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Pastor F, Charles E, Belmudes L, Chabrolles H, Cescato M, Rivoire M, Burger T, Passot G, Durantel D, Lucifora J, Couté Y, Salvetti A. Deciphering the phospho-signature induced by hepatitis B virus in primary human hepatocytes. Front Microbiol 2024; 15:1415449. [PMID: 38841065 PMCID: PMC11150682 DOI: 10.3389/fmicb.2024.1415449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
Phosphorylation is a major post-translation modification (PTM) of proteins which is finely tuned by the activity of several hundred kinases and phosphatases. It controls most if not all cellular pathways including anti-viral responses. Accordingly, viruses often induce important changes in the phosphorylation of host factors that can either promote or counteract viral replication. Among more than 500 kinases constituting the human kinome only few have been described as important for the hepatitis B virus (HBV) infectious cycle, and most of them intervene during early or late infectious steps by phosphorylating the viral Core (HBc) protein. In addition, little is known on the consequences of HBV infection on the activity of cellular kinases. The objective of this study was to investigate the global impact of HBV infection on the cellular phosphorylation landscape early after infection. For this, primary human hepatocytes (PHHs) were challenged or not with HBV, and a mass spectrometry (MS)-based quantitative phosphoproteomic analysis was conducted 2- and 7-days post-infection. The results indicated that while, as expected, HBV infection only minimally modified the cell proteome, significant changes were observed in the phosphorylation state of several host proteins at both time points. Gene enrichment and ontology analyses of up- and down-phosphorylated proteins revealed common and distinct signatures induced by infection. In particular, HBV infection resulted in up-phosphorylation of proteins involved in DNA damage signaling and repair, RNA metabolism, in particular splicing, and cytoplasmic cell-signaling. Down-phosphorylated proteins were mostly involved in cell signaling and communication. Validation studies carried out on selected up-phosphorylated proteins, revealed that HBV infection induced a DNA damage response characterized by the appearance of 53BP1 foci, the inactivation of which by siRNA increased cccDNA levels. In addition, among up-phosphorylated RNA binding proteins (RBPs), SRRM2, a major scaffold of nuclear speckles behaved as an antiviral factor. In accordance with these findings, kinase prediction analysis indicated that HBV infection upregulates the activity of major kinases involved in DNA repair. These results strongly suggest that HBV infection triggers an intrinsic anti-viral response involving DNA repair factors and RBPs that contribute to reduce HBV replication in cell culture models.
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Affiliation(s)
- Florentin Pastor
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Emilie Charles
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Lucid Belmudes
- Université Grenoble Alpes, CEA, INSERM, UA13 BGE, CEA, CNRS, FR2048, Grenoble, France
| | - Hélène Chabrolles
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Marion Cescato
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | | | - Thomas Burger
- Université Grenoble Alpes, CEA, INSERM, UA13 BGE, CEA, CNRS, FR2048, Grenoble, France
| | - Guillaume Passot
- Service de Chirurgie Générale et Oncologique, Hôpital Lyon Sud, Hospices Civils de Lyon Et CICLY, EA3738, Université Claude Bernard Lyon, Lyon, France
| | - David Durantel
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Julie Lucifora
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, UA13 BGE, CEA, CNRS, FR2048, Grenoble, France
| | - Anna Salvetti
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
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2
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Horner SM, Thompson MG. Challenges to mapping and defining m 6A function in viral RNA. RNA (NEW YORK, N.Y.) 2024; 30:482-490. [PMID: 38531643 PMCID: PMC11019751 DOI: 10.1261/rna.079959.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Viral RNA molecules contain multiple layers of regulatory information. This includes features beyond the primary sequence, such as RNA structures and RNA modifications, including N6-methyladenosine (m6A). Many recent studies have identified the presence and location of m6A in viral RNA and have found diverse regulatory roles for this modification during viral infection. However, to date, viral m6A mapping strategies have limitations that prevent a complete understanding of the function of m6A on individual viral RNA molecules. While m6A sites have been profiled on bulk RNA from many viruses, the resulting m6A maps of viral RNAs described to date present a composite picture of m6A across viral RNA molecules in the infected cell. Thus, for most viruses, it is unknown if unique viral m6A profiles exist throughout infection, nor if they regulate specific viral life cycle stages. Here, we describe several challenges to defining the function of m6A in viral RNA molecules and provide a framework for future studies to help in the understanding of how m6A regulates viral infection.
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Affiliation(s)
- Stacy M Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Matthew G Thompson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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Dhakal A, Salim C, Skelly M, Amichan Y, Lamm AT, Hundley HA. ADARs regulate cuticle collagen expression and promote survival to pathogen infection. BMC Biol 2024; 22:37. [PMID: 38360623 PMCID: PMC10870475 DOI: 10.1186/s12915-024-01840-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND In all organisms, the innate immune system defends against pathogens through basal expression of molecules that provide critical barriers to invasion and inducible expression of effectors that combat infection. The adenosine deaminase that act on RNA (ADAR) family of RNA-binding proteins has been reported to influence innate immunity in metazoans. However, studies on the susceptibility of ADAR mutant animals to infection are largely lacking. RESULTS Here, by analyzing adr-1 and adr-2 null mutants in well-established slow-killing assays, we find that both Caenorhabditis elegans ADARs are important for organismal survival to gram-negative and gram-positive bacteria, all of which are pathogenic to humans. Furthermore, our high-throughput sequencing and genetic analysis reveal that ADR-1 and ADR-2 function in the same pathway to regulate collagen expression. Consistent with this finding, our scanning electron microscopy studies indicate adr-1;adr-2 mutant animals also have altered cuticle morphology prior to pathogen exposure. CONCLUSIONS Our data uncover a critical role of the C. elegans ADAR family of RNA-binding proteins in promoting cuticular collagen expression, which represents a new post-transcriptional regulatory node that influences the extracellular matrix. In addition, we provide the first evidence that ADAR mutant animals have altered susceptibility to infection with several opportunistic human pathogens, suggesting a broader role of ADARs in altering physical barriers to infection to influence innate immunity.
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Affiliation(s)
- Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, 47405, USA
| | - Chinnu Salim
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Mary Skelly
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Yarden Amichan
- Faculty of Biology, Technion Institute of Technology, Haifa, Israel
| | - Ayelet T Lamm
- Faculty of Biology, Technion Institute of Technology, Haifa, Israel
| | - Heather A Hundley
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
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Amahong K, Zhang W, Liu Y, Li T, Huang S, Han L, Tao L, Zhu F. RVvictor: Virus RNA-directed molecular interactions for RNA virus infection. Comput Biol Med 2024; 169:107886. [PMID: 38157777 DOI: 10.1016/j.compbiomed.2023.107886] [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: 08/06/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
RNA viruses are major human pathogens that cause seasonal epidemics and occasional pandemic outbreaks. Due to the nature of their RNA genomes, it is anticipated that virus's RNA interacts with host protein (INTPRO), messenger RNA (INTmRNA), and non-coding RNA (INTncRNA) to perform their particular functions during their transcription and replication. In other words, thus, it is urgently needed to have such valuable data on virus RNA-directed molecular interactions (especially INTPROs), which are highly anticipated to attract broad research interests in the fields of RNA virus translation and replication. In this study, a new database was constructed to describe the virus RNA-directed interaction (INTPRO, INTmRNA, INTncRNA) for RNA virus (RVvictor). This database is unique in a) unambiguously characterizing the interactions between viruses RNAs and host proteins, b) providing, for the first time, the most systematic RNA-directed interaction data resources in providing clues to understand the molecular mechanisms of RNA viruses' translation, and replication, and c) in RVvictor, comprehensive enrichment analysis is conducted for each virus RNA based on its associated target genes/proteins, and the enrichment results were explicitly illustrated using various graphs. We found significant enrichment of a suite of pathways related to infection, translation, and replication, e.g., HIV infection, coronavirus disease, regulation of viral genome replication, and so on. Due to the devastating and persistent threat posed by the RNA virus, RVvictor constructed, for the first time, a possible network of cross-talk in RNA-directed interaction, which may ultimately explain the pathogenicity of RNA virus infection. The knowledge base might help develop new anti-viral therapeutic targets in the future. It's now free and publicly accessible at: https://idrblab.org/rvvictor/.
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Affiliation(s)
- Kuerbannisha Amahong
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China
| | - Wei Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China
| | - Yuhong Liu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Teng Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Shijie Huang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China
| | - Lianyi Han
- Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Shanghai, 315211, China.
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China.
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5
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Wang H, Cheng L, Yu L, Guo Z. Targeting the mammalian target of rapamycin pathway in neurological manifestations of Covid-19. Rev Med Virol 2024; 34:e2503. [PMID: 38282397 DOI: 10.1002/rmv.2503] [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: 11/21/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/30/2024]
Abstract
The diverse and severe nature of neurological manifestations associated with coronavirus disease 2019 (Covid-19) has garnered increasing attention. Exploring the potential to decrease neurological complications in Covid-19 patients involves targeting the mammalian target of rapamycin (mTOR) pathway as a therapeutic strategy. The mTOR pathway, widely recognised for its central role in essential cellular processes like synthesising proteins, facilitating autophagy, and modulating immune responses, has implications in various neurological disorders. Drawing parallels between these disorders and the observed neurological complications in Covid-19, we present a comprehensive review on the current understanding of mTOR signalling in the context of severe acute respiratory syndrome coronavirus 2 infection and neuroinflammation.
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Affiliation(s)
- Han Wang
- Department of Clinical Laboratory, The Affiliated Hospital to Changchun, University of Chinese Medicine, Changchun, China
| | - Li Cheng
- Department of Clinical Laboratory, The Affiliated Hospital to Changchun, University of Chinese Medicine, Changchun, China
| | - Lanlan Yu
- Department of Clinical Laboratory, The Affiliated Hospital to Changchun, University of Chinese Medicine, Changchun, China
| | - Zhigang Guo
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, China
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6
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Bello AJ, Popoola A, Okpuzor J, Ihekwaba-Ndibe AE, Olorunniji FJ. A Genetic Circuit Design for Targeted Viral RNA Degradation. Bioengineering (Basel) 2023; 11:22. [PMID: 38247899 PMCID: PMC10813695 DOI: 10.3390/bioengineering11010022] [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: 12/07/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
Advances in synthetic biology have led to the design of biological parts that can be assembled in different ways to perform specific functions. For example, genetic circuits can be designed to execute specific therapeutic functions, including gene therapy or targeted detection and the destruction of invading viruses. Viral infections are difficult to manage through drug treatment. Due to their high mutation rates and their ability to hijack the host's ribosomes to make viral proteins, very few therapeutic options are available. One approach to addressing this problem is to disrupt the process of converting viral RNA into proteins, thereby disrupting the mechanism for assembling new viral particles that could infect other cells. This can be done by ensuring precise control over the abundance of viral RNA (vRNA) inside host cells by designing biological circuits to target vRNA for degradation. RNA-binding proteins (RBPs) have become important biological devices in regulating RNA processing. Incorporating naturally upregulated RBPs into a gene circuit could be advantageous because such a circuit could mimic the natural pathway for RNA degradation. This review highlights the process of viral RNA degradation and different approaches to designing genetic circuits. We also provide a customizable template for designing genetic circuits that utilize RBPs as transcription activators for viral RNA degradation, with the overall goal of taking advantage of the natural functions of RBPs in host cells to activate targeted viral RNA degradation.
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Affiliation(s)
- Adebayo J. Bello
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
- Department of Biological Sciences, Redeemer’s University, Ede 232101, Osun State, Nigeria
| | - Abdulgafar Popoola
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
- Department of Medical Laboratory Science, Kwara State University, Malete, Ilorin 241102, Kwara State, Nigeria
| | - Joy Okpuzor
- Department of Cell Biology & Genetics, University of Lagos, Akoka, Lagos 101017, Lagos State, Nigeria;
| | | | - Femi J. Olorunniji
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
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7
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Chen Y, Lei X, Jiang Z, Humphries F, Parsi KM, Mustone NJ, Ramos I, Mutetwa T, Fernandez-Sesma A, Maehr R, Caffrey DR, Fitzgerald KA. Cellular nucleic acid-binding protein restricts SARS-CoV-2 by regulating interferon and disrupting RNA-protein condensates. Proc Natl Acad Sci U S A 2023; 120:e2308355120. [PMID: 37963251 PMCID: PMC10666094 DOI: 10.1073/pnas.2308355120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
A detailed understanding of the innate immune mechanisms involved in restricting SARS-CoV-2 infection and how the virus disrupts these processes could reveal new strategies to boost antiviral mechanisms and develop therapeutics for COVID-19. Here, we identify cellular nucleic acid-binding protein (CNBP) as a key host factor controlling SARS-CoV-2 infection. In response to RNA-sensing pathways, CNBP is phosphorylated and translocates from the cytosol to the nucleus where it binds to the interferon-β enhancer to initiate transcription. Because SARS-CoV-2 evades immune detection by the host's RNA-sensing pathways, CNBP is largely retained in the cytosol where it restricts SARS-CoV-2 directly, leading to a battle between the host and SARS-CoV-2 that extends beyond antiviral immune signaling pathways. We further demonstrated that CNBP binds SARS-CoV-2 viral RNA directly and competes with the viral nucleocapsid protein to prevent viral RNA and nucleocapsid protein from forming liquid-liquid phase separation (LLPS) condensates critical for viral replication. Consequently, cells and animals lacking CNBP have higher viral loads, and CNBP-deficient mice succumb rapidly to infection. Altogether, these findings identify CNBP as a key antiviral factor for SARS-CoV-2, functioning both as a regulator of antiviral IFN gene expression and a cell-intrinsic restriction factor that disrupts LLPS to limit viral replication and spread. In addition, our studies also highlight viral condensates as important targets and strategies for the development of drugs to combat COVID-19.
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Affiliation(s)
- Yongzhi Chen
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Xuqiu Lei
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Zhaozhao Jiang
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Fiachra Humphries
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Krishna Mohan Parsi
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Nicholas J. Mustone
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Irene Ramos
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Tinaye Mutetwa
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - René Maehr
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Daniel R. Caffrey
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Katherine A. Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01605
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8
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Tang D, Liu Y, Wang C, Li L, Al-Farraj SA, Chen X, Yan Y. Invasion by exogenous RNA: cellular defense strategies and implications for RNA inference. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:573-584. [PMID: 38045546 PMCID: PMC10689678 DOI: 10.1007/s42995-023-00209-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023]
Abstract
Exogenous RNA poses a continuous threat to genome stability and integrity across various organisms. Accumulating evidence reveals complex mechanisms underlying the cellular response to exogenous RNA, including endo-lysosomal degradation, RNA-dependent repression and innate immune clearance. Across a variety of mechanisms, the natural anti-sense RNA-dependent defensive strategy has been utilized both as a powerful gene manipulation tool and gene therapy strategy named RNA-interference (RNAi). To optimize the efficiency of RNAi silencing, a comprehensive understanding of the whole life cycle of exogenous RNA, from cellular entry to its decay, is vital. In this paper, we review recent progress in comprehending the recognition and elimination of foreign RNA by cells, focusing on cellular entrance, intracellular transportation, and immune-inflammatory responses. By leveraging these insights, we highlight the potential implications of these insights for advancing RNA interference efficiency, underscore the need for future studies to elucidate the pathways and fates of various exogenous RNA forms, and provide foundational information for more efficient RNA delivery methods in both genetic manipulation and therapy in different organisms.
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Affiliation(s)
- Danxu Tang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education) and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Yan Liu
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education) and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Chundi Wang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
| | - Saleh A. Al-Farraj
- Zoology Department, College of Science, King Saud University, 11451 Riyadh, Saudi Arabia
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
- Suzhou Research Institute, Shandong University, Suzhou, 215123 China
| | - Ying Yan
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education) and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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9
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Ray D, Laverty KU, Jolma A, Nie K, Samson R, Pour SE, Tam CL, von Krosigk N, Nabeel-Shah S, Albu M, Zheng H, Perron G, Lee H, Najafabadi H, Blencowe B, Greenblatt J, Morris Q, Hughes TR. RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Sci Rep 2023; 13:5238. [PMID: 37002329 PMCID: PMC10066285 DOI: 10.1038/s41598-023-32245-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Thousands of RNA-binding proteins (RBPs) crosslink to cellular mRNA. Among these are numerous unconventional RBPs (ucRBPs)-proteins that associate with RNA but lack known RNA-binding domains (RBDs). The vast majority of ucRBPs have uncharacterized RNA-binding specificities. We analyzed 492 human ucRBPs for intrinsic RNA-binding in vitro and identified 23 that bind specific RNA sequences. Most (17/23), including 8 ribosomal proteins, were previously associated with RNA-related function. We identified the RBDs responsible for sequence-specific RNA-binding for several of these 23 ucRBPs and surveyed whether corresponding domains from homologous proteins also display RNA sequence specificity. CCHC-zf domains from seven human proteins recognized specific RNA motifs, indicating that this is a major class of RBD. For Nudix, HABP4, TPR, RanBP2-zf, and L7Ae domains, however, only isolated members or closely related homologs yielded motifs, consistent with RNA-binding as a derived function. The lack of sequence specificity for most ucRBPs is striking, and we suggest that many may function analogously to chromatin factors, which often crosslink efficiently to cellular DNA, presumably via indirect recruitment. Finally, we show that ucRBPs tend to be highly abundant proteins and suggest their identification in RNA interactome capture studies could also result from weak nonspecific interactions with RNA.
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Affiliation(s)
- Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kaitlin U Laverty
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Arttu Jolma
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kate Nie
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Reuben Samson
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Sara E Pour
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Cyrus L Tam
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Niklas von Krosigk
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Mihai Albu
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Gabrielle Perron
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0C7, Canada
- McGill Genome Centre, Montréal, QC, H3A 0G1, Canada
| | - Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Hamed Najafabadi
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0C7, Canada
- McGill Genome Centre, Montréal, QC, H3A 0G1, Canada
| | - Benjamin Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jack Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Quaid Morris
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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10
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Girardi E, Messmer M, Lopez P, Fender A, Chicher J, Chane-Woon-Ming B, Hammann P, Pfeffer S. Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection. RNA (NEW YORK, N.Y.) 2023; 29:361-375. [PMID: 36617674 PMCID: PMC9945444 DOI: 10.1261/rna.079270.122] [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: 05/23/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Viruses are obligate intracellular parasites, which depend on the host cellular machineries to replicate their genome and complete their infectious cycle. Long double-stranded (ds)RNA is a common viral by-product originating during RNA virus replication and is universally sensed as a danger signal to trigger the antiviral response. As a result, viruses hide dsRNA intermediates into viral replication factories and have evolved strategies to hijack cellular proteins for their benefit. The characterization of the host factors associated with viral dsRNA and involved in viral replication remains a major challenge to develop new antiviral drugs against RNA viruses. Here, we performed anti-dsRNA immunoprecipitation followed by mass spectrometry analysis to fully characterize the dsRNA interactome in Sindbis virus (SINV) infected human cells. Among the identified proteins, we characterized SFPQ (splicing factor, proline-glutamine rich) as a new dsRNA-associated proviral factor upon SINV infection. We showed that SFPQ depletion reduces SINV infection in human HCT116 and SK-N-BE(2) cells, suggesting that SFPQ enhances viral production. We demonstrated that the cytoplasmic fraction of SFPQ partially colocalizes with dsRNA upon SINV infection. In agreement, we proved by RNA-IP that SFPQ can bind dsRNA and viral RNA. Furthermore, we showed that overexpression of a wild-type, but not an RNA binding mutant SFPQ, increased viral infection, suggesting that RNA binding is essential for its positive effect on the virus. Overall, this study provides the community with a compendium of dsRNA-associated factors during viral infection and identifies SFPQ as a new proviral dsRNA binding protein.
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Affiliation(s)
- Erika Girardi
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
| | - Mélanie Messmer
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
| | - Paula Lopez
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
| | - Aurélie Fender
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
| | - Johana Chicher
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Plateforme Protéomique Strasbourg-Esplanade, 67084 Strasbourg France
| | - Béatrice Chane-Woon-Ming
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
| | - Philippe Hammann
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Plateforme Protéomique Strasbourg-Esplanade, 67084 Strasbourg France
| | - Sébastien Pfeffer
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
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11
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Iselin L, Palmalux N, Kamel W, Simmonds P, Mohammed S, Castello A. Uncovering viral RNA-host cell interactions on a proteome-wide scale. Trends Biochem Sci 2022; 47:23-38. [PMID: 34509361 PMCID: PMC9187521 DOI: 10.1016/j.tibs.2021.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/12/2021] [Accepted: 08/06/2021] [Indexed: 01/14/2023]
Abstract
RNA viruses interact with a wide range of cellular RNA-binding proteins (RBPs) during their life cycle. The prevalence of these host-virus interactions has been highlighted by new methods that elucidate the composition of viral ribonucleoproteins (vRNPs). Applied to 11 viruses so far, these approaches have revealed hundreds of cellular RBPs that interact with viral (v)RNA in infected cells. However, consistency across methods is limited, raising questions about methodological considerations when designing and interpreting these studies. Here, we discuss these caveats and, through comparing available vRNA interactomes, describe RBPs that are consistently identified as vRNP components and outline their potential roles in infection. In summary, these novel approaches have uncovered a new universe of host-virus interactions holding great therapeutic potential.
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Affiliation(s)
- Louisa Iselin
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK,Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK)
| | - Wael Kamel
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK)
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK,The Rosalind Franklin Institute, Oxfordshire, OX11 0FA, UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK),Correspondence:
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12
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Bayoumi M, Munir M. Potential Use of CRISPR/Cas13 Machinery in Understanding Virus-Host Interaction. Front Microbiol 2021; 12:743580. [PMID: 34899631 PMCID: PMC8664230 DOI: 10.3389/fmicb.2021.743580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Prokaryotes have evolutionarily acquired an immune system to fend off invading mobile genetic elements, including viral phages and plasmids. Through recognizing specific sequences of the invading nucleic acid, prokaryotes mediate a subsequent degradation process collectively referred to as the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) (CRISPR-Cas) system. The CRISPR-Cas systems are divided into two main classes depending on the structure of the effector Cas proteins. Class I systems have effector modules consisting of multiple proteins, while class II systems have a single multidomain effector. Additionally, the CRISPR-Cas systems can also be categorized into types depending on the spacer acquisition components and their evolutionary features, namely, types I-VI. Among CRISPR/Cas systems, Cas9 is one of the most common multidomain nucleases that identify, degrade, and modulate DNA. Importantly, variants of Cas proteins have recently been found to target RNA, especially the single-effector Cas13 nucleases. The Cas13 has revolutionized our ability to study and perturb RNAs in endogenous microenvironments. The Cas13 effectors offer an excellent candidate for developing novel research tools in virological and biotechnological fields. Herein, in this review, we aim to provide a comprehensive summary of the recent advances of Cas13s for targeting viral RNA for either RNA-mediated degradation or CRISPR-Cas13-based diagnostics. Additionally, we aim to provide an overview of the proposed applications that could revolutionize our understanding of viral-host interactions using Cas13-mediated approaches.
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Affiliation(s)
- Mahmoud Bayoumi
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- Virology Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
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13
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Amarilla AA, Sng JDJ, Parry R, Deerain JM, Potter JR, Setoh YX, Rawle DJ, Le TT, Modhiran N, Wang X, Peng NYG, Torres FJ, Pyke A, Harrison JJ, Freney ME, Liang B, McMillan CLD, Cheung STM, Guevara DJDC, Hardy JM, Bettington M, Muller DA, Coulibaly F, Moore F, Hall RA, Young PR, Mackenzie JM, Hobson-Peters J, Suhrbier A, Watterson D, Khromykh AA. A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses. Nat Commun 2021; 12:3431. [PMID: 34103499 PMCID: PMC8187723 DOI: 10.1038/s41467-021-23779-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/03/2021] [Indexed: 02/06/2023] Open
Abstract
The current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We demonstrate that despite the large size of the viral RNA genome (~30 kb), infectious full-length cDNA is readily assembled in vitro by a circular polymerase extension reaction (CPER) methodology without the need for technically demanding intermediate steps. Overlapping cDNA fragments are generated from viral RNA and assembled together with a linker fragment containing CMV promoter into a circular full-length viral cDNA in a single reaction. Transfection of the circular cDNA into mammalian cells results in the recovery of infectious SARS-CoV-2 virus that exhibits properties comparable to the parental virus in vitro and in vivo. CPER is also used to generate insect-specific Casuarina virus with ~20 kb genome and the human pathogens Ross River virus (Alphavirus) and Norovirus (Calicivirus), with the latter from a clinical sample. Additionally, reporter and mutant viruses are generated and employed to study virus replication and virus-receptor interactions. Here the authors describe a simple reverse genetics method that relies on overlapping cDNA fragments for generation of positive-strand viruses including SARS-CoV-2 and characterize them in vitro and in vivo.
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Affiliation(s)
- Alberto A Amarilla
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Julian D J Sng
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Rhys Parry
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Joshua M Deerain
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - James R Potter
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Yin Xiang Setoh
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.,Microbiology and Molecular Epidemiology Division, Environmental Health Institute, National Environmental Agency, Singapore, Singapore
| | - Daniel J Rawle
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Thuy T Le
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Xiaohui Wang
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Nias Y G Peng
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Francisco J Torres
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Alyssa Pyke
- Queensland Health Forensic & Scientific Services, Queensland Department of Health, Coopers Plains, QLD, Australia
| | - Jessica J Harrison
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Morgan E Freney
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Benjamin Liang
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Christopher L D McMillan
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Stacey T M Cheung
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | | | - Joshua M Hardy
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Mark Bettington
- School of Medicine, University of Queensland, Kelvin Grove, QLD, Australia
| | - David A Muller
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Fasséli Coulibaly
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Frederick Moore
- Queensland Health Forensic & Scientific Services, Queensland Department of Health, Coopers Plains, QLD, Australia
| | - Roy A Hall
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Paul R Young
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Jason M Mackenzie
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.
| | - Jody Hobson-Peters
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia.
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia.
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia.
| | - Alexander A Khromykh
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia.
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14
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Innate immunity in hepatitis B and D virus infection: consequences for viral persistence, inflammation, and T cell recognition. Semin Immunopathol 2021; 43:535-548. [PMID: 34019142 PMCID: PMC8443521 DOI: 10.1007/s00281-021-00864-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022]
Abstract
Chronic infections with human hepatitis viruses continue to be a major health burden worldwide. Despite the availability of an effective prophylactic vaccine against the hepatitis B virus (HBV) and of antiviral agents efficiently suppressing HBV replication, more than 250 million people are currently chronically infected with this hepatotropic DNA virus, and resolution of chronic hepatitis B (CHB) is rarely achieved. Moreover, coinfection with the hepatitis D virus (HDV), a human RNA satellite virus requiring the envelope proteins of HBV for productive viral spreading, substantially aggravates the disease course of CHB. The molecular mechanisms by which these viruses interact with each other and with the intrinsic innate responses of the hepatocytes are not fully understood. While HBV appears to avoid innate immune recognition, HDV elicits a strong enhancement of innate responses. Notwithstanding, such induction does not hamper HDV replication but contributes to liver inflammation and pathogenesis. Intriguingly, HDV appears to influence the ability of T cells to recognize infected hepatocytes by boosting antigen presentation. This review focuses on current knowledge regarding how these viruses can shape and counteract the intrinsic innate responses of the hepatocytes, thus affecting the immune system and pathogenesis. Understanding the distinct strategies of persistence that HBV and HDV have evolved is central for advancing the development of curative therapies.
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15
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Saiz M, Martinez-Salas E. Uncovering targets of the Leader protease: Linking RNA-mediated pathways and antiviral defense. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1645. [PMID: 33605051 PMCID: PMC8244099 DOI: 10.1002/wrna.1645] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
RNA viruses have developed specialized mechanisms to subvert host RNA‐binding proteins (RBPs) favoring their own gene expression. The Leader (L) protein of foot‐and‐mouth disease virus, a member of the Picornaviridae family, is a papain‐like cysteine protease that self‐cleaves from the polyprotein. Early in infection, the L protease cleaves the translation initiation factors eIF4GI and eIF4GII, inducing the shutdown of cap‐dependent translation. However, the cleavage sites on the viral polyprotein, eIF4GI, and eIF4GII differ in sequence, challenging the definition of a consensus site for L targets. Identification of Gemin5 and Daxx proteolytic products in infected cells unveiled a motif centered on the RKAR sequence. The RBP Gemin5 is a member of the survival of motor neurons complex, a ribosome interacting protein, and a translation downregulator. Likewise, the Fas‐ligand Daxx is a multifunctional adaptor that plays key roles in transcription control, apoptosis, and innate immune antiviral response. Remarkably, the cleavage site on the RNA helicases MDA5 and LGP2, two relevant immune sensors of the retinoic acid‐inducible gene‐I (RIG‐I)‐like receptors family, resembles the L target site of Gemin5 and Daxx, and similar cleavage sites have been reported in ISG15 and TBK1, two proteins involved in type I interferon response and signaling pathway, respectively. In this review we dissect the features of the L cleavage sites in essential RBPs, eventually helping in the discovery of novel L targets. This article is categorized under:RNA in Disease and Development > RNA in Disease Translation > Translation Regulation
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Affiliation(s)
- Margarita Saiz
- Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa, Madrid, Spain
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