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Ghaleh SS, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Sisakht MM, Farhadi A, Bakhtiari MM, Kuehu DL, Deng Y. SARS-CoV-2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents. Virus Res 2023; 323:199016. [PMID: 36473671 PMCID: PMC9721189 DOI: 10.1016/j.virusres.2022.199016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Rapid transmission and reproduction of RNA viruses prepare conducive conditions to have a high rate of mutations in their genetic sequence. The viral mutations make adapt the severe acute respiratory syndrome coronavirus 2 in the host environment and help the evolution of the virus then also caused a high mortality rate by the virus that threatens worldwide health. Mutations and adaptation help the virus to escape confrontations that are done against it. METHODS In the present study, we analyzed 6,510,947 sequences of non-structural protein 1 as one of the conserved regions of the virus to find out frequent mutations and substitute amino acids in comparison with the wild type. NSP1 mutations rate divided into continents were different. RESULTS Based on this continental categorization, E87D in global vision and also in Europe notably increased. The E87D mutation has signed up to January 2022 as the first frequent mutation observed. The remarkable mutations, H110Y and R24C have the second and third frequencies, respectively. CONCLUSION According to the important role of non-structural protein 1 on the host mRNA translation, developing drug design against the protein could be so hopeful to find more effective ways the control and then treatment of the global pandemic coronavirus disease 2019.
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Affiliation(s)
| | - Karim Rahimian
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics. Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Bahar Mahdavi
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Tokhanbigli
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran (IAUPS)
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Amin Farhadi
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Mahsa Mousakhan Bakhtiari
- Pediatric Cell Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Donna Lee Kuehu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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Wang SM, Goguadze N, Kimura Y, Yasui Y, Pan B, Wang TY, Nakamura Y, Lin YT, Hogan QH, Wilson KL, Su TP, Wu HE. Genomic Action of Sigma-1 Receptor Chaperone Relates to Neuropathic Pain. Mol Neurobiol 2021; 58:2523-2541. [PMID: 33459966 PMCID: PMC8128747 DOI: 10.1007/s12035-020-02276-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/28/2020] [Indexed: 11/16/2022]
Abstract
Sigma-1 receptors (Sig-1Rs) are endoplasmic reticulum (ER) chaperones implicated in neuropathic pain. Here we examine if the Sig-1R may relate to neuropathic pain at the level of dorsal root ganglia (DRG). We focus on the neuronal excitability of DRG in a "spare nerve injury" (SNI) model of neuropathic pain in rats and find that Sig-1Rs likely contribute to the genesis of DRG neuronal excitability by decreasing the protein level of voltage-gated Cav2.2 as a translational inhibitor of mRNA. Specifically, during SNI, Sig-1Rs translocate from ER to the nuclear envelope via a trafficking protein Sec61β. At the nucleus, the Sig-1R interacts with cFos and binds to the promoter of 4E-BP1, leading to an upregulation of 4E-BP1 that binds and prevents eIF4E from initiating the mRNA translation for Cav2.2. Interestingly, in Sig-1R knockout HEK cells, Cav2.2 is upregulated. In accordance with those findings, we find that intra-DRG injection of Sig-1R agonist (+)pentazocine increases frequency of action potentials via regulation of voltage-gated Ca2+ channels. Conversely, intra-DRG injection of Sig-1R antagonist BD1047 attenuates neuropathic pain. Hence, we discover that the Sig-1R chaperone causes neuropathic pain indirectly as a translational inhibitor.
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MESH Headings
- Animals
- Calcium Channels, N-Type/genetics
- Calcium Channels, N-Type/metabolism
- Endoplasmic Reticulum/metabolism
- Eukaryotic Initiation Factor-4E/metabolism
- Ganglia, Spinal/metabolism
- Gene Expression Regulation
- Genome
- HEK293 Cells
- Humans
- Intracellular Signaling Peptides and Proteins/metabolism
- Male
- Nerve Tissue/injuries
- Nerve Tissue/pathology
- Neuralgia/genetics
- Nuclear Envelope/metabolism
- Promoter Regions, Genetic/genetics
- Protein Biosynthesis
- Proto-Oncogene Proteins c-fos/metabolism
- RNA Caps/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats, Sprague-Dawley
- Receptors, sigma/agonists
- Receptors, sigma/genetics
- Receptors, sigma/metabolism
- SEC Translocation Channels/metabolism
- Transcription, Genetic
- Sigma-1 Receptor
- Rats
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Affiliation(s)
- Shao-Ming Wang
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH/DHHS, Suite 3512, 333 Cassell Drive, Baltimore, MD, 21224, USA
| | - Nino Goguadze
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH/DHHS, Suite 3512, 333 Cassell Drive, Baltimore, MD, 21224, USA
| | - Yuriko Kimura
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH/DHHS, Suite 3512, 333 Cassell Drive, Baltimore, MD, 21224, USA
| | - Yuko Yasui
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH/DHHS, Suite 3512, 333 Cassell Drive, Baltimore, MD, 21224, USA
| | - Bin Pan
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Tzu-Yun Wang
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH/DHHS, Suite 3512, 333 Cassell Drive, Baltimore, MD, 21224, USA
- Department of Psychiatry, College of Medicine, National Cheng Kung University, Tainan City, 70101, Taiwan
| | - Yoki Nakamura
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH/DHHS, Suite 3512, 333 Cassell Drive, Baltimore, MD, 21224, USA
- Department of Pharmacology, Graduate School of Biomedical & Health Science, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Yu-Ting Lin
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH/DHHS, Suite 3512, 333 Cassell Drive, Baltimore, MD, 21224, USA
| | - Quinn H Hogan
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Katherine L Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Tsung-Ping Su
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH/DHHS, Suite 3512, 333 Cassell Drive, Baltimore, MD, 21224, USA.
| | - Hsiang-En Wu
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, NIH/DHHS, Suite 3512, 333 Cassell Drive, Baltimore, MD, 21224, USA
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Ciesiolka A, Stroynowska-Czerwinska A, Joachimiak P, Ciolak A, Kozlowska E, Michalak M, Dabrowska M, Olejniczak M, Raczynska KD, Zielinska D, Wozna-Wysocka M, Krzyzosiak WJ, Fiszer A. Artificial miRNAs targeting CAG repeat expansion in ORFs cause rapid deadenylation and translation inhibition of mutant transcripts. Cell Mol Life Sci 2021; 78:1577-96. [PMID: 32696070 DOI: 10.1007/s00018-020-03596-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Polyglutamine (polyQ) diseases are incurable neurological disorders caused by CAG repeat expansion in the open reading frames (ORFs) of specific genes. This type of mutation in the HTT gene is responsible for Huntington’s disease (HD). CAG repeat-targeting artificial miRNAs (art-miRNAs) were shown as attractive therapeutic approach for polyQ disorders as they caused allele-selective decrease in the level of mutant proteins. Here, using polyQ disease models, we aimed to demonstrate how miRNA-based gene expression regulation is dependent on target sequence features. We show that the silencing efficiency and selectivity of art-miRNAs is influenced by the localization of the CAG repeat tract within transcript and the specific sequence context. Furthermore, we aimed to reveal the events leading to downregulation of mutant polyQ proteins and found very rapid activation of translational repression and HTT transcript deadenylation. Slicer-activity of AGO2 was dispensable in this process, as determined in AGO2 knockout cells generated with CRISPR-Cas9 technology. We also showed highly allele-selective downregulation of huntingtin in human HD neural progenitors (NPs). Taken together, art-miRNA activity may serve as a model of the cooperative activity and targeting of ORF regions by endogenous miRNAs.
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Abstract
Antisense PNA-peptide conjugates targeting essential bacterial genes have shown interesting potential for discovery of novel precision antibiotics. In this context, the minimal inhibitory concentration (MIC) assay is used to assess and compare the antimicrobial activity of natural as well as synthetic antimicrobial compounds. Here, we describe the determination of the minimal inhibitory concentration of peptide-PNA conjugates against Escherichia coli. This method can be expanded to include minimal bactericidal concentration (MBC) determination and kill-curve kinetics.
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Affiliation(s)
- Lise Goltermann
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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5
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Jackowiak P, Hojka-Osinska A, Gasiorek K, Stelmaszczuk M, Gudanis D, Gdaniec Z, Figlerowicz M. Effects of G-quadruplex topology on translational inhibition by tRNA fragments in mammalian and plant systems in vitro. Int J Biochem Cell Biol 2017; 92:148-154. [PMID: 28989078 DOI: 10.1016/j.biocel.2017.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/05/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023]
Abstract
The folding of tRNA fragments (tRFs) into G-quadruplex structures and the implications of G-quadruplexes in translational inhibition have been studied mainly in mammalian systems. To increase our knowledge of these phenomena, we determined the influence of human and plant tRFs and model G-quadruplexes on translation in rabbit reticulocyte lysate and wheat germ extract. The efficiency of translational inhibition in the mammalian system was strongly associated with the type of G-quadruplex topology. In the plant system, the ability of a small RNA to adopt the G-quadruplex conformation was not sufficient to repress translation, indicating the importance of other structural determinants.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Hojka-Osinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Gasiorek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Michal Stelmaszczuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Dorota Gudanis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznan, Poland.
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McEwan DL, Feinbaum RL, Stroustrup N, Haas W, Conery AL, Anselmo A, Sadreyev R, Ausubel FM. Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway. BMC Biol 2016; 14:105. [PMID: 27927200 PMCID: PMC5143455 DOI: 10.1186/s12915-016-0334-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many pathogens secrete toxins that target key host processes resulting in the activation of immune pathways. The secreted Pseudomonas aeruginosa toxin Exotoxin A (ToxA) disrupts intestinal protein synthesis, which triggers the induction of a subset of P. aeruginosa-response genes in the nematode Caenorhabditis elegans. RESULTS We show here that one ToxA-induced C. elegans gene, the Tribbles pseudokinase ortholog nipi-3, is essential for host survival following exposure to P. aeruginosa or ToxA. We find that NIPI-3 mediates the post-developmental expression of intestinal immune genes and proteins and primarily functions in parallel to known immune pathways, including p38 MAPK signaling. Through mutagenesis screening, we identify mutants of the bZIP C/EBP transcription factor cebp-1 that suppress the hypersusceptibility defects of nipi-3 mutants. CONCLUSIONS NIPI-3 is a negative regulator of CEBP-1, which in turn negatively regulates protective immune mechanisms. This pathway represents a previously unknown innate immune signaling pathway in intestinal epithelial cells that is involved in the surveillance of cellular homeostasis. Because NIPI-3 and CEBP-1 are also essential for C. elegans development, NIPI-3 is analogous to other key innate immune signaling molecules such as the Toll receptors in Drosophila that have an independent role during development.
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Affiliation(s)
- Deborah L. McEwan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
| | - Rhonda L. Feinbaum
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
| | | | - Wilhelm Haas
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA USA
| | - Annie L. Conery
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
- Present Address: Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA USA
| | - Frederick M. Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA
- Department of Genetics, Harvard Medical School, Boston, MA USA
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