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Smart A, Gilmer O, Caliskan N. Translation Inhibition Mediated by Interferon-Stimulated Genes during Viral Infections. Viruses 2024; 16:1097. [PMID: 39066259 PMCID: PMC11281336 DOI: 10.3390/v16071097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Viruses often pose a significant threat to the host through the exploitation of cellular machineries for their own benefit. In the context of immune responses, myriad host factors are deployed to target viral RNAs and inhibit viral protein translation, ultimately hampering viral replication. Understanding how "non-self" RNAs interact with the host translation machinery and trigger immune responses would help in the development of treatment strategies for viral infections. In this review, we explore how interferon-stimulated gene products interact with viral RNA and the translation machinery in order to induce either global or targeted translation inhibition.
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Affiliation(s)
- Alexandria Smart
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Orian Gilmer
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Neva Caliskan
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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2
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Daniels MG, Werner ME, Li RT, Pascal SM. Exploration of Potential Broad-Spectrum Antiviral Targets in the Enterovirus Replication Element: Identification of Six Distinct 5' Cloverleaves. Viruses 2024; 16:1009. [PMID: 39066172 PMCID: PMC11281424 DOI: 10.3390/v16071009] [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: 05/16/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Enterovirus genomic replication initiates at a predicted RNA cloverleaf (5'CL) at the 5' end of the RNA genome. The 5'CL contains one stem (SA) and three stem-loops (SLB, SLC, SLD). Here, we present an analysis of 5'CL conservation and divergence for 209 human health-related serotypes from the enterovirus genus, including enterovirus and rhinovirus species. Phylogenetic analysis indicates six distinct 5'CL serotypes that only partially correlate with the species definition. Additional findings include that 5'CL sequence conservation is higher between the EV species than between the RV species, the 5'CL of EVA and EVB are nearly identical, and RVC has the lowest 5'CL conservation. Regions of high conservation throughout all species include SA and the loop and nearby bases of SLB, which is consistent with known protein interactions at these sites. In addition to the known protein binding site for the Poly-C binding protein in the loop of SLB, other conserved consecutive cytosines in the stems of SLB and SLC provide additional potential interaction sites that have not yet been explored. Other sites of conservation, including the predicted bulge of SLD and other conserved stem, loop, and junction regions, are more difficult to explain and suggest additional interactions or structural requirements that are not yet fully understood. This more intricate understanding of sequence and structure conservation and variability in the 5'CL may assist in the development of broad-spectrum antivirals against a wide range of enteroviruses, while better defining the range of virus isotypes expected to be affected by a particular antiviral.
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Affiliation(s)
- Morgan G. Daniels
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA; (M.G.D.); (M.E.W.)
| | - Meagan E. Werner
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA; (M.G.D.); (M.E.W.)
| | - Rockwell T. Li
- Math and Science Academy, Ocean Lakes High School, Virginia Beach, VA 23454, USA;
| | - Steven M. Pascal
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA; (M.G.D.); (M.E.W.)
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3
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Mahé M, Rios-Fuller T, Katsara O, Schneider RJ. Non-canonical mRNA translation initiation in cell stress and cancer. NAR Cancer 2024; 6:zcae026. [PMID: 38828390 PMCID: PMC11140632 DOI: 10.1093/narcan/zcae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/08/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
The now well described canonical mRNA translation initiation mechanism of m7G 'cap' recognition by cap-binding protein eIF4E and assembly of the canonical pre-initiation complex consisting of scaffolding protein eIF4G and RNA helicase eIF4A has historically been thought to describe all cellular mRNA translation. However, the past decade has seen the discovery of alternative mechanisms to canonical eIF4E mediated mRNA translation initiation. Studies have shown that non-canonical alternate mechanisms of cellular mRNA translation initiation, whether cap-dependent or independent, serve to provide selective translation of mRNAs under cell physiological and pathological stress conditions. These conditions typically involve the global downregulation of canonical eIF4E1/cap-mediated mRNA translation, and selective translational reprogramming of the cell proteome, as occurs in tumor development and malignant progression. Cancer cells must be able to maintain physiological plasticity to acquire a migratory phenotype, invade tissues, metastasize, survive and adapt to severe microenvironmental stress conditions that involve inhibition of canonical mRNA translation initiation. In this review we describe the emerging, important role of non-canonical, alternate mechanisms of mRNA translation initiation in cancer, particularly in adaptation to stresses and the phenotypic cell fate changes involved in malignant progression and metastasis. These alternate translation initiation mechanisms provide new targets for oncology therapeutics development.
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Affiliation(s)
- Mélanie Mahé
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Tiffany Rios-Fuller
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Olga Katsara
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Robert J Schneider
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
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4
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Jacobebbinghaus N, Lauersen KJ, Kruse O, Baier T. Bicistronic expression of nuclear transgenes in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1400-1412. [PMID: 38415961 DOI: 10.1111/tpj.16677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
In eukaryotic organisms, proteins are typically translated from monocistronic messenger RNAs containing a single coding sequence (CDS). However, recent long transcript sequencing identified 87 nuclear polycistronic mRNAs in Chlamydomonas reinhardtii natively carrying multiple co-expressed CDSs. In this study, we investigated the dynamics of 22 short intergenic sequences derived from these native polycistronic loci by their application in genetic constructs for synthetic transgene expression. A promising candidate sequence was identified based on the quantification of transformation efficiency and expression strength of a fluorescence reporter protein. Subsequently, the expression of independent proteins from one mRNA was verified by cDNA amplification and protein molecular mass characterization. We demonstrated engineered bicistronic expression in vivo to drive successful co-expression of several terpene synthases with the selection marker aphVIII. Bicistronic transgene design resulted in significantly increased (E)-α-bisabolene production of 7.95 mg L-1 from a single open reading frame, 18.1× fold higher than previous reports. Use of this strategy simplifies screening procedures for identification of high-level expressing transformants, does not require the application of additional fluorescence reporters, and reduces the nucleotide footprint compared to classical monocistronic expression cassettes. Although clear advantages for bicistronic transgene expression were observed, this strategy was found to be limited to the aphVIII marker, and further studies are necessary to gain insights into the underlying mechanism that uniquely permits this co-expression from the algal nuclear genome.
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Affiliation(s)
- Nick Jacobebbinghaus
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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5
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Chen QM. The Odds of Protein Translation Control Under Stress. Antioxid Redox Signal 2024; 40:943-947. [PMID: 38573012 DOI: 10.1089/ars.2023.0478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Physical or chemical stress is commonly known to inhibit protein translation at the cellular level. Since the process of protein translation requires catalysis by a multi-component machinery containing eukaryotic initiation factors (eIFs) and ribosomes in a sequence of reactions, how the process fails to proceed and whether certain genes can escape such blockade have provoked research efforts. Lines of evidence have demonstrated that phosphorylation of eIF4E or dephosphorylation of 4E-binding proteins (4E-BPs) prevents the formation of the eukaryotic translation initiation factor 4F (eIF4F) complex, whereas phosphorylation of eukaryotic translation initiation factor 2 alpha (eIF2α) due to activation of heme-regulated inhibitor (HRI), general control nonderepressible 2 (GCN2), protein kinase RNA-like endoplasmic reticulum kinase (PERK), or protein kinase R (PKR) by a diverse array of stressors prevents eIF2-GTP-tRNAiMet ternary complex assembly. These signal the abandonment of translation initiation via 5'-7-methylguanine (m7G) cap recognition by eIF4E. Stress can promote cleavage of tRNAs, impediment of rRNA processing, changes in the epitranscriptomic landscape, ribosome stalling or collision, activation of ribosomal surveillance systems, and assembly of the stress granules. Although these events contribute to the general inhibition of protein translation, a few proteins can bypass such negativity and become translated selectively. Such selective protein translation is primarily m7G cap independent through the integrated stress response or Internal Ribosomal Entry Site (IRES). The newly synthesized proteins often influence cell fate, facilitate cell survival, and build endogenous defense. Insights into the general inhibition of protein translation and selective translation of specific proteins will advance our understanding of the etiology or progression of human diseases involving cellular stress from viral infection or inflammation to myocardial infarction, stroke, or neurodegenerative disease. Antioxid. Redox Signal. 40, 943-947.
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Affiliation(s)
- Qin M Chen
- Holsclaw Endowed Professor of Pharmacology, Director of Pharmacogenomics, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
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6
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Li Y, Zhang L, Wang L, Li J, Zhao Y, Liu F, Wang Q. Structure and function of type IV IRES in picornaviruses: a systematic review. Front Microbiol 2024; 15:1415698. [PMID: 38855772 PMCID: PMC11157119 DOI: 10.3389/fmicb.2024.1415698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
The Picornaviridae is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a core of RNA genome. A typical genome of picornavirus harbors a well-conserved and highly structured RNA element known as the internal ribosome entry site (IRES), functionally essential for viral replication and protein translation. Based on differences in their structures and mechanisms of action, picornaviral IRESs have been categorized into five types: type I, II, III, IV, and V. Compared with the type IV IRES, the others not only are structurally complicated, but also involve multiple initiation factors for triggering protein translation. The type IV IRES, often referred to as hepatitis C virus (HCV)-like IRES due to its structural resemblance to the HCV IRES, exhibits a simpler and more compact structure than those of the other four. The increasing identification of picornaviruses with the type IV IRES suggests that this IRES type seems to reveal strong retention and adaptation in terms of viral evolution. Here, we systematically reviewed structural features and biological functions of the type IV IRES in picornaviruses. A comprehensive understanding of the roles of type IV IRESs will contribute to elucidating the replication mechanism and pathogenesis of picornaviruses.
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Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- Qingdao Center for Animal Disease Control and Prevention, Qingdao, China
| | - Lei Zhang
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, China
| | - Jing Li
- Market Supervision Administration of Huangdao District, Qingdao, China
| | - Yanwei Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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7
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Brennan JW, Sun Y. Defective viral genomes: advances in understanding their generation, function, and impact on infection outcomes. mBio 2024; 15:e0069224. [PMID: 38567955 PMCID: PMC11077978 DOI: 10.1128/mbio.00692-24] [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] [Indexed: 05/09/2024] Open
Abstract
Defective viral genomes (DVGs) are truncated derivatives of their parental viral genomes generated during an aberrant round of viral genomic replication. Distinct classes of DVGs have been identified in most families of both positive- and negative-sense RNA viruses. Importantly, DVGs have been detected in clinical samples from virally infected individuals and an emerging body of association studies implicates DVGs in shaping the severity of disease caused by viral infections in humans. Consequently, there is growing interest in understanding the molecular mechanisms of de novo DVG generation, how DVGs interact with the innate immune system, and harnessing DVGs as novel therapeutics and vaccine adjuvants to attenuate viral pathogenesis. This minireview focuses on single-stranded RNA viruses (excluding retroviridae), and summarizes the current knowledge of DVG generation, the functions and diversity of DVG species, the roles DVGs play in influencing disease progression, and their application as antivirals and vaccine adjuvants.
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Affiliation(s)
- Justin W. Brennan
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Yan Sun
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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8
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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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9
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Schrunk E, Dutka P, Hurt RC, Wu D, Shapiro MG. Bioorthogonal Labeling Enables In Situ Fluorescence Imaging of Expressed Gas Vesicle Nanostructures. Bioconjug Chem 2024; 35:333-339. [PMID: 38346316 PMCID: PMC10961726 DOI: 10.1021/acs.bioconjchem.3c00518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Gas vesicles (GVs) are proteinaceous nanostructures that, along with virus-like particles, encapsulins, nanocages, and other macromolecular assemblies, are being developed for potential biomedical applications. To facilitate such development, it would be valuable to characterize these nanostructures' subcellular assembly and localization. However, traditional fluorescent protein fusions are not tolerated by GVs' primary constituent protein, making optical microscopy a challenge. Here, we introduce a method for fluorescently visualizing intracellular GVs using the bioorthogonal label FlAsH, which becomes fluorescent upon reaction with the six-amino acid tetracysteine (TC) tag. We engineered the GV subunit protein, GvpA, to display the TC tag and showed that GVs bearing TC-tagged GvpA can be successfully assembled and fluorescently visualized in HEK 293T cells. Importantly, this was achieved by replacing only a fraction of GvpA with the tagged version. We used fluorescence images of the tagged GVs to study the GV size and distance distributions within these cells. This bioorthogonal and fractional labeling approach will enable research to provide a greater understanding of GVs and could be adapted to similar proteinaceous nanostructures.
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Affiliation(s)
- Erik Schrunk
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California 91125, United States
| | - Przemysław Dutka
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California 91125, United States
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Robert C Hurt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Di Wu
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California 91125, United States
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California 91125, United States
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Howard Hughes Medical Institute, Pasadena, California 91125, United States
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10
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Tamura T, Yamamoto H, Ogino S, Morioka Y, Tsujino S, Suzuki R, Hiono T, Suzuki S, Isoda N, Sakoda Y, Fukuhara T. A rapid and versatile reverse genetics approach for generating recombinant positive-strand RNA viruses that use IRES-mediated translation. J Virol 2024; 98:e0163823. [PMID: 38353536 PMCID: PMC10949505 DOI: 10.1128/jvi.01638-23] [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: 10/19/2023] [Accepted: 01/24/2024] [Indexed: 03/20/2024] Open
Abstract
Reverse genetics systems have played a central role in developing recombinant viruses for a wide spectrum of virus research. The circular polymerase extension reaction (CPER) method has been applied to studying positive-strand RNA viruses, allowing researchers to bypass molecular cloning of viral cDNA clones and thus leading to the rapid generation of recombinant viruses. However, thus far, the CPER protocol has only been established using cap-dependent RNA viruses. Here, we demonstrate that a modified version of the CPER method can be successfully applied to positive-strand RNA viruses that use cap-independent, internal ribosomal entry site (IRES)-mediated translation. As a proof-of-concept, we employed mammalian viruses with different types (classes I, II, and III) of IRES to optimize the CPER method. Using the hepatitis C virus (HCV, class III), we found that inclusion in the CPER assembly of an RNA polymerase I promoter and terminator, instead of those from polymerase II, allowed greater viral production. This approach was also successful in generating recombinant bovine viral diarrhea virus (class III) following transfection of MDBK/293T co-cultures to overcome low transfection efficiency. In addition, we successfully generated the recombinant viruses from clinical specimens. Our modified CPER could be used for producing hepatitis A virus (HAV, type I) as well as de novo generation of encephalomyocarditis virus (type II). Finally, we generated recombinant HCV and HAV reporter viruses that exhibited replication comparable to that of the wild-type parental viruses. The recombinant HAV reporter virus helped evaluate antivirals. Taking the findings together, this study offers methodological advances in virology. IMPORTANCE The lack of versatility of reverse genetics systems remains a bottleneck in viral research. Especially when (re-)emerging viruses reach pandemic levels, rapid characterization and establishment of effective countermeasures using recombinant viruses are beneficial in disease control. Indeed, numerous studies have attempted to establish and improve the methods. The circular polymerase extension reaction (CPER) method has overcome major obstacles in generating recombinant viruses. However, this method has not yet been examined for positive-strand RNA viruses that use cap-independent, internal ribosome entry site-mediated translation. Here, we engineered a suitable gene cassette to expand the CPER method for all positive-strand RNA viruses. Furthermore, we overcame the difficulty of generating recombinant viruses because of low transfection efficiency. Using this modified method, we also successfully generated reporter viruses and recombinant viruses from a field sample without virus isolation. Taking these findings together, our adapted methodology is an innovative technology that could help advance virologic research.
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Affiliation(s)
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Hirotaka Yamamoto
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Saho Ogino
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Yuhei Morioka
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Shuhei Tsujino
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Takahiro Hiono
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Norikazu Isoda
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshihiro Sakoda
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
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11
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McGee AV, Liu YV, Griffith AL, Szegletes ZM, Wen B, Kraus C, Miller NW, Steger RJ, Escude Velasco B, Bosch JA, Zirin JD, Viswanatha R, Sontheimer EJ, Goodale A, Greene MA, Green TM, Doench JG. Modular vector assembly enables rapid assessment of emerging CRISPR technologies. CELL GENOMICS 2024; 4:100519. [PMID: 38484704 PMCID: PMC10943585 DOI: 10.1016/j.xgen.2024.100519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/31/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
The diversity of CRISPR systems, coupled with scientific ingenuity, has led to an explosion of applications; however, to test newly described innovations in their model systems, researchers typically embark on cumbersome, one-off cloning projects to generate custom reagents that are optimized for their biological questions. Here, we leverage Golden Gate cloning to create the Fragmid toolkit, a modular set of CRISPR cassettes and delivery technologies, along with a web portal, resulting in a combinatorial platform that enables scalable vector assembly within days. We further demonstrate that multiple CRISPR technologies can be assessed in parallel in a pooled screening format using this resource, enabling the rapid optimization of both novel technologies and cellular models. These results establish Fragmid as a robust system for the rapid design of CRISPR vectors, and we anticipate that this assembly approach will be broadly useful for systematic development, comparison, and dissemination of CRISPR technologies.
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Affiliation(s)
- Abby V McGee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yanjing V Liu
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Audrey L Griffith
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zsofia M Szegletes
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bronte Wen
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carolyn Kraus
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nathan W Miller
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan J Steger
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Berta Escude Velasco
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan D Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Raghuvir Viswanatha
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew A Greene
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas M Green
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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12
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Fernández-García L, Ahumada-Marchant C, Lobos-Ávila P, Brauer B, Bustos FJ, Arriagada G. The Mytilus chilensis Steamer-like Element-1 Retrotransposon Antisense mRNA Harbors an Internal Ribosome Entry Site That Is Modulated by hnRNPK. Viruses 2024; 16:403. [PMID: 38543768 PMCID: PMC10974842 DOI: 10.3390/v16030403] [Citation(s) in RCA: 1] [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: 01/23/2024] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 05/23/2024] Open
Abstract
LTR-retrotransposons are transposable elements characterized by the presence of long terminal repeats (LTRs) directly flanking an internal coding region. They share genome organization and replication strategies with retroviruses. Steamer-like Element-1 (MchSLE-1) is an LTR-retrotransposon identified in the genome of the Chilean blue mussel Mytilus chilensis. MchSLE-1 is transcribed; however, whether its RNA is also translated and the mechanism underlying such translation remain to be elucidated. Here, we characterize the MchSLE-1 translation mechanism. We found that the MchSLE-1 5' and 3'LTRs command transcription of sense and antisense RNAs, respectively. Using luciferase reporters commanded by the untranslated regions (UTRs) of MchSLE-1, we found that in vitro 5'UTR sense is unable to initiate translation, whereas the antisense 5'UTR initiates translation even when the eIF4E-eIF4G interaction was disrupted, suggesting the presence of an internal ribosomal entry site (IRES). The antisense 5'UTR IRES activity was tested using bicistronic reporters. The antisense 5'UTR has IRES activity only when the mRNA is transcribed in the nucleus, suggesting that nuclear RNA-binding proteins are required to modulate its activity. Indeed, heterogeneous nuclear ribonucleoprotein K (hnRNPK) was identified as an IRES trans-acting factor (ITAF) of the MchSLE-1 IRES. To our knowledge, this is the first report describing an IRES in an antisense mRNA derived from a mussel LTR-retrotransposon.
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Affiliation(s)
| | | | | | | | | | - Gloria Arriagada
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 83700071, Chile; (L.F.-G.); (C.A.-M.); (P.L.-Á.); (B.B.); (F.J.B.)
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13
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Brito Querido J, Díaz-López I, Ramakrishnan V. The molecular basis of translation initiation and its regulation in eukaryotes. Nat Rev Mol Cell Biol 2024; 25:168-186. [PMID: 38052923 DOI: 10.1038/s41580-023-00624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 12/07/2023]
Abstract
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irene Díaz-López
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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14
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Bhatter N, Dmitriev SE, Ivanov P. Cell death or survival: Insights into the role of mRNA translational control. Semin Cell Dev Biol 2024; 154:138-154. [PMID: 37357122 PMCID: PMC10695129 DOI: 10.1016/j.semcdb.2023.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Cellular stress is an intrinsic part of cell physiology that underlines cell survival or death. The ability of mammalian cells to regulate global protein synthesis (aka translational control) represents a critical, yet underappreciated, layer of regulation during the stress response. Various cellular stress response pathways monitor conditions of cell growth and subsequently reshape the cellular translatome to optimize translational outputs. On the molecular level, such translational reprogramming involves an intricate network of interactions between translation machinery, RNA-binding proteins, mRNAs, and non-protein coding RNAs. In this review, we will discuss molecular mechanisms, signaling pathways, and targets of translational control that contribute to cellular adaptation to stress and to cell survival or death.
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Affiliation(s)
- Nupur Bhatter
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Harvard Initiative for RNA Medicine, Boston, Massachusetts, USA.
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15
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Hutchison V, Lynch A, Gutierrez-Gamez AM, Chen J. Inducible tricolor reporter mouse for parallel imaging of lysosomes, mitochondria, and microtubules. J Cell Biol 2024; 223:e202305086. [PMID: 37917008 PMCID: PMC10621751 DOI: 10.1083/jcb.202305086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/06/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023] Open
Abstract
Cell type-specific use of the same DNA blueprint generates diverse cell types. Such diversity must also be executed via differential deployment of the same subcellular machinery. However, our understanding of the size, distribution, and dynamics of subcellular machinery in native tissues and their connection to cellular diversity remains limited. We generate and characterize an inducible tricolor reporter mouse, dubbed "Kaleidoscope," for simultaneous imaging of lysosomes, mitochondria, and microtubules in any cell type and at a single-cell resolution. The expected subcellular compartments are labeled in culture and in tissues with no impact on cellular and organismal viability. Quantitative and live imaging of the tricolor reporter captures cell type-specific organelle features and kinetics in the lung, as well as their changes after Sendai virus infection. Yap/Taz mutant lung epithelial cells undergo accelerated lamellar body maturation, a subcellular manifestation of their molecular defects. A comprehensive toolbox of reporters for all subcellular structures is expected to transform our understanding of cell biology in tissues.
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Affiliation(s)
- Vera Hutchison
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Anne Lynch
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | | | - Jichao Chen
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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16
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Feng Z, Zhang X, Zhou J, Li Q, Chu L, Di G, Xu Z, Chen Q, Wang M, Jiang X, Xia H, Chen X. An in vitro-transcribed circular RNA targets the mitochondrial inner membrane cardiolipin to ablate EIF4G2 +/PTBP1 + pan-adenocarcinoma. NATURE CANCER 2024; 5:30-46. [PMID: 37845485 DOI: 10.1038/s43018-023-00650-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 09/07/2023] [Indexed: 10/18/2023]
Abstract
In vitro-transcribed (IVT) mRNA has arisen as a rapid method for the production of nucleic acid drugs. Here, we have constructed an oncolytic IVT mRNA that utilizes human rhinovirus type 2 (HRV2) internal ribosomal entry sites (IRESs) to selectively trigger translation in cancer cells with high expression of EIF4G2 and PTBP1. The oncolytic effect was provided by a long hGSDMDc .825 T>A/c.884 A>G-F1LCT mutant mRNA sequence with mitochondrial inner membrane cardiolipin targeting toxicity that triggers mitophagy. Utilizing the permuted intron-exon (PIE) splicing circularization strategy and lipid nanoparticle (LNP) encapsulation reduced immunogenicity of the mRNA and enabled delivery to eukaryotic cells in vivo. Engineered HRV2 IRESs-GSDMDp.D275E/E295G-F1LCT circRNA-LNPs (GSDMDENG circRNA) successfully inhibited EIF4G2+/PTBP1+ pan-adenocarcinoma xenografts growth. Importantly, in a spontaneous tumor model with abnormal EIF4G2 and PTBP1 caused by KRAS G12D mutation, GSDMDENG circRNA significantly prevented the occurrence of pancreatic, lung and colon adenocarcinoma, improved the survival rate and induced persistent KRAS G12D tumor antigen-specific cytotoxic T lymphocyte responses.
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Affiliation(s)
- Zunyong Feng
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Zhongda Hospital, School of Medicine & School of Biological Sciences and Medical Engineering, Advanced Institute for Life and Health & Interdisciplinary Innovation Institute for Medicine and Engineering, Southeast University, Nanjing, China
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore, Singapore
| | - Xuanbo Zhang
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore, Singapore
| | - Jing Zhou
- Department of Anatomy, School of Basic Medicine & School of Medical Imageology, Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu, China
| | - Qiang Li
- Department of Anatomy, School of Basic Medicine & School of Medical Imageology, Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu, China
| | - Liuxi Chu
- Zhongda Hospital, School of Medicine & School of Biological Sciences and Medical Engineering, Advanced Institute for Life and Health & Interdisciplinary Innovation Institute for Medicine and Engineering, Southeast University, Nanjing, China
| | - Guangfu Di
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Zhengyuan Xu
- Department of Anatomy, School of Basic Medicine & School of Medical Imageology, Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu, China
| | - Qun Chen
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Ming Wang
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaochun Jiang
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China.
| | - Hongping Xia
- Zhongda Hospital, School of Medicine & School of Biological Sciences and Medical Engineering, Advanced Institute for Life and Health & Interdisciplinary Innovation Institute for Medicine and Engineering, Southeast University, Nanjing, China.
- Department of Pathology, Nanjing Drum Tower Hospital Clinical College & Key Laboratory of Antibody Technique of National Health Commission & Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, China.
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore, Singapore.
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17
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Geng G, Yu C, Yuan X. Variable eIF4E-binding sites and their synergistic effect on cap-independent translation in a novel IRES of wheat yellow mosaic virus RNA2 isolates. Int J Biol Macromol 2024; 254:128062. [PMID: 37967597 DOI: 10.1016/j.ijbiomac.2023.128062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
Some viral proteins are translated cap-independently via the internal ribosome entry site (IRES), which maintains conservative characteristic among different isolates of the same virus species. However, IRES activity showed a 7-fold variance in RNA2 of wheat yellow mosaic virus (WYMV) HC and LYJN isolates in this study. Based on RNA structure probing and mutagenesis assay, the loosened middle stem of H1 and the hepta-nucleotide top loop of H2 in the LYJN isolate synergistically ensured higher IRES activity than that in the HC isolate. In addition, the conserved top loop of H1 ensured basic IRES activity in HC and LYJN isolates. WYMV RNA2 5'-UTR specifically interacted with the wheat eIF4E, accomplished by the top loop of H1 in the HC isolate or the top loop of H1 and H2 in the LYJN isolate. The high IRES activity of the WYMV RNA2 LYJN isolate was regulated by two eIF4E-binding sites, which showed a synergistic effect mediated by the proximity of the H1 and H2 top loops owing to the flexibility of the middle stem in H1. This report presents a novel evolution pattern of IRES, which altered the number of eIF4E-binding sites to regulate IRES activity.
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Affiliation(s)
- Guowei Geng
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Shandong Province Key Laboratory of Agricultural Microbiology, Tai'an 271018, PR China
| | - Chengming Yu
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Shandong Province Key Laboratory of Agricultural Microbiology, Tai'an 271018, PR China
| | - Xuefeng Yuan
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Shandong Province Key Laboratory of Agricultural Microbiology, Tai'an 271018, PR China.
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18
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Barrington CL, Galindo G, Koch AL, Horton ER, Morrison EJ, Tisa S, Stasevich TJ, Rissland OS. Synonymous codon usage regulates translation initiation. Cell Rep 2023; 42:113413. [PMID: 38096059 PMCID: PMC10790568 DOI: 10.1016/j.celrep.2023.113413] [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: 05/13/2023] [Revised: 08/30/2023] [Accepted: 10/25/2023] [Indexed: 12/30/2023] Open
Abstract
Nonoptimal synonymous codons repress gene expression, but the underlying mechanisms are poorly understood. We and others have previously shown that nonoptimal codons slow translation elongation speeds and thereby trigger messenger RNA (mRNA) degradation. Nevertheless, transcript levels are often insufficient to explain protein levels, suggesting additional mechanisms by which codon usage regulates gene expression. Using reporters in human and Drosophila cells, we find that transcript levels account for less than half of the variation in protein abundance due to codon usage. This discrepancy is explained by translational differences whereby nonoptimal codons repress translation initiation. Nonoptimal transcripts are also less bound by the translation initiation factors eIF4E and eIF4G1, providing a mechanistic explanation for their reduced initiation rates. Importantly, translational repression can occur without mRNA decay and deadenylation, and it does not depend on the known nonoptimality sensor, CNOT3. Our results reveal a potent mechanism of regulation by codon usage where nonoptimal codons repress further rounds of translation.
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Affiliation(s)
- Chloe L Barrington
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gabriel Galindo
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Amanda L Koch
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Emma R Horton
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Evan J Morrison
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Samantha Tisa
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Timothy J Stasevich
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Olivia S Rissland
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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19
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Dobrikov MI, Dobrikova EY, Nardone-White DT, McKay ZP, Brown MC, Gromeier M. Early enterovirus translation deficits extend viral RNA replication and elicit sustained MDA5-directed innate signaling. mBio 2023; 14:e0191523. [PMID: 37962360 PMCID: PMC10746184 DOI: 10.1128/mbio.01915-23] [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: 07/18/2023] [Accepted: 10/02/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Multiple pattern recognition receptors sense vRNAs and initiate downstream innate signaling: endosomal Toll-like receptors (TLRs) 3, 7, and 8 and cytoplasmic RIG-I-like receptors (RLRs) RIG-I, and MDA5. They engage distinct signaling scaffolds: mitochondrial antiviral signaling protein (RLR), MyD88, and TLR-adaptor interacting with SLC15A4 on the lysosome (TLR7 and TLR8) and toll/IL-1R domain-containing adaptor inducing IFN (TLR3). By virtue of their unusual vRNA structure and direct host cell entry path, the innate response to EVs uniquely is orchestrated by MDA5. We reported that PVSRIPO's profound attenuation and loss of cytopathogenicity triggers MDA5-directed polar TBK1-IRF3 signaling that generates priming of polyfunctional antitumor CD8+ T-cell responses and durable antitumor surveillance in vivo. Here we unraveled EV-host relations that control suppression of host type-I IFN responses and show that PVSRIPO's deficient immediate host eIF4G cleavage generates unopposed MDA5-directed downstream signaling cascades resulting in sustained type-I IFN release.
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Affiliation(s)
- Mikhail I. Dobrikov
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
| | - Elena Y. Dobrikova
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
| | - Dasean T. Nardone-White
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical School, Durham, North Carolina, USA
| | - Zachary P. McKay
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
| | - Michael C. Brown
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
| | - Matthias Gromeier
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical School, Durham, North Carolina, USA
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20
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Meyer L, Courtin B, Gomard M, Namane A, Permal E, Badis G, Jacquier A, Fromont-Racine M. eIF2A represses cell wall biogenesis gene expression in Saccharomyces cerevisiae. PLoS One 2023; 18:e0293228. [PMID: 38011112 PMCID: PMC10681259 DOI: 10.1371/journal.pone.0293228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/07/2023] [Indexed: 11/29/2023] Open
Abstract
Translation initiation is a complex and highly regulated process that represents an important mechanism, controlling gene expression. eIF2A was proposed as an alternative initiation factor, however, its role and biological targets remain to be discovered. To further gain insight into the function of eIF2A in Saccharomyces cerevisiae, we identified mRNAs associated with the eIF2A complex and showed that 24% of the most enriched mRNAs encode proteins related to cell wall biogenesis and maintenance. In agreement with this result, we showed that an eIF2A deletion sensitized cells to cell wall damage induced by calcofluor white. eIF2A overexpression led to a growth defect, correlated with decreased synthesis of several cell wall proteins. In contrast, no changes were observed in the transcriptome, suggesting that eIF2A controls the expression of cell wall-related proteins at a translational level. The biochemical characterization of the eIF2A complex revealed that it strongly interacts with the RNA binding protein, Ssd1, which is a negative translational regulator, controlling the expression of cell wall-related genes. Interestingly, eIF2A and Ssd1 bind several common mRNA targets and we found that the binding of eIF2A to some targets was mediated by Ssd1. Surprisingly, we further showed that eIF2A is physically and functionally associated with the exonuclease Xrn1 and other mRNA degradation factors, suggesting an additional level of regulation. Altogether, our results highlight new aspects of this complex and redundant fine-tuned regulation of proteins expression related to the cell wall, a structure required to maintain cell shape and rigidity, providing protection against harmful environmental stress.
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Affiliation(s)
- Laura Meyer
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, Paris, France
| | - Baptiste Courtin
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, Paris, France
| | - Maïté Gomard
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, Paris, France
| | - Abdelkader Namane
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, Paris, France
| | - Emmanuelle Permal
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, Paris, France
| | - Gwenael Badis
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, Paris, France
| | - Alain Jacquier
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, Paris, France
| | - Micheline Fromont-Racine
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, Paris, France
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21
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Lee KH. Internal ribosomal entry site-mediated translational activity of nitric oxide synthase 2. Anim Cells Syst (Seoul) 2023; 27:321-328. [PMID: 38414531 PMCID: PMC10898816 DOI: 10.1080/19768354.2023.2275613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/22/2023] [Indexed: 02/29/2024] Open
Abstract
The internal ribosome entry site (IRES) is a unique structure found in the 5' untranslated region (5'-UTR) of specific messenger RNAs (mRNAs) that allows ribosomes to bind and initiate translation without the need for a cap structure. In this study, we investigated the presence and functional properties of the IRES activity of nitric oxide synthase 2 (NOS2) mRNA, which encodes an enzyme that produces nitric oxide in response to various stimuli such as inflammation. Nitric oxide is a signaling molecule that plays a crucial role in various physiological processes, including immune responses and neuronal signaling. Our results showed the existence of IRES activity in the 5'-UTR of Nos2 mRNA in various cell types. IRES-mediated translation of NOS2 mRNA was higher in neuronal cells and its activity increased in response to lipopolysaccharide (LPS). Despite inhibition of cap-dependent translation, nitrite production was partially maintained. These results demonstrate the presence of IRES activity in the 5'-UTR of NOS2 mRNA and suggest that IRES-mediated translation plays a key role in controlling nitric oxide production in response to LPS, an inflammatory stimulus.
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Affiliation(s)
- Kyung-Ha Lee
- Department of Molecular Biology, Pusan National University, Busan, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, Republic of Korea
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22
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Ariza-Mateos A, Briones C, Perales C, Bayo-Jiménez MT, Domingo E, Gómez J. Viruses as archaeological tools for uncovering ancient molecular relationships. Ann N Y Acad Sci 2023; 1529:3-13. [PMID: 37801367 DOI: 10.1111/nyas.15071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
The entry of a virus into the host cell always implies the alteration of certain intracellular molecular relationships, some of which may involve the recovery of ancient cellular activities. In this sense, viruses are archaeological tools for identifying unexpressed activities in noninfected cells. Among these, activities that hinder virus propagation may represent cellular defense mechanisms, for example, activities that mutagenize the viral genome such as ADAR-1 or APOBEC activities. Instead, those that facilitate virus propagation can be interpreted as the result of viral adaptation to-or mimicking-cellular structures, enabling the virus to perform anthropomorphic activities, including hijacking, manipulating, and reorganizing cellular factors for their own benefit. The alternative we consider here is that some of these second set of cellular activities were already in the uninfected cell but silenced, under the negative control of the cell or lineage, and that they represent a necessary precondition for viral infection. For example, specifically loading an amino acid at the 3'-end of the mRNA of some plant viruses by aminoacyl-tRNA synthetases has proved essential for virus infection despite this reaction not occurring with cellular mRNAs. Other activities of this type are discussed here, together with the biological context in which they acquire a coherent meaning, that is, genetic latency and molecular conflict.
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Affiliation(s)
- Ascensión Ariza-Mateos
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
| | - María Teresa Bayo-Jiménez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Jordi Gómez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
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23
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Harris MT, Marr MT. The intrinsically disordered region of eIF5B stimulates IRES usage and nucleates biological granule formation. Cell Rep 2023; 42:113283. [PMID: 37862172 PMCID: PMC10680144 DOI: 10.1016/j.celrep.2023.113283] [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: 08/27/2022] [Revised: 03/22/2023] [Accepted: 09/29/2023] [Indexed: 10/22/2023] Open
Abstract
Cells activate stress response pathways to survive adverse conditions. Such responses involve the inhibition of global cap-dependent translation. This inhibition is a block that essential transcripts must escape via alternative methods of translation initiation, e.g., an internal ribosome entry site (IRES). IRESs have distinct structures and generally require a limited repertoire of translation factors. Cellular IRESs have been identified in many critical cellular stress response transcripts. We previously identified cellular IRESs in the murine insulin receptor (Insr) and insulin-like growth factor 1 receptor (Igf1r) transcripts and demonstrated their resistance to eukaryotic initiation factor 4F (eIF4F) inhibition. Here, we find that eIF5B preferentially promotes Insr, Igf1r, and hepatitis C virus IRES activity through a non-canonical mechanism that requires its highly charged and disordered N terminus. We find that the N-terminal region of eIF5B can drive cytoplasmic granule formation. This eIF5B granule is triggered by cellular stress and is sufficient to specifically promote IRES activity.
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Affiliation(s)
- Meghan T Harris
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02453, USA
| | - Michael T Marr
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02453, USA.
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24
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McGee AV, Liu YV, Griffith AL, Szegletes ZM, Wen B, Kraus C, Miller NW, Steger RJ, Velasco BE, Bosch JA, Zirin JD, Viswanatha R, Sontheimer EJ, Goodale A, Greene MA, Green TM, Doench JG. Modular vector assembly enables rapid assessment of emerging CRISPR technologies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564061. [PMID: 37961518 PMCID: PMC10634825 DOI: 10.1101/2023.10.25.564061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The diversity of CRISPR systems, coupled with scientific ingenuity, has led to an explosion of applications; however, to test newly-described innovations in their model systems, researchers typically embark on cumbersome, one-off cloning projects to generate custom reagents that are optimized for their biological questions. Here, we leverage Golden Gate cloning to create the Fragmid toolkit, a modular set of CRISPR cassettes and delivery technologies, along with a web portal, resulting in a combinatorial platform that enables scalable vector assembly within days. We further demonstrate that multiple CRISPR technologies can be assessed in parallel in a pooled screening format using this resource, enabling the rapid optimization of both novel technologies and cellular models. These results establish Fragmid as a robust system for the rapid design of CRISPR vectors, and we anticipate that this assembly approach will be broadly useful for systematic development, comparison, and dissemination of CRISPR technologies.
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Affiliation(s)
- Abby V McGee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yanjing V Liu
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Audrey L Griffith
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zsofia M Szegletes
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bronte Wen
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carolyn Kraus
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nathan W Miller
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan J Steger
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Berta Escude Velasco
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan D Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Raghuvir Viswanatha
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew A Greene
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas M Green
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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25
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Wang L, Cui X, Jiang F, Hu Y, Wan W, Li G, Lin Y, Xiao J. Circular RNA Translation in Cardiovascular Diseases. Curr Genomics 2023; 24:66-71. [PMID: 37994328 PMCID: PMC10662380 DOI: 10.2174/1389202924666230911121358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/08/2023] [Accepted: 08/09/2023] [Indexed: 11/24/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of endogenous functional RNA generated by back-splicing. Recently, circRNAs have been found to have certain coding potential. Proteins/peptides translated from circRNAs play essential roles in various diseases. Here, we briefly summarize the basic knowledge and technologies that are usually applied to study circRNA translation. Then, we focus on the research progress of circRNA translation in cardiovascular diseases and discuss the perspective and future direction of translatable circRNA study in cardiovascular diseases.
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Affiliation(s)
- Lijun Wang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Xinxin Cui
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Fei Jiang
- Department of Nursing, Union Hospital, Fujian Medical University Union Hospital, Fuzhou, 350001, China
- Fujian Provincial Special Reserve Talents Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Yuxue Hu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Wensi Wan
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Yanjuan Lin
- Department of Nursing, Union Hospital, Fujian Medical University Union Hospital, Fuzhou, 350001, China
- Fujian Provincial Special Reserve Talents Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
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26
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Clark NK, Harris MT, Dahl WB, Knotts Z, Marr MT. The Insulin Receptor and Insulin like Growth Factor Receptor 5' UTRs Support Translation Initiation Independently of EIF4G1. Mol Cell Biol 2023; 43:485-499. [PMID: 37724583 PMCID: PMC10569357 DOI: 10.1080/10985549.2023.2255120] [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: 07/22/2022] [Accepted: 08/25/2023] [Indexed: 09/21/2023] Open
Abstract
IRES mediated translation initiation requires a different repertoire of factors than canonical cap-dependent translation. Treatments that inhibit the canonical translation factor EIF4G1 have little or no effect on the ability of the Insr and Igf1r cellular IRESes to promote translation. Transcripts for two cellular receptors contain RNA elements that facilitate translation initiation without intact EIF4G1. Cellular IRES mechanisms may resemble viral type III IRESes allowing them to promote translate with a limited number of initiation factors allowing them to work under stress conditions when canonical translation is repressed.
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Affiliation(s)
- Nicholas K. Clark
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts, USA
| | - Meghan T. Harris
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
- Myeloid Therapeutics, Cambridge, Massachusetts, USA
| | - William B. Dahl
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Zachary Knotts
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Michael T. Marr
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
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27
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Zhou Y, Wu J, Yao S, Xu Y, Zhao W, Tong Y, Zhou Z. DeepCIP: A multimodal deep learning method for the prediction of internal ribosome entry sites of circRNAs. Comput Biol Med 2023; 164:107288. [PMID: 37542919 DOI: 10.1016/j.compbiomed.2023.107288] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/05/2023] [Accepted: 07/28/2023] [Indexed: 08/07/2023]
Abstract
Circular RNAs (circRNAs) have been found to have the ability to encode proteins through internal ribosome entry sites (IRESs), which are essential RNA regulatory elements for cap-independent translation. Identification of IRES elements in circRNA is crucial for understanding its function. Previous studies have presented IRES predictors based on machine learning techniques, but they were mainly designed for linear RNA IRES. In this study, we proposed DeepCIP (Deep learning method for CircRNA IRES Prediction), a multimodal deep learning approach that employs both sequence and structural information for circRNA IRES prediction. Our results demonstrate the effectiveness of the sequence and structure models used by DeepCIP in feature extraction and suggest that integrating sequence and structural information efficiently improves the accuracy of prediction. The comparison studies indicate that DeepCIP outperforms other comparative methods on the test set and real circRNA IRES dataset. Furthermore, through the integration of an interpretable analysis mechanism, we elucidate the sequence patterns learned by our model, which align with the previous discovery of motifs that facilitate circRNA translation. Thus, DeepCIP has the potential to enhance the study of the coding potential of circRNAs and contribute to the design of circRNA-based drugs. DeepCIP as a standalone program is freely available at https://github.org/zjupgx/DeepCIP.
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Affiliation(s)
- Yuxuan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang University Innovation Institute for Artificial Intelligence in Medicine - Aoming (Hangzhou) Biomedical Co., Ltd. Joint Laboratory, Hangzhou, 310018, China
| | - Jingcheng Wu
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shihao Yao
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China; China Jiliang University - Aoming (Hangzhou) Biomedical Co., Ltd. Joint Laboratory, Hangzhou, 310018, China
| | - Yulian Xu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China; China Jiliang University - Aoming (Hangzhou) Biomedical Co., Ltd. Joint Laboratory, Hangzhou, 310018, China
| | - Wenbin Zhao
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang University Innovation Institute for Artificial Intelligence in Medicine - Aoming (Hangzhou) Biomedical Co., Ltd. Joint Laboratory, Hangzhou, 310018, China
| | - Yunguang Tong
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; College of Life Sciences, China Jiliang University, Hangzhou, 310018, China; Aoming (Hangzhou) Biomedical Co., Ltd., Hangzhou, 310018, China; Zhejiang University Innovation Institute for Artificial Intelligence in Medicine - Aoming (Hangzhou) Biomedical Co., Ltd. Joint Laboratory, Hangzhou, 310018, China; China Jiliang University - Aoming (Hangzhou) Biomedical Co., Ltd. Joint Laboratory, Hangzhou, 310018, China.
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China.
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28
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Zhao Y, Rai J, Li H. Regulation of translation by ribosomal RNA pseudouridylation. SCIENCE ADVANCES 2023; 9:eadg8190. [PMID: 37595043 PMCID: PMC10438446 DOI: 10.1126/sciadv.adg8190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such as ribosome, however, remains elusive owing to the lack of structures without this natural modification. Here, we studied the translation of a hypopseudouridylated ribosome initiated by the internal ribosome entry site (IRES) elements. We analyzed eight cryo-electron microscopy structures of the ribosome bound with the Taura syndrome virus IRES in multiple functional states. We found widespread loss of pseudouridine-mediated interactions through water and long-range base pairings. In the presence of the translocase, eukaryotic elongation factor 2, and guanosine 5'-triphosphate hydrolysis, the hypopseudouridylated ribosome favors a rare unconducive conformation for decoding that is partially recouped in the ribosome population that remains modified at the P-site uridine. The structural principles learned establish the link between functional defects and modification loss and are likely applicable to other pseudouridine-associated processes.
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Affiliation(s)
- Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Jay Rai
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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29
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Islam RA, Rallis C. Ribosomal Biogenesis and Heterogeneity in Development, Disease, and Aging. EPIGENOMES 2023; 7:17. [PMID: 37606454 PMCID: PMC10443367 DOI: 10.3390/epigenomes7030017] [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: 07/20/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
Although reported in the literature, ribosome heterogeneity is a phenomenon whose extent and implications in cell and organismal biology is not fully appreciated. This has been the case due to the lack of the appropriate techniques and approaches. Heterogeneity can arise from alternative use and differential content of protein and RNA constituents, as well as from post-transcriptional and post-translational modifications. In the few examples we have, it is apparent that ribosomal heterogeneity offers an additional level and potential for gene expression regulation and might be a way towards tuning metabolism, stress, and growth programs to external and internal stimuli and needs. Here, we introduce ribosome biogenesis and discuss ribosomal heterogeneity in various reported occasions. We conclude that a systematic approach in multiple organisms will be needed to delineate this biological phenomenon and its contributions to growth, aging, and disease. Finally, we discuss ribosome mutations and their roles in disease.
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Affiliation(s)
- Rowshan Ara Islam
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK;
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Charalampos Rallis
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK;
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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30
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Chabronova A, van den Akker G, Housmans BAC, Caron MMJ, Cremers A, Surtel DAM, Peffers MJ, van Rhijn LW, Marchand V, Motorin Y, Welting TJM. Depletion of SNORA33 Abolishes ψ of 28S-U4966 and Affects the Ribosome Translational Apparatus. Int J Mol Sci 2023; 24:12578. [PMID: 37628759 PMCID: PMC10454564 DOI: 10.3390/ijms241612578] [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: 07/05/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Eukaryotic ribosomes are complex molecular nanomachines translating genetic information from mRNAs into proteins. There is natural heterogeneity in ribosome composition. The pseudouridylation (ψ) of ribosomal RNAs (rRNAs) is one of the key sources of ribosome heterogeneity. Nevertheless, the functional consequences of ψ-based ribosome heterogeneity and its relevance for human disease are yet to be understood. Using HydraPsiSeq and a chronic disease model of non-osteoarthritic primary human articular chondrocytes exposed to osteoarthritic synovial fluid, we demonstrated that the disease microenvironment is capable of instigating site-specific changes in rRNA ψ profiles. To investigate one of the identified differential rRNA ψ sites (28S-ψ4966), we generated SNORA22 and SNORA33 KO SW1353 cell pools using LentiCRISPRv2/Cas9 and evaluated the ribosome translational capacity by 35S-Met/Cys incorporation, assessed the mode of translation initiation and ribosomal fidelity using dual luciferase reporters, and assessed cellular and ribosomal proteomes by LC-MS/MS. We uncovered that the depletion of SNORA33, but not SNORA22, reduced 28S-ψ4966 levels. The resulting loss of 28S-ψ4966 affected ribosomal protein composition and function and led to specific changes in the cellular proteome. Overall, our pioneering findings demonstrate that cells dynamically respond to disease-relevant changes in their environment by altering their rRNA pseudouridylation profiles, with consequences for ribosome function and the cellular proteome relevant to human disease.
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Affiliation(s)
- Alzbeta Chabronova
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Guus van den Akker
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Bas A C Housmans
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Marjolein M J Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Andy Cremers
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Don A M Surtel
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Mandy J Peffers
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L8 7TX, UK
| | - Lodewijk W van Rhijn
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Virginie Marchand
- UAR2008 IBSLor CNRS-INSERM-Université de Lorraine, F54000 Nancy, France
| | - Yuri Motorin
- UAR2008 IBSLor CNRS-INSERM-Université de Lorraine, F54000 Nancy, France
- UMR7365 IMOPA, CNRS-Université de Lorraine, F54000 Nancy, France
| | - Tim J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center+ (MUMC+), 6229 HX Maastricht, The Netherlands
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31
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Seo JJ, Jung SJ, Yang J, Choi DE, Kim VN. Functional viromic screens uncover regulatory RNA elements. Cell 2023:S0092-8674(23)00675-X. [PMID: 37413987 DOI: 10.1016/j.cell.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 04/21/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023]
Abstract
The number of sequenced viral genomes has surged recently, presenting an opportunity to understand viral diversity and uncover unknown regulatory mechanisms. Here, we conducted a screening of 30,367 viral segments from 143 species representing 96 genera and 37 families. Using a library of viral segments in 3' UTR, we identified hundreds of elements impacting RNA abundance, translation, and nucleocytoplasmic distribution. To illustrate the power of this approach, we investigated K5, an element conserved in kobuviruses, and found its potent ability to enhance mRNA stability and translation in various contexts, including adeno-associated viral vectors and synthetic mRNAs. Moreover, we identified a previously uncharacterized protein, ZCCHC2, as a critical host factor for K5. ZCCHC2 recruits the terminal nucleotidyl transferase TENT4 to elongate poly(A) tails with mixed sequences, delaying deadenylation. This study provides a unique resource for virus and RNA research and highlights the potential of the virosphere for biological discoveries.
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Affiliation(s)
- Jenny J Seo
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Soo-Jin Jung
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jihye Yang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Da-Eun Choi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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32
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Wildi N, Seuberlich T. The Roles of the 5' and 3' Untranslated Regions in Human Astrovirus Replication. Viruses 2023; 15:1402. [PMID: 37376701 DOI: 10.3390/v15061402] [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: 05/02/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
Astroviruses are small nonenveloped single-stranded RNA viruses with a positive sense genome. They are known to cause gastrointestinal disease in a broad spectrum of species. Although astroviruses are distributed worldwide, a gap in knowledge of their biology and disease pathogenesis persists. Many positive-sense single-stranded RNA viruses show conserved and functionally important structures in their 5' and 3' untranslated regions (UTRs). However, not much is known about the role of the 5' and 3' UTRs in the viral replication of HAstV-1. We analyzed the UTRs of HAstV-1 for secondary RNA structures and mutated them, resulting in partial or total UTR deletion. We used a reverse genetic system to study the production of infectious viral particles and to quantify protein expression in the 5' and 3' UTR mutants, and we established an HAstV-1 replicon system containing two reporter cassettes in open reading frames 1a and 2, respectively. Our data show that 3' UTR deletions almost completely abolished viral protein expression and that 5' UTR deletions led to a reduction in infectious virus particles in infection experiments. This indicates that the presence of the UTRs is essential for the life cycle of HAstV-1 and opens avenues for further research.
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Affiliation(s)
- Nicole Wildi
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Torsten Seuberlich
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
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33
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Wu C, Wang S, Cao T, Huang T, Xu L, Wang J, Li Q, Wang Y, Qian L, Xu L, Xia Y, Huang X. Newly discovered mechanisms that mediate tumorigenesis and tumour progression: circRNA-encoded proteins. J Cell Mol Med 2023; 27:1609-1620. [PMID: 37070530 PMCID: PMC10273065 DOI: 10.1111/jcmm.17751] [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: 01/31/2023] [Revised: 03/18/2023] [Accepted: 04/08/2023] [Indexed: 04/19/2023] Open
Abstract
Proteins produced by cap-independent translation mediated by an internal ribosome entry site (IRES) in circular RNAs (circRNAs) play important roles in tumour progression. To date, numerous studies have been performed on circRNAs and the proteins they encode. In this review, we summarize the biogenesis of circRNAs and the mechanisms regulating circRNA-encoded proteins expression. We also describe relevant research methods and their applications to biological processes such as tumour cell proliferation, metastasis, epithelial-mesenchymal transition (EMT), apoptosis, autophagy and chemoresistance. This paper offers deeper insights into the roles that circRNA-encoded proteins play in tumours. It also provides a theoretical basis for the use of circRNA-encoded proteins as biomarkers of tumorigenesis and for the development of new targets for tumour therapy.
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Affiliation(s)
- Chengwei Wu
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Song Wang
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Tingting Cao
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Tao Huang
- Department of Thoracic SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
| | - Lishuai Xu
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Jiawei Wang
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Qian Li
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Ye Wang
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Long Qian
- The Second Affiliated Hospital of Wannan Medical CollegeWuhuChina
| | - Li Xu
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Yabin Xia
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Xiaoxu Huang
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
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Hutchison V, Lynch A, Gamez AMG, Chen J. An inducible tricolor reporter mouse for simultaneous imaging of lysosomes, mitochondria and microtubules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541817. [PMID: 37293075 PMCID: PMC10245888 DOI: 10.1101/2023.05.22.541817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cell-type-specific use of the same DNA blueprint generates diverse cell types. Such diversity must also be executed via differential deployment of the same subcellular machinery. However, our understanding of the size, distribution, and dynamics of subcellular machinery in native tissues, and their connection to cellular diversity, remain limited. We generate and characterize an inducible tricolor reporter mouse, dubbed "kaleidoscope", for simultaneous imaging of lysosomes, mitochondria and microtubules in any cell type and at a single cell resolution. The expected subcellular compartments are labeled in culture and in tissues with no impact on cellular and organismal viability. Quantitative and live imaging of the tricolor reporter captures cell-type-specific organelle features and kinetics in the lung, as well as their changes after Sendai virus infection. Yap/Taz mutant lung epithelial cells undergo accelerated lamellar body maturation, a subcellular manifestation of their molecular defects. A comprehensive toolbox of reporters for all subcellular structures is expected to transform our understanding of cell biology in tissues.
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Affiliation(s)
- Vera Hutchison
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Anne Lynch
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | - Jichao Chen
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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Loan Young T, Chang Wang K, James Varley A, Li B. Clinical Delivery of Circular RNA: Lessons Learned from RNA Drug Development. Adv Drug Deliv Rev 2023; 197:114826. [PMID: 37088404 DOI: 10.1016/j.addr.2023.114826] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
Circular RNAs (circRNA) represent a distinct class of covalently closed-loop RNA molecules, which play diverse roles in regulating biological processes and disease states. The enhanced stability of synthetic circRNAs compared to their linear counterparts has recently garnered considerable research interest, paving the way for new therapeutic applications. While clinical circRNA technology is still in its early stages, significant advancements in mRNA technology offer valuable insights into its potential future applications. Two primary obstacles that must be addressed are the development of efficient production methods and the optimization of delivery systems. To expedite progress in this area, this review aims to provide an overview of the current state of knowledge on circRNA structure and function, outline recent techniques for synthesizing circRNAs, highlight key delivery strategies and applications, and discuss the current challenges and future prospects in the field of circRNA-based therapeutics.
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Affiliation(s)
- Tiana Loan Young
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Kevin Chang Wang
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Andrew James Varley
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Bowen Li
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3M2, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada.
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36
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Kemmler CL, Moran HR, Murray BF, Scoresby A, Klem JR, Eckert RL, Lepovsky E, Bertho S, Nieuwenhuize S, Burger S, D'Agati G, Betz C, Puller AC, Felker A, Ditrychova K, Bötschi S, Affolter M, Rohner N, Lovely CB, Kwan KM, Burger A, Mosimann C. Next-generation plasmids for transgenesis in zebrafish and beyond. Development 2023; 150:dev201531. [PMID: 36975217 PMCID: PMC10263156 DOI: 10.1242/dev.201531] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
Transgenesis is an essential technique for any genetic model. Tol2-based transgenesis paired with Gateway-compatible vector collections has transformed zebrafish transgenesis with an accessible modular system. Here, we establish several next-generation transgenesis tools for zebrafish and other species to expand and enhance transgenic applications. To facilitate gene regulatory element testing, we generated Gateway middle entry vectors harboring the small mouse beta-globin minimal promoter coupled to several fluorophores, CreERT2 and Gal4. To extend the color spectrum for transgenic applications, we established middle entry vectors encoding the bright, blue-fluorescent protein mCerulean and mApple as an alternative red fluorophore. We present a series of p2A peptide-based 3' vectors with different fluorophores and subcellular localizations to co-label cells expressing proteins of interest. Finally, we established Tol2 destination vectors carrying the zebrafish exorh promoter driving different fluorophores as a pineal gland-specific transgenesis marker that is active before hatching and through adulthood. exorh-based reporters and transgenesis markers also drive specific pineal gland expression in the eye-less cavefish (Astyanax). Together, our vectors provide versatile reagents for transgenesis applications in zebrafish, cavefish and other models.
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Affiliation(s)
- Cassie L. Kemmler
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Hannah R. Moran
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Brooke F. Murray
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Aaron Scoresby
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - John R. Klem
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Rachel L. Eckert
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Elizabeth Lepovsky
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Sylvain Bertho
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Susan Nieuwenhuize
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Sibylle Burger
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Gianluca D'Agati
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Charles Betz
- Growth & Development, Biozentrum, Spitalstrasse 41, University of Basel, 4056 Basel, Switzerland
| | - Ann-Christin Puller
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Anastasia Felker
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Karolina Ditrychova
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Seraina Bötschi
- Department of Molecular Life Sciences, University of Zurich, 8057 Zürich, Switzerland
| | - Markus Affolter
- Growth & Development, Biozentrum, Spitalstrasse 41, University of Basel, 4056 Basel, Switzerland
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - C. Ben Lovely
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Kristen M. Kwan
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexa Burger
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Christian Mosimann
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
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Abstract
Viruses lack the properties to replicate independently due to the limited resources encoded in their genome; therefore, they hijack the host cell machinery to replicate and survive. Picornaviruses get the prerequisite for effective protein synthesis through specific sequences known as internal ribosome entry sites (IRESs). In the past 2 decades, significant progress has been made in identifying different types of IRESs in picornaviruses. This review will discuss the past and current findings related to the five different types of IRESs and various internal ribosome entry site trans-acting factors (ITAFs) that either promote or suppress picornavirus translation and replication. Some IRESs are inefficient and thus require ITAFs. To achieve their full efficiency, they recruit various ITAFs, which enable them to translate more effectively and efficiently, except type IV IRES, which does not require any ITAFs. Although there are two kinds of ITAFs, one promotes viral IRES-dependent translation, and the second type restricts. Picornaviruses IRESs are classified into five types based on their use of sequence, ITAFs, and initiation factors. Some ITAFs regulate IRES activity by localizing to the viral replication factories in the cytoplasm. Also, some drugs, chemicals, and herbal extracts also regulate viral IRES-dependent translation and replication. Altogether, this review will elaborate on our understanding of the past and recent advancements in the IRES-dependent translation and replication of picornaviruses. IMPORTANCE The family Picornaviridae is divided into 68 genera and 158 species. The viruses belonging to this family range from public health importance, such as poliovirus, enterovirus A71, and hepatitis A virus, to animal viruses of great economic importance, such as foot-and-mouth disease virus. The genomes of picornaviruses contain 5' untranslated regions (5' UTRs), which possess crucial and highly structured stem-loops known as IRESs. IRES assemble the ribosomes and facilitate the cap-independent translation. Virus-host interaction is a hot spot for researchers, which warrants deep insight into understanding viral pathogenesis better and discovering new tools and ways for viral restriction to improve human and animal health. The cap-independent translation in the majority of picornaviruses is modulated by ITAFs, which bind to various IRES regions to initiate the translation. The discoveries of ITAFs substantially contributed to understanding viral replication behavior and enhanced our knowledge about virus-host interaction more effectively than ever before. This review discussed the various types of IRESs found in Picornaviridae, past and present discoveries regarding ITAFs, and their mechanism of action. The herbal extracts, drugs, and chemicals, which indicated their importance in controlling viruses, were also summarized. In addition, we discussed the movement of ITAFs from the nucleus to viral replication factories. We believe this review will stimulate researchers to search for more novel ITAFs, drugs, herbal extracts, and chemicals, enhancing the understanding of virus-host interaction.
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Shestakova ED, Smirnova VV, Shatsky IN, Terenin IM. Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story. RNA (NEW YORK, N.Y.) 2023; 29:282-299. [PMID: 36517212 PMCID: PMC9945437 DOI: 10.1261/rna.079462.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The eukaryotic initiation factor 4G2 (eIF4G2, DAP5, Nat1, p97) was discovered in 1997. Over the past two decades, dozens of papers have presented contradictory data on eIF4G2 function. Since its identification, eIF4G2 has been assumed to participate in noncanonical translation initiation mechanisms, but recent results indicate that it can be involved in scanning as well. In particular, eIF4G2 provides leaky scanning through some upstream open reading frames (uORFs), which are typical for long 5' UTRs of mRNAs from higher eukaryotes. It is likely the protein can also help the ribosome overcome other impediments during scanning of the 5' UTRs of animal mRNAs. This may explain the need for eIF4G2 in higher eukaryotes, as many mRNAs that encode regulatory proteins have rather long and highly structured 5' UTRs. Additionally, they often bind to various proteins, which also hamper the movement of scanning ribosomes. This review discusses the suggested mechanisms of eIF4G2 action, denotes obscure or inconsistent results, and proposes ways to uncover other fundamental mechanisms in which this important protein factor may be involved in higher eukaryotes.
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Affiliation(s)
- Ekaterina D Shestakova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Victoria V Smirnova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
- Sirius University of Science and Technology, Sochi 354349, Russia
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Roles of circular RNAs in regulating the development of glioma. J Cancer Res Clin Oncol 2023; 149:979-993. [PMID: 35776196 DOI: 10.1007/s00432-022-04136-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Glioma is the most common malignant tumor in the central nervous system. In patients with glioma, the prognosis is poor and median survival is only 12-15 months. With the recent development of sequencing technology, important roles of noncoding RNAs are being discovered in cells, especially those of circular RNAs (circRNAs). Because circRNAs are stable, abundant, and highly conserved, they are regarded as novel biomarkers in the early diagnosis and prognosis of diseases. PURPOSE In this review, roles and mechanisms of circRNAs in the development of glioma are summarized. METHODS This paper collects and reviews relevant PubMed literature. CONCLUSION Several classes of circRNAs are highly expressed in glioma and are associated with malignant biological behaviors of gliomas, including proliferation, migration, invasion, apoptosis, angiogenesis, and drug resistance. Further studies are needed to clarify the roles of circRNAs in glioma and to determine whether it is possible to increase therapeutic effects on tumors through circRNA intervention.
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40
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Liu Y, Cui J, Hoffman AR, Hu JF. Eukaryotic translation initiation factor eIF4G2 opens novel paths for protein synthesis in development, apoptosis and cell differentiation. Cell Prolif 2023; 56:e13367. [PMID: 36547008 PMCID: PMC9977666 DOI: 10.1111/cpr.13367] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/21/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022] Open
Abstract
Protein translation is a critical regulatory event involved in nearly all physiological and pathological processes. Eukaryotic translation initiation factors are dedicated to translation initiation, the most highly regulated stage of protein synthesis. Eukaryotic translation initiation factor 4G2 (eIF4G2, also called p97, NAT1 and DAP5), an eIF4G family member that lacks the binding sites for 5' cap binding protein eIF4E, is widely considered to be a key factor for internal ribosome entry sites (IRESs)-mediated cap-independent translation. However, recent findings demonstrate that eIF4G2 also supports many other translation initiation pathways. In this review, we summarize the role of eIF4G2 in a variety of cap-independent and -dependent translation initiation events. Additionally, we also update recent findings regarding the role of eIF4G2 in apoptosis, cell survival, cell differentiation and embryonic development. These studies reveal an emerging new picture of how eIF4G2 utilizes diverse translational mechanisms to regulate gene expression.
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Affiliation(s)
- Yudi Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital, Jilin University, Changchun, Jilin, P.R. China
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital, Jilin University, Changchun, Jilin, P.R. China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, California, USA
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital, Jilin University, Changchun, Jilin, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, California, USA
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41
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Eastman C, Tapprich WE. RNA Structure in the 5' Untranslated Region of Enterovirus D68 Strains with Differing Neurovirulence Phenotypes. Viruses 2023; 15:295. [PMID: 36851509 PMCID: PMC9959730 DOI: 10.3390/v15020295] [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: 12/08/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Enterovirus-D68 (EV-D68) is a positive-sense single-stranded RNA virus within the family Picornaviridae. EV-D68 was initially considered a respiratory virus that primarily affected children. However, in 2014, EV-D68 outbreaks occurred causing the expected increase in respiratory illness cases, but also an increase in acute flaccid myelitis cases (AFM). Sequencing of 2014 outbreak isolates revealed variations in the 5' UTR of the genome compared to the historical Fermon strain. The structure of the 5' UTR RNA contributes to enterovirus virulence, including neurovirulence in poliovirus, and could contribute to neurovirulence in contemporary EV-D68 strains. In this study, the secondary and tertiary structures of 5' UTR RNA from the Fermon strain and 2014 isolate KT347251.1 are analyzed and compared. Secondary structures were determined using SHAPE-MaP and TurboFold II and tertiary structures were predicted using 3dRNAv2.0. Comparison of RNA structures between the EV-D68 strains shows significant remodeling at the secondary and tertiary levels. Notable secondary structure changes occurred in domains II, IV and V. Shifts in the secondary structure changed the tertiary structure of the individual domains and the orientation of the domains. Our comparative structural models for EV-D68 5' UTR RNA highlight regions of the molecule that could be targeted for treatment of neurotropic enteroviruses.
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Affiliation(s)
| | - William E. Tapprich
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
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Murphy JC, Harrington EM, Schumann S, Vasconcelos EJR, Mottram TJ, Harper KL, Aspden JL, Whitehouse A. Kaposi's sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs. Nat Commun 2023; 14:300. [PMID: 36653366 PMCID: PMC9849454 DOI: 10.1038/s41467-023-35914-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Historically, ribosomes were viewed as unchanged homogeneous macromolecular machines with no regulatory capacity for mRNA translation. An emerging concept is that heterogeneity of ribosomal composition exists, exerting a regulatory function or specificity in translational control. This is supported by recent discoveries identifying compositionally distinct specialised ribosomes that actively regulate mRNA translation. Viruses lack their own translational machinery and impose high translational demands on the host during replication. We explore the possibility that KSHV manipulates ribosome biogenesis producing specialised ribosomes which preferentially translate viral transcripts. Quantitative proteomic analysis identified changes in the stoichiometry and composition of precursor ribosomal complexes during the switch from latent to lytic replication. We demonstrate the enhanced association of ribosomal biogenesis factors BUD23 and NOC4L, and the KSHV ORF11 protein, with small ribosomal subunit precursor complexes during lytic replication. BUD23 depletion resulted in significantly reduced viral gene expression, culminating in dramatic reduction of infectious virion production. Ribosome profiling demonstrated BUD23 is essential for reduced association of ribosomes with KSHV uORFs in late lytic genes, required for the efficient translation of the downstream coding sequence. Results provide mechanistic insights into KSHV-mediated manipulation of cellular ribosome composition inducing a population of specialised ribosomes facilitating efficient translation of viral mRNAs.
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Affiliation(s)
- James C Murphy
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Elena M Harrington
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sophie Schumann
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Timothy J Mottram
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Katherine L Harper
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- LeedsOmics, University of Leeds, Leeds, LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
- LeedsOmics, University of Leeds, Leeds, LS2 9JT, UK.
- Department of Biochemistry & Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
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Liu C, Wu X, Gokulnath P, Li G, Xiao J. The Functions and Mechanisms of Translatable Circular RNAs. J Pharmacol Exp Ther 2023; 384:52-60. [PMID: 35609922 DOI: 10.1124/jpet.122.001085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 04/03/2022] [Accepted: 04/29/2022] [Indexed: 12/27/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed RNA produced by back-splicing. CircRNAs have been considered as a type of noncoding RNAs for a long time. However, recent studies have shown that circRNAs can be translated into functional proteins. Proteins specifically encoded by circRNAs have been proved to play important roles in cancer pathology. In this review, we introduce the methods commonly used to identify and validate circRNA translation in detail. We also describe the major mechanisms driving the translation of these circRNAs. In addition, we summarize the main functions of the circRNA-encoded proteins in both physiologic and pathologic conditions. Finally, we discuss the therapeutic potential and challenges in the usage of synthetic translatable circRNAs. This brief review highlights recent discoveries made in this field and the progress of therapy based on translatable circRNAs. SIGNIFICANCE STATEMENT: Understanding the translation of circRNA could facilitate the identification of novel drug targets in various diseases. Moreover, some circRNA encoded proteins were demonstrated to have therapeutic functions in cancer. The application of synthetic circRNAs as carriers to achieve stable protein expression in vitro and in vivo has tremendous therapeutic potential.
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Affiliation(s)
- Chang Liu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China (C.L., X.W., J.X.); Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China (C.L., X.W., J.X.); and Cardiovascular Division of the Massachusetts General Hospitaland Harvard Medical School, Boston, Massachusetts (P.G., G.L.)
| | - Xinying Wu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China (C.L., X.W., J.X.); Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China (C.L., X.W., J.X.); and Cardiovascular Division of the Massachusetts General Hospitaland Harvard Medical School, Boston, Massachusetts (P.G., G.L.)
| | - Priyanka Gokulnath
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China (C.L., X.W., J.X.); Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China (C.L., X.W., J.X.); and Cardiovascular Division of the Massachusetts General Hospitaland Harvard Medical School, Boston, Massachusetts (P.G., G.L.)
| | - Guoping Li
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China (C.L., X.W., J.X.); Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China (C.L., X.W., J.X.); and Cardiovascular Division of the Massachusetts General Hospitaland Harvard Medical School, Boston, Massachusetts (P.G., G.L.)
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China (C.L., X.W., J.X.); Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China (C.L., X.W., J.X.); and Cardiovascular Division of the Massachusetts General Hospitaland Harvard Medical School, Boston, Massachusetts (P.G., G.L.)
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44
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Polio and Its Epidemiology. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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Kim H, Aponte-Diaz D, Sotoudegan MS, Shengjuler D, Arnold JJ, Cameron CE. The enterovirus genome can be translated in an IRES-independent manner that requires the initiation factors eIF2A/eIF2D. PLoS Biol 2023; 21:e3001693. [PMID: 36689548 PMCID: PMC9894558 DOI: 10.1371/journal.pbio.3001693] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 02/02/2023] [Accepted: 01/04/2023] [Indexed: 01/24/2023] Open
Abstract
RNA recombination in positive-strand RNA viruses is a molecular-genetic process, which permits the greatest evolution of the genome and may be essential to stabilizing the genome from the deleterious consequences of accumulated mutations. Enteroviruses represent a useful system to elucidate the details of this process. On the biochemical level, it is known that RNA recombination is catalyzed by the viral RNA-dependent RNA polymerase using a template-switching mechanism. For this mechanism to function in cells, the recombining genomes must be located in the same subcellular compartment. How a viral genome is trafficked to the site of genome replication and recombination, which is membrane associated and isolated from the cytoplasm, is not known. We hypothesized that genome translation was essential for colocalization of genomes for recombination. We show that complete inactivation of internal ribosome entry site (IRES)-mediated translation of a donor enteroviral genome enhanced recombination instead of impairing it. Recombination did not occur by a nonreplicative mechanism. Rather, sufficient translation of the nonstructural region of the genome occurred to support subsequent steps required for recombination. The noncanonical translation initiation factors, eIF2A and eIF2D, were required for IRES-independent translation. Our results support an eIF2A/eIF2D-dependent mechanism under conditions in which the eIF2-dependent mechanism is inactive. Detection of an IRES-independent mechanism for translation of the enterovirus genome provides an explanation for a variety of debated observations, including nonreplicative recombination and persistence of enteroviral RNA lacking an IRES. The existence of an eIF2A/eIF2D-dependent mechanism in enteroviruses predicts the existence of similar mechanisms in other viruses.
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Affiliation(s)
- Hyejeong Kim
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - David Aponte-Diaz
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Mohamad S. Sotoudegan
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | | | - Jamie J. Arnold
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Craig E. Cameron
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
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46
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Brownsword MJ, Locker N. A little less aggregation a little more replication: Viral manipulation of stress granules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1741. [PMID: 35709333 PMCID: PMC10078398 DOI: 10.1002/wrna.1741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 01/31/2023]
Abstract
Recent exciting studies have uncovered how membrane-less organelles, also known as biocondensates, are providing cells with rapid response pathways, allowing them to re-organize their cellular contents and adapt to stressful conditions. Their assembly is driven by the phase separation of their RNAs and intrinsically disordered protein components into condensed foci. Among these, stress granules (SGs) are dynamic cytoplasmic biocondensates that form in response to many stresses, including activation of the integrated stress response or viral infections. SGs sit at the crossroads between antiviral signaling and translation because they concentrate signaling proteins and components of the innate immune response, in addition to translation machinery and stalled mRNAs. Consequently, they have been proposed to contribute to antiviral activities, and therefore are targeted by viral countermeasures. Equally, SGs components can be commandeered by viruses for their own efficient replication. Phase separation processes are an important component of the viral life cycle, for example, driving the assembly of replication factories or inclusion bodies. Therefore, in this review, we will outline the recent understanding of this complex interplay and tug of war between viruses, SGs, and their components. This article is categorized under: RNA in Disease and Development > RNA in Disease Translation > Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Matthew J. Brownsword
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
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47
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Liu Y, Wu Z, Wu D, Gao N, Lin J. Reconstitution of Multi-Protein Complexes through Ribozyme-Assisted Polycistronic Co-Expression. ACS Synth Biol 2022; 12:136-143. [PMID: 36512506 PMCID: PMC9872166 DOI: 10.1021/acssynbio.2c00416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In living cells, proteins often exert their functions by interacting with other proteins forming protein complexes. Obtaining homogeneous samples of protein complexes with correct fold and stoichiometry is critical for its biochemical and biophysical characterization as well as functional investigation. Here, we developed a Ribozyme-Assisted Polycistronic co-expression system (pRAP) for heterologous co-production and in vivo assembly of multi-subunit complexes. In the pRAP system, a polycistronic mRNA transcript is co-transcriptionally converted into individual mono-cistrons in vivo. Each cistron can initiate translation with comparable efficiency, resulting in balanced production for all subunits, thus permitting faithful protein complex assembly. With pRAP polycistronic co-expression, we have successfully reconstituted large functional multi-subunit complexes involved in mammalian translation initiation. Our invention provides a valuable tool for studying the molecular mechanisms of biological processes.
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Affiliation(s)
- Yan Liu
- State
Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan
Hospital, Fudan University, Shanghai 200438, China
| | - Zihan Wu
- State
Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan
Hospital, Fudan University, Shanghai 200438, China
| | - Damu Wu
- State
Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for
Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ning Gao
- State
Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for
Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jinzhong Lin
- State
Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan
Hospital, Fudan University, Shanghai 200438, China,. Tel.: +86-21-31246764
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48
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Wang X, Zhu J, Zhang D, Liu G. Ribosomal control in RNA virus-infected cells. Front Microbiol 2022; 13:1026887. [PMID: 36419416 PMCID: PMC9677555 DOI: 10.3389/fmicb.2022.1026887] [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: 08/24/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Viruses are strictly intracellular parasites requiring host cellular functions to complete their reproduction cycle involving virus infection of host cell, viral genome replication, viral protein translation, and virion release. Ribosomes are protein synthesis factories in cells, and viruses need to manipulate ribosomes to complete their protein synthesis. Viruses use translation initiation factors through their own RNA structures or cap structures, thereby inducing ribosomes to synthesize viral proteins. Viruses also affect ribosome production and the assembly of mature ribosomes, and regulate the recognition of mRNA by ribosomes, thereby promoting viral protein synthesis and inhibiting the synthesis of host antiviral immune proteins. Here, we review the remarkable mechanisms used by RNA viruses to regulate ribosomes, in particular, the mechanisms by which RNA viruses induce the formation of specific heterogeneous ribosomes required for viral protein translation. This review provides valuable insights into the control of viral infection and diseases from the perspective of viral protein synthesis.
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49
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Roles of RNA-binding proteins in immune diseases and cancer. Semin Cancer Biol 2022; 86:310-324. [PMID: 35351611 DOI: 10.1016/j.semcancer.2022.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 01/27/2023]
Abstract
Genetic information that is transcribed from DNA to mRNA, and then translated from mRNA to protein, is regulated by complex and sophisticated post-transcriptional mechanisms. Recently, it has become clear that mRNA degradation not only acts to remove unnecessary mRNA, but is also closely associated with the regulation of translation initiation, and is essential for maintaining cellular homeostasis. Various RNA-binding proteins (RBPs) have been reported to play central roles in the mechanisms of mRNA stability and translation initiation through various signal transduction pathways, and to modulate gene expression faster than the transcription process via post-transcriptional modifications in response to intracellular and extracellular stimuli, without de novo protein synthesis. On the other hand, inflammation is necessary for the elimination of pathogens associated with infection, and is tightly controlled to avoid the overexpression of inflammatory cytokines, such as interleukin 6 (IL-6) and tumor necrosis factor (TNF). It is increasingly becoming clear that RBPs play important roles in the post-transcriptional regulation of these immune responses. Furthermore, it has been shown that the aberrant regulation of RBPs leads to chronic inflammation and autoimmune diseases. Although it has been recognized since the time of Rudolf Virchow in the 19th century that cancer-associated inflammation contributes to tumor onset and progression, involvement of the disruption of the balance between anti-tumor immunity via the immune surveillance system and pro-tumor immunity by cancer-associated inflammation in the malignant transformation of cancer remains elusive. Recently, the dysregulated expression and activation of representative RBPs involved in regulation of the production of pro-inflammatory cytokines have been shown to be involved in tumor progression. In this review, we summarize the recent progress in our understanding of the functional roles of these RBPs in several types of immune responses, and the involvement of RBP dysregulation in the pathogenesis of immune diseases and cancer, and discuss possible therapeutic strategies against cancer by targeting RBPs, coupled with immunotherapy.
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Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential. Mol Cell 2022; 82:3840-3855.e8. [PMID: 36270248 PMCID: PMC9636002 DOI: 10.1016/j.molcel.2022.09.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/13/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
The use of alternative promoters, splicing, and cleavage and polyadenylation (APA) generates mRNA isoforms that expand the diversity and complexity of the transcriptome. Here, we uncovered thousands of previously undescribed 5' uncapped and polyadenylated transcripts (5' UPTs). We show that these transcripts resist exonucleases due to a highly structured RNA and N6-methyladenosine modification at their 5' termini. 5' UPTs appear downstream of APA sites within their host genes and are induced upon APA activation. Strong enrichment in polysomal RNA fractions indicates 5' UPT translational potential. Indeed, APA promotes downstream translation initiation, non-canonical protein output, and consistent changes to peptide presentation at the cell surface. Lastly, we demonstrate the biological importance of 5' UPTs using Bcl2, a prominent anti-apoptotic gene whose entire coding sequence is a 5' UPT generated from 5' UTR-embedded APA sites. Thus, APA is not only accountable for terminating transcripts, but also for generating downstream uncapped RNAs with translation potential and biological impact.
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