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Liu W, He X, Zhu Y, Li Y, Wang Z, Li P, Pan J, Wang J, Chu B, Yang G, Zhang M, He Q, Li Y, Li W, Zhang C. Identification of a conserved G-quadruplex within the E165R of African swine fever virus (ASFV) as a potential antiviral target. J Biol Chem 2024:107453. [PMID: 38852886 DOI: 10.1016/j.jbc.2024.107453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/11/2024] Open
Abstract
African swine fever virus (ASFV) is a double-stranded DNA arbovirus with high transmissibility and mortality rates. It has caused immense economic losses to the global pig industry. Currently, no effective vaccines or medications are to combat ASFV infection. G-quadruplex (G4) structures have attracted increasing interest because of their regulatory role in vital biological processes. In this study, we identified a conserved G-rich sequence within the E165R gene of ASFV. Subsequently, using various methods, we verified that this sequence could fold into a parallel G-quadruplex (G4). In addition, the G4-stabilizers pyridostatin (PDS) and 5,10,15,20-tetrakis-(N-methyl-4-pyridyl) porphin (TMPyP4) can bind and stabilize this G4 structure, thereby inhibiting E165R gene expression, and the inhibitory effect is associated with G4 formation. Moreover, the G4 ligand PDS substantially impeded ASFV proliferation in Vero cells by reducing gene copy number and viral protein expression. These compelling findings suggest that G4 structures may represent a promising and novel antiviral target against ASFV.
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Affiliation(s)
- Wenhao Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Xinglin He
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University; Hubei Hongshan Laboratory, Wuhan430070, China
| | - Yance Zhu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaqin Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhihao Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Pengfei Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University; Hubei Hongshan Laboratory, Wuhan430070, China
| | - Jiajia Pan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Beibei Chu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Guoyu Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Mengjia Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University; Hubei Hongshan Laboratory, Wuhan430070, China
| | - Qigai He
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University; Hubei Hongshan Laboratory, Wuhan430070, China
| | - Yongtao Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Wentao Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University; Hubei Hongshan Laboratory, Wuhan430070, China.
| | - Chao Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
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Figueroa GB, D'souza S, Pereira HS, Vasudeva G, Figueroa SB, Robinson ZE, Badmalia MD, Meier-Stephenson V, Corcoran JA, van Marle G, Ni Y, Urban S, Coffin CS, Patel TR. Development of a single-domain antibody to target a G-quadruplex located on the hepatitis B virus covalently closed circular DNA genome. J Med Virol 2024; 96:e29692. [PMID: 38804172 DOI: 10.1002/jmv.29692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
To achieve a virological cure for hepatitis B virus (HBV), innovative strategies are required to target the covalently closed circular DNA (cccDNA) genome. Guanine-quadruplexes (G4s) are a secondary structure that can be adopted by DNA and play a significant role in regulating viral replication, transcription, and translation. Antibody-based probes and small molecules have been developed to study the role of G4s in the context of the human genome, but none have been specifically made to target G4s in viral infection. Herein, we describe the development of a humanized single-domain antibody (S10) that can target a G4 located in the PreCore (PreC) promoter of the HBV cccDNA genome. MicroScale Thermophoresis demonstrated that S10 has a strong nanomolar affinity to the PreC G4 in its quadruplex form and a structural electron density envelope of the complex was determined using Small-Angle X-ray Scattering. Lentiviral transduction of S10 into HepG2-NTCP cells shows nuclear localization, and chromatin immunoprecipitation coupled with next-generation sequencing demonstrated that S10 can bind to the HBV PreC G4 present on the cccDNA. This research validates the existence of a G4 in HBV cccDNA and demonstrates that this DNA secondary structure can be targeted with high structural and sequence specificity using S10.
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Affiliation(s)
- Gerardo B Figueroa
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Simmone D'souza
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Higor S Pereira
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Gunjan Vasudeva
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Sara B Figueroa
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Zachary E Robinson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Maulik D Badmalia
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Vanessa Meier-Stephenson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jennifer A Corcoran
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Guido van Marle
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Yi Ni
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infection Research, Heidelberg University, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infection Research, Heidelberg University, Heidelberg, Germany
| | - Carla S Coffin
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
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Giraud G, El Achi K, Zoulim F, Testoni B. Co-Transcriptional Regulation of HBV Replication: RNA Quality Also Matters. Viruses 2024; 16:615. [PMID: 38675956 PMCID: PMC11053573 DOI: 10.3390/v16040615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Chronic hepatitis B (CHB) virus infection is a major public health burden and the leading cause of hepatocellular carcinoma. Despite the efficacy of current treatments, hepatitis B virus (HBV) cannot be fully eradicated due to the persistence of its minichromosome, or covalently closed circular DNA (cccDNA). The HBV community is investing large human and financial resources to develop new therapeutic strategies that either silence or ideally degrade cccDNA, to cure HBV completely or functionally. cccDNA transcription is considered to be the key step for HBV replication. Transcription not only influences the levels of viral RNA produced, but also directly impacts their quality, generating multiple variants. Growing evidence advocates for the role of the co-transcriptional regulation of HBV RNAs during CHB and viral replication, paving the way for the development of novel therapies targeting these processes. This review focuses on the mechanisms controlling the different co-transcriptional processes that HBV RNAs undergo, and their contribution to both viral replication and HBV-induced liver pathogenesis.
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Affiliation(s)
- Guillaume Giraud
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
| | - Khadija El Achi
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
| | - Fabien Zoulim
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
- Hospices Civils de Lyon, Hôpital Croix Rousse, Service d’Hépato-Gastroentérologie, 69004 Lyon, France
| | - Barbara Testoni
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
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4
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Giraud G, Rodà M, Huchon P, Michelet M, Maadadi S, Jutzi D, Montserret R, Ruepp MD, Parent R, Combet C, Zoulim F, Testoni B. G-quadruplexes control hepatitis B virus replication by promoting cccDNA transcription and phase separation in hepatocytes. Nucleic Acids Res 2024; 52:2290-2305. [PMID: 38113270 PMCID: PMC10954475 DOI: 10.1093/nar/gkad1200] [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: 04/05/2023] [Revised: 11/12/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Phase separation regulates fundamental processes in gene expression and is mediated by the local concentration of proteins and nucleic acids, as well as nucleic acid secondary structures such as G-quadruplexes (G4s). These structures play fundamental roles in both host gene expression and in viral replication due to their peculiar localisation in regulatory sequences. Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) is an episomal minichromosome whose persistence is at the basis of chronic infection. Identifying the mechanisms controlling its transcriptional activity is indispensable to develop new therapeutic strategies against chronic hepatitis B. The aim of this study was to determine whether G4s are formed in cccDNA and regulate viral replication. Combining biochemistry and functional studies, we demonstrate that cccDNA indeed contains ten G4s structures. Furthermore, mutations disrupting two G4s located in the enhancer I HBV regulatory region altered cccDNA transcription and viral replication. Finally, we showed for the first time that cccDNA undergoes phase separation in a G4-dependent manner to promote its transcription in infected hepatocytes. Altogether, our data give new insight in the transcriptional regulation of the HBV minichromosome that might pave the way for the identification of novel targets to destabilize or silence cccDNA.
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Affiliation(s)
- Guillaume Giraud
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
| | - Mélanie Rodà
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
| | - Pélagie Huchon
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
- Université Claude-Bernard Lyon I, 69003 Lyon, France
| | - Maud Michelet
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
| | - Sarah Maadadi
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 lyon, france; université claude-bernard lyon i, 69003 Lyon, France
| | - Daniel Jutzi
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, WC2R 2LS London, UK
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7 Passage du Vercors 69367Lyon, France
| | - Marc-David Ruepp
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, WC2R 2LS London, UK
| | - Romain Parent
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
| | - Christophe Combet
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
| | - Fabien Zoulim
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
- Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Service, Hospices Civils de Lyon, 69004 Lyon, France
| | - Barbara Testoni
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
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Zareie AR, Dabral P, Verma SC. G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection. Pathogens 2024; 13:60. [PMID: 38251367 PMCID: PMC10819198 DOI: 10.3390/pathogens13010060] [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: 11/15/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4's involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands' known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments.
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Affiliation(s)
| | | | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA; (A.R.Z.); (P.D.)
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Huang P, Li X, Tan Z, Wang Y, Yan J. Characterization of the G-quadruplexes in the transthyretin gene and its role in silencing transthyretin mRNA transcription. Bioorg Med Chem Lett 2024; 97:129568. [PMID: 38008337 DOI: 10.1016/j.bmcl.2023.129568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
Transthyretin Amyloidosis arises from the misfolding of monomers or oligomers of the normal transthyretin protein. Our investigation revealed that certain guanine-rich regions within the 5' UTR sequence of the transthyretin gene possess the ability to form G2-quadruplex structures, as determined through analysis with QGRS mapper. We demonstrated that small molecule ligands, including TMPyP4, Braco-19, NMM, and TO, have a significant impact on the stabilization of transthyretin G-quadruplexes. The objective of this study was to confirm the effect of ligands on transthyretin gene transcription through the stabilization of G-quadruplexes. To comprehend the interaction between ligands and transthyretin G-quadruplexes, a range of analytical techniques were employed, includingUV titration, fluorescence titration assays, circular dichroism, quantitative RT-PCR and cytotoxicity tests. The results revealed the presence of four putative G2-quadruplex sequences, which formed stable anti-parallel, parallel, and hybrid G2-quadruplex structures. Notably, Ttrg 3 (5'-GGAAGGAAGGGAGGGAGGG-3') exhibited the highest stability to form G-quadruplex. Furthermore, TmPyP4, Braco-19, NMM and TO were found to stabilize the parallel topology of Ttrg 3. After 48 h of incubation, the RT-PCR experiments revealed a significant reduction in transthyretin mRNA transcription in HepG2 cells when treated with 20 μM TmPyP4 and Braco-19, without inducing apoptosis. Our findings suggested that ligand-mediated stabilization of G-quadruplexes within the 5'-UTR can effectively silence transthyretin expression, highlighting the potential of G-quadruplex as a novel therapeutic target for Transthyretin Amyloidosis. This study might shed valuable lights for the development of innovative therapeutic approach against Transthyretin Amyloidosis.
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Affiliation(s)
- Peimin Huang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xu Li
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China
| | - Zhonghan Tan
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China
| | - Yuqing Wang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China.
| | - Jinwu Yan
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China.
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Kumar A, Kamuju V, Vivekanandan P. RNA G-quadruplexes inhibit translation of the PE/PPE transcripts in Mycobacterium tuberculosis. J Biol Chem 2024; 300:105567. [PMID: 38103641 PMCID: PMC10801317 DOI: 10.1016/j.jbc.2023.105567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/22/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023] Open
Abstract
The role of RNA G-quadruplexes (rG4s) in bacteria remains poorly understood. High G-quadruplex densities have been linked to organismal stress. Here we investigate rG4s in mycobacteria, which survive highly stressful conditions within the host. We show that rG4-enrichment is a unique feature exclusive to slow-growing pathogenic mycobacteria, and Mycobacterium tuberculosis (Mtb) transcripts contain an abundance of folded rG4s. Notably, the PE/PPE family of genes, unique to slow-growing pathogenic mycobacteria, contain over 50% of rG4s within Mtb transcripts. We found that RNA oligonucleotides of putative rG4s in PE/PPE genes form G-quadruplex structures in vitro, which are stabilized by the G-quadruplex ligand BRACO19. Furthermore, BRACO19 inhibits the transcription of PE/PPE genes and selectively suppresses the growth of Mtb but not Mycobacterium smegmatis or other rapidly growing bacteria. Importantly, the stabilization of rG4s inhibits the translation of Mtb PE/PPE genes (PPE56, PPE67, PPE68, PE_PGRS39, and PE_PGRS41) ectopically expressed in M. smegmatis or Escherichia coli. In addition, the rG4-mediated reduction in PE/PPE protein levels attenuates proinflammatory response upon infection of THP-1 cells. Our findings shed new light on the regulation of PE/PPE genes and highlight a pivotal role for rG4s in Mtb transcripts as regulators of post-transcriptional translational control. The rG4s in mycobacterial transcripts may represent potential drug targets for newer therapies.
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Affiliation(s)
- Ashish Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Vinay Kamuju
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India.
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Pathak R. G-Quadruplexes in the Viral Genome: Unlocking Targets for Therapeutic Interventions and Antiviral Strategies. Viruses 2023; 15:2216. [PMID: 38005893 PMCID: PMC10674748 DOI: 10.3390/v15112216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
G-quadruplexes (G4s) are unique non-canonical four-stranded nucleic acid secondary structures formed by guanine-rich DNA or RNA sequences. Sequences with the potential to form quadruplex motifs (pG4s) are prevalent throughout the genomes of all organisms, spanning from prokaryotes to eukaryotes, and are enriched within regions of biological significance. In the past few years, the identification of pG4s within most of the Baltimore group viruses has attracted increasing attention due to their occurrence in regulatory regions of the genome and the subsequent implications for regulating critical stages of viral life cycles. In this context, the employment of specific G4 ligands has aided in comprehending the intricate G4-mediated regulatory mechanisms in the viral life cycle, showcasing the potential of targeting viral G4s as a novel antiviral strategy. This review offers a thorough update on the literature concerning G4s in viruses, including their identification and functional significance across most of the human-infecting viruses. Furthermore, it delves into potential therapeutic avenues targeting G4s, encompassing various G4-binding ligands, G4-interacting proteins, and oligonucleotide-based strategies. Finally, the article highlights both progress and challenges in the field, providing valuable insights into leveraging this unusual nucleic acid structure for therapeutic purposes.
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Affiliation(s)
- Rajiv Pathak
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
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9
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Yan MP, Wee CE, Yen KP, Stevens A, Wai LK. G-quadruplex ligands as therapeutic agents against cancer, neurological disorders and viral infections. Future Med Chem 2023; 15:1987-2009. [PMID: 37933551 DOI: 10.4155/fmc-2023-0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
G-quadruplexes (G4s) within the human genome have undergone extensive molecular investigation, with a strong focus on telomeres, gene promoters and repetitive regulatory sequences. G4s play central roles in regulating essential biological processes, including telomere maintenance, replication, transcription and translation. Targeting these molecular processes with G4-binding ligands holds substantial therapeutic potential in anticancer treatments and has also shown promise in treating neurological, skeletal and muscular disorders. The presence of G4s in bacterial and viral genomes also suggests that G4-binding ligands could be a critical tool in fighting infections. This review provides an overview of the progress and applications of G4-binding ligands, their proposed mechanisms of action, challenges faced and prospects for their utilization in anticancer treatments, neurological disorders and antiviral activities.
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Affiliation(s)
- Mock Phooi Yan
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Chua Eng Wee
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Khor Poh Yen
- Faculty Pharmacy & Health Sciences, Universiti Kuala Lumpur, Royal College of Medicine Perak, 3, Jalan Greentown, Ipoh, Perak, 30450, Malaysia
| | - Aaron Stevens
- Department of Pathology & Molecular Medicine, University of Otago, Wellington, 6021, New Zealand
| | - Lam Kok Wai
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
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10
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Fang P, Xie C, Pan T, Cheng T, Chen W, Xia S, Ding T, Fang J, Zhou Y, Fang L, Wei D, Xiao S. Unfolding of an RNA G-quadruplex motif in the negative strand genome of porcine reproductive and respiratory syndrome virus by host and viral helicases to promote viral replication. Nucleic Acids Res 2023; 51:10752-10767. [PMID: 37739415 PMCID: PMC10602871 DOI: 10.1093/nar/gkad759] [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: 01/02/2023] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 09/24/2023] Open
Abstract
G-quadruplex (G4) is a unique secondary structure formed by guanine-rich nucleic acid sequences. Growing studies reported that the genomes of some viruses harbor G4 structures associated with viral replication, opening up a new field to dissect viral infection. Porcine reproductive and respiratory syndrome virus (PRRSV), a representative member of Arteriviridae, is an economically significant pathogen that has devastated the swine industry worldwide for over 30 years. In this study, we identified a highly conserved G-rich sequence with parallel-type G4 structure (named PRRSV-G4) in the negative strand genome RNA of PRRSV. Pyridostatin (PDS), a well-known G4-binding ligand, stabilized the PRRSV-G4 structure and inhibited viral replication. By screening the proteins interacting with PRRSV-G4 in PRRSV-infected cells and single-molecule magnetic tweezers analysis, we found that two helicases, host DDX18 and viral nsp10, interact with and efficiently unwound the PRRSV-G4 structure, thereby facilitating viral replication. Using a PRRSV reverse genetics system, we confirmed that recombinant PRRSV with a G4-disruptive mutation exhibited resistance to PDS treatment, thereby displaying higher replication than wild-type PRRSV. Collectively, these results demonstrate that the PRRSV-G4 structure plays a crucial regulatory role in viral replication, and targeting this structure represents a promising strategy for antiviral therapies.
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Affiliation(s)
- Puxian Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Congbao Xie
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, and Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Ting Pan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Ting Cheng
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Wei Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Sijin Xia
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Tong Ding
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Junkang Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, and Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yanrong Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Dengguo Wei
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, and Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
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11
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Wang J, Huang H, Zhao K, Teng Y, Zhao L, Xu Z, Zheng Y, Zhang L, Li C, Duan Y, Liang K, Zhou X, Cheng X, Xia Y. G-quadruplex in hepatitis B virus pregenomic RNA promotes its translation. J Biol Chem 2023; 299:105151. [PMID: 37567479 PMCID: PMC10485161 DOI: 10.1016/j.jbc.2023.105151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Hepatitis B virus (HBV) is a hepatotropic DNA virus that has a very compact genome. Due to this genomic density, several distinct mechanisms are used to facilitate the viral life cycle. Recently, accumulating evidence show that G-quadruplex (G4) in different viruses play essential regulatory roles in key steps of the viral life cycle. Although G4 structures in the HBV genome have been reported, their function in HBV replication remains elusive. In this study, we treated an HBV replication-competent cell line and HBV-infected cells with the G4 structure stabilizer pyridostatin (PDS) and evaluated different HBV replication markers to better understand the role played by the G4. In both models, we found PDS had no effect on viral precore RNA (pcRNA) or pre-genomic RNA (pgRNA), but treatment did increase HBeAg/HBc ELISA reads and intracellular levels of viral core/capsid protein (HBc) in a dose-dependent manner, suggesting post-transcriptional regulation. To further dissect the mechanism of G4 involvement, we used in vitro-synthesized HBV pcRNA and pgRNA. Interestingly, we found PDS treatment only enhanced HBc expression from pgRNA but not HBeAg expression from pcRNA. Our bioinformatic analysis and CD spectroscopy revealed that pgRNA harbors a conserved G4 structure. Finally, we introduced point mutations in pgRNA to disrupt its G4 structure and observed the resulting mutant failed to respond to PDS treatment and decreased HBc level in in vitro translation assay. Taken together, our data demonstrate that HBV pgRNA contains a G4 structure that plays a vital role in the regulation of viral mRNA translation.
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Affiliation(s)
- Jingjing Wang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Haiyan Huang
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yan Teng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Li Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Zaichao Xu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yingcheng Zheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Lu Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Conghui Li
- Department of Pathophysiology, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yurong Duan
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Kaiwei Liang
- Department of Pathophysiology, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China.
| | - Xiaoming Cheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China; Department of Pathology, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China; Hubei Jiangxia Laboratory, Wuhan, China.
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China; Hubei Jiangxia Laboratory, Wuhan, China.
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12
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Brázda V, Dobrovolná M, Bohálová N, Mergny JL. G-quadruplexes in the evolution of hepatitis B virus. Nucleic Acids Res 2023; 51:7198-7204. [PMID: 37395407 PMCID: PMC10415126 DOI: 10.1093/nar/gkad556] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/23/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023] Open
Abstract
Hepatitis B virus (HBV) is one of the most dangerous human pathogenic viruses found in all corners of the world. Recent sequencing of ancient HBV viruses revealed that these viruses have accompanied humanity for several millenia. As G-quadruplexes are considered to be potential therapeutic targets in virology, we examined G-quadruplex-forming sequences (PQS) in modern and ancient HBV genomes. Our analyses showed the presence of PQS in all 232 tested HBV genomes, with a total number of 1258 motifs and an average frequency of 1.69 PQS per kbp. Notably, the PQS with the highest G4Hunter score in the reference genome is the most highly conserved. Interestingly, the density of PQS motifs is lower in ancient HBV genomes than in their modern counterparts (1.5 and 1.9/kb, respectively). This modern frequency of 1.90 is very close to the PQS frequency of the human genome (1.93) using identical parameters. This indicates that the PQS content in HBV increased over time to become closer to the PQS frequency in the human genome. No statistically significant differences were found between PQS densities in HBV lineages found in different continents. These results, which constitute the first paleogenomics analysis of G4 propensity, are in agreement with our hypothesis that, for viruses causing chronic infections, their PQS frequencies tend to converge evolutionarily with those of their hosts, as a kind of 'genetic camouflage' to both hijack host cell transcriptional regulatory systems and to avoid recognition as foreign material.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
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13
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Narula P, Kiruthika S, Chowdhari S, Vivekanandan P, Chugh A. Inhibition of Hepatitis B Virus (HBV) by Tachyplesin, a Marine Antimicrobial Cell-Penetrating Peptide. Pharmaceutics 2023; 15:pharmaceutics15020672. [PMID: 36839994 PMCID: PMC9962029 DOI: 10.3390/pharmaceutics15020672] [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: 09/26/2022] [Revised: 12/05/2022] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
We investigate the role of Tachyplesin (Tpl), a marine antimicrobial cell-penetrating peptide, as an anti-HBV agent. Our findings, using confocal microscopy and flow cytometry, demonstrate the internalization of FITC-Tpl in both Huh7 and HepG2 cell lines. Further, our results show that Tpl inhibits the expression of HBV proteins, including hepatitis B surface antigen (HBsAg) and hepatitis B 'e' antigen (HBeAg) in cell supernatants of human liver cell lines transfected with 1.3× pHBV. Interestingly Tpl also reduces levels of HBV pre-core RNA and HBV pregenomic RNA, suggesting that Tpl-mediated inhibition occurs at the early stages of HBV replication, including viral transcription. In addition, Tpl led to a significant reduction in levels of hepatitis B virion secretion. In sum, here we demonstrate the potent anti-HBV activity of Tpl at non-cytotoxic concentrations indicating the potential of Tpl to emerge as an effective therapeutic peptide against HBV.
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14
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Makova KD, Weissensteiner MH. Noncanonical DNA structures are drivers of genome evolution. Trends Genet 2023; 39:109-124. [PMID: 36604282 PMCID: PMC9877202 DOI: 10.1016/j.tig.2022.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023]
Abstract
In addition to the canonical right-handed double helix, other DNA structures, termed 'non-B DNA', can form in the genomes across the tree of life. Non-B DNA regulates multiple cellular processes, including replication and transcription, yet its presence is associated with elevated mutagenicity and genome instability. These discordant cellular roles fuel the enormous potential of non-B DNA to drive genomic and phenotypic evolution. Here we discuss recent studies establishing non-B DNA structures as novel functional elements subject to natural selection, affecting evolution of transposable elements (TEs), and specifying centromeres. By highlighting the contributions of non-B DNA to repeated evolution and adaptation to changing environments, we conclude that evolutionary analyses should include a perspective of not only DNA sequence, but also its structure.
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Affiliation(s)
- Kateryna D Makova
- Department of Biology, Penn State University, 310 Wartik Laboratory, University Park, PA 16802, USA.
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15
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Yang J, Qin G, Niu J, Wei Y, Li X, Zhao C, Wang C, Ren J, Qu X. Targeting G-quadruplexes in an ageing epigenetic regulator promoter for rescuing mitochondrial dysfunction in Alzheimer's disease. Chem Commun (Camb) 2023; 59:1078-1081. [PMID: 36621881 DOI: 10.1039/d2cc05957f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Here, we provide an out-of-the-box G-quadruplex (G4) targeting-based strategy for rescuing mitochondrial dysfunction in Alzheimer's disease. We predict and verify the presence of G4s within the promoter of an ageing epigenetic regulator BAZ2B. G4-specific ligands targeting BAZ2B G4s could significantly down-regulate the BAZ2B expression and relieve mitochondrial dysfunction. Therefore, this work may provide a new way of rescuing mitochondrial dysfunction in AD by targeting G4s in a specific ageing epigenetic regulator promoter.
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Affiliation(s)
- Jie Yang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Geng Qin
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jingsheng Niu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yue Wei
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xuexia Li
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Chunyu Wang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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16
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Smeller L. Pressure Tuning Studies of Four-Stranded Nucleic Acid Structures. Int J Mol Sci 2023; 24:ijms24021803. [PMID: 36675317 PMCID: PMC9866529 DOI: 10.3390/ijms24021803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Four-stranded folded structures, such as G-quadruplexes and i-motifs in the genome, have attracted a growing interest nowadays since they have been discovered in the telomere and in several oncogene promoter regions. Their biological relevance is undeniable since their existence in living cells has been observed. In vivo they take part in the regulation of gene expression, in vitro they are used in the analytical biochemistry. They are attractive and promising targets for cancer therapy. Pressure studies can reveal specific aspects of the molecular processes. Pressure tuning experiments allow the determination of the volumetric parameters of the folded structures and of the folding-unfolding processes. Here, we review the thermodynamic parameters with a special focus on the volumetric ones, which were determined using pressure tuning spectroscopic experiments on the G-quadruplex and i-motif nucleic acid forms.
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Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
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17
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Lv L, Zhang L. G-quadruplexes in the monkeypox virus are potential antiviral targets. J Med Virol 2023; 95:e28299. [PMID: 36366981 DOI: 10.1002/jmv.28299] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022]
Abstract
Monkeypox virus (MPXV) is a member of Orthopoxvirus in the Poxviridae family, causing a Public Health Emergency of International Concern. The number of cases and geographic range has increased significantly in 2022. Identification of MPXV-specific therapeutic targets is urgent. G-quadruplex (GQ) secondary structures attract great attention as potential targets for antiviral strategy. Whether GQs are present in the MPXV genome remains inconclusive. In this study, we aim to characterize the GQs encoded by MPXV. Through a series of biophysical experiments, we characterized the formation potential of MPXV-encoded GQs and evaluated the binding and stabilization abilities of GQ ligands including BRACO-19, pyridostatin, and TMPyP4 to GQs encoded by MPXV. Moreover, GQ ligands suppressed the gene transcription of MPXV sequences containing GQ. BRACO-19 and TMPyP4 were able to inhibit vaccinia virus replication. We demonstrated the existence of MPXV GQ and reinforced the idea that GQs could be novel antiviral targets. Targeting these GQ sequences with GQ-binding molecules may represent a new approach for MPXV therapy.
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Affiliation(s)
- Lu Lv
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.,Institute of Infection and Immunity, Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Leiliang Zhang
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.,Institute of Infection and Immunity, Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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18
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Qin G, Zhao C, Yang J, Wang Z, Ren J, Qu X. Unlocking G-Quadruplexes as Targets and Tools against COVID-19. CHINESE J CHEM 2022; 41:CJOC202200486. [PMID: 36711116 PMCID: PMC9874442 DOI: 10.1002/cjoc.202200486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 02/01/2023]
Abstract
The applicability of G-quadruplexes (G4s) as antiviral targets, therapeutic agents and diagnostic tools for coronavirus disease 2019 (COVID-19) is currently being evaluated, which has drawn the extensive attention of the scientific community. During the COVID-19 pandemic, research in this field is rapidly accumulating. In this review, we summarize the latest achievements and breakthroughs in the use of G4s as antiviral targets, therapeutic agents and diagnostic tools for COVID-19, particularly using G4 ligands. Finally, strength and weakness regarding G4s in anti-SARS-CoV-2 field are highlighted for prospective future projects.
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Affiliation(s)
- Geng Qin
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Jie Yang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Zhao Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
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19
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Teng Y, Zhu M, Chi Y, Li L, Jin Y. Can G-quadruplex become a promising target in HBV therapy? Front Immunol 2022; 13:1091873. [PMID: 36591216 PMCID: PMC9797731 DOI: 10.3389/fimmu.2022.1091873] [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: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
The chronic infection with hepatitis B virus (HBV) is an important health problem that affects millions of people worldwide. Current therapies for HBV always suffer from a poor response rate, common side effects, and the need for lifelong treatment. Novel therapeutic targets are expected. Interestingly, non-canonical structures of nucleic acids play crucial roles in the regulation of gene expression. Especially the formation of G-quadruplexes (G4s) in G-rich strands has been demonstrated to affect many bioprocesses including replication, transcription, and translation, showing great potential as targets in anticancer and antiviral therapies. In this review, we summarize recent antiviral studies about G4s and discuss the potential roles of G4 structures in antiviral therapy for HBV.
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Affiliation(s)
- Ye Teng
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ming Zhu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yuan Chi
- Pharmaceutical Department, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Lijing Li
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Lijing Li, ; Ye Jin,
| | - Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Lijing Li, ; Ye Jin,
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20
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Sun H, Chang L, Yan Y, Ji H, Jiang X, Song S, Xiao Y, Lu Z, Wang L. Naturally occurring pre-S mutations promote occult HBV infection by affecting pre-S2/S promoter activity. Antiviral Res 2022; 208:105448. [DOI: 10.1016/j.antiviral.2022.105448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2022]
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21
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Advances in
G
‐quadruplexes‐based fluorescent imaging. Biopolymers 2022; 113:e23528. [DOI: 10.1002/bip.23528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
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22
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Kabbara A, Vialet B, Marquevielle J, Bonnafous P, Mackereth CD, Amrane S. RNA G-quadruplex forming regions from SARS-2, SARS-1 and MERS coronoviruses. Front Chem 2022; 10:1014663. [PMID: 36479439 PMCID: PMC9719988 DOI: 10.3389/fchem.2022.1014663] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/26/2022] [Indexed: 11/14/2023] Open
Abstract
COVID-19 (Corona Virus Disease 2019), SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome) are infectious diseases each caused by coronavirus outbreaks. Small molecules and other therapeutics are rapidly being developed to treat these diseases, but the threat of new variants and outbreaks argue for the identification of additional viral targets. Here we identify regions in each of the three coronavirus genomes that are able to form G-quadruplex (G4) structures. G4s are structures formed by DNA or RNA with a core of two or more stacked planes of guanosine tetrads. In recent years, numerous DNA and RNA G4s have emerged as promising pharmacological targets for the treatment of cancer and viral infection. We use a combination of bioinformatics and biophysical approaches to identify conserved RNA G4 regions from the ORF1A and S sequences of SARS-CoV, SARS-CoV-2 and MERS-CoV. Although a general depletion of G4-forming regions is observed in coronaviridae, the preservation of these selected G4 sequences support a significance in viral replication. Targeting these RNA structures may represent a new antiviral strategy against these viruses distinct from current approaches that target viral proteins.
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Affiliation(s)
| | | | | | | | | | - Samir Amrane
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, Bordeaux, France
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23
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Hepatitis B Virus-Encoded HBsAg Contributes to Hepatocarcinogenesis by Inducing the Oncogenic Long Noncoding RNA LINC00665 through the NF-κB Pathway. Microbiol Spectr 2022; 10:e0273121. [PMID: 35993712 PMCID: PMC9603668 DOI: 10.1128/spectrum.02731-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Clinical and in vivo studies have demonstrated a role for hepatitis B virus (HBV)-encoded HBsAg (hepatitis B surface antigen) in HBV-related hepatocellular carcinoma (HCC); however, the underlying mechanisms remain largely unknown. Here, we investigated the role of HBsAg in regulating long noncoding RNAs (lncRNAs) involved in HCC progression. Our analysis of microarray data sets identified LINC00665 as an HBsAg-regulated lncRNA. Furthermore, LINC00665 is upregulated in liver samples from HBV-infected patients as well as in HCC, specifically in HBV-related HCC liver samples. These findings were supported by our in vitro data demonstrating that HBsAg, as well as HBV, positively regulates LINC00665 in multiple HBV cell culture models. Next, we evaluated the oncogenic potential of LINC00665 by its overexpression and CRISPR interference (CRISPRi)-based knockdown in various cell-based assays. LINC00665 promoted cell proliferation, migration, and colony formation but inhibited cell apoptosis in vitro. We then identified the underlying mechanism of HBsAg-mediated regulation of LINC00665. We used immunofluorescence assays to show that HBsAg enhanced the nuclear translocation of NF-κB factors in HepG2 cells, confirming that HBsAg activates NF-κB. Inhibition of NF-κB signaling nullified HBsAg-mediated LINC00665 upregulation, suggesting that HBsAg acts through NF-κB to regulate LINC00665. Furthermore, the LINC00665 promoter contains NF-κB binding sites, and their disruption abrogated HBsAg-induced LINC00665 upregulation. Finally, HBsAg facilitated the enrichment of the NF-κB factors NF-κB1, RelA, and c-Rel in the LINC00665 promoter. Taken together, this work shows that HBsAg can drive hepatocarcinogenesis by upregulating oncogenic LINC000665 through the NF-κB pathway, thereby identifying a novel mechanism in HBV-related HCC. IMPORTANCE Hepatitis B virus (HBV) is a major risk factor for hepatocellular carcinoma (HCC). Numerous reports indicate an oncogenic role for HBV-encoded HBsAg; however, the underlying mechanisms are not well understood. Here, we studied the role of HBsAg in regulating lncRNAs involved in hepatocarcinogenesis. We demonstrate that HBsAg, as well as HBV, positively regulates oncogenic lncRNA LINC00665. The clinical significance of this lncRNA is highlighted by our observation that LINC00665 is upregulated in liver samples during HBV infection and HBV-related HCC. Furthermore, we show LINC00665 can drive hepatocarcinogenesis by promoting cell proliferation, colony formation, and cell migration and inhibiting apoptosis. Taken together, this work identified LINC00665 as a novel gene through which HBsAg can drive hepatocarcinogenesis. Finally, we show that HBsAg enhances LINC00665 levels in hepatocytes by activating the NF-κB pathway, thereby identifying a novel mechanism by which HBV may contribute to HCC.
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24
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Interface of G-quadruplex with both stabilizing and destabilizing ligands for targeting various diseases. Int J Biol Macromol 2022; 219:414-427. [DOI: 10.1016/j.ijbiomac.2022.07.248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 11/19/2022]
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25
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Zhai LY, Liu JF, Zhao JJ, Su AM, Xi XG, Hou XM. Targeting the RNA G-Quadruplex and Protein Interactome for Antiviral Therapy. J Med Chem 2022; 65:10161-10182. [PMID: 35862260 DOI: 10.1021/acs.jmedchem.2c00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, G-quadruplexes (G4s), types of noncanonical four-stranded nucleic acid structures, have been identified in many viruses that threaten human health, such as HIV and Epstein-Barr virus. In this context, G4 ligands were designed to target the G4 structures, among which some have shown promising antiviral effects. In this Perspective, we first summarize the diversified roles of RNA G4s in different viruses. Next, we introduce small-molecule ligands developed as G4 modulators and highlight their applications in antiviral studies. In addition to G4s, we comprehensively review the medical intervention of G4-interacting proteins from both the virus (N protein, viral-encoded helicases, severe acute respiratory syndrome-unique domain, and Epstein-Barr nuclear antigen 1) and the host (heterogeneous nuclear ribonucleoproteins, RNA helicases, zinc-finger cellular nucelic acid-binding protein, and nucleolin) by inhibitors as an alternative way to disturb the normal functions of G4s. Finally, we discuss the challenges and opportunities in G4-based antiviral therapy.
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Affiliation(s)
- Li-Yan Zhai
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jing-Fan Liu
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jian-Jin Zhao
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Ai-Min Su
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China.,Laboratory of Biology and Applied Pharmacology, CNRS UMR 8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
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26
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Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques. Int J Mol Sci 2022; 23:ijms23105761. [PMID: 35628571 PMCID: PMC9144967 DOI: 10.3390/ijms23105761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/06/2023] Open
Abstract
Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of high pressure (>100 MPa = 1 kbar) in biology. Studies of high pressure can give insight into the volumetric aspects of various biological systems; this information cannot be obtained otherwise. High-pressure treatment is a potentially useful alternative method to heat-treatment in food science. Elevated pressure (up to 120 MPa) is present in the deep sea, which is a considerable part of the biosphere. From a basic scientific point of view, the application of the gamut of modern spectroscopic techniques provides information about the conformational changes of biomolecules, fluctuations, and flexibility. This paper reviews first the thermodynamic aspects of pressure science, the important parameters affecting the volume of a molecule. The technical aspects of high pressure production are briefly mentioned, and the most common high-pressure-compatible spectroscopic techniques are also discussed. The last part of this paper deals with the main biomolecules, lipids, proteins, and nucleic acids: how they are affected by pressure and what information can be gained about them using pressure. I I also briefly mention a few supramolecular structures such as viruses and bacteria. Finally, a subjective view of the most promising directions of high pressure bioscience is outlined.
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27
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Characterization of G-Quadruplexes in Enterovirus A71 Genome and Their Interaction with G-Quadruplex Ligands. Microbiol Spectr 2022; 10:e0046022. [PMID: 35446122 PMCID: PMC9241713 DOI: 10.1128/spectrum.00460-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human enteroviruses cause many diseases; however, there is no specific therapeutic drug. G-quadruplex is an atypical secondary structure formed in the guanine rich region of DNA or RNA, which can exist in the viral genome. The different positions of G-quadruplex play an important role in the regulation of virus replication and infection. Whether G-quadruplexes are present in human enteroviruses is unknown. In current study, we analyzed the potential quadruplex forming sequences of human enteroviruses, especially EV-A71 virus, which causes hand, foot, and mouth disease. The results showed that there were a certain number of potential quadruplex-forming sequences in human enteroviruses. Through a variety of experimental methods, we evaluated the formation potential of EV-A71 encoded G-quadruplex and analyzed the binding ability of G-quadruplex ligands, including BRACO-19, pyridostatin and TMPyP4 to virus encoded G-quadruplexes. G-quadruplex ligands BRACO-19, PDS and TMPyP4 could inhibit the transcription of constructs containing EV-A71 G-quadruplex sequences. Moreover, we found that BRACO-19 was able to inhibit the replication of EV-A71, suggesting that targeting G-quadruplexes in EV-A71 genome by G-quadruplex ligands could be a novel antiviral way against EV-A71. Our finding not only uncovered the G-quadruplexes in human enteroviruses, but also would provide a new strategy for human enteroviruses therapy. IMPORTANCE G-quadruplex is a stable nucleic acid secondary structure formed by the folding of guanine rich nucleic acid. The important regulatory function of G-quadruplex makes it an attractive target of antiviral effect. Human enteroviruses cause a variety of human diseases, including common cold, nervous system diseases, cardiovascular damage, and diabetes. Enterovirus A71 (EV-A71) is one of pathogens causing hand, foot, and mouth disease; however, whether G-quadruplexes are present in the genomes of human enteroviruses is unknown. The function of G-quadruplexes in the EV-A71 genomes is not clear. We predicted and characterized G-quadruplex sequences in EV-A71. G-quadruplex ligands were identified to stabilize EV-A71 G-quadruplexes with high affinities. We also demonstrated G-quadruplex ligand BRACO-19 inhibited EV-A71 replication. Our studies provide a framework for targeting G-quadruplexes in the enteroviruses genome, which will be a new way to develop antiviral agents against human enteroviruses.
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28
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Kumar S, Ramamurthy C, Choudhary D, Sekar A, Patra A, Bhavesh NS, Vivekanandan P. Contrasting roles for G-quadruplexes in regulating human Bcl-2 and virus homologues KSHV KS-Bcl-2 and EBV BHRF1. Sci Rep 2022; 12:5019. [PMID: 35322051 PMCID: PMC8943185 DOI: 10.1038/s41598-022-08161-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/03/2022] [Indexed: 01/14/2023] Open
Abstract
Herpesviruses are known to acquire several genes from their hosts during evolution. We found that a significant proportion of virus homologues encoded by HSV-1, HSV-2, EBV and KSHV and their human counterparts contain G-quadruplex motifs in their promoters. We sought to understand the role of G-quadruplexes in the regulatory regions of viral Bcl-2 homologues encoded by KSHV (KS-Bcl-2) and EBV (BHRF1). We demonstrate that the KSHV KS-Bcl-2 and the EBV BHRF1 promoter G-quadruplex motifs (KSHV-GQ and EBV-GQ) form stable intramolecular G-quadruplexes. Ligand-mediated stabilization of KS-Bcl-2 and BHRF1 promoter G-quadruplexes significantly increased the promoter activity resulting in enhanced transcription of these viral Bcl-2 homologues. Mutations disrupting KSHV-GQ and EBV-GQ inhibit promoter activity and render the KS-Bcl-2 and the BHRF1 promoters non-responsive to G-quadruplex ligand. In contrast, promoter G-quadruplexes of human bcl-2 gene inhibit promoter activity. Further, KS-Bcl-2 and BHRF1 promoter G-quadruplexes augment RTA (a virus-encoded transcription factor)-mediated increase in viral bcl-2 promoter activity. In sum, this work highlights how human herpesviruses have evolved to exploit promoter G-quadruplexes to regulate virus homologues to counter their cellular counterparts.
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Affiliation(s)
- Shivani Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi, 110016, India
| | - Chitteti Ramamurthy
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi, 110016, India
| | - Divya Choudhary
- Department of Chemical Engineering, Indian Institute of Technology, Delhi, New Delhi, 110016, India
| | - Aashika Sekar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, New Delhi, 110016, India
| | - Anupam Patra
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, Delhi, New Delhi, 110067, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, Delhi, New Delhi, 110067, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi, 110016, India.
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29
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Mendes E, Aljnadi IM, Bahls B, Victor BL, Paulo A. Major Achievements in the Design of Quadruplex-Interactive Small Molecules. Pharmaceuticals (Basel) 2022; 15:ph15030300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022] Open
Abstract
Organic small molecules that can recognize and bind to G-quadruplex and i-Motif nucleic acids have great potential as selective drugs or as tools in drug target discovery programs, or even in the development of nanodevices for medical diagnosis. Hundreds of quadruplex-interactive small molecules have been reported, and the challenges in their design vary with the intended application. Herein, we survey the major achievements on the therapeutic potential of such quadruplex ligands, their mode of binding, effects upon interaction with quadruplexes, and consider the opportunities and challenges for their exploitation in drug discovery.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
| | - Israa M. Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bruno L. Victor
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Correspondence:
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30
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Lv L, Cui H, Chen Z, Zhou Y, Zhang L. G‐quadruplex ligands inhibit chikungunya virus replication. J Med Virol 2022; 94:2519-2527. [PMID: 35075669 DOI: 10.1002/jmv.27622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/27/2021] [Accepted: 01/21/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Lu Lv
- Department of Clinical Laboratory MedicineThe First Affifiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan HospitalJinanShandongChina
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Haoran Cui
- Department of Clinical Laboratory MedicineThe First Affifiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan HospitalJinanShandongChina
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Zhiyang Chen
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Yixuan Zhou
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Leiliang Zhang
- Department of Clinical Laboratory MedicineThe First Affifiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan HospitalJinanShandongChina
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
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31
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:2120-2124. [DOI: 10.1093/jac/dkac148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/12/2022] [Indexed: 11/15/2022] Open
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32
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Xu J, Huang H, Zhou X. G-Quadruplexes in Neurobiology and Virology: Functional Roles and Potential Therapeutic Approaches. JACS AU 2021; 1:2146-2161. [PMID: 34977886 PMCID: PMC8715485 DOI: 10.1021/jacsau.1c00451] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 05/11/2023]
Abstract
A G-quadruplex (G4) is a four-stranded nucleic acid secondary structure maintained by Hoogsteen hydrogen bonds established between four guanines. Experimental studies and bioinformatics predictions support the hypothesis that these structures are involved in different cellular functions associated with both DNA and RNA processes. An increasing number of diseases have been shown to be associated with abnormal G4 regulation. Here, we describe the existence of G4 and then discuss G4-related pathogenic mechanisms in neurodegenerative diseases and the viral life cycle. Furthermore, we focus on the role of G4s in the design of antiviral therapy and neuropharmacology, including G4 ligands, G4-based aptamers, G4-related proteins, and CRISPR-based sequence editing, along with a discussion of limitations and insights into the prospects of this unusual nucleic acid secondary structure in therapeutics. Finally, we highlight progress and challenges in this field and the potential G4-related research fields.
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Affiliation(s)
- Jinglei Xu
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
| | - Haiyan Huang
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Xiang Zhou
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
- Email to X.Z.:
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33
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Molnár OR, Végh A, Somkuti J, Smeller L. Characterization of a G-quadruplex from hepatitis B virus and its stabilization by binding TMPyP4, BRACO19 and PhenDC3. Sci Rep 2021; 11:23243. [PMID: 34853392 PMCID: PMC8636512 DOI: 10.1038/s41598-021-02689-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/12/2021] [Indexed: 12/22/2022] Open
Abstract
Specific guanine rich nucleic acid sequences can form non-canonical structures, like the four stranded G-quadruplex (GQ). We studied the GQ-forming sequence (named HepB) found in the genome of the hepatitis B virus. Fluorescence-, infrared- and CD-spectroscopy were used. HepB shows a hybrid form in presence of K+, but Na+, Li+, and Rb+ induce parallel structure. Higher concentrations of metal ions increase the unfolding temperature, which was explained by a short thermodynamic calculation. Temperature stability of the GQ structure was determined for all these ions. Na+ has stronger stabilizing effect on HepB than K+, which is highly unusual. The transition temperatures were 56.6, 53.8, 58.5 and 54.4 °C for Na+, K+, Li+, and Rb+ respectively. Binding constants for Na+ and K+ were 10.2 mM and 7.1 mM respectively. Study of three ligands designed in cancer research for GQ targeting (TMPyP4, BRACO19 and PhenDC3) showed unequivocally their binding to HepB. Binding was proven by the increased stability of the bound form. The stabilization was higher than 20 °C for TMPyP4 and PhenDC3, while it was considerably lower for BRACO19. These results might have medical importance in the fight against the hepatitis B virus.
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Affiliation(s)
- Orsolya Réka Molnár
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary
| | - András Végh
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary.,Department of Ophthalmology, Semmelweis University, Budapest, 1085, Hungary
| | - Judit Somkuti
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary.
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34
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Chen Y, Wei D, Deng M. Comparative Analysis of Serum Proteins Between Hepatitis B Virus Genotypes B and C Infection by DIA-Based Quantitative Proteomics. Infect Drug Resist 2021; 14:4701-4715. [PMID: 34795487 PMCID: PMC8592397 DOI: 10.2147/idr.s335666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022] Open
Abstract
Purpose In clinical practice, the clinicopathological profiles and outcomes of patients infected with hepatitis B virus (HBV) are different between genotypes B and C. However, little is known about the potential mechanism and differences in specific biological pathways associated with the different genotype. This study aimed to compare the serum protein profile between patients infected with HBV genotype B and those infected with HBV genotype C. Patients and Methods A total of 54 serum samples from patients with chronic HBV genotype B infection and those with chronic HBV genotype C infection, and healthy controls were used for the proteomic analysis (n = 18 samples in per group). Serum proteomic profiles were analyzed using data-independent acquisition (DIA)-based liquid chromatography-mass spectrometry to identify differentially expressed proteins (up- or downregulation of at least 1.5-fold) between serum samples from HBV patients infected with HBV genotype B and those infected with genotype C. Results We identified 1010 proteins, 53 of which were differentially expressed between the serum samples of the healthy controls and those of HBV genotype B infected patients, and 59 that were differentially expressed between the samples of the healthy controls and those of HBV genotype C infected patients. Furthermore, our results indicated that two proteins identified as being differentially expressed (VWF and C8B) have potential as biomarkers for distinguishing genotype B infected HBV patients from those infected with genotype C. Conclusion The results of our DIA-based quantitative proteomic analysis revealed that HBV genotypes B and C are associated with different molecular profiles and may provide fundamental information for further detailed investigations of the molecular mechanism underlying these differences.
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Affiliation(s)
- Yunqing Chen
- Department of Infectious Diseases, Affiliated Hospital of Jiaxing University, Jiaxing, People's Republic of China.,Department of Infectious Diseases, First Hospital of Jiaxing, Jiaxing, People's Republic of China
| | - Dahai Wei
- Department of Infectious Diseases, Affiliated Hospital of Jiaxing University, Jiaxing, People's Republic of China.,Department of Infectious Diseases, First Hospital of Jiaxing, Jiaxing, People's Republic of China.,Institute of Hepatology, Affiliated Hospital of Jiaxing University, Jiaxing, People's Republic of China
| | - Min Deng
- Department of Infectious Diseases, Affiliated Hospital of Jiaxing University, Jiaxing, People's Republic of China.,Department of Infectious Diseases, First Hospital of Jiaxing, Jiaxing, People's Republic of China.,Institute of Hepatology, Affiliated Hospital of Jiaxing University, Jiaxing, People's Republic of China
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35
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Somkuti J, Molnár OR, Grád A, Smeller L. Pressure Perturbation Studies of Noncanonical Viral Nucleic Acid Structures. BIOLOGY 2021; 10:1173. [PMID: 34827166 PMCID: PMC8615049 DOI: 10.3390/biology10111173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/16/2022]
Abstract
G-quadruplexes are noncanonical structures formed by guanine-rich sequences of the genome. They are found in crucial loci of the human genome, they take part in the regulation of important processes like cell proliferation and cell death. Much less is known about the subjects of this work, the viral G-quadruplexes. We have chosen three potentially G-quadruplex-forming sequences of hepatitis B. We measured the stability and the thermodynamic parameters of these quadruplexes. We also investigated the potential stabilization of these G-quadruplexes by binding a special ligand that was originally developed for cancer therapy. Fluorescence and infrared spectroscopic measurements were performed over wide temperature and pressure ranges. Our experiments indicate the small unfolding volume change of all three oligos. We found a difference between the unfolding of the 2-quartet and the 3-quartet G-quadruplexes. All three G-quadruplexes were stabilized by TMPyP4, which is a cationic porphyrin developed for stabilizing the human telomere.
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Affiliation(s)
| | | | | | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary; (J.S.); (O.R.M.); (A.G.)
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Zou M, Li JY, Zhang MJ, Li JH, Huang JT, You PD, Liu SW, Zhou CQ. G-quadruplex binder pyridostatin as an effective multi-target ZIKV inhibitor. Int J Biol Macromol 2021; 190:178-188. [PMID: 34461156 DOI: 10.1016/j.ijbiomac.2021.08.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
At present, there are still no anti-Zika virus (ZIKV) drugs or vaccines approved by FDA with accurate targets and antiviral mechanisms. Considering the RNA G-quadruplex sequences in ZIKV genome, it is very meaningful to develop G-quadruplex binders as potential anti-ZIKV drugs with novel and accurate targets. In this paper, five classical G-quadruplex binders including Ber, Braco 19, NiL, 360A and PDS have been chosen to discuss their interaction with ZIKV RNA G-quadruplexes. PDS shows higher binding affinity and thermal stability than the other G-quadruplex binders. This property is further evidenced in cells by immunofluorescence microscopy. And PDS shows higher anti-ZIKV activity (EC50 = 4.2 ± 0.4 μM) than the other G-quadruplex binders as well as the positive control ribavirin, with a low cytotoxicity. By time-of-addition assay, PDS exerts antiviral activity at the post-entry process of ZIKV replication cycle, thus inhibiting ZIKV mRNA replication and protein expression. Furthermore, PDS combines with ZIKV NS2B-NS3 protease and reduces its catalytic activity. This study suggests that G-quadruplex binder PDS is an effective multi-target ZIKV inhibitor, which provides more guidance to design some novel anti-ZIKV drugs targeting ZIKV RNA G-quadruplexes.
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Affiliation(s)
- Min Zou
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Jing-Yan Li
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Meng-Jia Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Jun-Hui Li
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Jun-Tao Huang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Pei-Dan You
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Shu-Wen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
| | - Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
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Ravichandran S, Razzaq M, Parveen N, Ghosh A, Kim KK. The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex. Nucleic Acids Res 2021; 49:10689-10706. [PMID: 34450640 PMCID: PMC8501965 DOI: 10.1093/nar/gkab739] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/10/2021] [Accepted: 08/24/2021] [Indexed: 12/29/2022] Open
Abstract
G-quadruplex (G4), a four-stranded DNA or RNA structure containing stacks of guanine tetrads, plays regulatory roles in many cellular functions. So far, conventional G4s containing loops of 1–7 nucleotides have been widely studied. Increasing experimental evidence suggests that unconventional G4s, such as G4s containing long loops (long-loop G4s), play a regulatory role in the genome by forming a stable structure. Other secondary structures such as hairpins in the loop might thus contribute to the stability of long-loop G4s. Therefore, investigation of the effect of the hairpin-loops on the structure and function of G4s is required. In this study, we performed a systematic biochemical investigation of model G4s containing long loops with various sizes and structures. We found that the long-loop G4s are less stable than conventional G4s, but their stability increased when the loop forms a hairpin (hairpin-G4). We also verified the biological significance of hairpin-G4s by showing that hairpin-G4s present in the genome also form stable G4s and regulate gene expression as confirmed by in cellulo reporter assays. This study contributes to expanding the scope and diversity of G4s, thus facilitating future studies on the role of G4s in the human genome.
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Affiliation(s)
- Subramaniyam Ravichandran
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Maria Razzaq
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Nazia Parveen
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Ambarnil Ghosh
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
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Ahluwalia S, Choudhary D, Tyagi P, Kumar V, Vivekanandan P. Vitamin D signaling inhibits HBV activity by directly targeting the HBV core promoter. J Biol Chem 2021; 297:101233. [PMID: 34562448 PMCID: PMC8517215 DOI: 10.1016/j.jbc.2021.101233] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Clinical and epidemiological studies support a role for vitamin D in suppressing hepatitis B virus (HBV). This antiviral role of vitamin D is widely attributed to vitamin D receptor (VDR)/retinoid X receptor-mediated regulation of host immunomodulatory genes through vitamin D response elements (VDREs) in their promoters. Here, we investigated the ability of calcitriol (1α,25-dihydroxyvitamin D3, metabolically activated vitamin D) to directly regulate HBV activity through this signaling pathway. We observed that calcitriol selectively inhibited only the HBV core promoter without affecting the HBV-PreS1, HBV-PreS2/S, or HBx promoters. We then identified a VDRE cluster in the HBV core promoter that is highly conserved across most HBV genotypes. Disruption of this VDRE cluster abrogated calcitriol-mediated suppression of the HBV core promoter. Furthermore, we showed that VDR interacts directly with the VDRE cluster in the HBV core promoter independent of retinoid X receptor. This demonstrates that calcitriol inhibits HBV core promoter activity through a noncanonical calcitriol-activated VDR pathway. Finally, we observed that calcitriol suppressed expression of the canonical HBV core promoter transcripts, pregenomic RNA, and precore RNA in multiple HBV cell culture models. In addition, calcitriol inhibited the secretion of hepatitis B "e" antigen and hepatitis B surface antigen (HBV-encoded proteins linked to poor disease prognosis), without affecting virion secretion. Our findings identify VDR as a novel regulator of HBV core promoter activity and also explain at least in part the correlation of vitamin D levels to HBV activity observed in clinical studies. Furthermore, this study has implications on the potential use of vitamin D along with anti-HBV therapies, and lays the groundwork for studies on vitamin D-mediated regulation of viruses through VDREs in virus promoters.
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Affiliation(s)
- Shivaksh Ahluwalia
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Divya Choudhary
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Purnima Tyagi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary sciences, New Delhi, India
| | - Vijay Kumar
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary sciences, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
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Wang E, Thombre R, Shah Y, Latanich R, Wang J. G-Quadruplexes as pathogenic drivers in neurodegenerative disorders. Nucleic Acids Res 2021; 49:4816-4830. [PMID: 33784396 PMCID: PMC8136783 DOI: 10.1093/nar/gkab164] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/20/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
G-quadruplexes (G4s), higher-order DNA and RNA secondary structures featuring guanine-rich nucleic acid sequences with various conformations, are widely distributed in the human genome. These structural motifs are known to participate in basic cellular processes, including transcription, splicing, and translation, and their functions related to health and disease are becoming increasingly recognized. In this review, we summarize the landscape of G4s involved in major neurodegenerative disorders, describing the genes that contain G4-forming sequences and proteins that have high affinity for G4-containing elements. The functions of G4s are diverse, with potentially protective or deleterious effects in the pathogenic cascades of various neurological diseases. While the studies of the functions of G4s in vivo, including those involved in pathophysiology, are still in their early stages, we will nevertheless discuss the evidence pointing to their biological relevance. A better understanding of this unique structural element in the biological context is important for unveiling its potential roles in the pathogenesis of diseases such as neurodegeneration and for designing new diagnostic and therapeutic strategies.
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Affiliation(s)
- Ernest Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ravi Thombre
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yajas Shah
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Rachel Latanich
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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40
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Pruška A, Marchand A, Zenobi R. Novel Insight into Proximal DNA Domain Interactions from Temperature-Controlled Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2021; 60:15390-15398. [PMID: 33822450 PMCID: PMC8251475 DOI: 10.1002/anie.202016757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/07/2021] [Indexed: 01/05/2023]
Abstract
Quadruplexes are non-canonical nucleic acid structures essential for many cellular processes. Hybrid quadruplex-duplex oligonucleotide assemblies comprised of multiple domains are challenging to study with conventional biophysical methods due to their structural complexity. Here, we introduce a novel method based on native mass spectrometry (MS) coupled with a custom-built temperature-controlled nanoelectrospray ionization (TCnESI) source designed to investigate interactions between proximal DNA domains. Thermal denaturation experiments were aimed to study unfolding of multi-stranded oligonucleotide constructs derived from biologically relevant structures and to identify unfolding intermediates. Using the TCnESI MS, we observed changes in Tm and thermodynamic characteristics of proximal DNA domains depending on the number of domains, their position, and order in a single experiment.
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Affiliation(s)
- Adam Pruška
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Adrien Marchand
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Renato Zenobi
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
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41
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Pruška A, Marchand A, Zenobi R. Novel Insight into Proximal DNA Domain Interactions from Temperature‐Controlled Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Adam Pruška
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Adrien Marchand
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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42
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Mishra S, Kota S, Chaudhary R, Misra HS. Guanine quadruplexes and their roles in molecular processes. Crit Rev Biochem Mol Biol 2021; 56:482-499. [PMID: 34162300 DOI: 10.1080/10409238.2021.1926417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The role of guanine quadruplexes (G4) in fundamental biological processes like DNA replication, transcription, translation and telomere maintenance is recognized. G4 structure dynamics is regulated by G4 structure binding proteins and is thought to be crucial for the maintenance of genome integrity in both prokaryotic and eukaryotic cells. Growing research over the last decade has expanded the existing knowledge of the functional diversity of G4 (DNA and RNA) structures across the working models. The control of G4 structure dynamics using G4 binding drugs has been suggested as the putative targets in the control of cancer and bacterial pathogenesis. This review has brought forth the collections of recent information that indicate G4 (mostly G4 DNA) roles in microbial pathogenesis, DNA damaging stress response in bacteria and mammalian cells. Studies in mitochondrial gene function regulation by G4s have also been underscored. Finally, the interdependence of G4s and epigenetic modifications and their speculated medical implications through G4 interacting proteins has been discussed.
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Affiliation(s)
- Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
| | - Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
| | - H S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
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Abstract
Quadruplex structures have been identified in a plethora of organisms where they play important functions in the regulation of molecular processes, and hence have been proposed as therapeutic targets for many diseases. In this paper we report the extensive bioinformatic analysis of the SARS-CoV-2 genome and related viruses using an upgraded version of the open-source algorithm G4-iM Grinder. This version improves the functionality of the software, including an easy way to determine the potential biological features affected by the candidates found. The quadruplex definitions of the algorithm were optimized for SARS-CoV-2. Using a lax quadruplex definition ruleset, which accepts amongst other parameters two residue G- and C-tracks, 512 potential quadruplex candidates were discovered. These sequences were evaluated by their in vitro formation probability, their position in the viral RNA, their uniqueness and their conservation rates (calculated in over seventeen thousand different COVID-19 clinical cases and sequenced at different times and locations during the ongoing pandemic). These results were then compared subsequently to other Coronaviridae members, other Group IV (+)ssRNA viruses and the entire viral realm. Sequences found in common with other viral species were further analyzed and characterized. Sequences with high scores unique to the SARS-CoV-2 were studied to investigate the variations amongst similar species. Quadruplex formation of the best candidates were then confirmed experimentally. Using NMR and CD spectroscopy, we found several highly stable RNA quadruplexes that may be suitable therapeutic targets for the SARS-CoV-2.
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A novel piperazine derivative that targets hepatitis B surface antigen effectively inhibits tenofovir resistant hepatitis B virus. Sci Rep 2021; 11:11723. [PMID: 34083665 PMCID: PMC8175705 DOI: 10.1038/s41598-021-91196-1] [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: 03/02/2021] [Accepted: 05/19/2021] [Indexed: 02/04/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection is a global problem. The loss of hepatitis B surface antigen (HBsAg) in serum is a therapeutic end point. Prolonged therapy with nucleoside/nucleotide analogues targeting the HBV-polymerase may lead to resistance and rarely results in the loss of HBsAg. Therefore, inhibitors targeting HBsAg may have potential therapeutic applications. Here, we used computational virtual screening, docking, and molecular dynamics simulations to identify potential small molecule inhibitors against HBsAg. After screening a million molecules from ZINC database, we identified small molecules with potential anti-HBV activity. Subsequently, cytotoxicity profiles and anti-HBV activities of these small molecules were tested using a widely used cell culture model for HBV. We identified a small molecule (ZINC20451377) which binds to HBsAg with high affinity, with a KD of 65.3 nM, as determined by Surface Plasmon Resonance spectroscopy. Notably, the small molecule inhibited HBsAg production and hepatitis B virion secretion (10 μM) at low micromolar concentrations and was also efficacious against a HBV quadruple mutant (CYEI mutant) resistant to tenofovir. We conclude that this small molecule exhibits strong anti-HBV properties and merits further testing.
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Abiri A, Lavigne M, Rezaei M, Nikzad S, Zare P, Mergny JL, Rahimi HR. Unlocking G-Quadruplexes as Antiviral Targets. Pharmacol Rev 2021; 73:897-923. [PMID: 34045305 DOI: 10.1124/pharmrev.120.000230] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Guanine-rich DNA and RNA sequences can fold into noncanonical nucleic acid structures called G-quadruplexes (G4s). Since the discovery that these structures may act as scaffolds for the binding of specific ligands, G4s aroused the attention of a growing number of scientists. The versatile roles of G4 structures in viral replication, transcription, and translation suggest direct applications in therapy or diagnostics. G4-interacting molecules (proteins or small molecules) may also affect the balance between latent and lytic phases, and increasing evidence reveals that G4s are implicated in generally suppressing viral processes, such as replication, transcription, translation, or reverse transcription. In this review, we focus on the discovery of G4s in viruses and the role of G4 ligands in the antiviral drug discovery process. After assessing the role of viral G4s, we argue that host G4s participate in immune modulation, viral tumorigenesis, cellular pathways involved in virus maturation, and DNA integration of viral genomes, which can be potentially employed for antiviral therapeutics. Furthermore, we scrutinize the impediments and shortcomings in the process of studying G4 ligands and drug discovery. Finally, some unanswered questions regarding viral G4s are highlighted for prospective future projects. SIGNIFICANCE STATEMENT: G-quadruplexes (G4s) are noncanonical nucleic acid structures that have gained increasing recognition during the last few decades. First identified as relevant targets in oncology, their importance in virology is now increasingly clear. A number of G-quadruplex ligands are known: viral transcription and replication are the main targets of these ligands. Both viral and cellular G4s may be targeted; this review embraces the different aspects of G-quadruplexes in both host and viral contexts.
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Affiliation(s)
- Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Marc Lavigne
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Masoud Rezaei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Sanaz Nikzad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Peyman Zare
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Jean-Louis Mergny
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Hamid-Reza Rahimi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
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Goswami P, Bartas M, Lexa M, Bohálová N, Volná A, Červeň J, Červeňová V, Pečinka P, Špunda V, Fojta M, Brázda V. SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci. Brief Bioinform 2021; 22:1338-1345. [PMID: 33341900 PMCID: PMC7799342 DOI: 10.1093/bib/bbaa385] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 genome. In this study, we inspected high-frequency mutations of SARS-CoV-2 and carried out systematic analyses of their overlay with inverted repeat (IR) loci and CpG islands. The main conclusion of our study is that SARS-CoV-2 hot-spot mutations are significantly enriched within both IRs and CpG island loci. This points to their role in genomic instability and may predict further mutational drive of the SARS-CoV-2 genome. Moreover, CpG islands are strongly enriched upstream from viral ORFs and thus could play important roles in transcription and the viral life cycle. We hypothesize that hypermethylation of these loci will decrease the transcription of viral ORFs and could therefore limit the progression of the disease.
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Affiliation(s)
- Pratik Goswami
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Matej Lexa
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Veronika Červeňová
- Department of Mathematics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Global Change Research Institute of the Czech Academy of Sciences, Brno, Czech Republic
| | - Miroslav Fojta
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
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47
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Dey U, Sarkar S, Teronpi V, Yella VR, Kumar A. G-quadruplex motifs are functionally conserved in cis-regulatory regions of pathogenic bacteria: An in-silico evaluation. Biochimie 2021; 184:40-51. [PMID: 33548392 DOI: 10.1016/j.biochi.2021.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
Abstract
The role of G-quadruplexes in the cellular physiology of human pathogenesis is an intriguing area of research. Nonetheless, their functional roles and evolutionary conservation have not been compared comprehensively in pathogenic forms of various bacterial genera and species. In the current in silico study, we addressed the role of G-quadruplex-forming sequences (G4 motifs) in the context of cis-regulation, expression variation, regulatory networks, gene orthology and ontology. Genome-wide screening across seven pathogenic genomes using the G4Hunter tool revealed the significant prevalence of G4 motifs in cis-regulatory regions compared to the intragenic regions. Significant conservation of G4 motifs was observed in the regulatory region of 300 orthologous genes. Further analysis of published ChIP-Seq data (Minch et al., 2015) of 91 DNA-binding proteins of the M. tuberculosis genome revealed significant links between G4 motifs and target sites of transcriptional regulators. Interestingly, the transcription factors entangled with virulence, in specific, CsoR, Rv0081, DevR/DosR, and TetR family are found to have G4 motifs in their target regulatory regions. Overall the current study applies positional-functional relationship computation to delve into the cis-regulation of G-quadruplex structures in the context of gene orthology in pathogenic bacteria.
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Affiliation(s)
- Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India
| | - Sharmilee Sarkar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India
| | - Valentina Teronpi
- Department of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, 784184, Assam, India
| | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522502, Andhra Pradesh, India.
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India.
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48
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Meier-Stephenson V, Badmalia MD, Mrozowich T, Lau KCK, Schultz SK, Gemmill DL, Osiowy C, van Marle G, Coffin CS, Patel TR. Identification and characterization of a G-quadruplex structure in the pre-core promoter region of hepatitis B virus covalently closed circular DNA. J Biol Chem 2021; 296:100589. [PMID: 33774051 PMCID: PMC8094906 DOI: 10.1016/j.jbc.2021.100589] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023] Open
Abstract
Approximately 250 million people worldwide are chronically infected with the hepatitis B virus (HBV) and are at increased risk of developing cirrhosis and hepatocellular carcinoma. The HBV genome persists as covalently closed circular DNA (cccDNA), which serves as the template for all HBV mRNA transcripts. Current nucleos(t)ide analogs used to treat HBV do not directly target the HBV cccDNA genome and thus cannot eradicate HBV infection. Here, we report the discovery of a unique G-quadruplex structure in the pre-core promoter region of the HBV genome that is conserved among nearly all genotypes. This region is central to critical steps in the viral life cycle, including the generation of pregenomic RNA, synthesis of core and polymerase proteins, and genome encapsidation; thus, an increased understanding of the HBV pre-core region may lead to the identification of novel anti-HBV cccDNA targets. We utilized biophysical methods (circular dichroism and small-angle X-ray scattering) to characterize the HBV G-quadruplex and the effect of three distinct G to A mutants. We also used microscale thermophoresis to quantify the binding affinity of G-quadruplex and its mutants with a known quadruplex-binding protein (DHX36). To investigate the physiological relevance of HBV G-quadruplex, we employed assays using DHX36 to pull-down cccDNA and compared HBV infection in HepG2 cells transfected with wild-type and mutant HBV plasmids by monitoring the levels of genomic DNA, pregenomic RNA, and antigens. Further evaluation of this critical host-protein interaction site in the HBV cccDNA genome may facilitate the development of novel anti-HBV therapeutics against the resilient cccDNA template.
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Affiliation(s)
- Vanessa Meier-Stephenson
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada; Department of Medicine, Cumming School of Medicine, Calgary, Alberta, Canada
| | - Maulik D Badmalia
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Tyler Mrozowich
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Keith C K Lau
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Sarah K Schultz
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Darren L Gemmill
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Carla Osiowy
- Viral Hepatitis and Bloodborne Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Guido van Marle
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Carla S Coffin
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada; Department of Medicine, Cumming School of Medicine, Calgary, Alberta, Canada.
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada; DiscoveryLab, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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49
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Chen M, Chen Q, Li Y, Yang Z, Taylor EW, Zhao L. A G-quadruplex nanoswitch in the SGK1 promoter regulates isoform expression by K +/Na + balance and resveratrol binding. Biochim Biophys Acta Gen Subj 2020; 1865:129778. [PMID: 33144140 DOI: 10.1016/j.bbagen.2020.129778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/05/2020] [Accepted: 10/28/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND High sodium intake can up-regulate the level of renal serum- and glucocorticoid-inducible kinase-1 (SGK1), which plays a pivotal role in controlling blood pressure via activation of the epithelial sodium channel (ENaC), which can lead to salt-sensitive hypertension. Increased potassium intake, or a vegetarian diet, counteracts salt-sensitive hypertension, but the underlying mechanisms are not fully understood. METHODS Bioinformatics and molecular modeling were used to identify G-quadruplex (G4) and their conformations in the SGK1 promoter. CD spectra and UV melting dynamics were measured to study the stability of G4 as influenced by potassium/sodium balance and resveratrol. RT-PCR and Western blot were employed to study the effects of potassium and resveratrol on the SGK1 isoform expression. RESULTS The SGK1 gene encodes a G4 structure in the proximal upstream of promoter-2; the G4 structure is stabilized by potassium or resveratrol, but destabilized by sodium. Super-physiological levels of sodium stimulate the transcription of all SGK1 isoforms, whereas resveratrol or potassium supplementation inhibits the transcription of iso-2 and iso-3, but not iso-1. CONCLUSIONS Stabilizing the G4 by potassium or resveratrol induces alternative promoter usage and/or pre-mRNA splicing in the transcription of SGK1. GENERAL SIGNIFICANCE Potassium/sodium ion balance or resveratrol binding can act to regulate G4 molecular switches for controlling SGK1 gene expression, thereby presenting a new avenue for drug development.
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Affiliation(s)
- Mengjie Chen
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Qi Chen
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yirui Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Zhenjun Yang
- School of Pharmaceutical Sciences, Peking University, Beijing 100083, China
| | - Ethan W Taylor
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA.
| | - Lijun Zhao
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
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50
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Kumar S, Choudhary D, Patra A, Bhavesh NS, Vivekanandan P. Analysis of G-quadruplexes upstream of herpesvirus miRNAs: evidence of G-quadruplex mediated regulation of KSHV miR-K12-1-9,11 cluster and HCMV miR-US33. BMC Mol Cell Biol 2020; 21:67. [PMID: 32972365 PMCID: PMC7513282 DOI: 10.1186/s12860-020-00306-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND G-quadruplexes regulate gene expression, recombination, packaging and latency in herpesviruses. Herpesvirus-encoded miRNAs have been linked to important biological functions. The presence and the biological role of G-quadruplexes have not been studied in the regulatory regions of virus miRNA. We hypothesized that herpesvirus-encoded miRNAs are regulated by G-quadruplexes in their promoters. RESULTS We analyzed the 1 kb regulatory regions of all herpesvirus-encoded miRNAs for the presence of putative quadruplex-forming sequences (PQS). Over two-third (67%) of the regulatory regions of herpesvirus miRNAs had atleast 1 PQS. The 200 bp region of the promoter proximal to herpesvirus miRNA is particularly enriched for PQS. We chose to study the G-quadruplex motifs in the promoters of miR-K12 cluster in Kaposi's sarcoma-associated Herpesvirus (KSHV miR-K12-1-9,11) and the miR-US33 encoded by Human Cytomegalovirus (HCMV miR-US33). Biophysical characterization indicates that the G-quadruplex motifs in the promoters of the KSHV miR-K12 cluster and the HCMV miR-US33 form stable intramolecular G-quadruplexes in vitro. Mutations disrupting the G-quadruplex motif in the promoter of the KSHV miR-K12 cluster significantly inhibits promoter activity, while those disrupting the motif in the promoter of HCMV miR-US33 significantly enhance the promoter activity as compared to that of the respective wild-type promoter. Similarly, the addition of G-quadruplex binding ligands resulted in the modulation of promoter activity of the wild-type promoters (with intact G-quadruplex) but not the mutant promoters (containing quadruplex-disrupting mutations). CONCLUSION Our findings highlight previously unknown mechanisms of regulation of virus-encoded miRNA and also shed light on new roles for G-quadruplexes in herpesvirus biology.
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Affiliation(s)
- Shivani Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Divya Choudhary
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Anupam Patra
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
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