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Parthasarathy S, Saenjamsai P, Hao H, Ferkul A, Pfannenstiel JJ, Suder EL, Bejan DS, Chen Y, Schwarting N, Aikawa M, Muhlberger E, Orozco RC, Sullivan CS, Cohen MS, Davido DJ, Hume AJ, Fehr AR. PARP14 is pro- and anti-viral host factor that promotes IFN production and affects the replication of multiple viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591186. [PMID: 38712082 PMCID: PMC11071520 DOI: 10.1101/2024.04.26.591186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
PARP14 is a 203 kDa multi-domain protein that is primarily known as an ADP-ribosyltransferase, and is involved in a variety of cellular functions including DNA damage, microglial activation, inflammation, and cancer progression. In addition, PARP14 is upregulated by interferon (IFN), indicating a role in the antiviral response. Furthermore, PARP14 has evolved under positive selection, again indicating that it is involved in host-pathogen conflict. We found that PARP14 is required for increased IFN-I production in response to coronavirus infection lacking ADP-ribosylhydrolase (ARH) activity and poly(I:C), however, whether it has direct antiviral function remains unclear. Here we demonstrate that the catalytic activity of PARP14 enhances IFN-I and IFN-III responses and restricts ARH-deficient murine hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. To determine if PARP14's antiviral functions extended beyond CoVs, we tested the ability of herpes simplex virus 1 (HSV-1) and several negative-sense RNA viruses, including vesicular stomatitis virus (VSV), Ebola virus (EBOV), and Nipah virus (NiV), to infect A549 PARP14 knockout (KO) cells. HSV-1 had increased replication in PARP14 KO cells, indicating that PARP14 restricts HSV-1 replication. In contrast, PARP14 was critical for the efficient infection of VSV, EBOV, and NiV, with EBOV infectivity at less than 1% of WT cells. A PARP14 active site inhibitor had no impact on HSV-1 or EBOV infection, indicating that its effect on these viruses was independent of its catalytic activity. These data demonstrate that PARP14 promotes IFN production and has both pro- and anti-viral functions targeting multiple viruses.
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Affiliation(s)
| | - Pradtahna Saenjamsai
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Hongping Hao
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Anna Ferkul
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | | | - Ellen L. Suder
- Department of Microbiology, Boston University School of Medicine, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, MA, 02118, USA
| | - Daniel S. Bejan
- Department of Chemical Physiology and Biochemistry, Oregon Health Sciences University, Portland, OR, 97239, USA
| | - Yating Chen
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Nancy Schwarting
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Masanori Aikawa
- Center for Excellence in Vascular Biology (P.K.J., M.A., E.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Center for Interdisciplinary Cardiovascular Sciences (M.A., E.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Channing Division of Network Medicine (M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Elke Muhlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, MA, 02118, USA
| | - Robin C. Orozco
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | | | - Michael S. Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health Sciences University, Portland, OR, 97239, USA
| | - David J. Davido
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Adam J. Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, MA, 02118, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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Zhu Z, Weng S, Zheng F, Zhao Q, Xu Y, Wu J. Identification of Poly(ADP-ribose) Polymerase 9 (PARP9) as a Potent Suppressor for Mycobacterium tuberculosis Infection. PHENOMICS (CHAM, SWITZERLAND) 2024; 4:158-170. [PMID: 38884060 PMCID: PMC11169154 DOI: 10.1007/s43657-023-00112-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/18/2024]
Abstract
ADP-ribosylation is a reversible and dynamic post-translational modification mediated by ADP-ribosyltransferases (ARTs). Poly(ADP-ribose) polymerases (PARPs) are an important family of human ARTs. ADP-ribosylation and PARPs have crucial functions in host-pathogen interaction, especially in viral infections. However, the functions and potential molecular mechanisms of ADP-ribosylation and PARPs in Mycobacterium infection remain unknown. In this study, bioinformatics analysis revealed significantly changed expression levels of several PARPs in tuberculosis patients compared to healthy individuals. Moreover, the expression levels of these PARPs returned to normal following tuberculosis treatment. Then, the changes in the expression levels of PARPs during Mycobacterium infection were validated in Tohoku Hospital Pediatrics-1 (THP1)-induced differentiated macrophages infected with Mycobacterium model strains bacillus Calmette-Guérin (BCG) and in human lung adenocarcinoma A549 cells infected with Mycobacterium smegmatis (Ms), respectively. The mRNA levels of PARP9, PARP10, PARP12, and PARP14 were most significantly increased during infection, with corresponding increases in protein levels, indicating the possible biological functions of these PARPs during Mycobacterium infection. In addition, the biological function of host PARP9 in Mycobacterium infection was further studied. PARP9 deficiency significantly increased the infection efficiency and intracellular proliferation ability of Ms, which was reversed by the reconstruction of PARP9. Collectively, this study updates the understanding of changes in PARP expression during Mycobacterium infection and provides evidence supporting PARP9 as a potent suppressor for Mycobacterium infection. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00112-2.
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Affiliation(s)
- Zhenyu Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Shufeng Weng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Fen Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Qi Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Ying Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Jiaxue Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
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Sobotka AA, Tempera I. PARP1 as an Epigenetic Modulator: Implications for the Regulation of Host-Viral Dynamics. Pathogens 2024; 13:131. [PMID: 38392869 PMCID: PMC10891851 DOI: 10.3390/pathogens13020131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The principal understanding of the Poly(ADP-ribose) polymerase (PARP) regulation of genomes has been focused on its role in DNA repair; however, in the past few years, an additional role for PARPs and PARylation has emerged in regulating viral-host interactions. In particular, in the context of DNA virus infection, PARP1-mediated mechanisms of gene regulations, such as the involvement with cellular protein complexes responsible for the folding of the genome into the nucleus, the formation of chromatin loops connecting distant regulatory genomic regions, and other methods of transcriptional regulation, provide additional ways through which PARPs can modulate the function of both the host and the viral genomes during viral infection. In addition, potential viral amplification of the activity of PARPs on the host genome can contribute to the pathogenic effect of viral infection, such as viral-driven oncogenesis, opening the possibility that PARP inhibition may represent a potential therapeutic approach to target viral infection. This review will focus on the role of PARPs, particularly PARP1, in regulating the infection of DNA viruses.
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Affiliation(s)
- Asher A. Sobotka
- Wistar Institute, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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4
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Maestri D, Napoletani G, Kossenkov A, Preston-Alp S, Caruso LB, Tempera I. The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC. Nucleic Acids Res 2023; 51:12092-12110. [PMID: 37889078 PMCID: PMC10711448 DOI: 10.1093/nar/gkad936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Epstein-Barr virus (EBV) establishes lifelong asymptomatic infection by replication of its chromatinized episomes with the host genome. EBV exhibits different latency-associated transcriptional repertoires, each with distinct three-dimensional structures. CTCF, Cohesin and PARP1 are involved in maintaining viral latency and establishing episome architecture. Epstein-Barr virus-associated gastric cancer (EBVaGC) represents 1.3-30.9% of all gastric cancers globally. EBV-positive gastric cancers exhibit an intermediate viral transcription profile known as 'Latency II', expressing specific viral genes and noncoding RNAs. In this study, we investigated the impact of PARP1 inhibition on CTCF/Cohesin binding in Type II latency. We observed destabilization of the binding of both factors, leading to a disrupted three-dimensional architecture of the episomes and an altered viral gene expression. Despite sharing the same CTCF binding profile, Type I, II and III latencies exhibit different 3D structures that correlate with variations in viral gene expression. Additionally, our analysis of H3K27ac-enriched interactions revealed differences between Type II latency episomes and a link to cellular transformation through docking of the EBV genome at specific sites of the Human genome, thus promoting oncogene expression. Overall, this work provides insights into the role of PARP1 in maintaining active latency and novel mechanisms of EBV-induced cellular transformation.
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Affiliation(s)
- Davide Maestri
- The Wistar Institute, Philadelphia, PA 19104, USA
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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Napoletani G, Soldan SS, Kannan T, Preston-Alp S, Vogel P, Maestri D, Caruso LB, Kossenkov A, Sobotka A, Lieberman PM, Tempera I. PARP1 Inhibition Halts EBV+ Lymphoma Progression by Disrupting the EBNA2/MYC Axis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547847. [PMID: 37461649 PMCID: PMC10350008 DOI: 10.1101/2023.07.05.547847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
PARP1 has been shown to regulate EBV latency. However, the therapeutic effect of PARP1 inhibitors on EBV+ lymphomagenesis has not yet been explored. Here, we show that PARPi BMN-673 has a potent anti-tumor effect on EBV-driven LCL in a mouse xenograft model. We found that PARP1 inhibition induces a dramatic transcriptional reprogramming of LCLs driven largely by the reduction of the MYC oncogene expression and dysregulation of MYC targets, both in vivo and in vitro. PARP1 inhibition also reduced the expression of viral oncoprotein EBNA2, which we previously demonstrated depends on PARP1 for activation of MYC. Further, we show that PARP1 inhibition blocks the chromatin association of MYC, EBNA2, and tumor suppressor p53. Overall, our study strengthens the central role of PARP1 in EBV malignant transformation and identifies the EBNA2/MYC pathway as a target of PARP1 inhibitors and its utility for the treatment of EBNA2-driven EBV-associated cancers.
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Affiliation(s)
| | | | | | | | - Peter Vogel
- Department of Comparative Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
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ADP-Ribosylation in Antiviral Innate Immune Response. Pathogens 2023; 12:pathogens12020303. [PMID: 36839575 PMCID: PMC9964302 DOI: 10.3390/pathogens12020303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Adenosine diphosphate (ADP)-ribosylation is a reversible post-translational modification catalyzed by ADP-ribosyltransferases (ARTs). ARTs transfer one or more ADP-ribose from nicotinamide adenine dinucleotide (NAD+) to the target substrate and release the nicotinamide (Nam). Accordingly, it comes in two forms: mono-ADP-ribosylation (MARylation) and poly-ADP-ribosylation (PARylation). ADP-ribosylation plays important roles in many biological processes, such as DNA damage repair, gene regulation, and energy metabolism. Emerging evidence demonstrates that ADP-ribosylation is implicated in host antiviral immune activity. Here, we summarize and discuss ADP-ribosylation modifications that occur on both host and viral proteins and their roles in host antiviral response.
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Epstein-Barr Virus Viral Processivity Factor EA-D Facilitates Virus Lytic Replication by Inducing Poly(ADP-Ribose) Polymerase 1 Degradation. J Virol 2022; 96:e0037122. [PMID: 36286483 PMCID: PMC9645209 DOI: 10.1128/jvi.00371-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PARP1 acts as a negative regulator of lytic replication in EBV. To successfully enter the reactivation cycle, EBV has developed multiple strategies to counteract the host’s repressive mechanisms.
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8
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Human Cytomegalovirus Utilizes Multiple Viral Proteins to Regulate the Basement Membrane Protein Nidogen 1. J Virol 2022; 96:e0133622. [PMID: 36218358 PMCID: PMC9599421 DOI: 10.1128/jvi.01336-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nidogen 1 (NID1) is an important basement membrane protein secreted by many cell types. We previously found that human cytomegalovirus (HCMV) infection rapidly induced chromosome 1 breaks and that the basement membrane protein NID1, encoded near the 1q42 break site, was downregulated. We have now determined that the specific breaks in and of themselves did not regulate NID1, rather interactions between several viral proteins and the cellular machinery and DNA regulated NID1. We screened a battery of viral proteins present by 24 hours postinfection (hpi) when regulation was induced, including components of the incoming virion and immediate early (IE) proteins. Adenovirus (Ad) delivery of the tegument proteins pp71 and UL35 and the IE protein IE1 influenced steady-state (ss) NID1 levels. IE1's mechanism of regulation was unclear, while UL35 influenced proteasomal regulation of ss NID1. Real-time quantitative PCR (RT-qPCR) experiments determined that pp71 downregulated NID1 transcription. Surprisingly, WF28-71, a fibroblast clone that expresses minute quantities of pp71, suppressed NID1 transcription as efficiently as HCMV infection, resulting in the near absence of ss NID1. Sequence analysis of the region surrounding the 1q42 break sites and NID1 promoter revealed CCCTC-binding factor (CTCF) binding sites. Chromatin immunoprecipitation experiments determined that pp71 and CTCF were both bound at these two sites during HCMV infection. Expression of pp71 alone replicated this binding. Binding was observed as early as 1 hpi, and colocalization of pp71 and CTCF occurred as quickly as 15 min postinfection (pi) in infected cell nuclei. In fibroblasts where CTCF was knocked down, Adpp71 infection did not decrease NID1 transcription nor ss NID1 protein levels. Our results emphasize another aspect of pp71 activity during infection and identify this viral protein as a key contributor to HCMV's efforts to eliminate NID1. Further, we show, for the first time, direct interaction between pp71 and the cellular genome. IMPORTANCE We have found that human cytomegalovirus (HCMV) utilizes multiple viral proteins in multiple pathways to regulate a ubiquitous cellular basement membrane protein, nidogen-1 (NID1). The extent of the resources and the redundant methods that the virus has evolved to affect this control strongly suggest that its removal provides a life cycle advantage to HCMV. Our discoveries that one of the proteins that HCMV uses to control NID1, pp71, binds directly to the cellular DNA and can exert control when present in vanishingly small quantities may have broad implications in a wide range of infection scenarios. Dysregulation of NID1 in an immunocompetent host is not known to manifest complications during infection; however, in the naive immune system of a developing fetus, disruption of this developmentally critical protein could initiate catastrophic HCMV-induced birth defects.
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Zhang W, Guo J, Chen Q. Role of PARP-1 in Human Cytomegalovirus Infection and Functional Partners Encoded by This Virus. Viruses 2022; 14:2049. [PMID: 36146855 PMCID: PMC9501325 DOI: 10.3390/v14092049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous pathogen that threats the majority of the world's population. Poly (ADP-ribose) polymerase 1 (PARP-1) and protein poly (ADP-ribosyl)ation (PARylation) regulates manifold cellular functions. The role of PARP-1 and protein PARylation in HCMV infection is still unknown. In the present study, we found that the pharmacological and genetic inhibition of PARP-1 attenuated HCMV replication, and PARG inhibition favors HCMV replication. PARP-1 and its enzymatic activity were required for efficient HCMV replication. HCMV infection triggered the activation of PARP-1 and induced the translocation of PARP-1 from nucleus to cytoplasm. PARG was upregulated in HCMV-infected cells and this upregulation was independent of viral DNA replication. Moreover, we found that HCMV UL76, a true late protein of HCMV, inhibited the overactivation of PARP-1 through direct binding to the BRCT domain of PARP-1. In addition, UL76 also physically interacted with poly (ADP-ribose) (PAR) polymers through the RG/RGG motifs of UL76 which mediates its recruitment to DNA damage sites. Finally, PARP-1 inhibition or depletion potentiated HCMV-triggered induction of type I interferons. Our results uncovered the critical role of PARP-1 and PARP-1-mediated protein PARylation in HCMV replication.
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Affiliation(s)
| | | | - Qiang Chen
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan 430071, China
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10
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Herbert A, Fedorov A, Poptsova M. Mono a Mano: ZBP1’s Love–Hate Relationship with the Kissing Virus. Int J Mol Sci 2022; 23:ijms23063079. [PMID: 35328502 PMCID: PMC8955656 DOI: 10.3390/ijms23063079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/24/2022] [Accepted: 03/09/2022] [Indexed: 12/27/2022] Open
Abstract
Z-DNA binding protein (ZBP1) very much represents the nuclear option. By initiating inflammatory cell death (ICD), ZBP1 activates host defenses to destroy infectious threats. ZBP1 is also able to induce noninflammatory regulated cell death via apoptosis (RCD). ZBP1 senses the presence of left-handed Z-DNA and Z-RNA (ZNA), including that formed by expression of endogenous retroelements. Viruses such as the Epstein–Barr “kissing virus” inhibit ICD, RCD and other cell death signaling pathways to produce persistent infection. EBV undergoes lytic replication in plasma cells, which maintain detectable levels of basal ZBP1 expression, leading us to suggest a new role for ZBP1 in maintaining EBV latency, one of benefit for both host and virus. We provide an overview of the pathways that are involved in establishing latent infection, including those regulated by MYC and NF-κB. We describe and provide a synthesis of the evidence supporting a role for ZNA in these pathways, highlighting the positive and negative selection of ZNA forming sequences in the EBV genome that underscores the coadaptation of host and virus. Instead of a fight to the death, a state of détente now exists where persistent infection by the virus is tolerated by the host, while disease outcomes such as death, autoimmunity and cancer are minimized. Based on these new insights, we propose actionable therapeutic approaches to unhost EBV.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia; (A.F.); (M.P.)
- Correspondence:
| | - Aleksandr Fedorov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia; (A.F.); (M.P.)
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia; (A.F.); (M.P.)
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11
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Morgan SM, Tanizawa H, Caruso LB, Hulse M, Kossenkov A, Madzo J, Keith K, Tan Y, Boyle S, Lieberman PM, Tempera I. The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity. Nat Commun 2022; 13:187. [PMID: 35039491 PMCID: PMC8764100 DOI: 10.1038/s41467-021-27894-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) persists in human B-cells by maintaining its chromatinized episomes within the nucleus. We have previously shown that cellular factor Poly [ADP-ribose] polymerase 1 (PARP1) binds the EBV genome, stabilizes CTCF binding at specific loci, and that PARP1 enzymatic activity correlates with maintaining a transcriptionally active latency program. To better understand PARP1's role in regulating EBV latency, here we functionally characterize the effect of PARP enzymatic inhibition on episomal structure through in situ HiC mapping, generating a complete 3D structure of the EBV genome. We also map intragenomic contact changes after PARP inhibition to global binding of chromatin looping factors CTCF and cohesin across the EBV genome. We find that PARP inhibition leads to fewer total unique intragenomic interactions within the EBV episome, yet new chromatin loops distinct from the untreated episome are also formed. This study also illustrates that PARP inhibition alters gene expression at the regions where chromatin looping is most effected. We observe that PARP1 inhibition does not alter cohesin binding sites but does increase its frequency of binding at those sites. Taken together, these findings demonstrate that PARP has an essential role in regulating global EBV chromatin structure and latent gene expression.
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Affiliation(s)
- Sarah M Morgan
- The Wistar Institute, Philadelphia, PA, USA
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | | | | | - Michael Hulse
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | | | - Jozef Madzo
- The Coriell Institute for Medical Research, Camden, NJ, USA
| | - Kelsey Keith
- The Coriell Institute for Medical Research, Camden, NJ, USA
| | - Yinfei Tan
- Fox Chase Cancer Center, Philadelphia, PA, USA
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12
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Chung WC, Song MJ. Virus–Host Interplay Between Poly (ADP-Ribose) Polymerase 1 and Oncogenic Gammaherpesviruses. Front Microbiol 2022; 12:811671. [PMID: 35095818 PMCID: PMC8795711 DOI: 10.3389/fmicb.2021.811671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
The gammaherpesviruses, include the Epstein–Barr virus, Kaposi’s sarcoma-associated herpesvirus, and murine gammaherpesvirus 68. They establish latent infection in the B lymphocytes and are associated with various lymphoproliferative diseases and tumors. The poly (ADP-ribose) polymerase-1 (PARP1), also called ADP-ribosyltransferase diphtheria-toxin-like 1 (ARTD1) is a nuclear enzyme that catalyzes the transfer of the ADP-ribose moiety to its target proteins and participates in important cellular activities, such as the DNA-damage response, cell death, transcription, chromatin remodeling, and inflammation. In gammaherpesvirus infection, PARP1 acts as a key regulator of the virus life cycle: lytic replication and latency. These viruses also develop various strategies to regulate PARP1, facilitating their replication. This review summarizes the roles of PARP1 in the viral life cycle as well as the viral modulation of host PARP1 activity and discusses the implications. Understanding the interactions between the PARP1 and oncogenic gammaherpesviruses may lead to the identification of effective therapeutic targets for the associated diseases.
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13
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NAD+-consuming enzymes in immune defense against viral infection. Biochem J 2021; 478:4071-4092. [PMID: 34871367 PMCID: PMC8718269 DOI: 10.1042/bcj20210181] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic reminds us that in spite of the scientific progress in the past century, there is a lack of general antiviral strategies. In analogy to broad-spectrum antibiotics as antibacterial agents, developing broad spectrum antiviral agents would buy us time for the development of vaccines and treatments for future viral infections. In addition to targeting viral factors, a possible strategy is to understand host immune defense mechanisms and develop methods to boost the antiviral immune response. Here we summarize the role of NAD+-consuming enzymes in the immune defense against viral infections, with the hope that a better understanding of this process could help to develop better antiviral therapeutics targeting these enzymes. These NAD+-consuming enzymes include PARPs, sirtuins, CD38, and SARM1. Among these, the antiviral function of PARPs is particularly important and will be a focus of this review. Interestingly, NAD+ biosynthetic enzymes are also implicated in immune responses. In addition, many viruses, including SARS-CoV-2 contain a macrodomain-containing protein (NSP3 in SARS-CoV-2), which serves to counteract the antiviral function of host PARPs. Therefore, NAD+ and NAD+-consuming enzymes play crucial roles in immune responses against viral infections and detailed mechanistic understandings in the future will likely facilitate the development of general antiviral strategies.
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14
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New Look of EBV LMP1 Signaling Landscape. Cancers (Basel) 2021; 13:cancers13215451. [PMID: 34771613 PMCID: PMC8582580 DOI: 10.3390/cancers13215451] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Epstein-Barr Virus (EBV) infection is associated with various lymphomas and carcinomas as well as other diseases in humans. The transmembrane protein LMP1 plays versatile roles in EBV life cycle and pathogenesis, by perturbing, reprograming, and regulating a large range of host cellular mechanisms and functions, which have been increasingly disclosed but not fully understood so far. We summarize recent research progress on LMP1 signaling, including the novel components LIMD1, p62, and LUBAC in LMP1 signalosome and LMP1 novel functions, such as its induction of p62-mediated selective autophagy, regulation of metabolism, induction of extracellular vehicles, and activation of NRF2-mediated antioxidative defense. A comprehensive understanding of LMP1 signal transduction and functions may allow us to leverage these LMP1-regulated cellular mechanisms for clinical purposes. Abstract The Epstein–Barr Virus (EBV) principal oncoprotein Latent Membrane Protein 1 (LMP1) is a member of the Tumor Necrosis Factor Receptor (TNFR) superfamily with constitutive activity. LMP1 shares many features with Pathogen Recognition Receptors (PRRs), including the use of TRAFs, adaptors, and kinase cascades, for signal transduction leading to the activation of NFκB, AP1, and Akt, as well as a subset of IRFs and likely the master antioxidative transcription factor NRF2, which we have gradually added to the list. In recent years, we have discovered the Linear UBiquitin Assembly Complex (LUBAC), the adaptor protein LIMD1, and the ubiquitin sensor and signaling hub p62, as novel components of LMP1 signalosome. Functionally, LMP1 is a pleiotropic factor that reprograms, balances, and perturbs a large spectrum of cellular mechanisms, including the ubiquitin machinery, metabolism, epigenetics, DNA damage response, extracellular vehicles, immune defenses, and telomere elongation, to promote oncogenic transformation, cell proliferation and survival, anchorage-independent cell growth, angiogenesis, and metastasis and invasion, as well as the development of the tumor microenvironment. We have recently shown that LMP1 induces p62-mediated selective autophagy in EBV latency, at least by contributing to the induction of p62 expression, and Reactive Oxygen Species (ROS) production. We have also been collecting evidence supporting the hypothesis that LMP1 activates the Keap1-NRF2 pathway, which serves as the key antioxidative defense mechanism. Last but not least, our preliminary data shows that LMP1 is associated with the deregulation of cGAS-STING DNA sensing pathway in EBV latency. A comprehensive understanding of the LMP1 signaling landscape is essential for identifying potential targets for the development of novel strategies towards targeted therapeutic applications.
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15
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Tan A, Doig CL. NAD + Degrading Enzymes, Evidence for Roles During Infection. Front Mol Biosci 2021; 8:697359. [PMID: 34485381 PMCID: PMC8415550 DOI: 10.3389/fmolb.2021.697359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
Declines in cellular nicotinamide adenine dinucleotide (NAD) contribute to metabolic dysfunction, increase susceptibility to disease, and occur as a result of pathogenic infection. The enzymatic cleavage of NAD+ transfers ADP-ribose (ADPr) to substrate proteins generating mono-ADP-ribose (MAR), poly-ADP-ribose (PAR) or O-acetyl-ADP-ribose (OAADPr). These important post-translational modifications have roles in both immune response activation and the advancement of infection. In particular, emergent data show viral infection stimulates activation of poly (ADP-ribose) polymerase (PARP) mediated NAD+ depletion and stimulates hydrolysis of existing ADP-ribosylation modifications. These studies are important for us to better understand the value of NAD+ maintenance upon the biology of infection. This review focuses specifically upon the NAD+ utilising enzymes, discusses existing knowledge surrounding their roles in infection, their NAD+ depletion capability and their influence within pathogenic infection.
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Affiliation(s)
- Arnold Tan
- Interdisciplinary Science and Technology Centre, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Craig L Doig
- Interdisciplinary Science and Technology Centre, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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16
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Ge Y, Tian T, Huang S, Wan F, Li J, Li S, Wang X, Yang H, Hong L, Wu N, Yuan E, Luo Y, Cheng L, Hu C, Lei Y, Shu H, Feng X, Jiang Z, Wu Y, Chi Y, Guo X, Cui L, Xiao L, Li Z, Yang C, Miao Z, Chen L, Li H, Zeng H, Zhao D, Zhu F, Shen X, Zeng J. An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. Signal Transduct Target Ther 2021; 6:165. [PMID: 33895786 PMCID: PMC8065335 DOI: 10.1038/s41392-021-00568-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/03/2021] [Accepted: 03/17/2021] [Indexed: 02/08/2023] Open
Abstract
The global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires an urgent need to find effective therapeutics for the treatment of coronavirus disease 2019 (COVID-19). In this study, we developed an integrative drug repositioning framework, which fully takes advantage of machine learning and statistical analysis approaches to systematically integrate and mine large-scale knowledge graph, literature and transcriptome data to discover the potential drug candidates against SARS-CoV-2. Our in silico screening followed by wet-lab validation indicated that a poly-ADP-ribose polymerase 1 (PARP1) inhibitor, CVL218, currently in Phase I clinical trial, may be repurposed to treat COVID-19. Our in vitro assays revealed that CVL218 can exhibit effective inhibitory activity against SARS-CoV-2 replication without obvious cytopathic effect. In addition, we showed that CVL218 can interact with the nucleocapsid (N) protein of SARS-CoV-2 and is able to suppress the LPS-induced production of several inflammatory cytokines that are highly relevant to the prevention of immunopathology induced by SARS-CoV-2 infection.
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Affiliation(s)
- Yiyue Ge
- grid.12527.330000 0001 0662 3178Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China ,grid.410734.5NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province China
| | - Tingzhong Tian
- grid.12527.330000 0001 0662 3178Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China ,grid.410734.5NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province China
| | - Suling Huang
- grid.9227.e0000000119573309Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Fangping Wan
- grid.12527.330000 0001 0662 3178Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Jingxin Li
- grid.410734.5NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province China
| | - Shuya Li
- grid.12527.330000 0001 0662 3178Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Xiaoting Wang
- grid.508210.eSilexon AI Technology Co., Ltd., Nanjing, Jiangsu Province China
| | - Hui Yang
- grid.508210.eSilexon AI Technology Co., Ltd., Nanjing, Jiangsu Province China
| | - Lixiang Hong
- grid.12527.330000 0001 0662 3178Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Nian Wu
- grid.12527.330000 0001 0662 3178Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Enming Yuan
- grid.12527.330000 0001 0662 3178Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Yunan Luo
- grid.35403.310000 0004 1936 9991Department of Computer Science, University of Illinois at Urbana-Champaign, Illinois, IL USA
| | - Lili Cheng
- grid.12527.330000 0001 0662 3178School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Chengliang Hu
- grid.12527.330000 0001 0662 3178School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yipin Lei
- grid.508210.eSilexon AI Technology Co., Ltd., Nanjing, Jiangsu Province China
| | - Hantao Shu
- grid.12527.330000 0001 0662 3178Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Xiaolong Feng
- grid.33199.310000 0004 0368 7223School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei Province China ,grid.33199.310000 0004 0368 7223Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province China
| | - Ziyuan Jiang
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, China
| | - Yunfu Wu
- Inner Mongolia Alashan League Organization Establishment Committee Office Electronic Support Center, Alashan, Inner Mongolia China
| | - Ying Chi
- grid.410734.5NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province China
| | - Xiling Guo
- grid.410734.5NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province China
| | - Lunbiao Cui
- grid.410734.5NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province China
| | - Liang Xiao
- grid.507918.2Convalife (Shanghai) Co., Ltd., Shanghai, China
| | - Zeng Li
- grid.507918.2Convalife (Shanghai) Co., Ltd., Shanghai, China
| | - Chunhao Yang
- grid.9227.e0000000119573309Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zehong Miao
- grid.9227.e0000000119573309Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ligong Chen
- grid.12527.330000 0001 0662 3178School of Pharmaceutical Sciences, Tsinghua University, Beijing, China ,grid.24696.3f0000 0004 0369 153XAdvanced Innovation Center for Human Brain Protection, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Haitao Li
- grid.12527.330000 0001 0662 3178Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Hainian Zeng
- grid.508210.eSilexon AI Technology Co., Ltd., Nanjing, Jiangsu Province China
| | - Dan Zhao
- grid.12527.330000 0001 0662 3178Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Fengcai Zhu
- grid.410734.5NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province China ,grid.89957.3a0000 0000 9255 8984Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu Province China
| | - Xiaokun Shen
- grid.507918.2Convalife (Shanghai) Co., Ltd., Shanghai, China
| | - Jianyang Zeng
- grid.12527.330000 0001 0662 3178Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
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17
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Ge Y, Tian T, Huang S, Wan F, Li J, Li S, Wang X, Yang H, Hong L, Wu N, Yuan E, Luo Y, Cheng L, Hu C, Lei Y, Shu H, Feng X, Jiang Z, Wu Y, Chi Y, Guo X, Cui L, Xiao L, Li Z, Yang C, Miao Z, Chen L, Li H, Zeng H, Zhao D, Zhu F, Shen X, Zeng J. An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. Signal Transduct Target Ther 2021; 6:165. [PMID: 33895786 DOI: 10.1101/2020.03.11.986836] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/03/2021] [Accepted: 03/17/2021] [Indexed: 05/21/2023] Open
Abstract
The global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires an urgent need to find effective therapeutics for the treatment of coronavirus disease 2019 (COVID-19). In this study, we developed an integrative drug repositioning framework, which fully takes advantage of machine learning and statistical analysis approaches to systematically integrate and mine large-scale knowledge graph, literature and transcriptome data to discover the potential drug candidates against SARS-CoV-2. Our in silico screening followed by wet-lab validation indicated that a poly-ADP-ribose polymerase 1 (PARP1) inhibitor, CVL218, currently in Phase I clinical trial, may be repurposed to treat COVID-19. Our in vitro assays revealed that CVL218 can exhibit effective inhibitory activity against SARS-CoV-2 replication without obvious cytopathic effect. In addition, we showed that CVL218 can interact with the nucleocapsid (N) protein of SARS-CoV-2 and is able to suppress the LPS-induced production of several inflammatory cytokines that are highly relevant to the prevention of immunopathology induced by SARS-CoV-2 infection.
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Affiliation(s)
- Yiyue Ge
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province, China
| | - Tingzhong Tian
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province, China
| | - Suling Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Fangping Wan
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Jingxin Li
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Xiaoting Wang
- Silexon AI Technology Co., Ltd., Nanjing, Jiangsu Province, China
| | - Hui Yang
- Silexon AI Technology Co., Ltd., Nanjing, Jiangsu Province, China
| | - Lixiang Hong
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Nian Wu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Enming Yuan
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Yunan Luo
- Department of Computer Science, University of Illinois at Urbana-Champaign, Illinois, IL, USA
| | - Lili Cheng
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Chengliang Hu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yipin Lei
- Silexon AI Technology Co., Ltd., Nanjing, Jiangsu Province, China
| | - Hantao Shu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Xiaolong Feng
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Ziyuan Jiang
- Department of Automation, Tsinghua University, Beijing, China
| | - Yunfu Wu
- Inner Mongolia Alashan League Organization Establishment Committee Office Electronic Support Center, Alashan, Inner Mongolia, China
| | - Ying Chi
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province, China
| | - Xiling Guo
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province, China
| | - Lunbiao Cui
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province, China
| | - Liang Xiao
- Convalife (Shanghai) Co., Ltd., Shanghai, China
| | - Zeng Li
- Convalife (Shanghai) Co., Ltd., Shanghai, China
| | - Chunhao Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zehong Miao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ligong Chen
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Advanced Innovation Center for Human Brain Protection, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Haitao Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Hainian Zeng
- Silexon AI Technology Co., Ltd., Nanjing, Jiangsu Province, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.
| | - Fengcai Zhu
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu Province, China.
- Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu Province, China.
| | - Xiaokun Shen
- Convalife (Shanghai) Co., Ltd., Shanghai, China.
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.
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18
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Rosado MM, Pioli C. ADP-ribosylation in evasion, promotion and exacerbation of immune responses. Immunology 2021; 164:15-30. [PMID: 33783820 DOI: 10.1111/imm.13332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
ADP-ribosylation is the addition of one or more (up to some hundreds) ADP-ribose moieties to acceptor proteins. This evolutionary ancient post-translational modification (PTM) is involved in fundamental processes including DNA repair, inflammation, cell death, differentiation and proliferation, among others. ADP-ribosylation is catalysed by two major families of enzymes: the cholera toxin-like ADP-ribosyltransferases (ARTCs) and the diphtheria toxin-like ADP-ribosyltransferases (ARTDs, also known as PARPs). ARTCs sense and use extracellular NAD, which may represent a danger signal, whereas ARTDs are present in the cell nucleus and/or cytoplasm. ARTCs mono-ADP-ribosylate their substrates, whereas ARTDs, according to the specific family member, are able to mono- or poly-ADP-ribosylate target proteins or are devoid of enzymatic activity. Both mono- and poly-ADP-ribosylation are dynamic processes, as specific hydrolases are able to remove single or polymeric ADP moieties. This dynamic equilibrium between addition and degradation provides plasticity for fast adaptation, a feature being particularly relevant to immune cell functions. ADP-ribosylation regulates differentiation and functions of myeloid, T and B cells. It also regulates the expression of cytokines and chemokines, production of antibodies, isotype switch and the expression of several immune mediators. Alterations in these processes involve ADP-ribosylation in virtually any acute and chronic inflammatory/immune-mediated disease. Besides, pathogens developed mechanisms to contrast the action of ADP-ribosylating enzymes by using their own hydrolases and/or to exploit this PTM to sustain their virulence. In the present review, we summarize and discuss recent findings on the role of ADP-ribosylation in immunobiology, immune evasion/subversion by pathogens and immune-mediated diseases.
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Affiliation(s)
| | - Claudio Pioli
- Division of Health Protection Technologies, ENEA, Rome, Italy
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19
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Malgras M, Garcia M, Jousselin C, Bodet C, Lévêque N. The Antiviral Activities of Poly-ADP-Ribose Polymerases. Viruses 2021; 13:v13040582. [PMID: 33808354 PMCID: PMC8066025 DOI: 10.3390/v13040582] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023] Open
Abstract
The poly-adenosine diphosphate (ADP)-ribose polymerases (PARPs) are responsible for ADP-ribosylation, a reversible post-translational modification involved in many cellular processes including DNA damage repair, chromatin remodeling, regulation of translation and cell death. In addition to these physiological functions, recent studies have highlighted the role of PARPs in host defenses against viruses, either by direct antiviral activity, targeting certain steps of virus replication cycle, or indirect antiviral activity, via modulation of the innate immune response. This review focuses on the antiviral activity of PARPs, as well as strategies developed by viruses to escape their action.
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Affiliation(s)
- Mathilde Malgras
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
| | - Magali Garcia
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86021 Poitiers, France
| | - Clément Jousselin
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86021 Poitiers, France
| | - Charles Bodet
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
| | - Nicolas Lévêque
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86021 Poitiers, France
- Correspondence: nicolas.lévê; Tel.: +33-(0)5-49-44-38-17
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20
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Hopp AK, Hottiger MO. Uncovering the Invisible: Mono-ADP-ribosylation Moved into the Spotlight. Cells 2021; 10:680. [PMID: 33808662 PMCID: PMC8003356 DOI: 10.3390/cells10030680] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Adenosine diphosphate (ADP)-ribosylation is a nicotinamide adenine dinucleotide (NAD+)-dependent post-translational modification that is found on proteins as well as on nucleic acids. While ARTD1/PARP1-mediated poly-ADP-ribosylation has extensively been studied in the past 60 years, comparably little is known about the physiological function of mono-ADP-ribosylation and the enzymes involved in its turnover. Promising technological advances have enabled the development of innovative tools to detect NAD+ and NAD+/NADH (H for hydrogen) ratios as well as ADP-ribosylation. These tools have significantly enhanced our current understanding of how intracellular NAD dynamics contribute to the regulation of ADP-ribosylation as well as to how mono-ADP-ribosylation integrates into various cellular processes. Here, we discuss the recent technological advances, as well as associated new biological findings and concepts.
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Affiliation(s)
| | - Michael O. Hottiger
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland;
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21
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Fehr AR, Singh SA, Kerr CM, Mukai S, Higashi H, Aikawa M. The impact of PARPs and ADP-ribosylation on inflammation and host-pathogen interactions. Genes Dev 2020; 34:341-359. [PMID: 32029454 PMCID: PMC7050484 DOI: 10.1101/gad.334425.119] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Poly-adenosine diphosphate-ribose polymerases (PARPs) promote ADP-ribosylation, a highly conserved, fundamental posttranslational modification (PTM). PARP catalytic domains transfer the ADP-ribose moiety from NAD+ to amino acid residues of target proteins, leading to mono- or poly-ADP-ribosylation (MARylation or PARylation). This PTM regulates various key biological and pathological processes. In this review, we focus on the roles of the PARP family members in inflammation and host-pathogen interactions. Here we give an overview the current understanding of the mechanisms by which PARPs promote or suppress proinflammatory activation of macrophages, and various roles PARPs play in virus infections. We also demonstrate how innovative technologies, such as proteomics and systems biology, help to advance this research field and describe unanswered questions.
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Affiliation(s)
- Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Catherine M Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Shin Mukai
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Center for Excellence in Vascular Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Human Pathology, I.M. Sechenov First Moscow State Medical University of the Ministry of Health, Moscow 119146, Russian Federation
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22
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Structural Basis for Cooperative Binding of EBNA1 to the Epstein-Barr Virus Dyad Symmetry Minimal Origin of Replication. J Virol 2019; 93:JVI.00487-19. [PMID: 31142669 DOI: 10.1128/jvi.00487-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/21/2019] [Indexed: 12/11/2022] Open
Abstract
Epstein-Barr virus is associated with several human malignancies, including nasopharyngeal carcinoma, gastric cancer, and lymphoma. Latently infected cells carry a circularized EBV episome where the origin of replication (oriP) is comprised of two elements: the family of repeats (FR) and dyad symmetry (DS). The viral protein Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) binds to FR and DS to promote EBV episome maintenance and DNA replication during latent infection in proliferating cells. EBNA1 binding to the DS constitutes a minimal origin of DNA replication. Here we report the crystal structure of two EBNA1 DNA-binding domain dimers bound to a DS half-site. This structure shows that the DNA is smoothly bent, allowing for stabilizing interactions between the dimers. The dimer-dimer interface requires an intricate hydrogen bonding network involving residues R491 and D581. When this interface is disrupted, we note loss of stable dimer-dimer complex formation on the DNA, compromised oriP-containing plasmid replication in cells, and impaired recruitment of the MCM3 complex to the oriP Surface conservation analysis reveals that these residues are part of a larger conserved surface that may be critical for recruitment of replication machinery to the oriP Our results reveal a new region of EBNA1 critical for its activity and one that may be exploited by targeted small molecules to treat EBV-associated disease.IMPORTANCE Epstein-Barr virus (EBV) is a causative agent of various malignancies and may also contribute to autoimmune disease. The latent and episomal form of the virus is known to drive EBV-associated oncogenesis. Persistence of the viral episome in proliferating tumor cells requires the interaction of Epstein-Barr virus nuclear antigen 1 (EBNA1) with the viral origin of plasmid replication (oriP). The dyad symmetry (DS) element in oriP is the essential minimal replicator of oriP Here we report the X-ray crystal structure of EBNA1 bound to DS. The structure reveals a previous unrecognized interface formed between dimers of EBNA1 necessary for cooperative DNA binding, recruitment of cellular replication machinery, and replication function. These findings provide new insights into the mechanism of EBNA1 function at the replication origin and new opportunities to inhibit EBV latent infection and pathogenesis.
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Grunewald ME, Chen Y, Kuny C, Maejima T, Lease R, Ferraris D, Aikawa M, Sullivan CS, Perlman S, Fehr AR. The coronavirus macrodomain is required to prevent PARP-mediated inhibition of virus replication and enhancement of IFN expression. PLoS Pathog 2019; 15:e1007756. [PMID: 31095648 PMCID: PMC6521996 DOI: 10.1371/journal.ppat.1007756] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/09/2019] [Indexed: 12/20/2022] Open
Abstract
ADP-ribosylation is a ubiquitous post-translational addition of either monomers or polymers of ADP-ribose to target proteins by ADP-ribosyltransferases, usually by interferon-inducible diphtheria toxin-like enzymes known as PARPs. While several PARPs have known antiviral activities, these activities are mostly independent of ADP-ribosylation. Consequently, less is known about the antiviral effects of ADP-ribosylation. Several viral families, including Coronaviridae, Togaviridae, and Hepeviridae, encode for macrodomain proteins that bind to and hydrolyze ADP-ribose from proteins and are critical for optimal replication and virulence. These results suggest that macrodomains counter cellular ADP-ribosylation, but whether PARPs or, alternatively, other ADP-ribosyltransferases cause this modification is not clear. Here we show that pan-PARP inhibition enhanced replication and inhibited interferon production in primary macrophages infected with macrodomain-mutant but not wild-type coronavirus. Specifically, knockdown of two abundantly expressed PARPs, PARP12 and PARP14, led to increased replication of mutant but did not significantly affect wild-type virus. PARP14 was also important for the induction of interferon in mouse and human cells, indicating a critical role for this PARP in the regulation of innate immunity. In summary, these data demonstrate that the macrodomain is required to prevent PARP-mediated inhibition of coronavirus replication and enhancement of interferon production. ADP-ribosylation, an understudied post-translational modification, facilitates the host response to virus infection. Several viruses, including all members of the coronavirus family, encode a macrodomain to reverse ADP-ribosylation and combat this immune response. As such, viruses with mutations in the macrodomain are highly attenuated and cause minimal disease in vivo. Here, using primary macrophages and mice infected with a pathogenic murine coronavirus, we identify PARPs, specifically PARP12 and PARP14, as host cell ADP-ribosylating enzymes important for the attenuation of these mutant viruses and confirm their importance using inhibitors and siRNAs. These data demonstrate a broad strategy of virus-host interactions and indicate that the macrodomain may be a useful target for antiviral therapy.
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Affiliation(s)
- Matthew E. Grunewald
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States of America
| | - Yating Chen
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States of America
| | - Chad Kuny
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States of America
| | - Takashi Maejima
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Robert Lease
- McDaniel College, Westminster, MD, United States of America
| | - Dana Ferraris
- McDaniel College, Westminster, MD, United States of America
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Christopher S. Sullivan
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States of America
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States of America
- * E-mail: (SP); (ARF)
| | - Anthony R. Fehr
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States of America
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States of America
- * E-mail: (SP); (ARF)
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24
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Wang H, Fang G, Wang H, Dou J, Bian Z, Li Y, Chai H, Wu Z, Yao Q. A diboronic acid fluorescent sensor for selective recognition of d-ribose via fluorescence quenching. NEW J CHEM 2019. [DOI: 10.1039/c8nj06229c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Herein we reported a novel boronic acid-based water-soluble sensor. It decreased the fluorescence by 50% when combined with 0.0146 M of d-ribose, while increased or not changed obviously after binding to other carbohydrates.
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Affiliation(s)
- Hao Wang
- School of Medicine and Life Sciences
- University of Jinan–Shandong Academy of Medical Sciences
- Jinan 250200
- China
- Institute of Materia Medica
| | - Guiqian Fang
- School of Medicine and Life Sciences
- University of Jinan–Shandong Academy of Medical Sciences
- Jinan 250200
- China
- Institute of Materia Medica
| | - Hongxiao Wang
- School of Medicine and Life Sciences
- University of Jinan–Shandong Academy of Medical Sciences
- Jinan 250200
- China
- Institute of Materia Medica
| | - Jindi Dou
- School of Medicine and Life Sciences
- University of Jinan–Shandong Academy of Medical Sciences
- Jinan 250200
- China
- Institute of Materia Medica
| | - Zhancun Bian
- School of Medicine and Life Sciences
- University of Jinan–Shandong Academy of Medical Sciences
- Jinan 250200
- China
- Institute of Materia Medica
| | - Ying Li
- School of Medicine and Life Sciences
- University of Jinan–Shandong Academy of Medical Sciences
- Jinan 250200
- China
- Institute of Materia Medica
| | - Huining Chai
- School of Medicine and Life Sciences
- University of Jinan–Shandong Academy of Medical Sciences
- Jinan 250200
- China
- Institute of Materia Medica
| | - Zhongyu Wu
- School of Medicine and Life Sciences
- University of Jinan–Shandong Academy of Medical Sciences
- Jinan 250200
- China
- Institute of Materia Medica
| | - Qingqiang Yao
- School of Medicine and Life Sciences
- University of Jinan–Shandong Academy of Medical Sciences
- Jinan 250200
- China
- Institute of Materia Medica
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25
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Poly(ADP-Ribose) Polymerases in Host-Pathogen Interactions, Inflammation, and Immunity. Microbiol Mol Biol Rev 2018; 83:83/1/e00038-18. [PMID: 30567936 DOI: 10.1128/mmbr.00038-18] [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] [Indexed: 12/27/2022] Open
Abstract
The literature review presented here details recent research involving members of the poly(ADP-ribose) polymerase (PARP) family of proteins. Among the 17 recognized members of the family, the human enzyme PARP1 is the most extensively studied, resulting in a number of known biological and metabolic roles. This review is focused on the roles played by PARP enzymes in host-pathogen interactions and in diseases with an associated inflammatory response. In mammalian cells, several PARPs have specific roles in the antiviral response; this is perhaps best illustrated by PARP13, also termed the zinc finger antiviral protein (ZAP). Plant stress responses and immunity are also regulated by poly(ADP-ribosyl)ation. PARPs promote inflammatory responses by stimulating proinflammatory signal transduction pathways that lead to the expression of cytokines and cell adhesion molecules. Hence, PARP inhibitors show promise in the treatment of inflammatory disorders and conditions with an inflammatory component, such as diabetes, arthritis, and stroke. These functions are correlated with the biophysical characteristics of PARP family enzymes. This work is important in providing a comprehensive understanding of the molecular basis of pathogenesis and host responses, as well as in the identification of inhibitors. This is important because the identification of inhibitors has been shown to be effective in arresting the progression of disease.
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26
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Poly(ADP-ribose) polymerase 1 is necessary for coactivating hypoxia-inducible factor-1-dependent gene expression by Epstein-Barr virus latent membrane protein 1. PLoS Pathog 2018; 14:e1007394. [PMID: 30395643 PMCID: PMC6237423 DOI: 10.1371/journal.ppat.1007394] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/15/2018] [Accepted: 10/09/2018] [Indexed: 12/20/2022] Open
Abstract
Latent membrane protein 1 (LMP1) is the major transforming protein of Epstein-Barr virus (EBV) and is critical for EBV-induced B-cell transformation in vitro. Poly(ADP-ribose) polymerase 1 (PARP1) regulates accessibility of chromatin, alters functions of transcriptional activators and repressors, and has been directly implicated in transcriptional activation. Previously we showed that LMP1 activates PARP1 and increases Poly(ADP-ribos)ylation (PARylation) through PARP1. Therefore, to identify targets of LMP1 that are regulated through PARP1, LMP1 was ectopically expressed in an EBV-negative Burkitt’s lymphoma cell line. These LMP1-expressing cells were then treated with the PARP inhibitor olaparib and prepared for RNA sequencing. The LMP1/PARP targets identified through this RNA-seq experiment are largely involved in metabolism and signaling. Interestingly, Ingenuity Pathway Analysis of RNA-seq data suggests that hypoxia-inducible factor 1-alpha (HIF-1α) is an LMP1 target mediated through PARP1. PARP1 is acting as a coactivator of HIF-1α-dependent gene expression in B cells, and this co-activation is enhanced by LMP1-mediated activation of PARP1. HIF-1α forms a PARylated complex with PARP1 and both HIF-1α and PARP1 are present at promoter regions of HIF-1α downstream targets, leading to accumulation of positive histone marks at these regions. Complex formation, PARylation and binding of PARP1 and HIF-1α at promoter regions of HIF-1α downstream targets can all be attenuated by PARP1 inhibition, subsequently leading to a buildup of repressive histone marks and loss of positive histone marks. In addition, LMP1 switches cells to a glycolytic ‘Warburg’ metabolism, preferentially using aerobic glycolysis over mitochondrial respiration. Finally, LMP1+ cells are more sensitive to PARP1 inhibition and, therefore, targeting PARP1 activity may be an effective treatment for LMP1+ EBV-associated malignancies. Epstein-Barr virus (EBV) is one of the most ubiquitous human viruses, with over 90% of adults worldwide harboring lifelong latent EBV infection in a small fraction of their B-lymphocytes. EBV is known to cause lymphoproliferative disorders and is associated with several other types of cancer, including Hodgkin's lymphoma, Burkitt's lymphoma and Nasopharyngeal carcinoma. However, in most cases, the approach to EBV-positive lymphomas does not differ from EBV-negative lymphomas of the same histology. Latent membrane protein 1 (LMP1) is the major transforming protein of EBV and is critical for EBV-induced B-cell transformation in vitro. LMP1 activates several epigenetic regulators to modify host gene expression, including the chromatin-modifying enzyme Poly(ADP-ribose) polymerase 1, or PARP1. In the current study we have determined that LMP1 can activate PARP1 to increase hypoxia-inducible factor 1-alpha (HIF-1α)-dependent gene expression, leading to a change in host cell metabolism indicative of a ‘Warburg effect’ (aerobic glycolysis). This subsequently provides a proliferative advantage to LMP1-expressing cells. The LMP1-induced increase in HIF-1α-dependent gene expression, alteration of cellular metabolism, and accelerated cellular proliferation, can be offset with the PARP inhibitor olaparib. Therefore, targeting PARP1 activity may be an effective treatment for LMP1+ EBV-associated malignancies.
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27
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Chung WC, Kim J, Kim BC, Kang HR, Son J, Ki H, Hwang KY, Song MJ. Structure-based mechanism of action of a viral poly(ADP-ribose) polymerase 1-interacting protein facilitating virus replication. IUCRJ 2018; 5:866-879. [PMID: 30443370 PMCID: PMC6211522 DOI: 10.1107/s2052252518013854] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/01/2018] [Indexed: 06/09/2023]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1), an enzyme that modifies nuclear proteins by poly(ADP-ribosyl)ation, regulates various cellular activities and restricts the lytic replication of oncogenic gammaherpesviruses by inhibiting the function of replication and transcription activator (RTA), a key switch molecule of the viral life cycle. A viral PARP-1-interacting protein (vPIP) encoded by murine gammaherpesvirus 68 (MHV-68) orf49 facilitates lytic replication by disrupting interactions between PARP-1 and RTA. Here, the structure of MHV-68 vPIP was determined at 2.2 Å resolution. The structure consists of 12 α-helices with characteristic N-terminal β-strands (Nβ) and forms a V-shaped-twist dimer in the asymmetric unit. Structure-based mutagenesis revealed that Nβ and the α1 helix (residues 2-26) are essential for the nuclear localization and function of vPIP; three residues were then identified (Phe5, Ser12 and Thr16) that were critical for the function of vPIP and its interaction with PARP-1. A recombinant MHV-68 harboring mutations of these three residues showed severely attenuated viral replication both in vitro and in vivo. Moreover, ORF49 of Kaposi's sarcoma-associated herpesvirus also directly interacted with PARP-1, indicating a conserved mechanism of action of vPIPs. The results elucidate the novel molecular mechanisms by which oncogenic gammaherpesviruses overcome repression by PARP-1 using vPIPs.
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Affiliation(s)
- Woo-Chang Chung
- Virus–Host Interactions Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Junsoo Kim
- Structural Proteomics Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Byung Chul Kim
- Virus–Host Interactions Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hye-Ri Kang
- Virus–Host Interactions Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - JongHyeon Son
- Structural Proteomics Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hosam Ki
- Structural Proteomics Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Kwang Yeon Hwang
- Structural Proteomics Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Moon Jung Song
- Virus–Host Interactions Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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28
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Fehr AR, Jankevicius G, Ahel I, Perlman S. Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis. Trends Microbiol 2018; 26:598-610. [PMID: 29268982 PMCID: PMC6003825 DOI: 10.1016/j.tim.2017.11.011] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/16/2017] [Accepted: 11/30/2017] [Indexed: 12/20/2022]
Abstract
Viruses from the Coronaviridae, Togaviridae, and Hepeviridae families all contain genes that encode a conserved protein domain, called a macrodomain; however, the role of this domain during infection has remained enigmatic. The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Here, we comprehensively review this rapidly expanding field, describing the structures and enzymatic activities of viral macrodomains, and discussing their roles in viral replication and pathogenesis.
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Affiliation(s)
- Anthony R Fehr
- University of Iowa, Department of Microbiology and Immunology, Iowa City, IA 52242, USA; These authors contributed equally to this manuscript.
| | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; These authors contributed equally to this manuscript
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Stanley Perlman
- University of Iowa, Department of Microbiology and Immunology, Iowa City, IA 52242, USA.
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29
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Grunewald ME, Fehr AR, Athmer J, Perlman S. The coronavirus nucleocapsid protein is ADP-ribosylated. Virology 2018; 517:62-68. [PMID: 29199039 PMCID: PMC5871557 DOI: 10.1016/j.virol.2017.11.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 11/25/2022]
Abstract
ADP-ribosylation is a common post-translational modification, although how it modulates RNA virus infection is not well understood. While screening for ADP-ribosylated proteins during coronavirus (CoV) infection, we detected a ~55kDa ADP-ribosylated protein in mouse hepatitis virus (MHV)-infected cells and in virions, which we identified as the viral nucleocapsid (N) protein. The N proteins of porcine epidemic diarrhea virus (PEDV), severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV were also ADP-ribosylated. ADP-ribosylation of N protein was also observed in cells exogenously expressing N protein by transduction using Venezuelan equine encephalitis virus replicon particles (VRPs). However, plasmid-derived N protein was not ADP-ribosylated following transient transfection but was ADP-ribosylated after MHV infection, indicating that this modification requires virus infection. In conclusion, we have identified a novel post-translation modification of the CoV N protein that may play a regulatory role for this important structural protein.
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Affiliation(s)
- Matthew E Grunewald
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242, United States
| | - Anthony R Fehr
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242, United States
| | - Jeremiah Athmer
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242, United States
| | - Stanley Perlman
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242, United States.
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30
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Palazzo L, Mikoč A, Ahel I. ADP-ribosylation: new facets of an ancient modification. FEBS J 2017; 284:2932-2946. [PMID: 28383827 PMCID: PMC7163968 DOI: 10.1111/febs.14078] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/20/2017] [Accepted: 04/04/2017] [Indexed: 12/11/2022]
Abstract
Rapid response to environmental changes is achieved by uni- and multicellular organisms through a series of molecular events, often involving modification of macromolecules, including proteins, nucleic acids and lipids. Amongst these, ADP-ribosylation is of emerging interest because of its ability to modify different macromolecules in the cells, and its association with many key biological processes, such as DNA-damage repair, DNA replication, transcription, cell division, signal transduction, stress and infection responses, microbial pathogenicity and aging. In this review, we provide an update on novel pathways and mechanisms regulated by ADP-ribosylation in organisms coming from all kingdoms of life.
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Affiliation(s)
- Luca Palazzo
- Sir William Dunn School of PathologyUniversity of OxfordUK
| | - Andreja Mikoč
- Division of Molecular BiologyRuđer Bošković InstituteZagrebCroatia
| | - Ivan Ahel
- Sir William Dunn School of PathologyUniversity of OxfordUK
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31
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Wang Z, Gao Y, Zhang C, Hu H, Guo D, Xu Y, Xu Q, Zhang W, Deng S, Lv P, Yang Y, Ding Y, Li Q, Weng C, Chen X, Gong S, Chen H, Niu J, Tang H. Quinolinate Phosphoribosyltransferase is an Antiviral Host Factor Against Hepatitis C Virus Infection. Sci Rep 2017; 7:5876. [PMID: 28724915 PMCID: PMC5517448 DOI: 10.1038/s41598-017-06254-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 06/09/2017] [Indexed: 01/09/2023] Open
Abstract
HCV infection can decrease NAD+/NADH ratio, which could convert lipid metabolism to favor HCV replication. In hepatocytes, quinolinate phosphoribosyl transferase (QPRT) catabolizes quinolinic acid (QA) to nicotinic acid mononucleotide (NAMN) for de novo NAD synthesis. However, whether and how HCV modulates QPRT hence the lipogenesis is unknown. In this work, we found QPRT was reduced significantly in livers of patients or humanized C/OTg mice with persistent HCV infection. Mechanistic studies indicated that HCV NS3/4A promoted proteasomal degradation of QPRT through Smurf2, an E3 ubiquitin-protein ligase, in Huh7.5.1 cells. Furthermore, QPRT enzymatic activity involved in suppression of HCV replication in cells. Activation of QPRT with clofibrate (CLO) or addition of QPRT catabolite NAD both inhibited HCV replication in cells, probably through NAD+-dependent Sirt1 inhibition of cellular lipogenesis. More importantly, administration of CLO, a hypolipidemic drug used in clinics, could significantly reduce the viral load in HCV infected C/OTg mice. Take together, these results suggested that HCV infection triggered proteasomal degradation of QPRT and consequently reduced de novo NAD synthesis and lipogenesis, in favor of HCV replication. Hepatic QPRT thus likely served as a cellular factor that dampened productive HCV replication.
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Affiliation(s)
- Zhilong Wang
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.,CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Yanhang Gao
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Chao Zhang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haiming Hu
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Dongwei Guo
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Heilong Jiang, 150001, China
| | - Yi Xu
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Qiuping Xu
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Weihong Zhang
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Sisi Deng
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Pingyun Lv
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Yan Yang
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Yanhua Ding
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Qingquan Li
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Changjiang Weng
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Heilong Jiang, 150001, China
| | - Xinwen Chen
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Sitang Gong
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Hairong Chen
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Junqi Niu
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Hong Tang
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China. .,CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
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32
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Whitaker AM, Schaich MA, Smith MR, Flynn TS, Freudenthal BD. Base excision repair of oxidative DNA damage: from mechanism to disease. Front Biosci (Landmark Ed) 2017; 22:1493-1522. [PMID: 28199214 DOI: 10.2741/4555] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Reactive oxygen species continuously assault the structure of DNA resulting in oxidation and fragmentation of the nucleobases. Both oxidative DNA damage itself and its repair mediate the progression of many prevalent human maladies. The major pathway tasked with removal of oxidative DNA damage, and hence maintaining genomic integrity, is base excision repair (BER). The aphorism that structure often dictates function has proven true, as numerous recent structural biology studies have aided in clarifying the molecular mechanisms used by key BER enzymes during the repair of damaged DNA. This review focuses on the mechanistic details of the individual BER enzymes and the association of these enzymes during the development and progression of human diseases, including cancer and neurological diseases. Expanding on these structural and biochemical studies to further clarify still elusive BER mechanisms, and focusing our efforts toward gaining an improved appreciation of how these enzymes form co-complexes to facilitate DNA repair is a crucial next step toward understanding how BER contributes to human maladies and how it can be manipulated to alter patient outcomes.
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Affiliation(s)
- Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Tony S Flynn
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160,
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33
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Grabowski JM, Gulia-Nuss M, Kuhn RJ, Hill CA. RNAi reveals proteins for metabolism and protein processing associated with Langat virus infection in Ixodes scapularis (black-legged tick) ISE6 cells. Parasit Vectors 2017; 10:24. [PMID: 28086865 PMCID: PMC5237174 DOI: 10.1186/s13071-016-1944-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 12/16/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Tick-borne flaviviruses (TBFs) cause thousands of human cases of encephalitis worldwide each year, with some TBF infections progressing to hemorrhagic fever. TBFs are of medical and veterinary importance and strategies to reduce flavivirus transmission by the tick vector may have significant application. Analyses of the proteome of ISE6 cells derived from the black legged tick, Ixodes scapularis infected with the TBF, Langat virus (LGTV), have provided insights into proteins and cellular processes involved with LGTV infection. METHODS RNA interference (RNAi)-induced knockdown of transcripts was used to investigate the role of ten tick proteins in the LGTV infection cycle in ISE6 cells. LGTV-infected cells were separately transfected with dsRNA corresponding to each gene of interest and the effect on LGTV genome replication and release of infectious virus was assessed by RT-qPCR and plaque assays, respectively. RESULTS RNAi-induced knockdown of transcripts for two enzymes that likely function in amino acid, carbohydrate, lipid, terpenoid/polykeytide and vitamin metabolism, and a transcript for one protein of unknown function were associated with decreased replication of the LGTV genome and release of infectious virus from cells. The knockdown of transcripts for five enzymes predicted to function in metabolism, a protein likely associated with folding, sorting and degradation, and a protein of unknown function was associated with a decrease only in the amount of infectious LGTV released from cells. CONCLUSIONS These data suggest tick proteins potentially associated with metabolism and protein processing may be involved in LGTV infection of ISE6 cells. Our study provides information to begin to elucidate the function of these proteins and identify targets for the development of new interventions aimed at controlling the transmission of TBFs.
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Affiliation(s)
- Jeffrey M Grabowski
- Department of Entomology, College of Agriculture, Purdue University, 901 W State Street, West Lafayette, IN, 47907, USA.,Markey Center for Structural Biology, Department of Biological Sciences, College of Science, Purdue University, 915 W State Street, West Lafayette, IN, 47907, USA.,Current Address: NIH/NIAID, Rocky Mountain Laboratories, Laboratory of Virology, Biology of Vector-Borne Viruses Section, 903 S 4th St, Hamilton, MT, 59840, USA
| | - Monika Gulia-Nuss
- Department of Entomology, College of Agriculture, Purdue University, 901 W State Street, West Lafayette, IN, 47907, USA.,Current Address: Department of Biochemistry and Molecular Biology, College of Agriculture, Biotechnology, and Natural Resources, University of Nevada-Reno, 1664 N Virginia Street, Reno, NV, 89503, USA
| | - Richard J Kuhn
- Markey Center for Structural Biology, Department of Biological Sciences, College of Science, Purdue University, 915 W State Street, West Lafayette, IN, 47907, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Catherine A Hill
- Department of Entomology, College of Agriculture, Purdue University, 901 W State Street, West Lafayette, IN, 47907, USA. .,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA.
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Epstein-Barr Virus Oncoprotein LMP1 Mediates Epigenetic Changes in Host Gene Expression through PARP1. J Virol 2016; 90:8520-30. [PMID: 27440880 DOI: 10.1128/jvi.01180-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 07/11/2016] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED The latent infection of Epstein-Barr virus (EBV) is associated with 1% of human cancer incidence. Poly(ADP-ribosyl)ation (PARylation) is a posttranslational modification catalyzed by poly(ADP-ribose) polymerases (PARPs) that mediate EBV replication during latency. In this study, we detail the mechanisms that drive cellular PARylation during latent EBV infection and the effects of PARylation on host gene expression and cellular function. EBV-infected B cells had higher PAR levels than EBV-negative B cells. Moreover, cellular PAR levels were up to 2-fold greater in type III than type I latently infected EBV B cells. We identified a positive association between expression of the EBV genome-encoded latency membrane protein 1 (LMP1) and PAR levels that was dependent upon PARP1. PARP1 regulates gene expression by numerous mechanisms, including modifying chromatin structure and altering the function of chromatin-modifying enzymes. Since LMP1 is essential in establishing EBV latency and promoting tumorigenesis, we explored the model that disruption in cellular PARylation, driven by LMP1 expression, subsequently promotes epigenetic alterations to elicit changes in host gene expression. PARP1 inhibition resulted in the accumulation of the repressive histone mark H3K27me3 at a subset of LMP1-regulated genes. Inhibition of PARP1, or abrogation of PARP1 expression, also suppressed the expression of LMP1-activated genes and LMP1-mediated cellular transformation, demonstrating an essential role for PARP1 activity in LMP1-induced gene expression and cellular transformation associated with LMP1. In summary, we identified a novel mechanism by which LMP1 drives expression of host tumor-promoting genes by blocking generation of the inhibitory histone modification H3K27me3 through PARP1 activation. IMPORTANCE EBV is causally linked to several malignancies and is responsible for 1% of cancer incidence worldwide. The EBV-encoded protein LMP1 is essential for promoting viral tumorigenesis by aberrant activation of several well-known intracellular signaling pathways. We have identified and defined an additional novel molecular mechanism by which LMP1 regulates the expression of tumor-promoting host genes. We found that LMP1 activates the cellular protein PARP1, leading to a decrease in a repressive histone modification, accompanied by induction in expression of multiple cancer-related genes. PARP1 inhibition or depletion led to a decrease in LMP1-induced cellular transformation. Therefore, targeting PARP1 activity may be an effective treatment for EBV-associated malignancies.
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36
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Qiu GH. Genome defense against exogenous nucleic acids in eukaryotes by non-coding DNA occurs through CRISPR-like mechanisms in the cytosol and the bodyguard protection in the nucleus. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 767:31-41. [DOI: 10.1016/j.mrrev.2016.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 10/22/2015] [Accepted: 01/03/2016] [Indexed: 02/07/2023]
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Zhang Y, Mao D, Roswit WT, Jin X, Patel AC, Patel DA, Agapov E, Wang Z, Tidwell RM, Atkinson JJ, Huang G, McCarthy R, Yu J, Yun NE, Paessler S, Lawson TG, Omattage NS, Brett TJ, Holtzman MJ. PARP9-DTX3L ubiquitin ligase targets host histone H2BJ and viral 3C protease to enhance interferon signaling and control viral infection. Nat Immunol 2015; 16:1215-27. [PMID: 26479788 PMCID: PMC4653074 DOI: 10.1038/ni.3279] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/26/2015] [Indexed: 12/12/2022]
Abstract
Enhancing the response to interferon could offer an immunological advantage to the host. In support of this concept, we used a modified form of the transcription factor STAT1 to achieve hyper-responsiveness to interferon without toxicity and markedly improve antiviral function in transgenic mice and transduced human cells. We found that the improvement depended on expression of a PARP9-DTX3L complex with distinct domains for interaction with STAT1 and for activity as an E3 ubiquitin ligase that acted on host histone H2BJ to promote interferon-stimulated gene expression and on viral 3C proteases to degrade these proteases via the immunoproteasome. Thus, PARP9-DTX3L acted on host and pathogen to achieve a double layer of immunity within a safe reserve in the interferon signaling pathway.
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Affiliation(s)
- Yong Zhang
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Dailing Mao
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - William T Roswit
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Xiaohua Jin
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Anand C Patel
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri USA
| | - Dhara A Patel
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Eugene Agapov
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Zhepeng Wang
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Rose M Tidwell
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Jeffrey J Atkinson
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Guangming Huang
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Ronald McCarthy
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Jinsheng Yu
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri USA
| | - Nadezhda E Yun
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas USA
| | - Slobodan Paessler
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas USA
| | - T Glen Lawson
- Department of Chemistry, Bates College, Lewiston, Maine USA
| | - Natalie S Omattage
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
| | - Tom J Brett
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
- Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri USA
- Department of Biochemistry, Washington University School of Medicine, St. Louis, Missouri USA
| | - Michael J Holtzman
- Department of Medicine, Drug Discovery Program, Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri USA
- Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri USA
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Hareendran S, Ramakrishna B, Jayandharan GR. Synergistic inhibition of PARP-1 and NF-κB signaling downregulates immune response against recombinant AAV2 vectors during hepatic gene therapy. Eur J Immunol 2015; 46:154-66. [PMID: 26443873 DOI: 10.1002/eji.201545867] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/04/2015] [Accepted: 09/30/2015] [Indexed: 02/02/2023]
Abstract
Host immune response remains a key obstacle to widespread application of adeno-associated virus (AAV) based gene therapy. Thus, targeted inhibition of the signaling pathways that trigger such immune responses will be beneficial. Previous studies have reported that DNA damage response proteins such as poly(ADP-ribose) polymerase-1 (PARP-1) negatively affect the integration of AAV in the host genome. However, the role of PARP-1 in regulating AAV transduction and the immune response against these vectors has not been elucidated. In this study, we demonstrate that repression of PARP-1 improves the transduction of single-stranded AAV vectors both in vitro (∼174%) and in vivo (two- to 3.4-fold). Inhibition of PARP-1, also significantly downregulated the expression of several proinflammatory and cytokine markers such as TLRs, ILs, NF-κB subunit proteins associated with the host innate response against self-complementary AAV2 vectors. The suppression of the inflammatory response targeted against these vectors was more effective upon combined inhibition of PARP-1 and NF-κB signaling. This strategy also effectively attenuated the AAV capsid-specific cytotoxic T-cell response, with minimal effect on vector transduction, as demonstrated in normal C57BL/6 and hemophilia B mice. These data suggest that targeting specific host cellular proteins could be useful to attenuate the immune barriers to AAV-mediated gene therapy.
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Affiliation(s)
- Sangeetha Hareendran
- Centre for Stem Cell Research, Christian Medical College, Vellore, Tamil Nadu, India
| | - Banumathi Ramakrishna
- Department of General Pathology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Giridhara R Jayandharan
- Centre for Stem Cell Research, Christian Medical College, Vellore, Tamil Nadu, India.,Department of Hematology, Christian Medical College, Vellore, Tamil Nadu, India.,Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh, India
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Goodier JL, Pereira GC, Cheung LE, Rose RJ, Kazazian HH. The Broad-Spectrum Antiviral Protein ZAP Restricts Human Retrotransposition. PLoS Genet 2015; 11:e1005252. [PMID: 26001115 PMCID: PMC4441479 DOI: 10.1371/journal.pgen.1005252] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 04/29/2015] [Indexed: 12/13/2022] Open
Abstract
Intrinsic immunity describes the set of recently discovered but poorly understood cellular mechanisms that specifically target viral pathogens. Their discovery derives in large part from intensive studies of HIV and SIV that revealed restriction factors acting at various stages of the retroviral life cycle. Recent studies indicate that some factors restrict both retroviruses and retrotransposons but surprisingly in ways that may differ. We screened known interferon-stimulated antiviral proteins previously untested for their effects on cell culture retrotransposition. Several factors, including BST2, ISG20, MAVS, MX2, and ZAP, showed strong L1 inhibition. We focused on ZAP (PARP13/ZC3HAV1), a zinc-finger protein that targets viruses of several families, including Retroviridae, Tiloviridae, and Togaviridae, and show that ZAP expression also strongly restricts retrotransposition in cell culture through loss of L1 RNA and ribonucleoprotein particle integrity. Association of ZAP with the L1 ribonucleoprotein particle is supported by co-immunoprecipitation and co-localization with ORF1p in cytoplasmic stress granules. We also used mass spectrometry to determine the protein components of the ZAP interactome, and identified many proteins that directly interact and colocalize with ZAP, including MOV10, an RNA helicase previously shown to suppress retrotransposons. The detection of a chaperonin complex, RNA degradation proteins, helicases, post-translational modifiers, and components of chromatin modifying complexes suggest mechanisms of ZAP anti-retroelement activity that function in the cytoplasm and perhaps also in the nucleus. The association of the ZAP ribonucleoprotein particle with many interferon-stimulated gene products indicates it may be a key player in the interferon response.
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Affiliation(s)
- John L. Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gavin C. Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Ling E. Cheung
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Rebecca J. Rose
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Haig H. Kazazian
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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40
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Martire S, Mosca L, d'Erme M. PARP-1 involvement in neurodegeneration: A focus on Alzheimer's and Parkinson's diseases. Mech Ageing Dev 2015; 146-148:53-64. [PMID: 25881554 DOI: 10.1016/j.mad.2015.04.001] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/26/2015] [Accepted: 04/06/2015] [Indexed: 12/17/2022]
Abstract
DNA damage is the prime activator of the enzyme poly(ADP-ribose)polymerase1 (PARP-1) whose overactivation has been proven to be associated with the pathogenesis of numerous central nervous system disorders, such as ischemia, neuroinflammation, and neurodegenerative diseases. Under oxidative stress conditions PARP-1 activity increases, leading to an accumulation of ADP-ribose polymers and NAD(+) depletion, that induces energy crisis and finally cell death. This review aims to explain the contribution of PARP-1 in neurodegenerative diseases, focusing on Alzheimer's and Parkinson's disease, to stimulate further studies on this issue and thereby engage a new perspective regarding the design of possible therapeutic agents or the identification of biomarkers.
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Affiliation(s)
- Sara Martire
- Department of Biochemical Sciences, Sapienza University of Roma, Italy
| | - Luciana Mosca
- Department of Biochemical Sciences, Sapienza University of Roma, Italy
| | - Maria d'Erme
- Department of Biochemical Sciences, Sapienza University of Roma, Italy.
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41
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Liu L, Lear Z, Hughes DJ, Wu W, Zhou EM, Whitehouse A, Chen H, Hiscox JA. Resolution of the cellular proteome of the nucleocapsid protein from a highly pathogenic isolate of porcine reproductive and respiratory syndrome virus identifies PARP-1 as a cellular target whose interaction is critical for virus biology. Vet Microbiol 2014; 176:109-19. [PMID: 25614100 PMCID: PMC4414928 DOI: 10.1016/j.vetmic.2014.11.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 11/24/2014] [Accepted: 11/26/2014] [Indexed: 02/01/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to the swine industry and food security worldwide. The nucleocapsid (N) protein is a major structural protein of PRRSV. The primary function of this protein is to encapsidate the viral RNA genome, and it is also thought to participate in the modulation of host cell biology and recruitment of cellular factors to facilitate virus infection. In order to the better understand these latter roles the cellular interactome of PRRSV N protein was defined using label free quantitative proteomics. This identified several cellular factors that could interact with the N protein including poly [ADP-ribose] polymerase 1 (PARP-1), a cellular protein, which can add adenosine diphosphate ribose to a protein. Use of the PARP-1 small molecule inhibitor, 3-AB, in PRRSV infected cells demonstrated that PARP-1 was required and acted as an enhancer factor for virus biology. Serial growth of PRRSV in different concentrations of 3-AB did not yield viruses that were able to grow with wild type kinetics, suggesting that by targeting a cellular protein crucial for virus biology, resistant phenotypes did not emerge. This study provides further evidence that cellular proteins, which are critical for virus biology, can also be targeted to ablate virus growth and provide a high barrier for the emergence of drug resistance.
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Affiliation(s)
- Long Liu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Zoe Lear
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - David J Hughes
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Weining Wu
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - En-min Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Hongying Chen
- College of Life Sciences, Northwest A&F University, Yangling, China.
| | - Julian A Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; College of Veterinary Medicine, Northwest A&F University, Yangling, China; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.
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42
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Wang RH, Lahusen TJ, Chen Q, Xu X, Jenkins LMM, Leo E, Fu H, Aladjem M, Pommier Y, Appella E, Deng CX. SIRT1 deacetylates TopBP1 and modulates intra-S-phase checkpoint and DNA replication origin firing. Int J Biol Sci 2014; 10:1193-202. [PMID: 25516717 PMCID: PMC4261203 DOI: 10.7150/ijbs.11066] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 11/24/2014] [Indexed: 12/22/2022] Open
Abstract
SIRT1, the mammalian homolog of yeast Sir2, is a founding member of a family of 7 protein and histone deacetylases that are involved in numerous biological functions. Previous studies revealed that SIRT1 deficiency results in genome instability, which eventually leads to cancer formation, yet the underlying mechanism is unclear. To investigate this, we conducted a proteomics study and found that SIRT1 interacted with many proteins involved in replication fork protection and origin firing. We demonstrated that loss of SIRT1 resulted in increased replication origin firing, asymmetric fork progression, defective intra-S-phase checkpoint, and chromosome damage. Mechanistically, SIRT1 deacetylates and affects the activity of TopBP1, which plays an essential role in DNA replication fork protection and replication origin firing. Our study demonstrated that ectopic over-expression of the deacetylated form of TopBP1 in SIRT1 mutant cells repressed replication origin firing, while the acetylated form of TopBP1 lost this function. Thus, SIRT1 acts upstream of TopBP1 and plays an essential role in maintaining genome stability by modulating DNA replication fork initiation and the intra-S-phase cell cycle checkpoint.
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Affiliation(s)
- Rui-Hong Wang
- 1. Genetics of Development and Disease Branch, 10/9N105, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland MD 20892, USA; ; 4. Faculty of Health Sciences, University of Macau, Macau, SAR of People's Republic of China
| | - Tyler J Lahusen
- 1. Genetics of Development and Disease Branch, 10/9N105, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Qiang Chen
- 1. Genetics of Development and Disease Branch, 10/9N105, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Xiaoling Xu
- 1. Genetics of Development and Disease Branch, 10/9N105, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland MD 20892, USA; ; 4. Faculty of Health Sciences, University of Macau, Macau, SAR of People's Republic of China
| | - Lisa M Miller Jenkins
- 2. Laboratory of Cell Biology, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Elisabetta Leo
- 3. Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Haiqing Fu
- 3. Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Mirit Aladjem
- 3. Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Yves Pommier
- 3. Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Ettore Appella
- 2. Laboratory of Cell Biology, National Institutes of Health, Bethesda, Maryland MD 20892, USA
| | - Chu-Xia Deng
- 1. Genetics of Development and Disease Branch, 10/9N105, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland MD 20892, USA; ; 4. Faculty of Health Sciences, University of Macau, Macau, SAR of People's Republic of China
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Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts. PLoS Genet 2014; 10:e1004403. [PMID: 24875882 PMCID: PMC4038475 DOI: 10.1371/journal.pgen.1004403] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/09/2014] [Indexed: 01/23/2023] Open
Abstract
Post-translational protein modifications such as phosphorylation and ubiquitinylation are common molecular targets of conflict between viruses and their hosts. However, the role of other post-translational modifications, such as ADP-ribosylation, in host-virus interactions is less well characterized. ADP-ribosylation is carried out by proteins encoded by the PARP (also called ARTD) gene family. The majority of the 17 human PARP genes are poorly characterized. However, one PARP protein, PARP13/ZAP, has broad antiviral activity and has evolved under positive (diversifying) selection in primates. Such evolution is typical of domains that are locked in antagonistic ‘arms races’ with viral factors. To identify additional PARP genes that may be involved in host-virus interactions, we performed evolutionary analyses on all primate PARP genes to search for signatures of rapid evolution. Contrary to expectations that most PARP genes are involved in ‘housekeeping’ functions, we found that nearly one-third of PARP genes are evolving under strong recurrent positive selection. We identified a >300 amino acid disordered region of PARP4, a component of cytoplasmic vault structures, to be rapidly evolving in several mammalian lineages, suggesting this region serves as an important host-pathogen specificity interface. We also found positive selection of PARP9, 14 and 15, the only three human genes that contain both PARP domains and macrodomains. Macrodomains uniquely recognize, and in some cases can reverse, protein mono-ADP-ribosylation, and we observed strong signatures of recurrent positive selection throughout the macro-PARP macrodomains. Furthermore, PARP14 and PARP15 have undergone repeated rounds of gene birth and loss during vertebrate evolution, consistent with recurrent gene innovation. Together with previous studies that implicated several PARPs in immunity, as well as those that demonstrated a role for virally encoded macrodomains in host immune evasion, our evolutionary analyses suggest that addition, recognition and removal of ADP-ribosylation is a critical, underappreciated currency in host-virus conflicts. The outcome of viral infections is determined by the repertoire and specificity of the antiviral genes in a particular animal species. The identification of candidate immunity genes and mechanisms is a key step in describing this repertoire. Despite advances in genome sequencing, identification of antiviral genes has largely remained dependent on demonstration of their activity against candidate viruses. However, antiviral proteins that directly interact with viral targets or antagonists also bear signatures of recurrent evolutionary adaptation, which can be used to identify candidate antivirals. Here, we find that five out of seventeen genes that contain a domain that can catalyze the post-translational addition ADP-ribose to proteins bear such signatures of recurrent genetic innovation. In particular, we find that all the genes that encode both ADP-ribose addition (via PARP domains) as well as recognition and/or removal (via macro domains) activities have evolved under extremely strong diversifying selection in mammals. Furthermore, such genes have undergone multiple episodes of gene duplications and losses throughout mammalian evolution. Combined with the knowledge that some viruses also encode macro domains to counteract host immunity, our evolutionary analyses therefore implicate ADP-ribosylation as an underappreciated key step in antiviral defense in mammalian genomes.
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Lodhi N, Kossenkov AV, Tulin AV. Bookmarking promoters in mitotic chromatin: poly(ADP-ribose)polymerase-1 as an epigenetic mark. Nucleic Acids Res 2014; 42:7028-38. [PMID: 24861619 PMCID: PMC4066802 DOI: 10.1093/nar/gku415] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Epigenetics are the heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence. After mitosis, it is thought that bookmarking transcription factors remain at promoters, regulating which genes become active and which remain silent. Herein, we demonstrate that poly(ADP-ribose)polymerase-1 (PARP-1) is a genome-wide epigenetic memory mark in mitotic chromatin, and we further show that the presence of PARP-1 is absolutely crucial for reactivation of transcription after mitosis. Based on these findings, a novel molecular model of epigenetic memory transmission through the cell cycle is proposed.
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Affiliation(s)
- Niraj Lodhi
- Fox Chase Cancer Center, Philadelphia, PA, 19111 USA
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Small molecule inhibition of Epstein-Barr virus nuclear antigen-1 DNA binding activity interferes with replication and persistence of the viral genome. Antiviral Res 2014; 104:73-83. [PMID: 24486954 DOI: 10.1016/j.antiviral.2014.01.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/12/2013] [Accepted: 01/06/2014] [Indexed: 11/20/2022]
Abstract
The replication and persistence of extra chromosomal Epstein-Barr virus (EBV) episome in latently infected cells are primarily dependent on the binding of EBV-encoded nuclear antigen 1 (EBNA1) to the cognate EBV oriP element. In continuation of the previous study, herein we characterized EBNA1 small molecule inhibitors (H20, H31) and their underlying inhibitory mechanisms. In silico docking analyses predicted that H20 fits into a pocket in the EBNA1 DNA binding domain (DBD). However, H20 did not significantly affect EBNA1 binding to its cognate sequence. A limited structure-relationship study of H20 identified a hydrophobic compound H31, as an EBNA1 inhibitor. An in vitro EBNA1 EMSA and in vivo EGFP-EBNA1 confocal microscopy analysis showed that H31 inhibited EBNA1-dependent oriP sequence-specific DNA binding activity, but not sequence-nonspecific chromosomal association. Consistent with this, H31 repressed the EBNA1-dependent transcription, replication, and persistence of an EBV oriP plasmid. Furthermore, H31 induced progressive loss of EBV episome. In addition, H31 selectively retarded the growth of EBV-infected LCL or Burkitt's lymphoma cells. These data indicate that H31 inhibition of EBNA1-dependent DNA binding decreases transcription from and persistence of EBV episome in EBV-infected cells. These new compounds might be useful probes for dissecting EBNA1 functions in vitro and in vivo.
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Martire S, Fuso A, Rotili D, Tempera I, Giordano C, De Zottis I, Muzi A, Vernole P, Graziani G, Lococo E, Faraldi M, Maras B, Scarpa S, Mosca L, d'Erme M. PARP-1 modulates amyloid beta peptide-induced neuronal damage. PLoS One 2013; 8:e72169. [PMID: 24086258 PMCID: PMC3782458 DOI: 10.1371/journal.pone.0072169] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 07/08/2013] [Indexed: 01/31/2023] Open
Abstract
Amyloid beta peptide (Aβ) causes neurodegeneration by several mechanisms including oxidative stress, which is known to induce DNA damage with the consequent activation of poly (ADP-ribose) polymerase (PARP-1). To elucidate the role of PARP-1 in the neurodegenerative process, SH-SY5Y neuroblastoma cells were treated with Aβ25–35 fragment in the presence or absence of MC2050, a new PARP-1 inhibitor. Aβ25–35 induces an enhancement of PARP activity which is prevented by cell pre-treatment with MC2050. These data were confirmed by measuring PARP-1 activity in CHO cells transfected with amylod precursor protein and in vivo in brains specimens of TgCRND8 transgenic mice overproducing the amyloid peptide. Following Aβ25–35 exposure a significant increase in intracellular ROS was observed. These data were supported by the finding that Aβ25–35 induces DNA damage which in turn activates PARP-1. Challenge with Aβ25–35 is also able to activate NF-kB via PARP-1, as demonstrated by NF-kB impairment upon MC2050 treatment. Moreover, Aβ25–35via PARP-1 induces a significant increase in the p53 protein level and a parallel decrease in the anti-apoptotic Bcl-2 protein. These overall data support the hypothesis of PARP-1 involvment in cellular responses induced by Aβ and hence a possible rationale for the implication of PARP-1 in neurodegeneration is discussed.
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Affiliation(s)
- Sara Martire
- Department of Biochemical Sciences, Sapienza University, Rome, Italy
| | - Andrea Fuso
- Department of Psychology-Sec.Neuroscience, Sapienza University, Rome, Italy
| | - Dante Rotili
- Department of Pharmaceutical Studies, Sapienza University, Rome, Italy
| | - Italo Tempera
- Fels Institute for Cancer Research & Molecular Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Cesare Giordano
- Department of Pharmaceutical Studies, Sapienza University, Rome, Italy
| | - Ivana De Zottis
- Department of Biochemical Sciences, Sapienza University, Rome, Italy
| | - Alessia Muzi
- Department of Neuroscience, University of Roma “Tor Vergata”, Rome, Italy
| | - Patrizia Vernole
- Department of Public Health and Cell Biology, University of Roma “Tor Vergata”, Rome, Italy
| | - Grazia Graziani
- Department of Neuroscience, University of Roma “Tor Vergata”, Rome, Italy
| | - Emanuela Lococo
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Martina Faraldi
- Department of Biochemical Sciences, Sapienza University, Rome, Italy
| | - Bruno Maras
- Department of Biochemical Sciences, Sapienza University, Rome, Italy
| | - Sigfrido Scarpa
- Department of Surgery “P.Valdoni”, Sapienza University, Rome, Italy
| | - Luciana Mosca
- Department of Biochemical Sciences, Sapienza University, Rome, Italy
| | - Maria d'Erme
- Department of Biochemical Sciences, Sapienza University, Rome, Italy
- Instituto Pasteur Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
- * E-mail:
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Abstract
ORC (origin recognition complex) serves as the initiator for the assembly of the pre-RC (pre-replication complex) and the subsequent DNA replication. Together with many of its non-replication functions, ORC is a pivotal regulator of various cellular processes. Notably, a number of reports connect ORC to numerous human diseases, including MGS (Meier-Gorlin syndrome), EBV (Epstein-Barr virus)-infected diseases, American trypanosomiasis and African trypanosomiasis. However, much of the underlying molecular mechanism remains unclear. In those genetic diseases, mutations in ORC alter its function and lead to the dysregulated phenotypes; whereas in some pathogen-induced symptoms, host ORC and archaeal-like ORC are exploited by these organisms to maintain their own genomes. In this review, I provide detailed examples of ORC-related human diseases, and summarize the current findings on how ORC is involved and/or dysregulated. I further discuss how these discoveries can be generalized as model systems, which can then be applied to elucidating other related diseases and revealing potential targets for developing effective therapies.
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Epigenetic regulation of EBV and KSHV latency. Curr Opin Virol 2013; 3:251-9. [PMID: 23601957 DOI: 10.1016/j.coviro.2013.03.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/07/2013] [Accepted: 03/13/2013] [Indexed: 12/25/2022]
Abstract
The gammaherpesviruses are unique for their capacity to establish a variety of gene expression programs during latent and lytic infection. This capacity enables the virus to control host-cell proliferation, prevent programmed cell death, elude immune cell detection, and ultimately adapt to a wide range of environmental and developmental changes in the host cell. This remarkable plasticity of gene expression results from the combined functionalities of viral and host factors that biochemically remodel and epigenetically modify the viral chromosome. These epigenetic modifications range from primary DNA methylations, to chromatin protein post-translational modifications, to higher-order chromosome conformations. In addition, gammaherpesviruses have acquired specialized tools to modulate the epigenetic processes that promote viral genome propagation and host-cell survival.
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Zhang YB, Liu TK, Jiang J, Shi J, Liu Y, Li S, Gui JF. Identification of a novel Gig2 gene family specific to non-amniote vertebrates. PLoS One 2013; 8:e60588. [PMID: 23593256 PMCID: PMC3617106 DOI: 10.1371/journal.pone.0060588] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/28/2013] [Indexed: 12/15/2022] Open
Abstract
Gig2 (grass carp reovirus (GCRV)-induced gene 2) is first identified as a novel fish interferon (IFN)-stimulated gene (ISG). Overexpression of a zebrafish Gig2 gene can protect cultured fish cells from virus infection. In the present study, we identify a novel gene family that is comprised of genes homologous to the previously characterized Gig2. EST/GSS search and in silico cloning identify 190 Gig2 homologous genes in 51 vertebrate species ranged from lampreys to amphibians. Further large-scale search of vertebrate and invertebrate genome databases indicate that Gig2 gene family is specific to non-amniotes including lampreys, sharks/rays, ray-finned fishes and amphibians. Phylogenetic analysis and synteny analysis reveal lineage-specific expansion of Gig2 gene family and also provide valuable evidence for the fish-specific genome duplication (FSGD) hypothesis. Although Gig2 family proteins exhibit no significant sequence similarity to any known proteins, a typical Gig2 protein appears to consist of two conserved parts: an N-terminus that bears very low homology to the catalytic domains of poly(ADP-ribose) polymerases (PARPs), and a novel C-terminal domain that is unique to this gene family. Expression profiling of zebrafish Gig2 family genes shows that some duplicate pairs have diverged in function via acquisition of novel spatial and/or temporal expression under stresses. The specificity of this gene family to non-amniotes might contribute to a large extent to distinct physiology in non-amniote vertebrates.
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Affiliation(s)
- Yi-Bing Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (YZ) (YZ); (JG) (JG)
| | - Ting-Kai Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jun Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jun Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ying Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (YZ) (YZ); (JG) (JG)
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The Sound of Silence: RNAi in Poly (ADP-Ribose) Research. Genes (Basel) 2012; 3:779-805. [PMID: 24705085 PMCID: PMC3899979 DOI: 10.3390/genes3040779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 11/05/2012] [Accepted: 11/06/2012] [Indexed: 02/07/2023] Open
Abstract
Poly(ADP-ribosyl)-ation is a nonprotein posttranslational modification of proteins and plays an integral part in cell physiology and pathology. The metabolism of poly(ADP-ribose) (PAR) is regulated by its synthesis by poly(ADP-ribose) polymerases (PARPs) and on the catabolic side by poly(ADP-ribose) glycohydrolase (PARG). PARPs convert NAD+ molecules into PAR chains that interact covalently or noncovalently with target proteins and thereby modify their structure and functions. PAR synthesis is activated when PARP1 and PARP2 bind to DNA breaks and these two enzymes account for almost all PAR formation after genotoxic stress. PARG cleaves PAR molecules into free PAR and finally ADP-ribose (ADPR) moieties, both acting as messengers in cellular stress signaling. In this review, we discuss the potential of RNAi to manipulate the levels of PARPs and PARG, and consequently those of PAR and ADPR, and compare the results with those obtained after genetic or chemical disruption.
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