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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: 1] [Impact Index Per Article: 1.0] [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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2
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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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3
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Palacios-Pérez M, José MV. A Proposal of the Ur-RNAome. Genes (Basel) 2023; 14:2158. [PMID: 38136981 PMCID: PMC10743229 DOI: 10.3390/genes14122158] [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: 10/14/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
It is widely accepted that the earliest RNA molecules were folded into hairpins or mini-helixes. Herein, we depict the 2D and 3D conformations of those earliest RNA molecules with only RNY triplets, which Eigen proposed as the primeval genetic code. We selected 26 species (13 bacteria and 13 archaea). We found that the free energy of RNY hairpins was consistently lower than that of their corresponding shuffled controls. We found traces of the three ribosomal RNAs (16S, 23S, and 5S), tRNAs, 6S RNA, and the RNA moieties of RNase P and the signal recognition particle. Nevertheless, at this stage of evolution there was no genetic code (as seen in the absence of the peptidyl transferase centre and any vestiges of the anti-Shine-Dalgarno sequence). Interestingly, we detected the anticodons of both glycine (GCC) and threonine (GGU) in the hairpins of proto-tRNA.
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Affiliation(s)
- Miryam Palacios-Pérez
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Network of Researchers on the Chemical Emergence of Life (NoRCEL), Leeds LS7 3RB, UK
- NoRCEL’s Latin America Hub, 113 Philosophy Hall, University of California, Berkeley, CA 94720, USA
| | - Marco V. José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Network of Researchers on the Chemical Emergence of Life (NoRCEL), Leeds LS7 3RB, UK
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4
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Li M, Li W, Zhao M, Li Z, Wang GL, Liu W, Liang C. Transcriptome analysis reveals a lncRNA-miRNA-mRNA regulatory network in OsRpp30-mediated disease resistance in rice. BMC Genomics 2023; 24:643. [PMID: 37884868 PMCID: PMC10604448 DOI: 10.1186/s12864-023-09748-w] [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: 07/20/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play critical roles in various biological processes in plants. Extensive studies utilizing high-throughput RNA sequencing have revealed that many lncRNAs are involved in plant disease resistance. Oryza sativa RNase P protein 30 (OsRpp30) has been identified as a positive regulator of rice immunity against fungal and bacterial pathogens. Nevertheless, the specific functions of lncRNAs in relation to OsRpp30-mediated disease resistance in rice remain elusive. RESULTS We conducted a comprehensive analysis of lncRNAs, miRNAs, and mRNAs expression patterns in wild type (WT), OsRpp30 overexpression (OsRpp30-OE), and OsRpp30 knockout (OsRpp30-KO) rice plants. In total, we identified 91 differentially expressed lncRNAs (DElncRNAs), 1671 differentially expressed mRNAs (DEmRNAs), and 41 differentially expressed miRNAs (DEmiRNAs) across the different rice lines. To gain further insights, we investigated the interaction between DElncRNAs and DEmRNAs, leading to the discovery of 10 trans- and 27 cis-targeting pairs specific to the OsRpp30-OE and OsRpp30-KO samples. In addition, we constructed a competing endogenous RNA (ceRNA) network comprising differentially expressed lncRNAs, miRNAs, and mRNAs to elucidate their intricate interplay in rice disease resistance. The ceRNA network analysis uncovered a set of gene targets regulated by lncRNAs and miRNAs, which were found to be involved in pathogen recognition, hormone pathways, transcription factor activation, and other biological processes related to plant immunity. CONCLUSIONS Our study provides a comprehensive expression profiling of lncRNAs, miRNAs, and mRNAs in a collection of defense mutants in rice. To decipher the putative functional significance of lncRNAs, we constructed trans- and cis-targeting networks involving differentially expressed lncRNAs and mRNAs, as well as a ceRNA network incorporating differentially expressed lncRNAs, miRNAs, and mRNAs. Together, the findings from this study provide compelling evidence supporting the pivotal roles of lncRNAs in OsRpp30-mediated disease resistance in rice.
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Affiliation(s)
- Minghua Li
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Wei Li
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA.
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA.
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5
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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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6
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Limouse C, Smith OK, Jukam D, Fryer KA, Greenleaf WJ, Straight AF. Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions. Nat Commun 2023; 14:6073. [PMID: 37770513 PMCID: PMC10539311 DOI: 10.1038/s41467-023-41848-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs are unknown. Here we use chromatin-associated RNA sequencing (ChAR-seq) to map the global network of ncRNA interactions with chromatin in human embryonic stem cells and the dynamic changes in interactions during differentiation into definitive endoderm. We uncover general principles governing the organization of the RNA-chromatin interactome, demonstrating that nearly all ncRNAs exclusively interact with genes in close three-dimensional proximity to their locus and provide a model predicting the interactome. We uncover RNAs that interact with many loci across the genome and unveil thousands of unannotated RNAs that dynamically interact with chromatin. By relating the dynamics of the interactome to changes in gene expression, we demonstrate that activation or repression of individual genes is unlikely to be controlled by a single ncRNA.
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Affiliation(s)
- Charles Limouse
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Owen K Smith
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - David Jukam
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Kelsey A Fryer
- Department of Biochemistry, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | | | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, California, USA.
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7
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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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8
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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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9
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Jarrous N, Liu F. Human RNase P: overview of a ribonuclease of interrelated molecular networks and gene-targeting systems. RNA (NEW YORK, N.Y.) 2023; 29:300-307. [PMID: 36549864 PMCID: PMC9945436 DOI: 10.1261/rna.079475.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/09/2022] [Indexed: 05/14/2023]
Abstract
The seminal discovery of ribonuclease P (RNase P) and its catalytic RNA by Sidney Altman has not only revolutionized our understanding of life, but also opened new fields for scientific exploration and investigation. This review focuses on human RNase P and its use as a gene-targeting tool, two topics initiated in Altman's laboratory. We outline early works on human RNase P as a tRNA processing enzyme and comment on its expanding nonconventional functions in molecular networks of transcription, chromatin remodeling, homology-directed repair, and innate immunity. The important implications and insights from these discoveries on the potential use of RNase P as a gene-targeting tool are presented. This multifunctionality calls to a modified structure-function partitioning of domains in human RNase P, as well as its relative ribonucleoprotein, RNase MRP. The role of these two catalysts in innate immunity is of particular interest in molecular evolution, as this dynamic molecular network could have originated and evolved from primordial enzymes and sensors of RNA, including predecessors of these two ribonucleoproteins.
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Affiliation(s)
- Nayef Jarrous
- Department of Microbiology and Molecular Genetics, The Hebrew University-Hadassah Medical School, Jerusalem 9112010, Israel
| | - Fenyong Liu
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, California 94720, USA
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10
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Tang J, Wang X, Xiao D, Liu S, Tao Y. The chromatin-associated RNAs in gene regulation and cancer. Mol Cancer 2023; 22:27. [PMID: 36750826 PMCID: PMC9903551 DOI: 10.1186/s12943-023-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Eukaryotic genomes are prevalently transcribed into many types of RNAs that translate into proteins or execute gene regulatory functions. Many RNAs associate with chromatin directly or indirectly and are called chromatin-associated RNAs (caRNAs). To date, caRNAs have been found to be involved in gene and transcriptional regulation through multiple mechanisms and have important roles in different types of cancers. In this review, we first present different categories of caRNAs and the modes of interaction between caRNAs and chromatin. We then detail the mechanisms of chromatin-associated nascent RNAs, chromatin-associated noncoding RNAs and emerging m6A on caRNAs in transcription and gene regulation. Finally, we discuss the roles of caRNAs in cancer as well as epigenetic and epitranscriptomic mechanisms contributing to cancer, which could provide insights into the relationship between different caRNAs and cancer, as well as tumor treatment and intervention.
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Affiliation(s)
- Jun Tang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078 Hunan China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078 Hunan China
| | - Xiang Wang
- grid.216417.70000 0001 0379 7164Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongguang Tao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China. .,Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China. .,Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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11
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Trang P, Smith A, Liu F. Mapping of RNase P Ribozyme Regions in Proximity with a Human RNase P Subunit Protein Using Fe(II)-EDTA Cleavage and Nuclease Footprint Analyses. Methods Mol Biol 2023; 2666:55-67. [PMID: 37166656 DOI: 10.1007/978-1-0716-3191-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Ribonuclease P (RNase P), which may consist of both protein subunits and a catalytic RNA part, is responsible for 5' maturation of tRNA by cleaving the 5'-leader sequence. In Escherichia coli, RNase P contains a catalytic RNA subunit (M1 RNA) and a protein factor (C5 protein). In human cells, RNase P holoenzyme consists of an RNA subunit (H1 RNA) and multiple protein subunits that include human RPP29 protein. M1GS, a sequence specific targeting ribozyme derived from M1 RNA, can be constructed to target a specific mRNA to degrade it in vitro. Recent studies have shown that M1GS ribozymes are efficient in blocking the expression of viral mRNAs in cultured cells and in animals. These results suggest that RNase P ribozymes have the potential to be useful in basic research and in clinical applications. It has been shown that RNase P binding proteins, such as C5 protein and RPP29, can enhance the activities of M1GS RNA in processing a natural tRNA substrate and a target mRNA. Understanding how RPP29 binds to M1GS RNA and enhances the enzyme's catalytic activity will provide great insight into developing more robust gene-targeting ribozymes for in vivo application. In this chapter, we describe the methods of using Fe(II)-ethylenediaminetetraacetic acid (EDTA) cleavage and nuclease footprint analyses to determine the regions of a M1GS ribozyme that are in proximity to RPP29 protein.
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Affiliation(s)
- Phong Trang
- School of Public Health, University of California, Berkeley, CA, USA.
| | - Adam Smith
- Program in Comparative Biochemistry, University of California, Berkeley, CA, USA
| | - Fenyong Liu
- School of Public Health, University of California, Berkeley, CA, USA.
- Program in Comparative Biochemistry, University of California, Berkeley, CA, USA.
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12
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Suzuki K, Tange M, Yamagishi R, Hanada H, Mukai S, Sato T, Tanaka T, Akashi T, Kadomatsu K, Maeda T, Miida T, Takeuchi I, Murakami H, Sekido Y, Murakami-Tonami Y. SMG6 regulates DNA damage and cell survival in Hippo pathway kinase LATS2-inactivated malignant mesothelioma. Cell Death Dis 2022; 8:446. [PMID: 36335095 PMCID: PMC9637146 DOI: 10.1038/s41420-022-01232-w] [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: 07/19/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/08/2022]
Abstract
Many genes responsible for Malignant mesothelioma (MM) have been identified as tumor suppressor genes and it is difficult to target these genes directly at a molecular level. We searched for the gene which showed synthetic lethal phenotype with LATS2, one of the MM causative genes and one of the kinases in the Hippo pathway. Here we showed that knockdown of SMG6 results in synthetic lethality in LATS2-inactivated cells. We found that this synthetic lethality required the nuclear translocation of YAP1 and TAZ. Both are downstream factors of the Hippo pathway. We also demonstrated that this synthetic lethality did not require SMG6 in nonsense-mediated mRNA decay (NMD) but in regulating telomerase reverse transcriptase (TERT) activity. In addition, the RNA-dependent DNA polymerase (RdDP) activity of TERT was required for this synthetic lethal phenotype. We confirmed the inhibitory effects of LATS2 and SMG6 on cell proliferation in vivo. The result suggests an interaction between the Hippo and TERT signaling pathways. We also propose that SMG6 and TERT are novel molecular target candidates for LATS2-inactivated cancers such as MM.
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Affiliation(s)
- Koya Suzuki
- grid.258269.20000 0004 1762 2738Department of Clinical Laboratory of Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan ,grid.258269.20000 0004 1762 2738Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan ,grid.412788.00000 0001 0536 8427Cancer Molecular Genetics Lab, Tokyo University of Technology Graduate School of Bionics, Tokyo, Japan ,grid.264706.10000 0000 9239 9995Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
| | - Masaki Tange
- grid.412788.00000 0001 0536 8427Cancer Molecular Genetics Lab, Tokyo University of Technology Graduate School of Bionics, Tokyo, Japan
| | - Ryota Yamagishi
- grid.258799.80000 0004 0372 2033Department of Pathophysiology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Hiroyuki Hanada
- grid.7597.c0000000094465255Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan
| | - Satomi Mukai
- grid.410800.d0000 0001 0722 8444Division of Cancer Biology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Tatsuhiro Sato
- grid.410800.d0000 0001 0722 8444Division of Cancer Biology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | | | - Tomohiro Akashi
- grid.27476.300000 0001 0943 978XDepartment of Integrative Cellular Informatics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenji Kadomatsu
- grid.27476.300000 0001 0943 978XDepartment of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan ,grid.27476.300000 0001 0943 978XInstitute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Tohru Maeda
- grid.411042.20000 0004 0371 5415College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
| | - Takashi Miida
- grid.258269.20000 0004 1762 2738Department of Clinical Laboratory of Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Ichiro Takeuchi
- grid.7597.c0000000094465255Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan ,grid.27476.300000 0001 0943 978XGraduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Hiroshi Murakami
- grid.443595.a0000 0001 2323 0843Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Yoshitaka Sekido
- grid.410800.d0000 0001 0722 8444Division of Cancer Biology, Aichi Cancer Center Research Institute, Nagoya, Japan ,grid.27476.300000 0001 0943 978XDivision of Molecular and Cellular Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuko Murakami-Tonami
- grid.258269.20000 0004 1762 2738Department of Clinical Laboratory of Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan ,grid.412788.00000 0001 0536 8427Cancer Molecular Genetics Lab, Tokyo University of Technology Graduate School of Bionics, Tokyo, Japan ,grid.410800.d0000 0001 0722 8444Division of Cancer Biology, Aichi Cancer Center Research Institute, Nagoya, Japan
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13
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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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14
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Abstract
Covalently closed, single-stranded circular RNAs can be produced from viral RNA genomes as well as from the processing of cellular housekeeping noncoding RNAs and precursor messenger RNAs. Recent transcriptomic studies have surprisingly uncovered that many protein-coding genes can be subjected to backsplicing, leading to widespread expression of a specific type of circular RNAs (circRNAs) in eukaryotic cells. Here, we discuss experimental strategies used to discover and characterize diverse circRNAs at both the genome and individual gene scales. We further highlight the current understanding of how circRNAs are generated and how the mature transcripts function. Some circRNAs act as noncoding RNAs to impact gene regulation by serving as decoys or competitors for microRNAs and proteins. Others form extensive networks of ribonucleoprotein complexes or encode functional peptides that are translated in response to certain cellular stresses. Overall, circRNAs have emerged as an important class of RNAmolecules in gene expression regulation that impact many physiological processes, including early development, immune responses, neurogenesis, and tumorigenesis.
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Affiliation(s)
- Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China;
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, Texas, USA;
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China;
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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15
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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: 2] [Impact Index Per Article: 1.0] [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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16
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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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17
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Liu R, Jia Y, Kong G, He A. Novel insights into roles of N6-methyladenosine reader YTHDF2 in cancer progression. J Cancer Res Clin Oncol 2022; 148:2215-2230. [PMID: 35763107 DOI: 10.1007/s00432-022-04134-7] [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: 03/18/2022] [Accepted: 06/10/2022] [Indexed: 12/19/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification. M6A RNA methylation is reversible: m6A is installed by "writers", removed by "erasers", and recognized by "readers". Readers are executors to regulate RNA metabolism by recognizing specific m6A sites, including RNA splicing, export, translation and decay. YTHDF2 is the first identified m6A reader protein. YTHDF2 interacts with m6A-containing transcripts to accelerate the degradation process and regulate various biological processes, such as viral infection, stem cell development and cancer progression. Although there are some reviews about m6A modification in physiological and pathological processes, few reviews focus on roles of YTHDF2 in cancers to date. Therefore, in this review, we attempted to systematically summarize m6A reader protein YTHDF2: its structure, mechanisms in regulating RNA metabolism, roles in cancer progression and potential application for cancer treatment, which might inspire new ideas for m6A research in cancers and provide novel insights into cancer treatment.
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Affiliation(s)
- Rui Liu
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157, 5th West Road, Xi'an, 710004, Shaanxi, China
| | - Yachun Jia
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157, 5th West Road, Xi'an, 710004, Shaanxi, China
| | - Guangyao Kong
- National-Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China
| | - Aili He
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157, 5th West Road, Xi'an, 710004, Shaanxi, China. .,National-Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China.
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18
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Van Bortle K, Marciano DP, Liu Q, Chou T, Lipchik AM, Gollapudi S, Geller BS, Monte E, Kamakaka RT, Snyder MP. A cancer-associated RNA polymerase III identity drives robust transcription and expression of snaR-A noncoding RNA. Nat Commun 2022; 13:3007. [PMID: 35637192 PMCID: PMC9151912 DOI: 10.1038/s41467-022-30323-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 04/13/2022] [Indexed: 11/09/2022] Open
Abstract
RNA polymerase III (Pol III) includes two alternate isoforms, defined by mutually exclusive incorporation of subunit POLR3G (RPC7α) or POLR3GL (RPC7β), in mammals. The contributions of POLR3G and POLR3GL to transcription potential has remained poorly defined. Here, we discover that loss of subunit POLR3G is accompanied by a restricted repertoire of genes transcribed by Pol III. Particularly sensitive is snaR-A, a small noncoding RNA implicated in cancer proliferation and metastasis. Analysis of Pol III isoform biases and downstream chromatin features identifies loss of POLR3G and snaR-A during differentiation, and conversely, re-establishment of POLR3G gene expression and SNAR-A gene features in cancer contexts. Our results support a model in which Pol III identity functions as an important transcriptional regulatory mechanism. Upregulation of POLR3G, which is driven by MYC, identifies a subgroup of patients with unfavorable survival outcomes in specific cancers, further implicating the POLR3G-enhanced transcription repertoire as a potential disease factor. RNA polymerase III changes its subunit composition during mammalian development. Here the authors report that loss of subunit POLR3G, which re-emerges in cancer, promotes expression of small NF90-associated RNA (snaR-A), a noncoding RNA implicated in cell proliferation and metastasis.
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19
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Huang Y, Zheng Y, Yao L, Qiao F, Hou Y, Hu X, Li D, Shao Z. RNA binding protein POP7 regulates ILF3 mRNA stability and expression to promote breast cancer progression. Cancer Sci 2022; 113:3801-3813. [PMID: 35579257 DOI: 10.1111/cas.15430] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 11/29/2022] Open
Abstract
RNA Binding Proteins(RBPs)play pivotal roles in breast cancer (BC) development. As a RBP, Processing of precursor 7 (POP7) is one of the subunits of RNase P and RNase MRP, however, its exact function and mechanism in BC remain unknown. Here, we showed that expression of POP7 was frequently increased in breast cancer cells and in primary breast tumors. Up-regulated POP7 significantly promoted BC cell proliferation in vitro and primary tumor growth in vivo. POP7 also increased cell migration, invasion in vitro and lung metastasis in vivo. Through RNA-immunoprecipitation coupled with sequencing (RIP-seq), we found that POP7 bound preferentially to intron regions and POP7-binding peak associated genes were mainly enriched in cancer-related pathways. Further, POP7 regulated Interleukin Enhancer Binding Factor 3 (ILF3) expression through influencing its mRNA stability. Knockdown of ILF3 significantly impaired the increased malignant potential of POP7 over-expressing cells, suggesting that POP7 enhances BC progression through regulating ILF3 expression. Collectively, our findings provide the first evidence for the important role of POP7 and its regulation of ILF3 in promoting breast cancer progression.
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Affiliation(s)
- Yanni Huang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yizi Zheng
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Thyroid and Breast Surgery, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Ling Yao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Feng Qiao
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yifeng Hou
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xin Hu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Daqiang Li
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhiming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
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20
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Biagini V, Busi F, Anelli V, Kerschbamer E, Baghini M, Gurrieri E, Notarangelo M, Pesce I, van Niel G, D’Agostino VG, Mione M. Zebrafish Melanoma-Derived Interstitial EVs Are Carriers of ncRNAs That Induce Inflammation. Int J Mol Sci 2022; 23:ijms23105510. [PMID: 35628321 PMCID: PMC9143139 DOI: 10.3390/ijms23105510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 02/05/2023] Open
Abstract
Extracellular vesicles (EVs) are membranous particles released by all cell types. Their role as functional carrier of bioactive molecules is boosted by cells that actively secrete them in biological fluids or in the intercellular space (interstitial EVs, iEVs). Here we have optimised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are around 140 nm in diameter, as determined by nanoparticle tracking and transmission electron microscopy (TEM) analysis. Western blot analysis shows enrichment for CD63 and Alix in the iEV fraction, but not in melanoma cell lysates. Super resolution and confocal microscopy reveal that purified zebrafish iEVs are green fluorescent protein positive (GFP+), indicating that they integrate the oncogene GFP-HRASV12G used to induce melanoma in this model within their vesicular membrane or luminal content. Analysis of RNA-Seq data found 118 non-coding (nc)RNAs differentially distributed between zebrafish melanoma and their iEVs, with only 17 of them being selectively enriched in iEVs. Among these, the RNA components of RNAses P and MRP, which process ribosomal RNA precursors, mitochondrial RNAs, and some mRNAs, were enriched in zebrafish and human melanoma EVs, but not in iEVs extracted from brain tumours. We found that melanoma iEVs induce an inflammatory response when injected in larvae, with increased expression of interferon responsive genes, and this effect is reproduced by MRP- or P-RNAs injected into circulation. This suggests that zebrafish melanoma iEVs are a source of MRP- and P-RNAs that can trigger inflammation in cells of the innate immune system.
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Affiliation(s)
- Valentina Biagini
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology (Cibio), University of Trento, 38123 Trento, Italy; (V.B.); (F.B.); (V.A.); (M.B.)
| | - Federica Busi
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology (Cibio), University of Trento, 38123 Trento, Italy; (V.B.); (F.B.); (V.A.); (M.B.)
| | - Viviana Anelli
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology (Cibio), University of Trento, 38123 Trento, Italy; (V.B.); (F.B.); (V.A.); (M.B.)
| | - Emanuela Kerschbamer
- Bioinformatic Facility, Department of Cellular, Computational and Integrative Biology (Cibio), University of Trento, 38123 Trento, Italy;
| | - Marta Baghini
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology (Cibio), University of Trento, 38123 Trento, Italy; (V.B.); (F.B.); (V.A.); (M.B.)
| | - Elena Gurrieri
- Laboratory of Biotechnology and Nanomedicine, Department of Cellular, Computational and Integrative Biology (Cibio), University of Trento, 38123 Trento, Italy; (E.G.); (M.N.); (V.G.D.)
| | - Michela Notarangelo
- Laboratory of Biotechnology and Nanomedicine, Department of Cellular, Computational and Integrative Biology (Cibio), University of Trento, 38123 Trento, Italy; (E.G.); (M.N.); (V.G.D.)
| | - Isabella Pesce
- Cell Analysis and Separation Core Facility, Department of Cellular, Computational and Integrative Biology (Cibio), University of Trento, 38123 Trento, Italy;
| | - Guillaume van Niel
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, F-75014 Paris, France;
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, F-75014 Paris, France
| | - Vito G. D’Agostino
- Laboratory of Biotechnology and Nanomedicine, Department of Cellular, Computational and Integrative Biology (Cibio), University of Trento, 38123 Trento, Italy; (E.G.); (M.N.); (V.G.D.)
| | - Marina Mione
- Experimental Cancer Biology, Department of Cellular, Computational and Integrative Biology (Cibio), University of Trento, 38123 Trento, Italy; (V.B.); (F.B.); (V.A.); (M.B.)
- Correspondence:
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21
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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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Understanding 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. n-Tr20 is a neuron-specific, cytoplasmic transfer RNAArgUCU (tRNAArgUCU) isodecoder that affects seizure susceptibility, neuronal excitability, and translation signaling in mice. In addition, the C50U substitution in n-Tr20 (n-Tr20C50U), which is found in the widely used C57BL/6J (B6J) inbred mouse line, contributes to neurodegeneration by epistatic interactions with mutations in Gtpbp1 or Gtpbp2, two factors that rescue ribosomal stalling. The brains of B6J mice have high levels of immature and low levels of mature n-Tr20C50U, implicating defective tRNA biogenesis as the basis for neuronal dysfunction, a hypothesis tested in this study. We demonstrate that partially purified mouse brain ribonuclease P, the endonuclease responsible for 5′ maturation of tRNAs, exhibits at 1 mM magnesium a 20-fold lower apparent cleavage rate for processing the n-Tr20C50U precursor than the wild-type precursor. Thermal denaturation studies unexpectedly revealed that substituting the native C50-G64 base pair with the U50-G64 wobble pair in n-Tr20C50U increased the Tm by as much as 8 °C, with the magnitude of the change dependent on [Mg2+]. Moreover, results from thermal denaturation, native gel electrophoresis, 1H nuclear magnetic resonance spectroscopy, and kinetic studies collectively support the presence of stable alternative folds for n-Tr20C50U that may also be sampled transiently and in low abundance by the wild-type tRNA. These findings suggest that mutation-driven restructuring could foster nonnative folds and that conformational toggling of tRNAs poses an intrinsic risk for dysfunction when point mutations selectively stabilize nonnative states. This model may be applicable for understanding the molecular basis of other diseases that are associated with tRNA mutations.
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22
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Gómez-Redondo I, Pericuesta E, Navarrete-Lopez P, Ramos-Ibeas P, Planells B, Fonseca-Balvís N, Vaquero-Rey A, Fernández-González R, Laguna-Barraza R, Horiuchi K, Gutiérrez-Adán A. Zrsr2 and functional U12-dependent spliceosome are necessary for follicular development. iScience 2022; 25:103860. [PMID: 35198906 PMCID: PMC8850803 DOI: 10.1016/j.isci.2022.103860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/26/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
ZRSR2 is a splicing factor involved in recognition of 3′-intron splice sites that is frequently mutated in myeloid malignancies and several tumors; however, the role of mutations of Zrsr2 in other tissues has not been analyzed. To explore the biological role of ZRSR2, we generated three Zrsr2 mutant mouse lines. All Zrsr2 mutant lines exhibited blood cell anomalies, and in two lines, oogenesis was blocked at the secondary follicle stage. RNA-seq of Zrsr2mu secondary follicles showed aberrations in gene expression and showed altered alternative splicing (AS) events involving enrichment of U12-type intron retention (IR), supporting the functional Zrsr2 action in minor spliceosomes. IR events were preferentially associated with centriole replication, protein phosphorylation, and DNA damage checkpoint. Notably, we found alterations in AS events of 50 meiotic genes. These results indicate that ZRSR2 mutations alter splicing mainly in U12-type introns, which may affect peripheral blood cells, and impede oogenesis and female fertility. Zrsr2mu mice allow us to identify functions of Zrsr2 in vivo Minor splicing factor Zrsr2 is essential for oogenesis and peripheral blood cells Zrsr2 impairment affects the splicing of U12-type intron-containing genes Zrsr2mu aberrant splicing causes a global alteration of gene expression
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Affiliation(s)
- Isabel Gómez-Redondo
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Eva Pericuesta
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Paula Navarrete-Lopez
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Priscila Ramos-Ibeas
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Benjamín Planells
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Noelia Fonseca-Balvís
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Aida Vaquero-Rey
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Raúl Fernández-González
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Ricardo Laguna-Barraza
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Keiko Horiuchi
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, 1-396 Kosugi-cho, Nakahara-ku, Kawasaki, Kanagawa 211-8533, Japan
| | - Alfonso Gutiérrez-Adán
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
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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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24
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Rawal HC, Ali S, Mondal TK. miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms. Brief Bioinform 2021; 23:6420093. [PMID: 34734232 DOI: 10.1093/bib/bbab448] [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: 08/20/2021] [Revised: 09/15/2021] [Accepted: 09/28/2021] [Indexed: 11/12/2022] Open
Abstract
In recent years, microRNAs (miRNAs) and tRNA-derived RNA fragments (tRFs) have been reported extensively following different approaches of identification and analysis. Comprehensively analyzing the present approaches to overcome the existing variations, we developed a benchmarking methodology each for the identification of miRNAs and tRFs, termed as miRNA Prediction Methodology (miRPreM) and tRNA-induced small non-coding RNA Prediction Methodology (tiRPreM), respectively. We emphasized the use of respective genome of organism under study for mapping reads, sample data with at least two biological replicates, normalized read count support and novel miRNA prediction by two standard tools with multiple runs. The performance of these methodologies was evaluated by using Oryza coarctata, a wild rice species as a case study for model and non-model organisms. With organism-specific reference genome approach, 98 miRNAs and 60 tRFs were exclusively found. We observed high accuracy (13 out of 15) when tested these genome-specific miRNAs in support of analyzing the data with respective organism. Such a strong impact of miRPreM, we have predicted more than double number of miRNAs (186) as compared with the traditional approaches (79) and with tiRPreM, we have predicted all known classes of tRFs within the same small RNA data. Moreover, the methodologies presented here are in standard form in order to extend its applicability to different organisms rather than restricting to plants. Hence, miRPreM and tiRPreM can fulfill the need of a comprehensive methodology for miRNA prediction and tRF identification, respectively, for model and non-model organisms.
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Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.,School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India.,Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India
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25
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Rid7C, a member of the YjgF/YER057c/UK114 (Rid) protein family, is a novel endoribonuclease that regulates the expression of a specialist RNA polymerase involved in differentiation in Nonomuraea gerenzanensis. J Bacteriol 2021; 204:e0046221. [PMID: 34694905 DOI: 10.1128/jb.00462-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The YjgF/YER057c/UK114 (Rid) is a protein family breadth conserved in all domains of life and includes the widely distributed archetypal RidA (YjgF) subfamily and seven other subfamilies (Rid1 to Rid7). Among these subfamilies, RidA is the only family to have been biochemically well characterized and is involved in the deamination of the reactive enamine/imine intermediates. In this study, we have characterized a protein of the Rid7 subfamily, named Rid7C, in Nonomuraea gerenzanensis, an actinomycete that is characterized by the presence of two types of RNA polymerases. This is due to the co-existence in its genome of two RNAP β chain-encoding genes: rpoB(S) (the wild-type rpoB gene) and rpoB(R) (a specialist, mutant-type rpoB gene) that controls A40926 antibiotic production and a wide range of metabolic adaptive behaviors. Here, we found that expression of rpoB(R) is regulated post-transcriptionally by RNA processing in the 5'-UTR of rpoB(R) mRNA, and that the endoribonuclease activity of Rid7C is responsible for mRNA processing thereby overseeing several tracts of morphological and biochemical differentiation. We also provide evidence that Rid7C may be associated with ribonuclease P M1 RNA, although M1 RNA is not required for rpoB(R) mRNA processing in vitro, and that Rid7C endoribonuclease activity is inhibited by A40926 suggesting the existence of a negative feedback loop on A40926 production, and a role of the endogenous synthesis of A40926 in the modulation of biochemical differentiation in this microorganism. Importance The YjgF/YER057c/UK114 family includes many proteins with diverse functions involved in detoxification, RNA maturation, and control of mRNA translation. We found that Rid7C is an endoribonuclease that is involved in processing of rpoB(R) mRNA, coding for a specialized RNA polymerase beta subunit that oversees morphological differentiation and A40926 antibiotic production in Nonomuraea gerenzanensis. Rid7C-mediated processing promotes rpoB(R) mRNA translation and antibiotic production, while Rid7C endoribonuclease activity is inhibited by A40926 suggesting a role of the endogenous synthesis of A40926 in modulation of biochemical differentiation in this microorganism. Finally, we show that recombinant Rid7C co-purified with M1 RNA (the RNA subunit of ribonuclease P) from Escherichia coli extract, suggesting a functional interaction between Rid7C and M1 RNA activities.
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Li W, Xiong Y, Lai LB, Zhang K, Li Z, Kang H, Dai L, Gopalan V, Wang G, Liu W. The rice RNase P protein subunit Rpp30 confers broad-spectrum resistance to fungal and bacterial pathogens. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1988-1999. [PMID: 33932077 PMCID: PMC8486239 DOI: 10.1111/pbi.13612] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/25/2021] [Accepted: 04/25/2021] [Indexed: 05/23/2023]
Abstract
RNase P functions either as a catalytic ribonucleoprotein (RNP) or as an RNA-free polypeptide to catalyse RNA processing, primarily tRNA 5' maturation. To the growing evidence of non-canonical roles for RNase P RNP subunits including regulation of chromatin structure and function, we add here a role for the rice RNase P Rpp30 in innate immunity. This protein (encoded by LOC_Os11g01074) was uncovered as the top hit in yeast two-hybrid assays performed with the rice histone deacetylase HDT701 as bait. We showed that HDT701 and OsRpp30 are localized to the rice nucleus, OsRpp30 expression increased post-infection by Pyricularia oryzae (syn. Magnaporthe oryzae), and OsRpp30 deacetylation coincided with HDT701 overexpression in vivo. Overexpression of OsRpp30 in transgenic rice increased expression of defence genes and generation of reactive oxygen species after pathogen-associated molecular pattern elicitor treatment, outcomes that culminated in resistance to a fungal (P. oryzae) and a bacterial (Xanthomonas oryzae pv. oryzae) pathogen. Knockout of OsRpp30 yielded the opposite phenotypes. Moreover, HA-tagged OsRpp30 co-purified with RNase P pre-tRNA cleavage activity. Interestingly, OsRpp30 is conserved in grass crops, including a near-identical C-terminal tail that is essential for HDT701 binding and defence regulation. Overall, our results suggest that OsRpp30 plays an important role in rice immune response to pathogens and provides a new approach to generate broad-spectrum disease-resistant rice cultivars.
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Affiliation(s)
- Wei Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests and College of Plant ProtectionHunan Agricultural UniversityChangshaHunanChina
- Department of Plant PathologyThe Ohio State UniversityColumbusOHUSA
| | - Yehui Xiong
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Lien B. Lai
- Department of Chemistry and BiochemistryCenter for RNA BiologyThe Ohio State UniversityColumbusOhioUSA
| | - Kai Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Liangying Dai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests and College of Plant ProtectionHunan Agricultural UniversityChangshaHunanChina
| | - Venkat Gopalan
- Department of Chemistry and BiochemistryCenter for RNA BiologyThe Ohio State UniversityColumbusOhioUSA
| | - Guo‐Liang Wang
- Department of Plant PathologyThe Ohio State UniversityColumbusOHUSA
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
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27
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Shaukat AN, Kaliatsi EG, Skeparnias I, Stathopoulos C. The Dynamic Network of RNP RNase P Subunits. Int J Mol Sci 2021; 22:ijms221910307. [PMID: 34638646 PMCID: PMC8509007 DOI: 10.3390/ijms221910307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Ribonuclease P (RNase P) is an important ribonucleoprotein (RNP), responsible for the maturation of the 5′ end of precursor tRNAs (pre-tRNAs). In all organisms, the cleavage activity of a single phosphodiester bond adjacent to the first nucleotide of the acceptor stem is indispensable for cell viability and lies within an essential catalytic RNA subunit. Although RNase P is a ribozyme, its kinetic efficiency in vivo, as well as its structural variability and complexity throughout evolution, requires the presence of one protein subunit in bacteria to several protein partners in archaea and eukaryotes. Moreover, the existence of protein-only RNase P (PRORP) enzymes in several organisms and organelles suggests a more complex evolutionary timeline than previously thought. Recent detailed structures of bacterial, archaeal, human and mitochondrial RNase P complexes suggest that, although apparently dissimilar enzymes, they all recognize pre-tRNAs through conserved interactions. Interestingly, individual protein subunits of the human nuclear and mitochondrial holoenzymes have additional functions and contribute to a dynamic network of elaborate interactions and cellular processes. Herein, we summarize the role of each RNase P subunit with a focus on the human nuclear RNP and its putative role in flawless gene expression in light of recent structural studies.
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28
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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: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/11/2021] [Accepted: 07/28/2021] [Indexed: 12/24/2022]
Abstract
RNase P is an essential enzyme that catalyzes removal of the 5' leader from precursor transfer RNAs. The ribonucleoprotein (RNP) form of RNase P is present in all domains of life and comprises a single catalytic RNA (ribozyme) and a variable number of protein cofactors. Recent cryo-electron microscopy structures of representative archaeal and eukaryotic (nuclear) RNase P holoenzymes bound to tRNA substrate/product provide high-resolution detail on subunit organization, topology, and substrate recognition in these large, multisubunit catalytic RNPs. These structures point to the challenges in understanding how proteins modulate the RNA functional repertoire and how the structure of an ancient RNA-based catalyst was reshaped during evolution by new macromolecular associations that were likely necessitated by functional/regulatory coupling.
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Affiliation(s)
- Hong-Duc Phan
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Lien B Lai
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Walter J Zahurancik
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
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29
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Delbarre E, Janicki SM. Modulation of H3.3 chromatin assembly by PML: A way to regulate epigenetic inheritance. Bioessays 2021; 43:e2100038. [PMID: 34423467 DOI: 10.1002/bies.202100038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Although the promyelocytic leukemia (PML) protein is renowned for regulating a wide range of cellular processes and as an essential component of PML nuclear bodies (PML-NBs), the mechanisms through which it exerts its broad physiological impact are far from fully elucidated. Here, we review recent studies supporting an emerging view that PML's pleiotropic effects derive, at least partially, from its role in regulating histone H3.3 chromatin assembly, a critical epigenetic mechanism. These studies suggest that PML maintains heterochromatin organization by restraining H3.3 incorporation. Examination of PML's contribution to H3.3 chromatin assembly in the context of the cell cycle and PML-NB assembly suggests that PML represses heterochromatic H3.3 deposition during S phase and that transcription and SUMOylation regulate PML's recruitment to heterochromatin. Elucidating PML' s contributions to H3.3-mediated epigenetic regulation will provide insight into PML's expansive influence on cellular physiology and open new avenues for studying oncogenesis linked to PML malfunction.
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Affiliation(s)
- Erwan Delbarre
- Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Susan M Janicki
- Drexel University Thomas R. Kline School of Law, Philadelphia, Pennsylvania, USA
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30
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Lata E, Choquet K, Sagliocco F, Brais B, Bernard G, Teichmann M. RNA Polymerase III Subunit Mutations in Genetic Diseases. Front Mol Biosci 2021; 8:696438. [PMID: 34395528 PMCID: PMC8362101 DOI: 10.3389/fmolb.2021.696438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/21/2021] [Indexed: 12/24/2022] Open
Abstract
RNA polymerase (Pol) III transcribes small untranslated RNAs such as 5S ribosomal RNA, transfer RNAs, and U6 small nuclear RNA. Because of the functions of these RNAs, Pol III transcription is best known for its essential contribution to RNA maturation and translation. Surprisingly, it was discovered in the last decade that various inherited mutations in genes encoding nine distinct subunits of Pol III cause tissue-specific diseases rather than a general failure of all vital functions. Mutations in the POLR3A, POLR3C, POLR3E and POLR3F subunits are associated with susceptibility to varicella zoster virus-induced encephalitis and pneumonitis. In addition, an ever-increasing number of distinct mutations in the POLR3A, POLR3B, POLR1C and POLR3K subunits cause a spectrum of neurodegenerative diseases, which includes most notably hypomyelinating leukodystrophy. Furthermore, other rare diseases are also associated with mutations in genes encoding subunits of Pol III (POLR3H, POLR3GL) and the BRF1 component of the TFIIIB transcription initiation factor. Although the causal relationship between these mutations and disease development is widely accepted, the exact molecular mechanisms underlying disease pathogenesis remain enigmatic. Here, we review the current knowledge on the functional impact of specific mutations, possible Pol III-related disease-causing mechanisms, and animal models that may help to better understand the links between Pol III mutations and disease.
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Affiliation(s)
- Elisabeth Lata
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Karine Choquet
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Francis Sagliocco
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Bernard Brais
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Geneviève Bernard
- Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Martin Teichmann
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
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31
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Jarrous N, Mani D, Ramanathan A. Coordination of transcription and processing of tRNA. FEBS J 2021; 289:3630-3641. [PMID: 33929081 DOI: 10.1111/febs.15904] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/02/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022]
Abstract
Coordination of transcription and processing of RNA is a basic principle in regulation of gene expression in eukaryotes. In the case of mRNA, coordination is primarily founded on a co-transcriptional processing mechanism by which a nascent precursor mRNA undergoes maturation via cleavage and modification by the transcription machinery. A similar mechanism controls the biosynthesis of rRNA. However, the coordination of transcription and processing of tRNA, a rather short transcript, remains unknown. Here, we present a model for high molecular weight initiation complexes of human RNA polymerase III that assemble on tRNA genes and process precursor transcripts to mature forms. These multifunctional initiation complexes may support co-transcriptional processing, such as the removal of the 5' leader of precursor tRNA by RNase P. Based on this model, maturation of tRNA is predetermined prior to transcription initiation.
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Affiliation(s)
- Nayef Jarrous
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Dhivakar Mani
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Aravind Ramanathan
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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32
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Abstract
The innate immune system has numerous signal transduction pathways that lead to the production of type I interferons in response to exposure of cells to external stimuli. One of these pathways comprises RNA polymerase (Pol) III that senses common DNA viruses, such as cytomegalovirus, vaccinia, herpes simplex virus-1 and varicella zoster virus. This polymerase detects and transcribes viral genomic regions to generate AU-rich transcripts that bring to the induction of type I interferons. Remarkably, Pol III is also stimulated by foreign non-viral DNAs and expression of one of its subunits is induced by an RNA virus, the Sindbis virus. Moreover, a protein subunit of RNase P, which is known to associate with Pol III in initiation complexes, is induced by viral infection. Accordingly, alliance of the two tRNA enzymes in innate immunity merits a consideration.
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Affiliation(s)
- Nayef Jarrous
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Israel-Canada
| | - Alexander Rouvinski
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Israel-Canada.,The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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33
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The search for RNA-binding proteins: a technical and interdisciplinary challenge. Biochem Soc Trans 2021; 49:393-403. [PMID: 33492363 PMCID: PMC7925008 DOI: 10.1042/bst20200688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins are customarily regarded as important facilitators of gene expression. In recent years, RNA–protein interactions have also emerged as a pervasive force in the regulation of homeostasis. The compendium of proteins with provable RNA-binding function has swelled from the hundreds to the thousands astride the partnership of mass spectrometry-based proteomics and RNA sequencing. At the foundation of these advances is the adaptation of RNA-centric capture methods that can extract bound protein that has been cross-linked in its native environment. These methods reveal snapshots in time displaying an extensive network of regulation and a wealth of data that can be used for both the discovery of RNA-binding function and the molecular interfaces at which these interactions occur. This review will focus on the impact of these developments on our broader perception of post-transcriptional regulation, and how the technical features of current capture methods, as applied in mammalian systems, create a challenging medium for interpretation by systems biologists and target validation by experimental researchers.
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34
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Zorn P, Misiak D, Gekle M, Köhn M. Identification and initial characterization of POLIII-driven transcripts by msRNA-sequencing. RNA Biol 2021; 18:1807-1817. [PMID: 33404286 PMCID: PMC8583065 DOI: 10.1080/15476286.2020.1871216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are powerful regulators of gene expression but medium-sized (50–300 nts in length) ncRNAs (msRNAs) are barely picked-up precisely by RNA-sequencing. Here we describe msRNA-sequencing (msRNAseq), a modified protocol that associated with a computational analyses pipeline identified about ~1800 msRNA loci, including over 300 putatively novel msRNAs, in human and murine cells. We focused on the identification and initial characterization of three POLIII-derived transcripts. The validation of these uncharacterized msRNAs identified an ncRNA in antisense orientation from the POLR3E locus transcribed by POLIII. This msRNA, termed POLAR (POLR3E Antisense RNA), has a strikingly short half-life, localizes to paraspeckles (PSPs) and associates with PSP-associated proteins indicating that msRNAseq identifies functional msRNAs. Thus, our analyses will pave the way for analysing the roles of msRNAs in cells, development and diseases.
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Affiliation(s)
| | - Danny Misiak
- Institute of Molecular Medicine, University of Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Gekle
- Julius-Bernstein-Institute of Physiology, University of Halle-Wittenberg, Germany
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35
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Mishra S, Verma SK. Differential expression of proteins in Pseudomonas mendocina SMSKVR-3 under arsenate stress. J Basic Microbiol 2021; 61:351-361. [PMID: 33448070 DOI: 10.1002/jobm.202000671] [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: 11/10/2020] [Revised: 12/15/2020] [Accepted: 01/02/2021] [Indexed: 11/07/2022]
Abstract
This study focuses on analyzing the protein expression pattern of intracellular proteins when Pseudomonas mendocina SMSKVR-3 exposed to 300 mM of arsenate to find out the proteins that are overexpressed or exclusively expressed in response to arsenate. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of protein expression at different time intervals showed the highest number of protein bands (14) that are overexpressed at 8 h of the time interval. It was also observed that treatment with at least 200 mM of As(V) is required to induce a difference in protein expression. Two-dimensional (2D)-PAGE analysis of 8-h sample exhibited 146 unique spots, 45 underexpressed, and 46 overexpressed spots in arsenate-treated sample. Based on the highest percent volume and fold change, three unique spots and one overexpressed spot were selected and analyzed by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF/TOF) mass spectrometry (MS) analysis followed by the MASCOT search. These proteins were identified as ribosome-recycling factor (20.13 kDa), polyphosphate:ADP/GDP phosphotransferase (40.88 kDa), ribonuclease P protein component (14.96 kDa) and cobalt-precorrin-5B C(1)-methyltransferase (38.43 kDa) with MASCOT score of 54, 81, 94, and 100, respectively. All of these proteins help the bacteria to overcome arsenate stress.
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Affiliation(s)
- Shraddha Mishra
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, India
| | - Sanjay K Verma
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, India
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36
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Molla-Herman A, Angelova MT, Ginestet M, Carré C, Antoniewski C, Huynh JR. tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation. Front Genet 2020; 11:518949. [PMID: 33193603 PMCID: PMC7586317 DOI: 10.3389/fgene.2020.518949] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/03/2020] [Indexed: 01/16/2023] Open
Abstract
tRNA fragments (tRFs) are a class of small non-coding RNAs (sncRNAs) derived from tRNAs. tRFs are highly abundant in many cell types including stem cells and cancer cells, and are found in all domains of life. Beyond translation control, tRFs have several functions ranging from transposon silencing to cell proliferation control. However, the analysis of tRFs presents specific challenges and their biogenesis is not well understood. They are very heterogeneous and highly modified by numerous post-transcriptional modifications. Here we describe a bioinformatic pipeline (tRFs-Galaxy) to study tRFs populations and shed light onto tRNA fragments biogenesis in Drosophila melanogaster. Indeed, we used small RNAs Illumina sequencing datasets extracted from wild type and mutant ovaries affecting two different highly conserved steps of tRNA biogenesis: 5'pre-tRNA processing (RNase-P subunit Rpp30) and tRNA 2'-O-methylation (dTrm7_34 and dTrm7_32). Using our pipeline, we show how defects in tRNA biogenesis affect nuclear and mitochondrial tRFs populations and other small non-coding RNAs biogenesis, such as small nucleolar RNAs (snoRNAs). This tRF analysis workflow will advance the current understanding of tRFs biogenesis, which is crucial to better comprehend tRFs roles and their implication in human pathology.
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Affiliation(s)
- Anahi Molla-Herman
- Collège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, France
| | - Margarita T. Angelova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Maud Ginestet
- Collège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, France
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Christophe Antoniewski
- ARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Jean-René Huynh
- Collège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, France
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Sandoval-Mojica AF, Altman S, Hunter WB, Pelz-Stelinski KS. Peptide conjugated morpholinos for management of the huanglongbing pathosystem. PEST MANAGEMENT SCIENCE 2020; 76:3217-3224. [PMID: 32358830 DOI: 10.1002/ps.5877] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/27/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND 'Candidatus Liberibacter asiaticus' (CLas) is the causal agent of the devastating citrus disease Huanglongbing (HLB) and is transmitted by the insect vector Diaphorina citri (Hemiptera: Liviidae). A potential approach for treating CLas infection is the use of synthetic nucleic acid-like oligomers to silence bacterial gene expression. Peptide conjugated morpholinos (PPMOs) targeting essential genes in CLas and the psyllid vector's endosymbiotic bacteria, Wolbachia (-Diaphorina, wDi), were evaluated using in vitro and in vivo assays. RESULTS Expression of the wDi gyrA gene was significantly reduced following incubation of wDi cells with PPMOs. In addition, the viability of isolated wDi cells was greatly reduced when treated with PPMOs as compared to untreated cells. Feeding D. citri adults with a complementary PPMO (CLgyrA-14) showed significantly reduced (70% lower) expression of the CLas gyrA gene. CLas relative density was significantly lower in the psyllids fed with CLgyrA-14, when compared to untreated insects. Psyllids that were treated with CLgyrA-14 were less successful in transmitting the pathogen into uninfected plants, compared to untreated insects. CONCLUSION The expression of essential genes in the D. citri symbiont, wDi and the HLB pathogen were suppressed in response to PPMO treatments. This study demonstrates the potential of PPMOs as a novel strategy for management of bacterial pathogens of fruit trees, such as HLB. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Andrés F Sandoval-Mojica
- Department of Entomology and Nematology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, USA
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT,, USA
| | - Wayne B Hunter
- U.S Department of Agriculture, Agricultural Research Service, Fort Pierce, FL, USA
| | - Kirsten S Pelz-Stelinski
- Department of Entomology and Nematology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, USA
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38
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Ma S, Kong S, Wang F, Ju S. CircRNAs: biogenesis, functions, and role in drug-resistant Tumours. Mol Cancer 2020; 19:119. [PMID: 32758239 PMCID: PMC7409473 DOI: 10.1186/s12943-020-01231-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Targeted treatment, which can specifically kill tumour cells without affecting normal cells, is a new approach for tumour therapy. However, tumour cells tend to acquire resistance to targeted drugs during treatment. Circular RNAs (circRNAs) are single-stranded RNA molecules with unique structures and important functions. With the development of RNA sequencing technology, circRNAs have been found to be widespread in tumour-resistant cells and to play important regulatory roles. In this review, we present the latest advances in circRNA research and summarize the various mechanisms underlying their regulation. Moreover, we review the role of circRNAs in the chemotherapeutic resistance of tumours and explore the clinical value of circRNA regulation in treating tumour resistance.
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Affiliation(s)
- Shuo Ma
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.,School of Public Health, Nantong University, NO. 9, Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Shan Kong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.,School of Public Health, Nantong University, NO. 9, Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Feng Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China. .,School of Public Health, Nantong University, NO. 9, Seyuan Road, Nantong, 226019, Jiangsu, China.
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39
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The expanding regulatory mechanisms and cellular functions of circular RNAs. Nat Rev Mol Cell Biol 2020; 21:475-490. [PMID: 32366901 DOI: 10.1038/s41580-020-0243-y] [Citation(s) in RCA: 773] [Impact Index Per Article: 193.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
Many protein-coding genes in higher eukaryotes can produce circular RNAs (circRNAs) through back-splicing of exons. CircRNAs differ from mRNAs in their production, structure and turnover and thereby have unique cellular functions and potential biomedical applications. In this Review, I discuss recent progress in our understanding of the biogenesis of circRNAs and the regulation of their abundance and of their biological functions, including in transcription and splicing, sequestering or scaffolding of macromolecules to interfere with microRNA activities or signalling pathways, and serving as templates for translation. I further discuss the emerging roles of circRNAs in regulating immune responses and cell proliferation, and the possibilities of applying circRNA technologies in biomedical research.
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40
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The emerging role of RNA modifications in the regulation of mRNA stability. Exp Mol Med 2020; 52:400-408. [PMID: 32210357 PMCID: PMC7156397 DOI: 10.1038/s12276-020-0407-z] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 01/02/2023] Open
Abstract
Many studies have highlighted the importance of the tight regulation of mRNA stability in the control of gene expression. mRNA stability largely depends on the mRNA nucleotide sequence, which affects the secondary and tertiary structures of the mRNAs, and the accessibility of various RNA-binding proteins to the mRNAs. Recent advances in high-throughput RNA-sequencing techniques have resulted in the elucidation of the important roles played by mRNA modifications and mRNA nucleotide sequences in regulating mRNA stability. To date, hundreds of different RNA modifications have been characterized. Among them, several RNA modifications, including N6-methyladenosine (m6A), N6,2′-O-dimethyladenosine (m6Am), 8-oxo-7,8-dihydroguanosine (8-oxoG), pseudouridine (Ψ), 5-methylcytidine (m5C), and N4-acetylcytidine (ac4C), have been shown to regulate mRNA stability, consequently affecting diverse cellular and biological processes. In this review, we discuss our current understanding of the molecular mechanisms underlying the regulation of mammalian mRNA stability by various RNA modifications. Messenger RNA molecules play their key role in directing the manufacture of proteins via translating the genetic information in DNA. Sung Ho Boo and Yoon Ki Kim at Korea University in Seoul review current understanding of the significance of modifications to messenger RNA with respect to RNA stability in mammalian cells. Recent advances in RNA sequencing technology have revealed hundreds of different modifications which, by influencing RNA stability, can control gene expression. The modifications largely involve small chemical groups added to any of the four nucleotide groups that make up an RNA molecule. This can affect all aspects of mature RNA biogenesis, including transcription, pre-mRNA splicing, RNA export form the nucleus to the cytoplasm, translation, and stability.
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41
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Molecular Mechanisms Driving mRNA Degradation by m 6A Modification. Trends Genet 2020; 36:177-188. [PMID: 31964509 DOI: 10.1016/j.tig.2019.12.007] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 02/08/2023]
Abstract
N6-Methyladenosine (m6A), the most prevalent internal modification associated with eukaryotic mRNAs, influences many steps of mRNA metabolism, including splicing, export, and translation, as well as stability. Recent studies have revealed that m6A-containing mRNAs undergo one of two distinct pathways of rapid degradation: deadenylation via the YT521-B homology (YTH) domain-containing family protein 2 (YTHDF2; an m6A reader protein)-CCR4/NOT (deadenylase) complex or endoribonucleolytic cleavage by the YTHDF2-HRSP12-ribonuclease (RNase) P/mitochondrial RNA-processing (MRP) (endoribonuclease) complex. Some m6A-containing circular RNAs (circRNAs) are also subject to endoribonucleolytic cleavage by YTHDF2-HRSP12-RNase P/MRP. Here, we highlight recent progress on the molecular mechanisms underlying rapid mRNA degradation via m6A and describe our current understanding of the dynamic regulation of m6A-mediated mRNA decay through the crosstalk between m6A (or YTHDF2) and other cellular factors.
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42
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Bouchoucha A, Waltz F, Bonnard G, Arrivé M, Hammann P, Kuhn L, Schelcher C, Zuber H, Gobert A, Giegé P. Determination of protein-only RNase P interactome in Arabidopsis mitochondria and chloroplasts identifies a complex between PRORP1 and another NYN domain nuclease. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:549-561. [PMID: 31319441 DOI: 10.1111/tpj.14458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/03/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
The essential type of endonuclease that removes 5' leader sequences from transfer RNA precursors is called RNase P. While ribonucleoprotein RNase P enzymes containing a ribozyme are found in all domains of life, another type of RNase P called 'PRORP', for 'PROtein-only RNase P', is composed of protein that occurs only in a wide variety of eukaryotes, in organelles and in the nucleus. Here, to find how PRORP functions integrate with other cell processes, we explored the protein interaction network of PRORP1 in Arabidopsis mitochondria and chloroplasts. Although PRORP proteins function as single subunit enzymes in vitro, we found that PRORP1 occurs in protein complexes and is present in high-molecular-weight fractions that contain mitochondrial ribosomes. The analysis of immunoprecipitated protein complexes identified proteins involved in organellar gene expression processes. In particular, direct interaction was established between PRORP1 and MNU2 a mitochondrial nuclease. A specific domain of MNU2 and a conserved signature of PRORP1 were found to be directly accountable for this protein interaction. Altogether, results revealed the existence of an RNA maturation complex in Arabidopsis mitochondria and suggested that PRORP proteins cooperated with other gene expression factors for RNA maturation in vivo.
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Affiliation(s)
- Ayoub Bouchoucha
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Florent Waltz
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Géraldine Bonnard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Mathilde Arrivé
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg-Esplanade, CNRS, Université de Strasbourg, 15 rue René Descartes, Strasbourg, F-67084, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg-Esplanade, CNRS, Université de Strasbourg, 15 rue René Descartes, Strasbourg, F-67084, France
| | - Cédric Schelcher
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Anthony Gobert
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Giegé
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
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43
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Seki T, Yamagata H, Uchida S, Chen C, Kobayashi A, Kobayashi M, Harada K, Matsuo K, Watanabe Y, Nakagawa S. Altered expression of long noncoding RNAs in patients with major depressive disorder. J Psychiatr Res 2019; 117:92-99. [PMID: 31351391 DOI: 10.1016/j.jpsychires.2019.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 07/10/2019] [Accepted: 07/18/2019] [Indexed: 02/06/2023]
Abstract
Although major depressive disorder (MDD) is a leading cause of disability worldwide, its pathophysiology is poorly understood. Increasing evidence suggests that aberrant regulation of transcription plays a key role in the pathophysiology of MDD. Recently, long noncoding RNAs (lncRNAs) have been recognized for their important functions in chromatin structure, gene expression, and the subsequent manifestation of various biological processes in the central nervous system. However, it is unclear whether the aberrant expression and function of lncRNAs are associated with the pathophysiology of MDD. In this study, we sought to evaluate the expression of lncRNAs in peripheral blood leukocytes as potential biomarkers for MDD. We measured the expression levels of 83 lncRNAs in the peripheral blood leukocytes of 29 MDD patients and 29 age- and gender-matched healthy controls using quantitative reverse transcription PCR (RT-qPCR) analysis. We found that MDD patients exhibited distinct expression signatures. Specifically, the expression level of one lncRNA (RMRP) was lower while the levels of four (Y5, MER11C, PCAT1, and PCAT29) were higher in MDD patients compared to healthy controls. The expression level of RMRP was correlated with depression severity as measured by the Hamilton Depression Rating Scale (HAM-D). Moreover, RMRP expression was lower in a mouse model of depression, corroborating the observation from MDD patients. Taken together, our data suggest that lower RMRP levels may serve as a potential biomarker for MDD.
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Affiliation(s)
- Tomoe Seki
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Hirotaka Yamagata
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Shusaku Uchida
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Chong Chen
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Ayumi Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Masaaki Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Kenichiro Harada
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Koji Matsuo
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Yoshifumi Watanabe
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Shin Nakagawa
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
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Perederina A, Berezin I, Krasilnikov AS. In vitro reconstitution and analysis of eukaryotic RNase P RNPs. Nucleic Acids Res 2019; 46:6857-6868. [PMID: 29722866 PMCID: PMC6061874 DOI: 10.1093/nar/gky333] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/22/2018] [Indexed: 12/23/2022] Open
Abstract
RNase P is a ubiquitous site-specific endoribonuclease primarily responsible for the maturation of tRNA. Throughout the three domains of life, the canonical form of RNase P is a ribonucleoprotein (RNP) built around a catalytic RNA. The core RNA is well conserved from bacteria to eukaryotes, whereas the protein parts vary significantly. The most complex and the least understood form of RNase P is found in eukaryotes, where multiple essential proteins playing largely unknown roles constitute the bulk of the enzyme. Eukaryotic RNase P was considered intractable to in vitro reconstitution, mostly due to insolubility of its protein components, which hindered its studies. We have developed a robust approach to the in vitro reconstitution of Saccharomyces cerevisiae RNase P RNPs and used it to analyze the interplay and roles of RNase P components. The results eliminate the major obstacle to biochemical and structural studies of eukaryotic RNase P, identify components required for the activation of the catalytic RNA, reveal roles of proteins in the enzyme stability, localize proteins on RNase P RNA, and demonstrate the interdependence of the binding of RNase P protein modules to the core RNA.
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Affiliation(s)
- Anna Perederina
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Igor Berezin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Andrey S Krasilnikov
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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45
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Schaffer AE, Pinkard O, Coller JM. tRNA Metabolism and Neurodevelopmental Disorders. Annu Rev Genomics Hum Genet 2019; 20:359-387. [PMID: 31082281 DOI: 10.1146/annurev-genom-083118-015334] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
tRNAs are short noncoding RNAs required for protein translation. The human genome includes more than 600 putative tRNA genes, many of which are considered redundant. tRNA transcripts are subject to tightly controlled, multistep maturation processes that lead to the removal of flanking sequences and the addition of nontemplated nucleotides. Furthermore, tRNAs are highly structured and posttranscriptionally modified. Together, these unique features have impeded the adoption of modern genomics and transcriptomics technologies for tRNA studies. Nevertheless, it has become apparent from human neurogenetic research that many tRNA biogenesis proteins cause brain abnormalities and other neurological disorders when mutated. The cerebral cortex, cerebellum, and peripheral nervous system show defects, impairment, and degeneration upon tRNA misregulation, suggesting that they are particularly sensitive to changes in tRNA expression or function. An integrated approach to identify tRNA species and contextually characterize tRNA function will be imperative to drive future tool development and novel therapeutic design for tRNA-associated disorders.
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Affiliation(s)
- Ashleigh E Schaffer
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
| | - Otis Pinkard
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
| | - Jeffery M Coller
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
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46
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Park OH, Ha H, Lee Y, Boo SH, Kwon DH, Song HK, Kim YK. Endoribonucleolytic Cleavage of m6A-Containing RNAs by RNase P/MRP Complex. Mol Cell 2019; 74:494-507.e8. [DOI: 10.1016/j.molcel.2019.02.034] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 01/14/2019] [Accepted: 02/22/2019] [Indexed: 12/21/2022]
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47
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Wellner K, Mörl M. Post-Transcriptional Regulation of tRNA Pools To Govern the Central Dogma: A Perspective. Biochemistry 2019; 58:299-304. [PMID: 30192518 DOI: 10.1021/acs.biochem.8b00862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since their initial discovery, tRNAs have risen from sole adapter molecules during protein synthesis to pivotal modulators of gene expression. Through their many interactions with tRNA-associated protein factors, they play a central role in maintaining cell homeostasis, especially regarding the fine-tuning in response to a rapidly changing cellular environment. Here, we provide a perspective on current tRNA topics with a spotlight on the regulation of post-transcriptional shaping of tRNA molecules. First, we give an update on aberrant structural features that a yet functional fraction of mitochondrial tRNAs can exhibit. Then, we outline several aspects of the regulatory contribution of ribonucleases with a focus on tRNA processing versus tRNA elimination. We close with a comment on the possible consequences for the intracellular examination of nascent tRNA precursors regarding respective processing factors that have been shown to associate with the tRNA transcription machinery in alternative moonlighting functions.
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Affiliation(s)
- Karolin Wellner
- Institute for Biochemistry , Leipzig University , Brüderstrasse 34 , 04103 Leipzig , Germany
| | - Mario Mörl
- Institute for Biochemistry , Leipzig University , Brüderstrasse 34 , 04103 Leipzig , Germany
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48
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Grafanaki K, Anastasakis D, Kyriakopoulos G, Skeparnias I, Georgiou S, Stathopoulos C. Translation regulation in skin cancer from a tRNA point of view. Epigenomics 2018; 11:215-245. [PMID: 30565492 DOI: 10.2217/epi-2018-0176] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein synthesis is a central and dynamic process, frequently deregulated in cancer through aberrant activation or expression of translation initiation factors and tRNAs. The discovery of tRNA-derived fragments, a new class of abundant and, in some cases stress-induced, small Noncoding RNAs has perplexed the epigenomics landscape and highlights the emerging regulatory role of tRNAs in translation and beyond. Skin is the biggest organ in human body, which maintains homeostasis of its multilayers through regulatory networks that induce translational reprogramming, and modulate tRNA transcription, modification and fragmentation, in response to various stress signals, like UV irradiation. In this review, we summarize recent knowledge on the role of translation regulation and tRNA biology in the alarming prevalence of skin cancer.
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Affiliation(s)
- Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece.,Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Dimitrios Anastasakis
- National Institute of Musculoskeletal & Arthritis & Skin, NIH, 50 South Drive, Room 1152, Bethesda, MD 20892, USA
| | - George Kyriakopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Sophia Georgiou
- Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
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49
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Wu J, Niu S, Tan M, Huang C, Li M, Song Y, Wang Q, Chen J, Shi S, Lan P, Lei M. Cryo-EM Structure of the Human Ribonuclease P Holoenzyme. Cell 2018; 175:1393-1404.e11. [PMID: 30454648 DOI: 10.1016/j.cell.2018.10.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/20/2018] [Accepted: 09/28/2018] [Indexed: 12/14/2022]
Abstract
Ribonuclease (RNase) P is a ubiquitous ribozyme that cleaves the 5' leader from precursor tRNAs. Here, we report cryo-electron microscopy structures of the human nuclear RNase P alone and in complex with tRNAVal. Human RNase P is a large ribonucleoprotein complex that contains 10 protein components and one catalytic RNA. The protein components form an interlocked clamp that stabilizes the RNA in a conformation optimal for substrate binding. Human RNase P recognizes the tRNA using a double-anchor mechanism through both protein-RNA and RNA-RNA interactions. Structural comparison of the apo and tRNA-bound human RNase P reveals that binding of tRNA induces a local conformational change in the catalytic center, transforming the ribozyme into an active state. Our results also provide an evolutionary model depicting how auxiliary RNA elements in bacterial RNase P, essential for substrate binding, and catalysis, were replaced by the much more complex and multifunctional protein components in higher organisms.
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Affiliation(s)
- Jian Wu
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Shuangshuang Niu
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ming Tan
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chenhui Huang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Mingyue Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yang Song
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Qianmin Wang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Juan Chen
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Shaohua Shi
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Pengfei Lan
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China.
| | - Ming Lei
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Key laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China.
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Davies-Sala C, Jani S, Zorreguieta A, Tolmasky ME. Identification of the Acinetobacter baumannii Ribonuclease P Catalytic Subunit: Cleavage of a Target mRNA in the Presence of an External Guide Sequence. Front Microbiol 2018; 9:2408. [PMID: 30349524 PMCID: PMC6186949 DOI: 10.3389/fmicb.2018.02408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/20/2018] [Indexed: 11/17/2022] Open
Abstract
The bacterial ribonuclease P or RNase P holoenzyme is usually composed of a catalytic RNA subunit, M1, and a cofactor protein, C5. This enzyme was first identified for its role in maturation of tRNAs by endonucleolytic cleavage of the pre-tRNA. The RNase P endonucleolytic activity is characterized by having structural but not sequence substrate requirements. This property led to development of EGS technology, which consists of utilizing a short antisense oligonucleotide that when forming a duplex with a target RNA induces its cleavage by RNase P. This technology is being explored for designing therapies that interfere with expression of genes, in the case of bacterial infections EGS technology could be applied to target essential, virulence, or antibiotic resistant genes. Acinetobacter baumannii is a problematic pathogen that is commonly resistant to multiple antibiotics, and EGS technology could be utilized to design alternative therapies. To better understand the A. baumannii RNase P we first identified and characterized the catalytic subunit. We identified a gene coding for an RNA species, M1Ab, with the expected features of the RNase P M1 subunit. A recombinant clone coding for M1Ab complemented the M1 thermosensitive mutant Escherichia coli BL21(DE3) T7A49, which upon transformation was able to grow at the non-permissive temperature. M1Ab showed in vitro catalytic activity in combination with the C5 protein cofactor from E. coli as well as with that from A. baumannii, which was identified, cloned and partially purified. M1Ab was also able to cleave a target mRNA in the presence of an EGS with efficiency comparable to that of the E. coli M1, suggesting that EGS technology could be a viable option for designing therapeutic alternatives to treat multiresistant A. baumannii infections.
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Affiliation(s)
- Carol Davies-Sala
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States.,Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Facultad de Ciencias Exactas y Naturales de la Universidad de Buenos Aires, University of Buenos Aires, Buenos Aires, Argentina
| | - Saumya Jani
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Facultad de Ciencias Exactas y Naturales de la Universidad de Buenos Aires, University of Buenos Aires, Buenos Aires, Argentina
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States
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