1
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Skeparnias I, Bou-Nader C, Anastasakis DG, Fan L, Wang YX, Hafner M, Zhang J. Structural basis of MALAT1 RNA maturation and mascRNA biogenesis. Nat Struct Mol Biol 2024:10.1038/s41594-024-01340-4. [PMID: 38956168 DOI: 10.1038/s41594-024-01340-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 05/29/2024] [Indexed: 07/04/2024]
Abstract
The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) long noncoding RNA (lncRNA) has key roles in regulating transcription, splicing, tumorigenesis, etc. Its maturation and stabilization require precise processing by RNase P, which simultaneously initiates the biogenesis of a 3' cytoplasmic MALAT1-associated small cytoplasmic RNA (mascRNA). mascRNA was proposed to fold into a transfer RNA (tRNA)-like secondary structure but lacks eight conserved linking residues required by the canonical tRNA fold. Here we report crystal structures of human mascRNA before and after processing, which reveal an ultracompact, quasi-tRNA-like structure. Despite lacking all linker residues, mascRNA faithfully recreates the characteristic 'elbow' feature of tRNAs to recruit RNase P and ElaC homolog protein 2 (ELAC2) for processing, which exhibit distinct substrate specificities. Rotation and repositioning of the D-stem and anticodon regions preclude mascRNA from aminoacylation, avoiding interference with translation. Therefore, a class of metazoan lncRNA loci uses a previously unrecognized, unusually streamlined quasi-tRNA architecture to recruit select tRNA-processing enzymes while excluding others to drive bespoke RNA biogenesis, processing and maturation.
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Affiliation(s)
- Ilias Skeparnias
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Dimitrios G Anastasakis
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-Ray Scattering Core Facility of National Cancer Institute, Frederick, MD, USA
| | - Yun-Xing Wang
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-Ray Scattering Core Facility of National Cancer Institute, Frederick, MD, USA
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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2
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Michelson M, Yosovich K, Bahar S, Yogev Y, Birk OS, Ginzberg M, Lev D. Novel phenotype associated with homozygous likely pathogenic variant in the POP1 gene. Clin Genet 2024; 105:671-675. [PMID: 38351533 DOI: 10.1111/cge.14502] [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: 10/25/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
The biallelic variants of the POP1 gene are associated with the anauxetic dysplasia (AAD OMIM 607095), a rare skeletal dysplasia, characterized by prenatal rhizomelic shortening of limbs and generalized joint hypermobility. Affected individuals usually have normal neurodevelopmental milestones. Here we present three cases from the same family with likely pathogenic homozygous POP1 variant and a completely novel phenotype: a girl with global developmental delay and autism, microcephaly, peculiar dysmorphic features and multiple congenital anomalies. Two subsequent pregnancies were terminated due to multiple congenital malformations. Fetal DNA samples revealed the same homozygous variant in the POP1 gene. Expression of the RMRP was reduced in the proband compared with control and slightly reduced in both heterozygous parents, carriers for this variant. To our knowledge, this is the first report of this new phenotype, associated with a novel likely pathogenic variant in POP1. Our findings expand the phenotypic spectrum of POP1-related disorders.
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Affiliation(s)
- Marina Michelson
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
- The Genetic Institute of Maccabi Health Medicinal Organization, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Keren Yosovich
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Sarit Bahar
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Genetics Institute, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Mira Ginzberg
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Dorit Lev
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
- The Genetic Institute of Maccabi Health Medicinal Organization, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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3
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Kirsebom LA, Liu F, McClain WH. The discovery of a catalytic RNA within RNase P and its legacy. J Biol Chem 2024; 300:107318. [PMID: 38677513 PMCID: PMC11143913 DOI: 10.1016/j.jbc.2024.107318] [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: 09/18/2023] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
Sidney Altman's discovery of the processing of one RNA by another RNA that acts like an enzyme was revolutionary in biology and the basis for his sharing the 1989 Nobel Prize in Chemistry with Thomas Cech. These breakthrough findings support the key role of RNA in molecular evolution, where replicating RNAs (and similar chemical derivatives) either with or without peptides functioned in protocells during the early stages of life on Earth, an era referred to as the RNA world. Here, we cover the historical background highlighting the work of Altman and his colleagues and the subsequent efforts of other researchers to understand the biological function of RNase P and its catalytic RNA subunit and to employ it as a tool to downregulate gene expression. We primarily discuss bacterial RNase P-related studies but acknowledge that many groups have significantly contributed to our understanding of archaeal and eukaryotic RNase P, as reviewed in this special issue and elsewhere.
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Affiliation(s)
- Leif A Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
| | - Fenyong Liu
- School of Public Health, University of California, Berkeley, California, USA.
| | - William H McClain
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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4
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Elder JJH, Papadopoulos R, Hayne CK, Stanley RE. The making and breaking of tRNAs by ribonucleases. Trends Genet 2024; 40:511-525. [PMID: 38641471 PMCID: PMC11152995 DOI: 10.1016/j.tig.2024.03.007] [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: 02/08/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Ribonucleases (RNases) play important roles in supporting canonical and non-canonical roles of tRNAs by catalyzing the cleavage of the tRNA phosphodiester backbone. Here, we highlight how recent advances in cryo-electron microscopy (cryo-EM), protein structure prediction, reconstitution experiments, tRNA sequencing, and other studies have revealed new insight into the nucleases that process tRNA. This represents a very diverse group of nucleases that utilize distinct mechanisms to recognize and cleave tRNA during different stages of a tRNA's life cycle including biogenesis, fragmentation, surveillance, and decay. In this review, we provide a synthesis of the structure, mechanism, regulation, and modes of tRNA recognition by tRNA nucleases, along with open questions for future investigation.
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Affiliation(s)
- Jessica J H Elder
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Ry Papadopoulos
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA; Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Cassandra K Hayne
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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5
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Wang P, Lin J, Zheng X, Xu X. RNase P: Beyond Precursor tRNA Processing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae016. [PMID: 38862431 DOI: 10.1093/gpbjnl/qzae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/18/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
Ribonuclease P (RNase P) was first described in the 1970's as an endoribonuclease acting in the maturation of precursor transfer RNAs (tRNAs). More recent studies, however, have uncovered non-canonical roles for RNase P and its components. Here, we review the recent progress of its involvement in chromatin assembly, DNA damage response, and maintenance of genome stability with implications in tumorigenesis. The possibility of RNase P as a therapeutic target in cancer is also discussed.
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Affiliation(s)
- Peipei Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China
| | - Juntao Lin
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Xiangyang Zheng
- Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine, Dehua Hospital, Dehua 362500, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China
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6
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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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7
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Zhou B, Wan F, Lei KX, Lan P, Wu J, Lei M. Coevolution of RNA and protein subunits in RNase P and RNase MRP, two RNA processing enzymes. J Biol Chem 2024; 300:105729. [PMID: 38336296 PMCID: PMC10966300 DOI: 10.1016/j.jbc.2024.105729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
RNase P and RNase mitochondrial RNA processing (MRP) are ribonucleoproteins (RNPs) that consist of a catalytic RNA and a varying number of protein cofactors. RNase P is responsible for precursor tRNA maturation in all three domains of life, while RNase MRP, exclusive to eukaryotes, primarily functions in rRNA biogenesis. While eukaryotic RNase P is associated with more protein cofactors and has an RNA subunit with fewer auxiliary structural elements compared to its bacterial cousin, the double-anchor precursor tRNA recognition mechanism has remarkably been preserved during evolution. RNase MRP shares evolutionary and structural similarities with RNase P, preserving the catalytic core within the RNA moiety inherited from their common ancestor. By incorporating new protein cofactors and RNA elements, RNase MRP has established itself as a distinct RNP capable of processing ssRNA substrates. The structural information on RNase P and MRP helps build an evolutionary trajectory, depicting how emerging protein cofactors harmonize with the evolution of RNA to shape different functions for RNase P and MRP. Here, we outline the structural and functional relationship between RNase P and MRP to illustrate the coevolution of RNA and protein cofactors, a key driver for the extant, diverse RNP world.
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Affiliation(s)
- Bin Zhou
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China
| | - Futang Wan
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China
| | - Kevin X Lei
- Shanghai High School International Division, Shanghai, China
| | - Pengfei Lan
- Shanghai Institute of Precision Medicine, Shanghai, China; Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jian Wu
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China.
| | - Ming Lei
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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8
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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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9
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Zhang J. Recognition of the tRNA structure: Everything everywhere but not all at once. Cell Chem Biol 2024; 31:36-52. [PMID: 38159570 PMCID: PMC10843564 DOI: 10.1016/j.chembiol.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/02/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
tRNAs are among the most abundant and essential biomolecules in cells. These spontaneously folding, extensively structured yet conformationally flexible anionic polymers literally bridge the worlds of RNAs and proteins, and serve as Rosetta stones that decipher and interpret the genetic code. Their ubiquitous presence, functional irreplaceability, and privileged access to cellular compartments and ribosomes render them prime targets for both endogenous regulation and exogenous manipulation. There is essentially no part of the tRNA that is not touched by another interaction partner, either as programmed or imposed by an external adversary. Recent progresses in genetic, biochemical, and structural analyses of the tRNA interactome produced a wealth of new knowledge into their interaction networks, regulatory functions, and molecular interfaces. In this review, I describe and illustrate the general principles of tRNA recognition by proteins and other RNAs, and discuss the underlying molecular mechanisms that deliver affinity, specificity, and functional competency.
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Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
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10
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Chamberlain AR, Huynh L, Huang W, Taylor DJ, Harris ME. The specificity landscape of bacterial ribonuclease P. J Biol Chem 2024; 300:105498. [PMID: 38013087 PMCID: PMC10731613 DOI: 10.1016/j.jbc.2023.105498] [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: 07/24/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
Developing quantitative models of substrate specificity for RNA processing enzymes is a key step toward understanding their biology and guiding applications in biotechnology and biomedicine. Optimally, models to predict relative rate constants for alternative substrates should integrate an understanding of structures of the enzyme bound to "fast" and "slow" substrates, large datasets of rate constants for alternative substrates, and transcriptomic data identifying in vivo processing sites. Such data are either available or emerging for bacterial ribonucleoprotein RNase P a widespread and essential tRNA 5' processing endonuclease, thus making it a valuable model system for investigating principles of biological specificity. Indeed, the well-established structure and kinetics of bacterial RNase P enabled the development of high throughput measurements of rate constants for tRNA variants and provided the necessary framework for quantitative specificity modeling. Several studies document the importance of conformational changes in the precursor tRNA substrate as well as the RNA and protein subunits of bacterial RNase P during binding, although the functional roles and dynamics are still being resolved. Recently, results from cryo-EM studies of E. coli RNase P with alternative precursor tRNAs are revealing prospective mechanistic relationships between conformational changes and substrate specificity. Yet, extensive uncharted territory remains, including leveraging these advances for drug discovery, achieving a complete accounting of RNase P substrates, and understanding how the cellular context contributes to RNA processing specificity in vivo.
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Affiliation(s)
| | - Loc Huynh
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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11
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Sabalette KB, Makarova L, Marcia M. G·U base pairing motifs in long non-coding RNAs. Biochimie 2023; 214:123-140. [PMID: 37353139 DOI: 10.1016/j.biochi.2023.06.003] [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: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts involved in gene expression regulation and associated with diseases. Despite the unprecedented molecular complexity of these transcripts, recent studies of the secondary and tertiary structure of lncRNAs are starting to reveal the principles of lncRNA structural organization, with important functional implications. It therefore starts to be possible to analyze lncRNA structures systematically. Here, using a set of prototypical and medically-relevant lncRNAs of known secondary structure, we specifically catalogue the distribution and structural environment of one of the first-identified and most frequently occurring non-canonical Watson-Crick interactions, the G·U base pair. We compare the properties of G·U base pairs in our set of lncRNAs to those of the G·U base pairs in other well-characterized transcripts, like rRNAs, tRNAs, ribozymes, and riboswitches. Furthermore, we discuss how G·U base pairs in these targets participate in establishing interactions with proteins or miRNAs, and how they enable lncRNA tertiary folding by forming intramolecular or metal-ion interactions. Finally, by identifying highly-G·U-enriched regions of yet unknown function in our target lncRNAs, we provide a new rationale for future experimental investigation of these motifs, which will help obtain a more comprehensive understanding of lncRNA functions and molecular mechanisms in the future.
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Affiliation(s)
- Karina Belen Sabalette
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Liubov Makarova
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France.
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12
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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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13
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Orlovetskie N, Mani D, Rouvinski A, Jarrous N. Human RNase P exhibits and controls distinct ribonucleolytic activities required for ordered maturation of tRNA. Proc Natl Acad Sci U S A 2023; 120:e2307185120. [PMID: 37831743 PMCID: PMC10589621 DOI: 10.1073/pnas.2307185120] [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: 04/30/2023] [Accepted: 09/05/2023] [Indexed: 10/15/2023] Open
Abstract
Precursor tRNAs are transcribed with flanking and intervening sequences known to be processed by specific ribonucleases. Here, we show that transcription complexes of RNA polymerase III assembled on tRNA genes comprise RNase P that cleaves precursor tRNA and subsequently degrades the excised 5' leader. Degradation is based on a 3'-5' exoribonucleolytic activity carried out by the protein subunit Rpp14, as determined by biochemical and reverse genetic analyses. Neither reconstituted nor purified RNase P displays this magnesium ion-dependent, processive exoribonucleolytic activity. Markedly, knockdown of Rpp14 by RNA interference leads to a wide-ranging inhibition of cleavage of flanking and intervening sequences of various precursor tRNAs in extracts and cells. This study reveals that RNase P controls tRNA splicing complex and RNase Z for ordered maturation of nascent precursor tRNAs by transcription complexes.
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Affiliation(s)
- Natalie Orlovetskie
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem9112010, Israel
| | - Dhivakar Mani
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem9112010, Israel
| | - Alexander Rouvinski
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem9112010, Israel
- The Kuvin Center for the Study of Infectious and Tropical Diseases, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem9112010, Israel
| | - Nayef Jarrous
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem9112010, Israel
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14
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Zhou S, Van Bortle K. The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1782. [PMID: 36754845 PMCID: PMC10498592 DOI: 10.1002/wrna.1782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL) and translation (tRNA, 5S rRNA). In higher eukaryotes, the Pol III transcriptome has expanded to include additional, recently evolved ncRNA species that effectively broaden the footprint of Pol III transcription to additional cellular activities. Newly evolved ncRNAs function as riboregulators of autophagy (vault), immune signaling cascades (nc886), and translation (Alu, BC200, snaR). Notably, upregulation of Pol III transcription is frequently observed in cancer, and multiple ncRNA species are linked to both cancer progression and poor survival outcomes among cancer patients. In this review, we outline the basic features and functions of the Pol III transcriptome, and the evidence for dysregulation and dysfunction for each ncRNA in cancer. When taken together, recurrent patterns emerge, ranging from shared functional motifs that include molecular scaffolding and protein sequestration, overlapping protein interactions, and immunostimulatory activities, to the biogenesis of analogous small RNA fragments and noncanonical miRNAs, augmenting the function of the Pol III transcriptome and further broadening its role in cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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15
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Elkholi IE, Boulais J, Thibault MP, Phan HD, Robert A, Lai LB, Faubert D, Smith MJ, Gopalan V, Côté JF. Mapping the MOB proteins' proximity network reveals a unique interaction between human MOB3C and the RNase P complex. J Biol Chem 2023; 299:105123. [PMID: 37536630 PMCID: PMC10480535 DOI: 10.1016/j.jbc.2023.105123] [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: 05/09/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023] Open
Abstract
Distinct functions mediated by members of the monopolar spindle-one-binder (MOB) family of proteins remain elusive beyond the evolutionarily conserved and well-established roles of MOB1 (MOB1A/B) in regulating tissue homeostasis within the Hippo pathway. Since MOB proteins are adaptors, understanding how they engage in protein-protein interactions and help assemble complexes is essential to define the full scope of their biological functions. To address this, we undertook a proximity-dependent biotin identification approach to define the interactomes of all seven human MOB proteins in HeLa and human embryonic kidney 293 cell lines. We uncovered >200 interactions, of which at least 70% are unreported on BioGrid. The generated dataset reliably recalled the bona fide interactors of the well-studied MOBs. We further defined the common and differential interactome between different MOBs on a subfamily and an individual level. We discovered a unique association between MOB3C and 7 of 10 protein subunits of the RNase P complex, an endonuclease that catalyzes tRNA 5' maturation. As a proof of principle for the robustness of the generated dataset, we validated the specific interaction of MOB3C with catalytically active RNase P by using affinity purification-mass spectrometry and pre-tRNA cleavage assays of MOB3C pulldowns. In summary, our data provide novel insights into the biology of MOB proteins and reveal the first interactors of MOB3C, components of the RNase P complex, and hence an exciting nexus with RNA biology.
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Affiliation(s)
- Islam E Elkholi
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada; Molecular Biology Programs, Université de Montréal, Montreal, Quebec, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada.
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | | | - Hong-Duc Phan
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Amélie Robert
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Lien B Lai
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Denis Faubert
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Venkat Gopalan
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jean-Franҫois Côté
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada; Molecular Biology Programs, Université de Montréal, Montreal, Quebec, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada.
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16
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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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17
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Biela A, Hammermeister A, Kaczmarczyk I, Walczak M, Koziej L, Lin TY, Glatt S. The diverse structural modes of tRNA binding and recognition. J Biol Chem 2023; 299:104966. [PMID: 37380076 PMCID: PMC10424219 DOI: 10.1016/j.jbc.2023.104966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
tRNAs are short noncoding RNAs responsible for decoding mRNA codon triplets, delivering correct amino acids to the ribosome, and mediating polypeptide chain formation. Due to their key roles during translation, tRNAs have a highly conserved shape and large sets of tRNAs are present in all living organisms. Regardless of sequence variability, all tRNAs fold into a relatively rigid three-dimensional L-shaped structure. The conserved tertiary organization of canonical tRNA arises through the formation of two orthogonal helices, consisting of the acceptor and anticodon domains. Both elements fold independently to stabilize the overall structure of tRNAs through intramolecular interactions between the D- and T-arm. During tRNA maturation, different modifying enzymes posttranscriptionally attach chemical groups to specific nucleotides, which not only affect translation elongation rates but also restrict local folding processes and confer local flexibility when required. The characteristic structural features of tRNAs are also employed by various maturation factors and modification enzymes to assure the selection, recognition, and positioning of specific sites within the substrate tRNAs. The cellular functional repertoire of tRNAs continues to extend well beyond their role in translation, partly, due to the expanding pool of tRNA-derived fragments. Here, we aim to summarize the most recent developments in the field to understand how three-dimensional structure affects the canonical and noncanonical functions of tRNA.
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Affiliation(s)
- Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Marta Walczak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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18
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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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19
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Patel S, Sexton AN, Strine MS, Wilen CB, Simon MD, Pyle AM. Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq. Nat Commun 2023; 14:3426. [PMID: 37296103 PMCID: PMC10255950 DOI: 10.1038/s41467-023-38623-1] [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: 09/12/2022] [Accepted: 05/09/2023] [Indexed: 06/12/2023] Open
Abstract
Compact RNA structural motifs control many aspects of gene expression, but we lack methods for finding these structures in the vast expanse of multi-kilobase RNAs. To adopt specific 3-D shapes, many RNA modules must compress their RNA backbones together, bringing negatively charged phosphates into close proximity. This is often accomplished by recruiting multivalent cations (usually Mg2+), which stabilize these sites and neutralize regions of local negative charge. Coordinated lanthanide ions, such as terbium (III) (Tb3+), can also be recruited to these sites, where they induce efficient RNA cleavage, thereby revealing compact RNA 3-D modules. Until now, Tb3+ cleavage sites were monitored via low-throughput biochemical methods only applicable to small RNAs. Here we present Tb-seq, a high-throughput sequencing method for detecting compact tertiary structures in large RNAs. Tb-seq detects sharp backbone turns found in RNA tertiary structures and RNP interfaces, providing a way to scan transcriptomes for stable structural modules and potential riboregulatory motifs.
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Affiliation(s)
- Shivali Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Alec N Sexton
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
| | - Anna Marie Pyle
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.
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20
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Kazmi MA, Thaler DS, Åberg KC, Mattheisen JM, Huber T, Sakmar TP. The Coronavirus Calendar (CoronaCal): a simplified SARS-CoV-2 test system for sampling and retrospective analysis. FRONTIERS IN EPIDEMIOLOGY 2023; 3:1146006. [PMID: 38455914 PMCID: PMC10910978 DOI: 10.3389/fepid.2023.1146006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/14/2023] [Indexed: 03/09/2024]
Abstract
Objectives To develop a biological diary (CoronaCal) that allows anyone in the community to collect and store serial saliva samples and chart symptoms on ordinary printer paper. Methods Diaries were analyzed for the presence of SARS-CoV-2 RNA using established polymerase chain reaction (PCR) procedures. CoronaCal diaries were distributed to volunteer subjects in the community during the peak of the COVID-19 outbreak in New York. Volunteers collected their own daily saliva samples and self-reported symptoms. Results SARS-CoV-2 RNA extracted from CoronaCals was measured using qPCR and RNA levels were correlated with reported symptoms. SARS-CoV-2 RNA was detected in CoronaCals from nine of nine people with COVID-19 symptoms or exposure to someone with COVID-19, and not in one asymptomatic person. CoronaCals were stored for up to 70 days at room temperature during collection and then frozen for up to four months before analysis, suggesting that SARS-CoV-2 RNA is stable once dried onto paper. Conclusions Sampling saliva on simple paper provides a useful method to study the natural history and epidemiology of COVID-19. The CoronaCal collection and testing method is easy to implement, inexpensive, non-invasive and scalable. The approach can inform the historical and epidemiological understanding of infections in individuals and populations.
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Affiliation(s)
- Manija A. Kazmi
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, United States
| | - David S. Thaler
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, United States
- Biozentrum, University of Basel, Basel, Switzerland
- Program for the Human Environment, The Rockefeller University, New York, NY, United States
| | - Karina C. Åberg
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, United States
| | - Jordan M. Mattheisen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, United States
- Tri-Institutional Program in Chemical Biology, New York, NYUnited States
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, United States
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, United States
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21
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Jeandard D, Smirnova A, Fasemore AM, Coudray L, Entelis N, Förstner K, Tarassov I, Smirnov A. CoLoC-seq probes the global topology of organelle transcriptomes. Nucleic Acids Res 2022; 51:e16. [PMID: 36537202 PMCID: PMC9943681 DOI: 10.1093/nar/gkac1183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Proper RNA localisation is essential for physiological gene expression. Various kinds of genome-wide approaches permit to comprehensively profile subcellular transcriptomes. Among them, cell fractionation methods, that couple RNase treatment of isolated organelles to the sequencing of protected transcripts, remain most widely used, mainly because they do not require genetic modification of the studied system and can be easily implemented in any cells or tissues, including in non-model species. However, they suffer from numerous false-positives since incompletely digested contaminant RNAs can still be captured and erroneously identified as resident transcripts. Here we introduce Controlled Level of Contamination coupled to deep sequencing (CoLoC-seq) as a new subcellular transcriptomics approach that efficiently bypasses this caveat. CoLoC-seq leverages classical enzymatic kinetics and tracks the depletion dynamics of transcripts in a gradient of an exogenously added RNase, with or without organellar membranes. By means of straightforward mathematical modelling, CoLoC-seq infers the localisation topology of RNAs and robustly distinguishes between genuinely resident, luminal transcripts and merely abundant surface-attached contaminants. Our generic approach performed well on human mitochondria and is in principle applicable to other membrane-bounded organelles, including plastids, compartments of the vacuolar system, extracellular vesicles, and viral particles.
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Affiliation(s)
| | | | | | - Léna Coudray
- UMR7156 – Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, F-67000, France
| | - Nina Entelis
- UMR7156 – Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, F-67000, France
| | - Konrad U Förstner
- ZB MED – Information Centre for Life Sciences, Cologne, D-50931, Germany,TH Köln – University of Applied Sciences, Faculty of Information Science and Communication Studies, Institute of Information Science, Cologne, D-50678, Germany
| | - Ivan Tarassov
- UMR7156 – Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, F-67000, France
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22
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Altered tRNA processing is linked to a distinct and unusual La protein in Tetrahymena thermophila. Nat Commun 2022; 13:7332. [PMID: 36443289 PMCID: PMC9705548 DOI: 10.1038/s41467-022-34796-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
Nascent pre-tRNAs are transcribed by RNA polymerase III and immediately bound by La proteins on the UUU-3'OH sequence, using a tandem arrangement of the La motif and an adjacent RNA recognition motif-1 (RRM1), resulting in protection from 3'-exonucleases and promotion of pre-tRNA folding. The Tetrahymena thermophila protein Mlp1 has been previously classified as a genuine La protein, despite the predicted absence of the RRM1. We find that Mlp1 functions as a La protein through binding of pre-tRNAs, and affects pre-tRNA processing in Tetrahymena thermophila and when expressed in fission yeast. However, unlike in other examined eukaryotes, depletion of Mlp1 results in 3'-trailer stabilization. The 3'-trailers in Tetrahymena thermophila are uniquely short relative to other examined eukaryotes, and 5'-leaders have evolved to disfavour pre-tRNA leader/trailer pairing. Our data indicate that this variant Mlp1 architecture is linked to an altered, novel mechanism of tRNA processing in Tetrahymena thermophila.
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23
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Chai P, Lan P, Li S, Yao D, Chang C, Cao M, Shen Y, Ge S, Wu J, Lei M, Fan X. Mechanistic insight into allosteric activation of human pyruvate carboxylase by acetyl-CoA. Mol Cell 2022; 82:4116-4130.e6. [DOI: 10.1016/j.molcel.2022.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/08/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
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24
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Wu J, Yu S, Wang Y, Zhu J, Zhang Z. New insights into the role of ribonuclease P protein subunit p30 from tumor to internal reference. Front Oncol 2022; 12:1018279. [PMID: 36313673 PMCID: PMC9606464 DOI: 10.3389/fonc.2022.1018279] [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: 08/17/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
Ribonuclease P protein subunit p30 (RPP30) is a highly conserved housekeeping gene that exists in many species and tissues throughout the three life kingdoms (archaea, bacteria, and eukaryotes). RPP30 is closely related to a few types of tumors in human diseases but has a very stable transcription level in most cases. Based on this feature, increasing number of studies have used RPP30 as an internal reference gene. Here, the structure and basic functions of RPP30 are summarized and the likely relationship between RPP30 and various diseases in plants and human is outlined. Finally, the current application of RPP30 as an internal reference gene and its advantages over traditional internal reference genes are reviewed. RPP30 characteristics suggest that it has a good prospect of being selected as an internal reference; more work is needed to develop this research avenue.
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Affiliation(s)
- Junchao Wu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Sijie Yu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yalan Wang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Jie Zhu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China
| | - Zhenhua Zhang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,*Correspondence: Zhenhua Zhang,
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25
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Structural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P. Nat Commun 2022; 13:5120. [PMID: 36045135 PMCID: PMC9433436 DOI: 10.1038/s41467-022-32843-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022] Open
Abstract
Binding of precursor tRNAs (ptRNAs) by bacterial ribonuclease P (RNase P) involves an encounter complex (ES) that isomerizes to a catalytic conformation (ES*). However, the structures of intermediates and the conformational changes that occur during binding are poorly understood. Here, we show that pairing between the 5′ leader and 3′RCCA extending the acceptor stem of ptRNA inhibits ES* formation. Cryo-electron microscopy single particle analysis reveals a dynamic enzyme that becomes ordered upon formation of ES* in which extended acceptor stem pairing is unwound. Comparisons of structures with alternative ptRNAs reveals that once unwinding is completed RNase P primarily uses stacking interactions and shape complementarity to accommodate alternative sequences at its cleavage site. Our study reveals active site interactions and conformational changes that drive molecular recognition by RNase P and lays the foundation for understanding how binding interactions are linked to helix unwinding and catalysis. Ribonuclease P efficiently processes all tRNA precursors despite sequence variation at the site of cleavage. Here, authors use high-throughput enzymology and cryoEM to reveal conformational changes that drive recognition by bacterial RNase P.
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26
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Tang J, Tian X, Min J, Hu M, Hong L. RPP40 is a prognostic biomarker and correlated with tumor microenvironment in uterine corpus endometrial carcinoma. Front Oncol 2022; 12:957472. [PMID: 36091104 PMCID: PMC9448918 DOI: 10.3389/fonc.2022.957472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022] Open
Abstract
Ribonuclease P/MRP Subunit P40 (RPP40), a component of ribonuclease P and multimeric ribonuclease P complex, was reported as one of the promoting factors for the chemoresistance of acute myeloid leukemia and a recurrence predictor of early-stage triple-negative breast cancer. However, the functional role of RPP40 in uterine corpus endometrial carcinoma (UCEC) is unclear. In this study, comprehensive bioinformatic analyses were conducted to explore the predictive role of RPP40 on UCEC diagnosis and prognosis, as well as the underlying mechanism. Differential analyses of multiple databases showed that both messenger RNA (mRNA) and the protein expression of RPP40 were significantly upregulated in UCEC tumor tissues. Furthermore, the RPP40 mRNA expression level was significantly correlated with the clinicopathological characteristics of UCEC patients, including the clinical stage, primary therapy outcome, histological type, histologic grade, overall survival event, disease-specific survival event, and progression-free interval event. Receiver operating characteristic (ROC) analysis showed that RPP40 was a reliable predictor for UCEC diagnosis with an area under the curve (AUC) of 0.775, a sensitivity of 0.829, and a specificity of 0.719. Kaplan–Meier, Cox regression, and nomogram analyses showed that high RPP40 expression was an independent prognostic factor for the 1-year, 3-year, and 5-year survival of UCEC patients. In addition, the enrichment analysis of RPP40-associated differentially expressed genes and correlation analyses showed that the expression of RPP40 was correlated with the regulation of extracellular matrix and immune cell infiltration. In conclusion, the upregulation of RPP40 is significantly correlated with the poor survival and tumor microenvironment of UCEC, suggesting that RPP40 is a promising biomarker of poor prognosis and a potential target of chemotherapy or immunotherapy in UCEC.
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Affiliation(s)
- Jianming Tang
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaoli Tian
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jie Min
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ming Hu
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Li Hong
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Li Hong,
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27
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Phan HD, Norris AS, Du C, Stachowski K, Khairunisa B, Sidharthan V, Mukhopadhyay B, Foster M, Wysocki V, Gopalan V. Elucidation of structure-function relationships in Methanocaldococcus jannaschii RNase P, a multi-subunit catalytic ribonucleoprotein. Nucleic Acids Res 2022; 50:8154-8167. [PMID: 35848927 PMCID: PMC9371926 DOI: 10.1093/nar/gkac595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/27/2022] [Indexed: 11/12/2022] Open
Abstract
RNase P is a ribonucleoprotein (RNP) that catalyzes removal of the 5' leader from precursor tRNAs in all domains of life. A recent cryo-EM study of Methanocaldococcus jannaschii (Mja) RNase P produced a model at 4.6-Å resolution in a dimeric configuration, with each holoenzyme monomer containing one RNase P RNA (RPR) and one copy each of five RNase P proteins (RPPs; POP5, RPP30, RPP21, RPP29, L7Ae). Here, we used native mass spectrometry (MS), mass photometry (MP), and biochemical experiments that (i) validate the oligomeric state of the Mja RNase P holoenzyme in vitro, (ii) find a different stoichiometry for each holoenzyme monomer with up to two copies of L7Ae, and (iii) assess whether both L7Ae copies are necessary for optimal cleavage activity. By mutating all kink-turns in the RPR, we made the discovery that abolishing the canonical L7Ae-RPR interactions was not detrimental for RNase P assembly and function due to the redundancy provided by protein-protein interactions between L7Ae and other RPPs. Our results provide new insights into the architecture and evolution of RNase P, and highlight the utility of native MS and MP in integrated structural biology approaches that seek to augment the information obtained from low/medium-resolution cryo-EM models.
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Affiliation(s)
- Hong-Duc Phan
- Department of Chemistry and Biochemistry, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, Columbus, OH 43210, USA
- Center for RNA Biology, Columbus, OH 43210, USA
| | - Andrew S Norris
- Department of Chemistry and Biochemistry, Columbus, OH 43210, USA
- Center for RNA Biology, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry-Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Chen Du
- Department of Chemistry and Biochemistry, Columbus, OH 43210, USA
- Center for RNA Biology, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry-Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kye Stachowski
- Department of Chemistry and Biochemistry, Columbus, OH 43210, USA
- Center for RNA Biology, Columbus, OH 43210, USA
| | - Bela H Khairunisa
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Genetics, Bioinformatics, and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA
| | - Vaishnavi Sidharthan
- Department of Chemistry and Biochemistry, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, Columbus, OH 43210, USA
- Center for RNA Biology, Columbus, OH 43210, USA
| | | | - Mark P Foster
- Department of Chemistry and Biochemistry, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, Columbus, OH 43210, USA
- Center for RNA Biology, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, Columbus, OH 43210, USA
- Center for RNA Biology, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry-Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, Columbus, OH 43210, USA
- Center for RNA Biology, Columbus, OH 43210, USA
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Kan Y, Lu X, Feng L, Yang X, Ma H, Gong J, Yang J. RPP30 is a novel diagnostic and prognostic biomarker for gastric cancer. Front Genet 2022; 13:888051. [PMID: 35928448 PMCID: PMC9343801 DOI: 10.3389/fgene.2022.888051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/27/2022] [Indexed: 12/24/2022] Open
Abstract
Objective: This study aimed to identify the hub gene in gastric cancer (GC) tumorigenesis. A biomarker prediction model was constructed and analyzed, and protein expression in histopathological samples was verified in a validation cohort. Methods: Differentially expressed genes (DEGs) were identified from GC projects in The Cancer Genome Atlas (TCGA) database. Functional enrichment analysis of DEGs was performed between the high- and low- Ribonuclease P protein subunit p30 (RPP30) expression groups. ROC analysis was performed to assess RPP30 expression to discriminate GC from normal tissues. Functional enrichment pathways and immune infiltration of DEGs were analyzed using GSEA and ssGSEA. Survival analysis and nomogram construction were performed to predict patient survival. Immunohistochemical staining of GC tissues was performed to validate RPP30 expression in GC and paracancerous samples. Results: Gene expression data and clinical information of 380 cases (375 GC samples and 32 para-cancerous tissues) were collected from TCGA database. The AUC for RPP30 expression was found to be 0.785. The G alpha S signaling pathway was the most significantly enriched signaling pathway. Primary therapy outcome (p < 0.001, HR = 0.243, 95% CI = 0.156–0.379), age (p = 0.012, HR = 1.748, 95% CI = 1.133–2.698), and RPP30 expression (p < 0.001, HR = 2.069, 95% CI = 1.346–3.181) were identified as independent prognostic factors. As a quantitative approach, a nomogram constructed based on RPP30 expression, age, and primary therapy outcome performed well in predicting patient survival. Nineteen of the 25 tissue samples from the validation cohort showed positive RPP30 expression in GC tissues, whereas 16 cases showed negative RPP30 staining in normal tissues. The difference between the two was statistically significant. Conclusion: High RPP30 expression was significantly correlated with disease progression and poor survival in GC, promoting tumorigenesis and angiogenesis via tRNA dysregulation. This study provides new and promising insights into the molecular pathogenesis of tRNA in GC.
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Affiliation(s)
- Ying Kan
- Department of Nuclear Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xia Lu
- Department of Nuclear Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lijuan Feng
- Department of Nuclear Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xu Yang
- Department of Nuclear Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Huan Ma
- Department of Nuclear Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jianhua Gong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Jigang Yang, ; Jianhua Gong,
| | - Jigang Yang
- Department of Nuclear Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- *Correspondence: Jigang Yang, ; Jianhua Gong,
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29
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Sekulovski S, Trowitzsch S. Transfer RNA processing - from a structural and disease perspective. Biol Chem 2022; 403:749-763. [PMID: 35728022 DOI: 10.1515/hsz-2021-0406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/24/2022] [Indexed: 01/05/2023]
Abstract
Transfer RNAs (tRNAs) are highly structured non-coding RNAs which play key roles in translation and cellular homeostasis. tRNAs are initially transcribed as precursor molecules and mature by tightly controlled, multistep processes that involve the removal of flanking and intervening sequences, over 100 base modifications, addition of non-templated nucleotides and aminoacylation. These molecular events are intertwined with the nucleocytoplasmic shuttling of tRNAs to make them available at translating ribosomes. Defects in tRNA processing are linked to the development of neurodegenerative disorders. Here, we summarize structural aspects of tRNA processing steps with a special emphasis on intron-containing tRNA splicing involving tRNA splicing endonuclease and ligase. Their role in neurological pathologies will be discussed. Identification of novel RNA substrates of the tRNA splicing machinery has uncovered functions unrelated to tRNA processing. Future structural and biochemical studies will unravel their mechanistic underpinnings and deepen our understanding of neurological diseases.
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Affiliation(s)
- Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
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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: 7] [Impact Index Per Article: 3.5] [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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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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Chen S, Zhang L, Yuan Q, Tan J. Current Advances in Aptamer-based Biomolecular Recognition and Biological Process Regulation. Chem Res Chin Univ 2022; 38:847-855. [PMID: 35573821 PMCID: PMC9077342 DOI: 10.1007/s40242-022-2087-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 12/01/2022]
Abstract
The interaction between biomolecules with their target ligands plays a great role in regulating biological functions. Aptamers are short oligonucleotide sequences that can specifically recognize target biomolecules via structural complementarity and thus regulate related biological functions. In the past ten years, aptamers have made great progress in target biomolecule recognition, becoming a powerful tool to regulate biological functions. At present, there are many reviews on aptamers applied in biomolecular recognition, but few reviews pay attention to aptamer-based regulation of biological functions. Here, we summarize the approaches to enhancing aptamer affinity and the advancements of aptamers in regulating enzymatic activity, cellular immunity and cellular behaviors. Furthermore, this review discusses the challenges and future perspectives of aptamers in target recognition and biological functions regulation, aiming to provide some promising ideas for future regulation of biomolecular functions in a complex biological environment.
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Affiliation(s)
- Sisi Chen
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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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: 8] [Impact Index Per Article: 4.0] [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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34
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Köferle A, Schlattl A, Hörmann A, Thatikonda V, Popa A, Spreitzer F, Ravichandran MC, Supper V, Oberndorfer S, Puchner T, Wieshofer C, Corcokovic M, Reiser C, Wöhrle S, Popow J, Pearson M, Martinez J, Weitzer S, Mair B, Neumüller RA. Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes. Cell Rep 2022; 39:110636. [PMID: 35417719 DOI: 10.1016/j.celrep.2022.110636] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023] Open
Abstract
Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of functional redundancies can create de novo vulnerabilities that are specific to cancer cells. Here, we systematically search for cancer-relevant paralog interactions using CRISPR screens and publicly available loss-of-function datasets. Our analysis reveals >2,000 candidate dependencies, several of which we validate experimentally, including CSTF2-CSTF2T, DNAJC15-DNAJC19, FAM50A-FAM50B, and RPP25-RPP25L. We provide evidence that RPP25L can physically and functionally compensate for the absence of RPP25 as a member of the RNase P/MRP complexes in tRNA processing. Our analysis also reveals unexpected redundancies between sex chromosome genes. We show that chrX- and chrY-encoded paralogs, such as ZFX-ZFY, DDX3X-DDX3Y, and EIF1AX-EIF1AY, are functionally linked. Tumor cell lines from male patients with loss of chromosome Y become dependent on the chrX-encoded gene. We propose targeting of chrX-encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y chromosome.
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Affiliation(s)
- Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Andreas Schlattl
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | | | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Corinna Wieshofer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Christoph Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
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35
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Cai MD, Xu ZQ, Liu YH, Liu JQ, Zhao SY, Wang XJ, Li YH, Yu XL, Li XX. LncRNA-mediated effects of vitrification temperatures and cryoprotectant concentrations on bovine oocyte development following vitrification at the GV stage. Theriogenology 2022; 186:135-145. [DOI: 10.1016/j.theriogenology.2022.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/05/2022]
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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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37
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Lai LB, Lai SM, Szymanski ES, Kapur M, Choi EK, Al-Hashimi HM, Ackerman SL, Gopalan V. Structural basis for impaired 5' processing of a mutant tRNA associated with defects in neuronal homeostasis. Proc Natl Acad Sci U S A 2022; 119:e2119529119. [PMID: 35238631 PMCID: PMC8915964 DOI: 10.1073/pnas.2119529119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/09/2022] [Indexed: 02/06/2023] Open
Abstract
SignificanceUnderstanding and treating neurological disorders are global priorities. Some of these diseases are engendered by mutations that cause defects in the cellular synthesis of transfer RNAs (tRNAs), which function as adapter molecules that translate messenger RNAs into proteins. During tRNA biogenesis, ribonuclease P catalyzes removal of the transcribed sequence upstream of the mature tRNA. Here, we focus on a cytoplasmic tRNAArgUCU that is expressed specifically in neurons and, when harboring a particular point mutation, contributes to neurodegeneration in mice. Our results suggest that this mutation favors stable alternative structures that are not cleaved by mouse ribonuclease P and motivate a paradigm that may help to understand the molecular basis for disease-associated mutations in other tRNAs.
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Affiliation(s)
- Lien B. Lai
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Stella M. Lai
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Eric S. Szymanski
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710
| | - Mridu Kapur
- Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California San Diego, La Jolla, CA 92093
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093
| | - Edric K. Choi
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710
| | - Susan L. Ackerman
- Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California San Diego, La Jolla, CA 92093
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093
| | - Venkat Gopalan
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells. Nat Commun 2022; 13:911. [PMID: 35177610 PMCID: PMC8854666 DOI: 10.1038/s41467-022-28602-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
Three-dimensional (3D) structures dictate the functions of RNA molecules in a wide variety of biological processes. However, direct determination of RNA 3D structures in vivo is difficult due to their large sizes, conformational heterogeneity, and dynamics. Here we present a method, Spatial 2′-Hydroxyl Acylation Reversible Crosslinking (SHARC), which uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA. Integrating crosslinking, exonuclease (exo) trimming, proximity ligation, and high throughput sequencing, SHARC enables transcriptome-wide tertiary structure contact maps at high accuracy and precision, revealing heterogeneous RNA structures and interactions. SHARC data provide constraints that improves Rosetta-based RNA 3D structure modeling at near-nanometer resolution. Integrating SHARC-exo with other crosslinking-based methods, we discover compact folding of the 7SK RNA, a critical regulator of transcriptional elongation. These results establish a strategy for measuring RNA 3D distances and alternative conformations in their native cellular context. Determination of RNA 3D structures in vivo is a challenging problem. Here, the authors describe a chemical crosslinking method (SHARC) that they use in combination with RNA sequencing to measure distances between nucleotides in RNA 3D structures.
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39
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Yu K, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. A hexameric ribozyme nanostructure formed by double-decker assembly of a pair of triangular ribozyme trimers. Chembiochem 2022; 23:e202100573. [PMID: 35088928 DOI: 10.1002/cbic.202100573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/29/2021] [Indexed: 11/12/2022]
Abstract
The modular architecture of naturally occurring ribozymes makes them a promising class of structural platforms to design and assemble three-dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can be installed. We have constructed and analyzed RNA nanostructures with polygonal-shaped (closed) ribozyme oligomers by assembling unit RNAs derived from the Tetrahymena group I intron with a typical modular architecture. In this study, we dimerized ribozyme trimers with a triangular shape by introducing three pillar units. The resulting double-decker nanostructures containing six ribozyme units were characterized biochemically and their structures were observed by atomic force microscopy. The double-decker hexamers exhibited higher catalytic activity than the parent ribozyme trimers.
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Affiliation(s)
- Kai Yu
- University of Toyama: Toyama Daigaku, Department of Chemistry, JAPAN
| | - Kumi Hidaka
- Kyoto University: Kyoto Daigaku, Department of Chemistry, JAPAN
| | | | | | | | - Yoshiya Ikawa
- University of Toyama, Chemistry, Gofuku 3190, 930-8555, Toyama, JAPAN
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40
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Xue Y. Architecture of RNA-RNA interactions. Curr Opin Genet Dev 2021; 72:138-144. [PMID: 34954430 DOI: 10.1016/j.gde.2021.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/04/2021] [Accepted: 11/23/2021] [Indexed: 11/30/2022]
Abstract
RNA molecules tend to form intricate tertiary structures via intramolecular RNA-RNA interactions (RRIs) to regulate transcription, RNA processing, and translation processes. In these biological processes, RNAs, especially noncoding RNAs, usually achieve their regulatory specificity through intermolecular RNA-RNA base pairing and execute their regulatory outcomes via associated RNA-binding proteins. Decoding intramolecular and intermolecular RRIs is a prerequisite for understanding the architecture of various RNA molecules and their regulatory roles in development, differentiation, and disease. Many sequencing-based methods have recently been invented and have revealed extraordinarily complicated RRIs in mammalian cells. Here, we discuss the technical advances and limitations of various methodologies developed for studying cellular RRIs, with a focus on the emerging architectural roles of RRIs in gene regulation.
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Affiliation(s)
- Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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41
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Skeparnias I, Zhang J. Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions. Noncoding RNA 2021; 7:ncrna7040081. [PMID: 34940761 PMCID: PMC8704770 DOI: 10.3390/ncrna7040081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation. By contrast, the nature of these interactions and characteristics of their interfaces, especially those that involve partially or wholly structured RNAs, remain elusive. Herein, we discuss different modalities of RNA–RNA interactions with an emphasis on those that depend on secondary, tertiary, or quaternary structure. We dissect recently structurally elucidated RNA–RNA complexes including RNA triplexes, riboswitches, ribozymes, and reverse transcription complexes. These analyses highlight a reciprocal relationship that intimately links RNA structure formation with RNA–RNA interactions. The interactions not only shape and sculpt RNA structures but also are enabled and modulated by the structures they create. Understanding this two-way relationship between RNA structure and interactions provides mechanistic insights into the expanding repertoire of noncoding RNA functions, and may inform the design of novel therapeutics that target RNA structures or interactions.
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42
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Zimmer MM, Kibe A, Rand U, Pekarek L, Ye L, Buck S, Smyth RP, Cicin-Sain L, Caliskan N. The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting. Nat Commun 2021; 12:7193. [PMID: 34893599 PMCID: PMC8664833 DOI: 10.1038/s41467-021-27431-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022] Open
Abstract
Programmed ribosomal frameshifting (PRF) is a fundamental gene expression event in many viruses, including SARS-CoV-2. It allows production of essential viral, structural and replicative enzymes that are encoded in an alternative reading frame. Despite the importance of PRF for the viral life cycle, it is still largely unknown how and to what extent cellular factors alter mechanical properties of frameshift elements and thereby impact virulence. This prompted us to comprehensively dissect the interplay between the SARS-CoV-2 frameshift element and the host proteome. We reveal that the short isoform of the zinc-finger antiviral protein (ZAP-S) is a direct regulator of PRF in SARS-CoV-2 infected cells. ZAP-S overexpression strongly impairs frameshifting and inhibits viral replication. Using in vitro ensemble and single-molecule techniques, we further demonstrate that ZAP-S directly interacts with the SARS-CoV-2 RNA and interferes with the folding of the frameshift RNA element. Together, these data identify ZAP-S as a host-encoded inhibitor of SARS-CoV-2 frameshifting and expand our understanding of RNA-based gene regulation.
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Affiliation(s)
- Matthias M Zimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Anuja Kibe
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Ulfert Rand
- Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Lukas Pekarek
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Liqing Ye
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Stefan Buck
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
- Medical Faculty, Julius-Maximilians University Würzburg, 97074, Würzburg, Germany
| | - Luka Cicin-Sain
- Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany.
- Medical Faculty, Julius-Maximilians University Würzburg, 97074, Würzburg, Germany.
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43
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Zhang D, Chen SJ, Zhou R. Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model. J Phys Chem B 2021; 125:11907-11915. [PMID: 34694128 DOI: 10.1021/acs.jpcb.1c07288] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncanonical base pairs contribute crucially to the three-dimensional architecture of large RNA molecules; however, how to accurately model them remains an open challenge in RNA 3D structure prediction. Here, we report a promising coarse-grained (CG) IsRNA2 model to predict noncanonical base pairs in large RNAs through molecular dynamics simulations. By introducing a five-bead per nucleotide CG representation to reserve the three interacting edges of nucleobases, IsRNA2 accurately models various base-pairing interactions, including both canonical and noncanonical base pairs. A benchmark test indicated that IsRNA2 achieves a comparable performance to the atomic model in de novo modeling of noncanonical RNA structures. In addition, IsRNA2 was able to refine the 3D structure predictions for large RNAs in RNA-puzzle challenges. Finally, the graphics processing unit acceleration was introduced to speed up the sampling efficiency in IsRNA2 for very large RNA molecules. Therefore, the CG IsRNA2 model reported here offers a reliable approach to predict the structures and dynamics of large RNAs.
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Affiliation(s)
- Dong Zhang
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Ruhong Zhou
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China
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44
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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: 7] [Impact Index Per Article: 2.3] [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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45
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Zeng D, Abzhanova A, Brown BP, Reiter NJ. Dissecting Monomer-Dimer Equilibrium of an RNase P Protein Provides Insight Into the Synergistic Flexibility of 5' Leader Pre-tRNA Recognition. Front Mol Biosci 2021; 8:730274. [PMID: 34540901 PMCID: PMC8447495 DOI: 10.3389/fmolb.2021.730274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/18/2021] [Indexed: 11/13/2022] Open
Abstract
Ribonuclease P (RNase P) is a universal RNA-protein endonuclease that catalyzes 5' precursor-tRNA (ptRNA) processing. The RNase P RNA plays the catalytic role in ptRNA processing; however, the RNase P protein is required for catalysis in vivo and interacts with the 5' leader sequence. A single P RNA and a P protein form the functional RNase P holoenzyme yet dimeric forms of bacterial RNase P can interact with non-tRNA substrates and influence bacterial cell growth. Oligomeric forms of the P protein can also occur in vitro and occlude the 5' leader ptRNA binding interface, presenting a challenge in accurately defining the substrate recognition properties. To overcome this, concentration and temperature dependent NMR studies were performed on a thermostable RNase P protein from Thermatoga maritima. NMR relaxation (R1, R2), heteronuclear NOE, and diffusion ordered spectroscopy (DOSY) experiments were analyzed, identifying a monomeric species through the determination of the diffusion coefficients (D) and rotational correlation times (τc). Experimental diffusion coefficients and τc values for the predominant monomer (2.17 ± 0.36 * 10-10 m2/s, τ c = 5.3 ns) or dimer (1.87 ± 0.40* 10-10 m2/s, τ c = 9.7 ns) protein assemblies at 45°C correlate well with calculated diffusion coefficients derived from the crystallographic P protein structure (PDB 1NZ0). The identification of a monomeric P protein conformer from relaxation data and chemical shift information enabled us to gain novel insight into the structure of the P protein, highlighting a lack of structural convergence of the N-terminus (residues 1-14) in solution. We propose that the N-terminus of the bacterial P protein is partially disordered and adopts a stable conformation in the presence of RNA. In addition, we have determined the location of the 5' leader RNA in solution and measured the affinity of the 5' leader RNA-P protein interaction. We show that the monomer P protein interacts with RNA at the 5' leader binding cleft that was previously identified using X-ray crystallography. Data support a model where N-terminal protein flexibility is stabilized by holoenzyme formation and helps to accommodate the 5' leader region of ptRNA. Taken together, local structural changes of the P protein and the 5' leader RNA provide a means to obtain optimal substrate alignment and activation of the RNase P holoenzyme.
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Affiliation(s)
- Danyun Zeng
- Department of Chemistry, Marquette University, Milwaukee, WI, United States
| | - Ainur Abzhanova
- Department of Chemistry, Marquette University, Milwaukee, WI, United States
| | - Benjamin P Brown
- Chemical and Physical Biology Program, Medical Scientist Training Program, Vanderbilt University, Nashville, TN, United States.,Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Nicholas J Reiter
- Department of Chemistry, Marquette University, Milwaukee, WI, United States
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46
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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: 26] [Impact Index Per Article: 8.7] [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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47
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Bhatta A, Dienemann C, Cramer P, Hillen HS. Structural basis of RNA processing by human mitochondrial RNase P. Nat Struct Mol Biol 2021; 28:713-723. [PMID: 34489609 PMCID: PMC8437803 DOI: 10.1038/s41594-021-00637-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
Human mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In contrast to nuclear or bacterial RNase P, mtRNase P is not a ribozyme but comprises three protein subunits that carry out RNA cleavage and methylation by unknown mechanisms. Here, we present the cryo-EM structure of human mtRNase P bound to precursor tRNA, which reveals a unique mechanism of substrate recognition and processing. Subunits TRMT10C and SDR5C1 form a subcomplex that binds conserved mitochondrial tRNA elements, including the anticodon loop, and positions the tRNA for methylation. The endonuclease PRORP is recruited and activated through interactions with its PPR and nuclease domains to ensure precise pre-tRNA cleavage. The structure provides the molecular basis for the first step of RNA processing in human mitochondria.
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Affiliation(s)
- Arjun Bhatta
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Hauke S Hillen
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
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48
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Alonso D, Mondragón A. Mechanisms of catalytic RNA molecules. Biochem Soc Trans 2021; 49:1529-1535. [PMID: 34415304 PMCID: PMC10583251 DOI: 10.1042/bst20200465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022]
Abstract
Ribozymes are folded catalytic RNA molecules that perform important biological functions. Since the discovery of the first RNA with catalytic activity in 1982, a large number of ribozymes have been reported. While most catalytic RNA molecules act alone, some RNA-based catalysts, such as RNase P, the ribosome, and the spliceosome, need protein components to perform their functions in the cell. In the last decades, the structure and mechanism of several ribozymes have been studied in detail. Aside from the ribosome, which catalyzes peptide bond formation during protein synthesis, the majority of known ribozymes carry out mostly phosphoryl transfer reactions, notably trans-esterification or hydrolysis reactions. In this review, we describe the main features of the mechanisms of various types of ribozymes that can function with or without the help of proteins to perform their biological functions.
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Affiliation(s)
- Dulce Alonso
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, U.S.A
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, U.S.A
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49
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Marathe IA, Lai SM, Zahurancik WJ, Poirier MG, Wysocki VH, Gopalan V. Protein cofactors and substrate influence Mg2+-dependent structural changes in the catalytic RNA of archaeal RNase P. Nucleic Acids Res 2021; 49:9444-9458. [PMID: 34387688 PMCID: PMC8450104 DOI: 10.1093/nar/gkab655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/02/2021] [Accepted: 07/23/2021] [Indexed: 01/07/2023] Open
Abstract
The ribonucleoprotein (RNP) form of archaeal RNase P comprises one catalytic RNA and five protein cofactors. To catalyze Mg2+-dependent cleavage of the 5′ leader from pre-tRNAs, the catalytic (C) and specificity (S) domains of the RNase P RNA (RPR) cooperate to recognize different parts of the pre-tRNA. While ∼250–500 mM Mg2+ renders the archaeal RPR active without RNase P proteins (RPPs), addition of all RPPs lowers the Mg2+ requirement to ∼10–20 mM and improves the rate and fidelity of cleavage. To understand the Mg2+- and RPP-dependent structural changes that increase activity, we used pre-tRNA cleavage and ensemble FRET assays to characterize inter-domain interactions in Pyrococcus furiosus (Pfu) RPR, either alone or with RPPs ± pre-tRNA. Following splint ligation to doubly label the RPR (Cy3-RPRC domain and Cy5-RPRS domain), we used native mass spectrometry to verify the final product. We found that FRET correlates closely with activity, the Pfu RPR and RNase P holoenzyme (RPR + 5 RPPs) traverse different Mg2+-dependent paths to converge on similar functional states, and binding of the pre-tRNA by the holoenzyme influences Mg2+ cooperativity. Our findings highlight how Mg2+ and proteins in multi-subunit RNPs together favor RNA conformations in a dynamic ensemble for functional gains.
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Affiliation(s)
- Ila A Marathe
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,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
| | - Stella M Lai
- 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.,Resource for Native Mass Spectrometry-Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Walter J Zahurancik
- 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
| | - Michael G Poirier
- 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.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- 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.,Resource for Native Mass Spectrometry-Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,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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50
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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: 12] [Impact Index Per Article: 4.0] [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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