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Moreno E, Ciordia S, Fátima SM, Jiménez D, Martínez-Sanz J, Vizcarra P, Ron R, Sánchez-Conde M, Bargiela R, Sanchez-Carrillo S, Moreno S, Corrales F, Ferrer M, Serrano-Villar S. Proteomic snapshot of saliva samples predicts new pathways implicated in SARS-CoV-2 pathogenesis. Clin Proteomics 2024; 21:37. [PMID: 38778280 PMCID: PMC11112864 DOI: 10.1186/s12014-024-09482-9] [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: 10/13/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Information on the microbiome's human pathways and active members that can affect SARS-CoV-2 susceptibility and pathogenesis in the salivary proteome is very scarce. Here, we studied a unique collection of samples harvested from April to June 2020 from unvaccinated patients. METHODS We compared 10 infected and hospitalized patients with severe (n = 5) and moderate (n = 5) coronavirus disease (COVID-19) with 10 uninfected individuals, including non-COVID-19 but susceptible individuals (n = 5) and non-COVID-19 and nonsusceptible healthcare workers with repeated high-risk exposures (n = 5). RESULTS By performing high-throughput proteomic profiling in saliva samples, we detected 226 unique differentially expressed (DE) human proteins between groups (q-value ≤ 0.05) out of 3376 unambiguously identified proteins (false discovery rate ≤ 1%). Major differences were observed between the non-COVID-19 and nonsusceptible groups. Bioinformatics analysis of DE proteins revealed human proteomic signatures related to inflammatory responses, central cellular processes, and antiviral activity associated with the saliva of SARS-CoV-2-infected patients (p-value ≤ 0.0004). Discriminatory biomarker signatures from human saliva include cystatins, protective molecules present in the oral cavity, calprotectins, involved in cell cycle progression, and histones, related to nucleosome functions. The expression levels of two human proteins related to protein transport in the cytoplasm, DYNC1 (p-value, 0.0021) and MAPRE1 (p-value, 0.047), correlated with angiotensin-converting enzyme 2 (ACE2) plasma activity. Finally, the proteomes of microorganisms present in the saliva samples showed 4 main microbial functional features related to ribosome functioning that were overrepresented in the infected group. CONCLUSION Our study explores potential candidates involved in pathways implicated in SARS-CoV-2 susceptibility, although further studies in larger cohorts will be necessary.
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Affiliation(s)
- Elena Moreno
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain.
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Santos Milhano Fátima
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Daniel Jiménez
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
| | - Javier Martínez-Sanz
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Pilar Vizcarra
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Raquel Ron
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Matilde Sánchez-Conde
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Rafael Bargiela
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Sergio Sanchez-Carrillo
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049, Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, 28049, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Facultad de Medicina, Universidad de Alcalá de Henares, 28801, Alcalá de Henares, Madrid, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049, Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
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LIU JUN, LI WENLI, LU RUYUE, XU JIAQING, JIANG CHUNHUI, DUAN JUNLIN, ZHANG LINGZHI, WANG GUANFU, CHEN JIAXI. Investigation of the feasibility of NRAV as a biomarker for hepatocellular carcinoma. Oncol Res 2024; 32:717-726. [PMID: 38560576 PMCID: PMC10972727 DOI: 10.32604/or.2023.043575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/23/2023] [Indexed: 04/04/2024] Open
Abstract
The long non-coding RNA, Negative Regulator of Antiviral Response (NRAV) has been identified as a participant in both respiratory virus replication and immune checkpoints, however, its involvement in pan-cancer immune regulation and prognosis, particularly those of hepatocellular carcinoma (HCC), remains unclear. To address this knowledge gap, we analyzed expression profiles obtained from The Cancer Genome Atlas (TCGA) database, comparing normal and malignant tumor tissues. We found that NRAV expression is significantly upregulated in tumor tissues compared to adjacent nontumor tissues. Kaplan-Meier (K-M) analysis revealed the prognostic power of NRAV, wherein overexpression was significantly linked to reduced overall survival in a diverse range of tumor patients. Furthermore, noteworthy associations were observed between NRAV, immune checkpoints, immune cell infiltration, genes related to autophagy, epithelial-mesenchymal transition (EMT), pyroptosis, tumor mutational burden (TMB), and microsatellite instability (MSI) across different cancer types, including HCC. Moreover, NRAV upregulation expression was associated with multiple pathological stages by clinical observations. Furthermore, our investigation revealed a substantial elevation in the expression of NRAV in both HCC tumor tissues and cells compared to normal tissues and cells. The inhibition of NRAV resulted in the inhibition of cell proliferation, migration, and invasion in HCC cells, while also influencing the expression of CD274 (PD-L1) and CD44, along with various biomarkers associated with EMT, autophagy, and pyroptosis. The aforementioned results propose NRAV as a promising prognostic biomarker for HCC.
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Affiliation(s)
- JUN LIU
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Taizhou, China
- Department of Clinical Laboratory, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, China
| | - WENLI LI
- Department of Clinical Laboratory, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, China
| | - RUYUE LU
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Taizhou, China
| | - JIAQING XU
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Taizhou, China
| | - CHUNHUI JIANG
- School of Basic Medical Sciences Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - JUNLIN DUAN
- Department of Clinical Laboratory, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, China
| | - LINGZHI ZHANG
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - GUANFU WANG
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - JIAXI CHEN
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Taizhou, China
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Zhang Y, Gao Y, Li F, Qi Q, Li Q, Gu Y, Zheng Z, Hu B, Wang T, Zhang E, Xu H, Liu L, Tian T, Jin G, Yan C. Long non-coding RNA NRAV in the 12q24.31 risk locus drives gastric cancer development through glucose metabolism reprogramming. Carcinogenesis 2024; 45:23-34. [PMID: 37950445 DOI: 10.1093/carcin/bgad080] [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: 03/21/2023] [Revised: 10/24/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) serve as vital candidates to mediate cancer risk. Here, we aimed to identify the risk single-nucleotide polymorphisms (SNPs)-induced lncRNAs and to investigate their roles in gastric cancer (GC) development. Through integrating the differential expression analysis of lncRNAs in GC tissues and expression quantitative trait loci analysis in normal stomach tissues and GC tissues, as well as genetic association analysis based on GC genome-wide association studies and an independent validation study, we identified four lncRNA-related SNPs consistently associated with GC risk, including SNHG7 [odds ratio (OR) = 1.16, 95% confidence interval (CI): 1.09-1.23], NRAV (OR = 1.11, 95% CI: 1.05-1.17), LINC01082 (OR = 1.16, 95% CI: 1.08-1.22) and FENDRR (OR = 1.16, 95% CI: 1.07-1.25). We further found that a functional SNP rs6489786 at 12q24.31 increases binding of MEOX1 or MEOX2 at a distal enhancer and results in up-regulation of NRAV. The functional assays revealed that NRAV accelerates GC cell proliferation while inhibits GC cell apoptosis. Mechanistically, NRAV decreases the expression of key subunit genes through the electron transport chain, thereby driving the glucose metabolism reprogramming from aerobic respiration to glycolysis. These findings suggest that regulating lncRNA expression is a crucial mechanism for risk-associated variants in promoting GC development.
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Affiliation(s)
- Yan Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Yun Gao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Fengyuan Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qi Qi
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qian Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuanliang Gu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhonghua Zheng
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Beiping Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tianpei Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Public Health Institute of Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Hao Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Liu
- Institute of Digestive Endoscopy, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tian Tian
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
- Public Health Institute of Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Caiwang Yan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Immunology, Key Laboratory of Immunological Environment and Disease, Nanjing Medical University, Nanjing, China
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Wuxi, China
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Shapira G, Volkov H, Fabian I, Mohr DW, Bettinotti M, Shomron N, Avery RK, Arav-Boger R. Genomic Markers Associated with Cytomegalovirus DNAemia in Kidney Transplant Recipients. Viruses 2023; 15:2227. [PMID: 38005904 PMCID: PMC10674338 DOI: 10.3390/v15112227] [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: 10/05/2023] [Revised: 10/29/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Human cytomegalovirus (CMV) is a major pathogen after solid organ transplantation, leading to high morbidity and mortality. Transplantation from a CMV-seropositive donor to a CMV-seronegative recipient (D+/R-) is associated with high risk of CMV disease. However, that risk is not uniform, suggesting a role for host factors in immune control of CMV. To identify host genetic factors that control CMV DNAemia post transplantation, we performed a whole-exome association study in two cohorts of D+/R- kidney transplant recipients. Quantitative CMV DNA was measured for at least one year following transplantation. Several CMV-protective single-nucleotide polymorphisms (SNPs) were identified in the first cohort (72 patients) but were not reproducible in the second cohort (126 patients). A meta-analysis of both cohorts revealed several SNPs that were significantly associated with protection from CMV DNAemia. The copy number variation of several genes was significantly different between recipients with and without CMV DNAemia. Amongst patients with CMV DNAemia in the second cohort, several variants of interest (p < 5 × 10-5), the most common of which was NLRC5, were associated with peak viral load. We provide new predictive genetic markers for protection of CMV DNAemia. These markers should be validated in larger cohorts.
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Affiliation(s)
- Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hadas Volkov
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Itai Fabian
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
| | - David W. Mohr
- Johns Hopkins Genetic Resources Core Facility, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maria Bettinotti
- Immunogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA;
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Robin K. Avery
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA;
| | - Ravit Arav-Boger
- Department of Pediatrics, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Shtykalova S, Deviatkin D, Freund S, Egorova A, Kiselev A. Non-Viral Carriers for Nucleic Acids Delivery: Fundamentals and Current Applications. Life (Basel) 2023; 13:903. [PMID: 37109432 PMCID: PMC10142071 DOI: 10.3390/life13040903] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Over the past decades, non-viral DNA and RNA delivery systems have been intensively studied as an alternative to viral vectors. Despite the most significant advantage over viruses, such as the lack of immunogenicity and cytotoxicity, the widespread use of non-viral carriers in clinical practice is still limited due to the insufficient efficacy associated with the difficulties of overcoming extracellular and intracellular barriers. Overcoming barriers by non-viral carriers is facilitated by their chemical structure, surface charge, as well as developed modifications. Currently, there are many different forms of non-viral carriers for various applications. This review aimed to summarize recent developments based on the essential requirements for non-viral carriers for gene therapy.
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Affiliation(s)
- Sofia Shtykalova
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint-Petersburg, Russia
- Faculty of Biology, Saint-Petersburg State University, Universitetskaya Embankment 7-9, 199034 Saint-Petersburg, Russia
| | - Dmitriy Deviatkin
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint-Petersburg, Russia
- Faculty of Biology, Saint-Petersburg State University, Universitetskaya Embankment 7-9, 199034 Saint-Petersburg, Russia
| | - Svetlana Freund
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint-Petersburg, Russia
- Faculty of Biology, Saint-Petersburg State University, Universitetskaya Embankment 7-9, 199034 Saint-Petersburg, Russia
| | - Anna Egorova
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint-Petersburg, Russia
| | - Anton Kiselev
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint-Petersburg, Russia
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Liu N, Li M, Xie F, Lv J, Gao X, Zhang H, Gao J, Zheng A. Efficacy of mimetic viral dynein binding peptide binding nanoparticles in blood-brain barrier model. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Girardin C, Maze D, Gonçalves C, Le Guen YT, Pluchon K, Pichon C, Montier T, Midoux P. Selective attachment of a microtubule interacting peptide to plasmid DNA via a triplex forming oligonucleotide for transfection improvement. Gene Ther 2022; 30:271-277. [PMID: 35794469 DOI: 10.1038/s41434-022-00354-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/20/2022] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
In nonviral gene therapy approaches, the linkage of signal molecules to plasmid DNA (pDNA) is of interest for guiding its delivery to the nucleus. Here, we report its linkage to a peptide (P79-98) mediating migration on microtubules by using a triplex-forming oligonucleotide (TFO). pDNA of 5 kbp and 21 kbp containing 6 and 36 oligopurine • oligopyrimidine sites (TH), respectively, inserted outside the luciferase gene sequence were used. TFO with a dibenzocyclooctyl (DBCO) group in 3' end comprising some Bridged Nucleic Acid bases was conjugated by click chemistry with the peptide carrying an azide function in the C-terminal end. We found the formation of 6 and 18 triplex with pDNA of 5 kbp and 21 kbp, respectively. A twofold increase of the transfection efficiency was observed in the hind-limbs upon Hydrodynamic Limb Vein (HLV) injection in mice of naked P79-98 -pDNA of 21 kbp. This work paves the way for the selective equipping of pDNA with intracellular targeting molecules while preserving the full expression of the encoded gene.
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Affiliation(s)
- Caroline Girardin
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071, Orléans cedex 02, France
| | - Delphine Maze
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071, Orléans cedex 02, France
| | - Cristine Gonçalves
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071, Orléans cedex 02, France
| | | | - Kevin Pluchon
- Univ Brest, INSERM, EFS, UMR 1078, GGB - GTCA Team, F-29200, Brest, France
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071, Orléans cedex 02, France
| | - Tristan Montier
- Univ Brest, INSERM, EFS, UMR 1078, GGB - GTCA Team, F-29200, Brest, France. .,Service de Génétique Médicale et Biologie de la Reproduction, Centre de référence des maladies rares 'Maladies neuromusculaires', CHRU de Brest, F-29200, Brest, France.
| | - Patrick Midoux
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071, Orléans cedex 02, France.
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Talà A, Guerra F, Calcagnile M, Romano R, Resta SC, Paiano A, Chiariello M, Pizzolante G, Bucci C, Alifano P. HrpA anchors meningococci to the dynein motor and affects the balance between apoptosis and pyroptosis. J Biomed Sci 2022; 29:45. [PMID: 35765029 PMCID: PMC9241232 DOI: 10.1186/s12929-022-00829-8] [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: 02/09/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Neisseria meningitidis the HrpA/HrpB two-partner secretion system (TPS) was implicated in diverse functions including meningococcal competition, biofilm formation, adherence to epithelial cells, intracellular survival and vacuolar escape. These diverse functions could be attributed to distinct domains of secreted HrpA. METHODS A yeast two-hybrid screening, in vitro pull-down assay and immunofluorescence microscopy experiments were used to investigate the interaction between HrpA and the dynein light-chain, Tctex-type 1 (DYNLT1). In silico modeling was used to analyze HrpA structure. Western blot analysis was used to investigate apoptotic and pyroptotic markers. RESULTS The HrpA carboxy-terminal region acts as a manganese-dependent cell lysin, while the results of a yeast two-hybrid screening demonstrated that the HrpA middle region has the ability to bind the dynein light-chain, Tctex-type 1 (DYNLT1). This interaction was confirmed by in vitro pull-down assay and immunofluorescence microscopy experiments showing co-localization of N. meningitidis with DYNLT1 in infected epithelial cells. In silico modeling revealed that the HrpA-M interface interacting with the DYNLT1 has similarity with capsid proteins of neurotropic viruses that interact with the DYNLT1. Indeed, we found that HrpA plays a key role in infection of and meningococcal trafficking within neuronal cells, and is implicated in the modulation of the balance between apoptosis and pyroptosis. CONCLUSIONS Our findings revealed that N. meningitidis is able to effectively infect and survive in neuronal cells, and that this ability is dependent on HrpA, which establishes a direct protein-protein interaction with DYNLTI in these cells, suggesting that the HrpA interaction with dynein could be fundamental for N. meningitidis spreading inside the neurons. Moreover, we found that the balance between apoptotic and pyroptotic pathways is heavily affected by HrpA.
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Affiliation(s)
- Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Flora Guerra
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Roberta Romano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Silvia Caterina Resta
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Aurora Paiano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Mario Chiariello
- Core Research Laboratory-Siena, Institute for Cancer Research and Prevention (ISPRO), 53100, Siena, Italy.,Institute of Clinical Physiology (IFC), National Research Council (CNR), 53100, Siena, Italy
| | - Graziano Pizzolante
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Cecilia Bucci
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy.
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy.
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Tati S, Alisaraie L. Recruitment of dynein and kinesin to viral particles. FASEB J 2022; 36:e22311. [DOI: 10.1096/fj.202101900rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/14/2022] [Accepted: 03/29/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Sayi’Mone Tati
- School of Pharmacy Memorial University of Newfoundland St. John’s Newfoundland Canada
| | - Laleh Alisaraie
- School of Pharmacy Memorial University of Newfoundland St. John’s Newfoundland Canada
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10
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Rodriguez Galvan J, Donner B, Veseley CH, Reardon P, Forsythe HM, Howe J, Fujimura G, Barbar E. Human Parainfluenza Virus 3 Phosphoprotein Is a Tetramer and Shares Structural and Interaction Features with Ebola Phosphoprotein VP35. Biomolecules 2021; 11:1603. [PMID: 34827601 PMCID: PMC8615749 DOI: 10.3390/biom11111603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
The human parainfluenza virus 3 (HPIV3) poses a risk for pneumonia development in young children and immunocompromised patients. To investigate mechanisms of HPIV3 pathogenesis, we characterized the association state and host protein interactions of HPIV3 phosphoprotein (HPIV3 P), an indispensable viral polymerase cofactor. Sequence analysis and homology modeling predict that HPIV3 P possesses a long, disordered N-terminal tail (PTAIL) a coiled-coil multimerization domain (PMD), similar to the well-characterized paramyxovirus phosphoproteins from measles and Sendai viruses. Using a recombinantly expressed and purified construct of PMD and PTAIL, we show that HPIV3 P in solution is primarily an alpha-helical tetramer that is stable up to 60 °C. Pulldown and isothermal titration calorimetry experiments revealed that HPIV3 P binds the host hub protein LC8, and turbidity experiments demonstrated a new role for LC8 in increasing the solubility of HPIV3 P in the presence of crowding agents such as RNA. For comparison, we show that the multimerization domain of the Zaire Ebola virus phosphoprotein VP35 is also a tetramer and binds LC8 but with significantly higher affinity. Comparative analysis of the domain architecture of various virus phosphoproteins in the order Mononegavirales show multiple predicted and verified LC8 binding motifs, suggesting its prevalence and importance in regulating viral phosphoprotein structures. Our work provides evidence for LC8 binding to phosphoproteins with multiple association states, either tetrameric, as in the HPIV3 and Ebola phosphoproteins shown here, or dimeric as in rabies virus phosphoprotein. Taken together the data suggest that the association states of a virus-specific phosphoprotein and the complex formed by binding of the phosphoprotein to host LC8 are important regulators of viral function.
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Affiliation(s)
- Joaquin Rodriguez Galvan
- Department of Biochemistry & Biophysics, College of Science, Corvallis, OR 97331, USA; (J.R.G.); (B.D.); (C.H.V.); (H.M.F.); (J.H.); (G.F.)
| | - Brianna Donner
- Department of Biochemistry & Biophysics, College of Science, Corvallis, OR 97331, USA; (J.R.G.); (B.D.); (C.H.V.); (H.M.F.); (J.H.); (G.F.)
| | - Cat Hoang Veseley
- Department of Biochemistry & Biophysics, College of Science, Corvallis, OR 97331, USA; (J.R.G.); (B.D.); (C.H.V.); (H.M.F.); (J.H.); (G.F.)
| | - Patrick Reardon
- NMR Facility, Oregon State University, Corvallis, OR 97331, USA;
| | - Heather M. Forsythe
- Department of Biochemistry & Biophysics, College of Science, Corvallis, OR 97331, USA; (J.R.G.); (B.D.); (C.H.V.); (H.M.F.); (J.H.); (G.F.)
| | - Jesse Howe
- Department of Biochemistry & Biophysics, College of Science, Corvallis, OR 97331, USA; (J.R.G.); (B.D.); (C.H.V.); (H.M.F.); (J.H.); (G.F.)
| | - Gretchen Fujimura
- Department of Biochemistry & Biophysics, College of Science, Corvallis, OR 97331, USA; (J.R.G.); (B.D.); (C.H.V.); (H.M.F.); (J.H.); (G.F.)
| | - Elisar Barbar
- Department of Biochemistry & Biophysics, College of Science, Corvallis, OR 97331, USA; (J.R.G.); (B.D.); (C.H.V.); (H.M.F.); (J.H.); (G.F.)
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11
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Chen L, Li Z, Zeng T, Zhang YH, Feng K, Huang T, Cai YD. Identifying COVID-19-Specific Transcriptomic Biomarkers with Machine Learning Methods. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9939134. [PMID: 34307679 PMCID: PMC8272456 DOI: 10.1155/2021/9939134] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/03/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022]
Abstract
COVID-19, a severe respiratory disease caused by a new type of coronavirus SARS-CoV-2, has been spreading all over the world. Patients infected with SARS-CoV-2 may have no pathogenic symptoms, i.e., presymptomatic patients and asymptomatic patients. Both patients could further spread the virus to other susceptible people, thereby making the control of COVID-19 difficult. The two major challenges for COVID-19 diagnosis at present are as follows: (1) patients could share similar symptoms with other respiratory infections, and (2) patients may not have any symptoms but could still spread the virus. Therefore, new biomarkers at different omics levels are required for the large-scale screening and diagnosis of COVID-19. Although some initial analyses could identify a group of candidate gene biomarkers for COVID-19, the previous work still could not identify biomarkers capable for clinical use in COVID-19, which requires disease-specific diagnosis compared with other multiple infectious diseases. As an extension of the previous study, optimized machine learning models were applied in the present study to identify some specific qualitative host biomarkers associated with COVID-19 infection on the basis of a publicly released transcriptomic dataset, which included healthy controls and patients with bacterial infection, influenza, COVID-19, and other kinds of coronavirus. This dataset was first analysed by Boruta, Max-Relevance and Min-Redundancy feature selection methods one by one, resulting in a feature list. This list was fed into the incremental feature selection method, incorporating one of the classification algorithms to extract essential biomarkers and build efficient classifiers and classification rules. The capacity of these findings to distinguish COVID-19 with other similar respiratory infectious diseases at the transcriptomic level was also validated, which may improve the efficacy and accuracy of COVID-19 diagnosis.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, shanghai 200444, China
- College of Information Engineering, Shanghai Maritime University, shanghai 201306, China
| | - Zhandong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, China
| | - Tao Zeng
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, shanghai 200031, China
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, shanghai 200444, China
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12
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Richards A, Berth SH, Brady S, Morfini G. Engagement of Neurotropic Viruses in Fast Axonal Transport: Mechanisms, Potential Role of Host Kinases and Implications for Neuronal Dysfunction. Front Cell Neurosci 2021; 15:684762. [PMID: 34234649 PMCID: PMC8255969 DOI: 10.3389/fncel.2021.684762] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/17/2021] [Indexed: 11/28/2022] Open
Abstract
Much remains unknown about mechanisms sustaining the various stages in the life cycle of neurotropic viruses. An understanding of those mechanisms operating before their replication and propagation could advance the development of effective anti-viral strategies. Here, we review our current knowledge of strategies used by neurotropic viruses to undergo bidirectional movement along axons. We discuss how the invasion strategies used by specific viruses might influence their mode of interaction with selected components of the host’s fast axonal transport (FAT) machinery, including specialized membrane-bounded organelles and microtubule-based motor proteins. As part of this discussion, we provide a critical evaluation of various reported interactions among viral and motor proteins and highlight limitations of some in vitro approaches that led to their identification. Based on a large body of evidence documenting activation of host kinases by neurotropic viruses, and on recent work revealing regulation of FAT through phosphorylation-based mechanisms, we posit a potential role of host kinases on the engagement of viruses in retrograde FAT. Finally, we briefly describe recent evidence linking aberrant activation of kinase pathways to deficits in FAT and neuronal degeneration in the context of human neurodegenerative diseases. Based on these findings, we speculate that neurotoxicity elicited by viral infection may involve deregulation of host kinases involved in the regulation of FAT and other cellular processes sustaining neuronal function and survival.
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Affiliation(s)
- Alexsia Richards
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States
| | - Sarah H Berth
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Scott Brady
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, United States
| | - Gerardo Morfini
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, United States
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13
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Mutiawati E, Syahrul S, Fahriani M, Fajar JK, Mamada SS, Maliga HA, Samsu N, Ilmawan M, Purnamasari Y, Asmiragani AA, Ichsan I, Emran TB, Rabaan AA, Masyeni S, Nainu F, Harapan H. Global prevalence and pathogenesis of headache in COVID-19: A systematic review and meta-analysis. F1000Res 2020; 9:1316. [PMID: 33953911 PMCID: PMC8063523 DOI: 10.12688/f1000research.27334.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/30/2020] [Indexed: 09/01/2023] Open
Abstract
Background: This study was conducted to determine the prevalence of headache in coronavirus disease 2019 (COVID-19) and to assess its association as a predictor for COVID-19. This study also aimed to discuss the possible pathogenesis of headache in COVID-19. Methods: Available articles from PubMed, Scopus, and Web of Science were searched as of September 2 nd, 2020. Data on characteristics of the study, headache and COVID-19 were extracted following the PRISMA guidelines. Biases were assessed using the Newcastle-Ottawa scale. The cumulative prevalence of headache was calculated for the general population (i.e. adults and children). The pooled odd ratio (OR) with 95% confidence intervals (95%CI) was calculated using the Z test to assess the association between headache and the presence of COVID-19 cases. Results: We included 104,751 COVID-19 cases from 78 eligible studies to calculate the global prevalence of headache in COVID-19 and 17 studies were included to calculate the association of headache and COVID-19. The cumulative prevalence of headache in COVID-19 was 25.2% (26,464 out of 104,751 cases). Headache was found to be more prevalent, approximately by two-fold, in COVID-19 patients than in non-COVID-19 patients with symptoms of other respiratory viral infections, OR: 1.73; 95% CI: 1.94, 2.5 with p=0.04. Conclusion: Headache is common among COVID-19 patients and seems to be more common in COVID-19 patients compared to those with the non-COVID-19 viral infection. No definitive mechanisms on how headache emerges in COVID-19 patients but several possible hypotheses have been proposed. However, extensive studies are warranted to elucidate the mechanisms. PROSPERO registration: CRD42020210332 (28/09/2020).
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Affiliation(s)
- Endang Mutiawati
- Department of Neurology, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Department of Neurology, Dr. Zainoel Abidin Hospital, Banda Aceh, Aceh, 23126, Indonesia
| | - Syahrul Syahrul
- Department of Neurology, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Department of Neurology, Dr. Zainoel Abidin Hospital, Banda Aceh, Aceh, 23126, Indonesia
| | - Marhami Fahriani
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
| | - Jonny Karunia Fajar
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Brawijaya Internal Medicine Research Center, Department of Internal Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia
| | - Sukamto S. Mamada
- Faculty of Pharmacy, Hasanuddin University, Makassar, South Sulawesi, 90245, Indonesia
| | | | - Nur Samsu
- Brawijaya Internal Medicine Research Center, Department of Internal Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia
| | - Muhammad Ilmawan
- Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65117, Indonesia
| | - Yeni Purnamasari
- Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65117, Indonesia
| | | | - Ichsan Ichsan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia
| | - Sri Masyeni
- Department of Internal Medicine, Faculty of Medicine and Health Sciences, Universitas Warmadewa, Denpasar, Bali, 80235, Indonesia
- Department of Internal Medicine, Sanjiwani Hospital, Denpasar, Bali, 80235, Indonesia
| | - Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, Makassar, South Sulawesi, 90245, Indonesia
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
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14
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Mutiawati E, Syahrul S, Fahriani M, Fajar JK, Mamada SS, Maliga HA, Samsu N, Ilmawan M, Purnamasari Y, Asmiragani AA, Ichsan I, Emran TB, Rabaan AA, Masyeni S, Nainu F, Harapan H. Global prevalence and pathogenesis of headache in COVID-19: A systematic review and meta-analysis. F1000Res 2020; 9:1316. [PMID: 33953911 PMCID: PMC8063523 DOI: 10.12688/f1000research.27334.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 01/19/2023] Open
Abstract
Background: This study was conducted to determine the prevalence of headache in coronavirus disease 2019 (COVID-19) and to assess its association as a predictor for COVID-19. This study also aimed to discuss the possible pathogenesis of headache in COVID-19. Methods: Available articles from PubMed, Scopus, and Web of Science were searched as of September 2 nd, 2020. Data on characteristics of the study, headache and COVID-19 were extracted following the PRISMA guidelines. Biases were assessed using the Newcastle-Ottawa scale. The cumulative prevalence of headache was calculated for the general population (i.e. adults and children). The pooled odd ratio (OR) with 95% confidence intervals (95%CI) was calculated using the Z test to assess the association between headache and the presence of COVID-19 cases. Results: We included 104,751 COVID-19 cases from 78 eligible studies to calculate the global prevalence of headache in COVID-19 and 17 studies were included to calculate the association of headache and COVID-19. The cumulative prevalence of headache in COVID-19 was 25.2% (26,464 out of 104,751 cases). Headache was found to be more prevalent, approximately by two-fold, in COVID-19 patients than in non-COVID-19 patients (other respiratory viral infections), OR: 1.73; 95% CI: 1.94, 2.5 with p=0.04. Conclusion: Headache is common among COVID-19 patients and seems to be more common in COVID-19 patients compared to those with the non-COVID-19 viral infection. No definitive mechanisms on how headache emerges in COVID-19 patients but several possible hypotheses have been proposed. However, extensive studies are warranted to elucidate the mechanisms. PROSPERO registration: CRD42020210332 (28/09/2020).
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Affiliation(s)
- Endang Mutiawati
- Department of Neurology, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Department of Neurology, Dr. Zainoel Abidin Hospital, Banda Aceh, Aceh, 23126, Indonesia
| | - Syahrul Syahrul
- Department of Neurology, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Department of Neurology, Dr. Zainoel Abidin Hospital, Banda Aceh, Aceh, 23126, Indonesia
| | - Marhami Fahriani
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
| | - Jonny Karunia Fajar
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Brawijaya Internal Medicine Research Center, Department of Internal Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia
| | - Sukamto S. Mamada
- Faculty of Pharmacy, Hasanuddin University, Makassar, South Sulawesi, 90245, Indonesia
| | | | - Nur Samsu
- Brawijaya Internal Medicine Research Center, Department of Internal Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia
| | - Muhammad Ilmawan
- Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65117, Indonesia
| | - Yeni Purnamasari
- Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65117, Indonesia
| | | | - Ichsan Ichsan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia
| | - Sri Masyeni
- Department of Internal Medicine, Faculty of Medicine and Health Sciences, Universitas Warmadewa, Denpasar, Bali, 80235, Indonesia
- Department of Internal Medicine, Sanjiwani Hospital, Denpasar, Bali, 80235, Indonesia
| | - Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, Makassar, South Sulawesi, 90245, Indonesia
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
- Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, 23111, Indonesia
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15
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Tosolini AP, Sleigh JN. Intramuscular Delivery of Gene Therapy for Targeting the Nervous System. Front Mol Neurosci 2020; 13:129. [PMID: 32765219 PMCID: PMC7379875 DOI: 10.3389/fnmol.2020.00129] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
Virus-mediated gene therapy has the potential to deliver exogenous genetic material into specific cell types to promote survival and counteract disease. This is particularly enticing for neuronal conditions, as the nervous system is renowned for its intransigence to therapeutic targeting. Administration of gene therapy viruses into skeletal muscle, where distal terminals of motor and sensory neurons reside, has been shown to result in extensive transduction of cells within the spinal cord, brainstem, and sensory ganglia. This route is minimally invasive and therefore clinically relevant for gene therapy targeting to peripheral nerve soma. For successful transgene expression, viruses administered into muscle must undergo a series of processes, including host cell interaction and internalization, intracellular sorting, long-range retrograde axonal transport, endosomal liberation, and nuclear import. In this review article, we outline key characteristics of major gene therapy viruses—adenovirus, adeno-associated virus (AAV), and lentivirus—and summarize the mechanisms regulating important steps in the virus journey from binding at peripheral nerve terminals to nuclear delivery. Additionally, we describe how neuropathology can negatively influence these pathways, and conclude by discussing opportunities to optimize the intramuscular administration route to maximize gene delivery and thus therapeutic potential.
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Affiliation(s)
- Andrew P Tosolini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - James N Sleigh
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.,UK Dementia Research Institute, University College London, London, United Kingdom
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16
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Pietrantoni G, Ibarra-Karmy R, Arriagada G. Microtubule Retrograde Motors and Their Role in Retroviral Transport. Viruses 2020; 12:v12040483. [PMID: 32344581 PMCID: PMC7232228 DOI: 10.3390/v12040483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/18/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022] Open
Abstract
Following entry into the host cell, retroviruses generate a dsDNA copy of their genomes via reverse transcription, and this viral DNA is subsequently integrated into the chromosomal DNA of the host cell. Before integration can occur, however, retroviral DNA must be transported to the nucleus as part of a ‘preintegration complex’ (PIC). Transporting the PIC through the crowded environment of the cytoplasm is challenging, and retroviruses have evolved different mechanisms to accomplish this feat. Within a eukaryotic cell, microtubules act as the roads, while the microtubule-associated proteins dynein and kinesin are the vehicles that viruses exploit to achieve retrograde and anterograde trafficking. This review will examine the various mechanisms retroviruses have evolved in order to achieve retrograde trafficking, confirming that each retrovirus has its own strategy to functionally subvert microtubule associated proteins.
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17
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Yousafi Q, Azhar M, Khan MS, Mehmood A, Saleem S, Sajid MW, Hussain A, Kamal MA. Interaction of human dynein light chain 1 (DYNLL1) with enterochelin esterase ( Salmonella typhimurium) and protective antigen ( Bacillus anthraci) might be the potential cause of human infection. Saudi J Biol Sci 2019; 27:1396-1402. [PMID: 32346352 PMCID: PMC7182775 DOI: 10.1016/j.sjbs.2019.11.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
The cytoplasmic dynein light chain 1 (DYNLL1) is an important constituent of motor proteins complex. In human it is encoded by DYNLL1 gene. It is involved in cargo transport functions and interacts with many viral proteins with the help of short linear consensus motif sequence (K/R) XTQT. Viral proteins bind to DYNLL1 through its consensus short linear motif (SLiM) sequence to reach the target site in the cell and cause different infections in the host. It is still unknown if bacterial proteins also contain the same conserved SLiMs sequence through which they bind to this motor protein and cause infections. So, it is important to investigate the role of DYNLL1 in human bacterial infections. The interaction partner proteins of DYNLL1 against conserved viral motif sequences were predicted through PDBSum. Pairwise sequence alignment, between viral motif sequence and that of predicted proteins, was performed to identify conserved region in predicted interaction partners. Docking between the DYNLL1 and new pathogenic interaction partners was performed, by using PatchDock, to explore the protein-protein binding quality. Interactions of docked complexes were visualized by DimPlot. Three pathogenic bacterial proteins i.e., enterochelin esterase (3MGA), protective antigen (3J9C) and putative lipoprotein (4KT3) were selected as candidate interaction partners of DYNLL1. The putative lipoprotein (4KT3) showed low quality binding with DYNLL1. So, enterochelin esterase (3MGA) and protective antigen (3J9C) were speculated to be involved in human bacterial infections by using DYNLL1 to reach their target sites.
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Affiliation(s)
- Qudsia Yousafi
- Dept. Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Maria Azhar
- Dept. Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | | | - Asim Mehmood
- Dept. Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Shahzad Saleem
- Dept. Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | | | - Abrar Hussain
- Dept. Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Mohammad Amjad Kamal
- King Fahd Medical Research Center, King Abdulaziz University, P. O. Box 80216, Jeddah 21589, Saudi Arabia.,Enzymoics, 7 Peterlee Place, Hebersham, NSW 2770, Australia.,Novel Global Community Educational Foundation, Australia
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18
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Generous AR, Harrison OJ, Troyanovsky RB, Mateo M, Navaratnarajah CK, Donohue RC, Pfaller CK, Alekhina O, Sergeeva AP, Indra I, Thornburg T, Kochetkova I, Billadeau DD, Taylor MP, Troyanovsky SM, Honig B, Shapiro L, Cattaneo R. Trans-endocytosis elicited by nectins transfers cytoplasmic cargo, including infectious material, between cells. J Cell Sci 2019; 132:jcs235507. [PMID: 31331966 PMCID: PMC6737912 DOI: 10.1242/jcs.235507] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
Here, we show that cells expressing the adherens junction protein nectin-1 capture nectin-4-containing membranes from the surface of adjacent cells in a trans-endocytosis process. We find that internalized nectin-1-nectin-4 complexes follow the endocytic pathway. The nectin-1 cytoplasmic tail controls transfer: its deletion prevents trans-endocytosis, while its exchange with the nectin-4 tail reverses transfer direction. Nectin-1-expressing cells acquire dye-labeled cytoplasmic proteins synchronously with nectin-4, a process most active during cell adhesion. Some cytoplasmic cargo remains functional after transfer, as demonstrated with encapsidated genomes of measles virus (MeV). This virus uses nectin-4, but not nectin-1, as a receptor. Epithelial cells expressing nectin-4, but not those expressing another MeV receptor in its place, can transfer infection to nectin-1-expressing primary neurons. Thus, this newly discovered process can move cytoplasmic cargo, including infectious material, from epithelial cells to neurons. We name the process nectin-elicited cytoplasm transfer (NECT). NECT-related trans-endocytosis processes may be exploited by pathogens to extend tropism. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Alex R Generous
- Department of Molecular Medicine, Mayo Clinic, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
- Virology and Gene Therapy Track, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Oliver J Harrison
- Departments of Biochemistry and Molecular Biophysics, Systems Biology and Medicine, Zuckerman Mind, Brain, Behavior Institute, Columbia University, New York, NY 10032, USA
| | - Regina B Troyanovsky
- Department of Dermatology, Northwestern University, The Feinberg School of Medicine, Chicago, IL 60611
| | - Mathieu Mateo
- Department of Molecular Medicine, Mayo Clinic, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Chanakha K Navaratnarajah
- Department of Molecular Medicine, Mayo Clinic, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Ryan C Donohue
- Department of Molecular Medicine, Mayo Clinic, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
- Virology and Gene Therapy Track, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Christian K Pfaller
- Department of Molecular Medicine, Mayo Clinic, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
- Virology and Gene Therapy Track, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Olga Alekhina
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Alina P Sergeeva
- Departments of Biochemistry and Molecular Biophysics, Systems Biology and Medicine, Zuckerman Mind, Brain, Behavior Institute, Columbia University, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Indrajyoti Indra
- Department of Dermatology, Northwestern University, The Feinberg School of Medicine, Chicago, IL 60611
| | - Theresa Thornburg
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Irina Kochetkova
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA
| | | | - Matthew P Taylor
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Sergey M Troyanovsky
- Department of Dermatology, Northwestern University, The Feinberg School of Medicine, Chicago, IL 60611
| | - Barry Honig
- Departments of Biochemistry and Molecular Biophysics, Systems Biology and Medicine, Zuckerman Mind, Brain, Behavior Institute, Columbia University, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Lawrence Shapiro
- Departments of Biochemistry and Molecular Biophysics, Systems Biology and Medicine, Zuckerman Mind, Brain, Behavior Institute, Columbia University, New York, NY 10032, USA
| | - Roberto Cattaneo
- Department of Molecular Medicine, Mayo Clinic, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
- Virology and Gene Therapy Track, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
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19
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Zhang Y, Gao W, Li J, Wu W, Jiu Y. The Role of Host Cytoskeleton in Flavivirus Infection. Virol Sin 2019; 34:30-41. [PMID: 30725318 DOI: 10.1007/s12250-019-00086-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/10/2018] [Indexed: 01/07/2023] Open
Abstract
The family of flaviviruses is one of the most medically important groups of emerging arthropod-borne viruses. Host cell cytoskeletons have been reported to have close contact with flaviviruses during virus entry, intracellular transport, replication, and egress process, although many detailed mechanisms are still unclear. This article provides a brief overview of the function of the most prominent flaviviruses-induced or -hijacked cytoskeletal structures including actin, microtubules and intermediate filaments, mainly focus on infection by dengue virus, Zika virus and West Nile virus. We suggest that virus interaction with host cytoskeleton to be an interesting area of future research.
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Affiliation(s)
- Yue Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Gao
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Li
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Weihua Wu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yaming Jiu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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20
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Wang F, Li J, Li Q, Liu R, Zheng M, Wang Q, Wen J, Zhao G. Changes of host DNA methylation in domestic chickens infected with Salmonella enterica. J Genet 2018; 96:545-550. [PMID: 28947702 DOI: 10.1007/s12041-017-0818-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cytosine methylation is an effective way to modulate gene transcription.However, very little is knownabout the epigenetic changes in the host that is infected with Salmonella enterica. In this study, we usedmethylatedDNA immunoprecipitation sequencing to analyse the genomewide DNA methylation changes in domestic chickens after infected with Salmonella. The level of DNA methylation was slightly higher in the genomic regions around the transcription start termination sites in a Salmonella-infected group compared to the controls. Overall, 879 peaks were differentially methylated between Salmonella-infected and control groups, among which 135 were located in the gene promoter regions. Genes including MHC class IV antigen, GABARAPL1, MR1 and KDM1B were shown to be methylated more heavily after infected with Salmonella, whereas DYNLRB2, SEC14L3 and ANKIB1 tended to have fewer methylated cytosine residues in the promoter regions.Gene interaction network analysis of differentiallymethylated genes in the promoter regions revealed extensive connections with immune-related genes, indicating the possible impact of infection with Salmonella on the epigenetic status of the host.
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Affiliation(s)
- Fei Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
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21
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Milev MP, Yao X, Berthoux L, Mouland AJ. Impacts of virus-mediated manipulation of host Dynein. DYNEINS 2018. [PMCID: PMC7150161 DOI: 10.1016/b978-0-12-809470-9.00010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In general viruses' modus operandi to propagate is achieved by the co-opting host cell components, membranes, proteins, and machineries to their advantage. This is true for virtually every aspect of a virus' replication cycle from virus entry to the budding or release of progeny virus particles. In this chapter, we will discuss new information on the impacts of virus-mediated manipulation of Dynein motor complexes and associated machineries and factors. We will highlight how these host cell components impact on pathogenicity and immune responses, as many of the virus-mediated hijacked components also play pivotal roles in immune responses to pathogen insult. There are several comprehensive reviews that define virus–Dynein interactions including the first edition of this book that describes how viruses manipulate the host cell machineries their advantage. An updated table is included to summarize these virus–host interactions. Notably, barriers to intracellular translocation represent major hurdles to viral components during de novo infection and during active replication and the generation of progeny virus particles. Clearly, the subversion of host cell molecular motor protein activities takes advantage of constitutive and regulated membrane trafficking events and will target virus components to intracytoplasmic locales and membrane assembly. Broadening our understanding of the interplay between viruses, Dynein and the cytoskeleton will likely inform on new types of therapies. Continual enhancement of the breadth of new information on how viruses manipulate host cell biology will inevitably aid in the identification of new targets that can be poisoned to block old, new, and emerging viruses alike in their tracks.
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22
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Bicaudal D2 facilitates the cytoplasmic trafficking and nuclear import of HIV-1 genomes during infection. Proc Natl Acad Sci U S A 2017; 114:E10707-E10716. [PMID: 29180435 DOI: 10.1073/pnas.1712033114] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Numerous viruses, including HIV-1, exploit the microtubule network to traffic toward the nucleus during infection. Although numerous studies have observed a role for the minus-end microtubule motor dynein in HIV-1 infection, the mechanism by which the viral core containing the viral genome associates with dynein and induces its perinuclear trafficking has remained unclear. Here, we report that the dynein adapter protein bicaudal D2 (BICD2) is able to interact with HIV-1 viral cores in target cells. We also observe that BICD2 can bind in vitro-assembled capsid tubes through its CC3 domain. We observe that BICD2 facilitates infection by promoting the trafficking of viral cores to the nucleus, thereby promoting nuclear entry of the viral genome and infection. Finally, we observe that depletion of BICD2 in the monocytic cell line THP-1 results in an induction of IFN-stimulated genes in these cells. Collectively, these results identify a microtubule adapter protein critical for trafficking of HIV-1 in the cytoplasm of target cells and evasion of innate sensing mechanisms in macrophages.
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23
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Peptides mediating DNA transport on microtubules and their impact on non-viral gene transfer efficiency. Biosci Rep 2017; 37:BSR20170995. [PMID: 28899926 PMCID: PMC5643739 DOI: 10.1042/bsr20170995] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 11/17/2022] Open
Abstract
Synthetic vectors such as cationic polymers and cationic lipids remain attractive tools for non-viral gene transfer which is a complex process whose effectiveness relies on the ability to deliver a plasmid DNA (pDNA) into the nucleus of non-dividing cells. Once in the cytosol, the transport of pDNAs towards the nuclear envelope is strongly impaired by their very low cytosolic mobility due to their large size. To promote their movement towards the cell nucleus, few strategies have been implemented to exploit dynein, the microtubule’s (MT’s) motor protein, for propagation of cytosolic pDNA along the MTs towards the cell nucleus. In the first part of this review, an overview on MTs, dynein, dynein/virus interaction feature is presented followed by a summary of the results obtained by exploitation of LC8 and TCTEL1 dynein light chain association sequence (DLC-AS) for non-viral transfection. The second part dedicated to the adenoviral protein E3-14.7K, reports the transfection efficiency of polyplexes and lipoplexes containing the E3-14.7K-derived P79-98 peptide linked to pDNA. Here, several lines of evidence are given showing that dynein can be targeted to improve cytosolic pDNA mobility and accumulate pDNA near nuclear envelope in order to facilitate its transport through the nuclear pores. The linkage of various DLC-AS to pDNA carriers led to modest transfection improvements and their direct interaction with MTs was not demonstrated. In contrast, pDNA linked to the P79-98 peptide interacting with TCTEL1 via a cytosolic protein (fourteen seven K-interacting protein-1 (FIP-1)), interaction with MTs is evidenced in cellulo and transfection efficiency is improved.
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24
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Abstract
Retroviruses are obligate intracellular parasites of eukaryotic cells. After reverse transcription, the viral DNA contained in the preintegration complex is delivered to the nucleus of the host cell, where it integrates. Before reaching the nucleus, the incoming particle and the preintegration complex must travel throughout the cytoplasm. Likewise, the newly synthesized viral proteins and viral particles must transit the cytoplasm during exit. The cytoplasm is a crowded environment, and simple diffusion is difficult. Therefore, viruses have evolved to utilize the cellular mechanisms of movement through the cytoplasm, where microtubules are the roads, and the ATP-dependent motors dynein and kinesin are the vehicles for retrograde and anterograde trafficking. This review will focus on how different retroviruses (Mazon-Pfizer monkey virus, prototype foamy virus, bovine immunodeficiency virus, human immunodeficiency virus type 1, and murine leukemia virus) have subjugated the microtubule-associated motor proteins for viral replication. Although there have been advances in our understanding of how retroviruses move along microtubules, the strategies are different among them. Thus, a better understanding of the mechanisms used by each retrovirus to functionally subvert microtubule motor proteins will provide important clues in the design of new antiretroviral drugs that can specifically disrupt intracellular viral trafficking.
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Affiliation(s)
- Gloria Arriagada
- Departamento de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Viña del Mar, Chile
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25
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Functional Evidence of the Involvement of the Dynein Light Chain DYNLRB2 in Murine Leukemia Virus Infection. J Virol 2017; 91:JVI.00129-17. [PMID: 28250122 DOI: 10.1128/jvi.00129-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 02/21/2017] [Indexed: 11/20/2022] Open
Abstract
How murine leukemia virus (MLV) travels from the cell membrane to the nucleus and the mechanism for nuclear entry of MLV DNA in dividing cells still remain unclear. It seems likely that the MLV preintegration complex (PIC) interacts with cellular proteins to perform these tasks. We recently published that the microtubule motor cytoplasmic dynein complex and its regulator proteins interact with the MLV PIC at early times of infection, suggesting a functional interaction between the incoming viral particles, the dynein complex, and dynein regulators. To better understand the role of the dynein complex in MLV infection, we performed short hairpin RNA (shRNA) screening of the dynein light chains on MLV infection. We found that silencing of a specific light chain of the cytoplasmic dynein complex, DYNLRB2, reduced the efficiency of infection by MLV reporter viruses without affecting HIV-1 infection. Furthermore, the overexpression of DYNLRB2 increased infection by MLV. We conclude that the DYNLRB2 light chain of the cytoplasmic dynein complex is an important and specific piece of the host machinery needed for MLV infection.IMPORTANCE Retroviruses must reach the chromatin of their host to integrate their viral DNA, but first they must get into the nucleus. The cytoplasm is a crowded environment in which simple diffusion is slow, and thus viruses utilize retrograde transport along the microtubule network, mediated by the dynein complex. Different viruses use different components of this multisubunit complex. We have found that murine leukemia virus (MLV) associates functionally and specifically with the dynein light chain DYNLRB2, which is required for infection. Our study provides more insight into the molecular requirements for retrograde transport of the MLV preintegration complex and demonstrates, for the first time, a role for DYNLRB2 in viral infection.
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26
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Portilho DM, Persson R, Arhel N. Role of non-motile microtubule-associated proteins in virus trafficking. Biomol Concepts 2017; 7:283-292. [PMID: 27879481 DOI: 10.1515/bmc-2016-0018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/04/2016] [Indexed: 11/15/2022] Open
Abstract
Viruses are entirely dependent on their ability to infect a host cell in order to replicate. To reach their site of replication as rapidly and efficiently as possible following cell entry, many have evolved elaborate mechanisms to hijack the cellular transport machinery to propel themselves across the cytoplasm. Long-range movements have been shown to involve motor proteins along microtubules (MTs) and direct interactions between viral proteins and dynein and/or kinesin motors have been well described. Although less well-characterized, it is also becoming increasingly clear that non-motile microtubule-associated proteins (MAPs), including structural MAPs of the MAP1 and MAP2 families, and microtubule plus-end tracking proteins (+TIPs), can also promote viral trafficking in infected cells, by mediating interaction of viruses with filaments and/or motor proteins, and modulating filament stability. Here we review our current knowledge on non-motile MAPs, their role in the regulation of cytoskeletal dynamics and in viral trafficking during the early steps of infection.
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27
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Abstract
The early steps of HBV entry remain largely unknown despite the recent discovery of an HBV-specific entry receptor. Following entry HBV capsids have to be transported through the cytoplasm to the nuclear periphery, followed by nuclear entry. These steps have to take place in a coordinated manner to allow delivery of the genome into the nucleus. Due to the viscosity of the cytoplasm, the intracytoplasmic translocation has to be active and directed.Here, we describe protocols that can be applied to investigations of the HBV capsid with the cytoplasmic transport systems. We have chosen to present two independent experimental approaches, which allow avoiding artifacts. Aside of the specific capsid detection system, the protocols can be applied to any other viral structure.
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Affiliation(s)
- Quentin Osseman
- University of Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
| | - Michael Kann
- University of Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France.
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France.
- Centre Hospitalier Universitaire de Bordeaux, Service de Virologie, Bordeaux, France.
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28
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Brice A, Whelan DR, Ito N, Shimizu K, Wiltzer-Bach L, Lo CY, Blondel D, Jans DA, Bell TDM, Moseley GW. Quantitative Analysis of the Microtubule Interaction of Rabies Virus P3 Protein: Roles in Immune Evasion and Pathogenesis. Sci Rep 2016; 6:33493. [PMID: 27649849 PMCID: PMC5030706 DOI: 10.1038/srep33493] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/25/2016] [Indexed: 12/21/2022] Open
Abstract
Although microtubules (MTs) are known to have important roles in intracellular transport of many viruses, a number of reports suggest that specific viral MT-associated proteins (MAPs) target MTs to subvert distinct MT-dependent cellular processes. The precise functional importance of these interactions and their roles in pathogenesis, however, remain largely unresolved. To assess the association with disease of the rabies virus (RABV) MAP, P3, we quantitatively compared the phenotypes of P3 from a pathogenic RABV strain, Nishigahara (Ni) and a non-pathogenic Ni-derivative strain, Ni-CE. Using confocal/live-cell imaging and dSTORM super-resolution microscopy to quantify protein interactions with the MT network and with individual MT filaments, we found that the interaction by Ni-CE-P3 is significantly impaired compared with Ni-P3. This correlated with an impaired capacity to effect association of the transcription factor STAT1 with MTs and to antagonize interferon (IFN)/STAT1-dependent antiviral signaling. Importantly, we identified a single mutation in Ni-CE-P3 that is sufficient to inhibit MT-association and IFN-antagonist function of Ni-P3, and showed that this mutation alone attenuates the pathogenicity of RABV. These data provide evidence that the viral protein-MT interface has important roles in pathogenesis, suggesting that this interface could provide targets for vaccine/antiviral drug development.
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Affiliation(s)
- Aaron Brice
- Viral Pathogenesis Laboratory, Department of Biochemistry and Molecular Biology, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Donna R Whelan
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Naoto Ito
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.,The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Kenta Shimizu
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Linda Wiltzer-Bach
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Viral Pathogenesis Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Camden Y Lo
- Monash Micro Imaging, 27-31 Wright Street, Clayton, Victoria, 3168, Australia
| | - Danielle Blondel
- Unité de Virologie Moleculaire et Structurale, CNRS, UPR 3296, 91198 Gif sur Yvette Cedex, France
| | - David A Jans
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Gregory W Moseley
- Viral Pathogenesis Laboratory, Department of Biochemistry and Molecular Biology, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, 3010, Australia
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29
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Merino-Gracia J, Zamora-Carreras H, Bruix M, Rodríguez-Crespo I. Molecular Basis for the Protein Recognition Specificity of the Dynein Light Chain DYNLT1/Tctex1: CHARACTERIZATION OF THE INTERACTION WITH ACTIVIN RECEPTOR IIB. J Biol Chem 2016; 291:20962-20975. [PMID: 27502274 DOI: 10.1074/jbc.m116.736884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Indexed: 01/19/2023] Open
Abstract
It has been suggested that DYNLT1, a dynein light chain known to bind to various cellular and viral proteins, can function both as a molecular clamp and as a microtubule-cargo adapter. Recent data have shown that the DYNLT1 homodimer binds to two dynein intermediate chains to subsequently link cargo proteins such as the guanine nucleotide exchange factor Lfc or the small GTPases RagA and Rab3D. Although over 20 DYNLT1-interacting proteins have been reported, the exact sequence requirements that enable their association to the canonical binding groove or to the secondary site within the DYNLT1 surface are unknown. We describe herein the sequence recognition properties of the hydrophobic groove of DYNLT1 known to accommodate dynein intermediate chain. Using a pepscan approach, we have substituted each amino acid within the interacting peptide for all 20 natural amino acids and identified novel binding sequences. Our data led us to propose activin receptor IIB as a novel DYNLT1 ligand and suggest that DYNLT1 functions as a molecular dimerization engine bringing together two receptor monomers in the cytoplasmic side of the membrane. In addition, we provide evidence regarding a dual binding mode adopted by certain interacting partners such as Lfc or the parathyroid hormone receptor. Finally, we have used NMR spectroscopy to obtain the solution structure of human DYNLT1 forming a complex with dynein intermediate chain of ∼74 kDa; it is the first mammalian structure available.
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Affiliation(s)
- Javier Merino-Gracia
- From the Departamento Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain and
| | - Héctor Zamora-Carreras
- Departamento Química Física Biológica, Instituto Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Marta Bruix
- Departamento Química Física Biológica, Instituto Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Ignacio Rodríguez-Crespo
- From the Departamento Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain and
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30
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Dynein Regulators Are Important for Ecotropic Murine Leukemia Virus Infection. J Virol 2016; 90:6896-6905. [PMID: 27194765 DOI: 10.1128/jvi.00863-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 05/12/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED During the early steps of infection, retroviruses must direct the movement of the viral genome into the nucleus to complete their replication cycle. This process is mediated by cellular proteins that interact first with the reverse transcription complex and later with the preintegration complex (PIC), allowing it to reach and enter the nucleus. For simple retroviruses, such as murine leukemia virus (MLV), the identities of the cellular proteins involved in trafficking of the PIC in infection are unknown. To identify cellular proteins that interact with the MLV PIC, we developed a replication-competent MLV in which the integrase protein was tagged with a FLAG epitope. Using a combination of immunoprecipitation and mass spectrometry, we established that the microtubule motor dynein regulator DCTN2/p50/dynamitin interacts with the MLV preintegration complex early in infection, suggesting a direct interaction between the incoming viral particles and the dynein complex regulators. Further experiments showed that RNA interference (RNAi)-mediated silencing of either DCTN2/p50/dynamitin or another dynein regulator, NudEL, profoundly reduced the efficiency of infection by ecotropic, but not amphotropic, MLV reporters. We propose that the cytoplasmic dynein regulators are a critical component of the host machinery needed for infection by the retroviruses entering the cell via the ecotropic envelope pathway. IMPORTANCE Retroviruses must access the chromatin of host cells to integrate the viral DNA, but before this crucial event, they must reach the nucleus. The movement through the cytoplasm-a crowded environment where diffusion is slow-is thought to utilize retrograde transport along the microtubule network by the dynein complex. Different viruses use different components of this multisubunit complex. We found that the preintegration complex of murine leukemia virus (MLV) interacts with the dynein complex and that regulators of this complex are essential for infection. Our study provides the first insight into the requirements for retrograde transport of the MLV preintegration complex.
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31
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Differentially-Expressed Pseudogenes in HIV-1 Infection. Viruses 2015; 7:5191-205. [PMID: 26426037 PMCID: PMC4632377 DOI: 10.3390/v7102869] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 12/14/2022] Open
Abstract
Not all pseudogenes are transcriptionally silent as previously thought. Pseudogene transcripts, although not translated, contribute to the non-coding RNA pool of the cell that regulates the expression of other genes. Pseudogene transcripts can also directly compete with the parent gene transcripts for mRNA stability and other cell factors, modulating their expression levels. Tissue-specific and cancer-specific differential expression of these “functional” pseudogenes has been reported. To ascertain potential pseudogene:gene interactions in HIV-1 infection, we analyzed transcriptomes from infected and uninfected T-cells and found that 21 pseudogenes are differentially expressed in HIV-1 infection. This is interesting because parent genes of one-third of these differentially-expressed pseudogenes are implicated in HIV-1 life cycle, and parent genes of half of these pseudogenes are involved in different viral infections. Our bioinformatics analysis identifies candidate pseudogene:gene interactions that may be of significance in HIV-1 infection. Experimental validation of these interactions would establish that retroviruses exploit this newly-discovered layer of host gene expression regulation for their own benefit.
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32
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Merino-Gracia J, García-Mayoral MF, Rapali P, Valero RA, Bruix M, Rodríguez-Crespo I. DYNLT (Tctex-1) forms a tripartite complex with dynein intermediate chain and RagA, hence linking this small GTPase to the dynein motor. FEBS J 2015; 282:3945-58. [PMID: 26227614 DOI: 10.1111/febs.13388] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 07/02/2015] [Accepted: 07/28/2015] [Indexed: 12/15/2022]
Abstract
It has been suggested that DYNLT, a dynein light chain known to bind to various cellular and viral proteins, can function as a microtubule-cargo adaptor. Recent data showed that DYNLT links the small GTPase Rab3D to microtubules and, for this to occur, the DYNLT homodimer needs to display a binding site for dynein intermediate chain together with a binding site for the small GTPase. We have analysed in detail how RagA, another small GTPase, associates to DYNLT. After narrowing down the binding site of RagA to DYNLT we could identify that a β strand, part of the RagA G3 box involved in nucleotide binding, mediates this association. Interestingly, we show that both microtubule-associated DYNLT and cytoplasmic DYNLT are equally able to bind to the small GTPases Rab3D and RagA. Using NMR spectroscopy, we analysed the binding of dynein intermediate chain and RagA to mammalian DYNLT. Our experiments identify residues of DYNLT affected by dynein intermediate chain binding and residues affected by RagA binding, hence distinguishing the docking site for each of them. In summary, our results shed light on the mechanisms adopted by DYNLT when binding to protein cargoes that become transported alongside microtubules bound to the dynein motor.
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Affiliation(s)
- Javier Merino-Gracia
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain
| | - María Flor García-Mayoral
- Departamento de Química Biológica, Instituto de Química-Física Rocasolano, CSIC, Serrano, Madrid, Spain
| | - Peter Rapali
- Dynamics of Cell Growth and Division, Institut de Biologie Cellulaire et de Génétique, Centre National de la Recherche Scientifique, Bordeaux, France
| | - Ruth Ana Valero
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain
| | - Marta Bruix
- Departamento de Química Biológica, Instituto de Química-Física Rocasolano, CSIC, Serrano, Madrid, Spain
| | - Ignacio Rodríguez-Crespo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain
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33
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Foo KY, Chee HY. Interaction between Flavivirus and Cytoskeleton during Virus Replication. BIOMED RESEARCH INTERNATIONAL 2015; 2015:427814. [PMID: 26347881 PMCID: PMC4546964 DOI: 10.1155/2015/427814] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/30/2015] [Accepted: 07/28/2015] [Indexed: 12/25/2022]
Abstract
Flaviviruses are potentially human pathogens that cause major epidemics worldwide. Flavivirus interacts with host cell factors to form a favourable virus replication site. Cell cytoskeletons have been observed to have close contact with flaviviruses, which expands the understanding of cytoskeleton functions during virus replication, although many detailed mechanisms are still unclear. The interactions between the virus and host cytoskeletons such as actin filaments, microtubules, and intermediate filaments have provided insight into molecular alterations during the virus infection, such as viral entry, in-cell transport, scaffold assembly, and egress. This review article focuses on the utilization of cytoskeleton by Flavivirus and the respective functions during virus replication.
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Affiliation(s)
- Kar Yue Foo
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Hui-Yee Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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Mital J, Lutter EI, Barger AC, Dooley CA, Hackstadt T. Chlamydia trachomatis inclusion membrane protein CT850 interacts with the dynein light chain DYNLT1 (Tctex1). Biochem Biophys Res Commun 2015; 462:165-70. [PMID: 25944661 DOI: 10.1016/j.bbrc.2015.04.116] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 04/24/2015] [Indexed: 11/24/2022]
Abstract
Chlamydia trachomatis actively subverts the minus-end directed microtubule motor, dynein, to traffic along microtubule tracks to the Microtubule Organizing Center (MTOC) where it remains within a membrane bound replicative vacuole for the duration of its intracellular development. Unlike most substrates of the dynein motor, disruption of the dynactin cargo-linking complex by over-expression of the p50 dynamitin subunit does not inhibit C. trachomatis transport. A requirement for chlamydial protein synthesis to initiate this process suggests that a chlamydial product supersedes a requirement for p50 dynamitin. A yeast 2-hybrid system was used to screen the chlamydia inclusion membrane protein CT850 against a HeLa cell cDNA library and identified an interaction with the dynein light chain DYNLT1 (Tctex1). This interaction was at least partially dependent upon an (R/K-R/K-X-X-R/K) motif that is characteristic of DYNLT1 binding domains. CT850 expressed ectopically in HeLa cells localized at the MTOC and this localization is similarly dependent upon the predicted DYNLT1 binding domain. Furthermore, DYNLT1 is enriched at focal concentrations of CT850 on the chlamydial inclusion membrane that are known to interact with dynein and microtubules. Depletion of DYNLT1 disrupts the characteristic association of the inclusion membrane with centrosomes. Collectively, the results suggest that CT850 interacts with DYNLT1 to promote appropriate positioning of the inclusion at the MTOC.
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Affiliation(s)
- Jeffrey Mital
- Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA; Quinnipiac University, Hamden, CT 06518, USA
| | - Erika I Lutter
- Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Alexandra C Barger
- Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Cheryl A Dooley
- Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Ted Hackstadt
- Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA.
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Ebola virus VP35 interaction with dynein LC8 regulates viral RNA synthesis. J Virol 2015; 89:5148-53. [PMID: 25741013 DOI: 10.1128/jvi.03652-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/19/2015] [Indexed: 11/20/2022] Open
Abstract
Ebola virus VP35 inhibits alpha/beta interferon production and functions as a viral polymerase cofactor. Previously, the 8-kDa cytoplasmic dynein light chain (LC8) was demonstrated to interact with VP35, but the functional consequences were unclear. Here we demonstrate that the interaction is direct and of high affinity and that binding stabilizes the VP35 N-terminal oligomerization domain and enhances viral RNA synthesis. Mutational analysis demonstrates that VP35 interaction is required for the functional effects of LC8.
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Human immunodeficiency virus type 1 employs the cellular dynein light chain 1 protein for reverse transcription through interaction with its integrase protein. J Virol 2015; 89:3497-511. [PMID: 25568209 DOI: 10.1128/jvi.03347-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED In this study, we examined the requirement for host dynein adapter proteins such as dynein light chain 1 (DYNLL1), dynein light chain Tctex-type 1 (DYNLT1), and p150(Glued) in early steps of human immunodeficiency virus type 1 (HIV-1) replication. We found that the knockdown (KD) of DYNLL1, but not DYNLT1 or p150(Glued), resulted in significantly lower levels of HIV-1 reverse transcription in cells. Following an attempt to determine how DYNLL1 could impact HIV-1 reverse transcription, we detected the DYNLL1 interaction with HIV-1 integrase (IN) but not with capsid (CA), matrix (MA), or reverse transcriptase (RT) protein. Furthermore, by mutational analysis of putative DYNLL1 interaction motifs in IN, we identified the motifs (52)GQVD and (250)VIQD in IN as essential for DYNLL1 interaction. The DYNLL1 interaction-defective IN mutant HIV-1 (HIV-1IN(Q53A/Q252A)) exhibited impaired reverse transcription. Through further investigations, we have also detected relatively smaller amounts of particulate CA in DYNLL1-KD cells or in infections with HIV-1IN(Q53A/Q252A) mutant virus. Overall, our study demonstrates the novel interaction between HIV-1 IN and cellular DYNLL1 proteins and suggests the requirement of this virus-cell interaction for proper uncoating and efficient reverse transcription of HIV-1. IMPORTANCE Host cellular DYNLL1, DYNLT1, and p150(Glued) proteins have been implicated in the replication of several viruses. However, their roles in HIV-1 replication have not been investigated. For the first time, we demonstrated that during viral infection, HIV-1 IN interacts with DYNLL1, and their interaction was found to have a role in proper uncoating and efficient reverse transcription of HIV-1. Thus, interaction of IN and DYNLL1 may be a potential target for future anti-HIV therapy. Moreover, while our study has evaluated the involvement of IN in HIV-1 uncoating and reverse transcription, it also predicts a possible mechanism by which IN contributes to these early viral replication steps.
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Ouyang J, Zhu X, Chen Y, Wei H, Chen Q, Chi X, Qi B, Zhang L, Zhao Y, Gao GF, Wang G, Chen JL. NRAV, a long noncoding RNA, modulates antiviral responses through suppression of interferon-stimulated gene transcription. Cell Host Microbe 2014; 16:616-26. [PMID: 25525793 PMCID: PMC7104942 DOI: 10.1016/j.chom.2014.10.001] [Citation(s) in RCA: 264] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 06/04/2014] [Accepted: 09/15/2014] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) modulate various biological processes, but their role in host antiviral responses is largely unknown. Here we identify a lncRNA as a key regulator of antiviral innate immunity. Following from the observation that a lncRNA that we call negative regulator of antiviral response (NRAV) was dramatically downregulated during infection with several viruses, we ectopically expressed NRAV in human cells or transgenic mice and found that it significantly promotes influenza A virus (IAV) replication and virulence. Conversely, silencing NRAV suppressed IAV replication and virus production, suggesting that reduction of NRAV is part of the host antiviral innate immune response to virus infection. NRAV negatively regulates the initial transcription of multiple critical interferon-stimulated genes (ISGs), including IFITM3 and MxA, by affecting histone modification of these genes. Our results provide evidence for a lncRNA in modulating the antiviral interferon response.
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Affiliation(s)
- Jing Ouyang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaomei Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Anhui University, Hefei 230601, China
| | - Yuhai Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Wei
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinghuang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaojuan Chi
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baomin Qi
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lianfeng Zhang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Beijing 100021, China
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoshun Wang
- Gene Therapy Program, Departments of Microbiology and Immunology, Medicine and Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Ji-Long Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Chlamydia psittaci inclusion membrane protein IncB associates with host protein Snapin. Int J Med Microbiol 2014; 304:542-53. [PMID: 24751478 DOI: 10.1016/j.ijmm.2014.03.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 11/23/2022] Open
Abstract
Chlamydia (C.) psittaci, the causative agent of psittacosis in birds and humans, is the most important zoonotic pathogen of the family Chlamydiaceae. During a unique developmental cycle of this obligate intracellular pathogen, the infectious elementary body gains access to the susceptible host cell, where it transforms into the replicative reticulate body. C. psittaci uses dynein motor proteins for optimal early development. Chlamydial proteins that mediate this process are unknown. Two-hybrid screening with the C. psittaci inclusion protein IncB as bait against a HeLa Yeast Two-hybrid (YTH) library revealed that the host protein Snapin interacts with IncB. Snapin is a cytoplasmic protein that plays a multivalent role in intracellular trafficking. Confocal fluorescence microscopy using an IncB-specific antibody demonstrated that IncB, Snapin, and dynein were co-localized near the inclusion of C. psittaci-infected HEp-2 cells. This co-localization was lost when Snapin was depleted by RNAi. The interaction of Snapin with both IncB and dynein has been shown in vitro and in vivo. We propose that Snapin connects chlamydial inclusions with the microtubule network by interacting with both IncB and dynein.
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Li W, Tang X, Xing J, Sheng X, Zhan W. Proteomic analysis of differentially expressed proteins in Fenneropenaeus chinensis hemocytes upon white spot syndrome virus infection. PLoS One 2014; 9:e89962. [PMID: 24587154 PMCID: PMC3937397 DOI: 10.1371/journal.pone.0089962] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/23/2014] [Indexed: 11/18/2022] Open
Abstract
To elucidate molecular responses of shrimp hemocytes to white spot syndrome virus (WSSV) infection, two-dimensional gel electrophoresis was applied to investigate differentially expressed proteins in hemocytes of Chinese shrimp (Fenneropenaeus chinensis) at 24 h post infection (hpi). Approximately 580 protein spots were detected in hemocytes of healthy and WSSV-infected shrimps. Quantitative intensity analysis revealed 26 protein spots were significantly up-regulated, and 19 spots were significantly down-regulated. By mass spectrometry, small ubiquitin-like modifier (SUMO) 1, cytosolic MnSOD, triosephosphate isomerase, tubulin alpha-1 chain, microtubule-actin cross-linking factor 1, nuclear receptor E75 protein, vacuolar ATP synthase subunit B L form, inositol 1,4,5-trisphosphate receptor, arginine kinase, etc., amounting to 33 differentially modulated proteins were identified successfully. According to Gene Ontology annotation, the identified proteins were classified into nine categories, consisting of immune related proteins, stimulus response proteins, proteins involved in glucose metabolic process, cytoskeleton proteins, DNA or protein binding proteins, proteins involved in steroid hormone mediated signal pathway, ATP synthases, proteins involved in transmembrane transport and ungrouped proteins. Meanwhile, the expression profiles of three up-regulated proteins (SUMO, heat shock protein 70, and arginine kinase) and one down-regulated protein (prophenoloxidase) were further analyzed by real-time RT-PCR at the transcription level after WSSV infection. The results showed that SUMO and heat shock protein 70 were significantly up-regulated at each sampling time point, while arginine kinase was significantly up-regulated at 12 and 24 hpi. In contrast, prophenoloxidase was significantly down-regulated at each sampling time point. The results of this work provided preliminary data on proteins in shrimp hemocytes involved in WSSV infection.
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Affiliation(s)
- Wei Li
- Laboratory of Pathology and Immunology of Aquatic Animals, Ocean University of China, Qingdao, Shandong, China
| | - Xiaoqian Tang
- Laboratory of Pathology and Immunology of Aquatic Animals, Ocean University of China, Qingdao, Shandong, China
| | - Jing Xing
- Laboratory of Pathology and Immunology of Aquatic Animals, Ocean University of China, Qingdao, Shandong, China
| | - Xiuzhen Sheng
- Laboratory of Pathology and Immunology of Aquatic Animals, Ocean University of China, Qingdao, Shandong, China
| | - Wenbin Zhan
- Laboratory of Pathology and Immunology of Aquatic Animals, Ocean University of China, Qingdao, Shandong, China
- * E-mail:
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Chiang HS, Zhao Y, Song JH, Liu S, Wang N, Terhorst C, Sharpe AH, Basavappa M, Jeffrey KL, Reinecker HC. GEF-H1 controls microtubule-dependent sensing of nucleic acids for antiviral host defenses. Nat Immunol 2013; 15:63-71. [PMID: 24270516 PMCID: PMC4066330 DOI: 10.1038/ni.2766] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/08/2013] [Indexed: 12/15/2022]
Abstract
Detailed understanding of the signaling intermediates that confer the sensing of intracellular viral nucleic acids for induction of type I interferons is critical for strategies to curtail viral mechanisms that impede innate immune defenses. Here we show that the activation of the microtubule-associated guanine nucleotide exchange factor GEF-H1, encoded by Arhgef2, is essential for sensing of foreign RNA by RIG-I-like receptors. Activation of GEF-H1 controls RIG-I and Mda5-dependent phosphorylation of IRF3 and induction of interferon-β expression in macrophages. Generation of Arhgef2−/− mice revealed a pronounced signaling defect that prevented antiviral host responses to encephalomyocarditis virus and influenza A virus. Microtubule networks sequester GEF-H1 that upon activation is released to enable antiviral signaling by intracellular nucleic acid detection pathways.
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Affiliation(s)
- Hao-Sen Chiang
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School
| | - Yun Zhao
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School
| | - Joo-Hye Song
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School
| | - Song Liu
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School
| | - Ninghai Wang
- Division of Immunology, Beth Israel Deaconess Medical Center and Center for the Study of Inflammatory Bowel Disease, Harvard Medical School
| | - Cox Terhorst
- Division of Immunology, Beth Israel Deaconess Medical Center and Center for the Study of Inflammatory Bowel Disease, Harvard Medical School
| | - Arlene H Sharpe
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Megha Basavappa
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School
| | - Kate L Jeffrey
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School
| | - Hans-Christian Reinecker
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School
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Kausar S, Asif M, Bibi N, Rashid S. Comparative molecular docking analysis of cytoplasmic dynein light chain DYNLL1 with pilin to explore the molecular mechanism of pathogenesis caused by Pseudomonas aeruginosa PAO. PLoS One 2013; 8:e76730. [PMID: 24098557 PMCID: PMC3789673 DOI: 10.1371/journal.pone.0076730] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/26/2013] [Indexed: 11/19/2022] Open
Abstract
Cytoplasmic dynein light chain 1 (DYNLL1) is a component of large protein complex, which is implicated in cargo transport processes, and is known to interact with many cellular and viral proteins through its short consensus motif (K/R)XTQT. Still, it remains to be explored that bacterial proteins also exhibit similar recognition sequences to make them vulnerable to host defense mechanism. We employed multiple docking protocols including AUTODOCK, PatchDock, ZDOCK, DOCK/PIERR and CLUSPRO to explore the DYNLL1 and Pilin interaction followed by molecular dynamics simulation assays. Subsequent structural comparison of the predicted binding site for DYNLL1-Pilin complex against the experimentally verified DYNLL1 binding partners was performed to cross check the residual contributions and to determine the binding mode. On the basis of in silico analysis, here we describe a novel interaction of DYNLL1 and receptor binding domain of Pilin (the main protein constituent of bacterial type IV Pili) of gram negative bacteria Pseudomonas aeruginosa (PAO), which is the third most common nosocomial pathogen associated with the life-threatening infections. Evidently, our results underscore that Pilin specific motif (KSTQD) exhibits a close structural similarity to that of Vaccinia virus polymerase, P protein Rabies and P protein Mokola viruses. We speculate that binding of DYNLL1 to Pilin may trigger an uncontrolled inflammatory response of the host immune system during P. aeruginosa chronic infections thereby opening a new pioneering area to investigate the role of DYNLL1 in gram negative bacterial infections other than viral infections. Moreover, by manifesting a strict correspondence between sequence and function, our study anticipates a novel drug target site to control the complications caused by P. aeruginosa infections.
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Affiliation(s)
- Samina Kausar
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Asif
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Nousheen Bibi
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sajid Rashid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
- * E-mail:
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42
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Brice A, Moseley GW. Viral interactions with microtubules: orchestrators of host cell biology? Future Virol 2013. [DOI: 10.2217/fvl.12.137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Viral interaction with the microtubule (MT) cytoskeleton is critical to infection by many viruses. Most data regarding virus–MT interaction indicate key roles in the subcellular transport of virions/viral genomic material to sites of replication, assembly and egress. However, the MT cytoskeleton orchestrates diverse processes in addition to subcellular cargo transport, including regulation of signaling pathways, cell survival and mitosis, suggesting that viruses, expert manipulators of the host cell, may use the virus–MT interface to control multiple aspects of cell biology. Several lines of evidence support this idea, indicating that specific viral proteins can modify MT dynamics and/or structure and regulate processes such as apoptosis and innate immune signaling through MT-dependent mechanisms. Here, the authors review general aspects of virus–MT interactions, with emphasis on viral mechanisms that modify MT dynamics and functions to affect processes beyond virion transport. The emerging importance of discrete viral protein–MT interactions in pathogenic processes indicates that these interfaces may represent new targets for future therapeutics and vaccine development.
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Affiliation(s)
- Aaron Brice
- Viral Immune Evasion & Pathogenicity Laboratory, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Gregory W Moseley
- Viral Immune Evasion & Pathogenicity Laboratory, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia.
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Bucci C, Bakke O, Progida C. Charcot-Marie-Tooth disease and intracellular traffic. Prog Neurobiol 2012; 99:191-225. [PMID: 22465036 PMCID: PMC3514635 DOI: 10.1016/j.pneurobio.2012.03.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 12/23/2011] [Accepted: 03/13/2012] [Indexed: 12/23/2022]
Abstract
Mutations of genes whose primary function is the regulation of membrane traffic are increasingly being identified as the underlying causes of various important human disorders. Intriguingly, mutations in ubiquitously expressed membrane traffic genes often lead to cell type- or organ-specific disorders. This is particularly true for neuronal diseases, identifying the nervous system as the most sensitive tissue to alterations of membrane traffic. Charcot-Marie-Tooth (CMT) disease is one of the most common inherited peripheral neuropathies. It is also known as hereditary motor and sensory neuropathy (HMSN), which comprises a group of disorders specifically affecting peripheral nerves. This peripheral neuropathy, highly heterogeneous both clinically and genetically, is characterized by a slowly progressive degeneration of the muscle of the foot, lower leg, hand and forearm, accompanied by sensory loss in the toes, fingers and limbs. More than 30 genes have been identified as targets of mutations that cause CMT neuropathy. A number of these genes encode proteins directly or indirectly involved in the regulation of intracellular traffic. Indeed, the list of genes linked to CMT disease includes genes important for vesicle formation, phosphoinositide metabolism, lysosomal degradation, mitochondrial fission and fusion, and also genes encoding endosomal and cytoskeletal proteins. This review focuses on the link between intracellular transport and CMT disease, highlighting the molecular mechanisms that underlie the different forms of this peripheral neuropathy and discussing the pathophysiological impact of membrane transport genetic defects as well as possible future ways to counteract these defects.
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Affiliation(s)
- Cecilia Bucci
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni, 73100 Lecce, Italy.
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Rapali P, García-Mayoral MF, Martínez-Moreno M, Tárnok K, Schlett K, Albar JP, Bruix M, Nyitray L, Rodriguez-Crespo I. LC8 dynein light chain (DYNLL1) binds to the C-terminal domain of ATM-interacting protein (ATMIN/ASCIZ) and regulates its subcellular localization. Biochem Biophys Res Commun 2011; 414:493-8. [PMID: 21971545 DOI: 10.1016/j.bbrc.2011.09.093] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 09/17/2011] [Indexed: 12/30/2022]
Abstract
LC8 dynein light chain (now termed DYNLL1 and DYNLL2 in mammals), a dimeric 89 amino acid protein, is a component of the dynein multi-protein complex. However a substantial amount of DYNLL1 is not associated to microtubules and it can thus interact with dozens of cellular and viral proteins that display well-defined, short linear motifs. Using DYNLL1 as bait in a yeast two-hybrid screen of a human heart library we identified ATMIN, an ATM kinase-interacting protein, as a DYNLL1-binding partner. Interestingly, ATMIN displays at least 18 SQ/TQ motifs in its sequence and DYNLL1 is known to bind to proteins with KXTQT motifs. Using pepscan and yeast two-hybrid techniques we show that DYNLL1 binds to multiple SQ/TQ motifs present in the carboxy-terminal domain of ATMIN. Recombinant expression and purification of the DYNLL1-binding region of ATMIN allowed us to obtain a polypeptide with an apparent molecular mass in gel filtration close to 400 kDa that could bind to DYNLL1 in vitro. The NMR data-driven modelled complexes of DYNLL1 with two selected ATMIN peptides revealed a similar mode of binding to that observed between DYNLL1 and other peptide targets. Remarkably, co-expression of mCherry-DYNLL1 and GFP-ATMIN mutually affected intracellular protein localization. In GFP-ATMIN expressing-cells DNA damage induced efficiently nuclear foci formation, which was partly impeded by the presence of mCherry-DYNLL1. Thus, our results imply a potential cellular interference between DYNLL1 and ATMIN functions.
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Affiliation(s)
- Péter Rapali
- Dept. Biochemistry, Eötvös Loránd University, Budapest, Hungary
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Rapali P, Szenes Á, Radnai L, Bakos A, Pál G, Nyitray L. DYNLL/LC8: a light chain subunit of the dynein motor complex and beyond. FEBS J 2011; 278:2980-96. [PMID: 21777386 DOI: 10.1111/j.1742-4658.2011.08254.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The LC8 family members of dynein light chains (DYNLL1 and DYNLL2 in vertebrates) are highly conserved ubiquitous eukaryotic homodimer proteins that interact, besides dynein and myosin 5a motor proteins, with a large (and still incomplete) number of proteins involved in diverse biological functions. Despite an earlier suggestion that LC8 light chains function as cargo adapters of the above molecular motors, they are now recognized as regulatory hub proteins that interact with short linear motifs located in intrinsically disordered protein segments. The most prominent LC8 function is to promote dimerization of their binding partners that are often scaffold proteins of various complexes, including the intermediate chains of the dynein motor complex. Structural and functional aspects of this intriguing hub protein will be highlighted in this minireview.
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Affiliation(s)
- Péter Rapali
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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46
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Abstract
Dynein, which is a minus-end-directed microtubule motor, is crucial to a range of cellular processes. The mass of its motor domain is about 10 times that of kinesin, the other microtubule motor. Its large size and the difficulty of expressing and purifying mutants have hampered progress in dynein research. Recently, however, electron microscopy, X-ray crystallography and single-molecule nanometry have shed light on several key unsolved questions concerning how the dynein molecule is organized, what conformational changes in the molecule accompany ATP hydrolysis, and whether two or three motor domains are coordinated in the movements of dynein. This minireview describes our current knowledge of the molecular organization and the force-generating mechanism of dynein, with emphasis on findings from electron microscopy and single-molecule nanometry.
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Affiliation(s)
- Hitoshi Sakakibara
- National Institute of Information and Communications Technology, Nishi-ku, Kobe, Japan
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