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Manjunatha Reddy GB, Sumana K, Yogisharadhya R, Mohan HV, Lavanya VK, Chethankumar BH, Shivasharanappa N, Saminathan M, Basavaraj S, Dhama K, Bhadravati Sathish S. Structural and sequence analysis of the RPO30 gene of sheeppox and goatpox viruses from India. Vet Q 2024; 44:1-12. [PMID: 38523527 DOI: 10.1080/01652176.2024.2331524] [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: 03/08/2023] [Accepted: 10/07/2023] [Indexed: 03/26/2024] Open
Abstract
Sheeppox and goatpox are transboundary viral diseases of sheep and goats that cause significant economic losses to small and marginal farmers worldwide, including India. Members of the genus Capripoxvirus (CaPV), namely Sheeppox virus (SPPV), Goatpox virus (GTPV), and Lumpy skin disease virus (LSDV), are antigenically similar, and species differentiation can only be accomplished using molecular approaches. The present study aimed to understand the molecular epidemiology and host specificity of SPPV and GTPV circulating in India through sequencing and structural analysis of the RNA polymerase subunit-30 kDa (RPO30) gene. A total of 29 field isolates from sheep (n = 19) and goats (n = 10) belonging to different geographical regions of India during the period: Year 2015 to 2023, were analyzed based on the sequence and structure of the full-length RPO30 gene/protein. Phylogenetically, all the CaPV isolates were separated into three major clusters: SPPV, GTPV, and LSDV. Multiple sequence alignment revealed a highly conserved RPO30 gene, with a stretch of 21 nucleotide deletion in all SPPV isolates. Additionally, the RPO30 gene of the Indian SPPV and GTPV isolates possessed several species-specific conserved signature residues/motifs that could act as genotyping markers. Secondary structure analysis of the RPO30 protein showed four α-helices, two loops, and three turns, similar to that of the E4L protein of vaccinia virus (VACV). All the isolates in the present study exhibited host preferences across different states of India. Therefore, in order to protect vulnerable small ruminants from poxviral infections, it is recommended to take into consideration a homologous vaccination strategy.
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Affiliation(s)
| | - Krishnappa Sumana
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Revanaiah Yogisharadhya
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Hosakote Venkatappa Mohan
- Veterinary College, Karnataka Veterinary, Animal & Fisheries Sciences University, Bengaluru, Karnataka, India
| | | | | | - Nayakwadi Shivasharanappa
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Mani Saminathan
- ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Sajjanar Basavaraj
- ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Kuldeep Dhama
- ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
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Ren S, Zhang Y, Gao X, Wang X, Tong L, Wang S, Sun Y, Yin X, Chen H. Platform establishment of the Cre-loxP recombination system for genetic manipulation of the Lumpy skin disease virus. Vet Microbiol 2024; 294:110122. [PMID: 38772074 DOI: 10.1016/j.vetmic.2024.110122] [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: 01/30/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
Lumpy skin disease virus (LSDV) is a rapidly emerging pathogen in Asia, including China. Genetic manipulation of the LSDV is essential for the elucidation of the pathogenic mechanism and biological function of the LSDV-encoded protein. In this study, we established a platform for the Cre-loxP recombination system under a modified early-late H5 promoter of the VACV for quick construction of the recombinant LSDV virus. The recombinant virus, LSDV-EGFP-ΔTK, was purified and obtained using serial limited dilution and picking the single cells methods. Using the lentiviral package system, a Cre recombinase enzyme stable expression MDBK cell line was established to supply the Cre recombinase for the reporter gene excision. A genetically stable, safe TK gene-deleted LSDV (LSDV-ΔTK) was constructed using homologous recombination and the Cre-loxP system. It was purified using limited dilution in the MDBK-Cre cell line. Establishing the Cre-loxP recombination system will enable sequential deletion of the interested genes from the LSDV genome and genetic manipulation of the LSDV genome, providing technical support and a platform for developing the attenuated LSDV vaccine.
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Affiliation(s)
- Shanhui Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Yuzhe Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Xiaolong Gao
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai 810016, PR China
| | - Xiangwei Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Lina Tong
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai 810016, PR China
| | - Shasha Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Yuefeng Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China.
| | - Xiangping Yin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China.
| | - Haotai Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China.
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Chen S, Jiang Z, Li Q, Pan W, Chen Y, Liu J. Viral RNA capping: Mechanisms and antiviral therapy. J Med Virol 2024; 96:e29622. [PMID: 38682614 DOI: 10.1002/jmv.29622] [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: 12/19/2023] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
RNA capping is an essential trigger for protein translation in eukaryotic cells. Many viruses have evolved various strategies for initiating the translation of viral genes and generating progeny virions in infected cells via synthesizing cap structure or stealing the RNA cap from nascent host messenger ribonucleotide acid (mRNA). In addition to protein translation, a new understanding of the role of the RNA cap in antiviral innate immunity has advanced the field of mRNA synthesis in vitro and therapeutic applications. Recent studies on these viral RNA capping systems have revealed startlingly diverse ways and molecular machinery. A comprehensive understanding of how viruses accomplish the RNA capping in infected cells is pivotal for designing effective broad-spectrum antiviral therapies. Here we systematically review the contemporary insights into the RNA-capping mechanisms employed by viruses causing human and animal infectious diseases, while also highlighting its impact on host antiviral innate immune response. The therapeutic applications of targeting RNA capping against viral infections and the development of RNA-capping inhibitors are also summarized.
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Affiliation(s)
- Saini Chen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhimin Jiang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qiuchen Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wenliang Pan
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yu Chen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jinhua Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
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You T, Wang M, Zhang H, Wang X, Gao X, Yin X, Sun Y, Wang G, Chen HT, Ren S. Identification of the murine osteoblastic cell MC3T3-E1 as a permissive cell line in response to lumpy skin disease virus. J Virol Methods 2024; 326:114916. [PMID: 38479589 DOI: 10.1016/j.jviromet.2024.114916] [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: 01/14/2024] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Lumpy skin disease virus (LSDV) is a rapidly emerging pathogen in China. Screening suitable cells for LSDV replication is vital for future research on pathogenic mechanisms and vaccine development. Previous comparative studies have identified that the rodent-derived BHK21 is a highly susceptible cell model to LSDV infection. Using western blot, indirect immune-fluorescence assay, flow cytometry, and transmission electron microscopy methods, this study is the first to identify the murine osteoblastic cell line MC3T3-E1 as a novel permissive cell model for LSDV infection. The establishment of MC3T3-E1 as a suitable infectious cell model enhances our understanding of the species range and cell types of the permissive cells and nonpermissive that support LSDV replication. It is helpful to accelerate future research on the pathogenesis, clinical application, and vaccine development of LSDV.
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Affiliation(s)
- Ting You
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China; Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Meng Wang
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Hongqiang Zhang
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Xiangwei Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Xiaolong Gao
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai 810016, PR China
| | - Xiangping Yin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Yuefeng Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Guirong Wang
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Hao-Tai Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China.
| | - Shanhui Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China.
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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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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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Mahony TJ, Briody TE, Ommeh SC. Can the Revolution in mRNA-Based Vaccine Technologies Solve the Intractable Health Issues of Current Ruminant Production Systems? Vaccines (Basel) 2024; 12:152. [PMID: 38400135 PMCID: PMC10893269 DOI: 10.3390/vaccines12020152] [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: 12/18/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
To achieve the World Health Organization's global Sustainable Development Goals, increased production of high-quality protein for human consumption is required while minimizing, ideally reducing, environmental impacts. One way to achieve these goals is to address losses within current livestock production systems. Infectious diseases are key limiters of edible protein production, affecting both quantity and quality. In addition, some of these diseases are zoonotic threats and potential contributors to the emergence of antimicrobial resistance. Vaccination has proven to be highly successful in controlling and even eliminating several livestock diseases of economic importance. However, many livestock diseases, both existing and emerging, have proven to be recalcitrant targets for conventional vaccination technologies. The threat posed by the COVID-19 pandemic resulted in unprecedented global investment in vaccine technologies to accelerate the development of safe and efficacious vaccines. While several vaccination platforms emerged as front runners to meet this challenge, the clear winner is mRNA-based vaccination. The challenge now is for livestock industries and relevant stakeholders to harness these rapid advances in vaccination to address key diseases affecting livestock production. This review examines the key features of mRNA vaccines, as this technology has the potential to control infectious diseases of importance to livestock production that have proven otherwise difficult to control using conventional approaches. This review focuses on the challenging diseases of ruminants due to their importance in global protein production. Overall, the current literature suggests that, while mRNA vaccines have the potential to address challenges in veterinary medicine, further developments are likely to be required for this promise to be realized for ruminant and other livestock species.
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Affiliation(s)
- Timothy J. Mahony
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (T.E.B.); (S.C.O.)
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Chaban A, Minakhin L, Goldobina E, Bae B, Hao Y, Borukhov S, Putzeys L, Boon M, Kabinger F, Lavigne R, Makarova KS, Koonin EV, Nair SK, Tagami S, Severinov K, Sokolova ML. Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail. Nat Commun 2024; 15:317. [PMID: 38182597 PMCID: PMC10770324 DOI: 10.1038/s41467-023-44630-z] [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: 05/15/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of the P23-45 RNAPs with other RNAPs suggest that, despite the extensive functional differences, the two P23-45 RNAPs originate from an ancient gene duplication in an ancestral phage. Our findings demonstrate striking adaptability of RNAPs that can be attained within a single virus species.
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Affiliation(s)
- Anastasiia Chaban
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, 19107, USA
| | - Ekaterina Goldobina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Brain Bae
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yue Hao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ, 08084-1489, USA
| | - Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Florian Kabinger
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Institute of Molecular Genetics National Kurchatov Center, Moscow, 123182, Russia.
| | - Maria L Sokolova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany.
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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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10
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Chan SH, Molé CN, Nye D, Mitchell L, Dai N, Buss J, Kneller DW, Whipple JM, Robb GB. Biochemical characterization of mRNA capping enzyme from Faustovirus. RNA (NEW YORK, N.Y.) 2023; 29:1803-1817. [PMID: 37625853 PMCID: PMC10578482 DOI: 10.1261/rna.079738.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
The mammalian mRNA 5' cap structures play important roles in cellular processes such as nuclear export, efficient translation, and evading cellular innate immune surveillance and regulating 5'-mediated mRNA turnover. Hence, installation of the proper 5' cap is crucial in therapeutic applications of synthetic mRNA. The core 5' cap structure, Cap-0, is generated by three sequential enzymatic activities: RNA 5' triphosphatase, RNA guanylyltransferase, and cap N7-guanine methyltransferase. Vaccinia virus RNA capping enzyme (VCE) is a heterodimeric enzyme that has been widely used in synthetic mRNA research and manufacturing. The large subunit of VCE D1R exhibits a modular structure where each of the three structural domains possesses one of the three enzyme activities, whereas the small subunit D12L is required to activate the N7-guanine methyltransferase activity. Here, we report the characterization of a single-subunit RNA capping enzyme from an amoeba giant virus. Faustovirus RNA capping enzyme (FCE) exhibits a modular array of catalytic domains in common with VCE and is highly efficient in generating the Cap-0 structure without an activation subunit. Phylogenetic analysis suggests that FCE and VCE are descended from a common ancestral capping enzyme. We found that compared to VCE, FCE exhibits higher specific activity, higher activity toward RNA containing secondary structures and a free 5' end, and a broader temperature range, properties favorable for synthetic mRNA manufacturing workflows.
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Affiliation(s)
- S Hong Chan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Christa N Molé
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Dillon Nye
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Lili Mitchell
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Nan Dai
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Jackson Buss
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | | | | | - G Brett Robb
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
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11
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Zgarbová M, Otava T, Silhan J, Nencka R, Weber J, Boura E. Inhibitors of mpox VP39 2'-O methyltransferase efficiently inhibit the monkeypox virus. Antiviral Res 2023; 218:105714. [PMID: 37689311 DOI: 10.1016/j.antiviral.2023.105714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/11/2023]
Abstract
The RNA 2'-O methyltransferase (MTase) VP39 of the monkeypox virus (MpxV) participates in RNA capping within poxviruses. Sub-micromolar inhibitors targeting this enzyme were already reported. However, these 7-deaza analogs of S-adenosyl methionine (SAH) had not been tested in cellular assays until now. In this study, we employed plaque assays and cytopathic effect-based assays to evaluate the effectiveness of these compounds. All tested compounds demonstrated antiviral activity against MpxV, with EC50 values ranging from 0.06 to 2.7 μM. Nevertheless, some of these compounds also exhibited cytotoxicity in HeLa cells, while others showed no toxicity. Notably, the non-toxic compounds featured a large aromatic substituent at the 7-deaza position, whereas the toxic compounds had a small substituent at the same position. These findings suggest that VP39 represents a bona fide target for the development of antiviral drugs against MpxV.
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Affiliation(s)
- Michala Zgarbová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
| | - Tomas Otava
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
| | - Jan Silhan
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic.
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic.
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12
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Chehelgerdi M, Chehelgerdi M. The use of RNA-based treatments in the field of cancer immunotherapy. Mol Cancer 2023; 22:106. [PMID: 37420174 PMCID: PMC10401791 DOI: 10.1186/s12943-023-01807-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/13/2023] [Indexed: 07/09/2023] Open
Abstract
Over the past several decades, mRNA vaccines have evolved from a theoretical concept to a clinical reality. These vaccines offer several advantages over traditional vaccine techniques, including their high potency, rapid development, low-cost manufacturing, and safe administration. However, until recently, concerns over the instability and inefficient distribution of mRNA in vivo have limited their utility. Fortunately, recent technological advancements have mostly resolved these concerns, resulting in the development of numerous mRNA vaccination platforms for infectious diseases and various types of cancer. These platforms have shown promising outcomes in both animal models and humans. This study highlights the potential of mRNA vaccines as a promising alternative approach to conventional vaccine techniques and cancer treatment. This review article aims to provide a thorough and detailed examination of mRNA vaccines, including their mechanisms of action and potential applications in cancer immunotherapy. Additionally, the article will analyze the current state of mRNA vaccine technology and highlight future directions for the development and implementation of this promising vaccine platform as a mainstream therapeutic option. The review will also discuss potential challenges and limitations of mRNA vaccines, such as their stability and in vivo distribution, and suggest ways to overcome these issues. By providing a comprehensive overview and critical analysis of mRNA vaccines, this review aims to contribute to the advancement of this innovative approach to cancer treatment.
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Affiliation(s)
- Mohammad Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran.
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Matin Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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13
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Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P. Structural insights into human co-transcriptional capping. Mol Cell 2023:S1097-2765(23)00424-0. [PMID: 37369200 DOI: 10.1016/j.molcel.2023.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/22/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights into the three major steps of human co-transcriptional pre-mRNA capping based on six different cryoelectron microscopy (cryo-EM) structures. The human mRNA capping enzyme, RNGTT, first docks to the Pol II stalk to position its triphosphatase domain near the RNA exit site. The capping enzyme then moves onto the Pol II surface, and its guanylyltransferase receives the pre-mRNA 5'-diphosphate end. Addition of a GMP moiety can occur when the RNA is ∼22 nt long, sufficient to reach the active site of the guanylyltransferase. For subsequent cap(1) methylation, the methyltransferase CMTR1 binds the Pol II stalk and can receive RNA after it is grown to ∼29 nt in length. The observed rearrangements of capping factors on the Pol II surface may be triggered by the completion of catalytic reaction steps and are accommodated by domain movements in the elongation factor DRB sensitivity-inducing factor (DSIF).
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Affiliation(s)
- Gaurika Garg
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lucas Farnung
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Juliane Schwarz
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bionalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Andreas Linden
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bionalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bionalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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14
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Abduljalil JM, Elfiky AA, Elgohary AM. Exploration of natural compounds against the human mpox virus DNA-dependent RNA polymerase in silico. J Infect Public Health 2023; 16:996-1003. [PMID: 37167647 PMCID: PMC10148721 DOI: 10.1016/j.jiph.2023.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/18/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Last year, the human monkeypox virus (hMPXV) emerged as an alarming threat to the community, with a detectable outbreak outside the African continent for the first time. According to The American Centers for Disease Control and Prevention (CDC), the virus is reported globally, with 86,746 confirmed cases (until April 08, 2023). DNA-dependent RNA polymerase (DdRp) is an essential protein for viral replication; hence it is a promising drug target for developing antiviral drugs against DNA viruses. Therefore, this study was conducted to search for natural compounds that could provide scaffolds for RNA polymerase inhibitors. METHODS In this study, the DdRp structure of hMPXV was modeled and used to screen the natural compounds database (COCONUT). The virtual screening revealed 15 compounds able to tightly bind to the active site of the DdRp (binding energies less than -7.0 kcal/mol) compared to the physiological nucleotide, guanosine triphosphate (GTP). Molecular dynamics simulation was then performed on the top four hits and compared to GTP RESULTS: The results revealed the potential of four compounds (comp289, comp295, comp441, and comp449) in binding the hMPXV DdRp active site with a comparable binding affinity (-17.06 ± 2.96, -11.6 ± 5.34, -14.85 ± 2.66, and -10.79 ± 4.49 kcal/mol) with GTP (-21.03 ± 7.55 kcal/mol) CONCLUSION: These findings may also pave the way for developing new hMPXV inhibitors based on natural product scaffolds. These results need further experimental validation but promising as it was validated by unbiased all-atom MD simulations and binding free energy calculations.
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Affiliation(s)
- Jameel M Abduljalil
- Department of Biological Sciences, Faculty of Applied Sciences, Thamar University, Dhamar, Yemen
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
| | - Alaa M Elgohary
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
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15
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Ohno H, Akamine S, Mochizuki M, Hayashi K, Akichika S, Suzuki T, Saito H. Versatile strategy using vaccinia virus-capping enzyme to synthesize functional 5' cap-modified mRNAs. Nucleic Acids Res 2023; 51:e34. [PMID: 36731515 PMCID: PMC10085709 DOI: 10.1093/nar/gkad019] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/23/2022] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
The potential of synthetic mRNA as a genetic carrier has increased its application in scientific fields. Because the 5' cap regulates the stability and translational activity of mRNAs, there are concerted efforts to search for and synthesize chemically-modified 5' caps that improve the functionality of mRNA. Here, we report an easy and efficient method to synthesize functional mRNAs by modifying multiple 5' cap analogs using a vaccinia virus-capping enzyme. We show that this enzyme can introduce a variety of GTP analogs to the 5' end of RNA to generate 5' cap-modified mRNAs that exhibit different translation levels. Notably, some of these modified mRNAs improve translation efficiency and can be conjugated to chemical structures, further increasing their functionality. Our versatile method to generate 5' cap-modified mRNAs will provide useful tools for RNA therapeutics and biological research.
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Affiliation(s)
- Hirohisa Ohno
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Sae Akamine
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Megumi Mochizuki
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Karin Hayashi
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinichiro Akichika
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hirohide Saito
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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16
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Abstract
The positive-sense flavivirus RNA genome bears a cap 1 structure essential for RNA stability and viral protein translation, and the formation of cap 1 requires the virally encoded nonstructural protein NS5 harboring guanylyltransferase (GTase), cap guanine N7 methyltransferase (N7 MTase), and 5'-nucleotide ribose 2'-O MTase activities in its single-domain MTase module. Despite numerous MTase-containing structures reported, the structural evidence for a critical GMP-enzyme intermediate formation and RNA repositioning when transitioning among different reactions is missing. Here, we report 10 high-resolution MTase crystal structures of Omsk hemorrhagic fever virus (OHFV), a representative high-consequence tick-borne flavivirus, capturing previously unidentified GMP-arginine adduct structures and a rarely observed capped RNA conformation. These structures help us thread capping events in the canonical model with a structure-based hypothesis involving the flipping of the 5' nucleotide, while the observation of an m7GMP-arginine adduct is compatible with an alternate capping model that decouples the N7 and 2'-O methylation steps. IMPORTANCE The methyltransferase (MTase) domain of flavivirus NS5 is unique in harboring guanylyltransferase (GTase), N7 MTase, and 2'-O MTase activities, playing a central role in viral RNA capping. However, the detailed mechanisms of the multistep capping process remain elusive. Here, we report 10 crystal structures of a flavivirus MTase to help understand the guanylyl transfer from GTP to the GTase itself and the transition between guanylyl transfer and methylation steps. In particular, a previously unobserved GMP-arginine covalent intermediate was captured multiple times in MTase crystal soaking trials with GTP present in the soaking solution, supporting its role in bridging the guanylyl transfer from GTP to the GTase and subsequent transfer to the 5'-diphosphate RNA.
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17
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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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18
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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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19
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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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20
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Singh M, Posse V, Peter B, Falkenberg M, Gustafsson C. Ribonucleotides embedded in template DNA impair mitochondrial RNA polymerase progression. Nucleic Acids Res 2022; 50:989-999. [PMID: 35018464 PMCID: PMC8789056 DOI: 10.1093/nar/gkab1251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 11/12/2022] Open
Abstract
Human mitochondria lack ribonucleotide excision repair pathways, causing misincorporated ribonucleotides (rNMPs) to remain embedded in the mitochondrial genome. Previous studies have demonstrated that human mitochondrial DNA polymerase γ can bypass a single rNMP, but that longer stretches of rNMPs present an obstacle to mitochondrial DNA replication. Whether embedded rNMPs also affect mitochondrial transcription has not been addressed. Here we demonstrate that mitochondrial RNA polymerase elongation activity is affected by a single, embedded rNMP in the template strand. The effect is aggravated at stretches with two or more consecutive rNMPs in a row and cannot be overcome by addition of the mitochondrial transcription elongation factor TEFM. Our findings lead us to suggest that impaired transcription may be of functional relevance in genetic disorders associated with imbalanced nucleotide pools and higher levels of embedded rNMPs.
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Affiliation(s)
- Meenakshi Singh
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Viktor Posse
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
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21
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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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22
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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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23
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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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24
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Ravindran S. Profile of Patrick Cramer. Proc Natl Acad Sci U S A 2021; 118:e2111728118. [PMID: 34301909 PMCID: PMC8325307 DOI: 10.1073/pnas.2111728118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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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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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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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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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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Grimm C, Hillen HS, Bedenk K, Bartuli J, Neyer S, Zhang Q, Hüttenhofer A, Erlacher M, Dienemann C, Schlosser A, Urlaub H, Böttcher B, Szalay AA, Cramer P, Fischer U. Structural Basis of Poxvirus Transcription: Vaccinia RNA Polymerase Complexes. Cell 2019; 179:1537-1550.e19. [DOI: 10.1016/j.cell.2019.11.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/20/2019] [Accepted: 11/14/2019] [Indexed: 01/06/2023]
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