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Cackett G, Sýkora M, Portugal R, Dulson C, Dixon L, Werner F. Transcription termination and readthrough in African swine fever virus. Front Immunol 2024; 15:1350267. [PMID: 38545109 PMCID: PMC10965686 DOI: 10.3389/fimmu.2024.1350267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/30/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction African swine fever virus (ASFV) is a nucleocytoplasmic large DNA virus (NCLDV) that encodes its own host-like RNA polymerase (RNAP) and factors required to produce mature mRNA. The formation of accurate mRNA 3' ends by ASFV RNAP depends on transcription termination, likely enabled by a combination of sequence motifs and transcription factors, although these are poorly understood. The termination of any RNAP is rarely 100% efficient, and the transcriptional "readthrough" at terminators can generate long mRNAs which may interfere with the expression of downstream genes. ASFV transcriptome analyses reveal a landscape of heterogeneous mRNA 3' termini, likely a combination of bona fide termination sites and the result of mRNA degradation and processing. While short-read sequencing (SRS) like 3' RNA-seq indicates an accumulation of mRNA 3' ends at specific sites, it cannot inform about which promoters and transcription start sites (TSSs) directed their synthesis, i.e., information about the complete and unprocessed mRNAs at nucleotide resolution. Methods Here, we report a rigorous analysis of full-length ASFV transcripts using long-read sequencing (LRS). We systematically compared transcription termination sites predicted from SRS 3' RNA-seq with 3' ends mapped by LRS during early and late infection. Results Using in-vitro transcription assays, we show that recombinant ASFV RNAP terminates transcription at polyT stretches in the non-template strand, similar to the archaeal RNAP or eukaryotic RNAPIII, unaided by secondary RNA structures or predicted viral termination factors. Our results cement this T-rich motif (U-rich in the RNA) as a universal transcription termination signal in ASFV. Many genes share the usage of the same terminators, while genes can also use a range of terminators to generate transcript isoforms varying enormously in length. A key factor in the latter phenomenon is the highly abundant terminator readthrough we observed, which is more prevalent during late compared with early infection. Discussion This indicates that ASFV mRNAs under the control of late gene promoters utilize different termination mechanisms and factors to early promoters and/or that cellular factors influence the viral transcriptome landscape differently during the late stages of infection.
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Affiliation(s)
- Gwenny Cackett
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | - Michal Sýkora
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | | | - Christopher Dulson
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | - Linda Dixon
- Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Finn Werner
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
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2
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Pilotto S, Sýkora M, Cackett G, Dulson C, Werner F. Structure of the recombinant RNA polymerase from African Swine Fever Virus. Nat Commun 2024; 15:1606. [PMID: 38383525 PMCID: PMC10881513 DOI: 10.1038/s41467-024-45842-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
African Swine Fever Virus is a Nucleo-Cytoplasmic Large DNA Virus that causes an incurable haemorrhagic fever in pigs with a high impact on global food security. ASFV replicates in the cytoplasm of the infected cell and encodes its own transcription machinery that is independent of cellular factors, however, not much is known about how this system works at a molecular level. Here, we present methods to produce recombinant ASFV RNA polymerase, functional assays to screen for inhibitors, and high-resolution cryo-electron microscopy structures of the ASFV RNAP in different conformational states. The ASFV RNAP bears a striking resemblance to RNAPII with bona fide homologues of nine of its twelve subunits. Key differences include the fusion of the ASFV assembly platform subunits RPB3 and RPB11, and an unusual C-terminal domain of the stalk subunit vRPB7 that is related to the eukaryotic mRNA cap 2´-O-methyltransferase 1. Despite the high degree of structural conservation with cellular RNA polymerases, the ASFV RNAP is resistant to the inhibitors rifampicin and alpha-amanitin. The cryo-EM structures and fully recombinant RNAP system together provide an important tool for the design, development, and screening of antiviral drugs in a low biosafety containment environment.
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Affiliation(s)
- Simona Pilotto
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Michal Sýkora
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Gwenny Cackett
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Christopher Dulson
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Finn Werner
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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3
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Lv P, Fang Z, Guan J, Lv L, Xu M, Liu X, Li Z, Lan Y, Li Z, Lu H, Song D, He W, Gao F, Wang D, Zhao K. Genistein is effective in inhibiting Orf virus infection in vitro by targeting viral RNA polymerase subunit RPO30 protein. Front Microbiol 2024; 15:1336490. [PMID: 38389526 PMCID: PMC10882098 DOI: 10.3389/fmicb.2024.1336490] [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: 11/16/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024] Open
Abstract
Orf virus (ORFV), a typical member of the genus Parapoxvirus, Poxvirus family, causes a contagious pustular dermatitis in sheep, goats, and humans. Poxviruses encode a multisubunit DNA-dependent RNA polymerase (vRNAP) that carries out viral gene expression in the host cytoplasm, which is a viral factor essential to poxvirus replication. Due to its vital role in viral life, vRNAP has emerged as one of the potential drug targets. In the present study, we investigated the antiviral effect of genistein against ORFV infection. We provided evidence that genistein exerted antiviral effect through blocking viral genome DNA transcription/replication and viral protein synthesis and reducing viral progeny, which were dosedependently decreased in genistein-treated cells. Furthermore, we identified that genistein interacted with the vRNAP RPO30 protein by CETSA, molecular modeling and Fluorescence quenching, a novel antiviral target for ORFV. By blocking vRNAP RPO30 protein using antibody against RPO30, we confirmed that the inhibitory effect exerted by genistein against ORFV infection is mediated through the interaction with RPO30. In conclusion, we demonstrate that genistein effectively inhibits ORFV transcription in host cells by targeting vRNAP RPO30, which might be a promising drug candidate against poxvirus infection.
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Affiliation(s)
- Pin Lv
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
- College of Animal Science, Jilin University, Changchun, China
| | - Ziyu Fang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jiyu Guan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Lijun Lv
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Mengshi Xu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xingyuan Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhuomei Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yungang Lan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zi Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Huijun Lu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Deguang Song
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wenqi He
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Feng Gao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Dacheng Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
- College of Animal Science, Jilin University, Changchun, China
| | - Kui Zhao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
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O'Brien MJ, Ansari A. Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140968. [PMID: 37863410 PMCID: PMC10872477 DOI: 10.1016/j.bbapap.2023.140968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Although TFIIB is widely regarded as an initiation factor, recent reports have implicated it in multiple aspects of eukaryotic transcription. To investigate the broader role of TFIIB in transcription, we performed quantitative proteomic analysis of yeast TFIIB. We purified two different populations of TFIIB; one from soluble cell lysate, which is not engaged in transcription, and the other from the chromatin fraction which yields the transcriptionally active form of the protein. TFIIB purified from the chromatin exhibits several interactions that explain its non-canonical roles in transcription. RNAPII, TFIIF and TFIIH were the only components of the preinitiation complex with a significant presence in chromatin TFIIB. A notable feature was enrichment of all subunits of CF1 and Rat1 3' end processing-termination complexes in chromatin-TFIIB preparation. Subunits of the CPF termination complex were also detected in both chromatin and soluble derived TFIIB preparations. These results may explain the presence of TFIIB at the 3' end of genes during transcription as well as its role in promoter-termination interaction.
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Affiliation(s)
- Michael J O'Brien
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, United States of America
| | - Athar Ansari
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, United States of America.
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Semenov DV, Vasileva NS, Dymova MA, Mishinov SV, Savinovskaya YI, Ageenko AB, Dome AS, Zinchenko ND, Stepanov GA, Kochneva GV, Richter VA, Kuligina EV. Transcriptome Changes in Glioma Cells upon Infection with the Oncolytic Virus VV-GMCSF-Lact. Cells 2023; 12:2616. [PMID: 37998351 PMCID: PMC10670333 DOI: 10.3390/cells12222616] [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: 09/25/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Oncolytic virotherapy is a rapidly evolving approach that aims to selectively kill cancer cells. We designed a promising recombinant vaccinia virus, VV-GMCSF-Lact, for the treatment of solid tumors, including glioma. We assessed how VV-GMCSF-Lact affects human cells using immortalized and patient-derived glioma cultures and a non-malignant brain cell culture. Studying transcriptome changes in cells 12 h or 24 h after VV-GMCSF-Lact infection, we detected the common activation of histone genes. Additionally, genes associated with the interferon-gamma response, NF-kappa B signaling pathway, and inflammation mediated by chemokine and cytokine signaling pathways showed increased expression. By contrast, genes involved in cell cycle progression, including spindle organization, sister chromatid segregation, and the G2/M checkpoint, were downregulated following virus infection. The upregulation of genes responsible for Golgi vesicles, protein transport, and secretion correlated with reduced sensitivity to the cytotoxic effect of VV-GMCSF-Lact. Higher expression of genes encoding proteins, which participate in the maturation of pol II nuclear transcripts and mRNA splicing, was associated with an increased sensitivity to viral cytotoxicity. Genes whose expression correlates with the sensitivity of cells to the virus are important for increasing the effectiveness of cancer virotherapy. Overall, the results highlight molecular markers, biological pathways, and gene networks influencing the response of glioma cells to VV-GMCSF-Lact.
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Affiliation(s)
- Dmitriy V. Semenov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue, 8, 630090 Novosibirsk, Russia; (N.S.V.); (M.A.D.); (Y.I.S.); (A.B.A.); (A.S.D.); (N.D.Z.); (G.A.S.); (V.A.R.); (E.V.K.)
| | - Natalia S. Vasileva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue, 8, 630090 Novosibirsk, Russia; (N.S.V.); (M.A.D.); (Y.I.S.); (A.B.A.); (A.S.D.); (N.D.Z.); (G.A.S.); (V.A.R.); (E.V.K.)
| | - Maya A. Dymova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue, 8, 630090 Novosibirsk, Russia; (N.S.V.); (M.A.D.); (Y.I.S.); (A.B.A.); (A.S.D.); (N.D.Z.); (G.A.S.); (V.A.R.); (E.V.K.)
| | - Sergey V. Mishinov
- Novosibirsk Research Institute of Traumatology and Orthopedics n.a. Ya.L. Tsivyan, Department of Neurosurgery, Frunze Street, 17, 630091 Novosibirsk, Russia;
| | - Yulya I. Savinovskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue, 8, 630090 Novosibirsk, Russia; (N.S.V.); (M.A.D.); (Y.I.S.); (A.B.A.); (A.S.D.); (N.D.Z.); (G.A.S.); (V.A.R.); (E.V.K.)
| | - Alisa B. Ageenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue, 8, 630090 Novosibirsk, Russia; (N.S.V.); (M.A.D.); (Y.I.S.); (A.B.A.); (A.S.D.); (N.D.Z.); (G.A.S.); (V.A.R.); (E.V.K.)
| | - Anton S. Dome
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue, 8, 630090 Novosibirsk, Russia; (N.S.V.); (M.A.D.); (Y.I.S.); (A.B.A.); (A.S.D.); (N.D.Z.); (G.A.S.); (V.A.R.); (E.V.K.)
| | - Nikita D. Zinchenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue, 8, 630090 Novosibirsk, Russia; (N.S.V.); (M.A.D.); (Y.I.S.); (A.B.A.); (A.S.D.); (N.D.Z.); (G.A.S.); (V.A.R.); (E.V.K.)
| | - Grigory A. Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue, 8, 630090 Novosibirsk, Russia; (N.S.V.); (M.A.D.); (Y.I.S.); (A.B.A.); (A.S.D.); (N.D.Z.); (G.A.S.); (V.A.R.); (E.V.K.)
| | - Galina V. Kochneva
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, 630559 Koltsovo, Russia;
| | - Vladimir A. Richter
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue, 8, 630090 Novosibirsk, Russia; (N.S.V.); (M.A.D.); (Y.I.S.); (A.B.A.); (A.S.D.); (N.D.Z.); (G.A.S.); (V.A.R.); (E.V.K.)
| | - Elena V. Kuligina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue, 8, 630090 Novosibirsk, Russia; (N.S.V.); (M.A.D.); (Y.I.S.); (A.B.A.); (A.S.D.); (N.D.Z.); (G.A.S.); (V.A.R.); (E.V.K.)
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6
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Wang X, Terashi G, Kihara D. CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning. Nat Methods 2023; 20:1739-1747. [PMID: 37783885 PMCID: PMC10841814 DOI: 10.1038/s41592-023-02032-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/24/2023] [Indexed: 10/04/2023]
Abstract
DNA and RNA play fundamental roles in various cellular processes, where their three-dimensional structures provide information critical to understanding the molecular mechanisms of their functions. Although an increasing number of nucleic acid structures and their complexes with proteins are determined by cryogenic electron microscopy (cryo-EM), structure modeling for DNA and RNA remains challenging particularly when the map is determined at a resolution coarser than atomic level. Moreover, computational methods for nucleic acid structure modeling are relatively scarce. Here, we present CryoREAD, a fully automated de novo DNA/RNA atomic structure modeling method using deep learning. CryoREAD identifies phosphate, sugar and base positions in a cryo-EM map using deep learning, which are traced and modeled into a three-dimensional structure. When tested on cryo-EM maps determined at 2.0 to 5.0 Å resolution, CryoREAD built substantially more accurate models than existing methods. We also applied the method to cryo-EM maps of biomolecular complexes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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Chanarat S. Transcription machinery of the minimalist: comparative genomic analysis provides insights into the (de)regulated transcription mechanism of microsporidia - fungal-relative parasites. Transcription 2023; 14:1-17. [PMID: 36757099 PMCID: PMC10353337 DOI: 10.1080/21541264.2023.2174765] [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: 11/14/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Microsporidia are eukaryotic obligate intracellular parasites closely related to fungi. Co-evolving with infected hosts, microsporidia have highly reduced their genomes and lacked several biological components. As it is beneficial for intracellular parasites like microsporidia to reduce their genome size, it is therefore reasonable to assume that genes encoding multifactorial complex machinery of transcription could be a potential target to be excluded from microsporidian genomes during the reductive evolution. In such a case, an evolutionary dilemma occurs because microsporidia cannot remove all transcription-machinery-encoding genes, products of which are essential for initialthe initial steps of gene expression. Here, I propose that while genes encoding core machinery are conserved, several genes known to function in fine-tune regulation of transcription are absent. This genome compaction strategy may come at the cost of loosely regulated or less controllable transcription. Alternatively, analogous to microsporidian polar tube, the parasites may have specialized factors to regulate their RNA synthesis.
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Affiliation(s)
- Sittinan Chanarat
- Laboratory of Molecular Cell Biology, Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
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8
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Mirzakhanyan Y, Jankevics A, Scheltema RA, Gershon PD. Combination of deep XLMS with deep learning reveals an ordered rearrangement and assembly of a major protein component of the vaccinia virion. mBio 2023; 14:e0113523. [PMID: 37646531 PMCID: PMC10653903 DOI: 10.1128/mbio.01135-23] [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: 05/03/2023] [Accepted: 07/11/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE An outstanding problem in the understanding of poxvirus biology is the molecular structure of the mature virion. Via deep learning methods combined with chemical cross-linking mass spectrometry, we have addressed the structure and assembly pathway of P4a, a key poxvirus virion core component.
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Affiliation(s)
- Yeva Mirzakhanyan
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
| | - Andris Jankevics
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands
| | - Paul David Gershon
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
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Mustafa G, Mahrosh HS, Salman M, Ali M, Arif R, Ahmed S, Ebaid H. In Silico Analysis of Honey Bee Peptides as Potential Inhibitors of Capripoxvirus DNA-Directed RNA Polymerase. Animals (Basel) 2023; 13:2281. [PMID: 37508058 PMCID: PMC10376589 DOI: 10.3390/ani13142281] [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: 05/26/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The genus Capripoxvirus belongs to the Poxviridae family. The sheeppox, goatpox, and lumpy skin disease viruses are three species of this genus with 96% identity in their genomes. These are financially devastating viral infections among cattle, which cause a reduction in animal products and lead to a loss in livestock industries. In the current study, the phylogenetic analysis was carried out to reveal the evolutionary relationships of Capripoxvirus species (i.e., sheeppox virus (SPPV), goatpox virus (GTPV), and lumpy skin disease virus (LSDV)) with other viruses from the Poxviridae family with >96% query coverage to find the similarity index among all members. The three viruses (i.e., SPPV, GTPV, and LSDV) joined the clade of Capripoxvirus of the Poxviridae family in the phylogenetic tree and exhibited close evolutionary relationships. The multiple sequence alignment using ClustalOmega revealed significant variations in the protein sequences of the DNA-dependent RNA polymerase of SPPV, GTPV, and LSDV. The three-dimensional structures of five selected bee peptides and DNA-directed RNA polymerase of SPPV, GTPV, and LSDV were predicted using trRosetta and I-TASSER and used for molecular docking and simulation studies. The protein-protein docking was carried out using HADDOCK server to explore the antiviral activity of peptides as honey bee proteins against SPPV, GTPV, and LSDV. In total, five peptides were docked to DNA-directed RNA polymerase of these viruses. The peptides mellitin and secapin-1 displayed the lowest binding scores (-106.9 +/- 7.2 kcal/mol and -101.4 +/- 11.3 kcal/mol, respectively) and the best patterns with stable complexes. The molecular dynamics simulation indicated that the complex of protein DNA-dependent RNA polymerase and the peptide melittin stayed firmly connected and the peptide binding to the receptor protein was stable. The findings of this study provide the evidence of bee peptides as potent antimicrobial agents against sheeppox, goatpox, and lumpy skin disease viruses with no complexity.
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Affiliation(s)
- Ghulam Mustafa
- Department of Biochemistry, Government College University Faisalabad, Faisalabad 38060, Pakistan
| | - Hafiza Salaha Mahrosh
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Mahwish Salman
- Department of Biochemistry, Government College University Faisalabad, Faisalabad 38060, Pakistan
| | - Muhammad Ali
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Rawaba Arif
- Department of Biochemistry, University of Jhang, Jhang 35200, Pakistan
| | - Sibtain Ahmed
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Biochemistry, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Hossam Ebaid
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Yu XD, Ke F, Zhang QY, Gui JF. Genome Characteristics of Two Ranavirus Isolates from Mandarin Fish and Largemouth Bass. Pathogens 2023; 12:pathogens12050730. [PMID: 37242400 DOI: 10.3390/pathogens12050730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Ranaviruses are promiscuous pathogens that threaten lower vertebrates globally. In the present study, two ranaviruses (SCRaV and MSRaV) were isolated from two fishes of the order Perciformes: mandarin fish (Siniperca chuatsi) and largemouth bass (Micropterus salmoides). The two ranaviruses both induced cytopathic effects in cultured cells from fish and amphibians and have the typical morphologic characteristics of ranaviruses. Complete genomes of the two ranaviruses were then sequenced and analyzed. Genomes of SCRaV and MSRaV have a length of 99, 405, and 99, 171 bp, respectively, and both contain 105 predicted open reading frames (ORFs). Eleven of the predicted proteins have differences between SCRaV and MSRaV, in which only one (79L) possessed a relatively large difference. A comparison of the sequenced six ranaviruses from the two fish species worldwide revealed that sequence identities of the six proteins (11R, 19R, 34L, 68L, 77L, and 103R) were related to the place where the virus was isolated. However, there were obvious differences in protein sequence identities between the two viruses and iridoviruses from other hosts, with more than half lower than 55%. Especially, 12 proteins of the two isolates had no homologs in viruses from other hosts. Phylogenetic analysis revealed that ranaviruses from the two fishes clustered in one clade. Further genome alignment showed five groups of genome arrangements of ranaviruses based on the locally collinear blocks, in which the ranaviruses, including SCRaV and MSRaV, constitute the fifth group. These results provide new information on the ranaviruses infecting fishes of Perciformes and also are useful for further research of functional genomics of the type of ranaviruses.
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Affiliation(s)
- Xue-Dong Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Ke
- The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qi-Ya Zhang
- The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian-Fang Gui
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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11
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Wang J, Shahed-Ai-Mahmud M, Chen A, Li K, Tan H, Joyce R. An Overview of Antivirals against Monkeypox Virus and Other Orthopoxviruses. J Med Chem 2023; 66:4468-4490. [PMID: 36961984 DOI: 10.1021/acs.jmedchem.3c00069] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The current monkeypox outbreaks during the COVID-19 pandemic have reignited interest in orthopoxvirus antivirals. Monkeypox belongs to the Orthopoxvirus genus of the Poxviridae family, which also includes the variola virus, vaccinia virus, and cowpox virus. Two orally bioavailable drugs, tecovirimat and brincidofovir, have been approved for treating smallpox infections. Given their human safety profiles and in vivo antiviral efficacy in animal models, both drugs have also been recommended to treat monkeypox infection. To facilitate the development of additional orthopoxvirus antivirals, we summarize the antiviral activity, mechanism of action, and mechanism of resistance of orthopoxvirus antivirals. This perspective covers both direct-acting and host-targeting antivirals with an emphasis on drug candidates showing in vivo antiviral efficacy in animal models. We hope to speed the orthopoxvirus antiviral drug discovery by providing medicinal chemists with insights into prioritizing proper drug targets and hits for further development.
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Affiliation(s)
- Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Md Shahed-Ai-Mahmud
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Angelo Chen
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Ryan Joyce
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
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12
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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 2023; 24:414-429. [PMID: 36732602 DOI: 10.1038/s41580-022-00573-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/04/2023]
Abstract
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.
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13
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Bisio H, Legendre M, Giry C, Philippe N, Alempic JM, Jeudy S, Abergel C. Evolution of giant pandoravirus revealed by CRISPR/Cas9. Nat Commun 2023; 14:428. [PMID: 36702819 PMCID: PMC9879987 DOI: 10.1038/s41467-023-36145-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
Giant viruses (GVs) are a hotspot of unresolved controversies since their discovery, including the definition of "Virus" and their origin. While increasing knowledge of genome diversity has accumulated, GV functional genomics was largely neglected. Here, we describe an experimental framework to genetically modify nuclear GVs and their host Acanthamoeba castellanii using CRISPR/Cas9, shedding light on the evolution from small icosahedral viruses to amphora-shaped GVs. Ablation of the icosahedral major capsid protein in the phylogenetically-related mollivirus highlights a transition in virion shape and size. We additionally demonstrate the existence of a reduced core essential genome in pandoravirus, reminiscent of their proposed smaller ancestors. This proposed genetic expansion led to increased genome robustness, indicating selective pressures for adaptation to uncertain environments. Overall, we introduce new tools for manipulation of the unexplored genome of nuclear GVs and provide experimental evidence suggesting that viral gigantism has aroused as an emerging trait.
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Affiliation(s)
- Hugo Bisio
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France.
| | - Matthieu Legendre
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France
| | - Claire Giry
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France
| | - Nadege Philippe
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France
| | - Jean-Marie Alempic
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France
| | - Sandra Jeudy
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France
| | - Chantal Abergel
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France.
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14
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Molteni C, Forni D, Cagliani R, Mozzi A, Clerici M, Sironi M. Evolution of the orthopoxvirus core genome. Virus Res 2023; 323:198975. [PMID: 36280003 PMCID: PMC9586335 DOI: 10.1016/j.virusres.2022.198975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022]
Abstract
Orthopoxviruses comprise several relevant pathogens, including the causative agent of smallpox and monkeypox virus. Analysis of orthopoxvirus genome evolution mainly focused on gene gains/losses. We instead analyzed core genes, which are conserved in all orthopoxviruses. We show that, despite their strong constraint, some genes involved in viral morphogenesis and transcription/replication were targets of pervasive positive selection, which was relatively uncommon in immunomodulatory genes. However at least three of the positively selected genes, E3L, A24R, and H3L, might have evolved in response to immune selection. Episodic positive selection was particularly common on the internal branches of the orthopox phylogeny and on the monkeypox virus lineage. The latter showed evidence of episodic positive selection at the D14L gene, which encodes a modulator of complement activation (MOPICE). Notably, two genes (B1R and A33R) targeted by episodic selection on more than one branch are involved in forms of intra-genomic conflict. Finally, we found that, in orthopoxvirus proteomes, intrinsically disordered regions (IDRs) tend to be less constrained and are common targets of positive selection. Extension of our analysis to all poxviruses showed no evidence that the IDR fraction differs with host range. Conversely, we found a strong effect of base composition, which was however not sufficient to explain IDR fraction. We thus suggest that, in poxviruses, the IDR fraction is maintained by modulating GC content to accommodate disorder-promoting codons. Overall, our data provide novel insight in orthopoxvirus evolution and provide a list of genes and sites that are expected to modulate viral phenotypes.
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Affiliation(s)
- Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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15
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Byareddy SN, Sharma K, Sachdev S, Reddy AS, Acharya A, Klaustermeier KM, Lorson CL, Singh K. Potential therapeutic targets for Mpox: the evidence to date. Expert Opin Ther Targets 2023; 27:419-431. [PMID: 37368464 PMCID: PMC10722886 DOI: 10.1080/14728222.2023.2230361] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/07/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
INTRODUCTION The global Mpox (MPX) disease outbreak caused by the Mpox virus (MPXV) in 2022 alarmed the World Health Organization (WHO) and health regulation agencies of individual countries leading to the declaration of MPX as a Public Health Emergency. Owing to the genetic similarities between smallpox-causing poxvirus and MPXV, vaccine JYNNEOS, and anti-smallpox drugs Brincidofovir and Tecovirimat were granted emergency use authorization by the United States Food and Drug Administration. The WHO also included cidofovir, NIOCH-14, and other vaccines as treatment options. AREAS COVERED This article covers the historical development of EUA-granted antivirals, resistance to these antivirals, and the projected impact of signature mutations on the potency of antivirals against currently circulating MPXV. Since a high prevalence of MPXV infections in individuals coinfected with HIV and MPXV, the treatment results among these individuals have been included. EXPERT OPINION All EUA-granted drugs have been approved for smallpox treatment. These antivirals show good potency against Mpox. However, conserved resistance mutation positions in MPXV and related poxviruses, and the signature mutations in the 2022 MPXV can potentially compromise the efficacy of the EUA-granted treatments. Therefore, MPXV-specific medications are required not only for the current but also for possible future outbreaks.
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Affiliation(s)
- Siddappa N Byareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | | | - Shrikesh Sachdev
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Athreya S. Reddy
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | | | - Christian L Lorson
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Kamal Singh
- Department of Pharmaceutical Chemistry, DPSRU, New Delhi-110017
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
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16
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Banerjee S, Smith C, Geballe AP, Rothenburg S, Kitzman JO, Brennan G. Gene amplification acts as a molecular foothold to facilitate cross-species adaptation and evasion of multiple antiviral pathways. Virus Evol 2022; 8:veac105. [PMID: 36483110 PMCID: PMC9724558 DOI: 10.1093/ve/veac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/06/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Cross-species spillover events are responsible for many of the pandemics in human history including COVID-19; however, the evolutionary mechanisms that enable these events are poorly understood. We have previously modeled this process using a chimeric vaccinia virus expressing the rhesus cytomegalovirus-derived protein kinase R (PKR) antagonist RhTRS1 in place of its native PKR antagonists: E3L and K3L (VACVΔEΔK + RhTRS1). Using this virus, we demonstrated that gene amplification of rhtrs1 occurred early during experimental evolution and was sufficient to fully rescue virus replication in partially resistant African green monkey (AGM) fibroblasts. Notably, this rapid gene amplification also allowed limited virus replication in otherwise completely non-permissive human fibroblasts, suggesting that gene amplification may act as a 'molecular foothold' to facilitate viral adaptation to multiple species. In this study, we demonstrate that there are multiple barriers to VACVΔEΔK + RhTRS1 replication in human cells, mediated by both PKR and ribonuclease L (RNase L). We experimentally evolved three AGM-adapted virus populations in human fibroblasts. Each population adapted to human cells bimodally, via an initial 10-fold increase in replication after only two passages followed by a second 10-fold increase in replication by passage 9. Using our Illumina-based pipeline, we found that some single nucleotide polymorphisms (SNPs) which had evolved during the prior AGM adaptation were rapidly lost, while thirteen single-base substitutions and short indels increased over time, including two SNPs unique to human foreskin fibroblast (HFF)-adapted populations. Many of these changes were associated with components of the viral RNA polymerase, although no variant was shared between all three populations. Taken together, our results demonstrate that rhtrs1 amplification was sufficient to increase viral tropism after passage in an 'intermediate species' and subsequently enabled the virus to adopt different, species-specific adaptive mechanisms to overcome distinct barriers to viral replication in AGM and human cells.
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Affiliation(s)
- Shefali Banerjee
- †Current address for SB: Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Adam P Geballe
- Departments of Human Genetics and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA,Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Jacob O Kitzman
- Departments of Microbiology and Medicine, University of Washington, Seattle, WA 98195, USA
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17
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Hyun J. Poxvirus under the eyes of electron microscope. Appl Microsc 2022; 52:11. [DOI: 10.1186/s42649-022-00080-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022] Open
Abstract
AbstractZoonotic poxvirus infections pose significant threat to human health as we have witnessed recent spread of monkeypox. Therefore, insights into molecular mechanism behind poxvirus replication cycle are needed for the development of efficient antiviral strategies. Virion assembly is one of the key steps that determine the fate of replicating poxviruses. However, in-depth understanding of poxvirus assembly is challenging due to the complex nature of multi-step morphogenesis and heterogeneous virion structures. Despite these challenges, decades of research have revealed virion morphologies at various maturation stages, critical protein components and interactions with host cell compartments. Transmission electron microscopy has been employed as an indispensable tool for the examination of virion morphology, and more recently for the structure determination of protein complexes. In this review, we describe some of the major findings in poxvirus morphogenesis and the contributions of continuously advancing electron microscopy techniques.
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18
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Banerjee S, Smith C, Geballe A, Rothenburg S, Kitzman JO, Brennan G. Gene amplification acts as a molecular foothold to facilitate cross-species adaptation and evasion of multiple antiviral pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.06.494757. [PMID: 35702158 PMCID: PMC9196108 DOI: 10.1101/2022.06.06.494757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cross-species spillover events are responsible for many of the pandemics in human history including COVID-19; however, the evolutionary mechanisms that enable these events are poorly understood. We have previously modeled this process using a chimeric vaccinia virus expressing the rhesus cytomegalovirus-derived PKR antagonist RhTRS1 in place of its native PKR antagonists; E3L and K3L (VACVΔEΔK+RhTRS1). Using this virus, we demonstrated that gene amplification of rhtrs1 occurred early during experimental evolution and was sufficient to fully rescue virus replication in partially resistant African green monkey (AGM) fibroblasts. Notably, this rapid gene amplification also allowed limited virus replication in otherwise completely non-permissive human fibroblasts, suggesting that gene amplification may act as a "molecular foothold" to facilitate viral adaptation to multiple species. In this study, we demonstrate that there are multiple barriers to VACVΔEΔK+RhTRS1 replication in human cells, mediated by both PKR and RNase L. We experimentally evolved three AGM-adapted virus populations in human fibroblasts. Each population adapted to human cells bimodally, via an initial 10-fold increase in replication after only two passages followed by a second 10-fold increase in replication by passage nine. Using our Illumina-based pipeline, we found that some SNPs which had evolved during the prior AGM adaptation were rapidly lost, while 13 single-base substitutions and short indels increased over time, including two SNPs unique to HFF adapted populations. Many of these changes were associated with components of the viral RNA polymerase, although no variant was shared between all three populations. Taken together, our results demonstrate that rhtrs1 amplification was sufficient to increase viral tropism after passage in an "intermediate species" and subsequently enabled the virus to adopt different, species-specific adaptive mechanisms to overcome distinct barriers to viral replication in AGM and human cells.
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Affiliation(s)
- Shefali Banerjee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Cathy Smith
- Departments of Human Genetics and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adam Geballe
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
- Departments of Microbiology and Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Jacob O Kitzman
- Departments of Human Genetics and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Greg Brennan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
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19
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Villalta A, Schmitt A, Estrozi LF, Quemin ERJ, Alempic JM, Lartigue A, Pražák V, Belmudes L, Vasishtan D, Colmant AMG, Honoré FA, Couté Y, Grünewald K, Abergel C. The giant mimivirus 1.2 Mb genome is elegantly organized into a 30-nm diameter helical protein shield. eLife 2022; 11:e77607. [PMID: 35900198 PMCID: PMC9512402 DOI: 10.7554/elife.77607] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Mimivirus is the prototype of the Mimiviridae family of giant dsDNA viruses. Little is known about the organization of the 1.2 Mb genome inside the membrane-limited nucleoid filling the ~0.5 µm icosahedral capsids. Cryo-electron microscopy, cryo-electron tomography, and proteomics revealed that it is encased into a ~30-nm diameter helical protein shell surprisingly composed of two GMC-type oxidoreductases, which also form the glycosylated fibrils decorating the capsid. The genome is arranged in 5- or 6-start left-handed super-helices, with each DNA-strand lining the central channel. This luminal channel of the nucleoprotein fiber is wide enough to accommodate oxidative stress proteins and RNA polymerase subunits identified by proteomics. Such elegant supramolecular organization would represent a remarkable evolutionary strategy for packaging and protecting the genome, in a state ready for immediate transcription upon unwinding in the host cytoplasm. The parsimonious use of the same protein in two unrelated substructures of the virion is unexpected for a giant virus with thousand genes at its disposal.
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Affiliation(s)
- Alejandro Villalta
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Alain Schmitt
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Leandro F Estrozi
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS)GrenobleFrance
| | - Emmanuelle RJ Quemin
- Centre for Structural Systems Biology, Leibniz Institute for Experimental Virology (HPI), University of HamburgHamburgGermany
| | - Jean-Marie Alempic
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Audrey Lartigue
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Vojtěch Pražák
- Centre for Structural Systems Biology, Leibniz Institute for Experimental Virology (HPI), University of HamburgHamburgGermany
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Lucid Belmudes
- Univ. Grenoble Alpes, CEA, INSERM, IRIG, BGEGrenobleFrance
| | - Daven Vasishtan
- Centre for Structural Systems Biology, Leibniz Institute for Experimental Virology (HPI), University of HamburgHamburgGermany
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Agathe MG Colmant
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Flora A Honoré
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Yohann Couté
- Univ. Grenoble Alpes, CEA, INSERM, IRIG, BGEGrenobleFrance
| | - Kay Grünewald
- Centre for Structural Systems Biology, Leibniz Institute for Experimental Virology (HPI), University of HamburgHamburgGermany
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Chantal Abergel
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
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20
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Shah PS, Beesabathuni NS, Fishburn AT, Kenaston MW, Minami SA, Pham OH, Tucker I. Systems Biology of Virus-Host Protein Interactions: From Hypothesis Generation to Mechanisms of Replication and Pathogenesis. Annu Rev Virol 2022; 9:397-415. [PMID: 35576593 PMCID: PMC10150767 DOI: 10.1146/annurev-virology-100520-011851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As obligate intracellular parasites, all viruses must co-opt cellular machinery to facilitate their own replication. Viruses often co-opt these cellular pathways and processes through physical interactions between viral and host proteins. In addition to facilitating fundamental aspects of virus replication cycles, these virus-host protein interactions can also disrupt physiological functions of host proteins, causing disease that can be advantageous to the virus or simply a coincidence. Consequently, unraveling virus-host protein interactions can serve as a window into molecular mechanisms of virus replication and pathogenesis. Identifying virus-host protein interactions using unbiased systems biology approaches provides an avenue for hypothesis generation. This review highlights common systems biology approaches for identification of virus-host protein interactions and the mechanistic insights revealed by these methods. We also review conceptual innovations using comparative and integrative systems biology that can leverage global virus-host protein interaction data sets to more rapidly move from hypothesis generation to mechanism. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Priya S Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA; .,Department of Chemical Engineering, University of California, Davis, California, USA
| | - Nitin S Beesabathuni
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Adam T Fishburn
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
| | - Matthew W Kenaston
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
| | - Shiaki A Minami
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Oanh H Pham
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
| | - Inglis Tucker
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA;
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21
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Grimm C, Bartuli J, Fischer U. Cytoplasmic gene expression: lessons from poxviruses. Trends Biochem Sci 2022; 47:892-902. [DOI: 10.1016/j.tibs.2022.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
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22
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Bartuli J, Lorenzi I, Backes S, Grimm C, Fischer U. A generic protocol for the affinity-purification of native macromolecular complexes from poxvirus-infected cells. STAR Protoc 2022; 3:101116. [PMID: 35118428 PMCID: PMC8792428 DOI: 10.1016/j.xpro.2021.101116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The functional and structural characterization of macromolecular complexes requires protocols for their native isolation. Here, we describe a protocol for this task based on the recombinant poxvirus Vaccinia expressing tagged proteins of interest in infected cells. Tagged proteins and their interactors can then be isolated via affinity chromatography. The procedure is illustrated for the Vaccinia virus encoded multi-subunit RNA polymerase. Our protocol also allows the expression and isolation of heterologous proteins and hence is suitable for a broader application. For complete details on the use and execution of this profile, please refer to Grimm et al. (2019). Generation of endogenously tagged Vaccinia virus (VACV) strains Generation of VACV strains expressing heterologous proteins Protocol for the affinity purification of native macromolecular complexes
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Affiliation(s)
- Julia Bartuli
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
- Corresponding author
| | - Isotta Lorenzi
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
- Corresponding author
| | - Simone Backes
- Institute for Virology and Immunobiology, University of Wuerzburg, Versbacher Straße 7, 97078 Wuerzburg, Germany
| | - Clemens Grimm
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Utz Fischer
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Wuerzburg, Germany
- Corresponding author
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23
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Ly M, Burgess HM, Shah SB, Mohr I, Glaunsinger BA. Vaccinia virus D10 has broad decapping activity that is regulated by mRNA splicing. PLoS Pathog 2022; 18:e1010099. [PMID: 35202449 PMCID: PMC8903303 DOI: 10.1371/journal.ppat.1010099] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/08/2022] [Accepted: 02/10/2022] [Indexed: 01/01/2023] Open
Abstract
The mRNA 5’ cap structure serves both to protect transcripts from degradation and promote their translation. Cap removal is thus an integral component of mRNA turnover that is carried out by cellular decapping enzymes, whose activity is tightly regulated and coupled to other stages of the mRNA decay pathway. The poxvirus vaccinia virus (VACV) encodes its own decapping enzymes, D9 and D10, that act on cellular and viral mRNA, but may be regulated differently than their cellular counterparts. Here, we evaluated the targeting potential of these viral enzymes using RNA sequencing from cells infected with wild-type and decapping mutant versions of VACV as well as in uninfected cells expressing D10. We found that D9 and D10 target an overlapping subset of viral transcripts but that D10 plays a dominant role in depleting the vast majority of human transcripts, although not in an indiscriminate manner. Unexpectedly, the splicing architecture of a gene influences how robustly its corresponding transcript is targeted by D10, as transcripts derived from intronless genes are less susceptible to enzymatic decapping by D10. As all VACV genes are intronless, preferential decapping of transcripts from intron-containing genes provides an unanticipated mechanism for the virus to disproportionately deplete host transcripts and remodel the infected cell transcriptome. Vaccinia virus (VACV) is a DNA virus of the poxviridae family that was used as a vaccine for immunization against smallpox, ultimately enabling eradication of the smallpox virus. Unusual for DNA viruses, poxviruses like VACV replicate in the cytoplasm and thus must encode their own DNA replication and RNA processing machinery. This includes a protein called D10, which is a decapping enzyme that removes the protective 5’ caps of messenger RNA transcripts, causing them to be degraded, which is hypothesized to decrease antiviral signaling. Here, we demonstrate that D10 targets the majority of cellular messenger RNA transcripts. However, the activity of D10 is influenced by the splicing background of a transcript, where mature transcripts that have been spliced are more targeted and degraded by D10 compared to mature transcripts that are unspliced. The ability of D10 to distinguish transcripts by their splicing history enables it to deplete human transcripts while sparing viral transcripts, reshaping the landscape in favor of viral translation.
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Affiliation(s)
- Michael Ly
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Hannah M. Burgess
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Sahil B. Shah
- Center for Computational Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Britt A. Glaunsinger
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, Berkeley, California, United States of America
- * E-mail:
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24
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Fischer U, Bartuli J, Grimm C. Structure and function of the poxvirus transcription machinery. Enzymes 2021; 50:1-20. [PMID: 34861934 DOI: 10.1016/bs.enz.2021.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Members of the Poxviridae family are large double-stranded DNA viruses that replicate exclusively in the cytoplasm of their hosts. This goes in hand with a high level of independence from the host cell, which supports transcription and replication events only in the nucleus or in DNA-containing organelles. Consequently, virus specific, rather than cellular enzymes mediate most processes involving DNA replication and mRNA synthesis. Recent technological advances allowed a detailed functional and structural investigation of the transcription machinery of the prototypic poxvirus vaccinia. The DNA-dependent RNA polymerase (RNAP) at its core displays distinct similarities to eukaryotic RNAPs. Strong idiosyncrasies, however, are apparent for viral factors that are associated with the viral RNAP during mRNA production. We expect that future studies will unravel more key aspects of poxvirus gene expression, helping also the understanding of nuclear transcription mechanisms.
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Affiliation(s)
- Utz Fischer
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Julia Bartuli
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Clemens Grimm
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany.
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25
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Beyond the canonical role of TFIIB in eukaryotic transcription. Curr Genet 2021; 68:61-67. [PMID: 34797379 PMCID: PMC8602988 DOI: 10.1007/s00294-021-01223-x] [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: 09/10/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/06/2023]
Abstract
The role of general transcription factor TFIIB in transcription extends well beyond its evolutionarily conserved function in initiation. Chromatin localization studies demonstrating binding of TFIIB to both the 5’ and 3’ ends of genes in a diverse set of eukaryotes strongly suggested a rather unexpected role of the factor in termination. TFIIB indeed plays a role in termination of transcription. TFIIB occupancy of the 3’ end is possibly due to its interaction with the termination factors residing there. Interaction of the promoter-bound TFIIB with factors occupying the 3’ end of a gene may be the basis of transcription-dependent gene looping. The proximity of the terminator-bound factors with the promoter in a gene loop has the potential to terminate promoter-initiated upstream anti-sense transcription thereby conferring promoter directionality. TFIIB, therefore, is emerging as a factor with pleiotropic roles in the transcription cycle. This could be the reason for preferential targeting of TFIIB by viruses. Further studies are needed to understand the critical role of TFIIB in viral pathogenesis in the context of its newly identified roles in termination, gene looping and promoter directionality.
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26
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Structural basis of the complete poxvirus transcription initiation process. Nat Struct Mol Biol 2021; 28:779-788. [PMID: 34556871 DOI: 10.1038/s41594-021-00655-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/28/2021] [Indexed: 01/19/2023]
Abstract
Poxviruses express their genes in the cytoplasm of infected cells using a virus-encoded multi-subunit polymerase (vRNAP) and unique transcription factors. We present cryo-EM structures that uncover the complete transcription initiation phase of the poxvirus vaccinia. In the pre-initiation complex, the heterodimeric early transcription factor VETFs/l adopts an arc-like shape spanning the polymerase cleft and anchoring upstream and downstream promoter elements. VETFI emerges as a TBP-like protein that inserts asymmetrically into the DNA major groove, triggers DNA melting, ensures promoter recognition and enforces transcription directionality. The helicase VETFs fosters promoter melting and the phospho-peptide domain (PPD) of vRNAP subunit Rpo30 enables transcription initiation. An unprecedented upstream promoter scrunching mechanism assisted by the helicase NPH-I probably fosters promoter escape and transition into elongation. Our structures shed light on unique mechanisms of poxviral gene expression and aid the understanding of thus far unexplained universal principles in transcription.
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27
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Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z. Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading. Cell 2021; 184:3474-3485.e11. [PMID: 34143953 PMCID: PMC8142856 DOI: 10.1016/j.cell.2021.05.033] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/20/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022]
Abstract
The capping of mRNA and the proofreading play essential roles in SARS-CoV-2 replication and transcription. Here, we present the cryo-EM structure of the SARS-CoV-2 replication-transcription complex (RTC) in a form identified as Cap(0)-RTC, which couples a co-transcriptional capping complex (CCC) composed of nsp12 NiRAN, nsp9, the bifunctional nsp14 possessing an N-terminal exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase), and nsp10 as a cofactor of nsp14. Nsp9 and nsp12 NiRAN recruit nsp10/nsp14 into the Cap(0)-RTC, forming the N7-CCC to yield cap(0) (7MeGpppA) at 5' end of pre-mRNA. A dimeric form of Cap(0)-RTC observed by cryo-EM suggests an in trans backtracking mechanism for nsp14 ExoN to facilitate proofreading of the RNA in concert with polymerase nsp12. These results not only provide a structural basis for understanding co-transcriptional modification of SARS-CoV-2 mRNA but also shed light on how replication fidelity in SARS-CoV-2 is maintained.
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Affiliation(s)
- Liming Yan
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yunxiang Yang
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Mingyu Li
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Ying Zhang
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Litao Zheng
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Life Sciences, Tsinghua University, Beijing, China
| | - Ji Ge
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yucen C Huang
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Zhenyu Liu
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Tao Wang
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shan Gao
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Ran Zhang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanyun Y Huang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Zihe Rao
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Life Sciences, Tsinghua University, Beijing, China; State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Guangzhou Laboratory, Guangzhou, China.
| | - Zhiyong Lou
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Guangzhou Laboratory, Guangzhou, China.
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28
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Transcriptome view of a killer: African swine fever virus. Biochem Soc Trans 2021; 48:1569-1581. [PMID: 32725217 PMCID: PMC7458399 DOI: 10.1042/bst20191108] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023]
Abstract
African swine fever virus (ASFV) represents a severe threat to global agriculture with the world's domestic pig population reduced by a quarter following recent outbreaks in Europe and Asia. Like other nucleocytoplasmic large DNA viruses, ASFV encodes a transcription apparatus including a eukaryote-like RNA polymerase along with a combination of virus-specific, and host-related transcription factors homologous to the TATA-binding protein (TBP) and TFIIB. Despite its high impact, the molecular basis and temporal regulation of ASFV transcription is not well understood. Our lab recently applied deep sequencing approaches to characterise the viral transcriptome and gene expression during early and late ASFV infection. We have characterised the viral promoter elements and termination signatures, by mapping the RNA-5' and RNA-3' termini at single nucleotide resolution. In this review, we discuss the emerging field of ASFV transcripts, transcription, and transcriptomics.
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29
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O'Brien MJ, Ansari A. Critical Involvement of TFIIB in Viral Pathogenesis. Front Mol Biosci 2021; 8:669044. [PMID: 33996913 PMCID: PMC8119876 DOI: 10.3389/fmolb.2021.669044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/08/2021] [Indexed: 11/23/2022] Open
Abstract
Viral infections and the harm they cause to their host are a perpetual threat to living organisms. Pathogenesis and subsequent spread of infection requires replication of the viral genome and expression of structural and non-structural proteins of the virus. Generally, viruses use transcription and translation machinery of the host cell to achieve this objective. The viral genome encodes transcriptional regulators that alter the expression of viral and host genes by manipulating initiation and termination steps of transcription. The regulation of the initiation step is often through interactions of viral factors with gene specific factors as well as general transcription factors (GTFs). Among the GTFs, TFIIB (Transcription Factor IIB) is a frequent target during viral pathogenesis. TFIIB is utilized by a plethora of viruses including human immunodeficiency virus, herpes simplex virus, vaccinia virus, Thogoto virus, hepatitis virus, Epstein-Barr virus and gammaherpesviruses to alter gene expression. A number of viral transcriptional regulators exhibit a direct interaction with host TFIIB in order to accomplish expression of their genes and to repress host transcription. Some viruses have evolved proteins with a three-dimensional structure very similar to TFIIB, demonstrating the importance of TFIIB for viral persistence. Upon viral infection, host transcription is selectively altered with viral transcription benefitting. The nature of viral utilization of TFIIB for expression of its own genes, along with selective repression of host antiviral genes and downregulation of general host transcription, makes TFIIB a potential candidate for antiviral therapies.
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Affiliation(s)
- Michael J O'Brien
- Department of Biological Science, Wayne State University, Detroit, MI, United States
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States
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30
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Abstract
Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
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31
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Koonin EV, Krupovic M, Ishino S, Ishino Y. The replication machinery of LUCA: common origin of DNA replication and transcription. BMC Biol 2020; 18:61. [PMID: 32517760 PMCID: PMC7281927 DOI: 10.1186/s12915-020-00800-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Origin of DNA replication is an enigma because the replicative DNA polymerases (DNAPs) are not homologous among the three domains of life, Bacteria, Archaea, and Eukarya. The homology between the archaeal replicative DNAP (PolD) and the large subunits of the universal RNA polymerase (RNAP) responsible for transcription suggests a parsimonious evolutionary scenario. Under this model, RNAPs and replicative DNAPs evolved from a common ancestor that functioned as an RNA-dependent RNA polymerase in the RNA-protein world that predated the advent of DNA replication. The replicative DNAP of the Last Universal Cellular Ancestor (LUCA) would be the ancestor of the archaeal PolD.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, 75015, Paris, France
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
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32
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Hillen HS, Bartuli J, Grimm C, Dienemann C, Bedenk K, Szalay AA, Fischer U, Cramer P. Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes. Cell 2020; 179:1525-1536.e12. [PMID: 31835031 DOI: 10.1016/j.cell.2019.11.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/20/2019] [Accepted: 11/14/2019] [Indexed: 11/26/2022]
Abstract
Poxviruses use virus-encoded multisubunit RNA polymerases (vRNAPs) and RNA-processing factors to generate m7G-capped mRNAs in the host cytoplasm. In the accompanying paper, we report structures of core and complete vRNAP complexes of the prototypic Vaccinia poxvirus (Grimm et al., 2019; in this issue of Cell). Here, we present the cryo-electron microscopy (cryo-EM) structures of Vaccinia vRNAP in the form of a transcribing elongation complex and in the form of a co-transcriptional capping complex that contains the viral capping enzyme (CE). The trifunctional CE forms two mobile modules that bind the polymerase surface around the RNA exit tunnel. RNA extends from the vRNAP active site through this tunnel and into the active site of the CE triphosphatase. Structural comparisons suggest that growing RNA triggers large-scale rearrangements on the surface of the transcription machinery during the transition from transcription initiation to RNA capping and elongation. Our structures unravel the basis for synthesis and co-transcriptional modification of poxvirus RNA.
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Affiliation(s)
- Hauke S Hillen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Julia Bartuli
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Würzburg, 97074 Würzburg, Germany
| | - Clemens Grimm
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Würzburg, 97074 Würzburg, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kristina Bedenk
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Würzburg, 97074 Würzburg, Germany
| | - Aladar A Szalay
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Würzburg, 97074 Würzburg, Germany; Genelux Corporation, 3030 Bunker Hill Street, San Diego, CA 92109, USA
| | - Utz Fischer
- Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor Boveri-Institute, University of Würzburg, 97074 Würzburg, Germany; Genelux Corporation, 3030 Bunker Hill Street, San Diego, CA 92109, USA; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany.
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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33
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Moss B. Investigating Viruses During the Transformation of Molecular Biology: Part II. Annu Rev Virol 2020; 7:15-36. [PMID: 32392458 DOI: 10.1146/annurev-virology-021020-100558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
My scientific career started at an extraordinary time, shortly after the discoveries of the helical structure of DNA, the central dogma of DNA to RNA to protein, and the genetic code. Part I of this series emphasizes my education and early studies highlighted by the isolation and characterization of numerous vaccinia virus enzymes, determination of the cap structure of messenger RNA, and development of poxviruses as gene expression vectors for use as recombinant vaccines. Here I describe a shift in my research focus to combine molecular biology and genetics for a comprehensive understanding of poxvirus biology. The dominant paradigm during the early years was to select a function, isolate the responsible proteins, and locate the corresponding gene, whereas later the common paradigm was to select a gene, make a mutation, and determine the altered function. Motivations, behind-the-scenes insights, importance of new technologies, and the vital roles of trainees and coworkers are emphasized.
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Affiliation(s)
- Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
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