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Roesmann F, Sertznig H, Klaassen K, Wilhelm A, Heininger D, Heß S, Elsner C, Marschalek R, Santiago ML, Esser S, Sutter K, Dittmer U, Widera M. The interferon-regulated host factor hnRNPA0 modulates HIV-1 production by interference with LTR activity, mRNA trafficking, and programmed ribosomal frameshifting. J Virol 2024:e0053424. [PMID: 38899932 DOI: 10.1128/jvi.00534-24] [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: 03/23/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The interplay between host factors and viral components impacts viral replication efficiency profoundly. Members of the cellular heterogeneous nuclear ribonucleoprotein family (hnRNPs) have been extensively studied as HIV-1 host dependency factors, but whether they play a role in innate immunity is currently unknown. This study aimed to identify hnRNPA0 as a type I interferon (IFN)-repressed host factor in HIV-1-infected cells. Knockdown of hnRNPA0, a situation that mirrors conditions under IFN stimulation, increased LTR activity, export of unspliced HIV-1 mRNA, viral particle production, and thus, increased infectivity. Conversely, hnRNPA0 overexpression primarily reduced plasmid-driven and integrated HIV-1 long terminal repeat (LTR) activity, significantly decreasing total viral mRNA and protein levels. In addition, high levels of hnRNPA0 significantly reduced the HIV-1 programmed ribosomal frameshifting efficiency, resulting in a shift in the HIV-1 p55/p15 ratio. The HIV-1 alternative splice site usage remained largely unaffected by altered hnRNPA0 levels suggesting that the synergistic inhibition of the LTR activity and viral mRNA transcription, as well as impaired ribosomal frameshifting efficiency, are critical factors for efficient HIV-1 replication regulated by hnRNPA0. The pleiotropic dose-dependent effects under high or low hnRNPA0 levels were further confirmed in HIV-1-infected Jurkat cells. Finally, our study revealed that hnRNPA0 levels in PBMCs were lower in therapy-naive HIV-1-infected individuals compared to healthy controls. Our findings highlight a significant role for hnRNPA0 in HIV-1 replication and suggest that its IFN-I-regulated expression levels are critical for viral fitness allowing replication in an antiviral environment.IMPORTANCERNA-binding proteins, in particular, heterogeneous nuclear ribonucleoproteins (hnRNPs), have been extensively studied. Some act as host dependency factors for HIV-1 since they are involved in multiple cellular gene expression processes. Our study revealed hnRNPA0 as an IFN-regulated host factor, that is differently expressed after IFN-I treatment in HIV-1 target cells and lower expressed in therapy-naïve HIV-1-infected individuals. Our findings demonstrate the significant pleiotropic role of hnRNPA0 in viral replication: In high concentrations, hnRNPA0 limits viral replication by negatively regulating Tat-LTR transcription, retaining unspliced mRNA in the nucleus, and significantly impairing programmed ribosomal frameshifting. Low hnRNPA0 levels as observed in IFN-treated THP-1 cells, particularly facilitate HIV LTR activity and unspliced mRNA export, suggesting a role in innate immunity in favor of HIV replication. Understanding the mode of action between hnRNPA0 and HIV-1 gene expression might help to identify novel therapeutically strategies against HIV-1 and other viruses.
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Affiliation(s)
- Fabian Roesmann
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Helene Sertznig
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Katleen Klaassen
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Alexander Wilhelm
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Delia Heininger
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Stefanie Heß
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Mario L Santiago
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Stefan Esser
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Dermatology, HPSTD Outpatient Clinic, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marek Widera
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
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Enguita FJ, Leitão AL, Mattick JS. RNA Regulatory Networks 2.0. Int J Mol Sci 2023; 24:ijms24109001. [PMID: 37240347 DOI: 10.3390/ijms24109001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The central role of RNA molecules in cell biology has been an expanding subject of study since the proposal of the "RNA world" hypothesis 60 years ago [...].
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Affiliation(s)
- Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ana Lúcia Leitão
- Department of Chemistry, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
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Sarshar M, Scribano D, Palamara AT, Ambrosi C, Masotti A. The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions. Front Mol Biosci 2022; 9:1088783. [PMID: 36619166 PMCID: PMC9810633 DOI: 10.3389/fmolb.2022.1088783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein-RNA and RNA-RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.
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Affiliation(s)
- Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,Department of Infectious Diseases, National Institute of Health, Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy,IRCCS San Raffaele Roma, Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
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Diallo I, Ho J, Lambert M, Benmoussa A, Husseini Z, Lalaouna D, Massé E, Provost P. A tRNA-derived fragment present in E. coli OMVs regulates host cell gene expression and proliferation. PLoS Pathog 2022; 18:e1010827. [PMID: 36108089 PMCID: PMC9514646 DOI: 10.1371/journal.ppat.1010827] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 09/27/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
RNA-sequencing has led to a spectacular increase in the repertoire of bacterial sRNAs and improved our understanding of their biological functions. Bacterial sRNAs have also been found in outer membrane vesicles (OMVs), raising questions about their potential involvement in bacteria-host relationship, but few studies have documented this issue. Recent RNA-Sequencing analyses of bacterial RNA unveiled the existence of abundant very small RNAs (vsRNAs) shorter than 16 nt. These especially include tRNA fragments (tRFs) that are selectively loaded in OMVs and are predicted to target host mRNAs. Here, in Escherichia coli (E. coli), we report the existence of an abundant vsRNA, Ile-tRF-5X, which is selectively modulated by environmental stress, while remaining unaffected by inhibition of transcription or translation. Ile-tRF-5X is released through OMVs and can be transferred to human HCT116 cells, where it promoted MAP3K4 expression. Our findings provide a novel perspective and paradigm on the existing symbiosis between bacteria and human cells. We previously outlined by RNA-Sequencing (RNA-seq) the existence of abundant very small (<16 nt) bacterial and eukaryote RNA (vsRNA) population with potential regulatory functions. However, it is not exceptional to see vsRNA species removed from the RNA-seq libraries or datasets because being considered as random degradation products. As a proof of concept, we present in this study a 13 nt in length isoleucine tRNA-derived fragment (Ile-tRF-5X) which is selectively modulated by nutritional and thermal stress while remaining unaffected by transcription and translation inhibitions. We also showed that OMVs and their Ile-tRF-5X vsRNAs are delivered into human HCT116 cells and both can promote host cell gene expression and proliferation. Ile-tRF-5X appears to regulate gene silencing properties of miRNAs by competition. Our findings provide a novel perspective and paradigm on the existing symbiosis between hosts and bacteria but also brings a new insight of host-pathogen interactions mediated by tRFs which remain so far poorly characterized in bacteria.
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Affiliation(s)
- Idrissa Diallo
- CHU de Québec-Université Laval Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Jeffrey Ho
- CHU de Québec-Université Laval Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Marine Lambert
- CHU de Québec-Université Laval Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Abderrahim Benmoussa
- CHU de Québec-Université Laval Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Zeinab Husseini
- CHU de Québec-Université Laval Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - David Lalaouna
- CRCHUS, RNA Group, Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Eric Massé
- CRCHUS, RNA Group, Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Patrick Provost
- CHU de Québec-Université Laval Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
- * E-mail:
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Diallo I, Ho J, Lalaouna D, Massé E, Provost P. RNA Sequencing Unveils Very Small RNAs With Potential Regulatory Functions in Bacteria. Front Mol Biosci 2022; 9:914991. [PMID: 35720117 PMCID: PMC9203972 DOI: 10.3389/fmolb.2022.914991] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/02/2022] [Indexed: 12/21/2022] Open
Abstract
RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of an eukaryotic 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma and, by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16 nt). Here we report the detailed profiling of vsRNAs in Escherichia coli, E. coli-derived outer membrane vesicles (OMVs) and five other bacterial strains (Pseudomonas aeruginosa PA7, P. aeruginosa PAO1, Salmonella enterica serovar Typhimurium 14028S, Legionella pneumophila JR32 Philadelphia-1 and Staphylococcus aureus HG001). vsRNAs of 8–15 nt in length [RNAs (8-15 nt)] were found to be more abundant than RNAs of 16–30 nt in length [RNAs (16–30 nt)]. vsRNA biotypes were distinct and varied within and across bacterial species and accounted for one third of reads identified in the 8–30 nt window. The tRNA-derived fragments (tRFs) have appeared as a major biotype among the vsRNAs, notably Ile-tRF and Ala-tRF, and were selectively loaded in OMVs. tRF-derived vsRNAs appear to be thermodynamically stable with at least 2 G-C basepairs and stem-loop structure. The analyzed tRF-derived vsRNAs are predicted to target several human host mRNAs with diverse functions. Bacterial vsRNAs and OMV-derived vsRNAs could be novel players likely modulating the intricate relationship between pathogens and their hosts.
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Affiliation(s)
- Idrissa Diallo
- CHU de Québec Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - Jeffrey Ho
- CHU de Québec Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - David Lalaouna
- CRCHUS, RNA Group, Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Eric Massé
- CRCHUS, RNA Group, Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Patrick Provost
- CHU de Québec Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- *Correspondence: Patrick Provost,
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An Expanded Landscape of Unusually Short RNAs in 11 Samples from Six Eukaryotic Organisms. Noncoding RNA 2022; 8:ncrna8030034. [PMID: 35645341 PMCID: PMC9149858 DOI: 10.3390/ncrna8030034] [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] [Received: 02/22/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 11/30/2022] Open
Abstract
Small RNA sequencing (sRNA-Seq) approaches unveiled sequences derived from longer non-coding RNAs, such as transfer RNA (tRNA) and ribosomal RNA (rRNA) fragments, known as tRFs and rRFs, respectively. However, rRNAs and RNAs shorter than 16 nt are often depleted from library preparations/sequencing analyses, although they may be functional. Here, we sought to obtain a complete repertoire of small RNAs by sequencing the total RNA from 11 samples of 6 different eukaryotic organisms, from yeasts to human, in an extended 8- to 30-nt window of RNA length. The 8- to 15-nt window essentially contained fragments of longer non-coding RNAs, such as microRNAs, PIWI-associated RNAs (piRNAs), small nucleolar RNAs (snoRNAs), tRNAs and rRNAs. Notably, unusually short RNAs < 16 nt were more abundant than those >16 nt in bilaterian organisms. A new RT-qPCR method confirmed that two unusually short rRFs of 12 and 13 nt were more overly abundant (~3-log difference) than two microRNAs. We propose to not deplete rRNA and to reduce the lower threshold of RNA length to include unusually short RNAs in sRNA-Seq analyses and datasets, as their abundance and diversity support their potential role and importance as biomarkers of disease and/or mediators of cellular function.
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A New Specific and Sensitive RT-qPCR Method Based on Splinted 5' Ligation for the Quantitative Detection of RNA Species Shorter than microRNAs. Noncoding RNA 2021; 7:ncrna7030059. [PMID: 34564321 PMCID: PMC8482087 DOI: 10.3390/ncrna7030059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 12/27/2022] Open
Abstract
Recently, we discovered a new family of unusually short RNAs mapping to 5.8S ribosomal RNA (rRNA) and which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. To confirm these small RNA-sequencing (RNA-Seq) data, validate the existence of the two overly abundant doRNAs-the minimal core 12-nt doRNA sequence and its + 1-nt variant bearing a 5' Cytosine, C-doRNA-and streamline their analysis, we developed a new specific and sensitive splinted 5' ligation reverse transcription (RT)-quantitative polymerase chain reaction (qPCR) method. This method is based on a splint-assisted ligation of an adapter to the 5' end of doRNAs, followed by RT-qPCR amplification and quantitation. Our optimized protocol, which may discriminate between doRNA, C-doRNA, mutated and precursor sequences, can accurately detect as low as 240 copies and is quantitatively linear over a range of 7 logs. This method provides a unique tool to expand and facilitate studies exploring the molecular and cellular biology of RNA species shorter than microRNAs.
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The coming together of allosteric and phosphorylation mechanisms in the molecular integration of A2A heteroreceptor complexes in the dorsal and ventral striatal-pallidal GABA neurons. Pharmacol Rep 2021; 73:1096-1108. [PMID: 34426901 PMCID: PMC8413191 DOI: 10.1007/s43440-021-00314-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022]
Abstract
The role of adenosine A2A receptor (A2AR) and striatal-enriched protein tyrosine phosphatase (STEP) interactions in the striatal-pallidal GABA neurons was recently discussed in relation to A2AR overexpression and cocaine-induced increases of brain adenosine levels. As to phosphorylation, combined activation of A2AR and metabotropic glutamate receptor 5 (mGluR5) in the striatal-pallidal GABA neurons appears necessary for phosphorylation of the GluA1 unit of the AMPA receptor to take place. Robert Yasuda (J Neurochem 152: 270–272, 2020) focused on finding a general mechanism by which STEP activation is enhanced by increased A2AR transmission in striatal-pallidal GABA neurons expressing A2AR and dopamine D2 receptor. In his Editorial, he summarized in a clear way the significant effects of A2AR activation on STEP in the dorsal striatal-pallidal GABA neurons which involves a rise of intracellular levels of calcium causing STEP activation through its dephosphorylation. However, the presence of the A2AR in an A2AR-fibroblast growth factor receptor 1 (FGFR1) heteroreceptor complex can be required in the dorsal striatal-pallidal GABA neurons for the STEP activation. Furthermore, Won et al. (Proc Natl Acad Sci USA 116: 8028–8037, 2019) found in mass spectrometry experiments that the STEP splice variant STEP61 can bind to mGluR5 and inactivate it. In addition, A2AR overexpression can lead to increased formation of A2AR-mGluR5 heterocomplexes in ventral striatal-pallidal GABA neurons. It involves enhanced facilitatory allosteric interactions leading to increased Gq-mediated mGluR5 signaling activating STEP. The involvement of both A2AR and STEP in the actions of cocaine on synaptic downregulation was also demonstrated. The enhancement of mGluR5 protomer activity by the A2AR protomer in A2AR-mGluR5 heterocomplexes in the nucleus accumbens shell appears to have a novel significant role in STEP mechanisms by both enhancing the activation of STEP and being a target for STEP61.
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