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Khan D, Fox PL. Host-like RNA Elements Regulate Virus Translation. Viruses 2024; 16:468. [PMID: 38543832 PMCID: PMC10976276 DOI: 10.3390/v16030468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/01/2024] Open
Abstract
Viruses are obligate, intracellular parasites that co-opt host cell machineries for propagation. Critical among these machineries are those that translate RNA into protein and their mechanisms of control. Most regulatory mechanisms effectuate their activity by targeting sequence or structural features at the RNA termini, i.e., at the 5' or 3' ends, including the untranslated regions (UTRs). Translation of most eukaryotic mRNAs is initiated by 5' cap-dependent scanning. In contrast, many viruses initiate translation at internal RNA regions at internal ribosome entry sites (IRESs). Eukaryotic mRNAs often contain upstream open reading frames (uORFs) that permit condition-dependent control of downstream major ORFs. To offset genome compression and increase coding capacity, some viruses take advantage of out-of-frame overlapping uORFs (oORFs). Lacking the essential machinery of protein synthesis, for example, ribosomes and other translation factors, all viruses utilize the host apparatus to generate virus protein. In addition, some viruses exhibit RNA elements that bind host regulatory factors that are not essential components of the translation machinery. SARS-CoV-2 is a paradigm example of a virus taking advantage of multiple features of eukaryotic host translation control: the virus mimics the established human GAIT regulatory element and co-opts four host aminoacyl tRNA synthetases to form a stimulatory binding complex. Utilizing discontinuous transcription, the elements are present and identical in all SARS-CoV-2 subgenomic RNAs (and the genomic RNA). Thus, the virus exhibits a post-transcriptional regulon that improves upon analogous eukaryotic regulons, in which a family of functionally related mRNA targets contain elements that are structurally similar but lacking sequence identity. This "thrifty" virus strategy can be exploited against the virus since targeting the element can suppress the expression of all subgenomic RNAs as well as the genomic RNA. Other 3' end viral elements include 3'-cap-independent translation elements (3'-CITEs) and 3'-tRNA-like structures. Elucidation of virus translation control elements, their binding proteins, and their mechanisms can lead to novel therapeutic approaches to reduce virus replication and pathogenicity.
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Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul L. Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Putlyaeva LV, Demin DE, Korneev KV, Kasyanov AS, Tatosyan KA, Kulakovskiy IV, Kuprash DV, Schwartz AM. Potential Markers of Autoimmune Diseases, Alleles rs115662534(T) and rs548231435(C), Disrupt the Binding of Transcription Factors STAT1 and EBF1 to the Regulatory Elements of Human CD40 Gene. BIOCHEMISTRY (MOSCOW) 2019; 83:1534-1542. [PMID: 30878028 DOI: 10.1134/s0006297918120118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
CD40 receptor is expressed on B lymphocytes and other professional antigen-presenting cells. The binding of CD40 to its ligand CD154 on the surface of T helper cells plays an important role in the activation of B lymphocytes required for production of antibodies, in particular, against autoantigens. Association of several single nucleotide polymorphisms (SNPs) located in the non-coding areas of human CD40 locus with the elevated risk of autoimmune diseases has been demonstrated. The most studied of these SNPs is rs4810485 located in the first intron of the CD40 gene. Expression of the CD40 gene in B lymphocytes of donors homozygous for the common allelic variant of this polymorphism (G) is higher than in B cells from donors carrying the minor (T) variant. We investigated the enhancer activity of this fragment of the CD40 locus in human B cell lines and showed that it is independent on the rs4810485 alleles. However, the minor allelic variants of the rs4810485-linked SNPs rs548231435 and rs115662534 were associated with a significant decrease in the activity of the CD40 promoter due to the impairments in the binding of EBF1 and STAT1 transcription factors, respectively.
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Affiliation(s)
- L V Putlyaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - D E Demin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, Dolgoprudny, Moscow Region, 141701, Russia
| | - K V Korneev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - A S Kasyanov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - K A Tatosyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - I V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia.,Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - D V Kuprash
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia. .,Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, Dolgoprudny, Moscow Region, 141701, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - A M Schwartz
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia. .,Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, Dolgoprudny, Moscow Region, 141701, Russia
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Gordiienko I, Shlapatska L, Kovalevska L, Sidorenko SP. SLAMF1/CD150 in hematologic malignancies: Silent marker or active player? Clin Immunol 2018; 204:14-22. [PMID: 30616923 DOI: 10.1016/j.clim.2018.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/12/2022]
Abstract
SLAMF1/CD150 receptor is a founder of signaling lymphocyte activation molecule (SLAM) family of cell-surface receptors. It is widely expressed on cells within hematopoietic system. In hematologic malignancies CD150 cell surface expression is restricted to cutaneous T-cell lymphomas, few types of B-cell non-Hodgkin's lymphoma, near half of cases of chronic lymphocytic leukemia, Hodgkin's lymphoma, and multiple myeloma. Differential expression among various types of hematological malignancies allows considering CD150 as diagnostical and potential prognostic marker. Moreover, CD150 may be a target for antibody-based or measles virus oncolytic therapy. Due to CD150 signaling properties it is involved in regulation of malignant cell fate decision and tumor microenvironment in Hodgkin's lymphoma and chronic lymphocytic leukemia. This review summarizes evidence for the important role of CD150 in pathogenesis of hematologic malignancies.
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Affiliation(s)
- Inna Gordiienko
- Department of Molecular and Cellular Pathobiology, R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology National Academy of Sciences of Ukraine, Kyiv, Ukraine.
| | - Larysa Shlapatska
- Department of Molecular and Cellular Pathobiology, R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Larysa Kovalevska
- Department of Molecular and Cellular Pathobiology, R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Svetlana P Sidorenko
- Department of Molecular and Cellular Pathobiology, R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology National Academy of Sciences of Ukraine, Kyiv, Ukraine
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Gunišová S, Hronová V, Mohammad MP, Hinnebusch AG, Valášek LS. Please do not recycle! Translation reinitiation in microbes and higher eukaryotes. FEMS Microbiol Rev 2018; 42:165-192. [PMID: 29281028 PMCID: PMC5972666 DOI: 10.1093/femsre/fux059] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/20/2017] [Indexed: 12/14/2022] Open
Abstract
Protein production must be strictly controlled at its beginning and end to synthesize a polypeptide that faithfully copies genetic information carried in the encoding mRNA. In contrast to viruses and prokaryotes, the majority of mRNAs in eukaryotes contain only one coding sequence, resulting in production of a single protein. There are, however, many exceptional mRNAs that either carry short open reading frames upstream of the main coding sequence (uORFs) or even contain multiple long ORFs. A wide variety of mechanisms have evolved in microbes and higher eukaryotes to prevent recycling of some or all translational components upon termination of the first translated ORF in such mRNAs and thereby enable subsequent translation of the next uORF or downstream coding sequence. These specialized reinitiation mechanisms are often regulated to couple translation of the downstream ORF to various stimuli. Here we review all known instances of both short uORF-mediated and long ORF-mediated reinitiation and present our current understanding of the underlying molecular mechanisms of these intriguing modes of translational control.
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Affiliation(s)
- Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Mahabub Pasha Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
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Schwartz AM, Putlyaeva LV, Covich M, Klepikova AV, Akulich KA, Vorontsov IE, Korneev KV, Dmitriev SE, Polanovsky OL, Sidorenko SP, Kulakovskiy IV, Kuprash DV. Early B-cell factor 1 (EBF1) is critical for transcriptional control of SLAMF1 gene in human B cells. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:1259-68. [PMID: 27424222 DOI: 10.1016/j.bbagrm.2016.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/01/2016] [Accepted: 07/12/2016] [Indexed: 10/21/2022]
Abstract
Signaling lymphocytic activation molecule family member 1 (SLAMF1)/CD150 is a co-stimulatory receptor expressed on a variety of hematopoietic cells, in particular on mature lymphocytes activated by specific antigen, costimulation and cytokines. Changes in CD150 expression level have been reported in association with autoimmunity and with B-cell chronic lymphocytic leukemia. We characterized the core promoter for SLAMF1 gene in human B-cell lines and explored binding sites for a number of transcription factors involved in B cell differentiation and activation. Mutations of SP1, STAT6, IRF4, NF-kB, ELF1, TCF3, and SPI1/PU.1 sites resulted in significantly decreased promoter activity of varying magnitude, depending on the cell line tested. The most profound effect on the promoter strength was observed upon mutation of the binding site for Early B-cell factor 1 (EBF1). This mutation produced a 10-20 fold drop in promoter activity and pinpointed EBF1 as the master regulator of human SLAMF1 gene in B cells. We also identified three potent transcriptional enhancers in human SLAMF1 locus, each containing functional EBF1 binding sites. Thus, EBF1 interacts with specific binding sites located both in the promoter and in the enhancer regions of the SLAMF1 gene and is critical for its expression in human B cells.
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Affiliation(s)
- Anton M Schwartz
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Lidia V Putlyaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Milica Covich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Kseniya A Akulich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ilya E Vorontsov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Kirill V Korneev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey E Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg L Polanovsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Svetlana P Sidorenko
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Kuprash
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
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