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Baier CJ, Barrantes FJ. Role of cholesterol-recognition motifs in the infectivity of SARS-CoV-2 variants. Colloids Surf B Biointerfaces 2023; 222:113090. [PMID: 36563415 PMCID: PMC9743692 DOI: 10.1016/j.colsurfb.2022.113090] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022]
Abstract
The presence of linear amino acid motifs with the capacity to recognize the neutral lipid cholesterol, known as Cholesterol Recognition/interaction Amino acid Consensus sequence (CRAC), and its inverse or mirror image, CARC, has recently been reported in the primary sequence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike S homotrimeric glycoprotein. These motifs also occur in the two other pathogenic coronaviruses, SARS-CoV, and Middle-East respiratory syndrome CoV (MERS-CoV), most conspicuously in the transmembrane domain, the fusion peptide, the amino-terminal domain, and the receptor binding domain of SARS-CoV-2 S protein. Here we analyze the presence of cholesterol-recognition motifs in these key regions of the spike glycoprotein in the pathogenic CoVs. We disclose the inherent pathophysiological implications of the cholesterol motifs in the virus-host cell interactions and variant infectivity.
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Affiliation(s)
- Carlos Javier Baier
- Laboratorio de Toxicología, Instituto de Ciencias Biológicas y Biomédicas del Sur (INBIOSUR), Universidad Nacional del Sur (UNS), Consejo de Investigaciones Científicas y Técnicas (CONICET), Departamento de Biología, Bioquímica y Farmacia (DBByF), San Juan 670, B8000ICN Bahía Blanca, Argentina,Correspondence to: INBIOSUR-CONICET-UNS, DBByF, San Juan 670, B8000ICN Bahía Blanca, Buenos Aires, Argentina
| | - Francisco J. Barrantes
- Laboratory of Molecular Neurobiology, BIOMED UCA-CONICET, 1600 Av. A. Moreau de Justo, C1107AAZ Buenos Aires, Argentina,Correspondence to: BIOMED UCA-CONICET, Av. Alicia Moreau de Justo 1600, C1107AFF Buenos Aires, Argentina
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2
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First molecular detection of SARS-CoV-2 virus in cockroaches. Biologia (Bratisl) 2023; 78:1153-1160. [PMID: 36741802 PMCID: PMC9890436 DOI: 10.1007/s11756-023-01332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
Coronavirus is one of the main pathogens that primarily targets the human respiratory system. There are several ways to transmit this virus, such as direct contact or droplets spread by coughing or sneezing, and direct contact with fomites and surfaces is another way. This cross-sectional study was conducted in Shiraz, southern Iran, in 2021. 5 locations, including 3 hospitals and 2 dormitories, were selected for the survey. The cockroaches were collected from selected locations and transferred to the Laboratory of Medical Entomology at Shiraz University of Medical Sciences. All specimens were identified morphologically. The external and gastrointestinal washouts of collected samples with sterile phosphate-buffered saline separately were used for molecular analysis. An RT-qPCR assay, which suggests the possible insect‑borne transmission, was used. External and gastrointestinal washout of B. germanica from Dastgheyb Dormitory and P. americana from Ali-Asghar Hospital were positive for contamination with the SARS-CoV-2. Cockroaches spread the virus in the environment and contaminate human food and various surfaces of buildings. Their role will be more important in crowded places such as hotels, lodging houses, restaurants, and hospitals; vector control programs should be carried out with more accuracy in such places.
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Barrantes FJ. Fluorescence microscopy imaging of a neurotransmitter receptor and its cell membrane lipid milieu. Front Mol Biosci 2022; 9:1014659. [PMID: 36518846 PMCID: PMC9743973 DOI: 10.3389/fmolb.2022.1014659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/01/2022] [Indexed: 05/02/2024] Open
Abstract
Hampered by the diffraction phenomenon, as expressed in 1873 by Abbe, applications of optical microscopy to image biological structures were for a long time limited to resolutions above the ∼200 nm barrier and restricted to the observation of stained specimens. The introduction of fluorescence was a game changer, and since its inception it became the gold standard technique in biological microscopy. The plasma membrane is a tenuous envelope of 4 nm-10 nm in thickness surrounding the cell. Because of its highly versatile spectroscopic properties and availability of suitable instrumentation, fluorescence techniques epitomize the current approach to study this delicate structure and its molecular constituents. The wide spectral range covered by fluorescence, intimately linked to the availability of appropriate intrinsic and extrinsic probes, provides the ability to dissect membrane constituents at the molecular scale in the spatial domain. In addition, the time resolution capabilities of fluorescence methods provide complementary high precision for studying the behavior of membrane molecules in the time domain. This review illustrates the value of various fluorescence techniques to extract information on the topography and motion of plasma membrane receptors. To this end I resort to a paradigmatic membrane-bound neurotransmitter receptor, the nicotinic acetylcholine receptor (nAChR). The structural and dynamic picture emerging from studies of this prototypic pentameric ligand-gated ion channel can be extrapolated not only to other members of this superfamily of ion channels but to other membrane-bound proteins. I also briefly discuss the various emerging techniques in the field of biomembrane labeling with new organic chemistry strategies oriented to applications in fluorescence nanoscopy, the form of fluorescence microscopy that is expanding the depth and scope of interrogation of membrane-associated phenomena.
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Affiliation(s)
- Francisco J. Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA)–National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
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4
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Single-cell RNA-sequencing data analysis reveals a highly correlated triphasic transcriptional response to SARS-CoV-2 infection. Commun Biol 2022; 5:1302. [PMID: 36435849 PMCID: PMC9701238 DOI: 10.1038/s42003-022-04253-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is currently one of the most powerful techniques available to study the transcriptional response of thousands of cells to an external perturbation. Here, we perform a pseudotime analysis of SARS-CoV-2 infection using publicly available scRNA-seq data from human bronchial epithelial cells and colon and ileum organoids. Our results reveal that, for most genes, the transcriptional response to SARS-CoV-2 infection follows a non-linear pattern characterized by an initial and a final down-regulatory phase separated by an intermediate up-regulatory stage. A correlation analysis of transcriptional profiles suggests a common mechanism regulating the mRNA levels of most genes. Interestingly, genes encoded in the mitochondria or involved in translation exhibited distinct pseudotime profiles. To explain our results, we propose a simple model where nuclear export inhibition of nsp1-sensitive transcripts will be sufficient to explain the transcriptional shutdown of SARS-CoV-2 infected cells.
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Trifan A, Gorgun D, Salim M, Li Z, Brace A, Zvyagin M, Ma H, Clyde A, Clark D, Hardy DJ, Burnley T, Huang L, McCalpin J, Emani M, Yoo H, Yin J, Tsaris A, Subbiah V, Raza T, Liu J, Trebesch N, Wells G, Mysore V, Gibbs T, Phillips J, Chennubhotla SC, Foster I, Stevens R, Anandkumar A, Vishwanath V, Stone JE, Tajkhorshid E, A. Harris S, Ramanathan A. Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. THE INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2022; 36:603-623. [PMID: 38464362 PMCID: PMC10923581 DOI: 10.1177/10943420221113513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.
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Affiliation(s)
- Anda Trifan
- Argonne National Laboratory
- University of Illinois Urbana-Champaign
| | - Defne Gorgun
- Argonne National Laboratory
- University of Illinois Urbana-Champaign
| | | | | | | | | | | | - Austin Clyde
- Argonne National Laboratory
- University of Chicago
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ian Foster
- Argonne National Laboratory
- University of Chicago
| | - Rick Stevens
- Argonne National Laboratory
- University of Chicago
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Barrantes FJ. The constellation of cholesterol-dependent processes associated with SARS-CoV-2 infection. Prog Lipid Res 2022; 87:101166. [PMID: 35513161 PMCID: PMC9059347 DOI: 10.1016/j.plipres.2022.101166] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 01/11/2023]
Abstract
The role of cholesterol in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other coronavirus-host cell interactions is currently being discussed in the context of two main scenarios: i) the presence of the neutral lipid in cholesterol-rich lipid domains involved in different steps of the viral infection and ii) the alteration of metabolic pathways by the virus over the course of infection. Cholesterol-enriched lipid domains have been reported to occur in the lipid envelope membrane of the virus, in the host-cell plasma membrane, as well as in endosomal and other intracellular membrane cellular compartments. These membrane subdomains, whose chemical and physical properties distinguish them from the bulk lipid bilayer, have been purported to participate in diverse phenomena, from virus-host cell fusion to intracellular trafficking and exit of the virions from the infected cell. SARS-CoV-2 recruits many key proteins that participate under physiological conditions in cholesterol and lipid metabolism in general. This review analyses the status of cholesterol and lipidome proteins in SARS-CoV-2 infection and the new horizons they open for therapeutic intervention.
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Affiliation(s)
- Francisco J. Barrantes
- Corresponding author at: BIOMED UCA-CONICET, Av. Alicia Moreau de Justo 1600, C1107AFF Buenos Aires, Argentina
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Electrostatic Map of the SARS-CoV-2 Virion Specifies Binding Sites of the Antiviral Cationic Photosensitizer. Int J Mol Sci 2022; 23:ijms23137304. [PMID: 35806316 PMCID: PMC9266743 DOI: 10.3390/ijms23137304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Electrostatics is an important part of virus life. Understanding the detailed distribution of charges over the surface of a virus is important to predict its interactions with host cells, antibodies, drugs, and different materials. Using a coarse-grained model of the entire viral envelope developed by D. Korkin and S.-J. Marrink’s scientific groups, we created an electrostatic map of the external surface of SARS-CoV-2 and found a highly heterogeneous distribution of the electrostatic potential field of the viral envelope. Numerous negative patches originate mainly from negatively charged lipid domains in the viral membrane and negatively charged areas on the “stalks” of the spike (S) proteins. Membrane (M) and envelope (E) proteins with the total positive charge tend to colocalize with the negatively charged lipids. In the E protein pentamer exposed to the outer surface, negatively charged glutamate residues and surrounding lipids form a negative electrostatic potential ring around the channel entrance. We simulated the interaction of the antiviral octacationic photosensitizer octakis(cholinyl)zinc phthalocyanine with the surface structures of the entire model virion using the Brownian dynamics computational method implemented in ProKSim software (version r661). All mentioned negatively charged envelope components attracted the photosensitizer molecules and are thus potential targets for reactive oxygen generated in photosensitized reactions.
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Menéndez SG, Martín Giménez VM, Holick MF, Barrantes FJ, Manucha W. COVID-19 and neurological sequelae: Vitamin D as a possible neuroprotective and/or neuroreparative agent. Life Sci 2022; 297:120464. [PMID: 35271880 PMCID: PMC8898786 DOI: 10.1016/j.lfs.2022.120464] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 12/16/2022]
Abstract
SARS-CoV-2, the etiological agent of the current COVID-19 pandemic, belongs to a broad family of coronaviruses that also affect humans. SARS-CoV-2 infection usually leads to bilateral atypical pneumonia with significant impairment of respiratory function. However, the infectious capacity of SARS-CoV-2 is not limited to the respiratory system, but may also affect other vital organs such as the brain. The central nervous system is vulnerable to cell damage via direct invasion or indirect virus-related effects leading to a neuroinflammatory response, processes possibly associated with a decrease in the activity of angiotensin II converting enzyme (ACE2), the canonical cell-surface receptor for SARS-CoV-2. This enzyme regulates neuroprotective and neuroimmunomodulatory functions and can neutralize both inflammation and oxidative stress generated at the cellular level. Furthermore, there is evidence of an association between vitamin D deficiency and predisposition to the development of severe forms of COVID-19, with its possible neurological and neuropsychiatric sequelae: vitamin D has the ability to down-modulate the effects of neuroinflammatory cytokines, among other anti-inflammatory/immunomodulatory effects, thus attenuating harmful consequences of COVID-19. This review critically analyzes current evidence supporting the notion that vitamin D may act as a neuroprotective and neuroreparative agent against the neurological sequelae of COVID-19.
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Affiliation(s)
- Sebastián García Menéndez
- Laboratorio de Farmacología Experimental Básica y Traslacional, Área de Farmacología, Departamento de Patología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina,Instituto de Medicina y Biología Experimental de Cuyo, Consejo Nacional de Investigación Científica y Tecnológica (IMBECU-CONICET), Mendoza, Argentina
| | - Virna Margarita Martín Giménez
- Instituto de Investigaciones en Ciencias Químicas, Facultad de Ciencias Químicas y Tecnológicas, Universidad Católica de Cuyo, San Juan, Argentina
| | - Michael F. Holick
- Section of Endocrinology, Diabetes, Nutrition and Weight Management, Department of Medicine, Boston University Medical Campus, 715 Albany St #437, Boston, MA 02118, USA
| | - Francisco J. Barrantes
- Laboratorio de Neurobiología Molecular, Instituto de Investigaciones Biomédicas (BIOMED), UCA-CONICET, Buenos Aires, Argentina
| | - Walter Manucha
- Laboratorio de Farmacología Experimental Básica y Traslacional, Área de Farmacología, Departamento de Patología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina,Instituto de Medicina y Biología Experimental de Cuyo, Consejo Nacional de Investigación Científica y Tecnológica (IMBECU-CONICET), Mendoza, Argentina,Corresponding author at: Pharmacology Area, Pathology Department, Medical Sciences College, National University of Cuyo, Mendoza CP5500, Argentina
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Soltani A, Jamalidoust M, Hosseinpour A, Vahedi M, Ashraf H, Yousefinejad S. First molecular-based detection of SARS-CoV-2 virus in the field-collected houseflies. Sci Rep 2021; 11:13884. [PMID: 34230585 PMCID: PMC8260644 DOI: 10.1038/s41598-021-93439-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/24/2021] [Indexed: 12/17/2022] Open
Abstract
This is the first report of SARS-CoV-2 detection on field-collected Musca domestica housefly surface and tissue samples using the high-sensitive PCR assay which suggests the possible insect-borne transmission. The study was conducted in Shiraz city, southern Iran, in May and Jun 2020. Adult flies were sampled at the outdoor areas of two hospitals treating COVID-19 patients. Fly samples were first washed twice to remove the insect surface attached to SARS-CoV-2 virions. After that, the disinfected fly samples were homogenized. Fly surface washout and homogenate samples were tested using Taq Man real-time PCR assay for the SARS-CoV-2 virus. In a total of 156 houseflies, 75% of samples from the body washout samples were positive for SARS-CoV-2. Strikingly, 37% of the homogenized specimens were positive for the SARS-CoV-2, suggesting the possible infection of the insects or uptake of the virion to the insect metabolism. The other possibility is the houseflies up took the blood or blood fluids of the patients and the RNA of the SARS-CoV-2 survived in the insect body without replicating. Our preliminary findings suggest that the houseflies could transmit SARS-CoV-2 as a mechanical or biological vector especially during the warm seasons while increasing the population and activity of houseflies.
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Affiliation(s)
- Aboozar Soltani
- Research Center for Health Sciences, Institute of Health, Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Marzieh Jamalidoust
- Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Hosseinpour
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mozaffar Vahedi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hadi Ashraf
- Communicable Disease Unit, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Yousefinejad
- Research Center for Health Sciences, Institute of Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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