1
|
Kim K, Shi AB, Kelley K, Chen XS. Unraveling the Enzyme-Substrate Properties for APOBEC3A-Mediated RNA Editing. J Mol Biol 2023; 435:168198. [PMID: 37442413 PMCID: PMC10528890 DOI: 10.1016/j.jmb.2023.168198] [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: 03/17/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
The APOBEC3 family of human cytidine deaminases is involved in various cellular processes, including the innate and acquired immune system, mostly through inducing C-to-U in single-stranded DNA and/or RNA mutations. Although recent studies have examined RNA editing by APOBEC3A (A3A), its intracellular target specificity are not fully characterized. To address this gap, we performed in-depth analysis of cellular RNA editing using our recently developed sensitive cell-based fluorescence assay. Our findings demonstrate that A3A and an A3A-loop1-containing APOBEC3B (A3B) chimera are capable of RNA editing. We observed that A3A prefers to edit specific RNA substrates which are not efficiently deaminated by other APOBEC members. The editing efficiency of A3A is influenced by the RNA sequence contexts and distinct stem-loop secondary structures. Based on the identified RNA specificity features, we predicted potential A3A-editing targets in the encoding region of cellular mRNAs and discovered novel RNA transcripts that are extensively edited by A3A. Furthermore, we found a trend of increased synonymous mutations at the sites for more efficient A3A-editing, indicating evolutionary adaptation to the higher editing rate by A3A. Our results shed light on the intracellular RNA editing properties of A3A and provide insights into new RNA targets and potential impact of A3A-mediated RNA editing.
Collapse
Affiliation(s)
- Kyumin Kim
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA. https://twitter.com/KYUMINK1324
| | - Alan B Shi
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kori Kelley
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Program, Departments of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA; Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
2
|
Rakhmetullina A, Akimniyazova A, Niyazova T, Pyrkova A, Tauassarova M, Ivashchenko A, Zielenkiewicz P. Interactions of piRNAs with the mRNA of Candidate Genes in Esophageal Squamous Cell Carcinoma. Curr Issues Mol Biol 2023; 45:6140-6153. [PMID: 37504303 PMCID: PMC10378052 DOI: 10.3390/cimb45070387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/29/2023] Open
Abstract
Recently, a database of human piRNAs (piwi-interacting RNAs) was created, which allows the study of the binding of many piRNAs to the mRNAs of genes involved in many diseases, including cancer. In the present work, we identified the piRNAs that can interact with candidate esophageal squamous cell carcinoma (ESCC) genes. The binding of 480 thousand piRNAs with the mRNAs of 66 candidate ESCC genes was studied. Bioinformatic studies found that piRNAs bind only to the mRNAs of nine candidate genes: AURKA, BMP7, GCOM1, ERCC1, MTHFR, SASH1, SIX4, SULT1A1, and TP53. It has been shown that piRNAs can bind to mRNA by overlapping nucleotide sequences in limited 3'UTR and 5'UTR regions called clusters of binding sites (BSs). The existence of clusters of piRNA BSs significantly reduces the proportion of the nucleotide sequences of these sites in the mRNA of target genes. Competition between piRNAs occurs for binding to the mRNA of target genes. Individual piRNAs and groups of piRNAs that have separate BSs and clusters of BSs in the mRNAs of two or more candidate genes have been identified in the mRNAs of these genes. This organization of piRNAs BSs indicates the interdependence of the expression of candidate genes through piRNAs. Significant differences in the ability of genes to interact with piRNAs prevent the side effects of piRNAs on genes with a lack of the ability to bind such piRNAs. Individual piRNAs and sets of piRNAs are proposed and recommended for the diagnosis and therapy of ESCC.
Collapse
Affiliation(s)
- Aizhan Rakhmetullina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Technology of Production of Livestock Products, A. Baitursynov Kostanay Regional University, Kostanay 110000, Kazakhstan
| | - Aigul Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Togzhan Niyazova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Anna Pyrkova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty 050060, Kazakhstan
| | - Makpal Tauassarova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | | | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| |
Collapse
|
3
|
Rakhmetullina A, Akimniyazova A, Niyazova T, Pyrkova A, Kamenova S, Kondybayeva A, Ryskulova AG, Ivashchenko A, Zielenkiewicz P. Endogenous piRNAs Can Interact with the Omicron Variant of the SARS-CoV-2 Genome. Curr Issues Mol Biol 2023; 45:2950-2964. [PMID: 37185717 PMCID: PMC10136802 DOI: 10.3390/cimb45040193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the COVID-19 pandemic, can still infect populations in many countries around the globe. The Omicron strain is the most mutated variant of SARS-CoV-2. The high transmissibility of the strain and its ability to evade immunity necessitate a priority study of its properties in order to quickly create effective means of preventing its spread. The current research aimed to examine the in silico interaction between PIWI-interacting RNAs (piRNAs) and the SARS-CoV-2 genome (gRNA) to identify endogenous piRNAs and propose synthetic piRNAs with strong antiviral activity for drug development. This study used validated bioinformatic approaches regarding the interaction of more than eight million piRNAs with the SARS-CoV-2 genome. The piRNAs’ binding sites (BSs) in the 5′UTR were located with overlapping nucleotide sequences termed clusters of BSs. Several BSs clusters have been found in the nsp3, nsp7, RNA-dependent RNA polymerase, endoRNAse, S surface glycoprotein, ORF7a, and nucleocapsid. Sixteen synthetic piRNAs that interact with gRNA have been proposed with free binding energy ranging from −170 kJ/mol to −175 kJ/mol, which can be used to create drugs that suppress the reproduction of SARS-CoV-2.
Collapse
Affiliation(s)
- Aizhan Rakhmetullina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Technology of Production of Livestock Products, A. Baitursynov Kostanay Regional University, Kostanay 110000, Kazakhstan
| | - Aigul Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Togzhan Niyazova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Anna Pyrkova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty 050060, Kazakhstan
| | - Saltanat Kamenova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Aida Kondybayeva
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Alma-Gul Ryskulova
- Department of Population Health and Social Sciences, Kazakhstan’s Medical University “KSPH”, Almaty 050060, Kazakhstan
| | | | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| |
Collapse
|
4
|
Souza TML, Pinho VD, Setim CF, Sacramento CQ, Marcon R, Fintelman-Rodrigues N, Chaves OA, Heller M, Temerozo JR, Ferreira AC, Mattos M, Momo PB, Dias SSG, Gesto JSM, Pereira-Dutra F, Viola JPB, Queiroz-Junior CM, Guimarães LC, Chaves IM, Guimarães PPG, Costa VV, Teixeira MM, Bou-Habib DC, Bozza PT, Aguillón AR, Siqueira-Junior J, Macedo-Junior S, Andrade EL, Fadanni GP, Tolouei SEL, Potrich FB, Santos AA, Marques NF, Calixto JB, Rabi JA. Preclinical development of kinetin as a safe error-prone SARS-CoV-2 antiviral able to attenuate virus-induced inflammation. Nat Commun 2023; 14:199. [PMID: 36639383 PMCID: PMC9837764 DOI: 10.1038/s41467-023-35928-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Orally available antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are necessary because of the continuous circulation of new variants that challenge immunized individuals. Because severe COVID-19 is a virus-triggered immune and inflammatory dysfunction, molecules endowed with both antiviral and anti-inflammatory activity are highly desirable. We identified here that kinetin (MB-905) inhibits the in vitro replication of SARS-CoV-2 in human hepatic and pulmonary cell lines. On infected monocytes, MB-905 reduced virus replication, IL-6 and TNFα levels. MB-905 is converted into its triphosphate nucleotide to inhibit viral RNA synthesis and induce error-prone virus replication. Coinhibition of SARS-CoV-2 exonuclease, a proofreading enzyme that corrects erroneously incorporated nucleotides during viral RNA replication, potentiated the inhibitory effect of MB-905. MB-905 shows good oral absorption, its metabolites are stable, achieving long-lasting plasma and lung concentrations, and this drug is not mutagenic nor cardiotoxic in acute and chronic treatments. SARS-CoV-2-infected hACE-mice and hamsters treated with MB-905 show decreased viral replication, lung necrosis, hemorrhage and inflammation. Because kinetin is clinically investigated for a rare genetic disease at regimens beyond the predicted concentrations of antiviral/anti-inflammatory inhibition, our investigation suggests the opportunity for the rapid clinical development of a new antiviral substance for the treatment of COVID-19.
Collapse
Affiliation(s)
- Thiago Moreno L Souza
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil. .,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil.
| | - Vagner D Pinho
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil
| | - Cristina F Setim
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Carolina Q Sacramento
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Rodrigo Marcon
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Otavio A Chaves
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Melina Heller
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Jairo R Temerozo
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil.,Laboratório de Pesquisa sobre o Timo, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - André C Ferreira
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil.,Universidade Iguaçu, Nova Iguaçu, RJ, Brazil
| | - Mayara Mattos
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Patrícia B Momo
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil
| | - Suelen S G Dias
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - João S M Gesto
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Filipe Pereira-Dutra
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - João P B Viola
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute (INCA), Rua André Cavalcanti 37, 5th floor, Centro, Rio de Janeiro, Brazil
| | - Celso Martins Queiroz-Junior
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Lays Cordeiro Guimarães
- Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ian Meira Chaves
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Pedro Pires Goulart Guimarães
- Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vivian Vasconcelos Costa
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Mauro Martins Teixeira
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Dumith Chequer Bou-Habib
- National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil.,Laboratório de Pesquisa sobre o Timo, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Patrícia T Bozza
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Anderson R Aguillón
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil
| | - Jarbas Siqueira-Junior
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Sergio Macedo-Junior
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Edineia L Andrade
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Guilherme P Fadanni
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Sara E L Tolouei
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Francine B Potrich
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Adara A Santos
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Naiani F Marques
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - João B Calixto
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil.
| | - Jaime A Rabi
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil.
| |
Collapse
|
5
|
Cao D, Gooneratne I, Mera C, Vy J, Royal M, Huang B, Park Y, Manjunath A, Liang B. Analysis of Template Variations on RNA Synthesis by Respiratory Syncytial Virus Polymerase. Viruses 2022; 15:47. [PMID: 36680087 PMCID: PMC9863079 DOI: 10.3390/v15010047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a significant threat to infants and elderly individuals globally. Currently, there are no effective therapies or treatments for RSV infection because of an insufficient understanding of the RSV viral machinery. In this study, we investigated the effects of the template variations on RNA synthesis by the RSV polymerase through in vitro RNA synthesis assays. We confirmed the previously reported back-priming activity of the RSV polymerase, which is likely due to the secondary structure of the RNA template. We found that the expansion of the hairpin loop size of the RNA template abolishes the RSV polymerase back-priming activity. At the same time, it seemingly does not affect the de novo RNA synthesis activities of the RSV polymerase. Interestingly, our results show that the RSV polymerase also has a new primer-based terminal extension activity that adds nucleotides to the template and primer in a nonspecific manner. We also mapped the impact of the RNA 5' chemical group on its mobility in a urea-denaturing RNA gel shift assay. Overall, these results enhance our knowledge about the RNA synthesis processes of the RSV polymerase and may guide future therapeutic efforts to develop effective antiviral drugs for RSV treatment.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
6
|
Kamenova S, Sharapkhanova A, Akimniyazova A, Kuzhybayeva K, Kondybayeva A, Rakhmetullina A, Pyrkova A, Ivashchenko A. piRNA and miRNA Can Suppress the Expression of Multiple Sclerosis Candidate Genes. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 13:nano13010022. [PMID: 36615932 PMCID: PMC9823834 DOI: 10.3390/nano13010022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/02/2022] [Accepted: 12/17/2022] [Indexed: 05/14/2023]
Abstract
Multiple sclerosis (MS) is a common inflammatory demyelinating disease with a high mortality rate. MS is caused by many candidate genes whose specific involvement has yet to be established. The aim of our study was to identify endogenous miRNAs and piRNAs involved in the regulation of MS candidate gene expression using bioinformatic methods. A program was used to quantify the interaction of miRNA and piRNA nucleotides with mRNA of the target genes. We used 7310 miRNAs from three databases and 40,000 piRNAs. The mRNAs of the candidate genes revealed miRNA binding sites (BSs), which were located separately or formed clusters of BSs with overlapping nucleotide sequences. The miRNAs from the studied databases were generally bound to mRNAs in different combinations, but miRNAs from only one database were bound to the mRNAs of some genes. For the first time, a direct interaction between the complete sequence of piRNA nucleotides and the nucleotides of their mRNA BSs of target genes was shown. One to several clusters of BSs of miRNA and piRNA were identified in the mRNA of ADAM17, AHI1, CD226, EOMES, EVI5, IL12B, IL2RA, KIF21B, MGAT5, MLANA, SOX8, TNFRSF1A, and ZBTB46 MS candidate genes. These piRNAs form the expression regulation system of the MS candidate genes to coordinate the synthesis of their proteins. Based on these findings, associations of miRNAs, piRNAs, and candidate genes for MS diagnosis are recommended.
Collapse
Affiliation(s)
- Saltanat Kamenova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Aksholpan Sharapkhanova
- Department of Nervous Diseases, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Aigul Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Karlygash Kuzhybayeva
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Aida Kondybayeva
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Aizhan Rakhmetullina
- Department of Technology of Production of Livestock Products, A. Baitursynov Kostanay Regional University, Kostanay 110000, Kazakhstan
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Anna Pyrkova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty 050060, Kazakhstan
| | - Anatoliy Ivashchenko
- Center for Bioinformatics and Nanomedicine, Almaty 050060, Kazakhstan
- Correspondence:
| |
Collapse
|
7
|
Akimniyazova AN, Niyazova TK, Yurikova OY, Pyrkova AY, Zhanuzakov MA, Ivashchenko AT. piRNAs may regulate expression of candidate genes of esophageal adenocarcinoma. Front Genet 2022; 13:1069637. [PMID: 36531220 PMCID: PMC9747755 DOI: 10.3389/fgene.2022.1069637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/18/2022] [Indexed: 07/29/2023] Open
Abstract
Elucidation of ways to regulate the expression of candidate cancer genes will contribute to the development of methods for cancer diagnosis and therapy. The aim of the present study was to show the role of piRNAs as efficient regulators of mRNA translation of esophageal adenocarcinoma (EAC) candidate genes. We used bioinformatic methods to study the interaction characteristics of up to 200 thousand piRNAs with mRNAs of 38 candidate EAC genes. The piRNAs capable of binding to mRNA of AR, BTG3, CD55, ERBB3, FKBP5, FOXP1, LEP, SEPP1, SMAD4, and TP53 genes with high free energy by the formation of hydrogen bonds between canonical (G-C, A-U) and noncanonical (G-U, A-C) piRNA and mRNA nucleotide pairs were revealed. The organization of piRNA binding sites (BSs) in the mRNA of candidate genes was found to overlap nucleotide sequences to form clusters. Clusters of piRNA BSs were detected in the 5'-untranslated region, coding domain sequence, and 3'-untranslated region of mRNA. Due to the formation of piRNA binding site clusters, compaction of BSs occurs and competition between piRNAs for binding to mRNA of candidate EAC genes occurs. Associations of piRNA and candidate genes were selected for use as markers for the diagnosis of EAC.
Collapse
Affiliation(s)
- A. N. Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - T. K. Niyazova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - O. Yu. Yurikova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - A. Yu. Pyrkova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty, Kazakhstan
| | - M. A. Zhanuzakov
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | |
Collapse
|
8
|
Kiliszek A, Pluta M, Bejger M, Rypniewski W. Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair. RNA (NEW YORK, N.Y.) 2022; 29:rna.079414.122. [PMID: 36319090 PMCID: PMC9808570 DOI: 10.1261/rna.079414.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The self-complementary triplet 5'UGG3'/5'UGG3' is a particular structural motif containing noncanonical G-G pair and two U·G wobble pairs. It constitutes a specific structural and electrostatic environment attracting metal ions, particularly Ba2+ ions. Crystallographic research has shown that two Ba2+ cations are located in the major groove of the helix and interact directly with the UGG triplet. A comparison with the unliganded structure has revealed global changes in the RNA structure in the presence of metal ions, whereas thermodynamic measurements have shown increased stability. Moreover, in the structure with Ba2+, an unusual noncanonical G(syn)-G(syn) pair is observed instead of the common G(anti)-G(syn). We further elucidate the metal binding properties of the UGG/UGG triplet by performing crystallographic and thermodynamic studies using DSC and UV melting with other metal ions. The results explain the preferences of the UGG sequence for Ba2+ cations and point to possible applications of this metal-binding propensity.
Collapse
|
9
|
Pacesa M, Lin CH, Cléry A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FHT, Palermo G, Cameron P, Donohoue PD, Jinek M. Structural basis for Cas9 off-target activity. Cell 2022; 185:4067-4081.e21. [PMID: 36306733 PMCID: PMC10103147 DOI: 10.1016/j.cell.2022.09.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/01/2022] [Accepted: 09/15/2022] [Indexed: 11/06/2022]
Abstract
The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is determined by complementarity to a 20-nucleotide segment in its guide RNA. However, Cas9 can bind and cleave partially complementary off-target sequences, which raises safety concerns for its use in clinical applications. Here, we report crystallographic structures of Cas9 bound to bona fide off-target substrates, revealing that off-target binding is enabled by a range of noncanonical base-pairing interactions within the guide:off-target heteroduplex. Off-target substrates containing single-nucleotide deletions relative to the guide RNA are accommodated by base skipping or multiple noncanonical base pairs rather than RNA bulge formation. Finally, PAM-distal mismatches result in duplex unpairing and induce a conformational change in the Cas9 REC lobe that perturbs its conformational activation. Together, these insights provide a structural rationale for the off-target activity of Cas9 and contribute to the improved rational design of guide RNAs and off-target prediction algorithms.
Collapse
Affiliation(s)
- Martin Pacesa
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Chun-Han Lin
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Antoine Cléry
- Institute of Biochemistry, ETH Zurich, Hönggerbergring 64, 8093 Zurich, Switzerland
| | - Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, USA
| | - Katja Bargsten
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthew J Irby
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Frédéric H-T Allain
- Institute of Biochemistry, ETH Zurich, Hönggerbergring 64, 8093 Zurich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, USA
| | - Peter Cameron
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Paul D Donohoue
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| |
Collapse
|
10
|
Akimniyazova A, Yurikova O, Pyrkova A, Rakhmetullina A, Niyazova T, Ryskulova AG, Ivashchenko A. In Silico Study of piRNA Interactions with the SARS-CoV-2 Genome. Int J Mol Sci 2022; 23:9919. [PMID: 36077317 PMCID: PMC9456458 DOI: 10.3390/ijms23179919] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/27/2022] [Accepted: 08/28/2022] [Indexed: 11/25/2022] Open
Abstract
A prolonged pandemic with numerous human casualties requires a rapid search for means to control the various strains of SARS-CoV-2. Since only part of the human population is affected by coronaviruses, there are probably endogenous compounds preventing the spread of these viral pathogens. It has been shown that piRNA (PIWI-interacting RNAs) interact with the mRNA of human genes and can block protein synthesis at the stage of translation. Estimated the effects of piRNA on SARS-CoV-2 genomic RNA (gRNA) in silico. A cluster of 13 piRNA binding sites (BS) in the SARS-CoV-2 gRNA region encoding the oligopeptide was identified. The second cluster of BSs 39 piRNAs also encodes the oligopeptide. The third cluster of 24 piRNA BS encodes the oligopeptide. Twelve piRNAs were identified that strongly interact with the gRNA. Based on the identified functionally important endogenous piRNAs, synthetic piRNAs (spiRNAs) are proposed that will suppress the multiplication of the coronavirus even more strongly. These spiRNAs and selected endogenous piRNAs have little effect on human 17494 protein-coding genes, indicating a low probability of side effects. The piRNA and spiRNA selection methodology created for the control of SARS-CoV-2 (NC_045512.2) can be used to control all strains of SARS-CoV-2.
Collapse
Affiliation(s)
- Aigul Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Oxana Yurikova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Anna Pyrkova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty 050060, Kazakhstan
| | - Aizhan Rakhmetullina
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Togzhan Niyazova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Alma-Gul Ryskulova
- Department of Population Health and Social Sciences, Kazakhstan’s Medical University “KSPH”, Almaty 050060, Kazakhstan
| | | |
Collapse
|
11
|
Bioinformatics Analysis of the Interaction of miRNAs and piRNAs with Human mRNA Genes Having di- and Trinucleotide Repeats. Genes (Basel) 2022; 13:genes13050800. [PMID: 35627185 PMCID: PMC9141802 DOI: 10.3390/genes13050800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
The variability of nucleotide repeats is considered one of the causes of diseases, but their biological function is not understood. In recent years, the interaction of miRNAs and piRNAs with the mRNAs of genes responsible for developing neurodegenerative and oncological diseases and diabetes have been actively studied. We explored candidate genes with nucleotide repeats to predict associations with miRNAs and piRNAs. The parameters of miRNAs and piRNA binding sites with mRNAs of human genes having nucleotide repeats were determined using the MirTarget program. This program defines the start of the initiation of miRNA and piRNA binding to mRNAs, the localization of miRNA and piRNA binding sites in the 5′-untranslated region (5′UTR), coding sequence (CDS) and 3′-untranslated region (3′UTR); the free energy of binding; and the schemes of nucleotide interactions of miRNAs and piRNAs with mRNAs. The characteristics of miRNAs and piRNA binding sites with mRNAs of 73 human genes were determined. The 5′UTR, 3′UTR and CDS of the mRNAs of genes are involved in the development of neurodegenerative, oncological and diabetes diseases with GU, AC dinucleotide and CCG, CAG, GCC, CGG, CGC trinucleotide repeats. The associations of miRNAs, piRNAs and candidate target genes could be recommended for developing methods for diagnosing diseases, including neurodegenerative diseases, oncological diseases and diabetes.
Collapse
|
12
|
Myrzabekova M, Labeit S, Niyazova R, Akimniyazova A, Ivashchenko A. Identification of Bovine miRNAs with the Potential to Affect Human Gene Expression. Front Genet 2022; 12:705350. [PMID: 35087564 PMCID: PMC8787201 DOI: 10.3389/fgene.2021.705350] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Milk and other products from large mammals have emerged during human evolution as an important source of nutrition. Recently, it has been recognized that exogenous miRNAs (mRNA inhibited RNA) contained in milk and other tissues of the mammalian body can enter the human body, which in turn have the ability to potentially regulate human metabolism by affecting gene expression. We studied for exogenous miRNAs from Bos taurus that are potentially contain miRNAs from milk and that could act postprandially as regulators of human gene expression. The interaction of 17,508 human genes with 1025 bta-miRNAs, including 245 raw milk miRNAs was studied. The milk bta-miR-151-5p, bta-miR-151-3p, bta-miRNA-320 each have 11 BSs (binding sites), and bta-miRNA-345-5p, bta-miRNA-614, bta-miRNA-1296b and bta-miRNA-149 has 12, 14, 15 and 26 BSs, respectively. The bta-miR-574-5p from cow’s milk had 209 human genes in mRNAs from one to 25 repeating BSs. We found 15 bta-miRNAs that have 100% complementarity to the mRNA of 13 human target genes. Another 12 miRNAs have BSs in the mRNA of 19 human genes with 98% complementarity. The bta-miR-11975, bta-miR-11976, and bta-miR-2885 BSs are located with the overlap of nucleotide sequences in the mRNA of human genes. Nucleotide sequences of BSs of these miRNAs in 5′UTR mRNA of human genes consisted of GCC repeats with a total length of 18 nucleotides (nt) in 18 genes, 21 nt in 11 genes, 24 nt in 14 genes, and 27–48 nt in nine genes. Nucleotide sequences of BSs of bta-miR-11975, bta-miR-11976, and bta-miR-2885 in CDS mRNA of human genes consisted of GCC repeats with a total length of 18 nt in 33 genes, 21 nt in 13 genes, 24 nt in nine genes, and 27–36 nt in 11 genes. These BSs encoded polyA or polyP peptides. In only one case, the polyR (SLC24A3 gene) was encoded. The possibility of regulating the expression of human genes by exogenous bovine miRNAs is discussed.
Collapse
Affiliation(s)
- Moldir Myrzabekova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Siegfried Labeit
- Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Myomedix GmbH, Neckargemuend, Germany
| | - Raigul Niyazova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aigul Akimniyazova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anatoliy Ivashchenko
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| |
Collapse
|
13
|
Satpathi S, Endoh T, Podbevšek P, Plavec J, Sugimoto N. Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated berberine activity. Nucleic Acids Res 2021; 49:8449-8461. [PMID: 33784402 PMCID: PMC8421223 DOI: 10.1093/nar/gkab189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/25/2021] [Accepted: 03/06/2021] [Indexed: 01/26/2023] Open
Abstract
Non-coding RNAs are regarded as promising targets for the discovery of innovative drugs due to their abundance in the genome and their involvement in many biological processes. Phytochemicals (PCs) are the primary source of ligand-based drugs due to their broad spectrum of biological activities. Since many PCs are heterocyclic and have chemical groups potentially involved in the interaction with nucleic acids, detailed interaction analysis between PCs and RNA is crucial to explore the effect of PCs on RNA functions. In this study, an integrated approach for investigating interactions between PCs and RNAs were demonstrated to verify the RNA-mediated PCs functions by using berberine (BRB) as a model PC. RNA screening of a transcriptome library followed by sequence refinement found minimal RNA motif consisting of a cytosine bulge with U-A and G-U neighbouring base pairs for interaction with BRB. NMR-based structure determination and physicochemical analyses using chemical analogues of BRB demonstrated the importance of electrostatic and stacking interactions for sequence selective interaction and RNA stabilization. The selective interaction with a relatively small RNA motif based on a chemical structure of a planer heterocyclic highlights the biological activities of various PCs mediated by the interactions with particular functional RNAs. In addition, the systematic and quantitative investigations demonstrated in this study could be useful for the development of therapeutic chemicals targeting functional RNAs, based on the PCs, in the future.
Collapse
Affiliation(s)
- Sagar Satpathi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
| | - Peter Podbevšek
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana SI-1000, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana SI-1000, Slovenia
- EN→FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, p. p. 537, SI-1000 Ljubljana, Slovenia
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
| |
Collapse
|
14
|
Garg A, Roske Y, Yamada S, Uehata T, Takeuchi O, Heinemann U. PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases. Nucleic Acids Res 2021; 49:5369-5381. [PMID: 33950203 PMCID: PMC8136824 DOI: 10.1093/nar/gkab316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022] Open
Abstract
The CCCH-type zinc finger (ZnF) containing ZC3H12 ribonucleases are crucial in post-transcriptional immune homoeostasis with ZC3H12A being the only structurally studied member of the family. In this study, we present a structural-biochemical characterization of ZC3H12C, which is linked with chronic immune disorders like psoriasis. We established that the RNA substrate is cooperatively recognized by the PIN and ZnF domains of ZC3H12C and analyzed the crystal structure of ZC3H12C bound to a single-stranded RNA substrate. The RNA engages in hydrogen-bonded contacts and stacking interactions with the PIN and ZnF domains simultaneously. The ZC3H12 ZnF shows unprecedented structural features not previously observed in any member of the CCCH-ZnF family and utilizes stacking interactions via a unique combination of spatially conserved aromatic residues to align the target transcript in a bent conformation onto the ZnF scaffold. Further comparative structural analysis of ZC3H12 CCCH-ZnF suggests that a trinucleotide sequence is recognized by ZC3H12 ZnF in target RNA. Our work not only describes the initial structure-biochemical study on ZC3H12C, but also provides the first molecular insight into RNA recognition by a ZC3H12 family member. Finally, our work points to an evolutionary code for RNA recognition adopted by CCCH-type ZnF proteins.
Collapse
Affiliation(s)
- Ankur Garg
- Macromolecular Structure and Interaction, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Yvette Roske
- Macromolecular Structure and Interaction, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Shinnosuke Yamada
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Udo Heinemann
- Macromolecular Structure and Interaction, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| |
Collapse
|
15
|
Kamenova S, Aralbayeva A, Kondybayeva A, Akimniyazova A, Pyrkova A, Ivashchenko A. Evolutionary Changes in the Interaction of miRNA With mRNA of Candidate Genes for Parkinson's Disease. Front Genet 2021; 12:647288. [PMID: 33859673 PMCID: PMC8042338 DOI: 10.3389/fgene.2021.647288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/11/2021] [Indexed: 12/20/2022] Open
Abstract
Parkinson’s disease (PD) exhibits the second-highest rate of mortality among neurodegenerative diseases. PD is difficult to diagnose and treat due to its polygenic nature. In recent years, numerous studies have established a correlation between this disease and miRNA expression; however, it remains necessary to determine the quantitative characteristics of the interactions between miRNAs and their target genes. In this study, using novel bioinformatics approaches, the quantitative characteristics of the interactions between miRNAs and the mRNAs of candidate PD genes were established. Of the 6,756 miRNAs studied, more than one hundred efficiently bound to mRNA of 61 candidate PD genes. The miRNA binding sites (BS) were located in the 5′-untranslated region (5′UTR), coding sequence (CDS) and 3′-untranslated region (3′UTR) of the mRNAs. In the mRNAs of many genes, the locations of miRNA BS with overlapping nucleotide sequences (clusters) were identified. Such clusters substantially reduced the proportion of nucleotide sequences of miRNA BS in the 5′UTRs, CDSs, and 3′UTRs. The organization of miRNA BS into clusters leads to competition among miRNAs to bind mRNAs. Differences in the binding characteristics of miRNAs to the mRNAs of genes expressed at different rates were identified. Single miRNA BS, polysites for the binding for one miRNA, and multiple BS for two or more miRNAs in one mRNA were identified. Evolutionary changes in the BS of miRNAs and their clusters in 5′UTRs, CDSs and 3′UTRs of mRNA of orthologous candidate PD genes were established. Based on the quantitative characteristics of the interactions between miRNAs and mRNAs candidate PD genes, several associations recommended as markers for the diagnosis of PD.
Collapse
Affiliation(s)
- Saltanat Kamenova
- Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Assel Aralbayeva
- Department of Neurology, Kazakh Medical University, Almaty, Kazakhstan
| | - Aida Kondybayeva
- Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aigul Akimniyazova
- Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anna Pyrkova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anatoliy Ivashchenko
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| |
Collapse
|
16
|
Predicting Associations of miRNAs and Candidate Gastric Cancer Genes for Nanomedicine. NANOMATERIALS 2021; 11:nano11030691. [PMID: 33801990 PMCID: PMC8000878 DOI: 10.3390/nano11030691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/17/2022]
Abstract
Nanoscale miRNAs regulate the synthesis of most human proteins involved in differentiation, proliferation, cell cycle, apoptosis, and other processes associated with the growth and the development of an organism. miRNAs also play a number of important roles in the development of gastric cancer. In this work, we studied the quantitative characteristics of miRNA interactions with 69 candidate gastric cancer genes using bioinformatics approaches. To this end, the MirTarget program was used, which determines the characteristics of miRNA binding to mRNA in the 5′UTR, CDS, and 3′UTR. Associations of miRNAs with alternative target genes and associations of genes with alternative miRNAs were established. The cluster organization of miRNA binding sites (BSs) in mRNA was revealed, leading to the emergence of miRNA competition for binding to the mRNA of a target gene. Groups of target genes with clusters of overlapping BSs include miR-5095, miR-619-5p, miR-1273 family, miR-466, ID01030.3p-miR, ID00436.3p-miR, miR-574-5p, and ID00470.5p-miR. In the defined associations of target genes and miRNAs, miRNA BSs are organized into clusters of multiple BSs, which facilitate the design and the development of a system of chips that can be used to control the state of miRNA and target genes associations in gastric cancer.
Collapse
|
17
|
Rakhmetullina A, Pyrkova A, Aisina D, Ivashchenko A. In silico prediction of human genes as potential targets for rice miRNAs. Comput Biol Chem 2020; 87:107305. [PMID: 32570176 DOI: 10.1016/j.compbiolchem.2020.107305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Exogenous microRNAs (miRNAs) enter the human body through food, and their effects on metabolic processes can be considerable. It is important to determine which miRNAs from plants affect the expression of human genes and the extent of their influence. METHOD The binding sites of 738Oryza sativa miRNAs (osa-miRNAs) that interact with 17 508 mRNAs of human genes were determined using the MirTarget program. RESULT The characteristics of the binding of 46 single osa-miRNAs to 86 mRNAs of human genes with a value of free energy (ΔG) interaction equal 94%-100% from maximum ΔG were established. The findings showed that osa-miR2102-5p, osa-miR5075-3p, osa-miR2097-5p, osa-miR2919 targeted the largest number of genes at 38, 36, 23, 19 sites, respectively. mRNAs of 86 human genes were identified as targets for 93 osa-miRNAs of all family osa-miRNAs with ΔG values equal 94%-98% from maximum ΔG. Each miRNA of the osa-miR156-5p, osa-miR164-5p, osa-miR168-5p, osa-miR395-3p, osa-miR396-3p, osa-miR396-5p, osa-miR444-3p, osa-miR529-3p, osa-miR1846-3p, osa-miR2907-3p families had binding sites in mRNAs of several human target genes. The binding sites of osa-miRNAs in mRNAs of the target genes for each family of osa-miRNAs were conserved when compared to flanking nucleotide sequences. CONCLUSION Target mRNA human genes of osa-miRNAs are also candidate genes of cancer, cardiovascular and neurodegenerative diseases.
Collapse
Affiliation(s)
- Aizhan Rakhmetullina
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan
| | - Anna Pyrkova
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan
| | - Dana Aisina
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan
| | - Anatoliy Ivashchenko
- Department of Biotechnology, SRI of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Al-Farabi 71, Almaty, 050040, Kazakhstan.
| |
Collapse
|
18
|
Abstract
In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense.
Collapse
|
19
|
Zhao J, Kennedy SD, Berger KD, Turner DH. Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:1968-1984. [PMID: 31904966 DOI: 10.1021/acs.jctc.9b00912] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA and DNA are rapidly emerging as targets for therapeutics and as potential frameworks for nanotechnology. Accurate methods for predicting and designing structures and dynamics of nucleic acids would accelerate progress in these and other applications. Suitable approximations for modeling nucleic acids are being developed but require validation against disparate experimental observations. Here, nuclear magnetic resonance spectra for RNA and DNA single strands, CAAU and UCAAUC, are used as benchmarks to test molecular dynamics simulations with AMBER force fields OL3 and ROC-RNA for RNA and BSC1 for DNA. A detailed scheme for making comparisons is also presented. The results reflect recent progress in approximations and reveal remaining challenges.
Collapse
Affiliation(s)
- Jianbo Zhao
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
| | - Scott D Kennedy
- Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States.,Department of Biochemistry and Biophysics, School of Medicine & Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Kyle D Berger
- Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States.,Department of Biochemistry and Biophysics, School of Medicine & Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Douglas H Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
| |
Collapse
|
20
|
Zhang X, Cao Y, Zhang W, Simmons MP. Adenine·cytosine substitutions are an alternative pathway of compensatory mutation in angiosperm ITS2. RNA (NEW YORK, N.Y.) 2020; 26:209-217. [PMID: 31748405 PMCID: PMC6961544 DOI: 10.1261/rna.072660.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/14/2019] [Indexed: 06/01/2023]
Abstract
Compensatory mutations are crucial for functional RNA because they maintain RNA configuration and thus function. Compensatory mutation has traditionally been considered to be a two-step substitution through the GU-base-pair intermediate. We tested for an alternative AC-mediated compensatory mutation (ACCM). We investigated ACCMs by using a comprehensive sampling of ribosomal internal transcribed spacer 2 (ITS2) from 3934 angiosperm species in 80 genera and 55 families. We predicted ITS2 consensus secondary structures by using LocARNA for structure-based alignment and partitioning paired and unpaired regions. We examined and compared the substitution rates and frequencies among base pairs by using RNA-specific models. Base-pair states of ACCMs were mapped onto the inferred phylogenetic trees to infer their evolution. All types of compensatory mutations involving the AC intermediate were observed, but the most frequent substitutions were with AU or GC pairs, which are part of the AU-AC-GC pathway. Compared with the GU intermediate, AC had a lower frequency and higher mutability. Within the AU-AC-GC pathway, the AU-AC substitution rate was much slower than the AC-GC substitution rate. No consistently higher overall rate was identified for either pathway among all 80 sampled lineages, though compensatory mutations through the AC intermediate averaged about half that through the GU intermediate. These results demonstrate an alternative compensatory mutation between AU and GC that helps address the controversial inference of inferred simultaneous double substitutions.
Collapse
Affiliation(s)
- Xinwan Zhang
- Marine College, Shandong University, Weihai 264209, China
| | - Yong Cao
- Marine College, Shandong University, Weihai 264209, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai 264209, China
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| |
Collapse
|