1
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Weiss A, Gilbert JW, Flores IVR, Belgrad J, Ferguson C, Dogan EO, Wightman N, Mocarski K, Echeverria D, Summers A, Bramato B, McHugh N, Furgal R, Yamada N, Cooper D, Monopoli K, Godinho BM, Hassler MR, Yamada K, Greer P, Henninger N, Brown RH, Khvorova A. RNAi-mediated silencing of SOD1 profoundly extends survival and functional outcomes in ALS mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599943. [PMID: 38979291 PMCID: PMC11230209 DOI: 10.1101/2024.06.20.599943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative condition, with 20% of familial and 2-3% of sporadic cases linked to mutations in the cytosolic superoxide dismutase (SOD1) gene. Mutant SOD1 protein is toxic to motor neurons, making SOD1 gene lowering a promising approach, supported by preclinical data and the 2023 FDA approval of the GapmeR ASO targeting SOD1, tofersen. Despite the approval of an ASO and the optimism it brings to the field, the pharmacodynamics and pharmacokinetics of therapeutic SOD1 modulation can be improved. Here, we developed a chemically stabilized divalent siRNA scaffold (di-siRNA) that effectively suppresses SOD1 expression in vitro and in vivo. With optimized chemical modification, it achieves remarkable CNS tissue permeation and SOD1 silencing in vivo. Administered intraventricularly, di-siRNASOD1 extended survival in SOD1-G93A ALS mice, surpassing survival previously seen in these mice by ASO modalities, slowed disease progression, and prevented ALS neuropathology. These properties offer an improved therapeutic strategy for SOD1-mediated ALS and may extend to other dominantly inherited neurological disorders.
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Affiliation(s)
- Alexandra Weiss
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
| | - James W. Gilbert
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | | | - Jillian Belgrad
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Chantal Ferguson
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Elif O. Dogan
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
| | - Nicholas Wightman
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
| | - Kit Mocarski
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School; Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Ashley Summers
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Brianna Bramato
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Raymond Furgal
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Nozomi Yamada
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - David Cooper
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Kathryn Monopoli
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | | | - Matthew R. Hassler
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Ken Yamada
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Paul Greer
- Program in Molecular Medicine, UMass Chan Medical School; Worcester, MA, USA
| | - Nils Henninger
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
- Department of Psychiatry, UMass Chan Medical School; Worcester, MA, USA
| | - Robert H. Brown
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School; Worcester, MA, USA
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2
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Unti MJ, Jaffrey SR. Highly efficient cellular expression of circular mRNA enables prolonged protein expression. Cell Chem Biol 2024; 31:163-176.e5. [PMID: 37883972 PMCID: PMC10841545 DOI: 10.1016/j.chembiol.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/25/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023]
Abstract
A major problem with mRNA therapeutics is that mRNA is usually degraded within a few hours after entering the cytosol. New approaches for in vitro synthesis of circular mRNA have allowed increased levels and duration of protein synthesis from mRNA therapeutics due to the long half-life of circular mRNA. However, it remains difficult to genetically encode circular mRNAs in mammalian cells. Here, we describe the adaptation of the Tornado (Twister-optimized RNA for durable overexpression) system to achieve in-cell synthesis of circular mRNAs. We screen different promoters and internal ribosomal entry sites (IRESs) and identify combinations that result in high levels of circular mRNA and protein expression. We show that these circular mRNAs can be packaged into virus-like particles (VLPs), thus enabling prolonged protein expression. Overall, these data describe a platform for synthesis of circular mRNAs and how these circular mRNAs can improve VLP therapeutics.
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Affiliation(s)
- Mildred J Unti
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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3
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Vu TV, Nguyen NT, Kim J, Hong JC, Kim J. Prime editing: Mechanism insight and recent applications in plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:19-36. [PMID: 37794706 PMCID: PMC10754014 DOI: 10.1111/pbi.14188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Prime editing (PE) technology utilizes an extended prime editing guide RNA (pegRNA) to direct a fusion peptide consisting of nCas9 (H840) and reverse transcriptase (RT) to a specific location in the genome. This enables the installation of base changes at the targeted site using the extended portion of the pegRNA through RT activity. The resulting product of the RT reaction forms a 3' flap, which can be incorporated into the genomic site through a series of biochemical steps involving DNA repair and synthesis pathways. PE has demonstrated its effectiveness in achieving almost all forms of precise gene editing, such as base conversions (all types), DNA sequence insertions and deletions, chromosomal translocation and inversion and long DNA sequence insertion at safe harbour sites within the genome. In plant science, PE could serve as a groundbreaking tool for precise gene editing, allowing the creation of desired alleles to improve crop varieties. Nevertheless, its application has encountered limitations due to efficiency constraints, particularly in dicotyledonous plants. In this review, we discuss the step-by-step mechanism of PE, shedding light on the critical aspects of each step while suggesting possible solutions to enhance its efficiency. Additionally, we present an overview of recent advancements and future perspectives in PE research specifically focused on plants, examining the key technical considerations of its applications.
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Affiliation(s)
- Tien V. Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Ngan Thi Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuKorea
- Division of Life ScienceGyeongsang National UniversityJinjuKorea
- Nulla Bio Inc.JinjuKorea
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4
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Unti MJ, Jaffrey SR. Highly efficient cellular expression of circular mRNA enables prolonged protein expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548538. [PMID: 37503010 PMCID: PMC10369907 DOI: 10.1101/2023.07.11.548538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
A major problem with mRNA therapeutics is the limited duration of protein expression due to the short half-life of mRNA. New approaches for generating highly stable circular mRNA in vitro have allowed increased duration of protein expression. However, it remains difficult to genetically encode circular mRNAs in mammalian cells, which limits the use of circular mRNA in cell-derived therapeutics. Here we describe the adaptation of the Tornado (Twister-optimized RNA for durable overexpression) system to achieve in-cell synthesis of circular mRNAs. We identify the promoter and internal ribosomal entry site (IRES) that result in high levels of protein expression in cells. We then show that these circular mRNAs can be packaged into virus-like particles (VLPs) thus enabling prolonged protein expression. Overall, these data describe a platform for synthesis of circular mRNAs and how these circular mRNAs can markedly enhance the ability of VLPs to function as a mRNA delivery tool.
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5
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Khojasteh SC, Argikar UA, Cho S, Crouch R, Heck CJS, Johnson KM, Kalgutkar AS, King L, Maw HH, Seneviratne HK, Wang S, Wei C, Zhang D, Jackson KD. Biotransformation Novel Advances - 2021 year in review. Drug Metab Rev 2022; 54:207-245. [PMID: 35815654 DOI: 10.1080/03602532.2022.2097253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Biotransformation field is constantly evolving with new molecular structures and discoveries of metabolic pathways that impact efficacy and safety. Recent review by Kramlinger et al (2022) nicely captures the future (and the past) of highly impactful science of biotransformation (see the first article). Based on the selected articles, this review was categorized into three sections: (1) new modalities biotransformation, (2) drug discovery biotransformation, and (3) drug development biotransformation (Table 1).
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Affiliation(s)
- S Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, MS412a, South San Francisco, CA, 94080, USA
| | - Upendra A Argikar
- Non-clinical Development, Bill & Melinda Gates Medical Research Institute, Cambridge, MA 02139, USA
| | - Sungjoon Cho
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, MS412a, South San Francisco, CA, 94080, USA
| | - Rachel Crouch
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, Nashville, TN, 37203, USA
| | - Carley J S Heck
- Medicine Design, Pfizer Worldwide Research, Development and Medical, Eastern Point Road, Groton, Connecticut, USA
| | - Kevin M Johnson
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, MS412a, South San Francisco, CA, 94080, USA
| | - Amit S Kalgutkar
- Medicine Design, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - Lloyd King
- Quantitative Drug Discovery, UCB Biopharma UK, 216 Bath Road, Slough, SL1 3WE, UK
| | - Hlaing Holly Maw
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, 06877, USA
| | - Herana Kamal Seneviratne
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shuai Wang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, MS412a, South San Francisco, CA, 94080, USA
| | - Cong Wei
- Drug Metabolism & Pharmacokinetics, Biogen Inc., Cambridge, MA, 02142, USA
| | - Donglu Zhang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, MS412a, South San Francisco, CA, 94080, USA
| | - Klarissa D Jackson
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
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6
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Nelson JW, Randolph PB, Shen SP, Everette KA, Chen PJ, Anzalone AV, An M, Newby GA, Chen JC, Hsu A, Liu DR. Engineered pegRNAs improve prime editing efficiency. Nat Biotechnol 2022; 40:402-410. [PMID: 34608327 PMCID: PMC8930418 DOI: 10.1038/s41587-021-01039-7] [Citation(s) in RCA: 283] [Impact Index Per Article: 141.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023]
Abstract
Prime editing enables the installation of virtually any combination of point mutations, small insertions or small deletions in the DNA of living cells. A prime editing guide RNA (pegRNA) directs the prime editor protein to the targeted locus and also encodes the desired edit. Here we show that degradation of the 3' region of the pegRNA that contains the reverse transcriptase template and the primer binding site can poison the activity of prime editing systems, impeding editing efficiency. We incorporated structured RNA motifs to the 3' terminus of pegRNAs that enhance their stability and prevent degradation of the 3' extension. The resulting engineered pegRNAs (epegRNAs) improve prime editing efficiency 3-4-fold in HeLa, U2OS and K562 cells and in primary human fibroblasts without increasing off-target editing activity. We optimized the choice of 3' structural motif and developed pegLIT, a computational tool to identify non-interfering nucleotide linkers between pegRNAs and 3' motifs. Finally, we showed that epegRNAs enhance the efficiency of the installation or correction of disease-relevant mutations.
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Affiliation(s)
- James W Nelson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Peyton B Randolph
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Simon P Shen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Kelcee A Everette
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Peter J Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Andrew V Anzalone
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Meirui An
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan C Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Alvin Hsu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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7
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Hsu TY, Hsu LN, Chen SY, Juang BT. MUT-7 Provides Molecular Insight into the Werner Syndrome Exonuclease. Cells 2021; 10:cells10123457. [PMID: 34943966 PMCID: PMC8700014 DOI: 10.3390/cells10123457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/01/2021] [Accepted: 12/05/2021] [Indexed: 11/24/2022] Open
Abstract
Werner syndrome (WS) is a rare recessive genetic disease characterized by premature aging. Individuals with this disorder develop normally during childhood, but their physiological conditions exacerbate the aging process in late adolescence. WS is caused by mutation of the human WS gene (WRN), which encodes two main domains, a 3′-5′ exonuclease and a 3′-5′ helicase. Caenorhabditis elegans expresses human WRN orthologs as two different proteins: MUT-7, which has a 3′-5′ exonuclease domain, and C. elegans WRN-1 (CeWRN-1), which has only helicase domains. These unique proteins dynamically regulate olfactory memory in C. elegans, providing insight into the molecular roles of WRN domains in humans. In this review, we specifically focus on characterizing the function of MUT-7 in small interfering RNA (siRNA) synthesis in the cytoplasm and the roles of siRNA in directing nuclear CeWRN-1 loading onto a heterochromatin complex to induce negative feedback regulation. Further studies on the different contributions of the 3′-5′ exonuclease and helicase domains in the molecular mechanism will provide clues to the accelerated aging processes in WS.
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Affiliation(s)
- Tsung-Yuan Hsu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan;
- Department of Cell and Tissue Biology, University of California, 513 Parnassus, San Francisco, CA 94143, USA
| | - Ling-Nung Hsu
- Occupational Safety and Health Office, Fu Jen Catholic University Hospital, New Taipei City 243, Taiwan;
| | - Shih-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan;
| | - Bi-Tzen Juang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan;
- Center for Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Chiao Tung University, Hsinchu 300, Taiwan
- Correspondence:
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8
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Ngwe Tun MM, Morita K, Ishikawa T, Urata S. The Antiviral Effect of the Chemical Compounds Targeting DED/EDh Motifs of the Viral Proteins on Lymphocytic Choriomeningitis Virus and SARS-CoV-2. Viruses 2021; 13:1220. [PMID: 34202565 PMCID: PMC8310078 DOI: 10.3390/v13071220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/14/2021] [Accepted: 06/23/2021] [Indexed: 01/01/2023] Open
Abstract
Arenaviruses and coronaviruses include several human pathogenic viruses, such as Lassa virus, Lymphocytic choriomeningitis virus (LCMV), SARS-CoV, MERS-CoV, and SARS-CoV-2. Although these viruses belong to different virus families, they possess a common motif, the DED/EDh motif, known as an exonuclease (ExoN) motif. In this study, proof-of-concept studies, in which the DED/EDh motif in these viral proteins, NP for arenaviruses, and nsp14 for coronaviruses, could be a drug target, were performed. Docking simulation studies between two structurally different chemical compounds, ATA and PV6R, and the DED/EDh motifs in these viral proteins indicated that these compounds target DED/EDh motifs. The concentration which exhibited modest cell toxicity was used with these compounds to treat LCMV and SARS-CoV-2 infections in two different cell lines, A549 and Vero 76 cells. Both ATA and PV6R inhibited the post-entry step of LCMV and SARS-CoV-2 infection. These studies strongly suggest that DED/EDh motifs in these viral proteins could be a drug target to combat two distinct viral families, arenaviruses and coronaviruses.
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Affiliation(s)
- Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine and Leading Program, Graduate School of Biomedical Science, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (M.M.N.T.); (K.M.)
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine and Leading Program, Graduate School of Biomedical Science, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (M.M.N.T.); (K.M.)
| | - Takeshi Ishikawa
- Department of Chemistry, Biotechnology and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan
| | - Shuzo Urata
- National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
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9
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Ye X, Axhemi A, Jankowsky E. Alternative RNA degradation pathways by the exonuclease Pop2p from Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2021; 27:465-476. [PMID: 33408095 PMCID: PMC7962489 DOI: 10.1261/rna.078006.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
The 3' to 5' exonuclease Pop2p (Caf1p) is part of the CCR4-NOT deadenylation complex that removes poly(A) tails from mRNAs in cells. Pop2p is structurally conserved in eukaryotes, but Saccharomyces cerevisiae Pop2p harbors noncanonical amino acids in its catalytic center. The enzymatic properties of S. cerevisiae Pop2p are not well defined. Here we characterize the RNA exonuclease activity of recombinant S. cerevisiae Pop2p. We find that S. cerevisiae Pop2p degrades RNAs via two alternative reactions pathways, one generating nucleotides with 5'-phosphates and RNA intermediates with 3'-hydroxyls, and the other generating nucleotides with 3'-phosphates and RNA intermediates with 3'-phosphates. The enzyme is not able to initiate the reaction on RNAs with a 3'-phosphate, which leads to accumulation of RNAs with 3'-phosphates that can exceed 10 nt and are resistant to further degradation by S. cerevisiae Pop2p. We further demonstrate that S. cerevisiae Pop2p degrades RNAs in three reaction phases: an initial distributive phase, a second processive phase and a third phase during which processivity gradually declines. We also show that mutations of subsets of amino acids in the catalytic center, including those previously thought to inactivate the enzyme, moderately reduce, but not eliminate activity. Only mutation of all five amino acids in the catalytic center diminishes activity of Pop2p to background levels. Collectively, our results reveal robust exonuclease activity of S. cerevisiae Pop2p with unusual enzymatic properties, characterized by alternative degradation pathways, multiple reaction phases and functional redundancy of amino acids in the catalytic core.
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Affiliation(s)
- Xuan Ye
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Armend Axhemi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
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10
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Abstract
The identification and characterization of rhythmically expressed mRNAs have been an active area of research over the past 20 years, as these mRNAs are believed to produce the daily rhythms in a wide range of biological processes. Circadian transcriptome studies have used mature mRNA as a primary readout and focused largely on rhythmic RNA synthesis as a regulatory mechanism underlying rhythmic mRNA expression. However, RNA synthesis, RNA degradation, or a combination of both must be rhythmic to drive rhythmic RNA profiles, and it is still unclear to what extent rhythmic synthesis leads to rhythmic RNA profiles. In addition, circadian RNA expression is also often tissue specific. Although a handful of genes cycle in all or most tissues, others are rhythmic only in certain tissues, even though the same core clock mechanism is believed to control the rhythmic RNA profiles in all tissues. This review focuses on the dynamics of rhythmic RNA synthesis and degradation and discusses how these steps collectively determine the rhythmicity, phase, and amplitude of RNA accumulation. In particular, we highlight a possible role of RNA degradation in driving tissue-specific RNA rhythms. By unifying findings from experimental and theoretical studies, we will provide a comprehensive overview of how rhythmic gene expression can be achieved and how each regulatory step contributes to tissue-specific circadian transcriptome output in mammals.
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Affiliation(s)
| | - Shihoko Kojima
- To whom all correspondence should be addressed: Shihoko Kojima, Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA; .
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11
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Lardelli RM, Lykke-Andersen J. Competition between maturation and degradation drives human snRNA 3' end quality control. Genes Dev 2020; 34:989-1001. [PMID: 32499401 PMCID: PMC7328512 DOI: 10.1101/gad.336891.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/29/2020] [Indexed: 12/11/2022]
Abstract
Polymerases and exonucleases act on 3' ends of nascent RNAs to promote their maturation or degradation but how the balance between these activities is controlled to dictate the fates of cellular RNAs remains poorly understood. Here, we identify a central role for the human DEDD deadenylase TOE1 in distinguishing the fates of small nuclear (sn)RNAs of the spliceosome from unstable genome-encoded snRNA variants. We found that TOE1 promotes maturation of all regular RNA polymerase II transcribed snRNAs of the major and minor spliceosomes by removing posttranscriptional oligo(A) tails, trimming 3' ends, and preventing nuclear exosome targeting. In contrast, TOE1 promotes little to no maturation of tested U1 variant snRNAs, which are instead targeted by the nuclear exosome. These observations suggest that TOE1 is positioned at the center of a 3' end quality control pathway that selectively promotes maturation and stability of regular snRNAs while leaving snRNA variants unprocessed and exposed to degradation in what could be a widespread mechanism of RNA quality control given the large number of noncoding RNAs processed by DEDD deadenylases.
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Affiliation(s)
- Rea M Lardelli
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Jens Lykke-Andersen
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
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12
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Humphreys SC, Thayer MB, Campbell J, Chen WLK, Adams D, Lade JM, Rock BM. Emerging siRNA Design Principles and Consequences for Biotransformation and Disposition in Drug Development. J Med Chem 2020; 63:6407-6422. [PMID: 32352779 DOI: 10.1021/acs.jmedchem.9b01839] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
After two decades teetering at the intersection of laboratory tool and therapeutic reality, with two siRNA drugs now clinically approved, this modality has finally come into fruition. Consistent with other emerging modalities, initial proof-of-concept efforts concentrated on coupling pharmacologic efficacy with desirable safety profiles. Consequently, thorough investigations of siRNA absorption, distribution, metabolism, and excretion (ADME) properties are lacking. Advancing ADME knowledge will aid establishment of in vitro-in vivo correlations and pharmacokinetic-pharmacodynamic relationships to optimize candidate selection through discovery and translation. Here, we outline the emerging siRNA design principles and discuss the consequences for siRNA disposition and biotransformation. We propose a conceptual framework for siRNA ADME evaluation, contextualizing the site of biotransformation product formation with PK-PD modulation, and end with a discussion around safety and regulatory considerations and future directions for this modality.
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Affiliation(s)
- Sara C Humphreys
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Mai B Thayer
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Jabbar Campbell
- Neuroscience Department, Amgen Research, 360 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Wen Li Kelly Chen
- Comparative Biology and Safety Sciences Department, Amgen Research, 360 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Dan Adams
- Comparative Biology and Safety Sciences Department, Amgen Research, 360 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Julie M Lade
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Brooke M Rock
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
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13
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Derech-Haim S, Friedman Y, Hizi A, Bakhanashvili M. p53 regulates its own expression by an intrinsic exoribonuclease activity through AU-rich elements. J Mol Med (Berl) 2020; 98:437-449. [PMID: 32016559 DOI: 10.1007/s00109-020-01884-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/26/2019] [Accepted: 01/28/2020] [Indexed: 11/25/2022]
Abstract
The onco-suppressor p53 protein plays also an important role in the control of various aspects of health and disease. p53 levels are low in normal cells and elevated under stress conditions. While low levels of p53 promote tumor formation, overactive p53 leads to premature aging and cell death. RNA degradation is a critical level of regulation contributing to the control of gene expression. p53, as an RNA-binding protein, exerts 3' → 5' exoribonuclease activity, mediating degradation of adenylate/uridylate-rich elements (ARE)-containing ssRNAs. The 3'-UTR of p53-mRNA, which is a target of p53 itself, harbors cis-acting AREs. Our results suggest that p53 controls its own expression through murine double-minute 2 (mdm2)-independent "RNA decay" function in cytoplasm. We demonstrate that p53 expresses an exoribonuclease activity through the binding to ARE sequences of p53-mRNA via translation-independent and translation-dependent polysome-associated pathways. Antagonistic interplay was detected between p53 levels and execution of its exoribonuclease function mirrored in low p53 levels in normal cells, due to the efficient exoribonuclease activity, and in the accumulation of p53 in cells exposed to p53-activating drugs in accordance with the reduced exoribonuclease activity. Apparently, p53, via control of its own mRNA stability and/or translation in cytoplasm, might act as a negative regulator of p53-mRNA levels. The observed connection between exoribonuclease activity and p53 abundance highlights the importance of this function affecting p53 expression, imperative for multiple functions, with implications for the steady-state levels of protein and for the p53 stress response. The modulation in expression of exoribonuclease activity would be translated into the alterations in p53 level. KEY MESSAGES: p53 controls its own expression through mdm2-independent "RNA decay" function in cytoplasm. p53 expresses an exoribonuclease activity through the binding to ARE sequences of p53-mRNA. Antagonistic interplay exists between stress-induced p53 and execution of its exoribonuclease function.
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Affiliation(s)
- Sanaz Derech-Haim
- Infectious Diseases Unit, Sheba Medical Center, 5265601, Tel-Hashomer, Israel
| | - Yael Friedman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Amnon Hizi
- Department of Cellular and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mary Bakhanashvili
- Infectious Diseases Unit, Sheba Medical Center, 5265601, Tel-Hashomer, Israel.
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat-Gan, Israel.
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14
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Cross ST, Michalski D, Miller MR, Wilusz J. RNA regulatory processes in RNA virus biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1536. [PMID: 31034160 PMCID: PMC6697219 DOI: 10.1002/wrna.1536] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
Numerous post‐transcriptional RNA processes play a major role in regulating the quantity, quality and diversity of gene expression in the cell. These include RNA processing events such as capping, splicing, polyadenylation and modification, but also aspects such as RNA localization, decay, translation, and non‐coding RNA‐associated regulation. The interface between the transcripts of RNA viruses and the various RNA regulatory processes in the cell, therefore, has high potential to significantly impact virus gene expression, regulation, cytopathology and pathogenesis. Furthermore, understanding RNA biology from the perspective of an RNA virus can shed considerable light on the broad impact of these post‐transcriptional processes in cell biology. Thus the goal of this article is to provide an overview of the richness of cellular RNA biology and how RNA viruses use, usurp and/or avoid the associated machinery to impact the outcome of infection. This article is categorized under:RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Shaun T Cross
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Daniel Michalski
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Megan R Miller
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
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15
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Wu H, Liu Q, Shi H, Xie J, Zhang Q, Ouyang Z, Li N, Yang Y, Liu Z, Zhao Y, Lai C, Ruan D, Peng J, Ge W, Chen F, Fan N, Jin Q, Liang Y, Lan T, Yang X, Wang X, Lei Z, Doevendans PA, Sluijter JPG, Wang K, Li X, Lai L. Engineering CRISPR/Cpf1 with tRNA promotes genome editing capability in mammalian systems. Cell Mol Life Sci 2018; 75:3593-3607. [PMID: 29637228 PMCID: PMC11105780 DOI: 10.1007/s00018-018-2810-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/20/2018] [Accepted: 04/03/2018] [Indexed: 12/13/2022]
Abstract
CRISPR/Cpf1 features a number of properties that are distinct from CRISPR/Cas9 and provides an excellent alternative to Cas9 for genome editing. To date, genome engineering by CRISPR/Cpf1 has been reported only in human cells and mouse embryos of mammalian systems and its efficiency is ultimately lower than that of Cas9 proteins from Streptococcus pyogenes. The application of CRISPR/Cpf1 for targeted mutagenesis in other animal models has not been successfully verified. In this study, we designed and optimized a guide RNA (gRNA) transcription system by inserting a transfer RNA precursor (pre-tRNA) sequence downstream of the gRNA for Cpf1, protecting gRNA from immediate digestion by 3'-to-5' exonucleases. Using this new gRNAtRNA system, genome editing, including indels, large fragment deletion and precise point mutation, was induced in mammalian systems, showing significantly higher efficiency than the original Cpf1-gRNA system. With this system, gene-modified rabbits and pigs were generated by embryo injection or somatic cell nuclear transfer (SCNT) with an efficiency comparable to that of the Cas9 gRNA system. These results demonstrated that this refined gRNAtRNA system can boost the targeting capability of CRISPR/Cpf1 toolkits.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Animals, Newborn
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Cas Systems/genetics
- Cells, Cultured
- Cloning, Molecular/methods
- Cloning, Organism/methods
- Embryo, Mammalian
- Endonucleases/genetics
- Endonucleases/metabolism
- Female
- Fetus
- Gene Editing/methods
- Genome/genetics
- HEK293 Cells
- HeLa Cells
- Humans
- Male
- Mammals/embryology
- Mammals/genetics
- Mutagenesis
- Nuclear Transfer Techniques
- Pregnancy
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Transfer/genetics
- Rabbits
- Swine
- Swine, Miniature
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Affiliation(s)
- Han Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Qishuai Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Hui Shi
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jingke Xie
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Quanjun Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Zhen Ouyang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Nan Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yi Yang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Zhaoming Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yu Zhao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Chengdan Lai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Degong Ruan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jiangyun Peng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Weikai Ge
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Fangbing Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Nana Fan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Qin Jin
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yanhui Liang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ting Lan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaoyu Yang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, China
| | - Xiaoshan Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Zhiyong Lei
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands
- Netherlands Heart Institute, 3584CX, Utrecht, The Netherlands
| | - Pieter A Doevendans
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands
- Netherlands Heart Institute, 3584CX, Utrecht, The Netherlands
| | - Joost P G Sluijter
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands
- Netherlands Heart Institute, 3584CX, Utrecht, The Netherlands
| | - Kepin Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Xiaoping Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Liangxue Lai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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16
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Valdés-Flores J, López-Rosas I, López-Camarillo C, Ramírez-Moreno E, Ospina-Villa JD, Marchat LA. Life and Death of mRNA Molecules in Entamoeba histolytica. Front Cell Infect Microbiol 2018; 8:199. [PMID: 29971219 PMCID: PMC6018208 DOI: 10.3389/fcimb.2018.00199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/28/2018] [Indexed: 02/05/2023] Open
Abstract
In eukaryotic cells, the life cycle of mRNA molecules is modulated in response to environmental signals and cell-cell communication in order to support cellular homeostasis. Capping, splicing and polyadenylation in the nucleus lead to the formation of transcripts that are suitable for translation in cytoplasm, until mRNA decay occurs in P-bodies. Although pre-mRNA processing and degradation mechanisms have usually been studied separately, they occur simultaneously and in a coordinated manner through protein-protein interactions, maintaining the integrity of gene expression. In the past few years, the availability of the genome sequence of Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, coupled to the development of the so-called “omics” technologies provided new opportunities for the study of mRNA processing and turnover in this pathogen. Here, we review the current knowledge about the molecular basis for splicing, 3′ end formation and mRNA degradation in amoeba, which suggest the conservation of events related to mRNA life throughout evolution. We also present the functional characterization of some key proteins and describe some interactions that indicate the relevance of cooperative regulatory events for gene expression in this human parasite.
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Affiliation(s)
- Jesús Valdés-Flores
- Departamento de Bioquímica, CINVESTAV, Ciudad de Mexico, Mexico City, Mexico
| | - Itzel López-Rosas
- CONACyT Research Fellow - Colegio de Postgraduados Campus Campeche, Campeche, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México Ciudad de Mexico, Mexico City, Mexico
| | - Esther Ramírez-Moreno
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
| | - Juan D Ospina-Villa
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
| | - Laurence A Marchat
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
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17
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Charley PA, Wilusz CJ, Wilusz J. Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1. J Biol Chem 2017; 293:285-295. [PMID: 29118186 DOI: 10.1074/jbc.m117.805796] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/06/2017] [Indexed: 12/22/2022] Open
Abstract
Regulated mRNA decay plays a vital role in determining both the level and quality of cellular gene expression. Viral RNAs must successfully evade this host RNA decay machinery to establish a productive infection. One way for RNA viruses to accomplish this is to target the cellular exoribonuclease XRN1, because this enzyme is accessible in the cytoplasm and plays a major role in mRNA decay. Members of the Flaviviridae use RNA structures in their 5'- or 3'-untranslated regions to stall and repress XRN1, effectively stabilizing viral RNAs while also causing significant dysregulation of host cell mRNA stability. Here, we use a series of biochemical assays to demonstrate that the 3'-terminal portion of the nucleocapsid (N) mRNA of Rift Valley fever virus, a phlebovirus of the Bunyaviridae family, also can effectively stall and repress XRN1. The region responsible for impeding XRN1 includes a G-rich portion that likely forms a G-quadruplex structure. The 3'-terminal portions of ambisense-derived transcripts of multiple arenaviruses also stalled XRN1. Therefore, we conclude that RNAs from two additional families of mammalian RNA viruses stall and repress XRN1. This observation. emphasizes the importance and commonality of this viral strategy to interfere with the 5'-to-3'-exoribonuclease component of the cytoplasmic RNA decay machinery.
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Affiliation(s)
- Phillida A Charley
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Carol J Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523.
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18
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Sharaf A, Mercati F, Elmaghraby I, Elbaz RM, Marei EM. Functional and comparative genome analysis of novel virulent actinophages belonging to Streptomyces flavovirens. BMC Microbiol 2017; 17:51. [PMID: 28257628 PMCID: PMC5336643 DOI: 10.1186/s12866-017-0940-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Background Next Generation Sequencing (NGS) technologies provide exciting possibilities for whole genome sequencing of a plethora of organisms including bacterial strains and phages, with many possible applications in research and diagnostics. No Streptomyces flavovirens phages have been sequenced to date; there is therefore a lack in available information about S. flavovirens phage genomics. We report biological and physiochemical features and use NGS to provide the complete annotated genomes for two new strains (Sf1 and Sf3) of the virulent phage Streptomyces flavovirens, isolated from Egyptian soil samples. Results The S. flavovirens phages (Sf1 and Sf3) examined in this study show higher adsorption rates (82 and 85%, respectively) than other actinophages, indicating a strong specificity to their host, and latent periods (15 and 30 min.), followed by rise periods of 45 and 30 min. As expected for actinophages, their burst sizes were 1.95 and 2.49 virions per mL. Both phages were stable and, as reported in previous experiments, showed a significant increase in their activity after sodium chloride (NaCl) and magnesium chloride (MgCl2.6H2O) treatments, whereas after zinc chloride (ZnCl2) application both phages showed a significant decrease in infection. The sequenced phage genomes are parts of a singleton cluster with sizes of 43,150 bp and 60,934 bp, respectively. Bioinformatics analyses and functional characterizations enabled the assignment of possible functions to 19 and 28 putative identified ORFs, which included phage structural proteins, lysis components and metabolic proteins. Thirty phams were identified in both phages, 10 (33.3%) of them with known function, which can be used in cluster prediction. Comparative genomic analysis revealed significant homology between the two phages, showing the highest hits among Sf1, Sf3 and the closest Streptomyces phage (VWB phages) in a specific 13Kb region. However, the phylogenetic analysis using the Major Capsid Protein (MCP) sequences highlighted that the isolated phages belong to the BG Streptomyces phage group but are clearly separated, representing a novel sub-cluster. Conclusion The results of this study provide the first physiological and genomic information for S. flavovirens phages and will be useful for pharmaceutical industries based on S. flavovirens and future phage evolution studies.
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Affiliation(s)
- A Sharaf
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt. .,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czechia.
| | - F Mercati
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR) of Italy, 90129, Palermo, Italy
| | - I Elmaghraby
- Central Lab. of Organic Agriculture, Agricultural Research Center, Giza, 12619, Egypt
| | - R M Elbaz
- Botany and Microbiology Department, Faculty of Science, Helwan University, Ain-Helwan, Cairo, 11970, Egypt
| | - E M Marei
- Microbiology Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt
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19
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Lazzaretti D, Veith K, Kramer K, Basquin C, Urlaub H, Irion U, Bono F. The bicoid mRNA localization factor Exuperantia is an RNA-binding pseudonuclease. Nat Struct Mol Biol 2016; 23:705-13. [PMID: 27376588 DOI: 10.1038/nsmb.3254] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/09/2016] [Indexed: 12/20/2022]
Abstract
Anterior patterning in Drosophila is mediated by the localization of bicoid (bcd) mRNA at the anterior pole of the oocyte. Exuperantia (Exu) is a putative exonuclease (EXO) associated with bcd and required for its localization. We present the crystal structure of Exu, which reveals a dimeric assembly with each monomer consisting of a 3'-5' EXO-like domain and a sterile alpha motif (SAM)-like domain. The catalytic site is degenerate and inactive. Instead, the EXO-like domain mediates dimerization and RNA binding. We show that Exu binds RNA directly in vitro, that the SAM-like domain is required for RNA binding activity and that Exu binds a structured element present in the bcd 3' untranslated region with high affinity. Through structure-guided mutagenesis, we show that Exu dimerization is essential for bcd localization. Our data demonstrate that Exu is a noncanonical RNA-binding protein with EXO-SAM-like domain architecture that interacts with its target RNA as a homodimer.
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Affiliation(s)
| | - Katharina Veith
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Katharina Kramer
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Claire Basquin
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Uwe Irion
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Fulvia Bono
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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SAMHD1, the Aicardi-Goutières syndrome gene and retroviral restriction factor, is a phosphorolytic ribonuclease rather than a hydrolytic ribonuclease. Biochem Biophys Res Commun 2016; 477:977-981. [PMID: 27387229 DOI: 10.1016/j.bbrc.2016.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 07/02/2016] [Indexed: 11/21/2022]
Abstract
SAMHD1 plays diverse roles in innate immunity, autoimmune diseases and HIV restriction, but the mechanisms involved are still unclear. SAMHD1 has been reported to have both dNTPase and RNase activities. However, whether SAMHD1 possesses RNase activity remains highly controversial. Here, we found that, unlike conventional hydrolytic exoribonucleases, SAMHD1 requires inorganic phosphate to degrade RNA substrates and produces nucleotide diphosphates rather than nucleoside monophosphates, which indicated that SAMHD1 is a phosphorolytic but not hydrolytic 3'-5' exoribonuclease. Furthermore, SAMHD1 preferentially cleaved single-stranded RNAs comprising A20 or U20, whereas neither C20 nor G20 was susceptible to SAMHD1-mediated degradation. Our findings will facilitate more advanced studies into the role of the SAMHD1 RNase function in the cellular pathogenesis implicated in nucleic acid-triggered inflammatory responses and the anti-retroviral function of SAMHD1.
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21
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Sandstedt M, Jonsson M, Asp J, Dellgren G, Lindahl A, Jeppsson A, Sandstedt J. Intracellular flow cytometry may be combined with good quality and high sensitivity RT-qPCR analysis. Cytometry A 2015; 87:1079-89. [PMID: 26348124 DOI: 10.1002/cyto.a.22783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/30/2015] [Accepted: 08/23/2015] [Indexed: 02/04/2023]
Abstract
Flow cytometry (FCM) has become a well-established method for analysis of both intracellular and cell-surface proteins, while quantitative RT-PCR (RT-qPCR) is used to determine gene expression with high sensitivity and specificity. Combining these two methods would be of great value. The effects of intracellular staining on RNA integrity and RT-qPCR sensitivity and quality have not, however, been fully examined. We, therefore, intended to assess these effects further. Cells from the human lung cancer cell line A549 were fixed, permeabilized and sorted by FCM. Sorted cells were analyzed using RT-qPCR. RNA integrity was determined by RNA quality indicator analysis. A549 cells were then mixed with cells of the mouse cardiomyocyte cell line HL-1. A549 cells were identified by the cell surface marker ABCG2, while HL-1 cells were identified by intracellular cTnT. Cells were sorted and analyzed by RT-qPCR. Finally, cell cultures from human atrial biopsies were used to evaluate the effects of fixation and permeabilization on RT-qPCR analysis of nonimmortalized cells stored prior to analysis by FCM. A large amount of RNA could be extracted even when cells had been fixed and permeabilized. Permeabilization resulted in increased RNA degradation and a moderate decrease in RT-qPCR sensitivity. Gene expression levels were also affected to a moderate extent. Sorted populations from the mixed A549 and HL-1 cell samples showed gene expression patterns that corresponded to FCM data. When samples were stored before FCM sorting, the RT-qPCR analysis could still be performed with high sensitivity and quality. In summary, our results show that intracellular FCM may be performed with only minor impairment of the RT-qPCR sensitivity and quality when analyzing sorted cells; however, these effects should be considered when comparing RT-qPCR data of not fixed samples with those of fixed and permeabilized samples.
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Affiliation(s)
- Mikael Sandstedt
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Marianne Jonsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Julia Asp
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Göran Dellgren
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Cardiothoracic Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anders Lindahl
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anders Jeppsson
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Cardiothoracic Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Joakim Sandstedt
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
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22
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Lv H, Zhu Y, Qiu Y, Niu L, Teng M, Li X. Structural analysis of Dis3l2, an exosome-independent exonuclease from Schizosaccharomyces pombe. ACTA ACUST UNITED AC 2015; 71:1284-94. [PMID: 26057668 DOI: 10.1107/s1399004715005805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/23/2015] [Indexed: 01/04/2023]
Abstract
After deadenylation and decapping, cytoplasmic mRNA can be digested in two opposite directions: in the 5'-3' direction by Xrn1 or in the 3'-5' direction by the exosome complex. Recently, a novel 3'-5' RNA-decay pathway involving Dis3l2 has been described that differs from degradation by Xrn1 and the exosome. The product of the Schizosaccharomyces pombe gene SPAC2C4.07c was identified as a homologue of human Dis3l2. In this work, the 2.8 Å resolution X-ray crystal structure of S. pombe Dis3l2 (SpDis3l2) is reported, the conformation of which is obviously different from that in the homologous mouse Dis3l2-RNA complex. Fluorescence polarization assay experiments showed that RNB and S1 are the primary RNA-binding domains and that the CSDs (CSD1 and CSD2) play an indispensable role in the RNA-binding process of SpDis3l2. Taking the structure comparison and mutagenic experiments together, it can be inferred that the RNA-recognition pattern of SpDis3l2 resembles that of its mouse homologue rather than that of the Escherichia coli RNase II-RNA complex. Furthermore, a drastic conformation change could occur following the binding of the RNA substrate to SpDis3l2.
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Affiliation(s)
- Hui Lv
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yuwei Zhu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yu Qiu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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23
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Sokhi UK, Bacolod MD, Emdad L, Das SK, Dumur CI, Miles MF, Sarkar D, Fisher PB. Analysis of global changes in gene expression induced by human polynucleotide phosphorylase (hPNPase(old-35)). J Cell Physiol 2014; 229:1952-62. [PMID: 24729470 PMCID: PMC4149605 DOI: 10.1002/jcp.24645] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/09/2014] [Indexed: 01/19/2023]
Abstract
As a strategy to identify gene expression changes affected by human polynucleotide phosphorylase (hPNPase(old-35)), we performed gene expression analysis of HeLa cells in which hPNPase(old-35) was overexpressed. The observed changes were then compared to those of HO-1 melanoma cells in which hPNPase(old-35) was stably knocked down. Through this analysis, 90 transcripts, which positively or negatively correlated with hPNPase(old-35) expression, were identified. The majority of these genes were associated with cell communication, cell cycle, and chromosomal organization gene ontology categories. For a number of these genes, the positive or negative correlations with hPNPase(old-35) expression were consistent with transcriptional data extracted from the TCGA (The Cancer Genome Atlas) expression datasets for colon adenocarcinoma (COAD), skin cutaneous melanoma (SKCM), ovarian serous cyst adenocarcinoma (OV), and prostate adenocarcinoma (PRAD). Further analysis comparing the gene expression changes between Ad.hPNPase(old-35) infected HO-1 melanoma cells and HeLa cells overexpressing hPNPase(old-35) under the control of a doxycycline-inducible promoter, revealed global changes in genes involved in cell cycle and mitosis. Overall, this study provides further evidence that hPNPase(old-35) is associated with global changes in cell cycle-associated genes and identifies potential gene targets for future investigation.
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Affiliation(s)
- Upneet K. Sokhi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Manny D. Bacolod
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Luni Emdad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Swadesh K. Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Catherine I. Dumur
- Department of Pathology, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Michael F. Miles
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- Department of Neurology, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Paul B. Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
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24
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Taylor LL, Jackson RN, Rexhepaj M, King AK, Lott LK, van Hoof A, Johnson SJ. The Mtr4 ratchet helix and arch domain both function to promote RNA unwinding. Nucleic Acids Res 2014; 42:13861-72. [PMID: 25414331 PMCID: PMC4267639 DOI: 10.1093/nar/gku1208] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosome-mediated 3′-5′ turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like helicase core and a large arch domain that spans the core. The ‘ratchet helix’ is positioned to interact with RNA substrates as they move through the helicase. However, the contribution of the ratchet helix in Mtr4 activity is poorly understood. Here we show that strict conservation along the ratchet helix is particularly extensive for Ski2-like RNA helicases compared to related helicases. Mutation of residues along the ratchet helix alters in vitro activity in Mtr4 and TRAMP and causes slow growth phenotypes in vivo. We also identify a residue on the ratchet helix that influences Mtr4 affinity for polyadenylated substrates. Previous work indicated that deletion of the arch domain has minimal effect on Mtr4 unwinding activity. We now show that combining the arch deletion with ratchet helix mutations abolishes helicase activity and produces a lethal in vivo phenotype. These studies demonstrate that the ratchet helix modulates helicase activity and suggest that the arch domain plays a previously unrecognized role in unwinding substrates.
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Affiliation(s)
- Lacy L Taylor
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Ryan N Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Megi Rexhepaj
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Alejandra Klauer King
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Lindsey K Lott
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Sean J Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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25
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The genetic architecture of multiple myeloma. Adv Hematol 2014; 2014:864058. [PMID: 24803933 PMCID: PMC3996928 DOI: 10.1155/2014/864058] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/16/2014] [Indexed: 11/18/2022] Open
Abstract
Multiple myeloma is a malignant proliferation of monoclonal plasma cells leading to clinical features that include hypercalcaemia, renal dysfunction, anaemia, and bone disease (frequently referred to by the acronym CRAB) which represent evidence of end organ failure. Recent evidence has revealed myeloma to be a highly heterogeneous disease composed of multiple molecularly-defined subtypes each with varying clinicopathological features and disease outcomes. The major division within myeloma is between hyperdiploid and nonhyperdiploid subtypes. In this division, hyperdiploid myeloma is characterised by trisomies of certain odd numbered chromosomes, namely, 3, 5, 7, 9, 11, 15, 19, and 21 whereas nonhyperdiploid myeloma is characterised by translocations of the immunoglobulin heavy chain alleles at chromosome 14q32 with various partner chromosomes, the most important of which being 4, 6, 11, 16, and 20. Hyperdiploid and nonhyperdiploid changes appear to represent early or even initiating mutagenic events that are subsequently followed by secondary aberrations including copy number abnormalities, additional translocations, mutations, and epigenetic modifications which lead to plasma cell immortalisation and disease progression. The following review provides a comprehensive coverage of the genetic and epigenetic events contributing to the initiation and progression of multiple myeloma and where possible these abnormalities have been linked to disease prognosis.
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26
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Sokhi UK, DeSalle R, Bacolod MD, Das SK, Dasgupta S, Sarkar D, Fisher PB. Evolutionary dynamics of Polynucelotide phosphorylases. Mol Phylogenet Evol 2014; 73:77-86. [PMID: 24503483 DOI: 10.1016/j.ympev.2014.01.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 01/09/2014] [Accepted: 01/21/2014] [Indexed: 11/17/2022]
Abstract
Polynucleotide phosphorylase (PNPase) is an evolutionarily conserved 3'→5' phosphate-dependent exoribonucease belonging to the PDX family of proteins. It consists of two catalytic RNase PH domains (PNP1 and PNP2), an α-helical domain and two RNA-binding domains. The PNP1 and PNP2 domains share substantial sequence and structural homology with RNase PH (RPH), which is another PDX family member found in all the three major kingdoms of life, suggesting that these three domains originated from a common ancestor. Phylogenetic analysis (based on the PNPase/RNase PH sequence information for 43 vertebrate taxa) shows that PNP2 and RPH are sister taxa which arose through duplication of the ancestral PNP1 domain. Also, all three domains (PNP1, PNP2 and RPH), along with the KH and S1 domains have undergone significant and directional sequence change, as determined by branch and site-specific dN/dS analyses. In general, codons that show dN/dS ratios that are significantly greater than 1.0 are outside the ordered regions (α-helices and β-sheets) of these protein domains. In addition, sites that have been selected for mutagenesis in these proteins lie embedded in regions where there is a preponderance of codons with dN/dS values that are not significantly different from 0.0. Overall, this report is an attempt to further our understanding of the evolutionary history of these three protein domains, and define the evolutionary events that led to their refinement in the vertebrate lineage leading to mammals.
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Affiliation(s)
- Upneet K Sokhi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Rob DeSalle
- American Museum of Natural History, New York University, New York, NY, United States.
| | - Manny D Bacolod
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Swadesh K Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Santanu Dasgupta
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Paul B Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
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27
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Svec D, Andersson D, Pekny M, Sjöback R, Kubista M, Ståhlberg A. Direct cell lysis for single-cell gene expression profiling. Front Oncol 2013; 3:274. [PMID: 24224157 PMCID: PMC3819639 DOI: 10.3389/fonc.2013.00274] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 10/22/2013] [Indexed: 11/23/2022] Open
Abstract
The interest to analyze single and few cell samples is rapidly increasing. Numerous extraction protocols to purify nucleic acids are available, but most of them compromise severely on yield to remove contaminants and are therefore not suitable for the analysis of samples containing small numbers of transcripts only. Here, we evaluate 17 direct cell lysis protocols for transcript yield and compatibility with downstream reverse transcription quantitative real-time PCR. Four endogenously expressed genes are assayed together with RNA and DNA spikes in the samples. We found bovine serum albumin (BSA) to be the best lysis agent, resulting in efficient cell lysis, high RNA stability, and enhanced reverse transcription efficiency. Furthermore, we found direct cell lysis with BSA superior to standard column based extraction methods, when analyzing from 1 up to 512 mammalian cells. In conclusion, direct cell lysis protocols based on BSA can be applied with most cell collection methods and are compatible with most analytical workflows to analyze single-cells as well as samples composed of small numbers of cells.
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Affiliation(s)
- David Svec
- Institute of Biotechnology AS CR , Prague , Czech Republic ; TATAA Biocenter , Gothenburg , Sweden
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28
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Sokhi UK, Bacolod MD, Dasgupta S, Emdad L, Das SK, Dumur CI, Miles MF, Sarkar D, Fisher PB. Identification of genes potentially regulated by human polynucleotide phosphorylase (hPNPase old-35) using melanoma as a model. PLoS One 2013; 8:e76284. [PMID: 24143183 PMCID: PMC3797080 DOI: 10.1371/journal.pone.0076284] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/23/2013] [Indexed: 11/18/2022] Open
Abstract
Human Polynucleotide Phosphorylase (hPNPaseold-35 or PNPT1) is an evolutionarily conserved 3′→5′ exoribonuclease implicated in the regulation of numerous physiological processes including maintenance of mitochondrial homeostasis, mtRNA import and aging-associated inflammation. From an RNase perspective, little is known about the RNA or miRNA species it targets for degradation or whose expression it regulates; except for c-myc and miR-221. To further elucidate the functional implications of hPNPaseold-35 in cellular physiology, we knocked-down and overexpressed hPNPaseold-35 in human melanoma cells and performed gene expression analyses to identify differentially expressed transcripts. Ingenuity Pathway Analysis indicated that knockdown of hPNPaseold-35 resulted in significant gene expression changes associated with mitochondrial dysfunction and cholesterol biosynthesis; whereas overexpression of hPNPaseold-35 caused global changes in cell-cycle related functions. Additionally, comparative gene expression analyses between our hPNPaseold-35 knockdown and overexpression datasets allowed us to identify 77 potential “direct” and 61 potential “indirect” targets of hPNPaseold-35 which formed correlated networks enriched for cell-cycle and wound healing functional association, respectively. These results provide a comprehensive database of genes responsive to hPNPaseold-35 expression levels; along with the identification new potential candidate genes offering fresh insight into cellular pathways regulated by PNPT1 and which may be used in the future for possible therapeutic intervention in mitochondrial- or inflammation-associated disease phenotypes.
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Affiliation(s)
- Upneet K. Sokhi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Manny D. Bacolod
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Santanu Dasgupta
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Luni Emdad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Swadesh K. Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Catherine I. Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael F. Miles
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Neurology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Paul B. Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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29
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Brooks SA, Blackshear PJ. Tristetraprolin (TTP): interactions with mRNA and proteins, and current thoughts on mechanisms of action. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:666-79. [PMID: 23428348 PMCID: PMC3752887 DOI: 10.1016/j.bbagrm.2013.02.003] [Citation(s) in RCA: 296] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/25/2013] [Accepted: 02/04/2013] [Indexed: 12/14/2022]
Abstract
Changes in mRNA stability and translation are critical control points in the regulation of gene expression, particularly genes encoding growth factors, inflammatory mediators, and proto-oncogenes. Adenosine and uridine (AU)-rich elements (ARE), often located in the 3' untranslated regions (3'UTR) of mRNAs, are known to target transcripts for rapid decay. They are also involved in the regulation of mRNA stability and translation in response to extracellular cues. This review focuses on one of the best characterized ARE binding proteins, tristetraprolin (TTP), the founding member of a small family of CCCH tandem zinc finger proteins. In this survey, we have reviewed the current status of TTP interactions with mRNA and proteins, and discussed current thinking about TTP's mechanism of action to promote mRNA decay. We also review the proposed regulation of TTP's functions by phosphorylation. Finally, we have discussed emerging evidence for TTP operating as a translational regulator. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Seth A. Brooks
- Veterans Affairs Medical Center, White River Junction, Vermont, USA
- Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Perry J. Blackshear
- The Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
- Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina USA
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30
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Chlebowski A, Lubas M, Jensen TH, Dziembowski A. RNA decay machines: the exosome. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:552-60. [PMID: 23352926 DOI: 10.1016/j.bbagrm.2013.01.006] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
The multisubunit RNA exosome complex is a major ribonuclease of eukaryotic cells that participates in the processing, quality control and degradation of virtually all classes of RNA in Eukaryota. All this is achieved by about a dozen proteins with only three ribonuclease activities between them. At first glance, the versatility of the pathways involving the exosome and the sheer multitude of its substrates are astounding. However, after fifteen years of research we have some understanding of how exosome activity is controlled and applied inside the cell. The catalytic properties of the eukaryotic exosome are fairly well described and attention is now drawn to how the interplay between these activities impacts cell physiology. Also, it has become evident that exosome function relies on many auxiliary factors, which are intensely studied themselves. In this way, the focus of exosome research is slowly leaving the test tube and moving back into the cell. The exosome also has an interesting evolutionary history, which is evident within the eukaryotic lineage but only fully appreciated when considering similar protein complexes found in Bacteria and Archaea. Thus, while we keep this review focused on the most comprehensively described yeast and human exosomes, we shall point out similarities or dissimilarities to prokaryotic complexes and proteins where appropriate. The article is divided into three parts. In Part One we describe how the exosome is built and how it manifests in cells of different organisms. In Part Two we detail the enzymatic properties of the exosome, especially recent data obtained for holocomplexes. Finally, Part Three presents an overview of the RNA metabolism pathways that involve the exosome. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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31
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Sokhi UK, Das SK, Dasgupta S, Emdad L, Shiang R, DeSalle R, Sarkar D, Fisher PB. Human polynucleotide phosphorylase (hPNPaseold-35): should I eat you or not--that is the question? Adv Cancer Res 2013; 119:161-90. [PMID: 23870512 DOI: 10.1016/b978-0-12-407190-2.00005-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
RNA degradation plays a fundamental role in maintaining cellular homeostasis whether it occurs as a surveillance mechanism eliminating aberrant mRNAs or during RNA processing to generate mature transcripts. 3'-5' exoribonucleases are essential mediators of RNA decay pathways, and one such evolutionarily conserved enzyme is polynucleotide phosphorylase (PNPase). The human homologue of this fascinating enzymatic protein (hPNPaseold-35) was cloned a decade ago in the context of terminal differentiation and senescence through a novel "overlapping pathway screening" approach. Since then, significant insights have been garnered about this exoribonuclease and its repertoire of expanding functions. The objective of this review is to provide an up-to-date perspective of the recent discoveries made relating to hPNPaseold-35 and the impact they continue to have on our comprehension of its expanding and diverse array of functions.
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Hsiao YY, Duh Y, Chen YP, Wang YT, Yuan HS. How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes. Nucleic Acids Res 2012; 40:8144-54. [PMID: 22718982 PMCID: PMC3439924 DOI: 10.1093/nar/gks548] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Exonucleases are key enzymes in the maintenance of genome stability, processing of immature RNA precursors and degradation of unnecessary nucleic acids. However, it remains unclear how exonucleases digest nucleic acids to generate correct end products for next-step processing. Here we show how the exonuclease RNase T stops its trimming precisely. The crystal structures of RNase T in complex with a stem-loop DNA, a GG dinucleotide and single-stranded DNA with different 3′-end sequences demonstrate why a duplex with a short 3′-overhang, a dinucleotide and a ssDNA with a 3′-end C cannot be further digested by RNase T. Several hydrophobic residues in RNase T change their conformation upon substrate binding and induce an active or inactive conformation in the active site that construct a precise machine to determine which substrate should be digested based on its sequence, length and structure. These studies thus provide mechanistic insights into how RNase T prevents over digestion of its various substrates, and the results can be extrapolated to the thousands of members of the DEDDh family of exonucleases.
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Affiliation(s)
- Yu-Yuan Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan, ROC
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33
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Bernstein J, Toth EA. Yeast nuclear RNA processing. World J Biol Chem 2012; 3:7-26. [PMID: 22312453 PMCID: PMC3272586 DOI: 10.4331/wjbc.v3.i1.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 11/27/2011] [Accepted: 12/04/2011] [Indexed: 02/05/2023] Open
Abstract
Nuclear RNA processing requires dynamic and intricately regulated machinery composed of multiple enzymes and their cofactors. In this review, we summarize recent experiments using Saccharomyces cerevisiae as a model system that have yielded important insights regarding the conversion of pre-RNAs to functional RNAs, and the elimination of aberrant RNAs and unneeded intermediates from the nuclear RNA pool. Much progress has been made recently in describing the 3D structure of many elements of the nuclear degradation machinery and its cofactors. Similarly, the regulatory mechanisms that govern RNA processing are gradually coming into focus. Such advances invariably generate many new questions, which we highlight in this review.
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Affiliation(s)
- Jade Bernstein
- Jade Bernstein, Eric A Toth, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, United States
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Silva IJ, Saramago M, Dressaire C, Domingues S, Viegas SC, Arraiano CM. Importance and key events of prokaryotic RNA decay: the ultimate fate of an RNA molecule. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:818-36. [PMID: 21976285 DOI: 10.1002/wrna.94] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Inês Jesus Silva
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, Oeiras, Portugal
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35
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Initial genome sequencing and analysis of multiple myeloma. Nature 2011; 471:467-72. [PMID: 21430775 PMCID: PMC3560292 DOI: 10.1038/nature09837] [Citation(s) in RCA: 1131] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 01/17/2011] [Indexed: 12/16/2022]
Abstract
Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumor genomes and their comparison to matched normal DNAs. Several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the dataset. These include the mutation of genes involved in protein translation (seen in nearly half of the patients), genes involved in histone methylation, and genes involved in blood coagulation. In addition, a broader than anticipated role of NF-κB signaling was suggested by mutations in 11 members of the NF-κB pathway. Of potential immediate clinical relevance, activating mutations of the kinase BRAF were observed in 4% of patients, suggesting the evaluation of BRAF inhibitors in multiple myeloma clinical trials. These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.
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36
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RNA channelling by the eukaryotic exosome. EMBO Rep 2010; 11:936-42. [PMID: 21072061 DOI: 10.1038/embor.2010.164] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 09/13/2010] [Accepted: 09/16/2010] [Indexed: 11/09/2022] Open
Abstract
The eukaryotic exosome is a key nuclease for the degradation, processing and quality control of a wide variety of RNAs. Here, we report electron microscopic reconstructions and pseudo-atomic models of the ten-subunit Saccharomyces cerevisiae exosome in the unbound and RNA-bound states. In the RNA-bound structures, extra density that is visible at the entry and exit sites of the exosome channel indicates that a substrate-threading mechanism is used by the eukaryotic exosome. This channelling mechanism seems to be conserved in exosome-like complexes from all domains of life, and might have been present in the most recent common ancestor.
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Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance. Proc Natl Acad Sci U S A 2010; 107:12139-44. [PMID: 20566885 DOI: 10.1073/pnas.1004953107] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mtr4 is a conserved RNA helicase that functions together with the nuclear exosome. It participates in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA). It also interacts with the polyadenylating Trf4-Air2 heterodimer to form the so-called TRAMP (Trf4-Air2-Mtr4 Polyadenylation) complex. TRAMP is involved in exosome-mediated degradation of aberrant RNAs in nuclear surveillance pathways. We report the 2.9-A resolution crystal structure of Saccharomyces cerevisiae Mtr4 in complex with ADP and RNA. The structure shows a central ATPase core similar to that of other DExH helicases. Inserted in the DExH core is a region characteristic of Mtr4 orthologues that folds into an elongated stalk connected to a beta-barrel domain. This domain shows unexpected similarity to the KOW domain of L24, a ribosomal protein that binds 23S rRNA. We find that indeed the KOW domain of Mtr4 is able to bind in vitro transcribed tRNA(iMet), suggesting it might assist in presenting RNA substrates to the helicase core. The interaction of Mtr4 with Trf4-Air2 is mediated not by the stalk/KOW insertion but by the DExH core. We find that in the context of the TRAMP complex, the DExH core functions independently in vitro as an RNA helicase and a protein-binding platform. Mtr4 has thus evolved specific structural and surface features to perform its multiple functions.
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38
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Brooks SA. Functional interactions between mRNA turnover and surveillance and the ubiquitin proteasome system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:240-52. [PMID: 21935888 DOI: 10.1002/wrna.11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proteasome is a critical regulator of protein levels within the cell and is essential for maintaining homeostasis. A functional proteasome is required for effective mRNA surveillance and turnover. During transcription, the proteasome localizes to sites of DNA breaks, degrading RNA polymerase II and terminating transcription. For fully transcribed and processed messages, cytoplasmic surveillance is initiated with the pioneer round of translation. The proteasome is recruited to messages bearing premature termination codons, which trigger nonsense-mediated decay (NMD), as well as messages lacking a termination codon, which trigger nonstop decay, to degrade the aberrant protein produced from these messages. A number of proteins involved in mRNA translation are regulated in part by proteasome-mediated decay, including the initiation factors eIF4G, eIF4E, and eIF3a, and the poly(A)-binding protein (PABP) interacting protein, Paip2. eIF4E-BP (4E-BP) is differentially regulated by the proteasome: truncated to generate a protein with higher eIF4B binding or completely degraded, depending on its phosphorylation status. Finally, a functional proteasome is required for AU-rich-element (ARE)-mediated decay but the specific role the proteasome plays is unclear. There is data indicating the proteasome can bind to AREs, act as an endonuclease, and degrade ARE-binding proteins. How these events interact with the 5'-to-3' and 3'-to-5' decay pathways is unclear at this time; however, data is provided indicating that proteasomes colocalize with Xrn1 and the exosome RNases Rrp44 and Rrp6 in untreated HeLa cells.
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Affiliation(s)
- Seth A Brooks
- Veterans Administration Medical Center Research, White River Junction, VT 05009, USA.
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Lemay JF, D'Amours A, Lemieux C, Lackner DH, St-Sauveur VG, Bähler J, Bachand F. The nuclear poly(A)-binding protein interacts with the exosome to promote synthesis of noncoding small nucleolar RNAs. Mol Cell 2010; 37:34-45. [PMID: 20129053 DOI: 10.1016/j.molcel.2009.12.019] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 08/11/2009] [Accepted: 11/09/2009] [Indexed: 11/19/2022]
Abstract
Poly(A)-binding proteins (PABPs) are important to eukaryotic gene expression. In the nucleus, the PABP PABPN1 is thought to function in polyadenylation of pre-mRNAs. Deletion of fission yeast pab2, the homolog of mammalian PABPN1, results in transcripts with markedly longer poly(A) tails, but the nature of the hyperadenylated transcripts and the mechanism that leads to RNA hyperadenylation remain unclear. Here we report that Pab2 functions in the synthesis of noncoding RNAs, contrary to the notion that PABPs function exclusively on protein-coding mRNAs. Accordingly, the absence of Pab2 leads to the accumulation of polyadenylated small nucleolar RNAs (snoRNAs). Our findings suggest that Pab2 promotes poly(A) tail trimming from pre-snoRNAs by recruiting the nuclear exosome. This work unveils a function for the nuclear PABP in snoRNA synthesis and provides insights into exosome recruitment to polyadenylated RNAs.
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Affiliation(s)
- Jean-François Lemay
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC JIH 5N4, Canada
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Borowski LS, Szczesny RJ, Brzezniak LK, Stepien PP. RNA turnover in human mitochondria: more questions than answers? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1066-70. [PMID: 20117077 DOI: 10.1016/j.bbabio.2010.01.028] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 01/19/2010] [Accepted: 01/25/2010] [Indexed: 01/16/2023]
Abstract
Protein complexes responsible for RNA degradation play important role in three key aspects of RNA metabolism: they control stability of physiologically functional transcripts, remove the unnecessary RNA processing intermediates and destroy aberrantly formed RNAs. In mitochondria the post-transcriptional events seem to play a major role in regulation of gene expression, therefore RNA turnover is of particular importance. Despite many years of research, the details of this process are still a challenge. This review summarizes emerging landscape of interplay between the Suv3p helicase (SUPV3L1, Suv3), poly(A) polymerase and polynucleotide phosphorylase in controlling RNA degradation in human mitochondria.
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Affiliation(s)
- Lukasz S Borowski
- Institute of Genetics and Biotechnology, Faculty of Biology, Warsaw University, Pawinskiego 5a, 02-106 Warsaw, Poland
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Bonneau F, Basquin J, Ebert J, Lorentzen E, Conti E. The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation. Cell 2009; 139:547-59. [DOI: 10.1016/j.cell.2009.08.042] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 07/15/2009] [Accepted: 08/26/2009] [Indexed: 10/20/2022]
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Andrade JM, Hajnsdorf E, Régnier P, Arraiano CM. The poly(A)-dependent degradation pathway of rpsO mRNA is primarily mediated by RNase R. RNA (NEW YORK, N.Y.) 2009; 15:316-326. [PMID: 19103951 PMCID: PMC2648712 DOI: 10.1261/rna.1197309] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 10/27/2008] [Indexed: 05/27/2023]
Abstract
Polyadenylation is an important factor controlling RNA degradation and RNA quality control mechanisms. In this report we demonstrate for the first time that RNase R has in vivo affinity for polyadenylated RNA and can be a key enzyme involved in poly(A) metabolism. RNase II and PNPase, two major RNA exonucleases present in Escherichia coli, could not account for all the poly(A)-dependent degradation of the rpsO mRNA. RNase II can remove the poly(A) tails but fails to degrade the mRNA as it cannot overcome the RNA termination hairpin, while PNPase plays only a modest role in this degradation. We now demonstrate that in the absence of RNase E, RNase R is the relevant factor in the poly(A)-dependent degradation of the rpsO mRNA. Moreover, we have found that the RNase R inactivation counteracts the extended degradation of this transcript observed in RNase II-deficient cells. Elongated rpsO transcripts harboring increasing poly(A) tails are specifically recognized by RNase R and strongly accumulate in the absence of this exonuclease. The 3' oligo(A) extension may stimulate the binding of RNase R, allowing the complete degradation of the mRNA, as RNase R is not susceptible to RNA secondary structures. Moreover, this regulation is shown to occur despite the presence of PNPase. Similar results were observed with the rpsT mRNA. This report shows that polyadenylation favors in vivo the RNase R-mediated pathways of RNA degradation.
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Affiliation(s)
- José M Andrade
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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