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Athukorala A, Helbig KJ, McSharry BP, Forwood JK, Sarker S. An optimised protocol for the expression and purification of adenovirus core protein VII. J Virol Methods 2024; 326:114907. [PMID: 38432358 DOI: 10.1016/j.jviromet.2024.114907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Adenovirus protein VII (pVII) is a highly basic core protein, bearing resemblance to mammalian histones. Despite its diverse functions, a comprehensive understanding of its structural intricacies and the mechanisms underlying its functions remain elusive, primarily due to the complexity of producing a good amount of soluble pVII. This study aimed to optimise the expression and purification of recombinant pVII from four different adenoviruses with a simple vector construct. This study successfully determined the optimal conditions for efficiently purifying pVII across four adenovirus species, revealing the differential preference for bacterial expression systems. The One Shot BL21 Star (DE3) proved favourable over Rosetta 2 (DE3) pLysS with consistent levels of expression between IPTG-induced and auto-induction. We demonstrated that combining chemical and mechanical cell lysis is possible and highly effective. Other noteworthy benefits were observed in using RNase during sample processing. The addition of RNase has significantly improved the quality and quantity of the purified protein as confirmed by chromatographic and western blot analyses. These findings established a solid groundwork for pVII purification methodologies and carry the significant potential to assist in unveiling the core structure of pVII, its arrangement within the core, DNA condensation intricacies, and potential pathways for nuclear transport.
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Affiliation(s)
- Ajani Athukorala
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| | - Karla J Helbig
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| | - Brian P McSharry
- School of Dentistry and Medical Sciences Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Sciences Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Subir Sarker
- Biomedical Sciences and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia.
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2
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Neef A, Nath BK, Das T, Luque D, Forwood JK, Raidal SR, Das S. Recombinantly expressed virus-like particles (VLPs) of canine circovirus for development of an indirect ELISA. Vet Res Commun 2024; 48:1121-1133. [PMID: 38163840 DOI: 10.1007/s11259-023-10290-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Canine circovirus (CanineCV) is an emerging pathogen in domestic dogs, detected in multiple countries in association with varying clinical and pathological presentations including diarrhoea, vasculitis, granulomatous inflammation, and respiratory signs. Understanding the pathology of CanineCV is confounded by the fact that it has been detected in asymptomatic dogs as well as in diseased dogs concurrently infected with known pathogens. Recombinantly expressed self-assembling Virus-like particles (VLPs) lack viral genomic material but imitate the capsid surface conformations of wild type virion, allowing arrays of biological applications including subunit vaccine development and immunodiagnostics. In this study, full length CanineCV capsid gene was expressed in Escherichia coli followed by two-step purification process to yield soluble capsid protein in high concentration. Transmission electron microscopy (TEM) confirmed the capsid antigen self-assembled into 17-20 nm VLPs in glutathione S-transferase (GST) buffer, later utilised to develop an indirect enzyme-linked immunosorbent assay (iELISA). The respective sensitivity and specificity of the proposed iELISA were 94.10% and 88.40% compared with those obtained from Western blot. The mean OD450 value for western blot positive samples was 1.22 (range 0.12-3.39) and negative samples was 0.21 (range 0.07-0.41). An optimal OD450 cut-off of 0.35 was determined by ROC curve analysis. Median inter-assay and intra-assay validation revealed that the iELISA test results were reproducible with coefficients of variation 7.70 (range 5.6-11.9) and 4.21 (range 1.2-7.4). Our results demonstrated that VLP-based iELISA is a highly sensitive method for serological diagnosis of CanineCV infections in dogs, suitable for large-scale epidemiological studies.
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Affiliation(s)
- Alison Neef
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Babu Kanti Nath
- Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia.
| | - Tridip Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Daniel Luque
- Electron Microscope Unit, Mark Wainwright Analytical Centre, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Jade K Forwood
- Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
- School of Dentistry and Medical Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
- Training Hub Promoting Regional Industry and Innovation in Virology and Epidemiology, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Shane R Raidal
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
- Training Hub Promoting Regional Industry and Innovation in Virology and Epidemiology, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Shubhagata Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
- Training Hub Promoting Regional Industry and Innovation in Virology and Epidemiology, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
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3
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Hoad M, Roby JA, Forwood JK. Structural basis for nuclear import of bat adeno-associated virus capsid protein. J Gen Virol 2024; 105:001960. [PMID: 38441555 PMCID: PMC10999750 DOI: 10.1099/jgv.0.001960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 01/22/2024] [Indexed: 03/07/2024] Open
Abstract
Adeno-associated viruses (AAV) are one of the world's most promising gene therapy vectors and as a result, are one of the most intensively studied viral vectors. Despite a wealth of research into these vectors, the precise characterisation of AAVs to translocate into the host cell nucleus remains unclear. Recently we identified the nuclear localization signals of an AAV porcine strain and determined its mechanism of binding to host importin proteins. To expand our understanding of diverse AAV import mechanisms we sought to determine the mechanism in which the Cap protein from a bat-infecting AAV can interact with transport receptor importins for translocation into the nucleus. Using a high-resolution crystal structure and quantitative assays, we were able to not only determine the exact region and residues of the N-terminal domain of the Cap protein which constitute the functional NLS for binding with the importin alpha two protein, but also reveal the differences in binding affinity across the importin-alpha isoforms. Collectively our results allow for a detailed molecular view of the way AAV Cap proteins interact with host proteins for localization into the cell nucleus.
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Affiliation(s)
- Mikayla Hoad
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Justin A. Roby
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
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4
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Cross EM, Akbari N, Ghassabian H, Hoad M, Pavan S, Ariawan D, Donnelly CM, Lavezzo E, Petersen GF, Forwood JK, Alvisi G. A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin α-dependent nuclear localization signals. Protein Sci 2024; 33:e4876. [PMID: 38108201 PMCID: PMC10807245 DOI: 10.1002/pro.4876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
Nucleocytoplasmic transport regulates the passage of proteins between the nucleus and cytoplasm. In the best characterized pathway, importin (IMP) α bridges cargoes bearing basic, classical nuclear localization signals (cNLSs) to IMPβ1, which mediates transport through the nuclear pore complex. IMPα recognizes three types of cNLSs via two binding sites: the major binding site accommodates monopartite cNLSs, the minor binding site recognizes atypical cNLSs, while bipartite cNLSs simultaneously interact with both major and minor sites. Despite the growing knowledge regarding IMPα-cNLS interactions, our understanding of the evolution of cNLSs is limited. We combined bioinformatic, biochemical, functional, and structural approaches to study this phenomenon, using polyomaviruses (PyVs) large tumor antigens (LTAs) as a model. We characterized functional cNLSs from all human (H)PyV LTAs, located between the LXCXE motif and origin binding domain. Surprisingly, the prototypical SV40 monopartite NLS is not well conserved; HPyV LTA NLSs are extremely heterogenous in terms of structural organization, IMPα isoform binding, and nuclear targeting abilities, thus influencing the nuclear accumulation properties of full-length proteins. While several LTAs possess bipartite cNLSs, merkel cell PyV contains a hybrid bipartite cNLS whose upstream stretch of basic amino acids can function as an atypical cNLS, specifically binding to the IMPα minor site upon deletion of the downstream amino acids after viral integration in the host genome. Therefore, duplication of a monopartite cNLS and subsequent accumulation of point mutations, optimizing interaction with distinct IMPα binding sites, led to the evolution of bipartite and atypical NLSs binding at the minor site.
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Affiliation(s)
- Emily M. Cross
- School of Dentistry and Medical SciencesCharles Sturt UniversityWagga WaggaAustralia
- Diamond Light SourceHarwell Science and Innovation CampusDidcotUnited Kingdom
| | - Nasim Akbari
- Department of Molecular MedicineUniversity of PadovaPadovaItaly
| | | | - Mikayla Hoad
- School of Dentistry and Medical SciencesCharles Sturt UniversityWagga WaggaAustralia
| | - Silvia Pavan
- Department of Molecular MedicineUniversity of PadovaPadovaItaly
| | - Daryl Ariawan
- Dementia Research CentreMacquarie UniversitySydneyAustralia
| | - Camilla M. Donnelly
- School of Dentistry and Medical SciencesCharles Sturt UniversityWagga WaggaAustralia
| | - Enrico Lavezzo
- Department of Molecular MedicineUniversity of PadovaPadovaItaly
| | | | - Jade K. Forwood
- School of Dentistry and Medical SciencesCharles Sturt UniversityWagga WaggaAustralia
- Gulbali InstituteCharles Sturt UniversityWagga WaggaAustralia
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5
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Cross EM, Marin O, Ariawan D, Aragão D, Cozza G, Di Iorio E, Forwood JK, Alvisi G. Structural determinants of phosphorylation-dependent nuclear transport of HCMV DNA polymerase processivity factor UL44. FEBS Lett 2024; 598:199-209. [PMID: 38158756 DOI: 10.1002/1873-3468.14797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Human cytomegalovirus DNA polymerase processivity factor UL44 is transported into the nucleus by importin (IMP) α/β through a classical nuclear localization signal (NLS), and this region is susceptible to cdc2-mediated phosphorylation at position T427. Whilst phosphorylation within and close to the UL44 NLS regulates nuclear transport, the details remain elusive, due to the paucity of structural information regarding the role of negatively charged cargo phosphate groups. We addressed this issue by studying the effect of UL44 T427 phosphorylation on interaction with several IMPα isoforms by biochemical and structural approaches. Phosphorylation decreased UL44/IMPα affinity 10-fold, and a comparative structural analysis of UL44 NLS phosphorylated and non-phosphorylated peptides complexed with mouse IMPα2 revealed the structural rearrangements responsible for phosphorylation-dependent inhibition of UL44 nuclear import.
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Affiliation(s)
- Emily M Cross
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, Australia
- Diamond Light Source, Didcot, UK
| | - Oriano Marin
- Department of Biomedical Sciences, University of Padova, Italy
| | - Daryl Ariawan
- Dementia Research Centre, Macquarie University, Sydney, Australia
| | | | - Giorgio Cozza
- Department of Molecular Medicine, University of Padua, Italy
| | - Enzo Di Iorio
- Department of Molecular Medicine, University of Padua, Italy
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, Australia
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Athukorala A, Donnelly CM, Pavan S, Nematollahzadeh S, Djossou VA, Nath B, Helbig KJ, Di Iorio E, McSharry BP, Alvisi G, Forwood JK, Sarker S. Structural and functional characterization of siadenovirus core protein VII nuclear localization demonstrates the existence of multiple nuclear transport pathways. J Gen Virol 2024; 105. [PMID: 38261399 DOI: 10.1099/jgv.0.001928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Adenovirus protein VII (pVII) plays a crucial role in the nuclear localization of genomic DNA following viral infection and contains nuclear localization signal (NLS) sequences for the importin (IMP)-mediated nuclear import pathway. However, functional analysis of pVII in adenoviruses to date has failed to fully determine the underlying mechanisms responsible for nuclear import of pVII. Therefore, in the present study, we extended our analysis by examining the nuclear trafficking of adenovirus pVII from a non-human species, psittacine siadenovirus F (PsSiAdV). We identified a putative classical (c)NLS at pVII residues 120-128 (120PGGFKRRRL128). Fluorescence polarization and electrophoretic mobility shift assays demonstrated direct, high-affinity interaction with both IMPα2 and IMPα3 but not IMPβ. Structural analysis of the pVII-NLS/IMPα2 complex confirmed a classical interaction, with the major binding site of IMPα occupied by K124 of pVII-NLS. Quantitative confocal laser scanning microscopy showed that PsSiAdV pVII-NLS can confer IMPα/β-dependent nuclear localization to GFP. PsSiAdV pVII also localized in the nucleus when expressed in the absence of other viral proteins. Importantly, in contrast to what has been reported for HAdV pVII, PsSiAdV pVII does not localize to the nucleolus. In addition, our study demonstrated that inhibition of the IMPα/β nuclear import pathway did not prevent PsSiAdV pVII nuclear targeting, indicating the existence of alternative pathways for nuclear localization, similar to what has been previously shown for human adenovirus pVII. Further examination of other potential NLS signals, characterization of alternative nuclear import pathways, and investigation of pVII nuclear targeting across different adenovirus species is recommended to fully elucidate the role of varying nuclear import pathways in the nuclear localization of pVII.
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Affiliation(s)
- Ajani Athukorala
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| | - Camilla M Donnelly
- School of Dentistry and Medical Sciences, Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Silvia Pavan
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Sepehr Nematollahzadeh
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | | | - Babu Nath
- School of Dentistry and Medical Sciences, Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Karla J Helbig
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| | - Enzo Di Iorio
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Brian P McSharry
- School of Dentistry and Medical Sciences, Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Gualtiero Alvisi
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Subir Sarker
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
- Biomedical Sciences & Molecular Biology, College of Public Health Medical, and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
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7
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Vogel OA, Forwood JK, Leung DW, Amarasinghe GK, Basler CF. Viral Targeting of Importin Alpha-Mediated Nuclear Import to Block Innate Immunity. Cells 2023; 13:71. [PMID: 38201275 PMCID: PMC10778312 DOI: 10.3390/cells13010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Cellular nucleocytoplasmic trafficking is mediated by the importin family of nuclear transport proteins. The well-characterized importin alpha (IMPA) and importin beta (IMPB) nuclear import pathway plays a crucial role in the innate immune response to viral infection by mediating the nuclear import of transcription factors such as IRF3, NFκB, and STAT1. The nuclear transport of these transcription factors ultimately leads to the upregulation of a wide range of antiviral genes, including IFN and IFN-stimulated genes (ISGs). To replicate efficiently in cells, viruses have developed mechanisms to block these signaling pathways. One strategy to evade host innate immune responses involves blocking the nuclear import of host antiviral transcription factors. By binding IMPA proteins, these viral proteins prevent the nuclear transport of key transcription factors and suppress the induction of antiviral gene expression. In this review, we describe examples of proteins encoded by viruses from several different families that utilize such a competitive inhibition strategy to suppress the induction of antiviral gene expression.
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Affiliation(s)
- Olivia A. Vogel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - Daisy W. Leung
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA;
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA;
| | - Christopher F. Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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Donnelly CM, Stewart M, Roby JA, Sundaramoorthy V, Forwood JK. Structural Determination of the Australian Bat Lyssavirus Nucleoprotein and Phosphoprotein Complex. Viruses 2023; 16:33. [PMID: 38229694 PMCID: PMC7615531 DOI: 10.3390/v16010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Australian bat lyssavirus (ABLV) shows similar clinical symptoms as rabies, but there are currently no protein structures available for ABLV proteins. In lyssaviruses, the interaction between nucleoprotein (N) and phosphoprotein (N) in the absence of RNA generates a complex (N0P) that is crucial for viral assembly, and understanding the interface between these two proteins has the potential to provide insight into a key feature: the viral lifecycle. In this study, we used recombinant chimeric protein expression and X-ray crystallography to determine the structure of ABLV nucleoprotein bound to residues 1-40 of its phosphoprotein chaperone. Comparison of our results with the recently generated structure of RABV CVS-11 N0P demonstrated a highly conserved interface in this complex. Because the N0P interface is conserved in the lyssaviruses of phylogroup I, it is an attractive therapeutic target for multiple rabies-causing viral species.
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Affiliation(s)
- Camilla M. Donnelly
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Diagnostics, Surveillance and Response, Australian Centre for Disease Preparedness, CSIRO, Geelong, VIC 3219, Australia
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Justin A. Roby
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Vinod Sundaramoorthy
- Diagnostics, Surveillance and Response, Australian Centre for Disease Preparedness, CSIRO, Geelong, VIC 3219, Australia
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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Nath BK, Das T, Peters A, Gupta SD, Sarker S, Forwood JK, Raidal SR, Das S. Australasian Pigeon Circoviruses Demonstrate Natural Spillover Infection. Viruses 2023; 15:2025. [PMID: 37896802 PMCID: PMC10611180 DOI: 10.3390/v15102025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Pigeon circovirus (PiCV) is considered to be genetically diverse, with a relatively small circular single-stranded DNA genome of 2 kb that encodes for a capsid protein (Cap) and a replication initiator protein (Rep). Australasia is known to be the origin of diverse species of the Order Columbiformes, but limited data on the PiCV genome sequence has hindered phylogeographic studies in this species. To fill this gap, this study was conducted to investigate PiCV in 118 characteristic samples from different birds across Australia using PCR and sequencing. Eighteen partial PiCV Rep sequences and one complete PiCV genome sequence were recovered from reservoir and aberrant hosts. Phylogenetic analyses revealed that PiCV circulating in Australia was scattered across three different subclades. Importantly, one subclade dominated within the PiCV sequenced from Australia and Poland, whereas other PiCV sequenced in this study were more closely related to the PiCV sequenced from China, USA and Japan. In addition, PiCV Rep sequences obtained from clinically affected plumed whistling duck, blue billed duck and Australian magpie demonstrated natural spillover of PiCV unveiled host generalist characteristics of the pigeon circovirus. These findings indicate that PiCV genomes circulating in Australia lack host adapted population structure but demonstrate natural spillover infection.
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Affiliation(s)
- Babu Kanti Nath
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (T.D.); (A.P.); (S.R.R.); (S.D.)
- Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (S.D.G.); (J.K.F.)
| | - Tridip Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (T.D.); (A.P.); (S.R.R.); (S.D.)
| | - Andrew Peters
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (T.D.); (A.P.); (S.R.R.); (S.D.)
- Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (S.D.G.); (J.K.F.)
| | - Suman Das Gupta
- Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (S.D.G.); (J.K.F.)
| | - Subir Sarker
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4814, Australia;
| | - Jade K. Forwood
- Biosecurity Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (S.D.G.); (J.K.F.)
- School of Dentistry and Medical Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Training Hub Promoting Regional Industry and Innovation in Virology and Epidemiology, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Shane R. Raidal
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (T.D.); (A.P.); (S.R.R.); (S.D.)
| | - Shubhagata Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (T.D.); (A.P.); (S.R.R.); (S.D.)
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10
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Ghafoori SM, Abdollahpour S, Shirmast P, Forwood JK. Crystallographic structure determination and analysis of a potential short-chain dehydrogenase/reductase (SDR) from multi-drug resistant Acinetobacter baumannii. PLoS One 2023; 18:e0289992. [PMID: 37616198 PMCID: PMC10449147 DOI: 10.1371/journal.pone.0289992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/30/2023] [Indexed: 08/26/2023] Open
Abstract
Bacterial antibiotic resistance remains an ever-increasing worldwide problem, requiring new approaches and enzyme targets. Acinetobacter baumannii is recognised as one of the most significant antibiotic-resistant bacteria, capable of carrying up to 45 different resistance genes, and new drug discovery targets for this organism is an urgent priority. Short-chain dehydrogenase/reductase enzymes are a large protein family with >60,000 members involved in numerous biosynthesis pathways. Here, we determined the structure of an SDR protein from A. baumannii and assessed the putative co-factor comparisons with previously co-crystalised enzymes and cofactors. This study provides a basis for future studies to examine these potential co-factors in vitro.
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Affiliation(s)
- Seyed Mohammad Ghafoori
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga, Wagga, NSW, Australia
| | - Soha Abdollahpour
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga, Wagga, NSW, Australia
| | - Paniz Shirmast
- Menzies Health Institute Queensland and School of Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga, Wagga, NSW, Australia
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11
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Kumar M, Teakel SL, Swarbrick C, Chowdhury IS, Thorn DC, Sunde M, Carver JA, Forwood JK. Amyloid fibril formation, structure and domain swapping of acyl-coenzyme A thioesterase-7. FEBS J 2023; 290:4057-4073. [PMID: 37042241 DOI: 10.1111/febs.16795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/23/2023] [Accepted: 04/11/2023] [Indexed: 04/13/2023]
Abstract
Acyl-coenzyme A thioesterase (Acot) enzymes are involved in a broad range of essential intracellular roles including cell signalling, lipid metabolism, inflammation and the opening of ion channels. Dysregulation in lipid metabolism has been linked to neuroinflammatory and neurological disorders such as Alzheimer's and Parkinson's diseases. Structurally, Acot enzymes adopt a circularised trimeric arrangement with each monomer containing an N- and a C-terminal hotdog domain. Acot7 spontaneously forms amyloid fibrils in vitro under physiological conditions. The resultant amyloid fibrillar structures were characterised by dye-binding fluorescence assays, far-UV circular dichroism spectroscopy, transmission electron microscopy and X-ray fibre diffraction. Acot7 has an unusual mechanism of aggregation with no lag phase. The initial phase (~ 18 h) of aggregation involves conformational rearrangement within the oligomers to form species of enhanced β-sheet character. The subsequent loss of α-helical structure is accompanied by large-scale amyloid fibril formation. The crystal structure of Acot7 revealed an unexpected arrangement of the two domains within the circularised trimeric structure, which is the basis for a proposed mechanism of amyloid fibril formation involving domain swapping during the initial phase of aggregation. Acot7 formed fibrils in the presence of its substrate arachidonoyl-CoA and its inhibitors and maintained its enzyme activity during fibril assembly. It is proposed that the Acot7 fibrillar form acts as functional amyloid.
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Affiliation(s)
- Manjeet Kumar
- Research School of Chemistry, The Australian National University, Acton, Australia
| | - Sarah L Teakel
- School of Dentistry and Medical Science, Charles Sturt University, Wagga Wagga, Australia
| | - Crystall Swarbrick
- School of Dentistry and Medical Science, Charles Sturt University, Wagga Wagga, Australia
| | - Intifar S Chowdhury
- Research School of Chemistry, The Australian National University, Acton, Australia
| | - David C Thorn
- Research School of Chemistry, The Australian National University, Acton, Australia
| | - Margaret Sunde
- School of Medical Sciences, The University of Sydney, Australia
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Science, Charles Sturt University, Wagga Wagga, Australia
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12
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Tsimbalyuk S, Shornikov A, Srivastava P, Le VTB, Warren I, Khandokar YB, Kuhn ML, Forwood JK. Structural and Kinetic Characterization of the SpeG Spermidine/Spermine N-acetyltransferase from Methicillin-Resistant Staphylococcus aureus USA300. Cells 2023; 12:1829. [PMID: 37508494 PMCID: PMC10378331 DOI: 10.3390/cells12141829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Polyamines are simple yet critical molecules with diverse roles in numerous pathogenic and non-pathogenic organisms. Regulating polyamine concentrations affects the transcription and translation of genes and proteins important for cell growth, stress, and toxicity. One way polyamine concentrations are maintained within the cell is via spermidine/spermine N-acetyltransferases (SSATs) that acetylate intracellular polyamines so they can be exported. The bacterial SpeG enzyme is an SSAT that exhibits a unique dodecameric structure and allosteric site compared to other SSATs that have been previously characterized. While its overall 3D structure is conserved, its presence and role in different bacterial pathogens are inconsistent. For example, not all bacteria have speG encoded in their genomes; in some bacteria, the speG gene is present but has become silenced, and in other bacteria, it has been acquired on mobile genetic elements. The latter is the case for methicillin-resistant Staphylococcus aureus (MRSA) USA300, where it appears to aid pathogenesis. To gain a greater understanding of the structure/function relationship of SpeG from the MRSA USA300 strain (SaSpeG), we determined its X-ray crystal structure in the presence and absence of spermine. Additionally, we showed the oligomeric state of SaSpeG is dynamic, and its homogeneity is affected by polyamines and AcCoA. Enzyme kinetic assays showed that pre-incubation with polyamines significantly affected the positive cooperativity toward spermine and spermidine and the catalytic efficiency of the enzyme. Furthermore, we showed bacterial SpeG enzymes do not have equivalent capabilities to acetylate aminopropyl versus aminbutyl ends of spermidine. Overall, this study provides new insight that will assist in understanding the SpeG enzyme and its role in pathogenic and non-pathogenic bacteria at a molecular level.
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Affiliation(s)
- Sofiya Tsimbalyuk
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Aleksander Shornikov
- Deparment of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Parul Srivastava
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Van Thi Bich Le
- Deparment of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Imani Warren
- Deparment of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Yogesh B Khandokar
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Misty L Kuhn
- Deparment of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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13
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Tu WJ, Melino M, Dunn J, McCuaig RD, Bielefeldt-Ohmann H, Tsimbalyuk S, Forwood JK, Ahuja T, Vandermeide J, Tan X, Tran M, Nguyen Q, Zhang L, Nam A, Pan L, Liang Y, Smith C, Lineburg K, Nguyen TH, Sng JDJ, Tong ZWM, Chew KY, Short KR, Le Grand R, Seddiki N, Rao S. In vivo inhibition of nuclear ACE2 translocation protects against SARS-CoV-2 replication and lung damage through epigenetic imprinting. Nat Commun 2023; 14:3680. [PMID: 37369668 DOI: 10.1038/s41467-023-39341-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
In vitro, ACE2 translocates to the nucleus to induce SARS-CoV-2 replication. Here, using digital spatial profiling of lung tissues from SARS-CoV-2-infected golden Syrian hamsters, we show that a specific and selective peptide inhibitor of nuclear ACE2 (NACE2i) inhibits viral replication two days after SARS-CoV-2 infection. Moreover, the peptide also prevents inflammation and macrophage infiltration, and increases NK cell infiltration in bronchioles. NACE2i treatment increases the levels of the active histone mark, H3K27ac, restores host translation in infected hamster bronchiolar cells, and leads to an enrichment in methylated ACE2 in hamster bronchioles and lung macrophages, a signature associated with virus protection. In addition, ACE2 methylation is increased in myeloid cells from vaccinated patients and associated with reduced SARS-CoV-2 spike protein expression in monocytes from individuals who have recovered from infection. This protective epigenetic scarring of ACE2 is associated with a reduced latent viral reservoir in monocytes/macrophages and enhanced immune protection against SARS-CoV-2. Nuclear ACE2 may represent a therapeutic target independent of the variant and strain of viruses that use the ACE2 receptor for host cell entry.
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Affiliation(s)
- Wen Juan Tu
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michelle Melino
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jenny Dunn
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Robert D McCuaig
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Helle Bielefeldt-Ohmann
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Sofiya Tsimbalyuk
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Taniya Ahuja
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - John Vandermeide
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Xiao Tan
- Genomics and Machine Learning Lab, Division of Genetics and Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Minh Tran
- Genomics and Machine Learning Lab, Division of Genetics and Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Quan Nguyen
- Genomics and Machine Learning Lab, Division of Genetics and Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Liang Zhang
- NanoString Technologies Inc., Seattle, WA, 98109, USA
| | - Andy Nam
- NanoString Technologies Inc., Seattle, WA, 98109, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA, 98109, USA
| | - Yan Liang
- NanoString Technologies Inc., Seattle, WA, 98109, USA
| | - Corey Smith
- Translational and Human Immunology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Katie Lineburg
- Translational and Human Immunology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Tam H Nguyen
- Flow and Imaging Facility, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Julian D J Sng
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Zhen Wei Marcus Tong
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Keng Yih Chew
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Roger Le Grand
- Université Paris-Saclay, INSERM U1184, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - Nabila Seddiki
- Université Paris-Saclay, INSERM U1184, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - Sudha Rao
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
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14
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Donnelly CM, Vogel OA, Edwards MR, Taylor PE, Roby JA, Forwood JK, Basler CF. Henipavirus Matrix Protein Employs a Non-Classical Nuclear Localization Signal Binding Mechanism. Viruses 2023; 15:1302. [PMID: 37376602 DOI: 10.3390/v15061302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Nipah virus (NiV) and Hendra virus (HeV) are highly pathogenic species from the Henipavirus genus within the paramyxovirus family and are harbored by Pteropus Flying Fox species. Henipaviruses cause severe respiratory disease, neural symptoms, and encephalitis in various animals and humans, with human mortality rates exceeding 70% in some NiV outbreaks. The henipavirus matrix protein (M), which drives viral assembly and budding of the virion, also performs non-structural functions as a type I interferon antagonist. Interestingly, M also undergoes nuclear trafficking that mediates critical monoubiquitination for downstream cell sorting, membrane association, and budding processes. Based on the NiV and HeV M X-ray crystal structures and cell-based assays, M possesses a putative monopartite nuclear localization signal (NLS) (residues 82KRKKIR87; NLS1 HeV), positioned on an exposed flexible loop and typical of how many NLSs bind importin alpha (IMPα), and a putative bipartite NLS (244RR-10X-KRK258; NLS2 HeV), positioned within an α-helix that is far less typical. Here, we employed X-ray crystallography to determine the binding interface of these M NLSs and IMPα. The interaction of both NLS peptides with IMPα was established, with NLS1 binding the IMPα major binding site, and NLS2 binding as a non-classical NLS to the minor site. Co-immunoprecipitation (co-IP) and immunofluorescence assays (IFA) confirm the critical role of NLS2, and specifically K258. Additionally, localization studies demonstrated a supportive role for NLS1 in M nuclear localization. These studies provide additional insight into the critical mechanisms of M nucleocytoplasmic transport, the study of which can provide a greater understanding of viral pathogenesis and uncover a potential target for novel therapeutics for henipaviral diseases.
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Affiliation(s)
- Camilla M Donnelly
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Olivia A Vogel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan R Edwards
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
- School of Population and Public Health, Faculty of Medicine, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Paige E Taylor
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Justin A Roby
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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15
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Ghafoori SM, Petersen GF, Conrady DG, Calhoun BM, Stigliano MZZ, Baydo RO, Grice R, Abendroth J, Lorimer DD, Edwards TE, Forwood JK. Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site. Sci Rep 2023; 13:6940. [PMID: 37117205 PMCID: PMC10140725 DOI: 10.1038/s41598-023-33529-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/14/2023] [Indexed: 04/30/2023] Open
Abstract
Influenza virus (IV) causes several outbreaks of the flu each year resulting in an economic burden to the healthcare system in the billions of dollars. Several influenza pandemics have occurred during the last century and estimated to have caused 100 million deaths. There are four genera of IV, A (IVA), B (IVB), C (IVC), and D (IVD), with IVA being the most virulent to the human population. Hemagglutinin (HA) is an IVA surface protein that allows the virus to attach to host cell receptors and enter the cell. Here we have characterised the high-resolution structures of seven IVA HAs, with one in complex with the anti-influenza head-binding antibody C05. Our analysis revealed conserved receptor binding residues in all structures, as seen in previously characterised IV HAs. Amino acid conservation is more prevalent on the stalk than the receptor binding domain (RBD; also called the head domain), allowing the virus to escape from antibodies targeting the RBD. The equivalent site of C05 antibody binding to A/Denver/57 HA appears hypervariable in the other H1N1 IV HAs. Modifications within this region appear to disrupt binding of the C05 antibody, as these HAs no longer bind the C05 antibody by analytical SEC. Our study brings new insights into the structural and functional recognition of IV HA proteins and can contribute to further development of anti-influenza vaccines.
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Affiliation(s)
- Seyed Mohammad Ghafoori
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Gayle F Petersen
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Deborah G Conrady
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Brandy M Calhoun
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Matthew Z Z Stigliano
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Ruth O Baydo
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Rena Grice
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Donald D Lorimer
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Thomas E Edwards
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia.
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16
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Nath BK, Das S, Tidd N, Das T, Forwood JK, Raidal SR. Lesions and viral loads in racing pigeons naturally coinfected with pigeon circovirus and columbid alphaherpesvirus 1 in Australia. J Vet Diagn Invest 2023; 35:278-283. [PMID: 36896657 DOI: 10.1177/10406387231156839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Columbid alphaherpesvirus 1 (CoHV1) is associated with oral or upper respiratory tract lesions, encephalitis, and occasional fatal systemic disease in naive or immunosuppressed pigeons. Clinical disease is often reported with CoHV1 and coinfecting viruses, including pigeon circovirus (PiCV), which may cause host immunosuppression and augment lesion development. A natural outbreak of CoHV1 and PiCV coinfection occurred in a flock of 60 racing rock pigeons (Columba livia), in which 4 pigeons succumbed within 7 d of clinical onset. Lesions included suppurative stomatitis, pharyngitis, cloacitis, meningitis, and tympanitis, with eosinophilic intranuclear inclusion bodies consistent with herpesviral infection. In addition, large numbers of botryoid intracytoplasmic inclusion bodies were present in the skin, oral mucosa, and bursa of Fabricius, suggestive of circoviral infection, which was confirmed by immunohistochemistry. The concurrent viral load of CoHV1 and PiCV was high in liver, oropharynx, and bursa of Fabricius. We found PiCV in oro-cloacal swabs from 44 of 46 additional birds of variable clinical status, PiCV alone in 23 birds, and coinfection with CoHV1 in 21 birds. Viral copy numbers were significantly higher (p < 0.0001) for both viruses in clinically affected pigeons than in subclinical qPCR-positive birds. The CoHV1-induced lesions might have been exacerbated by concomitant PiCV infection.
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Affiliation(s)
- Babu K Nath
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, New South Wales, Australia.,Department of Dairy and Poultry Science, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Shubhagata Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Naomie Tidd
- Veterinary Diagnostic Laboratory, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Tridip Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Shane R Raidal
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, New South Wales, Australia
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17
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Hoad M, Cross EM, Donnelly CM, Sarker S, Roby JA, Forwood JK. Structural Characterization of Porcine Adeno-Associated Virus Capsid Protein with Nuclear Trafficking Protein Importin Alpha Reveals a Bipartite Nuclear Localization Signal. Viruses 2023; 15:v15020315. [PMID: 36851528 PMCID: PMC9964314 DOI: 10.3390/v15020315] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Adeno-associated viruses (AAV) are important vectors for gene therapy, and accordingly, many aspects of their cell transduction pathway have been well characterized. However, the specific mechanisms that AAV virions use to enter the host nucleus remain largely unresolved. We therefore aimed to reveal the interactions between the AAV Cap protein and the nuclear transport protein importin alpha (IMPα) at an atomic resolution. Herein we expanded upon our earlier research into the Cap nuclear localization signal (NLS) of a porcine AAV isolate, by examining the influence of upstream basic regions (BRs) towards IMPα binding. Using a high-resolution crystal structure, we identified that the IMPα binding determinants of the porcine AAV Cap comprise a bipartite NLS with an N-terminal BR binding at the minor site of IMPα, and the previously identified NLS motif binding at the major site. Quantitative assays showed a vast difference in binding affinity between the previously determined monopartite NLS, and bipartite NLS described in this study. Our results provide a detailed molecular view of the interaction between AAV capsids and the nuclear import receptor, and support the findings that AAV capsids enter the nucleus by binding the nuclear import adapter IMPα using the classical nuclear localization pathway.
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Affiliation(s)
- Mikayla Hoad
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Emily M. Cross
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Camilla M. Donnelly
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Subir Sarker
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| | - Justin A. Roby
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Correspondence:
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18
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Selinger M, Novotný R, Sýs J, Roby JA, Tykalová H, Ranjani GS, Vancová M, Jaklová K, Kaufman F, Bloom ME, Zdráhal Z, Grubhoffer L, Forwood JK, Hrabal R, Rumlová M, Štěrba J. Tick-borne encephalitis virus capsid protein induces translational shut-off as revealed by its structural-biological analysis. J Biol Chem 2022; 298:102585. [PMID: 36223838 PMCID: PMC9664413 DOI: 10.1016/j.jbc.2022.102585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/05/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is the most medically relevant tick-transmitted Flavivirus in Eurasia, targeting the host central nervous system and frequently causing severe encephalitis. The primary function of its capsid protein (TBEVC) is to recruit the viral RNA and form a nucleocapsid. Additional functionality of Flavivirus capsid proteins has been documented, but further investigation is needed for TBEVC. Here, we show the first capsid protein 3D structure of a member of the tick-borne flaviviruses group. The structure of monomeric Δ16-TBEVC was determined using high-resolution multidimensional NMR spectroscopy. Based on natural in vitro TBEVC homodimerization, the dimeric interfaces were identified by hydrogen deuterium exchange mass spectrometry (MS). Although the assembly of flaviviruses occurs in endoplasmic reticulum-derived vesicles, we observed that TBEVC protein also accumulated in the nuclei and nucleoli of infected cells. In addition, the predicted bipartite nuclear localization sequence in the TBEVC C-terminal part was confirmed experimentally, and we described the interface between TBEVC bipartite nuclear localization sequence and import adapter protein importin-alpha using X-ray crystallography. Furthermore, our coimmunoprecipitation coupled with MS identification revealed 214 interaction partners of TBEVC, including viral envelope and nonstructural NS5 proteins and a wide variety of host proteins involved mainly in rRNA processing and translation initiation. Metabolic labeling experiments further confirmed that TBEVC and other flaviviral capsid proteins are able to induce translational shutoff and decrease of 18S rRNA. These findings may substantially help to design a targeted therapy against TBEV.
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19
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Teakel S, Marama M, Aragão D, Tsimbalyuk S, Mackie ERR, Soares da‐Costa TP, Forwood JK, Cahill MA. Structural characterization of a
MAPR
‐related archaeal cytochrome
b
5M
protein. FEBS Lett 2022; 596:2409-2417. [DOI: 10.1002/1873-3468.14471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Sarah Teakel
- School of Dentistry and Medical Sciences Charles Sturt University Wagga Wagga NSW 2678 Australia
| | - Michealla Marama
- School of Animal and Veterinary Sciences Charles Sturt University Wagga Wagga NSW 2678 Australia
| | - David Aragão
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation 800 Blackburn Road Clayton VIC 3168 Australia
- Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0DE UK
| | - Sofiya Tsimbalyuk
- School of Dentistry and Medical Sciences Charles Sturt University Wagga Wagga NSW 2678 Australia
| | - Emily R. R. Mackie
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Bundoora VIC 3086 Australia
- School of Agriculture, Food & Wine and Waite Research Institute, University of Adelaide Waite Campus Glen Osmond SA 5064 Australia
| | - Tatiana P. Soares da‐Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science La Trobe University Bundoora VIC 3086 Australia
- School of Agriculture, Food & Wine and Waite Research Institute, University of Adelaide Waite Campus Glen Osmond SA 5064 Australia
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences Charles Sturt University Wagga Wagga NSW 2678 Australia
| | - Michael A. Cahill
- School of Dentistry and Medical Sciences Charles Sturt University Wagga Wagga NSW 2678 Australia
- The John Curtin School of Medical Research The Australian National University ACT 2601 Australia
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20
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Nath BK, Das S, Das T, Forwood JK, Raidal SR. Development and applications of a TaqMan based quantitative real-time PCR for the rapid detection of Pigeon circovirus (PiCV). J Virol Methods 2022; 308:114588. [PMID: 35870671 DOI: 10.1016/j.jviromet.2022.114588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022]
Abstract
TaqMan probe based quantitative polymerase reaction (TaqMan qPCR) is a robust and reliable technique for detecting and quantifying target DNA copies. Quantitative molecular diagnosis of genetically diverse single stranded DNA (ssDNA) virus such as Pigeon circovirus (PiCV) can be challenging owing to difficulties in primer binding or low abundance of template DNA copies in clinical specimens. Several methods have been described for the detection of PiCV, being qPCR the most simple and reliable. As far as is known, two qPCR systems described until now are based on SYBR green. This study reports development and validation of a highly sensitive TaqMan qPCR targeted to Rep for the detection of highly diverse PiCV in pigeon samples with excellent reproducibility, specificity, and sensitivity. The limit of detection was determined as low as 2 (two) plasmid copies. Estimations of 100 % specificity and 100 % sensitivity were obtained based on the qPCR results with panel of 60 samples (known PiCV positive, n = 30; known PiCV negative, n = 20; samples positive to Beak and feather disease virus (BFDV), n = 5 and samples positive to canine circovirus, n = 5). Co-efficient of variation (CV) for Ct values ranged between 0.27 % and 0.78 % in the same assay and 1.84-2.87 % in different assays.
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Affiliation(s)
- Babu K Nath
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia
| | - Shubhagata Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia
| | - Tridip Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia
| | - Shane R Raidal
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia; School of Dentistry and Medical Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales 2678, Australia.
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21
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Tsimbalyuk S, Cross EM, Hoad M, Donnelly CM, Roby JA, Forwood JK. Correction: Tsimbalyuk et al. The Intrinsically Disordered W Protein Is Multifunctional during Henipavirus Infection, Disrupting Host Signalling Pathways and Nuclear Import. Cells2020, 9, 1913. Cells 2022; 11:cells11081290. [PMID: 35456054 PMCID: PMC9027788 DOI: 10.3390/cells11081290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/25/2022] [Indexed: 11/25/2022] Open
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22
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Wang S, Chan KWK, Tan MJA, Flory C, Luo D, Lescar J, Forwood JK, Vasudevan SG. A conserved arginine in NS5 binds genomic 3' stem-loop RNA for primer-independent initiation of flavivirus RNA replication. RNA 2022; 28:177-193. [PMID: 34759006 PMCID: PMC8906541 DOI: 10.1261/rna.078949.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
The commitment to replicate the RNA genome of flaviviruses without a primer involves RNA-protein interactions that have been shown to include the recognition of the stem-loop A (SLA) in the 5' untranslated region (UTR) by the nonstructural protein NS5. We show that DENV2 NS5 arginine 888, located within the carboxy-terminal 18 residues, is completely conserved in all flaviviruses and interacts specifically with the top-loop of 3'SL in the 3'UTR which contains the pentanucleotide 5'-CACAG-3' previously shown to be critical for flavivirus RNA replication. We present virological and biochemical data showing the importance of this Arg 888 in virus viability and de novo initiation of RNA polymerase activity in vitro. Based on our binding studies, we hypothesize that ternary complex formation of NS5 with 3'SL, followed by dimerization, leads to the formation of the de novo initiation complex that could be regulated by the reversible zipping and unzipping of cis-acting RNA elements.
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Affiliation(s)
- Sai Wang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Min Jie Alvin Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Charlotte Flory
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 636921 Singapore
| | - Julian Lescar
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
- Department of Microbiology and Immunology, National University of Singapore, 117545 Singapore
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia
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23
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Tsimbalyuk S, Donnelly CM, Forwood JK. Structural characterization of human importin alpha 7 in its cargo-free form at 2.5 Å resolution. Sci Rep 2022; 12:315. [PMID: 35013395 PMCID: PMC8748863 DOI: 10.1038/s41598-021-03729-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/24/2021] [Indexed: 11/22/2022] Open
Abstract
Shuttling of macromolecules between nucleus and cytoplasm is a tightly regulated process mediated through specific interactions between cargo and nuclear transport proteins. In the classical nuclear import pathway, importin alpha recognizes cargo exhibiting a nuclear localization signal, and this complex is transported through the nuclear pore complex by importin beta. Humans possess seven importin alpha isoforms that can be grouped into three subfamilies, with many cargoes displaying specificity towards these importin alpha isoforms. The cargo binding sites within importin alpha isoforms are highly conserved in sequence, suggesting that specificity potentially relies on structural differences. Structures of some importin alpha isoforms, both in cargo-bound and free states, have been previously solved. However, there are currently no known structures of cargo free importin alpha isoforms within subfamily 3 (importin alpha 5, 6, 7). Here, we present the first crystal structure of human importin alpha 7 lacking the IBB domain solved at 2.5 Å resolution. The structure reveals a typical importin alpha architecture comprised of ten armadillo repeats and is most structurally conserved with importin alpha 5. Very little difference in structure was observed between the cargo-bound and free states, implying that importin alpha 7 does not undergo conformational change when binding cargo. These structural insights provide a strong platform for further evaluation of structure–function relationships and understanding how isoform specificity within the importin alpha family plays a role in nuclear transport in health and disease.
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Affiliation(s)
- S Tsimbalyuk
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - C M Donnelly
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - J K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia. .,School of Dentistry and Medical Sciences, Charles Sturt University, Room 2, National Life Sciences Hub, Wagga Wagga, NSW, 2678, Australia.
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24
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Hoad M, Roby JA, Forwood JK. Structural characterization of the porcine adeno-associated virus Po1 capsid protein binding to the nuclear trafficking protein importin alpha. FEBS Lett 2021; 595:2793-2804. [PMID: 34661283 DOI: 10.1002/1873-3468.14209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 11/05/2022]
Abstract
Adeno-associated viruses (AAVs) are key vectors for gene therapy; thus, many aspects of their cell transduction pathway have been revealed in detail. However, the specific mechanisms AAV virions use to enter the host nucleus remain largely unresolved. We therefore aimed to reveal the structural interactions between the AAV capsid (Cap) protein and the nuclear transport protein importin alpha (IMPα). A putative nuclear localization sequence (NLS) in the virion protein 1 capsid protein of the porcine AAV Po1 was identified. This region was complexed with IMPα and a structure solved at 2.26 Å. This is the first time that an NLS of AAV Cap complexed with IMPα has been determined structurally. Our results support the findings that AAV capsids enter the nucleus through binding the nuclear import adapter IMPα.
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Affiliation(s)
- Mikayla Hoad
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Justin A Roby
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
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25
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Tu WJ, McCuaig RD, Melino M, Rawle DJ, Le TT, Yan K, Suhrbier A, Johnston RL, Koufariotis LT, Waddell N, Cross EM, Tsimbalyuk S, Bain A, Ahern E, Collinson N, Phipps S, Forwood JK, Seddiki N, Rao S. Targeting novel LSD1-dependent ACE2 demethylation domains inhibits SARS-CoV-2 replication. Cell Discov 2021; 7:37. [PMID: 34031383 PMCID: PMC8143069 DOI: 10.1038/s41421-021-00279-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/24/2021] [Indexed: 02/07/2023] Open
Abstract
Treatment options for COVID-19 remain limited, especially during the early or asymptomatic phase. Here, we report a novel SARS-CoV-2 viral replication mechanism mediated by interactions between ACE2 and the epigenetic eraser enzyme LSD1, and its interplay with the nuclear shuttling importin pathway. Recent studies have shown a critical role for the importin pathway in SARS-CoV-2 infection, and many RNA viruses hijack this axis to re-direct host cell transcription. LSD1 colocalized with ACE2 at the cell surface to maintain demethylated SARS-CoV-2 spike receptor-binding domain lysine 31 to promote virus-ACE2 interactions. Two newly developed peptide inhibitors competitively inhibited virus-ACE2 interactions, and demethylase access to significantly inhibit viral replication. Similar to some other predominantly plasma membrane proteins, ACE2 had a novel nuclear function: its cytoplasmic domain harbors a nuclear shuttling domain, which when demethylated by LSD1 promoted importin-α-dependent nuclear ACE2 entry following infection to regulate active transcription. A novel, cell permeable ACE2 peptide inhibitor prevented ACE2 nuclear entry, significantly inhibiting viral replication in SARS-CoV-2-infected cell lines, outperforming other LSD1 inhibitors. These data raise the prospect of post-exposure prophylaxis for SARS-CoV-2, either through repurposed LSD1 inhibitors or new, nuclear-specific ACE2 inhibitors.
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Affiliation(s)
- Wen Juan Tu
- grid.1049.c0000 0001 2294 1395Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Robert D. McCuaig
- grid.1049.c0000 0001 2294 1395Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Michelle Melino
- grid.1049.c0000 0001 2294 1395Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Daniel J. Rawle
- grid.1049.c0000 0001 2294 1395The Inflammation Biology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Thuy T. Le
- grid.1049.c0000 0001 2294 1395The Inflammation Biology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Kexin Yan
- grid.1049.c0000 0001 2294 1395The Inflammation Biology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Andreas Suhrbier
- grid.1049.c0000 0001 2294 1395The Inflammation Biology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Rebecca L. Johnston
- grid.1049.c0000 0001 2294 1395Medical Genomics, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Lambros T. Koufariotis
- grid.1049.c0000 0001 2294 1395Medical Genomics, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Nicola Waddell
- grid.1049.c0000 0001 2294 1395Medical Genomics, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Emily M. Cross
- grid.1037.50000 0004 0368 0777School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW Australia
| | - Sofiya Tsimbalyuk
- grid.1037.50000 0004 0368 0777School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW Australia
| | - Amanda Bain
- grid.1049.c0000 0001 2294 1395Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Elizabeth Ahern
- grid.419789.a0000 0000 9295 3933Department of Medical Oncology, Monash Health, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857School of Clinical Sciences, Monash University, Clayton, VIC Australia
| | - Natasha Collinson
- grid.1049.c0000 0001 2294 1395Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Simon Phipps
- grid.1049.c0000 0001 2294 1395Respiratory Immunology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Jade K. Forwood
- grid.1037.50000 0004 0368 0777School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW Australia
| | - Nabila Seddiki
- U955, Equipe 16, Créteil, France ,grid.410511.00000 0001 2149 7878Université Paris-Est Créteil, Faculté de médecine, Créteil, France ,grid.511001.4Vaccine Research Institute (VRI), Créteil, France
| | - Sudha Rao
- grid.1049.c0000 0001 2294 1395Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
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26
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Le VTB, Tsimbalyuk S, Lim EQ, Solis A, Gawat D, Boeck P, Lim EQ, Renolo R, Forwood JK, Kuhn ML. The Vibrio cholerae SpeG Spermidine/Spermine N-Acetyltransferase Allosteric Loop and β6-β7 Structural Elements Are Critical for Kinetic Activity. Front Mol Biosci 2021; 8:645768. [PMID: 33928120 PMCID: PMC8076852 DOI: 10.3389/fmolb.2021.645768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 11/27/2022] Open
Abstract
Polyamines regulate many important biological processes including gene expression, intracellular signaling, and biofilm formation. Their intracellular concentrations are tightly regulated by polyamine transport systems and biosynthetic and catabolic pathways. Spermidine/spermine N-acetyltransferases (SSATs) are catabolic enzymes that acetylate polyamines and are critical for maintaining intracellular polyamine homeostasis. These enzymes belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily and adopt a highly conserved fold found across all kingdoms of life. SpeG is an SSAT protein found in a variety of bacteria, including the human pathogen Vibrio cholerae. This protein adopts a dodecameric structure and contains an allosteric site, making it unique compared to other SSATs. Currently, we have a limited understanding of the critical structural components of this protein that are required for its allosteric behavior. Therefore, we explored the importance of two key regions of the SpeG protein on its kinetic activity. To achieve this, we created various constructs of the V. cholerae SpeG protein, including point mutations, a deletion, and chimeras with residues from the structurally distinct and non-allosteric human SSAT protein. We measured enzyme kinetic activity toward spermine for ten constructs and crystallized six of them. Ultimately, we identified specific portions of the allosteric loop and the β6-β7 structural elements that were critical for enzyme kinetic activity. These results provide a framework for further study of the structure/function relationship of SpeG enzymes from other organisms and clues toward the structural evolution of members of the GNAT family across domains of life.
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Affiliation(s)
- Van Thi Bich Le
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Sofiya Tsimbalyuk
- School of Biomedical Science, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Ee Qi Lim
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Allan Solis
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Darwin Gawat
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Paloma Boeck
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Ee Qing Lim
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Rosselini Renolo
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Jade K. Forwood
- School of Biomedical Science, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Misty L. Kuhn
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
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Jagga B, Edwards M, Pagin M, Wagstaff KM, Aragão D, Roman N, Nanson JD, Raidal SR, Dominado N, Stewart M, Jans DA, Hime GR, Nicolis SK, Basler CF, Forwood JK. Structural basis for nuclear import selectivity of pioneer transcription factor SOX2. Nat Commun 2021; 12:28. [PMID: 33397924 PMCID: PMC7782513 DOI: 10.1038/s41467-020-20194-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
SOX (SRY-related HMG-box) transcription factors perform critical functions in development and cell differentiation. These roles depend on precise nuclear trafficking, with mutations in the nuclear targeting regions causing developmental diseases and a range of cancers. SOX protein nuclear localization is proposed to be mediated by two nuclear localization signals (NLSs) positioned within the extremities of the DNA-binding HMG-box domain and, although mutations within either cause disease, the mechanistic basis has remained unclear. Unexpectedly, we find here that these two distantly positioned NLSs of SOX2 contribute to a contiguous interface spanning 9 of the 10 ARM domains on the nuclear import adapter IMPα3. We identify key binding determinants and show this interface is critical for neural stem cell maintenance and for Drosophila development. Moreover, we identify a structural basis for the preference of SOX2 binding to IMPα3. In addition to defining the structural basis for SOX protein localization, these results provide a platform for understanding how mutations and post-translational modifications within these regions may modulate nuclear localization and result in clinical disease, and also how other proteins containing multiple NLSs may bind IMPα through an extended recognition interface. The SOX2 pioneer transcription factor performs critical roles in pluripotency and self-renewal of embryonic stem cells. Here the authors show that SOX2’s two nuclear localization signal sequences form a contiguous binding interface on the nuclear import receptor importin-α3, and provide a structural basis for the preference of SOX2 binding to IMPα3.
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Affiliation(s)
- Bikshapathi Jagga
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Megan Edwards
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, 30303, USA
| | - Miriam Pagin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, piazza della Scienza 2, 20126, Milano, Italy
| | - Kylie M Wagstaff
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - David Aragão
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Noelia Roman
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Nicole Dominado
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - David A Jans
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Gary R Hime
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, piazza della Scienza 2, 20126, Milano, Italy
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, 30303, USA
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia.
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28
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Nath BK, Das S, Roby JA, Sarker S, Luque D, Raidal SR, Forwood JK. Structural Perspectives of Beak and Feather Disease Virus and Porcine Circovirus Proteins. Viral Immunol 2020; 34:49-59. [PMID: 33275868 DOI: 10.1089/vim.2020.0097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Circoviruses represent a rapidly expanding group of viruses that infect both vertebrate and invertebrate hosts. Members are responsible for diseases of veterinary and economic importance, including postweaning multisystemic wasting syndrome in pigs, and beak and feather disease (BFD) in birds. These viruses are associated with lymphoid depletion and immunosuppressive conditions in infected animals leading to systemic illness. Circoviruses are small nonenveloped DNA viruses containing a single-stranded circular genome, encoding two major proteins: the capsid-associated protein (Cap), comprising the entirety of the viral capsid, and the replication-associated protein (Rep). Cap is the only protein component of the virion and plays crucial roles throughout the virus replication cycle, including viral attachment, cell entry, genome uncoating, and packaging of newly formed viral particles. Rep mediates recognition of replication origin motifs in the viral genome sequence and is responsible for endonuclease activity enabling nicking of the circular DNA and initiation of rolling-circle replication (RCR). Porcine circovirus 2 (PCV2) was the first circovirus capsid structure to be solved at atomic resolution using X-ray crystallography. The structure revealed an assembly comprising 60 monomeric subunits to form virus-like particles. Each Cap monomer harbors a canonical viral jelly roll domain composed of two, four-stranded antiparallel β-sheets. Crystal structures of two distinct macromolecular assemblies from BFD virus Cap were also resolved at high resolution. In these structures, the exposure of the N-terminal arginine-rich motif, responsible for DNA binding and nuclear localization is reversed. Additional structural investigations have also elucidated a PCV2 type-specific neutralizing epitope, and interaction between the PCV2 capsid and polymers such as heparin. In this review, we provide a snapshot of the structural and functional aspects of circovirus proteins.
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Affiliation(s)
- Babu Kanti Nath
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Justin A Roby
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Daniel Luque
- Centro Nacional de Microbiología/ISCIII, Majadahonda, Madrid, Spain
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
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29
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Donnelly CM, Roby JA, Scott CJ, Raidal SR, Forwood JK. The Structural Features of Henipavirus Matrix Protein Driving Intracellular Trafficking. Viral Immunol 2020; 34:27-40. [PMID: 33021467 DOI: 10.1089/vim.2020.0056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Henipaviruses are single-stranded RNA viruses that have recently emerged as zoonotic pathogens, capable of causing severe acute respiratory disease and encephalitis in humans. The prototypical henipaviruses, Hendra henipavirus and Nipah henipavirus, are a major health concern as they have high mortality rates and no currently approved human vaccine or drug therapy. Understanding the mechanisms of viral replication and pathogenicity is of critical importance for therapeutic developments. A novel target for such therapies is the Henipavirus Matrix (M) protein, a multifunctional protein that drives viral assembly and inhibits the innate immune response. These multifunctional attributes promote a complicated lifecycle: while viral replication occurs in the cytoplasm, M traffics to the nucleus, where it is ubiquitinated, for correct cellular targeting and virion packaging. In this study, we review the relationship between the structure and functions of M. In specific cases, the compatibility between structural accessibility and protein functionality is not always evident, and we highlight areas that require further investigation.
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Affiliation(s)
- Camilla M Donnelly
- School of Biomedical Sciences and Charles Sturt University, Wagga Wagga, Australia
| | - Justin A Roby
- School of Biomedical Sciences and Charles Sturt University, Wagga Wagga, Australia
| | - Christopher J Scott
- School of Biomedical Sciences and Charles Sturt University, Wagga Wagga, Australia
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Jade K Forwood
- School of Biomedical Sciences and Charles Sturt University, Wagga Wagga, Australia
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30
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Athukorala A, Forwood JK, Phalen DN, Sarker S. Molecular Characterisation of a Novel and Highly Divergent Passerine Adenovirus 1. Viruses 2020; 12:v12091036. [PMID: 32957674 PMCID: PMC7551158 DOI: 10.3390/v12091036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/09/2020] [Accepted: 09/15/2020] [Indexed: 01/16/2023] Open
Abstract
Wild birds harbour a large number of adenoviruses that remain uncharacterised with respect to their genomic organisation, diversity, and evolution within complex ecosystems. Here, we present the first complete genome sequence of an atadenovirus from a passerine bird that is tentatively named Passerine adenovirus 1 (PaAdV-1). The PaAdV-1 genome is 39,664 bp in length, which was the longest atadenovirus to be sequenced, to the best of our knowledge, and contained 42 putative genes. Its genome organisation was characteristic of the members of genus Atadenovirus; however, the novel PaAdV-1 genome was highly divergent and showed the highest sequence similarity with psittacine adenovirus-3 (55.58%). Importantly, PaAdV-1 complete genome was deemed to contain 17 predicted novel genes that were not present in any other adenoviruses sequenced to date, with several of these predicted novel genes encoding proteins that harbour transmembrane helices. Subsequent analysis of the novel PaAdV-1 genome positioned phylogenetically to a distinct sub-clade with all others sequenced atadenoviruses and did not show any obvious close evolutionary relationship. This study concluded that the PaAdV-1 complete genome described here is not closely related to any other adenovirus isolated from avian or other natural host species and that it should be considered a separate species.
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Affiliation(s)
- Ajani Athukorala
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia;
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - David N. Phalen
- Sydney School of Veterinary Science, University of Sydney, Camden, NSW 2570, Australia;
- Schubot Exotic Bird Health, Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX 77843-4467, USA
| | - Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia;
- Correspondence: ; Tel.: +61-3-9479-2317; Fax: +61-3-9479-1222
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Edwards MR, Hoad M, Tsimbalyuk S, Menicucci AR, Messaoudi I, Forwood JK, Basler CF. Henipavirus W Proteins Interact with 14-3-3 To Modulate Host Gene Expression. J Virol 2020; 94:e00373-20. [PMID: 32321809 PMCID: PMC7343215 DOI: 10.1128/jvi.00373-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/12/2020] [Indexed: 01/21/2023] Open
Abstract
Nipah virus (NiV) and Hendra virus (HeV), members of the Henipavirus genus in the Paramyxoviridae family, are recently emerged, highly lethal zoonotic pathogens. The NiV and HeV nonsegmented, negative-sense RNA genomes encode nine proteins, including the W protein. Expressed from the P gene through mRNA editing, W shares a common N-terminus with P and V but has a unique C-terminus. Expressed alone, W modulates innate immune responses by several mechanisms, and elimination of W from NiV alters the course of infection in experimentally infected ferrets. However, the specific host interactions that allow W to modulate innate immunity are incompletely understood. This study demonstrates that the NiV and HeV W proteins interact with all seven isoforms of the 14-3-3 family, regulatory molecules that preferentially bind phosphorylated target proteins to regulate a wide range of cellular functions. The interaction is dependent on the penultimate amino acid residue in the W sequence, a conserved, phosphorylated serine. The cocrystal structure of the W C-terminal binding motif with 14-3-3 provides only the second structure of a complex containing a mode III interactor, which is defined as a 14-3-3 interaction with a phosphoserine/phosphothreonine at the C-termini of the target protein. Transcriptomic analysis of inducible cell lines infected with an RNA virus and expressing either wild-type W or W lacking 14-3-3 binding, identifies new functions for W. These include the regulation of cellular metabolic processes, extracellular matrix organization, and apoptosis.IMPORTANCE Nipah virus (NiV) and Hendra virus (HeV), members of the Henipavirus genus, are recently emerged, highly lethal zoonotic pathogens that cause yearly outbreaks. NiV and HeV each encode a W protein that has roles in regulating host signaling pathways, including antagonism of the innate immune response. However, the mechanisms used by W to regulate these host responses are not clear. Here, characterization of the interaction of NiV and HeV W with 14-3-3 identifies modulation of 14-3-3-regulated host signaling pathways not previously associated with W, suggesting new avenues of research. The cocrystal structure of the NiV W:14-3-3 complex, as only the second structure of a 14-3-3 mode III interactor, provides further insight into this less-well-understood 14-3-3 binding motif.
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Affiliation(s)
- Megan R Edwards
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Mikayla Hoad
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Sofiya Tsimbalyuk
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Andrea R Menicucci
- Department of Molecular Biology and Biochemistry, College of Biological Sciences, University of California, Irvine, Irvine, California, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, College of Biological Sciences, University of California, Irvine, Irvine, California, USA
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
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Swarbrick CMD, Nanson JD, Patterson EI, Forwood JK. Structure, function, and regulation of thioesterases. Prog Lipid Res 2020; 79:101036. [PMID: 32416211 DOI: 10.1016/j.plipres.2020.101036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 01/15/2023]
Abstract
Thioesterases are present in all living cells and perform a wide range of important biological functions by catalysing the cleavage of thioester bonds present in a diverse array of cellular substrates. Thioesterases are organised into 25 families based on their sequence conservation, tertiary and quaternary structure, active site configuration, and substrate specificity. Recent structural and functional characterisation of thioesterases has led to significant changes in our understanding of the regulatory mechanisms that govern enzyme activity and their respective cellular roles. The resulting dogma changes in thioesterase regulation include mechanistic insights into ATP and GDP-mediated regulation by oligomerisation, the role of new key regulatory regions, and new insights into a conserved quaternary structure within TE4 family members. Here we provide a current and comparative snapshot of our understanding of thioesterase structure, function, and regulation across the different thioesterase families.
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Affiliation(s)
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience, Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Edward I Patterson
- Centre for Neglected Tropical Diseases, Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales, Australia.
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Tsimbalyuk S, Shornikov A, Thi Bich Le V, Kuhn ML, Forwood JK. SpeG polyamine acetyltransferase enzyme from Bacillus thuringiensis forms a dodecameric structure and exhibits high catalytic efficiency. J Struct Biol 2020; 210:107506. [PMID: 32283314 DOI: 10.1016/j.jsb.2020.107506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/24/2020] [Accepted: 04/08/2020] [Indexed: 11/30/2022]
Abstract
Polyamines are important for regulating biofilms and the exopolysaccharide of the biofilm matrix of Bacillus subtilis. Understanding how enzymes can regulate polyamine concentrations is critical for learning more about how these processes occur in diverse bacteria. Here, we describe the structure and function of another member of the spermidine/spermine acetyltransferases (SSAT) found in Bacilli. The SpeG enzyme from B. thuringiensis (BtSpeG) binds polyamines in its allosteric site and adopts a dodecameric oligomeric state similar to other SpeG enzymes from Gram-negative bacteria. Our kinetic results show the catalytic efficiency of BtSpeG was greater than any previously characterized SpeG to date, and in contrast to other SpeG proteins it exhibited very similar kinetic properties toward both spermine and spermidine. Similar to the SpeG enzyme from E. coli, BtSpeG was able to acetylate spermidine on the N1 and N8 positions. The turnover of BtSpeG toward spermine and spermidine was also two to three orders of magnitude greater than any other Bacilli SSAT enzyme that has been previously characterized. SpeG proteins from Bacilli, including B. cereus, B. thuringiensis and B. anthracis share nearly identical sequences and therefore our results likely provide insight into the structure/function relationship across multiple Bacillus species.
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Affiliation(s)
- Sofiya Tsimbalyuk
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Aleksander Shornikov
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Van Thi Bich Le
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA.
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia.
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Díaz-García C, Hornos F, Giudici AM, Cámara-Artigas A, Luque-Ortega JR, Arbe A, Rizzuti B, Alfonso C, Forwood JK, Iovanna JL, Gómez J, Prieto M, Coutinho A, Neira JL. Human importin α3 and its N-terminal truncated form, without the importin-β-binding domain, are oligomeric species with a low conformational stability in solution. Biochim Biophys Acta Gen Subj 2020; 1864:129609. [PMID: 32234409 DOI: 10.1016/j.bbagen.2020.129609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/13/2020] [Accepted: 03/26/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Eukaryotic cells have a continuous transit of macromolecules between the cytoplasm and the nucleus. Several carrier proteins are involved in this transport. One of them is importin α, which must form a complex with importin β to accomplish its function, by domain-swapping its 60-residue-long N terminus. There are several human isoforms of importin α; among them, importin α3 has a particularly high flexibility. METHODS We studied the conformational stability of intact importin α3 (Impα3) and its truncated form, where the 64-residue-long, N-terminal importin-β-binding domain (IBB) has been removed (ΔImpα3), in a wide pH range, with several spectroscopic, biophysical, biochemical methods and with molecular dynamics (MD). RESULTS Both species acquired native-like structure between pH 7 and 10.0, where Impα3 was a dimer (with an apparent self-association constant of ~10 μM) and ΔImpα3 had a higher tendency to self-associate than the intact species. The acquisition of secondary, tertiary and quaternary structure, and the burial of hydrophobic patches, occurred concomitantly. Both proteins unfolded irreversibly at physiological pH, by using either temperature or chemical denaturants, through several partially folded intermediates. The MD simulations support the presence of these intermediates. CONCLUSIONS The thermal stability of Impα3 at physiological pH was very low, but was higher than that of ΔImpα3. Both proteins were stable in a narrow pH range, and they unfolded at physiological pH populating several intermediate species. GENERAL SIGNIFICANCE The low conformational stability explains the flexibility of Impα3, which is needed to carry out its recognition of complex cargo sequences.
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Affiliation(s)
- Clara Díaz-García
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Felipe Hornos
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | | | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- ceiA3, 04120 Almería, Spain
| | - Juan Román Luque-Ortega
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Materials Physics Center (MPC), 20018 San Sebastián, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
| | - Javier Gómez
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - Manuel Prieto
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Ana Coutinho
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1649-004 Lisboa, Portugal
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain.
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Khandokar Y, Srivastava P, Raidal S, Sarker S, Forwood JK. Structural basis for disulphide-CoA inhibition of a butyryl-CoA hexameric thioesterase. J Struct Biol 2020; 210:107477. [PMID: 32027968 DOI: 10.1016/j.jsb.2020.107477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/30/2020] [Accepted: 02/02/2020] [Indexed: 10/25/2022]
Abstract
Acyl-coenzyme A thioesterases (ACTs) catalyse the hydrolysis of thioester bonds between fatty-acyl chains and coenzyme A (CoA), producing a free fatty-acyl chain and CoA. These enzymes are expressed ubiquitously across prokaryotes and eukaryotes, and play important roles in lipid metabolism. There are 25 thioesterase families, subdivided based on their active site configuration, protein oligomerization, and substrate specificity. Understanding the mechanism of regulation within these families is important due to their roles in controlling the cell concentration of a range of fatty acids and CoA-bound compounds. Here we report a structural basis for a novel mode of inhibition of an ACT from Staphylococcus aureus. The enzyme displays a hotdog fold composed of five β-strands wrapping around a central α-helix, and an additional 30 residue α-helix located at its C-terminus. We show that the enzyme is a hexamer and has specificity towards butyryl-CoA. Structural analysis revealed putative catalytic residues, and we show through site directed mutagenesis that Asn28, Asp43, and Thr60 are critical for activity. Additionally, we show that the Asn28Ala destabilises the enzyme oligomeric state into two distinct populations. Co-crystallization of the enzyme with the substrate butyryl-CoA produced a crystal with three CoA ligands bound in the enzyme active sites: CoA, butyryl-CoA, and disulphide-CoA, the latter of which inhibits enzyme activity. Our study provides new insights into the structure and specificity of hexameric thioesterases, inhibitory feedback mechanisms, and possible biotechnological applications in short-chain fatty acid production such as biofuels, pharmaceuticals, and industrial compounds.
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Affiliation(s)
- Yogesh Khandokar
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3052 Australia; School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Parul Srivastava
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Shane Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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Sarker S, Batinovic S, Talukder S, Das S, Park F, Petrovski S, Forwood JK, Helbig KJ, Raidal SR. Molecular characterisation of a novel pathogenic avipoxvirus from the Australian magpie (Gymnorhina tibicen). Virology 2019; 540:1-16. [PMID: 31726310 DOI: 10.1016/j.virol.2019.11.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 11/18/2022]
Abstract
Avipoxviruses are significant pathogens infecting a wide range of wild and domestic bird species globally. Here, we describe a novel genome sequence of magpiepox virus (MPPV) isolated from an Australian magpie. In the present study, histopathologically confirmed cutaneous pox lesions were used for transmission electron microscopic analysis, which demonstrated brick-shaped virions with regular spaced thread-like ridges, indicative of likely infectious particles. Subsequent analysis of the recovered MPPV genome positioned phylogenetically to a distinct sub-clade with the recently isolated avipoxvirus genome sequences from shearwater and canary bird species, and demonstrates a high degree of sequence similarity with CNPV (96.14%) and SWPV-2 (95.87%). The novel MPPV complete genome is missing 19 genes with a further 41 genes being truncated/fragmented compared to SWPV-2 and contains nine predicted unique genes. This is the first avipoxvirus complete genome sequence that infects Australian magpie.
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Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Steven Batinovic
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Saranika Talukder
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia, 3010
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Fiona Park
- Canley Heights Veterinary Clinic, Canley Heights, NSW, 2166, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Karla J Helbig
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
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Sarker S, Talukder S, Sutherland M, Forwood JK, Helbig K, Raidal SR. Characterization of the first mitochondrial genome of a little Corella ( Cacatua sanguinea) and its phylogenetic implications. Mitochondrial DNA B Resour 2019; 4:3792-3794. [PMID: 33366194 PMCID: PMC7707406 DOI: 10.1080/23802359.2019.1682481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/13/2019] [Indexed: 11/04/2022] Open
Abstract
This study was designed to sequence the first complete mitochondrial genome from a little corella (Cacatua sanguinea). The mitogenome sequence was circular and 16,695 bp in length. In comparison to other available mitogenome sequences belongs to Psittacidae species, this mitogenome encoded a conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes. The lengths of 12S and 16S ribosomal RNA were 975 bp and 1582 bp, respectively. The overall base composition of the mitogenome of C. sanguinea was dominated by higher AT (53.0%) than GC (47.0%) content. The complete mitogenome sequence determined in this study is useful for understanding the more profound evolutionary history and the conservation of C. sanguinea.
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Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Albury, New South Wales, Australia
| | - Saranika Talukder
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | | | - Jade K. Forwood
- School of Biomedical Sciences, Faculty of Science, Charles Sturt University, Albury, New South Wales, Australia
| | - Karla Helbig
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Shane R. Raidal
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Albury, New South Wales, Australia
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Sarker S, Sutherland M, Talukder S, Das S, Forwood JK, Helbig K, Raidal SR. The first complete mitogenome of Indian ringneck (Psittacula krameri) demonstrates close phylogenetic relationship with Eclectus parrot. Mitochondrial DNA B Resour 2019; 4:3579-3581. [PMID: 33366094 PMCID: PMC7707189 DOI: 10.1080/23802359.2019.1676676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
This study was aimed to sequence the first complete mitochondrial genome from an Indian ringneck parrot (Psittacula krameri). The mitogenome sequence was circular and 16,413 bp in length. In comparison to other available mitogenome sequences belonging to Psittacidae species, this mitogenome encoded a conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, 21 tRNA genes and a control region; however, this mitogenome missing a tRNA-Glu. The lengths of 12S and 16S ribosomal RNA were 975 bp and 1582 bp, respectively. The overall base composition of the mitogenome of P. krameri was dominated by higher AT (53.5%) than GC (46.5%) content. The complete mitogenome sequence determined in this study would be useful to track the more profound evolutionary history and the conservation of P. krameri.
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Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia.,School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, Australia
| | | | - Saranika Talukder
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Faculty of Science, Charles Sturt University, >Wagga Wagga, Australia
| | - Karla Helbig
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, Australia
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Das S, Smith K, Sarker S, Peters A, Adriaanse K, Eden P, Ghorashi SA, Forwood JK, Raidal SR. Assessing circovirus gene flow in multiple spill-over events. Virus Genes 2019; 55:802-814. [PMID: 31463770 DOI: 10.1007/s11262-019-01702-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 08/19/2019] [Indexed: 11/29/2022]
Abstract
The establishment of viral pathogens in new host environments following spillover events probably requires adaptive changes within both the new host and pathogen. After many generations, signals for ancient cross-species transmission may become lost and a strictly host-adapted phylogeny may mimic true co-divergence while the virus may retain an inherent ability to jump host species. The mechanistic basis for such processes remains poorly understood. To study the dynamics of virus-host co-divergence and the arbitrary chances of spillover in various reservoir hosts with equal ecological opportunity, we examined structural constraints of capsid protein in extant populations of Beak and feather disease virus (BFDV) during known spillover events. By assessing reservoir-based genotype stratification, we identified co-divergence defying signatures in the evolution BFDV which highlighted primordial processes of cryptic host adaptation and competing forces of host co-divergence and cross-species transmission. We demonstrate that, despite extensive surface plasticity gathered over a longer span of evolution, structural constraints of the capsid protein allow opportunistic host switching in host-adapted populations. This study provides new insights into how small populations of endangered psittacine species may face multidirectional forces of infection from reservoirs with apparently co-diverging genotypes.
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Affiliation(s)
- Shubhagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia
| | - Kate Smith
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia
| | - Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, 3086, Australia
| | - Andrew Peters
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia
| | - Katherine Adriaanse
- Healesville Sanctuary, Zoos Victoria, Badger Creek Road, Healesville, VIC, 3777, Australia
| | - Paul Eden
- Healesville Sanctuary, Zoos Victoria, Badger Creek Road, Healesville, VIC, 3777, Australia
| | - Seyed A Ghorashi
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW, 2650, Australia.
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Patterson EI, Nanson JD, Abendroth J, Bryan C, Sankaran B, Myler PJ, Forwood JK. Structural characterization of β-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites. Proteins 2019; 88:47-56. [PMID: 31237717 DOI: 10.1002/prot.25765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/30/2019] [Accepted: 06/07/2019] [Indexed: 11/08/2022]
Abstract
The bacterial fatty acid pathway is essential for membrane synthesis and a range of other metabolic and cellular functions. The β-ketoacyl-ACP synthases carry out the initial elongation reaction of this pathway, utilizing acetyl-CoA as a primer to elongate malonyl-ACP by two carbons, and subsequent elongation of the fatty acyl-ACP substrate by two carbons. Here we describe the structures of the β-ketoacyl-ACP synthase I from Brucella melitensis in complex with platencin, 7-hydroxycoumarin, and (5-thiophen-2-ylisoxazol-3-yl)methanol. The enzyme is a dimer and based on structural and sequence conservation, harbors the same active site configuration as other β-ketoacyl-ACP synthases. The platencin binding site overlaps with the fatty acyl compound supplied by ACP, while 7-hydroxyl-coumarin and (5-thiophen-2-ylisoxazol-3-yl)methanol bind at the secondary fatty acyl binding site. These high-resolution structures, ranging between 1.25 and 1.70 å resolution, provide a basis for in silico inhibitor screening and optimization, and can aid in rational drug design by revealing the high-resolution binding interfaces of molecules at the malonyl-ACP and acyl-ACP active sites.
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Affiliation(s)
- Edward I Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia.,The Institute for Molecular Biosciences (IMB), University of Queensland, Brisbane, QLD, Australia
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington.,UCB Beryllium Discovery Corp, Bainbridge Island, Washington
| | - Cassie Bryan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
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41
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Sarker S, Das S, Ghorashi SA, Forwood JK, Raidal SR. Pigeon circoviruses from feral pigeons in Australia demonstrate extensive recombination and genetic admixture with other circoviruses. Avian Pathol 2019; 48:512-520. [PMID: 31199167 DOI: 10.1080/03079457.2019.1629391] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Like other avian circovirus species, Pigeon circovirus (PiCV) is known to be genetically diverse with a relatively small circular single-stranded DNA genome of 2 kb that encodes for a capsid protein (Cap) and a replication initiator protein (Rep). Recent paleoviral evidence hints towards a probable Gondwanan origin of avian circoviruses, paralleling the evolution and dispersal of their hosts. Limited availability of PiCV genome sequence data in Australia has hindered phylogeographic studies in this species, so we screened clinically normal rock doves (Columba livia) in regional New South Wales, and demonstrated a high prevalence (76%) of PiCV infection by PCR. We also recovered 12 complete novel PiCV genomes and phylogenetic analyses revealed that PiCV circulating in Australian feral pigeons formed two strongly supported monophyletic clades. One clade resided with PiCV genomes from Poland, Australia, United Kingdom, Belgium, China, and Japan, and another basal clade was more closely related to PiCV genomes from Poland. A novel more distantly-related PiCV rep gene formed a solitary clade with weak posterior support. So we further analysed all selected partial rep gene sequences to demonstrate a likely naturally occurring spillover infection from a passerine circovirus candidate. The findings suggest that there is a high degree of genetic variation within PiCV in Columbiformes with potential greater admixture between avian circoviruses within Australia than previously known. RESEARCH HIGHLIGHTS Confirmed high prevalence rate of PiCV circulating in Australian wild pigeons. Highlighted extensive recombination events within Australian PiCV. Demonstrated a likely naturally occurring spillover infection from a passerine circovirus candidate.
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Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University , Melbourne , Australia.,School of Animal and Veterinary Sciences, Charles Sturt University , Wagga Wagga , Australia
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University , Wagga Wagga , Australia
| | - Seyed A Ghorashi
- School of Animal and Veterinary Sciences, Charles Sturt University , Wagga Wagga , Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University , Wagga Wagga , Australia
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University , Wagga Wagga , Australia.,Veterinary Diagnostic Laboratory, Charles Sturt University , Wagga Wagga , Australia
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42
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Ng IHW, Chan KWK, Tan MJA, Gwee CP, Smith KM, Jeffress SJ, Saw WG, Swarbrick CMD, Watanabe S, Jans DA, Grüber G, Forwood JK, Vasudevan SG. Zika Virus NS5 Forms Supramolecular Nuclear Bodies That Sequester Importin-α and Modulate the Host Immune and Pro-Inflammatory Response in Neuronal Cells. ACS Infect Dis 2019; 5:932-948. [PMID: 30848123 DOI: 10.1021/acsinfecdis.8b00373] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Zika virus (ZIKV) epidemic in the Americas was alarming because of its link with microcephaly in neonates and Guillain-Barré syndrome in adults. The unusual pathologies induced by ZIKV infection and the knowledge that the flaviviral nonstructural protein 5 (NS5), the most conserved protein in the flavivirus proteome, can modulate the host immune response during ZIKV infection prompted us to investigate the subcellular localization of NS5 during ZIKV infection and explore its functional significance. A monopartite nuclear localization signal (NLS) sequence within ZIKV NS5 was predicted by the cNLS Mapper program, and we observed localization of ZIKV NS5 in the nucleus of infected cells by immunostaining with specific antibodies. Strikingly, ZIKV NS5 forms spherical shell-like nuclear bodies that exclude DNA. The putative monopartite NLS 390KRPR393 is necessary to direct FLAG-tagged NS5 to the nucleus as the NS5 390ARPA393 mutant protein accumulates in the cytoplasm. Furthermore, coimmunostaining experiments reveal that NS5 localizes with and sequesters importin-α, but not importin-β, in the observed nuclear bodies during virus infection. Structural and biochemical data demonstrate binding of ZIKV NS5 with importin-α and reveal important binding determinants required for their interaction and formation of complexes that give rise to the supramolecular nuclear bodies. Significantly, we demonstrate a neuronal-specific activation of the host immune response to ZIKV infection and a possible role of ZIKV NS5's nuclear localization toward this activation. This suggests that ZIKV pathogenesis may arise from a tissue-specific host response to ZIKV infection.
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Affiliation(s)
- Ivan H. W. Ng
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Kitti Wing-Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
- Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, Singapore 117545
| | - Min Jie Alvin Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
- Genome Institute of Singapore, Agency for Science & Technology Research (A*STAR), 60 Biopolis Street, Singapore 138672
| | - Chin Piaw Gwee
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Kate M. Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Sarah J. Jeffress
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Wuan-Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Crystall M. D. Swarbrick
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - David A. Jans
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Subhash G. Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, Singapore 117545
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43
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Tan AHY, Tu W, McCuaig R, Hardy K, Donovan T, Tsimbalyuk S, Forwood JK, Rao S. Lysine-Specific Histone Demethylase 1A Regulates Macrophage Polarization and Checkpoint Molecules in the Tumor Microenvironment of Triple-Negative Breast Cancer. Front Immunol 2019; 10:1351. [PMID: 31249575 PMCID: PMC6582666 DOI: 10.3389/fimmu.2019.01351] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/28/2019] [Indexed: 12/14/2022] Open
Abstract
Macrophages play an important role in regulating the tumor microenvironment (TME). Here we show that classical (M1) macrophage polarization reduced expression of LSD1, nuclear REST corepressor 1 (CoREST), and the zinc finger protein SNAIL. The LSD1 inhibitor phenelzine targeted both the flavin adenine dinucleotide (FAD) and CoREST binding domains of LSD1, unlike the LSD1 inhibitor GSK2879552, which only targeted the FAD domain. Phenelzine treatment reduced nuclear demethylase activity and increased transcription and expression of M1-like signatures both in vitro and in a murine triple-negative breast cancer model. Overall, the LSD1 inhibitors phenelzine and GSK2879552 are useful tools for dissecting the contribution of LSD1 demethylase activity and the nuclear LSD1-CoREST complex to switching macrophage polarization programs. These findings suggest that inhibitors must have dual FAD and CoREST targeting abilities to successfully initiate or prime macrophages toward an anti-tumor M1-like phenotype in triple-negative breast cancer.
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Affiliation(s)
- Abel H Y Tan
- Epigenetics and Transcription Laboratory Melanie Swan Memorial Translational Centre, Sci-Tech, University of Canberra, Canberra, ACT, Australia
| | - WenJuan Tu
- Epigenetics and Transcription Laboratory Melanie Swan Memorial Translational Centre, Sci-Tech, University of Canberra, Canberra, ACT, Australia
| | - Robert McCuaig
- Epigenetics and Transcription Laboratory Melanie Swan Memorial Translational Centre, Sci-Tech, University of Canberra, Canberra, ACT, Australia
| | - Kristine Hardy
- Epigenetics and Transcription Laboratory Melanie Swan Memorial Translational Centre, Sci-Tech, University of Canberra, Canberra, ACT, Australia
| | - Thomasina Donovan
- Epigenetics and Transcription Laboratory Melanie Swan Memorial Translational Centre, Sci-Tech, University of Canberra, Canberra, ACT, Australia
| | - Sofiya Tsimbalyuk
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Sudha Rao
- Epigenetics and Transcription Laboratory Melanie Swan Memorial Translational Centre, Sci-Tech, University of Canberra, Canberra, ACT, Australia
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44
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Yang SNY, Atkinson SC, Fraser JE, Wang C, Maher B, Roman N, Forwood JK, Wagstaff KM, Borg NA, Jans DA. Novel Flavivirus Antiviral That Targets the Host Nuclear Transport Importin α/β1 Heterodimer. Cells 2019; 8:cells8030281. [PMID: 30909636 PMCID: PMC6468590 DOI: 10.3390/cells8030281] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/20/2022] Open
Abstract
Dengue virus (DENV) threatens almost 70% of the world’s population, with no effective vaccine or therapeutic currently available. A key contributor to infection is nuclear localisation in the infected cell of DENV nonstructural protein 5 (NS5) through the action of the host importin (IMP) α/β1 proteins. Here, we used a range of microscopic, virological and biochemical/biophysical approaches to show for the first time that the small molecule GW5074 has anti-DENV action through its novel ability to inhibit NS5–IMPα/β1 interaction in vitro as well as NS5 nuclear localisation in infected cells. Strikingly, GW5074 not only inhibits IMPα binding to IMPβ1, but can dissociate preformed IMPα/β1 heterodimer, through targeting the IMPα armadillo (ARM) repeat domain to impact IMPα thermal stability and α-helicity, as shown using analytical ultracentrifugation, thermostability analysis and circular dichroism measurements. Importantly, GW5074 has strong antiviral activity at low µM concentrations against not only DENV-2, but also zika virus and West Nile virus. This work highlights DENV NS5 nuclear targeting as a viable target for anti-flaviviral therapeutics.
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Affiliation(s)
- Sundy N Y Yang
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
| | - Sarah C Atkinson
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
| | - Johanna E Fraser
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
| | - Chunxiao Wang
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
| | - Belinda Maher
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
| | - Noelia Roman
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
| | - Kylie M Wagstaff
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
| | - Natalie A Borg
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
| | - David A Jans
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
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45
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Sarker S, Das S, Forwood JK, Raidal SR. The first complete mitogenome of Australia’s largest raptor, the wedge-tailed eagle ( Aquila audax). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1553529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Shane R. Raidal
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, Australia
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46
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Smith KM, Tsimbalyuk S, Edwards MR, Cross EM, Batra J, Soares da Costa TP, Aragão D, Basler CF, Forwood JK. Structural basis for importin alpha 3 specificity of W proteins in Hendra and Nipah viruses. Nat Commun 2018; 9:3703. [PMID: 30209309 PMCID: PMC6135763 DOI: 10.1038/s41467-018-05928-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
Seven human isoforms of importin α mediate nuclear import of cargo in a tissue- and isoform-specific manner. How nuclear import adaptors differentially interact with cargo harbouring the same nuclear localisation signal (NLS) remains poorly understood, as the NLS recognition region is highly conserved. Here, we provide a structural basis for the nuclear import specificity of W proteins in Hendra and Nipah viruses. We determine the structural interfaces of these cargo bound to importin α1 and α3, identifying a 2.4-fold more extensive interface and > 50-fold higher binding affinity for importin α3. Through the design of importin α1 and α3 chimeric and mutant proteins, together with structures of cargo-free importin α1 and α3 isoforms, we establish that the molecular basis of specificity resides in the differential positioning of the armadillo repeats 7 and 8. Overall, our study provides mechanistic insights into a range of important nucleocytoplasmic transport processes reliant on isoform adaptor specificity.
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Affiliation(s)
- Kate M Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Sofiya Tsimbalyuk
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Megan R Edwards
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, 30303, USA
| | - Emily M Cross
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Jyoti Batra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, 30303, USA
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - David Aragão
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC, 3168, Australia
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, 30303, USA.
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia.
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47
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Sarker S, Das S, Ghorashi SA, Forwood JK, Helbig K, Raidal SR. The first complete mitogenome of red-bellied parrot ( Poicephalus rufiventris) resolves phylogenetic status within Psittacidae. Mitochondrial DNA B Resour 2018; 3:195-197. [PMID: 33474115 PMCID: PMC7800220 DOI: 10.1080/23802359.2018.1437818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 01/18/2018] [Indexed: 12/02/2022] Open
Abstract
This paper describes the genomic architecture of a complete mitogenome from a red-bellied parrot (Poicephalus rufiventris). The mitogenome sequence was circular and 15,524 bp in length. Compared to other Psittacidae species, the genome encoded a conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, 21 tRNA genes, and two control regions, however, the mitogenome was missing a part of control region and a tRNA-Leu. The lengths of 12S and 16S ribosomal RNA were 975 bp and 1569 bp, respectively. The overall base composition of the mitogenome of P. rufiventris was dominated by higher AT (51.6%) than GC (48.4%) content. The complete mitogenome sequence determined in this study would be useful to track the deeper evolutionary history and the conservation of P. rufiventris.
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Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Albury, Australia
| | - Seyed A. Ghorashi
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Albury, Australia
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Albury, Australia
| | - Karla Helbig
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Shane R. Raidal
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Albury, Australia
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48
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Wang C, Yang SNY, Smith K, Forwood JK, Jans DA. Nuclear import inhibitor N-(4-hydroxyphenyl) retinamide targets Zika virus (ZIKV) nonstructural protein 5 to inhibit ZIKV infection. Biochem Biophys Res Commun 2017; 493:1555-1559. [PMID: 28988109 DOI: 10.1016/j.bbrc.2017.10.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 12/31/2022]
Abstract
In the absence of approved therapeutics, Zika virus (ZIKV)'s recent prolific outbreaks in the Americas, together with impacts on unborn fetuses of infected mothers, make it a pressing human health concern worldwide. Although a key player in viral replication in the infected host cell cytoplasm, ZIKV non-structural protein 5 (NS5) appears to contribute integrally to pathogenesis by localising in the host cell nucleus, in similar fashion to NS5 from Dengue virus (DENV). We show here for the first time that ZIKV NS5 is recognized with high nanomolar affinity by the host cell importin α/β1 heterodimer, and that this interaction can be blocked by the novel DENV NS5 targeting inhibitor N-(4-hydroxyphenyl) retinamide (4-HPR). Importantly, we show that 4-HPR has potent anti-ZIKV activity at low μM concentrations. With an established safety profile for human use, 4-HPR represents an exciting possibility as an anti-ZIKV agent.
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Affiliation(s)
- Chunxiao Wang
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia
| | - Sundy N Y Yang
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia
| | - Kate Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - David A Jans
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic. 3800, Australia.
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49
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Khandokar YB, Srivastava P, Cowieson N, Sarker S, Aragao D, Das S, Smith KM, Raidal SR, Forwood JK. Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase. J Biol Chem 2017; 292:20461-20471. [PMID: 28972175 DOI: 10.1074/jbc.m117.800227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/12/2017] [Indexed: 11/06/2022] Open
Abstract
Thioesterases catalyze the cleavage of thioester bonds within many activated fatty acids and acyl-CoA substrates. They are expressed ubiquitously in both prokaryotes and eukaryotes and are subdivided into 25 thioesterase families according to their catalytic active site, protein oligomerization, and substrate specificity. Although many of these enzyme families are well-characterized in terms of function and substrate specificity, regulation across most thioesterase families is poorly understood. Here, we characterized a TE6 thioesterase from the bacterium Neisseria meningitidis Structural analysis with X-ray crystallographic diffraction data to 2.0-Å revealed that each protein subunit harbors a hot dog-fold and that the TE6 enzyme forms a hexamer with D3 symmetry. An assessment of thioesterase activity against a range of acyl-CoA substrates revealed the greatest activity against acetyl-CoA, and structure-guided mutagenesis of putative active site residues identified Asn24 and Asp39 as being essential for activity. Our structural analysis revealed that six GDP nucleotides bound the enzyme in close proximity to an intersubunit disulfide bond interactions that covalently link thioesterase domains in a double hot dog dimer. Structure-guided mutagenesis of residues within the GDP-binding pocket identified Arg93 as playing a key role in the nucleotide interaction and revealed that GDP is required for activity. All mutations were confirmed to be specific and not to have resulted from structural perturbations by X-ray crystallography. This is the first report of a bacterial GDP-regulated thioesterase and of covalent linkage of thioesterase domains through a disulfide bond, revealing structural similarities with ADP regulation in the human ACOT12 thioesterase.
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Affiliation(s)
| | | | - Nathan Cowieson
- the Life Sciences Division, Diamond Light Source, Didcot OX11 0DE, United Kingdom
| | - Subir Sarker
- the Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Victoria 3086, Australia, and
| | - David Aragao
- the Australian National Synchrotron, Melbourne, Victoria 3168, Australia
| | - Shubagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia
| | | | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia
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50
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Sarker S, Das S, Frith S, Forwood JK, Helbig K, Raidal SR. Complete mitochondrial genome sequence of an Australian little penguin ( Eudyptula minor novaehollandia, J.R. Forster, 1781). Mitochondrial DNA B Resour 2017; 2:428-429. [PMID: 33473850 PMCID: PMC7799458 DOI: 10.1080/23802359.2017.1357446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this paper, we report the complete mitochondrial genome of an Australian little penguin (Eudyptula minor novaehollandia). The mitogenome sequence has been found to be circular, and 17,608 bp in length. Similar to other Spheniscidae species, the genome encoded a typically conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes, as well as all protein coding sequences started with methionine. The lengths of 12S ribosomal RNA and 16S ribosomal RNA were 977 bp and 1612 bp, respectively, and were located between tRNA-Phe and tRNA-Leu. The overall base composition of the mitogenome of E. minor novaehollandia had slightly higher AT (55.5%) content than GC (45.5%). The complete mitogenome sequence determined in this study would be useful to track the deeper evolutionary history and conservation of E. minor novaehollandia.
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Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, Australia
| | | | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Karla Helbig
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, Australia
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