1
|
Sterrenberg VT, Stalling D, Knaack JIH, Soh TK, Bosse JB, Meier C. A TriPPPro-Nucleotide Reporter with Optimized Cell-Permeable Dyes for Metabolic Labeling of Cellular and Viral DNA in Living Cells. Angew Chem Int Ed Engl 2023; 62:e202308271. [PMID: 37435767 DOI: 10.1002/anie.202308271] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
The metabolic labeling of nucleic acids in living cells is highly desirable to track the dynamics of nucleic acid metabolism in real-time and has the potential to provide novel insights into cellular biology as well as pathogen-host interactions. Catalyst-free inverse electron demand Diels-Alder reactions (iEDDA) with nucleosides carrying highly reactive moieties such as axial 2-trans-cyclooctene (2TCOa) would be an ideal tool to allow intracellular labeling of DNA. However, cellular kinase phosphorylation of the modified nucleosides is needed after cellular uptake as triphosphates are not membrane permeable. Unfortunately, the narrow substrate window of most endogenous kinases limits the use of highly reactive moieties. Here, we apply our TriPPPro (triphosphate pronucleotide) approach to directly deliver a highly reactive 2TCOa-modified 2'-deoxycytidine triphosphate reporter into living cells. We show that this nucleoside triphosphate is metabolically incorporated into de novo synthesized cellular and viral DNA and can be labeled with highly reactive and cell-permeable fluorescent dye-tetrazine conjugates via iEDDA to visualize DNA in living cells directly. Thus, we present the first comprehensive method for live-cell imaging of cellular and viral nucleic acids using a two-step labeling approach.
Collapse
Affiliation(s)
- Vincente T Sterrenberg
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Dörte Stalling
- CSSB Centre for Structural Systems Biology, Notkestraße 85, Building 15, 22607, Hamburg, Germany
- Institute of Virology, Hannover Medical School (MHH), 30625, Hannover, Germany
- Leibniz Institute of Virology (LIV), 20251, Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625, Hannover, Germany
| | - J Iven H Knaack
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Timothy K Soh
- CSSB Centre for Structural Systems Biology, Notkestraße 85, Building 15, 22607, Hamburg, Germany
- Institute of Virology, Hannover Medical School (MHH), 30625, Hannover, Germany
- Leibniz Institute of Virology (LIV), 20251, Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625, Hannover, Germany
| | - Jens B Bosse
- CSSB Centre for Structural Systems Biology, Notkestraße 85, Building 15, 22607, Hamburg, Germany
- Institute of Virology, Hannover Medical School (MHH), 30625, Hannover, Germany
- Leibniz Institute of Virology (LIV), 20251, Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625, Hannover, Germany
| | - Chris Meier
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| |
Collapse
|
2
|
Kyriakou E, Magiorkinis G. Interplay between endogenous and exogenous human retroviruses. Trends Microbiol 2023; 31:933-946. [PMID: 37019721 DOI: 10.1016/j.tim.2023.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/07/2023]
Abstract
In humans, retroviruses thrive more as symbionts than as parasites. Apart from the only two modern exogenous human retroviruses (human T-cell lymphotropic and immunodeficiency viruses; HTLV and HIV, respectively), ~8% of the human genome is occupied by ancient retroviral DNA [human endogenous retroviruses (HERVs)]. Here, we review the recent discoveries about the interactions between the two groups, the impact of infection by exogenous retroviruses on the expression of HERVs, the effect of HERVs on the pathogenicity of HIV and HTLV and on the severity of the diseases caused by them, and the antiviral protection that HERVs can allegedly provide to the host. Tracing the crosstalk between contemporary retroviruses and their endogenized ancestors will provide better understanding of the retroviral world.
Collapse
Affiliation(s)
- Eleni Kyriakou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
| |
Collapse
|
3
|
Jun YW, Kant M, Coskun E, Kato TA, Jaruga P, Palafox E, Dizdaroglu M, Kool ET. Possible Genetic Risks from Heat-Damaged DNA in Food. ACS CENTRAL SCIENCE 2023; 9:1170-1179. [PMID: 37396864 PMCID: PMC10311654 DOI: 10.1021/acscentsci.2c01247] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 07/04/2023]
Abstract
The consumption of foods prepared at high temperatures has been associated with numerous health risks. To date, the chief identified source of risk has been small molecules produced in trace levels by cooking and reacting with healthy DNA upon consumption. Here, we considered whether the DNA in food itself also presents a hazard. We hypothesize that high-temperature cooking may cause significant damage to the DNA in food, and this damage might find its way into cellular DNA by metabolic salvage. We tested cooked and raw foods and found high levels of hydrolytic and oxidative damage to all four DNA bases upon cooking. Exposing cultured cells to damaged 2'-deoxynucleosides (particularly pyrimidines) resulted in elevated DNA damage and repair responses in the cells. Feeding a deaminated 2'-deoxynucleoside (2'-deoxyuridine), and DNA containing it, to mice resulted in substantial uptake into intestinal genomic DNA and promoted double-strand chromosomal breaks there. The results suggest the possibility of a previously unrecognized pathway whereby high-temperature cooking may contribute to genetic risks.
Collapse
Affiliation(s)
- Yong Woong Jun
- Department of Chemistry, Sarafan ChEM-H, and Stanford Cancer InstituteStanford University, Stanford, California 94305, United States
| | - Melis Kant
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Erdem Coskun
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Institute
for Bioscience & Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States
| | - Takamitsu A. Kato
- Department
of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Pawel Jaruga
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Elizabeth Palafox
- Department of Chemistry, Sarafan ChEM-H, and Stanford Cancer InstituteStanford University, Stanford, California 94305, United States
| | - Miral Dizdaroglu
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Eric T. Kool
- Department of Chemistry, Sarafan ChEM-H, and Stanford Cancer InstituteStanford University, Stanford, California 94305, United States
| |
Collapse
|
4
|
Verrier ER, Ligat G, Heydmann L, Doernbrack K, Miller J, Maglott-Roth A, Jühling F, El Saghire H, Heuschkel MJ, Fujiwara N, Hsieh SY, Hoshida Y, Root DE, Felli E, Pessaux P, Mukherji A, Mailly L, Schuster C, Brino L, Nassal M, Baumert TF. Cell-based cccDNA reporter assay combined with functional genomics identifies YBX1 as HBV cccDNA host factor and antiviral candidate target. Gut 2022; 72:gutjnl-2020-323665. [PMID: 36591611 PMCID: PMC10423543 DOI: 10.1136/gutjnl-2020-323665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 11/24/2022] [Indexed: 01/03/2023]
Abstract
OBJECTIVES Chronic hepatitis B virus (HBV) infection is a leading cause of liver disease and hepatocellular carcinoma. A key feature of HBV replication is the synthesis of the covalently close circular (ccc)DNA, not targeted by current treatments and whose elimination would be crucial for viral cure. To date, little is known about cccDNA formation. One major challenge to address this urgent question is the absence of robust models for the study of cccDNA biology. DESIGN We established a cell-based HBV cccDNA reporter assay and performed a loss-of-function screen targeting 239 genes encoding the human DNA damage response machinery. RESULTS Overcoming the limitations of current models, the reporter assay enables to quantity cccDNA levels using a robust ELISA as a readout. A loss-of-function screen identified 27 candidate cccDNA host factors, including Y box binding protein 1 (YBX1), a DNA binding protein regulating transcription and translation. Validation studies in authentic infection models revealed a robust decrease in HBV cccDNA levels following silencing, providing proof-of-concept for the importance of YBX1 in the early steps of the HBV life cycle. In patients, YBX1 expression robustly correlates with both HBV load and liver disease progression. CONCLUSION Our cell-based reporter assay enables the discovery of HBV cccDNA host factors including YBX1 and is suitable for the characterisation of cccDNA-related host factors, antiviral targets and compounds.
Collapse
Affiliation(s)
- Eloi R Verrier
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
| | - Gaëtan Ligat
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
| | - Laura Heydmann
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
| | - Katharina Doernbrack
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Julija Miller
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | | | - Frank Jühling
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
| | - Houssein El Saghire
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
| | - Margaux J Heuschkel
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
| | - Naoto Fujiwara
- Department of Internal Medicine, Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sen-Yung Hsieh
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yujin Hoshida
- Department of Internal Medicine, Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Emanuele Felli
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Patrick Pessaux
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Atish Mukherji
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
| | - Laurent Mailly
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
| | - Catherine Schuster
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
| | - Laurent Brino
- IGBMC, Plateforme de Criblage Haut-débit, Illkirch, France
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Thomas F Baumert
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMRS 1110, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| |
Collapse
|
5
|
Afzal S, Fiaz K, Noor A, Sindhu AS, Hanif A, Bibi A, Asad M, Nawaz S, Zafar S, Ayub S, Hasnain SB, Shahid M. Interrelated Oncogenic Viruses and Breast Cancer. Front Mol Biosci 2022; 9:781111. [PMID: 35419411 PMCID: PMC8995849 DOI: 10.3389/fmolb.2022.781111] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/15/2022] [Indexed: 12/23/2022] Open
Abstract
Breast Cancer is a multifactorial disease and recent evidence that viruses have a greater role in its aetiology and pathophysiology than previously hypothesized, has garnered a lot of attention in the past couple of years. After the role of Mouse Mammary Tumour Virus (MMTV) in the oncogenesis of breast cancer has been proved in mice, search for similar viruses found quite a plausible relation of Human Papilloma Virus (HPV), Epstein–Barr virus (EBV), and Bovine Leukaemia Virus (BLV) with breast cancer. However, despite practical efforts to provide some clarity in this issue, the evidence that viruses cause breast cancer still remains inconclusive. Therefore, this article aims to clarify some ambiguity and elucidate the correlation of breast cancer and those particular viruses which are found to bring about the development of tumorigenesis by a previous infection or by their own oncogenic ability to manipulate the molecular mechanisms and bypass the immune system of the human body. Although many studies have reported, both, the individual and co-existing presence of HPV, EBV, MMTV, and BLV in patient sample tissues, particularly in Western women, and proposed oncogenic mechanisms, majority of the collective survey of literature fails to provide a delineated and strong conclusive evidence that viruses do, in fact, cause breast cancer. Measures to prevent these viral infections may curb breast cancer cases, especially in the West. More studies are needed to provide a definite conclusion.
Collapse
|
6
|
Boso G, Fleck K, Carley S, Liu Q, Buckler-White A, Kozak CA. The Oldest Co-opted gag Gene of a Human Endogenous Retrovirus Shows Placenta-Specific Expression and Is Upregulated in Diffuse Large B-Cell Lymphomas. Mol Biol Evol 2021; 38:5453-5471. [PMID: 34410386 PMCID: PMC8662612 DOI: 10.1093/molbev/msab245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Vertebrate genomes contain endogenous retroviruses (ERVs) that represent remnants of past germline infections by ancient retroviruses. Despite comprising 8% of the human genome, the human ERVs (HERVs) do not encode a replication competent retrovirus. However, some HERV genes have been co-opted to serve host functions, most notably the viral envelope-derived syncytins involved in placentation. Here, we identify the oldest HERV intact gag gene with an open reading frame, gagV1. Its provirus contains an intact env, envV1, and the first open reading frame found in an HERV gag leader, pre-gagV1, which encodes a novel protein. This HERV is linked to a related gag gene, gagV3, and these three genes all show patterns of evolutionary conservation in primates. gagV1 and pre-gagV1 orthologs are present in all simian primate lineages indicating that this HERV entered the germline of the common simian primate ancestor at least 43 Ma, whereas gagV3 is found in Old and New World monkeys. gagV1 and gagV3 have undergone recurrent gene conversion events and positive selection. Expression of gagV1, gagV3, and pre-gagV1 is restricted to the placenta in humans and macaques suggesting co-option for placenta-specific host functions. Transcriptomic analysis of human tumors also found upregulated levels of gagV1 transcripts in diffuse large B-cell lymphomas. These findings suggest that these HERV-V genes may be useful markers for the most common type of non-Hodgkin's lymphoma and that they may have contributed to the successive domestications of env and gag genes in eutherians involved in the ongoing ERV-driven evolution of the placenta.
Collapse
Affiliation(s)
- Guney Boso
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Katherine Fleck
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Samuel Carley
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Qingping Liu
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Alicia Buckler-White
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Christine A Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| |
Collapse
|
7
|
Shi J, Li X, Zhu M, Chi H, Song Y, Wang J, Huang J. The dUTPase of caprine arthritis-encephalitis virus negatively regulates interferon signaling pathway. IRANIAN JOURNAL OF VETERINARY RESEARCH 2021; 22:209-216. [PMID: 34777521 DOI: 10.22099/ijvr.2021.38240.5568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 05/19/2021] [Accepted: 06/27/2021] [Indexed: 09/30/2022]
Abstract
Background Deoxyuracil triphosphate nucleotide (dUTP) pyrophosphatase (dUTPase, DU) is an enzyme of caprine arthritis-encephalitis virus (CAEV) that minimizes incorporation of dUTP into the DNA. Caprine arthritis-encephalitis virus relies partly on its ability to escape from innate immunity to cause persistent infections. Interferon β (IFN-β) is an important marker for evaluating the innate immune system, and it has a broad spectrum of antiviral activity. Aims This study was conducted to investigate the details of the IFN-β response to CAEV infection. Methods The expression of IFN-β and the proliferation of Sendai virus (SeV) and vesicular stomatitis virus (VSV) were determined by real-time quantitative polymerase chain reaction (qPCR). The effect of DU on the IFN signaling pathway was evaluated using luciferase reporter assays. Results In our study, the expression of IFN-β was significantly inhibited and the proliferation of SeV and VSV was promoted in cells overexpressing CAEV-DU. DU affected interferon stimulated response element (ISRE) and IFN-β promoter activities induced by RIG-I/MDA5/MAVS/TBK1 pathway, while did not affect them induced by interferon regulatory factor 3 (IRF3-5D). Conclusion DU protein downregulated the production of IFN-β by inhibiting the activity of the signal transduction molecules upstream of IRF3, thereby, helping CAEV escape innate immunity. Findings of this work provide an evidence to understand the persistent infection and multiple system inflammation of CAEV.
Collapse
Affiliation(s)
- J Shi
- MSc Student in Biology, Department of Microbiology & Immunology, School of Life Sciences, Tianjin University, Tianjin, 300072, China.,These authors contributed equally to this work
| | - X Li
- Departmet of Microbiology & Immunology, School of Life Sciences, Tianjin University, Tianjin, 300072, China.,These authors contributed equally to this work
| | - M Zhu
- MSc Student in Biology, Department of Microbiology & Immunology, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - H Chi
- MSc Student in Biology, Department of Microbiology & Immunology, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Y Song
- MSc Student in Biology, Department of Microbiology & Immunology, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - J Wang
- MSc Student in Biology, Department of Microbiology & Immunology, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - J Huang
- Departmet of Microbiology & Immunology, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| |
Collapse
|
8
|
Yedavalli VRK, Patil A, Parrish J, Kozak CA. A novel class III endogenous retrovirus with a class I envelope gene in African frogs with an intact genome and developmentally regulated transcripts in Xenopus tropicalis. Retrovirology 2021; 18:20. [PMID: 34261506 PMCID: PMC8278194 DOI: 10.1186/s12977-021-00564-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/29/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Retroviruses exist as exogenous infectious agents and as endogenous retroviruses (ERVs) integrated into host chromosomes. Such endogenous retroviruses (ERVs) are grouped into three classes roughly corresponding to the seven genera of infectious retroviruses: class I (gamma-, epsilonretroviruses), class II (alpha-, beta-, delta-, lentiretroviruses) and class III (spumaretroviruses). Some ERVs have counterparts among the known infectious retroviruses, while others represent paleovirological relics of extinct or undiscovered retroviruses. RESULTS Here we identify an intact ERV in the Anuran amphibian, Xenopus tropicalis. XtERV-S has open reading frames (ORFs) for gag, pol (polymerase) and env (envelope) genes, with a small additional ORF in pol and a serine tRNA primer binding site. It has unusual features and domain relationships to known retroviruses. Analyses based on phylogeny and functional motifs establish that XtERV-S gag and pol genes are related to the ancient env-less class III ERV-L family but the surface subunit of env is unrelated to known retroviruses while its transmembrane subunit is class I-like. LTR constructs show transcriptional activity, and XtERV-S transcripts are detected in embryos after the maternal to zygotic mid-blastula transition and before the late tailbud stage. Tagged Gag protein shows typical subcellular localization. The presence of ORFs in all three protein-coding regions along with identical 5' and 3' LTRs (long terminal repeats) indicate this is a very recent germline acquisition. There are older, full-length, nonorthologous, defective copies in Xenopus laevis and the distantly related African bullfrog, Pyxicephalus adspersus. Additional older, internally deleted copies in X. tropicalis carry a 300 bp LTR substitution. CONCLUSIONS XtERV-S represents a genera-spanning member of the largely env-less class III ERV that has ancient and modern copies in Anurans. This provirus has an env ORF with a surface subunit unrelated to known retroviruses and a transmembrane subunit related to class I gammaretroviruses in sequence and organization, and is expressed in early embryogenesis. Additional XtERV-S-related but defective copies are present in X. tropicalis and other African frog taxa. XtERV-S is an unusual class III ERV variant, and it may represent an important transitional retroviral form that has been spreading in African frogs for tens of millions of years.
Collapse
Affiliation(s)
- Venkat R K Yedavalli
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Akash Patil
- Department of Biomedical Engineering, John Hopkins University, Baltimore, MD, 21205, USA
| | - Janay Parrish
- Internal Medicine, Northwell Health, Lenox Hill Hospital, New York, NY, 10075, USA
| | - Christine A Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA.
| |
Collapse
|
9
|
James AM, Seal SE, Bailey AM, Foster GD. Viral inosine triphosphatase: A mysterious enzyme with typical activity, but an atypical function. MOLECULAR PLANT PATHOLOGY 2021; 22:382-389. [PMID: 33471956 PMCID: PMC7865087 DOI: 10.1111/mpp.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 05/03/2023]
Abstract
Plant viruses typically have highly condensed genomes, yet the plant-pathogenic viruses Cassava brown streak virus, Ugandan cassava brown streak virus, and Euphorbia ringspot virus are unusual in encoding an enzyme not yet found in any other virus, the "house-cleaning" enzyme inosine triphosphatase. Inosine triphosphatases (ITPases) are highly conserved enzymes that occur in all kingdoms of life and perform a house-cleaning function by hydrolysing the noncanonical nucleotide inosine triphosphate to inosine monophosphate. The ITPases encoded by cassava brown streak virus and Ugandan cassava brown streak virus have been characterized biochemically and are shown to have typical ITPase activity. However, their biological role in virus infection has yet to be elucidated. Here we review what is known of viral-encoded ITPases and speculate on potential roles in infection with the aim of generating a greater understanding of cassava brown streak viruses, a group of the world's most devastating viruses.
Collapse
Affiliation(s)
- Amy M. James
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Susan E. Seal
- Natural Resources Institute, Chatham MaritimeGillinghamUK
| | - Andy M. Bailey
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Gary D. Foster
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| |
Collapse
|
10
|
Huang X, Jiao N, Zhang R. The genomic content and context of auxiliary metabolic genes in roseophages. Environ Microbiol 2021; 23:3743-3757. [PMID: 33511765 DOI: 10.1111/1462-2920.15412] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/24/2021] [Indexed: 11/26/2022]
Abstract
Marine bacteriophages frequently possess auxiliary metabolic genes (AMGs) that accelerate host metabolism during phage infection. The significance of AMGs in phage infecting the ecologically important Roseobacter clade, found predominantly in marine environments, remains to be determined. Here, we analysed the distribution and genomic context of 180 AMGs, annotated into 20 types, across 50 roseophage genomes. Roseophages share seven high-frequency AMGs (trx, grx, RNR, thyX, DCD, phoH, and mazG), most of them involved in the nucleotide biosynthesis pathway that represent conserved intra and inter operational taxonomic units (OTUs), and share ≥97% full-length DNA sequence similarity. Sporadic AMGs (dUTPase, lexA, degS, Que, NAPRT, AHL, pcnB, ctrA, RTX, RNR-nrdA, RNR-nrdE, wclP, and flgJ), present in only one or two OTUs, show high functional diversity. The roseophage AMG repertoire weakly correlates with environmental factors, while host range partially explains the sporadic AMG distribution. Locally co-linear blocks distribution index (LDI) analysis indicated that high-frequency roseopodovirus AMGs are restricted to particular genomic islands, possibly originating from limited historical acquisition events. Low-frequency roseopodovirus AMGs and all roseosiphovirus AMGs have high LDI values, implying multiple historical acquisition events. In summary, roseophages have acquired a range of AMGs through horizontal gene transfer, and the forces shaping the evolution of roseophages are described.
Collapse
Affiliation(s)
- Xingyu Huang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China
| |
Collapse
|
11
|
Identification of a herpes simplex virus 1 gene encoding neurovirulence factor by chemical proteomics. Nat Commun 2020; 11:4894. [PMID: 32994400 PMCID: PMC7524712 DOI: 10.1038/s41467-020-18718-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/09/2020] [Indexed: 01/10/2023] Open
Abstract
Identification of the complete set of translated genes of viruses is important to understand viral replication and pathogenesis as well as for therapeutic approaches to control viral infection. Here, we use chemical proteomics, integrating bio-orthogonal non-canonical amino acid tagging and high-resolution mass spectrometry, to characterize the newly synthesized herpes simplex virus 1 (HSV-1) proteome in infected cells. In these infected cells, host cellular protein synthesis is shut-off, increasing the chance to preferentially detect viral proteomes. We identify nine previously cryptic orphan protein coding sequences whose translated products are expressed in HSV-1-infected cells. Functional characterization of one identified protein, designated piUL49, shows that it is critical for HSV-1 neurovirulence in vivo by regulating the activity of virally encoded dUTPase, a key enzyme that maintains accurate DNA replication. Our results demonstrate that cryptic orphan protein coding genes of HSV-1, and probably other large DNA viruses, remain to be identified. Here the authors use chemical proteomics to identify the herpes simplex virus 1 encoded proteome in infected cells. Functional characterization of one of the nine identified proteins, designated piUL49, shows that it acts as neurovirulence factor in mice by regulating a virally encoded dUTPase.
Collapse
|
12
|
Munis AM. Gene Therapy Applications of Non-Human Lentiviral Vectors. Viruses 2020; 12:v12101106. [PMID: 33003635 PMCID: PMC7599719 DOI: 10.3390/v12101106] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 12/14/2022] Open
Abstract
Recent commercialization of lentiviral vector (LV)-based cell therapies and successful reports of clinical studies have demonstrated the untapped potential of LVs to treat diseases and benefit patients. LVs hold notable and inherent advantages over other gene transfer agents based on their ability to transduce non-dividing cells, permanently transform target cell genome, and allow stable, long-term transgene expression. LV systems based on non-human lentiviruses are attractive alternatives to conventional HIV-1-based LVs due to their lack of pathogenicity in humans. This article reviews non-human lentiviruses and highlights their unique characteristics regarding virology and molecular biology. The LV systems developed based on these lentiviruses, as well as their successes and shortcomings, are also discussed. As the field of gene therapy is advancing rapidly, the use of LVs uncovers further challenges and possibilities. Advances in virology and an improved understanding of lentiviral biology will aid in the creation of recombinant viral vector variants suitable for translational applications from a variety of lentiviruses.
Collapse
Affiliation(s)
- Altar M Munis
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| |
Collapse
|
13
|
Talotta R, Atzeni F, Laska MJ. Retroviruses in the pathogenesis of systemic lupus erythematosus: Are they potential therapeutic targets? Autoimmunity 2020; 53:177-191. [PMID: 32321325 DOI: 10.1080/08916934.2020.1755962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The pathogenesis of systemic lupus erythematosus (SLE) is characterised by the hyper-activation of immunologic pathways related to the antiviral response. Exogenous and endogenous retroviruses, by integrating their DNA templates in the host cell genome, may epigenetically control the transcription of genes involved in the immune response. Furthermore, their nucleic acids or neo-synthesized proteins could stimulate the sensor molecules placed upstream the inflammatory cascade. Exogenous retroviruses, like human immunodeficiency virus, have been associated to SLE-like manifestations or to a fair SLE diagnosis. In addition, there is some evidence confirming a pathogenic role of human endogenous retroviruses in SLE. In line with these data, the use of antiretroviral agents could represent an attractive opportunity in the future therapeutic algorithms of this disease, but studies are still missing.
Collapse
Affiliation(s)
- Rossella Talotta
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University Hospital "Gaetano Martino", Messina, Italy
| | - Fabiola Atzeni
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University Hospital "Gaetano Martino", Messina, Italy
| | | |
Collapse
|
14
|
Sharma D, Sharma A, Singh B, Verma SK. Bioinformatic Exploration of Metal-Binding Proteome of Zoonotic Pathogen Orientia tsutsugamushi. Front Genet 2019; 10:797. [PMID: 31608099 PMCID: PMC6769048 DOI: 10.3389/fgene.2019.00797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/30/2019] [Indexed: 12/21/2022] Open
Abstract
Metal ions are involved in many essential biological processes and are crucial for the survival of all organisms. Identification of metal-binding proteins (MBPs) of human affecting pathogens may provide the blueprint for understanding biological metal usage and their putative roles in pathogenesis. This study is focused on the analysis of MBPs from Orientia tsutsugamushi (Ott), a causal agent of scrub typhus in humans. A total of 321 proteins were predicted as putative MBPs, based on sequence search and three-dimensional structure analysis. Majority of proteins could bind with magnesium, and the order of metal binding was Mg > Ca > Zn > Mn > Fe > Cd > Ni > Co > Cu, respectively. The predicted MBPs were functionally classified into nine broad classes. Among them, gene expression and regulation, metabolism, cell signaling, and transport classes were dominant. It was noted that the putative MBPs were localized in all subcellular compartments of Ott, but majorly found in the cytoplasm. Additionally, it was revealed that out of 321 predicted MBPs 245 proteins were putative bacterial toxins and among them, 98 proteins were nonhomologous to human proteome. Sixty putative MBPs showed the ability to interact with drug or drug-like molecules, which indicate that they may be used as broad-spectrum drug targets. These predicted MBPs from Ott could play vital role(s) in various cellular activities and virulence, hence may serve as plausible therapeutic targets to design metal-based drugs to curtail its infection.
Collapse
Affiliation(s)
- Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| |
Collapse
|
15
|
Pálinkás HL, Rácz GA, Gál Z, Hoffmann OI, Tihanyi G, Róna G, Gócza E, Hiripi L, Vértessy BG. CRISPR/Cas9-Mediated Knock-Out of dUTPase in Mice Leads to Early Embryonic Lethality. Biomolecules 2019; 9:biom9040136. [PMID: 30987342 PMCID: PMC6523736 DOI: 10.3390/biom9040136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 01/05/2023] Open
Abstract
Sanitization of nucleotide pools is essential for genome maintenance. Deoxyuridine 5′-triphosphate nucleotidohydrolase (dUTPase) is a key enzyme in this pathway since it catalyzes the cleavage of 2′-deoxyuridine 5′-triphosphate (dUTP) into 2′-deoxyuridine 5′-monophosphate (dUMP) and inorganic pyrophosphate. Through its action dUTPase efficiently prevents uracil misincorporation into DNA and at the same time provides dUMP, the substrate for de novo thymidylate biosynthesis. Despite its physiological significance, knock-out models of dUTPase have not yet been investigated in mammals, but only in unicellular organisms, such as bacteria and yeast. Here we generate CRISPR/Cas9-mediated dUTPase knock-out in mice. We find that heterozygous dut +/– animals are viable while having decreased dUTPase levels. Importantly, we show that dUTPase is essential for embryonic development since early dut −/− embryos reach the blastocyst stage, however, they die shortly after implantation. Analysis of pre-implantation embryos indicates perturbed growth of both inner cell mass (ICM) and trophectoderm (TE). We conclude that dUTPase is indispensable for post-implantation development in mice.
Collapse
Affiliation(s)
- Hajnalka Laura Pálinkás
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720 Szeged, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
| | - Gergely Attila Rácz
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
| | - Zoltán Gál
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, H-2100 Gödöllő, Hungary.
| | - Orsolya Ivett Hoffmann
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, H-2100 Gödöllő, Hungary.
| | - Gergely Tihanyi
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
| | - Gergely Róna
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| | - Elen Gócza
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, H-2100 Gödöllő, Hungary.
| | - László Hiripi
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, H-2100 Gödöllő, Hungary.
| | - Beáta G Vértessy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Hungary.
| |
Collapse
|
16
|
Lehrer S, Rheinstein PH. Mouse mammary tumor viral env sequences are not present in the human genome but are present in breast tumors and normal breast tissues. Virus Res 2019; 266:43-47. [PMID: 30951792 DOI: 10.1016/j.virusres.2019.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 01/28/2023]
Abstract
In 1936, John Joseph Bittner identified mouse mammary tumor virus (MMTV), a milk transmitted beta retrovirus, a form of single-stranded positive-sense RNA virus. A retrovirus inserts a copy of its genome into the DNA of a host cell, thus altering the cell's genome. In the current analysis, we searched for MMTV sequences within the human genome. To compare the MMTV genome to the human genome, we used BLAT, the Blast-Like Alignment Tool of the UCSC Genome Browser. BLAT can align a user sequence of 25 bases or more to the genome. 60 MMTV sequences were in the human genome. Of 56 sequences from the MMTV POL gene, 36 POL sequences were from the same part of the gene, beginning at viral nucleotide 4800 but of different lengths. 8 viral sequences began at nucleotide ∼3430 of the POL gene. Four viral sequences were from GAGdUTPase, encoded by the MMTV PRO gene. Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is an enzyme present in several major retroviral families. In MMTV dUTPase may be essential for viral replication. Since BLAT identified no MMTV envelope (env) sequence in the human genome, the env sequences from breast tumors and normal breast tissue found in other studies may have come from an MMTV infection. However, no one is certain how MMTV could enter human cells, since the cells do not have a cellular receptor for MMTV, as do mouse cells.
Collapse
Affiliation(s)
- Steven Lehrer
- Department of Radiation Oncolog, Icahn School of Medicine at Mount Sinai, New York, United States.
| | | |
Collapse
|
17
|
Abstract
Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.
Collapse
Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
- Corresponding author: E-mail:
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
| |
Collapse
|
18
|
Zhu H, Gifford RJ, Murcia PR. Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes. J Virol 2018; 92:e00927-18. [PMID: 30209175 PMCID: PMC6232481 DOI: 10.1128/jvi.00927-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/01/2018] [Indexed: 01/01/2023] Open
Abstract
The evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian order Perissodactyla, with a view to understanding their impact on the evolution of modern equids (family Equidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization, and time of activity. Our results show that subsequent to their ancestral divergence from rhinoceroses and tapirs, equids acquired four novel ERV lineages. We show that two of these ERV lineages proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germ line colonization by retroviruses for more than 54 million years-longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution.IMPORTANCE ERVs in the host genome are highly informative about the long-term interactions of retroviruses and hosts. They are also interesting because they have influenced the evolution of mammalian genomes in various ways. In this study, we derive a calibrated timeline describing the process through which ERV diversity has been generated in the equine germ line. We determined the distribution and diversity of perissodactyl ERV lineages and inferred their retrotranspositional activity during evolution, thereby gaining insight into the long-term coevolutionary history of retroviruses and mammals. Our study provides a platform for future investigations to identify equine ERV loci involved in physiological processes and/or pathological conditions.
Collapse
Affiliation(s)
- Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Pablo Ramiro Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| |
Collapse
|
19
|
Murine cytomegalovirus M72 promotes acute virus replication in vivo and is a substrate of the TRiC/CCT complex. Virology 2018; 522:92-105. [PMID: 30029015 DOI: 10.1016/j.virol.2018.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/05/2018] [Accepted: 07/07/2018] [Indexed: 01/30/2023]
Abstract
Betaherpesvirus dUTPase homologs are core herpesvirus proteins, but little is known about their role during infection. Human cytomegalovirus (HCMV) UL72 and murine cytomegalovirus (MCMV) M72 have been designated dUTPase homologs, and previous studies indicate UL72 is dispensable for replication and enzymatically inactive. Here, we report the initial characterization of MCMV M72. M72 does not possess dUTPase activity, and is expressed as a leaky-late gene product with multiple protein isoforms. Importantly, M72 augments MCMV replication in vitro and during the early stage of acute infection in vivo. We identify and confirm interaction of M72 with the eukaryotic chaperonin tailless complex protein -1 (TCP-1) ring complex (TRiC) or chaperonin containing tailless complex polypeptide 1 (CCT). Accumulating biochemical evidence indicates M72 forms homo-oligomers and is a substrate of TRiC/CCT. Taken together, we provide the first evidence of M72's contribution to viral pathogenesis, and identify a novel interaction with the TRiC/CCT complex.
Collapse
|
20
|
Cavalieri V, Baiamonte E, Lo Iacono M. Non-Primate Lentiviral Vectors and Their Applications in Gene Therapy for Ocular Disorders. Viruses 2018; 10:E316. [PMID: 29890733 PMCID: PMC6024700 DOI: 10.3390/v10060316] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 12/18/2022] Open
Abstract
Lentiviruses have a number of molecular features in common, starting with the ability to integrate their genetic material into the genome of non-dividing infected cells. A peculiar property of non-primate lentiviruses consists in their incapability to infect and induce diseases in humans, thus providing the main rationale for deriving biologically safe lentiviral vectors for gene therapy applications. In this review, we first give an overview of non-primate lentiviruses, highlighting their common and distinctive molecular characteristics together with key concepts in the molecular biology of lentiviruses. We next examine the bioengineering strategies leading to the conversion of lentiviruses into recombinant lentiviral vectors, discussing their potential clinical applications in ophthalmological research. Finally, we highlight the invaluable role of animal organisms, including the emerging zebrafish model, in ocular gene therapy based on non-primate lentiviral vectors and in ophthalmology research and vision science in general.
Collapse
Affiliation(s)
- Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Edificio 16, 90128 Palermo, Italy.
- Advanced Technologies Network (ATeN) Center, University of Palermo, Viale delle Scienze Edificio 18, 90128 Palermo, Italy.
| | - Elena Baiamonte
- Campus of Haematology Franco e Piera Cutino, Villa Sofia-Cervello Hospital, 90146 Palermo, Italy.
| | - Melania Lo Iacono
- Campus of Haematology Franco e Piera Cutino, Villa Sofia-Cervello Hospital, 90146 Palermo, Italy.
| |
Collapse
|
21
|
Design of a Broad-Range Bacteriophage Cocktail That Reduces Pseudomonas aeruginosa Biofilms and Treats Acute Infections in Two Animal Models. Antimicrob Agents Chemother 2018; 62:AAC.02573-17. [PMID: 29555626 PMCID: PMC5971607 DOI: 10.1128/aac.02573-17] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/08/2018] [Indexed: 12/20/2022] Open
Abstract
The alarming diffusion of multidrug-resistant (MDR) bacterial strains requires investigations on nonantibiotic therapies. Among such therapies, the use of bacteriophages (phages) as antimicrobial agents, namely, phage therapy, is a promising treatment strategy supported by the findings of recent successful compassionate treatments in Europe and the United States. In this work, we combined host range and genomic information to design a 6-phage cocktail killing several clinical strains of Pseudomonas aeruginosa, including those collected from Italian cystic fibrosis (CF) patients, and analyzed the cocktail performance. We demonstrated that the cocktail composed of four novel phages (PYO2, DEV, E215 and E217) and two previously characterized phages (PAK_P1 and PAK_P4) was able to lyse P. aeruginosa both in planktonic liquid cultures and in biofilms. In addition, we showed that the phage cocktail could cure acute respiratory infection in mice and treat bacteremia in wax moth (Galleria mellonella) larvae. Furthermore, administration of the cocktail to larvae prior to bacterial infection provided prophylaxis. In this regard, the efficiency of the phage cocktail was found to be unaffected by the MDR or mucoid phenotype of the pseudomonal strain. The cocktail was found to be superior to the individual phages in destroying biofilms and providing a faster treatment in mice. We also found the Galleria larva model to be cost-effective for testing the susceptibility of clinical strains to phages, suggesting that it could be implemented in the frame of developing personalized phage therapies.
Collapse
|
22
|
Bala JA, Balakrishnan KN, Abdullah AA, Mohamed R, Haron AW, Jesse FFA, Noordin MM, Mohd-Azmi ML. The re-emerging of orf virus infection: A call for surveillance, vaccination and effective control measures. Microb Pathog 2018; 120:55-63. [PMID: 29709684 DOI: 10.1016/j.micpath.2018.04.057] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/01/2023]
Abstract
Orf disease is known to be enzootic among small ruminants in Asia, Africa, and some other parts of the world. The disease caused by orf virus is highly contagious among small ruminant species. Unfortunately, it has been neglected for decades because of the general belief that it only causes a self-limiting disease. On the other hand, in the past it has been reported to cause huge cumulative financial losses in livestock farming. Orf disease is characterized by localized proliferative and persistent skin nodule lesions that can be classified into three forms: generalized, labial and mammary or genitals. It can manifest as benign or malignant types. The later type of orf can remain persistent, often fatal and usually causes a serious outbreak among small ruminant population. Morbidity and mortality rates of orf are higher especially in newly infected kids and lambs. Application of antibiotics together with antipyretic and/or analgesic is highly recommended as a supportive disease management strategy for prevention of subsequent secondary microbial invasion. The presence of various exotic orf virus strains of different origin has been reported in many countries mostly due to poorly controlled cross-border virus transmission. There have been several efforts to develop orf virus vaccines and it was with variable success. The use of conventional vaccines to control orf is a debatable topic due to the concern of short term immunity development. Following re-infection in previously vaccinated animals, it is uncommon to observe the farms involved to experience rapid virus spread and disease outbreak. Meanwhile, cases of zoonosis from infected animals to animal handler are not uncommon. Despite failures to contain the spread of orf virus by the use of conventional vaccines, vaccination of animals with live orf virus is still considered as one of the best choice. The review herein described pertinent issues with regard to the development and use of potential effective vaccines as a control measure against orf virus infection.
Collapse
Affiliation(s)
- Jamilu Abubakar Bala
- Virology Unit, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University Putra Malaysia, Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia; Microbiology Unit, Department of Medical Laboratory Science, Faculty of Allied Health Sciences, Bayero University Kano, Nigeria, P.M.B. 3011, Kano, Nigeria
| | - Krishnan Nair Balakrishnan
- Virology Unit, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University Putra Malaysia, Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia
| | - Ashwaq Ahmed Abdullah
- Institute of Bioscience, University Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia; Department of Microbiology, Faculty of Applied Science, Taiz University, Taiz, Yemen
| | - Ramlan Mohamed
- Institut Penyelidikan Haiwan, (IPH), Veterinary Research Institute, Ipoh, 59, Jalan Sultan Azlan Shah, 31400 Ipoh, Perak, Malaysia
| | - Abd Wahid Haron
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia
| | - Faez Firdaus Abdullah Jesse
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia
| | - Mustapha M Noordin
- Virology Unit, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University Putra Malaysia, Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia
| | - Mohd Lila Mohd-Azmi
- Virology Unit, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University Putra Malaysia, Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia.
| |
Collapse
|
23
|
Ji D, Kietrys AM, Lee Y, Kool ET. ATP-Linked Chimeric Nucleotide as a Specific Luminescence Reporter of Deoxyuridine Triphosphatase. Bioconjug Chem 2018; 29:1614-1621. [PMID: 29578692 DOI: 10.1021/acs.bioconjchem.8b00124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleotide surveillance enzymes play important roles in human health, by monitoring damaged monomers in the nucleotide pool and deactivating them before they are incorporated into chromosomal DNA or disrupt nucleotide metabolism. In particular, deamination of cytosine, leading to uracil in DNA and in the nucleotide pool, can be deleterious, causing DNA damage. The enzyme deoxyuridine triphosphatase (dUTPase) is currently under study as a therapeutic and prognostic target for cancer. Measuring the activity of this enzyme is important both in basic research and in clinical applications involving this pathway, but current methods are nonselective, detecting pyrophosphate, which is produced by many enzymes. Here we describe the design and synthesis of a dUTPase enzyme-specific chimeric dinucleotide (DUAL) that replaces the pyrophosphate leaving group of the native substrate with ATP, enabling sensitive detection via luciferase luminescence signaling. The DUAL probe functions sensitively and selectively to quantify enzyme activities in vitro and in cell lysates. We further report the first measurements of dUTPase activities in eight different cell lines, which are found to vary by a factor of 7-fold. We expect that the new probe can be of considerable utility in research involving this clinically significant enzyme.
Collapse
Affiliation(s)
- Debin Ji
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Anna M Kietrys
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yujeong Lee
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Eric T Kool
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| |
Collapse
|
24
|
Saragani Y, Hizi A, Rahav G, Zaouch S, Bakhanashvili M. Cytoplasmic p53 contributes to the removal of uracils misincorporated by HIV-1 reverse transcriptase. Biochem Biophys Res Commun 2018; 497:804-810. [PMID: 29470985 DOI: 10.1016/j.bbrc.2018.02.159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 02/18/2018] [Indexed: 01/15/2023]
Abstract
HIV-1 reverse transcriptase (RT) in the cytoplasm of HIV-infected cells efficiently inserts the non-canonical dUTP into the proviral DNA, and extends the dU-terminated DNA. The misincorporation of dUTP leads to mutagenesis, and uracils can down-regulate viral gene expression. However, uracilation might also protect HIV DNA from auto-integration in the cytoplasm. Tumor suppressor p53 protein, exhibiting inherent 3'→5' exonuclease activity, provides a potential host-derived repair mechanism during HIV reverse transcription for the misincorporation of various wrong nucleotides, leading to both base-base mismatches and incorporated non-canonical ribonucleotides. Since the presence of proofreading activity is essential for DNA synthesis accuracy, we elucidated the potential involvement of cytoplasmic p53 in the U-editing activities during insertion of dUTP into DNA by recombinant HIV-1 RT (using isogenic p53-proficient and -deficient HCT116 cells). The biochemical data show that p53 in cytoplasm can participate through the intermolecular pathway in a dU-damage-associated repair mechanism by its ability to remove preformed 3'-terminal dUs, thus preventing further extension of 3' dU-terminated primer during DNA synthesis by HIV-1 RT. The specific depletion of p53 from cytoplasmic lysates of repair-proficient p53-harboring cells reduced this negative effect. Accordingly, the increased abundance of p53 in nutlin-treated cells correlates with enhanced error-correction functions, namely, removal of incorporated uracil. The data substantiate the significance of p53 as a potential proofreader for removal of non-canonical dUTP from HIV DNA, thus preventing the consequences of dUTP misincorporation in cell-type specific infectivity of HIV.
Collapse
Affiliation(s)
- Yossi Saragani
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel
| | - Amnon Hizi
- Dep. Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Galia Rahav
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel
| | - Sara Zaouch
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel
| | - Mary Bakhanashvili
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel.
| |
Collapse
|
25
|
Lawson JS, Salmons B, Glenn WK. Oncogenic Viruses and Breast Cancer: Mouse Mammary Tumor Virus (MMTV), Bovine Leukemia Virus (BLV), Human Papilloma Virus (HPV), and Epstein-Barr Virus (EBV). Front Oncol 2018; 8:1. [PMID: 29404275 PMCID: PMC5786831 DOI: 10.3389/fonc.2018.00001] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/03/2018] [Indexed: 12/18/2022] Open
Abstract
Background Although the risk factors for breast cancer are well established, namely female gender, early menarche and late menopause plus the protective influence of early pregnancy, the underlying causes of breast cancer remain unknown. The development of substantial recent evidence indicates that a handful of viruses may have a role in breast cancer. These viruses are mouse mammary tumor virus (MMTV), bovine leukemia virus (BLV), human papilloma viruses (HPVs), and Epstein–Barr virus (EBV-also known as human herpes virus type 4). Each of these viruses has documented oncogenic potential. The aim of this review is to inform the scientific and general community about this recent evidence. The evidence MMTV and human breast cancer—the evidence is detailed and comprehensive but cannot be regarded as conclusive. BLV and human breast cancer—the evidence is limited. However, in view of the emerging information about BLV in human breast cancer, it is prudent to encourage the elimination of BLV in cattle, particularly in the dairy industry. HPVs and breast cancer—the evidence is substantial but not conclusive. The availability of effective preventive vaccines is a major advantage and their use should be encouraged. EBV and breast cancer—the evidence is also substantial but not conclusive. Currently, there are no practical means of either prevention or treatment. Although there is evidence of genetic predisposition, and cancer in general is a culmination of events, there is no evidence that inherited genetic traits are causal. Conclusion The influence of oncogenic viruses is currently the major plausible hypothesis for a direct cause of human breast cancer.
Collapse
Affiliation(s)
- James S Lawson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | | | - Wendy K Glenn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
26
|
Benedek A, Pölöskei I, Ozohanics O, Vékey K, Vértessy BG. The Stl repressor from Staphylococcus aureus is an efficient inhibitor of the eukaryotic fruitfly dUTPase. FEBS Open Bio 2017; 8:158-167. [PMID: 29435406 PMCID: PMC5794464 DOI: 10.1002/2211-5463.12302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/25/2017] [Accepted: 06/30/2017] [Indexed: 11/17/2022] Open
Abstract
DNA metabolism and repair is vital for the maintenance of genome integrity. Specific proteinaceous inhibitors of key factors in this process have high potential for deciphering pathways of DNA metabolism and repair. The dUTPase enzyme family is responsible for guarding against erroneous uracil incorporation into DNA. Here, we investigate whether the staphylococcal Stl repressor may interact with not only bacterial but also eukaryotic dUTPase. We provide experimental evidence for the formation of a strong complex between Stl and Drosophila melanogasterdUTPase. We also find that dUTPase activity is strongly diminished in this complex. Our results suggest that the dUTPase protein sequences involved in binding to Stl are at least partially conserved through evolution from bacteria to eukaryotes.
Collapse
Affiliation(s)
- András Benedek
- Institute of Enzymology Research Centre for Natural Sciences Hungarian Academy of Sciences Budapest Hungary.,Department of Applied Biotechnology Budapest University of Technology and Economics Hungary
| | - István Pölöskei
- Department of Applied Biotechnology Budapest University of Technology and Economics Hungary
| | - Olivér Ozohanics
- Institute of Organic Chemistry Research Centre for Natural Sciences Hungarian Academy of Sciences Budapest Hungary
| | - Károly Vékey
- Institute of Organic Chemistry Research Centre for Natural Sciences Hungarian Academy of Sciences Budapest Hungary
| | - Beáta G Vértessy
- Institute of Enzymology Research Centre for Natural Sciences Hungarian Academy of Sciences Budapest Hungary.,Department of Applied Biotechnology Budapest University of Technology and Economics Hungary
| |
Collapse
|
27
|
Sinha A, Johnson WE. Retroviruses of the RDR superinfection interference group: ancient origins and broad host distribution of a promiscuous Env gene. Curr Opin Virol 2017; 25:105-112. [PMID: 28837888 DOI: 10.1016/j.coviro.2017.07.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/08/2017] [Accepted: 07/23/2017] [Indexed: 12/24/2022]
Abstract
Due to recombination, different regions of a retrovirus genome can have distinct phylogenetic histories. The RD114-and-D-type-retrovirus (RDR) interference group provides an extreme example: the RDR group comprises a variety of taxonomically distinct retroviruses, isolated from diverse mammalian and avian hosts, that share a homologous env gene and use the same cell-surface entry receptor. RDR env homologs are also found among ancient endogenous retrovirus (ERV) sequences, including the syncytin genes of humans and rabbits, indicating that RDR Env glycoproteins have likely mediated endogenization on multiple occasions in diverse vertebrate lineages. The distribution of RDR env among exogenous and endogenous retroviruses indicates that it has been swapped between viruses many times, and that it likely facilitated multiple cross-species transmission events spanning millions of years of vertebrate evolution.
Collapse
Affiliation(s)
- Anindita Sinha
- Biology Department, Boston College, 355 Higgins Hall, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA
| | - Welkin E Johnson
- Biology Department, Boston College, 355 Higgins Hall, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA.
| |
Collapse
|
28
|
Rodriguez F, Kenefick AW, Arkhipova IR. LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types. Viruses 2017; 9:v9040078. [PMID: 28398238 PMCID: PMC5408684 DOI: 10.3390/v9040078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/16/2022] Open
Abstract
Rotifers of the class Bdelloidea, microscopic freshwater invertebrates, possess a highlydiversified repertoire of transposon families, which, however, occupy less than 4% of genomic DNA in the sequenced representative Adineta vaga. We performed a comprehensive analysis of A. vaga retroelements, and found that bdelloid long terminal repeat (LTR)retrotransposons, in addition to conserved open reading frame (ORF) 1 and ORF2 corresponding to gag and pol genes, code for an unusually high variety of ORF3 sequences. Retrovirus-like LTR families in A. vaga belong to four major lineages, three of which are rotiferspecific and encode a dUTPase domain. However only one lineage contains a canonical envlike fusion glycoprotein acquired from paramyxoviruses (non-segmented negative-strand RNA viruses), although smaller ORFs with transmembrane domains may perform similar roles. A different ORF3 type encodes a GDSL esterase/lipase, which was previously identified as ORF1 in several clades of non-LTR retrotransposons, and implicated in membrane targeting. Yet another ORF3 type appears in unrelated LTR-retrotransposon lineages, and displays strong homology to DEDDy-type exonucleases involved in 3'-end processing of RNA and single-stranded DNA. Unexpectedly, each of the enzymatic ORF3s is also associated with different subsets of Penelope-like Athena retroelement families. The unusual association of the same ORF types with retroelements from different classes reflects their modular structure with a high degree of flexibility, and points to gene sharing between different groups of retroelements.
Collapse
Affiliation(s)
- Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
| | - Aubrey W Kenefick
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
- Present address: UC Davis Genome Center-GBSF, University of California, Davis, CA 95616, USA.
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
| |
Collapse
|
29
|
Podolny Y, Herzig E, Hizi A. Insights into the molecular and biological features of the dUTPase-related gene of bovine immunodeficiency virus. Virology 2017; 506:55-63. [PMID: 28342388 DOI: 10.1016/j.virol.2017.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/06/2017] [Accepted: 03/16/2017] [Indexed: 01/20/2023]
Abstract
This study was stimulated by our previous research of the dUTPase-related protein from bovine immunodeficiency virus (BIV) (Voronin et al., 2014). Despite the lack of detectable enzymatic BIV dUTPase activity (both of the recombinant protein and in virions), mutating the dUTPase gene was deleterious to viral production. However, cDNA synthesis and integration were apparently unaffected. Consequently, we have studied here two important issues. First, we showed that in cDNA produced by the dUTPase-mutated virions, the incidence of mutations was not higher than that found in wild-type BIV-infected cells. Second, single mutations, introduced in preserved dUTPase residues Asp48 and Asn57 (in the putative dUTPase active site or close to it), have led to abortive BIV infections (except for the conservative Asp48Glu mutation). Therefore, we postulate that the BIV dUTPase-related protein has a critical role in retroviral replication at steps that take place after viral cDNA synthesis and integration.
Collapse
Affiliation(s)
- Yulia Podolny
- From the Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Eytan Herzig
- From the Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Amnon Hizi
- From the Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| |
Collapse
|
30
|
Skliros D, Kalatzis PG, Katharios P, Flemetakis E. Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell. Front Microbiol 2016; 7:1807. [PMID: 27895630 PMCID: PMC5107563 DOI: 10.3389/fmicb.2016.01807] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/27/2016] [Indexed: 01/21/2023] Open
Abstract
Sequencing and annotation was performed for two large double stranded DNA bacteriophages, φGrn1 and φSt2 of the Myoviridae family, considered to be of great interest for phage therapy against Vibrios in aquaculture live feeds. In addition, phage–host metabolic interactions and exploitation was studied by transcript profiling of selected viral and host genes. Comparative genomic analysis with other large Vibrio phages was also performed to establish the presence and location of homing endonucleases highlighting distinct features for both phages. Phylogenetic analysis revealed that they belong to the “schizoT4like” clade. Although many reports of newly sequenced viruses have provided a large set of information, basic research related to the shift of the bacterial metabolism during infection remains stagnant. The function of many viral protein products in the process of infection is still unknown. Genome annotation identified the presence of several viral open reading frames (ORFs) participating in metabolism, including a Sir2/cobB (sirtuin) protein and a number of genes involved in auxiliary NAD+ and nucleotide biosynthesis, necessary for phage DNA replication. Key genes were subsequently selected for detail study of their expression levels during infection. This work suggests a complex metabolic interaction and exploitation of the host metabolic pathways and biochemical processes, including a possible post-translational protein modification, by the virus during infection.
Collapse
Affiliation(s)
- Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens Athens, Greece
| | - Panos G Kalatzis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HeraklionCrete, Greece; Marine Biological Section, University of CopenhagenHelsingør, Denmark
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion Crete, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens Athens, Greece
| |
Collapse
|
31
|
Nagy GN, Suardíaz R, Lopata A, Ozohanics O, Vékey K, Brooks BR, Leveles I, Tóth J, Vértessy BG, Rosta E. Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases. J Am Chem Soc 2016; 138:15035-15045. [PMID: 27740761 DOI: 10.1021/jacs.6b09012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arginine finger is a highly conserved and essential residue in many GTPase and AAA+ ATPase enzymes that completes the active site from a distinct protomer, forming contacts with the γ-phosphate of the nucleotide. To date, no pyrophosphatase has been identified that employs an arginine finger fulfilling all of the above properties; all essential arginine fingers are used to catalyze the cleavage of the γ-phosphate. Here, we identify and unveil the role of a conserved arginine residue in trimeric dUTPases that meets all the criteria established for arginine fingers. We found that the conserved arginine adjacent to the P-loop-like motif enables structural organization of the active site for efficient catalysis via its nucleotide coordination, while its direct electrostatic role in transition state stabilization is secondary. An exhaustive structure-based comparison of analogous, conserved arginines from nucleotide hydrolases and transferases revealed a consensus amino acid location and orientation for contacting the γ-phosphate of the substrate nucleotide. Despite the structurally equivalent position, functional differences between arginine fingers of dUTPases and NTPases are explained on the basis of the unique chemistry performed by the pyrophosphatase dUTPases.
Collapse
Affiliation(s)
- Gergely N Nagy
- Department of Biotechnology and Food Sciences, Budapest University of Technology and Economics , Budapest 1111, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Reynier Suardíaz
- Department of Chemistry, King's College London , London SE1 1DB, United Kingdom
| | - Anna Lopata
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Olivér Ozohanics
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Károly Vékey
- Core Technologies Centre, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , Rockville, Maryland 10892-9314, United States
| | - Ibolya Leveles
- Department of Biotechnology and Food Sciences, Budapest University of Technology and Economics , Budapest 1111, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Beata G Vértessy
- Department of Biotechnology and Food Sciences, Budapest University of Technology and Economics , Budapest 1111, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Edina Rosta
- Department of Chemistry, King's College London , London SE1 1DB, United Kingdom
| |
Collapse
|
32
|
Genome-Wide Screening of Retroviral Envelope Genes in the Nine-Banded Armadillo (Dasypus novemcinctus, Xenarthra) Reveals an Unfixed Chimeric Endogenous Betaretrovirus Using the ASCT2 Receptor. J Virol 2016; 90:8132-49. [PMID: 27384664 DOI: 10.1128/jvi.00483-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/24/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Retroviruses enter host cells through the interaction of their envelope (Env) protein with a cell surface receptor, which triggers the fusion of viral and cellular membranes. The sodium-dependent neutral amino acid transporter ASCT2 is the common receptor of the large RD114 retrovirus interference group, whose members display frequent env recombination events. Germ line retrovirus infections have led to numerous inherited endogenous retroviruses (ERVs) in vertebrate genomes, which provide useful insights into the coevolutionary history of retroviruses and their hosts. Rare ERV-derived genes display conserved viral functions, as illustrated by the fusogenic syncytin env genes involved in placentation. Here, we searched for functional env genes in the nine-banded armadillo (Dasypus novemcinctus) genome and identified dasy-env1.1, which clusters with RD114 interference group env genes and with two syncytin genes sharing ASCT2 receptor usage. Using ex vivo pseudotyping and cell-cell fusion assays, we demonstrated that the Dasy-Env1.1 protein is fusogenic and can use both human and armadillo ASCT2s as receptors. This gammaretroviral env gene belongs to a provirus with betaretrovirus-like features, suggesting acquisition through recombination. Provirus insertion was found in several Dasypus species, where it has not reached fixation, whereas related family members integrated before diversification of the genus Dasypus >12 million years ago (Mya). This newly described ERV lineage is potentially useful as a population genetic marker. Our results extend the usage of ASCT2 as a retrovirus receptor to the mammalian clade Xenarthra and suggest that the acquisition of an ASCT2-interacting env gene is a major selective force driving the emergence of numerous chimeric viruses in vertebrates. IMPORTANCE Retroviral infection is initiated by the binding of the viral envelope glycoprotein to a host cell receptor(s), triggering membrane fusion. Ancient germ line infections have generated numerous endogenous retroviruses (ERVs) in nearly all vertebrate genomes. Here, we report a previously uncharacterized ERV lineage from the genome of a xenarthran species, the nine-banded armadillo (Dasypus novemcinctus). It entered the Dasypus genus >12 Mya, with one element being inserted more recently in some Dasypus species, where it could serve as a useful marker for population genetics. This element exhibits an env gene, acquired by recombination events, with conserved viral fusogenic properties through binding to ASCT2, a receptor used by a wide range of recombinant retroviruses infecting other vertebrate orders. This specifies the ASCT2 transporter as a successful receptor for ERV endogenization and suggests that ASCT2-binding env acquisition events have favored the emergence of numerous chimeric viruses in a wide range of species.
Collapse
|