1
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Tomecki R, Drazkowska K, Madaj R, Mamot A, Dunin-Horkawicz S, Sikorski PJ. Expanding the Available RNA Labeling Toolbox With CutA Nucleotidyltransferase for Efficient Transcript Labeling with Purine and Pyrimidine Nucleotide Analogs. Chembiochem 2024:e202400202. [PMID: 38818670 DOI: 10.1002/cbic.202400202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/01/2024]
Abstract
RNA labeling is an invaluable tool for investigation of the function and localization of nucleic acids. Labels are commonly incorporated into 3' end of RNA and the primary enzyme used for this purpose is RNA poly(A) polymerase (PAP), which belongs to the class of terminal nucleotidyltransferases (NTases). However, PAP preferentially adds ATP analogs, thus limiting the number of available substrates. Here, we report the use of another NTase, CutA from the fungus Thielavia terrestris. Using this enzyme, we were able to incorporate into the 3' end of RNA not only purine analogs, but also pyrimidine analogs. We engaged strain-promoted azide-alkyl cycloaddition (SPAAC) to obtain fluorescently labeled or biotinylated transcripts from RNAs extended with azide analogs by CutA. Importantly, modified transcripts retained their biological properties. Furthermore, fluorescently labeled mRNAs were suitable for visualization in cultured mammalian cells. Finally, we demonstrate that either affinity studies or molecular dynamic (MD) simulations allow for rapid screening of NTase substrates, what opens up new avenues in the search for the optimal substrates for this class of enzymes.
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Affiliation(s)
- Rafal Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Karolina Drazkowska
- Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Rafal Madaj
- Laboratory of Structural Bioinformatics, Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Adam Mamot
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Pawel J Sikorski
- Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
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2
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Yamashita S, Tomita K. Mechanism of U6 snRNA oligouridylation by human TUT1. Nat Commun 2023; 14:4686. [PMID: 37563152 PMCID: PMC10415362 DOI: 10.1038/s41467-023-40420-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
U6 snRNA is a catalytic RNA responsible for pre-mRNA splicing reactions and undergoes various post-transcriptional modifications during its maturation process. The 3'-oligouridylation of U6 snRNA by the terminal uridylyltransferase, TUT1, provides the Lsm-binding site in U6 snRNA for U4/U6 di-snRNP formation and this ensures pre-mRNA splicing. Here, we present the crystal structure of human TUT1 (hTUT1) complexed with U6 snRNA, representing the post-uridylation of U6 snRNA by hTUT1. The N-terminal ZF-RRM and catalytic palm clamp the single-stranded AUA motif between the 5'-short stem and the 3'-telestem of U6 snRNA, and the ZF-RRM specifically recognizes the AUA motif. The ZF and the fingers hold the telestem, and the 3'-end of U6 snRNA is placed in the catalytic pocket of the palm for oligouridylation. The oligouridylation of U6 snRNA depends on the internal four-adenosine tract in the 5'-part of the telestem of U6 snRNA, and hTUT1 adds uridines until the internal adenosine tract can form base-pairs with the 3'-oligouridine tract. Together, the recognition of the specific structure and sequence of U6 snRNA by the multi-domain TUT1 protein and the intrinsic sequence and structure of U6 snRNA ensure the oligouridylation of U6 snRNA.
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Affiliation(s)
- Seisuke Yamashita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
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3
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Liudkovska V, Krawczyk PS, Brouze A, Gumińska N, Wegierski T, Cysewski D, Mackiewicz Z, Ewbank JJ, Drabikowski K, Mroczek S, Dziembowski A. TENT5 cytoplasmic noncanonical poly(A) polymerases regulate the innate immune response in animals. SCIENCE ADVANCES 2022; 8:eadd9468. [PMID: 36383655 PMCID: PMC9668313 DOI: 10.1126/sciadv.add9468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Innate immunity is the first line of host defense against pathogens. Here, through global transcriptome and proteome analyses, we uncover that newly described cytoplasmic poly(A) polymerase TENT-5 (terminal nucleotidyltransferase 5) enhances the expression of secreted innate immunity effector proteins in Caenorhabditis elegans. Direct RNA sequencing revealed that multiple mRNAs with signal peptide-encoding sequences have shorter poly(A) tails in tent-5-deficient worms. Those mRNAs are translated at the endoplasmic reticulum where a fraction of TENT-5 is present, implying that they represent its direct substrates. Loss of tent-5 makes worms more susceptible to bacterial infection. Notably, the role of TENT-5 in innate immunity is evolutionarily conserved. Its orthologs, TENT5A and TENT5C, are expressed in macrophages and induced during their activation. Analysis of macrophages devoid of TENT5A/C revealed their role in the regulation of secreted proteins involved in defense response. In summary, our study reveals cytoplasmic polyadenylation to be a previously unknown component of the posttranscriptional regulation of innate immunity in animals.
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Affiliation(s)
- Vladyslava Liudkovska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Paweł S Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Aleksandra Brouze
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Natalia Gumińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Tomasz Wegierski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Zuzanna Mackiewicz
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jonathan J Ewbank
- Aix Marseille University, INSERM, CNRS, CIML, Turing Centre for Living Systems, Marseille, France
| | - Krzysztof Drabikowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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4
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Hu Q, Yang H, Li M, Zhu L, Lv M, Li F, Zhang Z, Ren G, Gong Q. Molecular mechanism underlying the di-uridylation activity of Arabidopsis TUTase URT1. Nucleic Acids Res 2022; 50:10614-10625. [PMID: 36177876 PMCID: PMC9561377 DOI: 10.1093/nar/gkac839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/09/2022] [Accepted: 09/19/2022] [Indexed: 11/14/2022] Open
Abstract
In Arabidopsis, HESO1 and URT1 act cooperatively on unmethylated miRNA and mRNA uridylation to induce their degradation. Their collaboration significantly impacts RNA metabolism in plants. However, the molecular mechanism determining the functional difference and complementarity of these two enzymes remains unclear. We previously solved the three-dimensional structure of URT1 in the absence and presence of UTP. In this study, we further determined the structure of URT1 in complex with a 5′-AAAU-3′ RNA stretch that mimics the post-catalytic state of the mRNA poly(A) tail after the addition of the first uridine. Structural analysis and enzymatic assays revealed that L527 and Y592 endow URT1 with a preference to interact with purine over pyrimidine at the -1 RNA binding position, thus controlling the optimal number of uridine added to the 3′ extremity of poly(A) as two. In addition, we observed that a large-scale conformational rearrangement in URT1 occurs upon binding with RNA from an ‘open’ to a ‘closed’ state. Molecular dynamic simulation supports an open-closed conformational selection mechanism employed by URT1 to interact with RNA substrates and maintain distributive enzymatic activity. Based on the above results, a model regarding the catalytic cycle of URT1 is proposed to explain its di-uridylation activity.
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Affiliation(s)
- Qian Hu
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Huiru Yang
- State Key Laboratory of Genetic Engineering, Zhangjiang mRNA Innovation and Translation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Mingwei Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Lingru Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Mengqi Lv
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Fudong Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Zhiyong Zhang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Zhangjiang mRNA Innovation and Translation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qingguo Gong
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
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5
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Stein RL, Wilson DM. Kinetic and Mechanistic Studies of the Terminal Uridylyltransferase, Zcchc11 (TUT4). Biochemistry 2022; 61:1614-1624. [PMID: 35797480 DOI: 10.1021/acs.biochem.2c00146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Zcchc11 (TUT4, TENT3A, Z11) is a nucleotidyltransferase that catalyzes the 3'-polyuridylation of RNA. Our interest in this enzyme stems from its role in blocking the biogenesis of let-7, a family of microRNAs whose members act as tumor suppressors. Z11 polyuridylates pre-let-7, the precursor of let-7, when pre-let-7 is complexed with LIN28, an RNA-binding protein. Polyuridylation of pre-let-7 marks it for degradation. In addition to this LIN28-dependent activity, Z11 also has LIN28-independent activities. In this paper, we report the results of experiments that characterize LIN28-independent activities of Z11. Significant observations include the following. (1) Z11 uridylates not only mature let-7 species but also substrates as small as dinucleotides. (2) For both let-7i and the diribonucleotide AG, Z11 follows a steady-state ordered mechanism, with UTP adding before RNA. (3) Uridylation kinetics of let-7i (UGAGGUAGUAGUUUGUGCUGUU) and two truncated derivatives, GCUGUU and UU, indicate that Z11 manifests selectivity in Km,RNA; kcat,RNA values for the three substrates are nearly identical. (4) Z11 preferentially uridylates RNA lacking base-pairing near the 3' terminus. (5) Selectivity of Z11 toward ribonucleoside triphosphates is similar for let-7i and AG, with XTP preference: UTP > CTP > ATP ≫ GTP. Selectivity is manifested in Km,XTP, with kcat,XTP values being similar for UTP, CTP, and ATP. (6) Kinetic parameters for RNA turnover are dependent on the structure of the nucleoside triphosphate, consistent with recent structural data indicating stacking of the nucleoside triphosphate base with the base of the 3'-nucleotide of the substrate RNA (Faehnle et al., Nat. Struct. Mol. Biol. 2017, 24, 658).
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Affiliation(s)
- Ross L Stein
- Twentyeight-Seven Therapeutics, 490 Arsenal Way, Watertown, Massachusetts 02472, United States
| | - David M Wilson
- Twentyeight-Seven Therapeutics, 490 Arsenal Way, Watertown, Massachusetts 02472, United States
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6
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Tinti M, Kelner-Mirôn A, Marriott LJ, Ferguson MA. Polysomal mRNA Association and Gene Expression in Trypanosoma brucei. Wellcome Open Res 2022; 6:36. [PMID: 34250262 PMCID: PMC8240603 DOI: 10.12688/wellcomeopenres.16430.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 11/20/2022] Open
Abstract
Background: The contrasting physiological environments of
Trypanosoma brucei procyclic (insect vector) and bloodstream (mammalian host) forms necessitates deployment of different molecular processes and, therefore, changes in protein expression. Transcriptional regulation is unusual in
T. brucei because the arrangement of genes is polycistronic; however, genes which are transcribed together are subsequently cleaved into separate mRNAs by
trans-splicing. Following pre-mRNA processing, the regulation of mature mRNA stability is a tightly controlled cellular process. While many stage-specific transcripts have been identified, previous studies using RNA-seq suggest that changes in overall transcript level do not necessarily reflect the abundance of the corresponding protein. Methods: To better understand the regulation of gene expression in
T. brucei, we performed a bioinformatic analysis of RNA-seq on total, sub-polysomal, and polysomal mRNA samples. We further cross-referenced our dataset with a previously published proteomics dataset to identify new protein coding sequences. Results: Our analyses showed that several long non-coding RNAs are more abundant in the sub-polysome samples, which possibly implicates them in regulating cellular differentiation in
T. brucei. We also improved the annotation of the
T.brucei genome by identifying new putative protein coding transcripts that were confirmed by mass spectrometry data. Conclusions: Several long non-coding RNAs are more abundant in the sub-polysome cellular fractions and might pay a role in the regulation of gene expression. We hope that these data will be of wide general interest, as well as being of specific value to researchers studying gene regulation expression and life stage transitions in
T. brucei.
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Affiliation(s)
- Michele Tinti
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
| | - Anna Kelner-Mirôn
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
| | - Lizzie J. Marriott
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
| | - Michael A.J. Ferguson
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
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7
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Blümler A, Schwalbe H, Heckel A. Solid‐Phase‐Supported Chemoenzymatic Synthesis of a Light‐Activatable tRNA Derivative. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Anja Blümler
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance BMRZ Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
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8
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Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
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Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
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9
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Blümler A, Schwalbe H, Heckel A. Solid-Phase-Supported Chemoenzymatic Synthesis of a Light-Activatable tRNA Derivative. Angew Chem Int Ed Engl 2021; 61:e202111613. [PMID: 34738704 PMCID: PMC9299214 DOI: 10.1002/anie.202111613] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 12/14/2022]
Abstract
Herein, we present a multi‐cycle chemoenzymatic synthesis of modified RNA with simplified solid‐phase handling to overcome size limitations of RNA synthesis. It combines the advantages of classical chemical solid‐phase synthesis and enzymatic synthesis using magnetic streptavidin beads and biotinylated RNA. Successful introduction of light‐controllable RNA nucleotides into the tRNAMet sequence was confirmed by gel electrophoresis and mass spectrometry. The methods tolerate modifications in the RNA phosphodiester backbone and allow introductions of photocaged and photoswitchable nucleotides as well as photocleavable strand breaks and fluorophores.
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Affiliation(s)
- Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany.,Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance BMRZ, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
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10
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Low-bias ncRNA libraries using ordered two-template relay: Serial template jumping by a modified retroelement reverse transcriptase. Proc Natl Acad Sci U S A 2021; 118:2107900118. [PMID: 34649994 PMCID: PMC8594491 DOI: 10.1073/pnas.2107900118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2021] [Indexed: 02/07/2023] Open
Abstract
Retrotransposons are noninfectious, mobile genetic elements that proliferate in host genomes via an RNA intermediate that is copied into DNA by a reverse transcriptase (RT) enzyme. RTs are important for biotechnological applications involving information capture from RNA since RNA is first converted into complementary DNA for detection or sequencing. Here, we biochemically characterized RTs from two retroelements and uncovered several activities that allowed us to design a streamlined, efficient workflow for determining the inventory of RNA sequences in processed RNA pools. The unique properties of nonretroviral RT activities obviate many technical issues associated with current methods of RNA sequence analysis, with wide applications in research, biotechnology, and diagnostics. Selfish, non-long terminal repeat (non-LTR) retroelements and mobile group II introns encode reverse transcriptases (RTs) that can initiate DNA synthesis without substantial base pairing of primer and template. Biochemical characterization of these enzymes has been limited by recombinant expression challenges, hampering understanding of their properties and the possible exploitation of their properties for research and biotechnology. We investigated the activities of representative RTs using a modified non-LTR RT from Bombyx mori and a group II intron RT from Eubacterium rectale. Only the non-LTR RT supported robust and serial template jumping, producing one complementary DNA (cDNA) from several templates each copied end to end. We also discovered an unexpected terminal deoxynucleotidyl transferase activity of the RTs that adds nucleotide(s) of choice to 3′ ends of single- and/or double-stranded RNA or DNA. Combining these two types of activity with additional insights about nontemplated nucleotide additions to duplexed cDNA product, we developed a streamlined protocol for fusion of next-generation sequencing adaptors to both cDNA ends in a single RT reaction. When benchmarked using a reference pool of microRNAs (miRNAs), library production by Ordered Two-Template Relay (OTTR) using recombinant non-LTR retroelement RT outperformed all commercially available kits and rivaled the low bias of technically demanding home-brew protocols. We applied OTTR to inventory RNAs purified from extracellular vesicles, identifying miRNAs as well as myriad other noncoding RNAs (ncRNAs) and ncRNA fragments. Our results establish the utility of OTTR for automation-friendly, low-bias, end-to-end RNA sequence inventories of complex ncRNA samples.
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11
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Tinti M, Kelner-Mirôn A, Marriott LJ, Ferguson MAJ. Polysomal mRNA Association and Gene Expression in Trypanosoma brucei. Wellcome Open Res 2021; 6:36. [PMID: 34250262 DOI: 10.12688/wellcomeopenres.16430.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
Background: The contrasting physiological environments of Trypanosoma brucei procyclic (insect vector) and bloodstream (mammalian host) forms necessitates deployment of different molecular processes and, therefore, changes in protein expression. Transcriptional regulation is unusual in T. brucei because the arrangement of genes is polycistronic; however, genes which are transcribed together are subsequently cleaved into separate mRNAs by trans-splicing. Following pre-mRNA processing, the regulation of mature mRNA stability is a tightly controlled cellular process. While many stage-specific transcripts have been identified, previous studies using RNA-seq suggest that changes in overall transcript level do not necessarily reflect the abundance of the corresponding protein. Methods: To better understand the regulation of gene expression in T. brucei, we performed a bioinformatic analysis of RNA-seq on total, sub-polysomal, and polysomal mRNA samples. We further cross-referenced our dataset with a previously published proteomics dataset to identify new protein coding sequences. Results: Our analyses showed that several long non-coding RNAs are more abundant in the sub-polysome samples, which possibly implicates them in regulating cellular differentiation in T. brucei. We also improved the annotation of the T.brucei genome by identifying new putative protein coding transcripts that were confirmed by mass spectrometry data. Conclusions: Several long non-coding RNAs are more abundant in the sub-polysome cellular fractions and might pay a role in the regulation of gene expression. We hope that these data will be of wide general interest, as well as being of specific value to researchers studying gene regulation expression and life stage transitions in T. brucei.
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Affiliation(s)
- Michele Tinti
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
| | - Anna Kelner-Mirôn
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
| | - Lizzie J Marriott
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
| | - Michael A J Ferguson
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
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12
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Tinti M, Kelner-Mirôn A, Marriott LJ, Ferguson MAJ. Polysomal mRNA Association and Gene Expression in Trypanosoma brucei. Wellcome Open Res 2021; 6:36. [PMID: 34250262 DOI: 10.12688/wellcomeopenres.16430.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2021] [Indexed: 11/20/2022] Open
Abstract
Background: The contrasting physiological environments of Trypanosoma brucei procyclic (insect vector) and bloodstream (mammalian host) forms necessitates deployment of different molecular processes and, therefore, changes in protein expression. Transcriptional regulation is unusual in T. brucei because the arrangement of genes is polycistronic; however, genes which are transcribed together are subsequently cleaved into separate mRNAs by trans-splicing. Following pre-mRNA processing, the regulation of mature mRNA stability is a tightly controlled cellular process. While many stage-specific transcripts have been identified, previous studies using RNA-seq suggest that changes in overall transcript level do not necessarily reflect the abundance of the corresponding protein. Methods: To better understand the regulation of gene expression in T. brucei, we performed a bioinformatic analysis of RNA-seq on total, sub-polysomal, and polysomal mRNA samples. We further cross-referenced our dataset with a previously published proteomics dataset to identify new protein coding sequences. Results: Our analyses showed that several long non-coding RNAs are more abundant in the sub-polysome samples, which possibly implicates them in regulating cellular differentiation in T. brucei. We also improved the annotation of the T.brucei genome by identifying new putative protein coding transcripts that were confirmed by mass spectrometry data. Conclusions: Several long non-coding RNAs are more abundant in the sub-polysome cellular fractions and might pay a role in the regulation of gene expression. We hope that these data will be of wide general interest, as well as being of specific value to researchers studying gene regulation expression and life stage transitions in T. brucei.
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Affiliation(s)
- Michele Tinti
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
| | - Anna Kelner-Mirôn
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
| | - Lizzie J Marriott
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
| | - Michael A J Ferguson
- Wellcome Centre for Anti-Infectives Research (WCAIR), School of Life Sciences, University of Dundee, Dundee, Dundee, UK
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13
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Erber L, Betat H, Mörl M. CCA-Addition Gone Wild: Unusual Occurrence and Phylogeny of Four Different tRNA Nucleotidyltransferases in Acanthamoeba castellanii. Mol Biol Evol 2021; 38:1006-1017. [PMID: 33095240 PMCID: PMC7947759 DOI: 10.1093/molbev/msaa270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
tRNAs are important players in the protein synthesis machinery, where they act as adapter molecules for translating the mRNA codons into the corresponding amino acid sequence. In a series of highly conserved maturation steps, the primary transcripts are converted into mature tRNAs. In the amoebozoan Acanthamoeba castellanii, a highly unusual evolution of some of these processing steps was identified that are based on unconventional RNA polymerase activities. In this context, we investigated the synthesis of the 3′-terminal CCA-end that is added posttranscriptionally by a specialized polymerase, the tRNA nucleotidyltransferase (CCA-adding enzyme). The majority of eukaryotic organisms carry only a single gene for a CCA-adding enzyme that acts on both the cytosolic and the mitochondrial tRNA pool. In a bioinformatic analysis of the genome of this organism, we identified a surprising multitude of genes for enzymes that contain the active site signature of eukaryotic/eubacterial tRNA nucleotidyltransferases. In vitro activity analyses of these enzymes revealed that two proteins represent bona fide CCA-adding enzymes, one of them carrying an N-terminal sequence corresponding to a putative mitochondrial target signal. The other enzymes have restricted activities and represent CC- and A-adding enzymes, respectively. The A-adding enzyme is of particular interest, as its sequence is closely related to corresponding enzymes from Proteobacteria, indicating a horizontal gene transfer. Interestingly, this unusual diversity of nucleotidyltransferase genes is not restricted to Acanthamoeba castellanii but is also present in other members of the Acanthamoeba genus, indicating an ancient evolutionary trait.
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Affiliation(s)
- Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
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14
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15
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Malik D, Kobyłecki K, Krawczyk P, Poznański J, Jakielaszek A, Napiórkowska A, Dziembowski A, Tomecki R, Nowotny M. Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine. Nucleic Acids Res 2020; 48:9387-9405. [PMID: 32785623 PMCID: PMC7498324 DOI: 10.1093/nar/gkaa647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/14/2020] [Accepted: 07/27/2020] [Indexed: 11/12/2022] Open
Abstract
Template-independent terminal ribonucleotide transferases (TENTs) catalyze the addition of nucleotide monophosphates to the 3′-end of RNA molecules regulating their fate. TENTs include poly(U) polymerases (PUPs) with a subgroup of 3′ CUCU-tagging enzymes, such as CutA in Aspergillus nidulans. CutA preferentially incorporates cytosines, processively polymerizes only adenosines and does not incorporate or extend guanosines. The basis of this peculiar specificity remains to be established. Here, we describe crystal structures of the catalytic core of CutA in complex with an incoming non-hydrolyzable CTP analog and an RNA with three adenosines, along with biochemical characterization of the enzyme. The binding of GTP or a primer with terminal guanosine is predicted to induce clashes between 2-NH2 of the guanine and protein, which would explain why CutA is unable to use these ligands as substrates. Processive adenosine polymerization likely results from the preferential binding of a primer ending with at least two adenosines. Intriguingly, we found that the affinities of CutA for the CTP and UTP are very similar and the structures did not reveal any apparent elements for specific NTP binding. Thus, the properties of CutA likely result from an interplay between several factors, which may include a conformational dynamic process of NTP recognition.
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Affiliation(s)
- Deepshikha Malik
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland
| | - Kamil Kobyłecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw 02-106, Poland
| | - Paweł Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw 02-106, Poland
| | - Aleksandra Jakielaszek
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland
| | - Agnieszka Napiórkowska
- Structural Biology Center, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw 02-106, Poland
| | - Rafał Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw 02-106, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, Warsaw 02-106, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland
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16
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Abstract
Ro60 ribonucleoproteins (RNPs), composed of the ring-shaped Ro 60-kDa (Ro60) protein and noncoding RNAs called Y RNAs, are present in all three domains of life. Ro60 was first described as an autoantigen in patients with rheumatic disease, and Ro60 orthologs have been identified in 3% to 5% of bacterial genomes, spanning the majority of phyla. Their functions have been characterized primarily in Deinococcus radiodurans, the first sequenced bacterium with a recognizable ortholog. In D. radiodurans, the Ro60 ortholog enhances the ability of 3'-to-5' exoribonucleases to degrade structured RNA during several forms of environmental stress. Y RNAs are regulators that inhibit or allow the interactions of Ro60 with other proteins and RNAs. Studies of Ro60 RNPs in other bacteria hint at additional functions, since the most conserved Y RNA contains a domain that is a close tRNA mimic and Ro60 RNPs are often encoded adjacent to components of RNA repair systems.
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Affiliation(s)
- Soyeong Sim
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Kevin Hughes
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Xinguo Chen
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
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17
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Erber L, Hoffmann A, Fallmann J, Hagedorn M, Hammann C, Stadler PF, Betat H, Prohaska S, Mörl M. Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in Dictyostelium discoideum. Int J Mol Sci 2020; 21:ijms21155210. [PMID: 32717856 PMCID: PMC7432833 DOI: 10.3390/ijms21155210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 01/12/2023] Open
Abstract
Dictyostelium discoideum, the model organism for the evolutionary supergroup of Amoebozoa, is a social amoeba that, upon starvation, undergoes transition from a unicellular to a multicellular organism. In its genome, we identified two genes encoding for tRNA nucleotidyltransferases. Such pairs of tRNA nucleotidyltransferases usually represent collaborating partial activities catalyzing CC- and A-addition to the tRNA 3'-end, respectively. In D. discoideum, however, both enzymes exhibit identical activities, representing bona-fide CCA-adding enzymes. Detailed characterization of the corresponding activities revealed that both enzymes seem to be essential and are regulated inversely during different developmental stages of D. discoideum. Intriguingly, this is the first description of two functionally equivalent CCA-adding enzymes using the same set of tRNAs and showing a similar distribution within the cell. This situation seems to be a common feature in Dictyostelia, as other members of this phylum carry similar pairs of tRNA nucleotidyltransferase genes in their genome.
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Affiliation(s)
- Lieselotte Erber
- Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (H.B.)
| | - Anne Hoffmann
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
| | - Jörg Fallmann
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
| | - Monica Hagedorn
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany; (M.H.); (C.H.)
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany; (M.H.); (C.H.)
| | - Peter F. Stadler
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Leipzig University, 04103 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Carrera 45 No. 26-85, Colombia
- Santa Fe Institute for Complex Systems, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
- Department of Theoretical Chemistry of the University of Vienna, A-1090 Vienna, Austria
| | - Heike Betat
- Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (H.B.)
| | - Sonja Prohaska
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; (A.H.); (J.F.); (P.F.S.); (S.P.)
- Computational EvoDevo Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (H.B.)
- Correspondence: ; Tel.: +49-341-9736-911; Fax: +49-341-9736-919
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18
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Liudkovska V, Dziembowski A. Functions and mechanisms of RNA tailing by metazoan terminal nucleotidyltransferases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1622. [PMID: 33145994 PMCID: PMC7988573 DOI: 10.1002/wrna.1622] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022]
Abstract
Termini often determine the fate of RNA molecules. In recent years, 3' ends of almost all classes of RNA species have been shown to acquire nontemplated nucleotides that are added by terminal nucleotidyltransferases (TENTs). The best-described role of 3' tailing is the bulk polyadenylation of messenger RNAs in the cell nucleus that is catalyzed by canonical poly(A) polymerases (PAPs). However, many other enzymes that add adenosines, uridines, or even more complex combinations of nucleotides have recently been described. This review focuses on metazoan TENTs, which are either noncanonical PAPs or terminal uridylyltransferases with varying processivity. These enzymes regulate RNA stability and RNA functions and are crucial in early development, gamete production, and somatic tissues. TENTs regulate gene expression at the posttranscriptional level, participate in the maturation of many transcripts, and protect cells against viral invasion and the transposition of repetitive sequences. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Vladyslava Liudkovska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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19
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A tale of non-canonical tails: gene regulation by post-transcriptional RNA tailing. Nat Rev Mol Cell Biol 2020; 21:542-556. [PMID: 32483315 DOI: 10.1038/s41580-020-0246-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2020] [Indexed: 01/06/2023]
Abstract
RNA tailing, or the addition of non-templated nucleotides to the 3' end of RNA, is the most frequent and conserved type of RNA modification. The addition of tails and their composition reflect RNA maturation stages and have important roles in determining the fate of the modified RNAs. Apart from canonical poly(A) polymerases, which add poly(A) tails to mRNAs in a transcription-coupled manner, a family of terminal nucleotidyltransferases (TENTs), including terminal uridylyltransferases (TUTs), modify RNAs post-transcriptionally to control RNA stability and activity. The human genome encodes 11 different TENTs with distinct substrate specificity, intracellular localization and tissue distribution. In this Review, we discuss recent advances in our understanding of non-canonical RNA tails, with a focus on the functions of human TENTs, which include uridylation, mixed tailing and post-transcriptional polyadenylation of mRNAs, microRNAs and other types of non-coding RNA.
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20
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Abstract
Specific chemical modifications of biological molecules are an efficient way of regulating molecular function, and a plethora of downstream signalling pathways are influenced by the modification of DNA and proteins. Many of the enzymes responsible for regulating protein and DNA modifications are targets of current cancer therapies. RNA epitranscriptomics, the study of RNA modifications, is the new frontier of this arena. Despite being known since the 1970s, eukaryotic RNA modifications were mostly identified on transfer RNA and ribosomal RNA until the last decade, when they have been identified and characterized on mRNA and various non-coding RNAs. Increasing evidence suggests that RNA modification pathways are also misregulated in human cancers and may be ideal targets of cancer therapy. In this Review we highlight the RNA epitranscriptomic pathways implicated in cancer, describing their biological functions and their connections to the disease.
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Affiliation(s)
- Isaia Barbieri
- The Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- Division of Cellular and Molecular Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
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21
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poly(UG)-tailed RNAs in genome protection and epigenetic inheritance. Nature 2020; 582:283-288. [PMID: 32499657 PMCID: PMC8396162 DOI: 10.1038/s41586-020-2323-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/16/2020] [Indexed: 12/17/2022]
Abstract
Mobile genetic elements threaten genome integrity in all organisms. MUT-2/RDE-3 is a ribonucleotidyltransferase required for transposon silencing and RNA interference (RNAi) in C. elegans1–4. When tethered to RNAs in heterologous expression systems, RDE-3 can add long stretches of alternating non-templated uridine (U) and guanosine (G) ribonucleotides to the 3’ termini of these RNAs (poly(UG) or pUG tails)5. Here we show that, in its natural context in C. elegans, RDE-3 adds pUG tails to targets of RNAi, as well as to transposon RNAs. pUG tails with more than 16 perfectly alternating 3’ U and G nucleotides convert RNA fragments into agents of gene silencing. pUG tails promote gene silencing by recruiting RNA-dependent RNA polymerases (RdRPs), which use pUG-tailed RNAs (pUG RNAs) as templates to synthesize small interfering RNAs (siRNAs). Our results show that cycles of pUG RNA–templated siRNA synthesis and siRNA-directed mRNA pUGylation underlie dsRNA-directed transgenerational epigenetic inheritance in the C. elegans germline. We speculate that this pUG RNA/siRNA silencing loop allows parents to inoculate progeny against the expression of unwanted or parasitic genetic elements
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22
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Structural and Functional Analyses of the FAM46C/Plk4 Complex. Structure 2020; 28:910-921.e4. [PMID: 32433990 DOI: 10.1016/j.str.2020.04.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/23/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023]
Abstract
FAM46C, a non-canonical poly(A) polymerase, is frequently mutated in multiple myeloma. Loss of function of FAM46C promotes cell survival of multiple myeloma, suggesting a tumor-suppressive role. FAM46C is also essential for fastening sperm head and flagellum, indispensable for male fertility. The molecular mechanisms of these functions of FAM46C remain elusive. We report the crystal structure of FAM46C to provide the basis for its poly(A) polymerase activity and rationalize mutations associated with multiple myeloma. In addition, we found that FAM46C interacts directly with the serine/threonine kinase Plk4, the master regulator of centrosome duplication. We present the structure of FAM46C in complex with the Cryptic Polo-Box 1-2 domains of Plk4. Our structure-based mutational analyses show that the interaction with Plk4 recruits FAM46C to centrosomes. Our data suggest that Plk4-mediated localization of FAM46C enables its regulation of centrosome structure and functions, which may underlie the roles for FAM46C in cell proliferation and sperm development.
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23
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Zhu L, Hu Q, Cheng L, Jiang Y, Lv M, Liu Y, Li F, Shi Y, Gong Q. Crystal structure of Arabidopsis terminal uridylyl transferase URT1. Biochem Biophys Res Commun 2020; 524:490-496. [PMID: 32008746 DOI: 10.1016/j.bbrc.2020.01.124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 11/19/2022]
Abstract
3' uridylation is an essential modification associated with coding and noncoding RNA degradation in eukaryotes. In Arabidopsis, HESO1 was first identified as the major nucleotidyl transferase that uridylates most unmethylated miRNAs, and URT1 was later reported to play a redundant but important role in miRNA uridylation when HESO1 is absent. Two enzymes work sequentially and collaboratively to tail different forms of the same miRNAs in vivo. For mRNA, however, URT1 becomes the main enzyme to uridylate the majority of mRNA and repairs their deadenylated ends to restore the binding site for Poly(A) Binding Protein (PABP). HESO1, on the other hand, targets mostly the mRNAs with very short oligo(A) tails and fails in fulfilling the same task. To understand the structural basis these two functional homologues possess for their different substrate preferences and catalytic behaviors, we first determined the crystal structures of URT1 in the absence and presence of UTP. Our structures, together with functional assay and sequence analysis, indicated that URT1 has a conserved UTP-recognition mechanism analogue to the terminal uridylyl transferases from other species whereas HESO1 may evolve separately to recognize UTP in a different way. Moreover, URT1 N552 may be an important residue in interacting with 3' nucleotide of RNA substrate. The URT1 structure we determined represents the first structure of uridylyl transferase from plants, shedding light on the mechanisms of URT1/HESO1-dependent RNA metabolism.
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Affiliation(s)
- Lingru Zhu
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230027, China
| | - Qian Hu
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230027, China
| | - Lin Cheng
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230027, China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230027, China
| | - Mengqi Lv
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230027, China
| | - Yongrui Liu
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230027, China
| | - Fudong Li
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230027, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230027, China
| | - Qingguo Gong
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230027, China.
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Erber L, Franz P, Betat H, Prohaska S, Mörl M. Divergent Evolution of Eukaryotic CC- and A-Adding Enzymes. Int J Mol Sci 2020; 21:ijms21020462. [PMID: 31936900 PMCID: PMC7014341 DOI: 10.3390/ijms21020462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/06/2020] [Accepted: 01/09/2020] [Indexed: 12/04/2022] Open
Abstract
Synthesis of the CCA end of essential tRNAs is performed either by CCA-adding enzymes or as a collaboration between enzymes restricted to CC- and A-incorporation. While the occurrence of such tRNA nucleotidyltransferases with partial activities seemed to be restricted to Bacteria, the first example of such split CCA-adding activities was reported in Schizosaccharomyces pombe. Here, we demonstrate that the choanoflagellate Salpingoeca rosetta also carries CC- and A-adding enzymes. However, these enzymes have distinct evolutionary origins. Furthermore, the restricted activity of the eukaryotic CC-adding enzymes has evolved in a different way compared to their bacterial counterparts. Yet, the molecular basis is very similar, as highly conserved positions within a catalytically important flexible loop region are missing in the CC-adding enzymes. For both the CC-adding enzymes from S. rosetta as well as S. pombe, introduction of the loop elements from closely related enzymes with full activity was able to restore CCA-addition, corroborating the significance of this loop in the evolution of bacterial as well as eukaryotic tRNA nucleotidyltransferases. Our data demonstrate that partial CC- and A-adding activities in Bacteria and Eukaryotes are based on the same mechanistic principles but, surprisingly, originate from different evolutionary events.
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Affiliation(s)
- Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (P.F.); (H.B.)
| | - Paul Franz
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (P.F.); (H.B.)
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (P.F.); (H.B.)
| | - Sonja Prohaska
- Computational EvoDevo Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany;
- Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
- Santa Fe Institute for Complex Systems, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (L.E.); (P.F.); (H.B.)
- Correspondence: ; Tel.: +49-341-9736-911; Fax: +49-341-9736-919
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25
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Chung CZ, Jaramillo JE, Ellis MJ, Bour DYN, Seidl LE, Jo DHS, Turk MA, Mann MR, Bi Y, Haniford DB, Duennwald ML, Heinemann IU. RNA surveillance by uridylation-dependent RNA decay in Schizosaccharomyces pombe. Nucleic Acids Res 2019; 47:3045-3057. [PMID: 30715470 PMCID: PMC6451125 DOI: 10.1093/nar/gkz043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 12/14/2022] Open
Abstract
Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In this study, we investigate the prevalence and impact of uridylation-dependent RNA decay in S. pombe by transcriptionally profiling cid1 and dis3L2 deletion strains. We found that the exonuclease Dis3L2 represents a bottleneck in uridylation-dependent mRNA decay, whereas Cid1 plays a redundant role that can be complemented by other Tutases. Deletion of dis3L2 elicits a cellular stress response, upregulating transcription of genes involved in protein folding and degradation. Misfolded proteins accumulate in both deletion strains, yet only trigger a strong stress response in dis3L2 deficient cells. While a deletion of cid1 increases sensitivity to protein misfolding stress, a dis3L2 deletion showed no increased sensitivity or was even protective. We furthermore show that uridylyl- and adenylyltransferases cooperate to generate a 5'-NxAUUAAAA-3' RNA motif on dak2 mRNA. Our studies elucidate the role of uridylation-dependent RNA decay as part of a global mRNA surveillance, and we found that perturbation of this pathway leads to the accumulation of misfolded proteins and elicits cellular stress responses.
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Affiliation(s)
- Christina Z Chung
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Julia E Jaramillo
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Michael J Ellis
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Daniel Y N Bour
- Department of Pathology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Lauren E Seidl
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - David H S Jo
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Matthew A Turk
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Mitchell R Mann
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Yumin Bi
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - David B Haniford
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Martin L Duennwald
- Department of Pathology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada
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26
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Cheng L, Li F, Jiang Y, Yu H, Xie C, Shi Y, Gong Q. Structural insights into a unique preference for 3' terminal guanine of mirtron in Drosophila TUTase tailor. Nucleic Acids Res 2019; 47:495-508. [PMID: 30407553 PMCID: PMC6326804 DOI: 10.1093/nar/gky1116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/23/2018] [Indexed: 01/19/2023] Open
Abstract
Terminal uridylyl transferase (TUTase) is one type of enzyme that modifies RNA molecules by facilitating the post-transcriptional addition of uridyl ribonucleotides to their 3' ends. Recent researches have reported that Drosophila TUTase, Tailor, exhibits an intrinsic preference for RNA substrates ending in 3'G, distinguishing it from any other known TUTases. Through this unique feature, Tailor plays a crucial role as the repressor in the biogenesis pathway of splicing-derived mirtron pre-miRNAs. Here we describe crystal structures of core catalytic domain of Tailor and its complexes with RNA stretches 5'-AGU-3' and 5'-AGUU-3'. We demonstrate that R327 and N347 are two key residues contributing cooperatively to Tailor's preference for 3'G, and R327 may play an extra role in facilitating the extension of polyuridylation chain. We also demonstrate that conformational stability of the exit of RNA-binding groove also contributes significantly to Tailor's activity. Overall, our work reveals useful insights to explain why Drosophila Tailor can preferentially select RNA substrates ending in 3'G and provides important values for further understanding the biological significances of biogenesis pathway of mirtron in flies.
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Affiliation(s)
- Lin Cheng
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China
| | - Fudong Li
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China
| | - Hailong Yu
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China
| | - Changlin Xie
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China.,High Magnet Field Laboratory, Chinese Academy of Science, 50 Shushanhu Road, Hefei, Anhui 230031, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China
| | - Qingguo Gong
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China
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27
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Kroupova A, Ivascu A, Reimão-Pinto MM, Ameres SL, Jinek M. Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor. Nucleic Acids Res 2019; 47:1030-1042. [PMID: 30462292 PMCID: PMC6344859 DOI: 10.1093/nar/gky1164] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/12/2018] [Indexed: 11/16/2022] Open
Abstract
Non-templated 3′-uridylation of RNAs has emerged as an important mechanism for regulating the processing, stability and biological function of eukaryotic transcripts. In Drosophila, oligouridine tailing by the terminal uridylyl transferase (TUTase) Tailor of numerous RNAs induces their degradation by the exonuclease Dis3L2, which serves functional roles in RNA surveillance and mirtron RNA biogenesis. Tailor preferentially uridylates RNAs terminating in guanosine or uridine nucleotides but the structural basis underpinning its RNA substrate selectivity is unknown. Here, we report crystal structures of Tailor bound to a donor substrate analog or mono- and oligouridylated RNA products. These structures reveal specific amino acid residues involved in donor and acceptor substrate recognition, and complementary biochemical assays confirm the critical role of an active site arginine in conferring selectivity toward 3′-guanosine terminated RNAs. Notably, conservation of these active site features suggests that other eukaryotic TUTases, including mammalian TUT4 and TUT7, might exhibit similar, hitherto unknown, substrate selectivity. Together, these studies provide critical insights into the specificity of 3′-uridylation in eukaryotic post-transcriptional gene regulation.
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Affiliation(s)
- Alena Kroupova
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Anastasia Ivascu
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Madalena M Reimão-Pinto
- Institute of Molecular Biotechnology, IMBA, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology, IMBA, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
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28
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Snoek BC, Babion I, Koppers-Lalic D, Pegtel DM, Steenbergen RD. Altered microRNA processing proteins in HPV-induced cancers. Curr Opin Virol 2019; 39:23-32. [PMID: 31408800 DOI: 10.1016/j.coviro.2019.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/15/2022]
Abstract
High-risk human papilloma virus (hrHPV) infections are associated with the development of anogenital cancers, in particular cervical cancer, and a subset of head and neck cancers. Previous studies have shown that microRNAs (miRNAs) contribute to the development and progression of HPV-induced malignancies. miRNAs are small non-coding RNAs that exist as multiple length and sequence variants, termed isomiRs. Efficient processing of miRNAs and generation of isomiRs is accomplished by several processing proteins. Deregulation of Drosha, AGO2, and TENT2, among others, has been observed in HPV-induced cancers and was even found at the precancerous stage. This suggests that miRNA processing proteins may be involved during early cancer development and that the generated isomiRs could provide promising biomarkers for early cancer diagnosis.
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Affiliation(s)
- Barbara C Snoek
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Iris Babion
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Danijela Koppers-Lalic
- Amsterdam UMC, Vrije Universiteit Amsterdam, Neurosurgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Dirk M Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Renske Dm Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands.
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29
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Yang A, Bofill-De Ros X, Shao TJ, Jiang M, Li K, Villanueva P, Dai L, Gu S. 3' Uridylation Confers miRNAs with Non-canonical Target Repertoires. Mol Cell 2019; 75:511-522.e4. [PMID: 31178353 PMCID: PMC6688926 DOI: 10.1016/j.molcel.2019.05.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/14/2019] [Accepted: 05/09/2019] [Indexed: 12/14/2022]
Abstract
Many microRNAs (miRNAs) exist alongside abundant miRNA isoforms (isomiRs), most of which arise from post-maturation sequence modifications such as 3' uridylation. However, the ways in which these sequence modifications affect miRNA function remain poorly understood. Here, using human miR-27a in cell lines as a model, we discovered that a nonfunctional target site unable to base-pair extensively with the miRNA seed sequence can regain function when an upstream adenosine is able to base-pair with a post-transcriptionally added uridine in the miR-27a tail. This tail-U-mediated repression (TUMR) is abolished in cells lacking the uridylation enzymes TUT4 and TUT7, indicating that uridylation alters miRNA function by modulating target recognition. We identified a set of non-canonical targets in human cells that are specifically regulated by uridylated miR-27a. We provide evidence that TUMR expands the targets of other endogenous miRNAs. Our study reveals a function of uridylated isomiRs in regulating non-canonical miRNA targets.
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Affiliation(s)
- Acong Yang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Xavier Bofill-De Ros
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Tie-Juan Shao
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; School of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Minjie Jiang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Katherine Li
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Patricia Villanueva
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisheng Dai
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Shuo Gu
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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30
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Zhang Y, Ramming A, Heinke L, Altschmied L, Slotkin RK, Becker JD, Kappel C, Lenhard M. The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:655-672. [PMID: 31009115 DOI: 10.1111/tpj.14348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/21/2019] [Accepted: 04/08/2019] [Indexed: 05/28/2023]
Abstract
RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence-labelling strategy, we have characterized this defect in more detail using RNA and small-RNA sequencing. In addition to global defects in the expression of pollen-differentiation genes, paps1 null-mutant pollen shows a strong overaccumulation of transposable element (TE) transcripts, yet a depletion of 21- and particularly 24-nucleotide-long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding TEs. Double-mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4, mutations. In particular, the double-mutant of paps1 and rna-dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast.
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Affiliation(s)
- Yunming Zhang
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Anna Ramming
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Lisa Heinke
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Lothar Altschmied
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse 3, D-06466 Seeland, OT, Gatersleben, Germany
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
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31
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Preston MA, Porter DF, Chen F, Buter N, Lapointe CP, Keles S, Kimble J, Wickens M. Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase. Nat Methods 2019; 16:437-445. [PMID: 30988468 PMCID: PMC6613791 DOI: 10.1038/s41592-019-0370-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/24/2019] [Accepted: 03/05/2019] [Indexed: 12/22/2022]
Abstract
Ribonucleotidyl transferases (rNTases) add untemplated ribonucleotides to diverse RNAs. We have developed TRAID-seq, a screening strategy in Saccharomyces cerevisiae to identify sequences added to a reporter RNA at single-nucleotide resolution by overexpressed candidate enzymes from different organisms. The rNTase activities of 22 previously unexplored enzymes were determined. In addition to poly(A)- and poly(U)-adding enzymes, we identified a cytidine-adding enzyme that is likely to be part of a two-enzyme system that adds CCA to tRNAs in a eukaryote; a nucleotidyl transferase that adds nucleotides to RNA without apparent nucleotide preference; and a poly(UG) polymerase, Caenorhabditis elegans MUT-2, that adds alternating uridine and guanosine nucleotides to form poly(UG) tails. MUT-2 is known to be required for certain forms of RNA silencing, and mutants of the enzyme that result in defective silencing did not add poly(UG) tails in our assay. We propose that MUT-2 poly(UG) polymerase activity is required to promote genome integrity and RNA silencing.
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Affiliation(s)
- Melanie A Preston
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Promega Corporation, Madison, WI, USA
| | - Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Program in Epithelial Biology, Stanford University Medical School, Stanford, CA, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
| | - Natascha Buter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Promega Corporation, Madison, WI, USA
| | - Christopher P Lapointe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | - Sunduz Keles
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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32
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Crystal structure of the Lin28-interacting module of human terminal uridylyltransferase that regulates let-7 expression. Nat Commun 2019; 10:1960. [PMID: 31036859 PMCID: PMC6488673 DOI: 10.1038/s41467-019-09966-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/10/2019] [Indexed: 01/02/2023] Open
Abstract
Lin28-dependent oligo-uridylylation of precursor let-7 (pre-let-7) by terminal uridylyltransferase 4/7 (TUT4/7) represses let-7 expression by blocking Dicer processing, and regulates cell differentiation and proliferation. The interaction between the Lin28:pre-let-7 complex and the N-terminal Lin28-interacting module (LIM) of TUT4/7 is required for pre-let-7 oligo-uridylylation by the C-terminal catalytic module (CM) of TUT4/7. Here, we report crystallographic and biochemical analyses of the LIM of human TUT4. The LIM consists of the N-terminal Cys2His2-type zinc finger (ZF) and the non-catalytic nucleotidyltransferase domain (nc-NTD). The ZF of LIM adopts a distinct structural domain, and its structure is homologous to those of double-stranded RNA binding zinc fingers. The interaction between the ZF and pre-let-7 stabilizes the Lin28:pre-let-7:TUT4 ternary complex, and enhances the oligo-uridylylation reaction by the CM. Thus, the ZF in LIM and the zinc-knuckle in the CM, which interacts with the oligo-uridylylated tail, together facilitate Lin28-dependent pre-let-7 oligo-uridylylation.
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33
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Mohanty BK, Kushner SR. New Insights into the Relationship between tRNA Processing and Polyadenylation in Escherichia coli. Trends Genet 2019; 35:434-445. [PMID: 31036345 DOI: 10.1016/j.tig.2019.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/28/2019] [Accepted: 03/12/2019] [Indexed: 11/30/2022]
Abstract
Recent studies suggest that poly(A) polymerase I (PAP I)-mediated polyadenylation in Escherichia coli is highly prevalent among mRNAs as well as tRNA precursors. Primary tRNA transcripts are initially processed endonucleolytically to generate pre-tRNA species, which undergo 5'-end maturation by the ribozyme RNase P. Subsequently, a group of 3' → 5' exonucleases mature the 3' ends of the majority of tRNAs with few exceptions. PAP I competes with the 3' → 5' exonucleases for pre-tRNA substrates adding short poly(A) tails, which not only modulate the stability of the pre-tRNAs, but also regulate the availability of functional tRNAs. In this review, we discuss the recent discoveries of new tRNA processing pathways and the implications of polyadenylation in tRNA metabolism in E. coli.
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Affiliation(s)
- Bijoy K Mohanty
- Department of Genetics, University of Georgia, Athens, GA 30605, USA
| | - Sidney R Kushner
- Department of Genetics, University of Georgia, Athens, GA 30605, USA; Department of Microbiology, University of Georgia, Athens, GA 30605, USA.
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34
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Thomas C, Rusanov T, Hoang T, Augustin T, Kent T, Gaspar I, Pomerantz RT. One-step enzymatic modification of RNA 3' termini using polymerase θ. Nucleic Acids Res 2019; 47:3272-3283. [PMID: 30818397 PMCID: PMC6468238 DOI: 10.1093/nar/gkz029] [Citation(s) in RCA: 5] [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: 04/10/2018] [Revised: 01/13/2019] [Accepted: 02/13/2019] [Indexed: 11/27/2022] Open
Abstract
Site-specific modification of synthetic and cellular RNA such as with specific nucleobases, fluorophores and attachment chemistries is important for a variety of basic and applied research applications. However, simple and efficient methods to modify RNA such as at the 3' terminus with specific nucleobases or nucleotide analogs conjugated to various chemical moieties are lacking. Here, we develop and characterize a one-step enzymatic method to modify RNA 3' termini using recombinant human polymerase theta (Polθ). We demonstrate that Polθ efficiently adds 30-50 2'-deoxyribonucleotides to the 3' terminus of RNA molecules of various lengths and sequences, and extends RNA 3' termini with an assortment of 2'-deoxy and 2',3'-dideoxy ribonucleotide analogs containing functional chemistries, such as high affinity attachment moieties and fluorophores. In contrast to Polθ, terminal deoxynucleotidyl transferase (TdT) is unable to use RNA as a substrate altogether. Overall, Polθ shows a strong preference for adding deoxyribonucleotides to RNA, but can also add ribonucleotides with relatively high efficiency in particular sequence contexts. We anticipate that this unique activity of Polθ will become invaluable for applications requiring 3' terminal modification of RNA and potentially enzymatic synthesis of RNA.
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Affiliation(s)
- Crystal Thomas
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Timur Rusanov
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Trung Hoang
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Taurai Augustin
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Tatiana Kent
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Imre Gaspar
- European Molecular Biology Laboratory, Heidelberg, Meyerhofstrasse 1, 69117, Germany
| | - Richard T Pomerantz
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
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35
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Liu Y, Wang M, Liu X, Quan J, Fang Y, Liu Y, Qiu Y, Yu Y, Zhou X. Drosophila Trf4-1 involves in mRNA and primary miRNA transcription. Biochem Biophys Res Commun 2019; 511:806-812. [PMID: 30837153 DOI: 10.1016/j.bbrc.2019.02.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 02/23/2019] [Indexed: 11/16/2022]
Abstract
Drosophila Trf4-1 (DmTrf4-1) is a polyadenylation polymerase or terminal nucleotidyl transferase (PAP/TENT) that has been reported to add poly(A) tails to snRNAs in nucleus or mRNAs in cytoplasm. Here, we found that the loss of Trf4-1 resulted in the reduction of mRNAs and primary miRNAs (pri-miRNAs) in both Drosophila S2 cells and adult flies. Interestingly, the role of Trf4-1 in transcription is independent of its PAP/TENT activity. Moreover, using the chromatin immunoprecipitation assay, we uncovered that the loss of Trf4-1 led to abnormal RNA polymerase II accumulation and reduced H3K4me3 binding in promoter regions. Thus, our study indicates a positive role of Trf4-1 in the transcription of mRNAs and pri-miRNAs.
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Affiliation(s)
- Yongxiang Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China; Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Ming Wang
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Jia Quan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China; Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Yuan Fang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China; Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Yujie Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Yang Qiu
- Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Yang Yu
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China; Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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36
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Analysis of 3' End Modifications in microRNAs by High-Throughput Sequencing. Methods Mol Biol 2019; 1823:115-139. [PMID: 29959678 DOI: 10.1007/978-1-4939-8624-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
MicroRNAs are ~22 nt small, non-coding RNAs that direct posttranscriptional silencing of gene expression to regulate animal development, physiology, and disease. An emerging mechanism that controls the biogenesis of microRNAs is the addition of non-templated nucleotides, predominantly uridine, to the 3' end of precursor-microRNAs, in a process that is commonly referred to as tailing. Here, we describe methods that enable the systematic characterization of tailing events in mature microRNAs and their precursors. We report protocols for untargeted and targeted cDNA library preparation procedures, as exemplified in the context of the model organism Drosophila melanogaster and focusing on precursor-microRNAs. We also refer to a dedicated computational framework for the subsequent analysis of untemplated nucleotide additions in cDNA libraries. The described methods for the systematic characterization of posttranscriptional modifications in gene regulatory small RNAs and their precursors will be instrumental in clarifying regulatory concepts that control posttranscriptional gene silencing.
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37
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Yashiro Y, Tomita K. Function and Regulation of Human Terminal Uridylyltransferases. Front Genet 2018; 9:538. [PMID: 30483311 PMCID: PMC6240794 DOI: 10.3389/fgene.2018.00538] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/24/2018] [Indexed: 11/21/2022] Open
Abstract
RNA uridylylation plays a pivotal role in the biogenesis and metabolism of functional RNAs, and regulates cellular gene expression. RNA uridylylation is catalyzed by a subset of proteins from the non-canonical terminal nucleotidyltransferase family. In human, three proteins (TUT1, TUT4, and TUT7) have been shown to exhibit template-independent uridylylation activity at 3′-end of specific RNAs. TUT1 catalyzes oligo-uridylylation of U6 small nuclear (sn) RNA, which catalyzes mRNA splicing. Oligo-uridylylation of U6 snRNA is required for U6 snRNA maturation, U4/U6-di-snRNP formation, and U6 snRNA recycling during mRNA splicing. TUT4 and TUT7 catalyze mono- or oligo-uridylylation of precursor let-7 (pre–let-7). Let-7 RNA is broadly expressed in somatic cells and regulates cellular proliferation and differentiation. Mono-uridylylation of pre–let-7 by TUT4/7 promotes subsequent Dicer processing to up-regulate let-7 biogenesis. Oligo-uridylylation of pre–let-7 by TUT4/7 is dependent on an RNA-binding protein, Lin28. Oligo-uridylylated pre–let-7 is less responsive to processing by Dicer and degraded by an exonuclease DIS3L2. As a result, let-7 expression is repressed. Uridylylation of pre–let-7 depends on the context of the 3′-region of pre–let-7 and cell type. In this review, we focus on the 3′ uridylylation of U6 snRNA and pre-let-7, and describe the current understanding of mechanism of activity and regulation of human TUT1 and TUT4/7, based on their crystal structures that have been recently solved.
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Affiliation(s)
- Yuka Yashiro
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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38
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Zigáčková D, Vaňáčová Š. The role of 3' end uridylation in RNA metabolism and cellular physiology. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0171. [PMID: 30397107 DOI: 10.1098/rstb.2018.0171] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2018] [Indexed: 12/14/2022] Open
Abstract
Most eukaryotic RNAs are posttranscriptionally modified. The majority of modifications promote RNA maturation, others may regulate function and stability. The 3' terminal non-templated oligouridylation is a widespread modification affecting many cellular RNAs at some stage of their life cycle. It has diverse roles in RNA metabolism. The most prevalent is the regulation of stability and quality control. On the cellular and organismal level, it plays a critical role in a number of pathways, such as cell cycle regulation, cell death, development or viral infection. Defects in uridylation have been linked to several diseases. This review summarizes the current knowledge about the role of the 3' terminal oligo(U)-tailing in biology of various RNAs in eukaryotes and describes key factors involved in these pathways.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Dagmar Zigáčková
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5/A35, Brno 625 00, Czech Republic
| | - Štěpánka Vaňáčová
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5/A35, Brno 625 00, Czech Republic
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39
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Warkocki Z, Liudkovska V, Gewartowska O, Mroczek S, Dziembowski A. Terminal nucleotidyl transferases (TENTs) in mammalian RNA metabolism. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0162. [PMID: 30397099 PMCID: PMC6232586 DOI: 10.1098/rstb.2018.0162] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2018] [Indexed: 12/15/2022] Open
Abstract
In eukaryotes, almost all RNA species are processed at their 3′ ends and most mRNAs are polyadenylated in the nucleus by canonical poly(A) polymerases. In recent years, several terminal nucleotidyl transferases (TENTs) including non-canonical poly(A) polymerases (ncPAPs) and terminal uridyl transferases (TUTases) have been discovered. In contrast to canonical polymerases, TENTs' functions are more diverse; some, especially TUTases, induce RNA decay while others, such as cytoplasmic ncPAPs, activate translationally dormant deadenylated mRNAs. The mammalian genome encodes 11 different TENTs. This review summarizes the current knowledge about the functions and mechanisms of action of these enzymes. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
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Affiliation(s)
- Zbigniew Warkocki
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, Poland
| | - Vladyslava Liudkovska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Olga Gewartowska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland .,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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40
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de Almeida C, Scheer H, Gobert A, Fileccia V, Martinelli F, Zuber H, Gagliardi D. RNA uridylation and decay in plants. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0163. [PMID: 30397100 DOI: 10.1098/rstb.2018.0163] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2018] [Indexed: 12/13/2022] Open
Abstract
RNA uridylation consists of the untemplated addition of uridines at the 3' extremity of an RNA molecule. RNA uridylation is catalysed by terminal uridylyltransferases (TUTases), which form a subgroup of the terminal nucleotidyltransferase family, to which poly(A) polymerases also belong. The key role of RNA uridylation is to regulate RNA degradation in a variety of eukaryotes, including fission yeast, plants and animals. In plants, RNA uridylation has been mostly studied in two model species, the green algae Chlamydomonas reinhardtii and the flowering plant Arabidopsis thaliana Plant TUTases target a variety of RNA substrates, differing in size and function. These RNA substrates include microRNAs (miRNAs), small interfering silencing RNAs (siRNAs), ribosomal RNAs (rRNAs), messenger RNAs (mRNAs) and mRNA fragments generated during post-transcriptional gene silencing. Viral RNAs can also get uridylated during plant infection. We describe here the evolutionary history of plant TUTases and we summarize the diverse molecular functions of uridylation during RNA degradation processes in plants. We also outline key points of future research.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Caroline de Almeida
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Hélène Scheer
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Anthony Gobert
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Veronica Fileccia
- Dipartimento di Scienze Agrarie Alimentari Forestali, Università degli Studi di Palermo, viale delle scienze ed. 4, Palermo 90128, Italy
| | - Federico Martinelli
- Dipartimento di Scienze Agrarie Alimentari Forestali, Università degli Studi di Palermo, viale delle scienze ed. 4, Palermo 90128, Italy
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
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41
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Fuchs Wightman F, Giono LE, Fededa JP, de la Mata M. Target RNAs Strike Back on MicroRNAs. Front Genet 2018; 9:435. [PMID: 30333855 PMCID: PMC6175985 DOI: 10.3389/fgene.2018.00435] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/13/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are extensively studied regulatory non-coding small RNAs that silence animal genes throughout most biological processes, typically doing so by binding to partially complementary sequences within target RNAs. A plethora of studies has described detailed mechanisms for microRNA biogenesis and function, as well as their temporal and spatial regulation during development. By inducing translational repression and/or degradation of their target RNAs, microRNAs can contribute to achieve highly specific cell- or tissue-specific gene expression, while their aberrant expression can lead to disease. Yet an unresolved aspect of microRNA biology is how such small RNA molecules are themselves cleared from the cell, especially under circumstances where fast microRNA turnover or specific degradation of individual microRNAs is required. In recent years, it was unexpectedly found that binding of specific target RNAs to microRNAs with extensive complementarity can reverse the outcome, triggering degradation of the bound microRNAs. This emerging pathway, named TDMD for Target RNA-Directed MicroRNA Degradation, leads to microRNA 3'-end tailing by the addition of A/U non-templated nucleotides, trimming or shortening from the 3' end, and highly specific microRNA loss, providing a new layer of microRNA regulation. Originally described in flies and known to be triggered by viral RNAs, novel endogenous instances of TDMD have been uncovered and are now starting to be understood. Here, we review our current knowledge of this pathway and its potential role in the control and diversification of microRNA expression patterns.
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Affiliation(s)
- Federico Fuchs Wightman
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Luciana E Giono
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Juan Pablo Fededa
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Manuel de la Mata
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
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42
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Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway. Methods 2018; 152:23-30. [PMID: 30138674 DOI: 10.1016/j.ymeth.2018.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/02/2018] [Accepted: 08/14/2018] [Indexed: 02/07/2023] Open
Abstract
Over the past decade, modifications to microRNAs (miRNAs) via 3' end nucleotide addition have gone from a deep-sequencing curiosity to experimentally confirmed drivers of a range of regulatory activities. Here we overview the methods that have been deployed by researchers seeking to untangle these diverse functional roles and include characterizing not only the nucleotidyl transferases catalyzing the additions but also the nucleotides being added, and the timing of their addition during the miRNA pathway. These methods and their further development are key to clarifying the diverse and sometimes contradictory functional findings presently attributed to these nucleotide additions.
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43
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Calderon BM, Conn GL. A human cellular noncoding RNA activates the antiviral protein 2'-5'-oligoadenylate synthetase 1. J Biol Chem 2018; 293:16115-16124. [PMID: 30126839 DOI: 10.1074/jbc.ra118.004747] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/10/2018] [Indexed: 12/16/2022] Open
Abstract
The 2'-5'-oligoadenylate synthetase (OAS) family of enzymes sense cytosolic dsRNA, a potent signal of viral infection. In response to dsRNA binding, OAS proteins synthesize the second messenger 2'-5'-linked oligoadenylate that activates the latent ribonuclease L (RNase L). RNase L-mediated degradation of viral and cellular RNAs effectively halts viral replication and further stimulates innate immune responses by inducing type I interferon. The OAS/RNase L pathway is therefore central in innate immune recognition and promotion of antiviral host responses. However, the potential for specific RNA sequences or structures to drive OAS1 activation and the molecular mechanisms by which they act are not currently fully understood. Moreover, the cellular regulators of OAS activity are not well defined. Here, we demonstrate that the human cellular noncoding RNA 886 (nc886) activates OAS1 both in vitro and in human A549 cells. We show that a unique structure present only in one of the two structural conformers adopted by nc886 drives potent OAS1 activation. In contrast, the conformer lacking this unique structure activated OAS1 only very weakly. We also found that formation of this OAS1-activating structural motif depends on the nucleotides in the apical-most loop of nc886 and the adjacent helix. These findings identify a cellular RNA capable of activating the OAS/RNase L pathway in human cells and illustrate the importance of structural elements, and their context, in potentiating OAS1 activity.
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Affiliation(s)
- Brenda M Calderon
- From the Department of Biochemistry and.,Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Emory University School of Medicine, Atlanta, Georgia 30322
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44
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A tRNA's fate is decided at its 3' end: Collaborative actions of CCA-adding enzyme and RNases involved in tRNA processing and degradation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:433-441. [PMID: 29374586 DOI: 10.1016/j.bbagrm.2018.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 02/07/2023]
Abstract
tRNAs are key players in translation and are additionally involved in a wide range of distinct cellular processes. The vital importance of tRNAs becomes evident in numerous diseases that are linked to defective tRNA molecules. It is therefore not surprising that the structural intactness of tRNAs is continuously scrutinized and defective tRNAs are eliminated. In this process, erroneous tRNAs are tagged with single-stranded RNA sequences that are recognized by degrading exonucleases. Recent discoveries have revealed that the CCA-adding enzyme - actually responsible for the de novo synthesis of the 3'-CCA end - plays an indispensable role in tRNA quality control by incorporating a second CCA triplet that is recognized as a degradation tag. In this review, we give an update on the latest findings regarding tRNA quality control that turns out to represent an interplay of the CCA-adding enzyme and RNases involved in tRNA degradation and maturation. In particular, the RNase-induced turnover of the CCA end is now recognized as a trigger for the CCA-adding enzyme to repeatedly scrutinize the structural intactness of a tRNA. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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45
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Yang C, Liu F, Chen S, Wang M, Jia R, Zhu D, Liu M, Sun K, Yang Q, Wu Y, Chen X, Cheng A. Identification of 2'-5'-Oligoadenylate Synthetase-Like Gene in Goose: Gene Structure, Expression Patterns, and Antiviral Activity Against Newcastle Disease Virus. J Interferon Cytokine Res 2018; 36:563-72. [PMID: 27576097 DOI: 10.1089/jir.2015.0167] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
2'-5'-oligoadenylate synthetase-like (OASL) is a kind of antiviral protein induced by interferons (IFNs), which plays an important role in the IFNs-mediated antiviral signaling pathway. In this study, we cloned and identified OASL in the Chinese goose for the first time. Goose 2'-5'-oligoadenylate synthetase-like (goOASL), including an ORF of 1527bp, encoding a protein of 508 amino acids. GoOASL protein contains 3 conserved motifs: nucleotidyltransferase (NTase) domain, 2'-5'-oligoadenylate synthetase (OAS) domain, and 2 ubiquitin-like (UBL) repeats. The tissue distribution profile of goOASL in 2-week-old gosling and adult goose were identified by Real-Time quantitative PCR, which revealed that the highest level of goOASL mRNA transcription was detected in the blood of adult goose and gosling. The mRNA transcription level of goOASL was upregulated in all tested tissues of duck Tembusu virus (DTMUV)-infected 3-day-old goslings, compared with control groups. Furthermore, using the stimulus Poly(I: C), ODN2006, R848, and lipopolysaccharide (LPS) as well as the viral pathogens DTMUV, H9N2 avian influenza virus (AIV), and gosling plague virus (GPV) to treat goose peripheral blood mononuclear cells (PBMCs) for 6 h, goOASL transcripts level was significantly upregulated in all treated groups. To further investigate the antiviral activity of goOASL, pcDNA3.1(+)-goOASL-His plasmid was constructed, and goOASL was expressed by the goose embryo fibroblast cells (GEFs) transfected with pcDNA3.1(+)-goOASL-His. Our research data suggested that Newcastle disease virus (NDV) replication (viral copies and viral titer) in GEFs was significantly reduced by the overexpression of goOASL protein. These data were meaningful for the antiviral immunity research of goose and shed light on the future prevention of NDV in fowl.
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Affiliation(s)
- Chao Yang
- 1 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
| | - Fei Liu
- 2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University , Chengdu, China
| | - Shun Chen
- 1 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University , Chengdu, China .,2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University , Chengdu, China .,3 Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
| | - Mingshu Wang
- 1 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University , Chengdu, China .,2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University , Chengdu, China .,3 Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
| | - Renyong Jia
- 1 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University , Chengdu, China .,2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University , Chengdu, China .,3 Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
| | - Dekang Zhu
- 2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University , Chengdu, China .,3 Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
| | - Mafeng Liu
- 1 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
| | - Kunfeng Sun
- 1 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University , Chengdu, China .,2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University , Chengdu, China .,3 Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
| | - Qiao Yang
- 1 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University , Chengdu, China .,2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University , Chengdu, China .,3 Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
| | - Ying Wu
- 1 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University , Chengdu, China .,2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University , Chengdu, China .,3 Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
| | - Xiaoyue Chen
- 2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University , Chengdu, China .,3 Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
| | - Anchun Cheng
- 1 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University , Chengdu, China .,2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University , Chengdu, China .,3 Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University , Chengdu, China
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Yu Y, Jia T, Chen X. The 'how' and 'where' of plant microRNAs. THE NEW PHYTOLOGIST 2017; 216:1002-1017. [PMID: 29048752 PMCID: PMC6040672 DOI: 10.1111/nph.14834] [Citation(s) in RCA: 253] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/21/2017] [Indexed: 05/18/2023]
Abstract
Contents 1002 I. 1002 II. 1007 III. 1010 IV. 1013 1013 References 1013 SUMMARY: MicroRNAs (miRNAs) are small non-coding RNAs, of typically 20-24 nt, that regulate gene expression post-transcriptionally through sequence complementarity. Since the identification of the first miRNA, lin-4, in the nematode Caenorhabditis elegans in 1993, thousands of miRNAs have been discovered in animals and plants, and their regulatory roles in numerous biological processes have been uncovered. In plants, research efforts have established the major molecular framework of miRNA biogenesis and modes of action, and are beginning to elucidate the mechanisms of miRNA degradation. Studies have implicated restricted and surprising subcellular locations in which miRNA biogenesis or activity takes place. In this article, we summarize the current knowledge on how plant miRNAs are made and degraded, and how they repress target gene expression. We discuss not only the players involved in these processes, but also the subcellular sites in which these processes are known or implicated to take place. We hope to raise awareness that the cell biology of miRNAs holds the key to a full understanding of these enigmatic molecules.
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Affiliation(s)
- Yu Yu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Tianran Jia
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA
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47
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Kobyłecki K, Kuchta K, Dziembowski A, Ginalski K, Tomecki R. Biochemical and structural bioinformatics studies of fungal CutA nucleotidyltransferases explain their unusual specificity toward CTP and increased tendency for cytidine incorporation at the 3'-terminal positions of synthesized tails. RNA (NEW YORK, N.Y.) 2017; 23:1902-1926. [PMID: 28947555 PMCID: PMC5689010 DOI: 10.1261/rna.061010.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 09/12/2017] [Indexed: 05/25/2023]
Abstract
Noncanonical RNA nucleotidyltransferases (NTases), including poly(A), poly(U) polymerases (PAPs/PUPs), and C/U-adding enzymes, modify 3'-ends of different transcripts affecting their functionality and stability. They contain PAP/OAS1 substrate-binding domain (SBD) with inserted NTase domain. Aspergillus nidulans CutA (AnCutA), synthesizes C/U-rich 3'-terminal extensions in vivo. Here, using high-throughput sequencing of the 3'-RACE products for tails generated by CutA proteins in vitro in the presence of all four NTPs, we show that even upon physiological ATP excess synthesized tails indeed contain an unprecedented number of cytidines interrupted by uridines and stretches of adenosines, and that the majority end with two cytidines. Strikingly, processivity assays documented that in the presence of CTP as a sole nucleotide, the enzyme terminates after adding two cytidines only. Comparison of our CutA 3D model to selected noncanonical NTases of known structures revealed substantial differences in the nucleotide recognition motif (NRM) within PAP/OAS1 SBD. We demonstrate that CutA specificity toward CTP can be partially changed to PAP or PUP by rational mutagenesis within NRM and, analogously, Cid1 PUP can be converted into a C/U-adding enzyme. Collectively, we suggest that a short cluster of amino acids within NRM is a determinant of NTases' substrate preference, which may allow us to predict their specificity.
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Affiliation(s)
- Kamil Kobyłecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Krzysztof Kuchta
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
| | - Rafał Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
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48
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Lima CR, Gomes CC, Santos MF. Role of microRNAs in endocrine cancer metastasis. Mol Cell Endocrinol 2017; 456:62-75. [PMID: 28322989 DOI: 10.1016/j.mce.2017.03.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/12/2017] [Accepted: 03/13/2017] [Indexed: 12/20/2022]
Abstract
The deregulation of transcription and processing of microRNAs (miRNAs), as well as their function, has been involved in the pathogenesis of several human diseases, including cancer. Despite advances in therapeutic approaches, cancer still represents one of the major health problems worldwide. Cancer metastasis is an aggravating factor in tumor progression, related to increased treatment complexity and a worse prognosis. After more than one decade of extensive studies of miRNAs, the fundamental role of these molecules in cancer progression and metastasis is beginning to be elucidated. Recent evidences have demonstrated a significant role of miRNAs on the metastatic cascade, acting either as pro-metastatic or anti-metastatic. They are involved in distinct steps of metastasis including epithelial-to-mesenchymal transition, migration/invasion, anoikis survival, and distant organ colonization. Studies on the roles of miRNAs in cancer have focused mainly on two fronts: the establishment of a miRNA signature for different tumors, which may aid in early diagnosis using these miRNAs as markers, and functional studies of specific miRNAs, determining their targets, function and regulation. Functional miRNA studies on endocrine cancers are still scarce and represent an important area of research, since some tumors, although not frequent, present a high mortality rate. Among the endocrine tumors, thyroid cancer is the most common and best studied. Several miRNAs show lowered expression in endocrine cancers (i.e. miR-200s, miR-126, miR-7, miR-29a, miR-30a, miR-137, miR-206, miR-101, miR-613, miR-539, miR-205, miR-9, miR-195), while others are commonly overexpressed (i.e. miR-21, miR-183, miR-31, miR-let7b, miR-584, miR-146b, miR-221, miR-222, miR-25, miR-595). Additionally, some miRNAs were found in serum exosomes (miR-151, miR-145, miR-31), potentially serving as diagnostic tools. In this review, we summarize studies concerning the discovery and functions of miRNAs and their regulatory roles in endocrine cancer metastasis, which may contribute for the finding of novel therapeutic targets. The review focus on miRNAs with at least some identified targets, with established functions and, if possible, upstream regulation.
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Affiliation(s)
- Cilene Rebouças Lima
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1524, Prédio I, CEP 05508-000, São Paulo, SP, Brazil.
| | - Cibele Crastequini Gomes
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1524, Prédio I, CEP 05508-000, São Paulo, SP, Brazil.
| | - Marinilce Fagundes Santos
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1524, Prédio I, CEP 05508-000, São Paulo, SP, Brazil.
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49
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Shin J, Paek KY, Ivshina M, Stackpole EE, Richter JD. Essential role for non-canonical poly(A) polymerase GLD4 in cytoplasmic polyadenylation and carbohydrate metabolism. Nucleic Acids Res 2017; 45:6793-6804. [PMID: 28383716 PMCID: PMC5499868 DOI: 10.1093/nar/gkx239] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/30/2017] [Indexed: 11/16/2022] Open
Abstract
Regulation of gene expression at the level of cytoplasmic polyadenylation is important for many biological phenomena including cell cycle progression, mitochondrial respiration, and learning and memory. GLD4 is one of the non-canonical poly(A) polymerases that regulates cytoplasmic polyadenylation-induced translation, but its target mRNAs and role in cellular physiology is not well known. To assess the full panoply of mRNAs whose polyadenylation is controlled by GLD4, we performed an unbiased whole genome-wide screen using poy(U) chromatography and thermal elution. We identified hundreds of mRNAs regulated by GLD4, several of which are involved in carbohydrate metabolism including GLUT1, a major glucose transporter. Depletion of GLD4 not only reduced GLUT1 poly(A) tail length, but also GLUT1 protein. GLD4-mediated translational control of GLUT1 mRNA is dependent of an RNA binding protein, CPEB1, and its binding elements in the 3΄ UTR. Through regulating GLUT1 level, GLD4 affects glucose uptake into cells and lactate levels. Moreover, GLD4 depletion impairs glucose deprivation-induced GLUT1 up-regulation. In addition, we found that GLD4 affects glucose-dependent cellular phenotypes such as migration and invasion in glioblastoma cells. Our observations delineate a novel post-transcriptional regulatory network involving carbohydrate metabolism and glucose homeostasis mediated by GLD4.
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Affiliation(s)
- Jihae Shin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ki Young Paek
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Maria Ivshina
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Emily E Stackpole
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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50
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De Almeida C, Scheer H, Zuber H, Gagliardi D. RNA uridylation: a key posttranscriptional modification shaping the coding and noncoding transcriptome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [PMID: 28984054 DOI: 10.1002/wrna.1440] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 12/27/2022]
Abstract
RNA uridylation is a potent and widespread posttranscriptional regulator of gene expression. RNA uridylation has been detected in a range of eukaryotes including trypanosomes, animals, plants, and fungi, but with the noticeable exception of budding yeast. Virtually all classes of eukaryotic RNAs can be uridylated and uridylation can also tag viral RNAs. The untemplated addition of a few uridines at the 3' end of a transcript can have a decisive impact on RNA's fate. In rare instances, uridylation is an intrinsic step in the maturation of noncoding RNAs like for the U6 spliceosomal RNA or mitochondrial guide RNAs in trypanosomes. Uridylation can also switch specific miRNA precursors from a degradative to a processing mode. This switch depends on the number of uridines added which is regulated by the cellular context. Yet, the typical consequence of uridylation on mature noncoding RNAs or their precursors is to accelerate decay. Importantly, mRNAs are also tagged by uridylation. In fact, the advent of novel high throughput sequencing protocols has recently revealed the pervasiveness of mRNA uridylation, from plants to humans. As for noncoding RNAs, the main function to date for mRNA uridylation is to promote degradation. Yet, additional roles begin to be ascribed to U-tailing such as the control of mRNA deadenylation, translation control and possibly storage. All these new findings illustrate that we are just beginning to appreciate the diversity of roles played by RNA uridylation and its full temporal and spatial implication in regulating gene expression. WIREs RNA 2018, 9:e1440. doi: 10.1002/wrna.1440 This article is categorized under: RNA Processing > 3' End Processing RNA Processing > RNA Editing and Modification RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Caroline De Almeida
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
| | - Hélène Scheer
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University of Strasbourg, Strasbourg, France
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