRNAs have already been implicated in translation, catalysis, as guides for RNA modification, as spliceosome components and regulatory RNA. However, recent studies are adding new mncRNA functions including regulation of gene expression and alternative splicing. In this review, we describe the different classes, characteristics and emerging functions of mncRNAs and their relative expression patterns. Finally, we provide a portrait of the challenges facing their detection and annotation in databases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Vincent Boivin
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Laurence Faucher-Giguère
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Michelle Scott
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sherif Abou-Elela
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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32
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Daniels CJ, Lai LB, Chen TH, Gopalan V. Both kinds of RNase P in all domains of life: surprises galore. RNA (NEW YORK, N.Y.) 2019; 25:286-291. [PMID: 30578286 PMCID: PMC6380272 DOI: 10.1261/rna.068379.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/18/2018] [Indexed: 05/03/2023]
Abstract
RNase P, an essential housekeeping endonuclease needed for 5'-processing of tRNAs, exists in two distinct forms: one with an RNA- and the other with a protein-based active site. The notion that the protein form of RNase P exists only in eukaryotes has been upended by the recent discovery of a protein-only variant in Bacteria and Archaea. The use of these two divergent scaffolds, shaped by convergent evolution, in all three domains of life inspires questions relating to the ancestral form of RNase P, as well as their origins and function(s) in vivo. Results from our analysis of publicly available bacterial and archaeal genomes suggest that the widespread RNA-based ribonucleoprotein variant is likely the ancient form. We also discuss the possible genetic origins and function of RNase P, including how the simultaneous presence of its variants may contribute to the fitness of their host organisms.
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Affiliation(s)
- Charles J Daniels
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Lien B Lai
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Tien-Hao Chen
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Venkat Gopalan
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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33
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Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. FEMS Microbiol Rev 2018; 42:579-613. [PMID: 29684129 DOI: 10.1093/femsre/fuy016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022] Open
Abstract
RNA-processing pathways are at the centre of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes are still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally, prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.
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Affiliation(s)
- Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Yves Quentin
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
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34
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Affiliation(s)
- William G Scott
- Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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35
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Chen TH, Sotomayor M, Gopalan V. Biochemical Studies Provide Insights into the Necessity for Multiple Arabidopsis thaliana Protein-Only RNase P Isoenzymes. J Mol Biol 2018; 431:615-624. [PMID: 30414965 DOI: 10.1016/j.jmb.2018.11.004] [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: 08/19/2018] [Revised: 10/22/2018] [Accepted: 11/04/2018] [Indexed: 10/27/2022]
Abstract
RNase P catalyzes removal of the 5' leader from precursor tRNAs (pre-tRNAs) in all three domains of life. Some eukaryotic cells contain multiple forms of the protein-only RNase P (PRORP) variant, prompting efforts to unravel this seeming redundancy. Previous studies concluded that there were only modest differences in the processing of typical pre-tRNAs by the three isoforms in Arabidopsis thaliana [AtPRORP1 (organellar), AtPRORP2 and AtPRORP3 (nuclear)]. Here, we investigated if different physical attributes of the three isoforms might engender payoffs under specific conditions. Our temperature-activity profiling studies revealed that AtPRORPs display substrate-identity dependent behavior at elevated temperatures (37-45 °C), with the organellar variant outperforming the nuclear counterparts. Echoing these findings, molecular dynamics simulations revealed that AtPRORP2 relative to AtPRORP1 samples a wider conformational ensemble that deviates from the crystal structure. Results from our biochemical studies and molecular dynamics simulations support the idea that AtPRORPs have overlapping but not necessarily redundant attributes and inspire new perspectives on the suitability of each variant to perform its function(s) in a specific cellular locale.
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Affiliation(s)
- Tien-Hao Chen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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36
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Condon C, Piton J, Braun F. Distribution of the ribosome associated endonuclease Rae1 and the potential role of conserved amino acids in codon recognition. RNA Biol 2018; 15:683-688. [PMID: 29557713 DOI: 10.1080/15476286.2018.1454250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We recently identified a novel ribonuclease in Bacillus subtilis called Rae1 that cleaves mRNAs in a translation-dependent manner. Rae1 is a member of the NYN/PIN family of ribonucleases and is highly conserved in the Firmicutes, the Cyanobacteria and the chloroplasts of photosynthetic algae and plants. We have proposed a model in which Rae1 enters the A-site of ribosomes that are paused following translation of certain sequences that are still ill-defined. In the only case identified thus far, Rae1 cleaves between a conserved glutamate and lysine codon during translation of a short peptide called S1025. Certain other codons are also tolerated on either side of the cleavage site, but these are recognized less efficiently. The model of Rae1 docked in the A-site allows us to make predictions about which conserved residues may be important for recognition of mRNA, the tRNA in the adjacent P-site and binding to the 50S ribosome subunit.
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Affiliation(s)
- Ciarán Condon
- a UMR 8261 (CNRS - Univ. Paris Diderot), Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, Paris , France
| | | | - Frédérique Braun
- a UMR 8261 (CNRS - Univ. Paris Diderot), Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, Paris , France
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