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Achleitner L, Winter M, Aguilar PP, Lingg N, Jungbauer A, Klausberger M, Satzer P. Robust and resource-efficient production process suitable for large-scale production of baculovirus through high cell density seed train and optimized infection strategy. N Biotechnol 2024; 80:46-55. [PMID: 38302001 DOI: 10.1016/j.nbt.2024.01.002] [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: 10/24/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
The aim of this study was the development of a scalable production process for high titer (108 pfu/mL and above) recombinant baculovirus stocks with low cell line-derived impurities for the production of virus-like particles (VLP). To achieve this, we developed a high cell density (HCD) culture for low footprint cell proliferation, compared different infection strategies at multiplicity of infection (MOI) 0.05 and 0.005, different infection strategies and validated generally applicable harvest criteria of cell viability ≤ 80%. We also investigated online measurable parameters to observe the baculovirus production. The infection strategy employing a very low virus inoculum of MOI 0.005 and a 1:2 dilution with fresh medium one day after infection proved to be the most resource efficient. There, we achieved higher cell-specific titers and lower host cell protein concentrations at harvest than other tested infection strategies with the same MOI, while saving half of the virus stock for infecting the culture compared to other tested infection strategies. HCD culture by daily medium exchange was confirmed as suitable for seed train propagation, infection, and baculovirus production, equally efficient as the conventionally propagated seed train. Online measurable parameters for cell concentration and average cell diameter were found to be effective in monitoring the production process. The study concluded that a more efficient VLP production process in large scale can be achieved using this virus stock production strategy, which could also be extended to produce other proteins or extracellular vesicles with the baculovirus expression system.
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Affiliation(s)
- Lena Achleitner
- acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria; Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Martina Winter
- acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria; Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Patricia Pereira Aguilar
- acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria; Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Nico Lingg
- acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria; Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Alois Jungbauer
- acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria; Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Miriam Klausberger
- Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Peter Satzer
- acib - Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria; Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.
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2
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Sharma S, Mahadevan J, Giri L, Mitra K. Identification of optimal flow rate for culture media, cell density, and oxygen toward maximization of virus production in a fed-batch baculovirus-insect cell system. Biotechnol Bioeng 2023; 120:3529-3542. [PMID: 37749905 DOI: 10.1002/bit.28558] [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: 09/09/2022] [Revised: 08/03/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
In recent times, it has been realized that novel vaccines are required to combat emerging disease outbreaks, and faster optimization is required to respond to global vaccine demands. Although, fed-batch operations offer better productivity, experiment-based optimization of a new fed-batch process remains expensive and time-consuming. In this context, we propose a novel computational framework that can be used for process optimization and control of a fed-batch baculovirus-insect cell system. Since the baculovirus expression vector system (BEVS) is known to be widely used platforms for recombinant protein/vaccine production, we chose this system to demonstrate the identification of optimal profile. Toward this, first, we constructed a mathematical model that captures the time course of cell and virus growth in a baculovirus-insect cell system. Second, the proposed model was used for numerical analysis to determine the optimal operating profiles of control variables such as culture media, cell density, and oxygen based on a multiobjective optimal control formulation. Third, a detailed comparison between batch and fed-batch culture was perfromed along with a comparison between various alternatives of fed-batch operation. Finally, we demonstrate that a model-based quantification of controlled feed addition in fed-batch culture is capable of providing better productivity as compared to a batch culture. The proposed framework can be utilized for the estimation of optimal operating regions of different control variables to achieve maximum infected cell density and virus yield while minimizing the substrate/media, uninfected cell, and oxygen consumption.
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Affiliation(s)
- Surbhi Sharma
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, Telangana, India
| | - Jagadeesh Mahadevan
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, Telangana, India
| | - Lopamudra Giri
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, Telangana, India
| | - Kishalay Mitra
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, Telangana, India
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3
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Jia X, Gao Y, Huang Y, Sun L, Li S, Li H, Zhang X, Li Y, He J, Wu W, Venkannagari H, Yang K, Baker ML, Zhang Q. Architecture of the baculovirus nucleocapsid revealed by cryo-EM. Nat Commun 2023; 14:7481. [PMID: 37980340 PMCID: PMC10657434 DOI: 10.1038/s41467-023-43284-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/03/2023] [Indexed: 11/20/2023] Open
Abstract
Baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) has been widely used as a bioinsecticide and a protein expression vector. Despite their importance, very little is known about the structure of most baculovirus proteins. Here, we show a 3.2 Å resolution structure of helical cylindrical body of the AcMNPV nucleocapsid, composed of VP39, as well as 4.3 Å resolution structures of both the head and the base of the nucleocapsid composed of over 100 protein subunits. AcMNPV VP39 demonstrates some features of the HK97-like fold and utilizes disulfide-bonds and a set of interactions at its C-termini to mediate nucleocapsid assembly and stability. At both ends of the nucleocapsid, the VP39 cylinder is constricted by an outer shell ring composed of proteins AC104, AC142 and AC109. AC101(BV/ODV-C42) and AC144(ODV-EC27) form a C14 symmetric inner layer at both capsid head and base. In the base, these proteins interact with a 7-fold symmetric capsid plug, while a portal-like structure is seen in the central portion of head. Additionally, we propose an application of AlphaFold2 for model building in intermediate resolution density.
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Affiliation(s)
- Xudong Jia
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Yuanzhu Gao
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
- Cryo-EM Facility Center, Southern University of Science and Technology, Shenzhen, China
| | - Yuxuan Huang
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Linjun Sun
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Siduo Li
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Hongmei Li
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Xueqing Zhang
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Yinyin Li
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Jian He
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Wenbi Wu
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Harikanth Venkannagari
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Kai Yang
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center, Houston, TX, 77030, USA.
| | - Qinfen Zhang
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China.
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4
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Aguilar Rangel M, Dolan PT, Taguwa S, Xiao Y, Andino R, Frydman J. High-resolution mapping reveals the mechanism and contribution of genome insertions and deletions to RNA virus evolution. Proc Natl Acad Sci U S A 2023; 120:e2304667120. [PMID: 37487061 PMCID: PMC10400975 DOI: 10.1073/pnas.2304667120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/07/2023] [Indexed: 07/26/2023] Open
Abstract
RNA viruses rapidly adapt to selective conditions due to the high intrinsic mutation rates of their RNA-dependent RNA polymerases (RdRps). Insertions and deletions (indels) in viral genomes are major contributors to both deleterious mutational load and evolutionary novelty, but remain understudied. To characterize the mechanistic details of their formation and evolutionary dynamics during infection, we developed a hybrid experimental-bioinformatic approach. This approach, called MultiMatch, extracts insertions and deletions from ultradeep sequencing experiments, including those occurring at extremely low frequencies, allowing us to map their genomic distribution and quantify the rates at which they occur. Mapping indel mutations in adapting poliovirus and dengue virus populations, we determine the rates of indel generation and identify mechanistic and functional constraints shaping indel diversity. Using poliovirus RdRp variants of distinct fidelity and genome recombination rates, we demonstrate tradeoffs between fidelity and Indel generation. Additionally, we show that maintaining translation frame and viral RNA structures constrain the Indel landscape and that, due to these significant fitness effects, Indels exert a significant deleterious load on adapting viral populations. Conversely, we uncover positively selected Indels that modulate RNA structure, generate protein variants, and produce defective interfering genomes in viral populations. Together, our analyses establish the kinetic and mechanistic tradeoffs between misincorporation, recombination, and Indel rates and reveal functional principles defining the central role of Indels in virus evolution, emergence, and the regulation of viral infection.
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Affiliation(s)
| | - Patrick T. Dolan
- Department of Biology, Stanford University, Stanford, CA94305
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA94143
| | - Shuhei Taguwa
- Department of Biology, Stanford University, Stanford, CA94305
- Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka565-0871, Japan
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA94143
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA94143
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA94305
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5
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Tran NT, Lecomte E, Saleun S, Namkung S, Robin C, Weber K, Devine E, Blouin V, Adjali O, Ayuso E, Gao G, Penaud-Budloo M, Tai PW. Human and Insect Cell-Produced Recombinant Adeno-Associated Viruses Show Differences in Genome Heterogeneity. Hum Gene Ther 2022; 33:371-388. [PMID: 35293222 PMCID: PMC9063199 DOI: 10.1089/hum.2022.050] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
In the past two decades, adeno-associated virus (AAV) vector manufacturing has made remarkable advancements to meet large-scale production demands for preclinical and clinical trials. In addition, AAV vectors have been extensively studied for their safety and efficacy. In particular, the presence of empty AAV capsids and particles containing "inaccurate" vector genomes in preparations has been a subject of concern. Several methods exist to separate empty capsids from full particles; but thus far, no single technique can produce vectors that are free of empty or partial (non-unit length) capsids. Unfortunately, the exact genome compositions of full, intermediate, and empty capsids remain largely unknown. In this work, we used AAV-genome population sequencing to explore the compositions of DNase-resistant, encapsidated vector genomes produced by two common production pipelines: plasmid transfection in human embryonic kidney cells (pTx/HEK293) and baculovirus expression vectors in Spodoptera frugiperda insect cells (rBV/Sf9). Intriguingly, our results show that vectors originating from the same construct design that were manufactured by the rBV/Sf9 system produced a higher degree of truncated and unresolved species than those generated by pTx/HEK293 production. We also demonstrate that empty particles purified by cesium chloride gradient ultracentrifugation are not truly empty but are instead packaged with genomes composed of a single truncated and/or unresolved inverted terminal repeat (ITR). Our data suggest that the frequency of these "mutated" ITRs correlates with the abundance of inaccurate genomes in all fractions. These surprising findings shed new light on vector efficacy, safety, and how clinical vectors should be quantified and evaluated.
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Affiliation(s)
- Ngoc Tam Tran
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Emilie Lecomte
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Sylvie Saleun
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Suk Namkung
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Cécile Robin
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | | | - Eric Devine
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Veronique Blouin
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Oumeya Adjali
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Eduard Ayuso
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Guangping Gao
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA
- Li Weibo Institute of Rare Diseases Research; UMass Chan Medical School, Worcester, Massachusetts, USA
| | | | - Phillip W.L. Tai
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA
- Li Weibo Institute of Rare Diseases Research; UMass Chan Medical School, Worcester, Massachusetts, USA
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6
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Abstract
The success of many viruses depends upon cooperative interactions between viral genomes. However, whenever cooperation occurs, there is the potential for 'cheats' to exploit that cooperation. We suggest that: (1) the biology of viruses makes viral cooperation particularly susceptible to cheating; (2) cheats are common across a wide range of viruses, including viral entities that are already well studied, such as defective interfering genomes, and satellite viruses. Consequently, the evolutionary theory of cheating could help us understand and manipulate viral dynamics, while viruses also offer new opportunities to study the evolution of cheating.
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Affiliation(s)
- Asher Leeks
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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7
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Das A, Dutta S, Sen M, Saxena A, Kumar J, Giri L, Murhammer DW, Chakraborty J. A detailed model and Monte Carlo simulation for predicting DIP genome length distribution in baculovirus infection of insect cells. Biotechnol Bioeng 2020; 118:238-252. [PMID: 32936454 DOI: 10.1002/bit.27566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/04/2020] [Accepted: 09/09/2020] [Indexed: 01/14/2023]
Abstract
Baculoviruses have enormous potential for use as biopesticides to control insect pest populations without the adverse environmental effects posed by the widespread use of chemical pesticides. However, continuous baculovirus production is susceptible to DNA mutation and the subsequent production of defective interfering particles (DIPs). The amount of DIPs produced and their genome length distribution are of great interest not only for baculoviruses but for many other DNA and RNA viruses. In this study, we elucidate this aspect of virus replication using baculovirus as an example system and both experimental and modeling studies. The existing mathematical models for the virus replication process consider DIPs as a lumped quantity and do not consider the genome length distribution of the DIPs. In this study, a detailed population balance model for the cell-virus culture is presented, which predicts the genome length distribution of the DIP population along with their relative proportion. The model is simulated using the kinetic Monte Carlo algorithm, and the results agree well with the experimental results. Using this model, a practical strategy to maintain the DIP fraction to near to its maximum and minimum limits has been demonstrated.
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Affiliation(s)
- Ashok Das
- Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Soumajit Dutta
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | | | - Abha Saxena
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, Telangana, India
| | - Jitendra Kumar
- Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Lopamudra Giri
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, Telangana, India
| | - David W Murhammer
- Department of Chemical and Biochemical Engineering, The University of Iowa, Iowa City, California, USA
| | - Jayanta Chakraborty
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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8
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Saxena A, Ravutla S, Upadhyay V, Jana S, Murhammer D, Giri L. Statistical modeling of cell-to-cell variability in viral infection during passaging in suspension cell culture: Application in Monte-Carlo simulation. Biotechnol Bioeng 2020; 117:1483-1501. [PMID: 32017023 DOI: 10.1002/bit.27295] [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: 08/02/2019] [Revised: 12/13/2019] [Accepted: 02/03/2020] [Indexed: 11/09/2022]
Abstract
Packaging during the passaging of viruses in cell cultures yields various phenotypes and is regulated by viral protein expression in infected cells. Although such a packaging mechanism has a profound effect in controlling the virus yield, little is known about the underlying statistical models followed by virus packaging and protein expression among cells infected with the virus. A predictive framework combining identification of the probability density function (PDF) based on log-likelihood and using the PDF for Monte-Carlo simulations is developed. The Birnbaum-Saunders distribution was found to be consistent with all three-virus packaging levels, including nucleocapsids/occlusion-derived virus (ODV), ODVs/polyhedra, and polyhedra/cell for both wild-type and genetically modified AcMNPV. Next, it was demonstrated that PDF fitting could be used to compare two viruses having distinctly different genetic configurations. Finally, the identified PDF can be incorporated in RNA synthesis parameters for baculovirus infection to predict the cell-to-cell variability in protein expression using Monte-Carlo simulations. The proposed tool can be used for the estimation of uncertainty in the kinetic parameter and prediction of cell-to-cell variability for other biological systems.
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Affiliation(s)
- Abha Saxena
- Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Suryateja Ravutla
- Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Vikas Upadhyay
- Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Soumya Jana
- Electrical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - David Murhammer
- Department of Chemical and Biochemical Engineering, The University of Iowa, Iowa City, Iowa
| | - Lopamudra Giri
- Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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9
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Saxena A, Upadhyay V, Dhyani V, Jana S, Giri L. Cell-to-Cell Variability in Protein Expression during Viral Infection: Monte-Carlo Simulation and Validation based on Confocal Imaging .. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2019:138-141. [PMID: 31945863 DOI: 10.1109/embc.2019.8856612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
One of the major challenges is to identify the statistical model underlying the heterogeneity in viral protein expression in single cells. In this endeavor, we propose a computational tool to address the cell-to-cell variability in protein expression by random variate generation following probability distributions. Here, we show that statistical modeling using the probability density function of various distribution offers considerable potential for providing stochastic inputs to Monte Carlo simulation. Specifically, we present the ranking between three distribution families including gamma, normal and Weibull distribution using a comparison of cumulative frequency obtained from experiment and simulation. The major contribution of the proposed simulation method is to identify the underlying statistical model in kinetic parameters that capture the variability in protein expression in single cells obtained through imaging using confocal microscopy.
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10
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Continuous influenza virus production in a tubular bioreactor system provides stable titers and avoids the "von Magnus effect". PLoS One 2019; 14:e0224317. [PMID: 31689309 PMCID: PMC6830746 DOI: 10.1371/journal.pone.0224317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/10/2019] [Indexed: 01/23/2023] Open
Abstract
Continuous cell culture-based influenza vaccine production could significantly reduce footprint and manufacturing costs compared to current batch processing. However, yields of influenza virus in continuous mode can be affected by oscillations in virus titers caused by periodic accumulation of defective interfering particles. The generation of such particles has also been observed previously in cascades of continuous stirred tank reactors (CSTRs) and is known as the “von Magnus effect”. To improve virus yields and to avoid these oscillations, we have developed a novel continuous tubular bioreactor system for influenza A virus production. It was built using a 500 mL CSTR for cell growth linked to a 105 m long tubular plug-flow bioreactor (PFBR). Virus propagation took place only in the PFBR with a nominal residence time of 20 h and a production capacity of 0.2 mL/min. The bioreactor was first tested with suspension MDCK cells at different multiplicities of infection (MOI), and then with suspension avian AGE1.CR.pIX cells at a fixed nominal MOI of 0.02. Maximum hemagglutinin (HA) titers of 2.4 and 1.6 log10(HA units/100 μL) for suspension MDCK cells and AGE1.CR.pIX cells, respectively, were obtained. Flow cytometric analysis demonstrated that 100% infected cells with batch-like HA titers can be obtained at a MOI of at least 0.1. Stable HA and TCID50 titers over 18 days of production were confirmed using the AGE1.CR.pIX cell line, and PCR analysis demonstrated stable production of full-length genome. The contamination level of segments with deletions (potentially defective interfering particles), already present in the virus seed, was low and did not increase. Control experiments using batch and semi-continuous cultures confirmed these findings. A comparison showed that influenza virus production can be achieved with the tubular bioreactor system in about half the time with a space-time-yield up to two times higher than for typical batch cultures. In summary, a novel continuous tubular bioreactor system for cell culture-based influenza virus production was developed. One main advantage, an essentially single-passage amplification of viruses, should enable efficient production of vaccines as well as vectors for gene and cancer therapy.
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11
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Saxena A, Byram PK, Singh SK, Chakraborty J, Murhammer D, Giri L. A structured review of baculovirus infection process: integration of mathematical models and biomolecular information on cell–virus interaction. J Gen Virol 2018; 99:1151-1171. [DOI: 10.1099/jgv.0.001108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Abha Saxena
- 1Indian Institute of Technology Hyderabad, Chemical Engineering, Village Kandi, Sangareddy, Hyderabad, Telangana 502205, India
| | - Prasanna Kumar Byram
- 1Indian Institute of Technology Hyderabad, Chemical Engineering, Village Kandi, Sangareddy, Hyderabad, Telangana 502205, India
| | - Suraj Kumar Singh
- 1Indian Institute of Technology Hyderabad, Chemical Engineering, Village Kandi, Sangareddy, Hyderabad, Telangana 502205, India
| | - Jayanta Chakraborty
- 2Indian Institute of Technology Kharagpur, Chemical Engineering, Kharagpur, West Bengal 721302, India
| | - David Murhammer
- 3The University of Iowa, Department of Chemical and Biochemical Engineering, Iowa City, IA 52242-1527, USA
| | - Lopamudra Giri
- 1Indian Institute of Technology Hyderabad, Chemical Engineering, Village Kandi, Sangareddy, Hyderabad, Telangana 502205, India
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12
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Direct sequencing of the white spot syndrome virus from Brazil: Genome assembly and new insights on phylogeny. Virus Res 2018; 245:52-61. [DOI: 10.1016/j.virusres.2017.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 11/19/2022]
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13
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Martínez-Solís M, Jakubowska AK, Herrero S. Expression of the lef5 gene from Spodoptera exigua multiple nucleopolyhedrovirus contributes to the baculovirus stability in cell culture. Appl Microbiol Biotechnol 2017; 101:7579-7588. [DOI: 10.1007/s00253-017-8495-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/25/2017] [Accepted: 08/03/2017] [Indexed: 12/17/2022]
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14
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The Autographa californica Multiple Nucleopolyhedrovirus ac83 Gene Contains a cis-Acting Element That Is Essential for Nucleocapsid Assembly. J Virol 2017; 91:JVI.02110-16. [PMID: 28031366 DOI: 10.1128/jvi.02110-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023] Open
Abstract
Baculoviridae is a family of insect-specific viruses that have a circular double-stranded DNA genome packaged within a rod-shaped capsid. The mechanism of baculovirus nucleocapsid assembly remains unclear. Previous studies have shown that deletion of the ac83 gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) blocks viral nucleocapsid assembly. Interestingly, the ac83-encoded protein Ac83 is not a component of the nucleocapsid, implying a particular role for ac83 in nucleocapsid assembly that may be independent of its protein product. To examine this possibility, Ac83 synthesis was disrupted by insertion of a chloramphenicol resistance gene into its coding sequence or by deleting its promoter and translation start codon. Both mutants produced progeny viruses normally, indicating that the Ac83 protein is not required for nucleocapsid assembly. Subsequently, complementation assays showed that the production of progeny viruses required the presence of ac83 in the AcMNPV genome instead of its presence in trans Therefore, we reasoned that ac83 is involved in nucleocapsid assembly via an internal cis-acting element, which we named the nucleocapsid assembly-essential element (NAE). The NAE was identified to lie within nucleotides 1651 to 1850 of ac83 and had 8 conserved A/T-rich regions. Sequences homologous to the NAE were found only in alphabaculoviruses and have a conserved positional relationship with another essential cis-acting element that was recently identified. The identification of the NAE may help to connect the data of viral cis-acting elements and related proteins in the baculovirus nucleocapsid assembly, which is important for elucidating DNA-protein interaction events during this process.IMPORTANCE Virus nucleocapsid assembly usually requires specific cis-acting elements in the viral genome for various processes, such as the selection of the viral genome from the cellular nucleic acids, the cleavage of concatemeric viral genome replication intermediates, and the encapsidation of the viral genome into procapsids. In linear DNA viruses, such elements generally locate at the ends of the viral genome; however, most of these elements remain unidentified in circular DNA viruses (including baculovirus) due to their circular genomic conformation. Here, we identified a nucleocapsid assembly-essential element in the AcMNPV (the archetype of baculovirus) genome. This finding provides an important reference for studies of nucleocapsid assembly-related elements in baculoviruses and other circular DNA viruses. Moreover, as most of the previous studies of baculovirus nucleocapsid assembly have been focused on viral proteins, our study provides a novel entry point to investigate this mechanism via cis-acting elements in the viral genome.
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Nguyen Q, Tb Tran T, Chan LC, Nielsen LK, Reid S. In vitro production of baculoviruses: identifying host and virus genes associated with high productivity. Appl Microbiol Biotechnol 2016; 100:9239-9253. [PMID: 27613424 DOI: 10.1007/s00253-016-7774-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/25/2016] [Accepted: 08/01/2016] [Indexed: 01/22/2023]
Abstract
Baculoviruses are recognized as viral workhorses of biotechnology, being used for production of vaccines, complex recombinant proteins, gene delivery vectors' and safe biological pesticides. Improving production yields and understanding the interactions of the virus and its host cell are important aspects of ensuring baculovirus-based processes are commercially competitive. This study aims at potential optimization of host cells used in in vitro virus production by systemically investigating changes in host gene expression in response to virus replication and transcription inside host cells. The study focuses on in vitro interactions of the Helicoverpa armigera virus with Helicoverpa zea insect cells. We used 22 genome-wide microarrays to simultaneously measure both virus and host genes in infected cells in multiple batch suspension cultures, representing high- and low-producing infection conditions. Among 661 differentially expressed genes, we identified a core set of 59 host genes consistently overexpressed post infection, with strong overrepresentation of genes involved in retrotransposition, protein processing in the endoplasmic reticulum, and ubiquitin-mediated proteolysis. Applying a whole genome correlation network analysis to link gene expression to productivity, we revealed 18 key genes significantly associated to virus yield. In addition, this study is among the first to perform a genome-wide expression study for a major baculovirus group II strain, the H. armigera virus, extending current understanding of baculovirus-insect interactions, which mainly focuses on group I viruses.
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Affiliation(s)
- Quan Nguyen
- Livestock Genomics, CSIRO (The Commonwealth Scientific and Industrial Research Organisation) Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
| | - Trinh Tb Tran
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Leslie Cl Chan
- Patheon Biologics, 37 Kent street, Brisbane, QLD, 4102, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Steven Reid
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Hattori T, Nakanishi K, Mori T, Tomita M, Tsumoto K. The method used to culture host cells (Sf9 cells) can affect the qualities of baculovirus budding particles expressing recombinant proteins. Biosci Biotechnol Biochem 2016; 80:445-51. [DOI: 10.1080/09168451.2015.1101331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Budded virus (BV) particles of baculovirus (Autographa californica nucleopolyhedrovirus, AcNPV) are harvested from the supernatant of liquid culture of Sf9 host cells by ultracentrifugation. Using polyacrylamide gel electrophoresis, Western blot and transmission electron microscopy (TEM) of BV samples fractionated closely by sucrose density gradient centrifugation, we observed that BVs exhibited different qualities depending on whether they had been harvested from the supernatant from a standing (static), shaking (suspension), or standing/shaking (pre-/post-infection) culture of Sf9 cells. The amount of BV protein apparently increased in the order of standing, standing/shaking, and shaking procedure, and the yield of intact particles showed an opposite trend. TEM observation clearly showed that appropriate fractions of the standing and standing/shaking cultures contained more intact BV particles than those from the shaking culture. These results suggest that the qualities of recombinant BV particles may be related to the culture conditions of the host cells.
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Affiliation(s)
- Tomomi Hattori
- Division of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Japan
| | - Kohei Nakanishi
- Division of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Japan
| | - Takaaki Mori
- Division of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Japan
| | - Masahiro Tomita
- Division of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Japan
| | - Kanta Tsumoto
- Division of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Japan
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The FP25K Acts as a Negative Factor for the Infectivity of AcMNPV Budded Virus. PLoS One 2015; 10:e0128471. [PMID: 26020780 PMCID: PMC4447387 DOI: 10.1371/journal.pone.0128471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/27/2015] [Indexed: 01/11/2023] Open
Abstract
Baculoviruses generally produce two progeny phenotypes—the budded virus (BV) and the occlusion-derived virus (ODV)—and the intricate mechanisms that regulate the temporal synthesis of the two phenotypes are critical for the virus replication cycle, which are far from being clearly understood. FP25K was reported to be responsible for the regulation of BV/ODV, and the mutations within result in a decrease of normal ODVs formation and an increase of BVs production. In this study, we demonstrated that the increase of BV titer in an fp25k knockout recombinant (fp25k-negative) was a result of higher infectivity of BVs rather than an increased production of BVs. The constitution of the major structural proteins and genome of parental and fp25k-negative BVs were analyzed. The results showed that the integrity of the majority of DNA packaged into the fp25k-negative BVs was intact; i.e., the genomic DNA of fp25k-negative BV had better transformation and transfection efficiency than that of the parental virus, indicating more intact genomes in the virions. Although the analysis of proteins associated with BVs revealed that more envelope protein GP64 were incorporated into the fp25k-negative BVs, subsequent experiments suggested that overexpression of GP64 did not improve the titer of BVs. Thus, we conclude that the main reason for higher infectivity of BVs is due to better genome integrity, which benefits from the deletion of fp25k resulting in increased stability of the genome and produce a higher proportion of infectious BVs. FP25K acts as a negative factor for the infectivity of BV.
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Matindoost L, Nielsen LK, Reid S. Intracellular Trafficking of Baculovirus Particles: A Quantitative Study of the HearNPV/HzAM1 Cell and AcMNPV/Sf9 Cell Systems. Viruses 2015; 7:2288-307. [PMID: 25951488 PMCID: PMC4452906 DOI: 10.3390/v7052288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/21/2015] [Accepted: 04/28/2015] [Indexed: 01/29/2023] Open
Abstract
To replace the in vivo production of baculovirus-based biopesticides with a more convenient in vitro produced product, the limitations imposed by in vitro production have to be solved. One of the main problems is the low titer of HearNPV budded virions (BV) in vitro as the use of low BV titer stocks can result in non-homogenous infections resulting in multiple virus replication cycles during scale up that leads to low Occlusion Body yields. Here we investigate the baculovirus traffic in subcellular fractions of host cells throughout infection with an emphasis on AcMNPV/Sf9 and HearNPV/HzAM1 systems distinguished as "good" and "bad" BV producers, respectively. qPCR quantification of viral DNA in the nucleus, cytoplasm and extracellular fractions demonstrated that although the HearNPV/HzAM1 system produces twice the amount of vDNA as the AcMNPV/Sf9 system, its percentage of BV to total progeny vDNA was lower. vDNA egress from the nucleus to the cytoplasm is sufficient in both systems, however, a higher percentage of vDNA in the HearNPV/HzAM1 system remain in the cytoplasm and do not bud out of the cells compared to the AcMNPV/Sf9 system. In both systems more than 75% of the vDNA produced in the nuclear fraction go unused, without budding or being encapsulated in OBs showing the capacity for improvements that could result from the engineering of the virus/cell line systems to achieve better productivities for both BV and OB yields.
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Affiliation(s)
- Leila Matindoost
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Steve Reid
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia.
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Frensing T. Defective interfering viruses and their impact on vaccines and viral vectors. Biotechnol J 2015; 10:681-9. [DOI: 10.1002/biot.201400429] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/13/2015] [Accepted: 01/27/2015] [Indexed: 11/12/2022]
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Lau CH, Zhu H, Tay JCK, Li Z, Tay FC, Chen C, Tan WK, Du S, Sia VK, Phang RZ, Tang SY, Yang C, Chi Z, Liang CC, Ning E, Wang S. Genetic rearrangements of variable di-residue (RVD)-containing repeat arrays in a baculoviral TALEN system. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2014; 1:14050. [PMID: 26015987 PMCID: PMC4362386 DOI: 10.1038/mtm.2014.50] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 08/17/2014] [Indexed: 01/24/2023]
Abstract
Virus-derived gene transfer vectors have been successfully employed to express the transcription activator-like effector nucleases (TALENs) in mammalian cells. Since the DNA-binding domains of TALENs consist of the variable di-residue (RVD)-containing tandem repeat modules and virus genome with repeated sequences is susceptible to genetic recombination, we investigated several factors that might affect TALEN cleavage efficiency of baculoviral vectors. Using a TALEN system designed to target the AAVS1 locus, we observed increased sequence instability of the TALE repeat arrays when a higher multiplicity of infection (MOI) of recombinant viruses was used to produce the baculoviral vectors. We also detected more deleterious mutations in the TALE DNA-binding domains when both left and right TALEN arms were placed into a single expression cassette as compared to the viruses containing one arm only. The DNA sequence changes in the domains included deletion, addition, substitution, and DNA strand exchange between the left and right TALEN arms. Based on these observations, we have developed a protocol using a low MOI to produce baculoviral vectors expressing TALEN left and right arms separately. Cotransduction of the viruses produced by this optimal protocol provided an improved TALEN cleavage efficiency and enabled effective site-specific transgene integration in human cells.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Haibao Zhu
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Johan Chin-Kang Tay
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Zhendong Li
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Felix Chang Tay
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Can Chen
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Wee-Kiat Tan
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Shouhui Du
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Vic-Ki Sia
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Rui-Zhe Phang
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Shin-Yi Tang
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Chiyun Yang
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Zhixia Chi
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Chieh-Ching Liang
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Er Ning
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Shu Wang
- Department of Biological Sciences, National University of Singapore , Singapore, Singapore ; Institute of Bioengineering and Nanotechnology , Singapore, Singapore
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Thézé J, Cabodevilla O, Palma L, Williams T, Caballero P, Herniou EA. Genomic diversity in European Spodoptera exigua multiple nucleopolyhedrovirus isolates. J Gen Virol 2014; 95:2297-2309. [PMID: 24854001 DOI: 10.1099/vir.0.064766-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Key virus traits such as virulence and transmission strategies rely on genetic variation that results in functional changes in the interactions between hosts and viruses. Here, comparative genomic analyses of seven isolates of Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) with differing phenotypes were employed to pinpoint candidate genes that may be involved in host-virus interactions. These isolates obtained after vertical or horizontal transmission of infection in insects differed in virulence. Apart from one genome containing a piggyBac transposon, all European SeMNPV isolates had a similar genome size and content. Complete genome analyses of single nucleotide polymorphisms and insertions/deletions identified mutations in 48 ORFs that could result in functional changes. Among these, 13 ORFs could be correlated with particular phenotypic characteristics of SeMNPV isolates. Mutations were found in all gene functional classes and most of the changes we highlighted could potentially be associated with differences in transmission. The regulation of DNA replication (helicase, lef-7) and transcription (lef-9, p47) might be important for the establishment of sublethal infection prior to and following vertical transmission. Virus-host cell interactions also appear instrumental in the modulation of viral transmission as significant mutations were detected in virion proteins involved in primary (AC150) or secondary infections (ME35) and in apoptosis inhibition (IAP2, AC134). Baculovirus populations naturally harbour high genomic variation located in genes involved at different levels of the complex interactions between virus and host during the course of an infection. The comparative analyses performed here suggest that the differences in baculovirus virulence and transmission phenotypes involve multiple molecular pathways.
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Affiliation(s)
- Julien Thézé
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France
| | - Oihana Cabodevilla
- Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, 31192 Mutilva Baja, Navarra, Spain
| | - Leopoldo Palma
- Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, 31192 Mutilva Baja, Navarra, Spain
| | | | - Primitivo Caballero
- Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Navarra, Spain.,Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, 31192 Mutilva Baja, Navarra, Spain
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France
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Nguyen Q, Nielsen LK, Reid S. Genome scale transcriptomics of baculovirus-insect interactions. Viruses 2013; 5:2721-47. [PMID: 24226166 PMCID: PMC3856412 DOI: 10.3390/v5112721] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/28/2013] [Accepted: 11/04/2013] [Indexed: 01/25/2023] Open
Abstract
Baculovirus-insect cell technologies are applied in the production of complex proteins, veterinary and human vaccines, gene delivery vectors' and biopesticides. Better understanding of how baculoviruses and insect cells interact would facilitate baculovirus-based production. While complete genomic sequences are available for over 58 baculovirus species, little insect genomic information is known. The release of the Bombyx mori and Plutella xylostella genomes, the accumulation of EST sequences for several Lepidopteran species, and especially the availability of two genome-scale analysis tools, namely oligonucleotide microarrays and next generation sequencing (NGS), have facilitated expression studies to generate a rich picture of insect gene responses to baculovirus infections. This review presents current knowledge on the interaction dynamics of the baculovirus-insect system' which is relatively well studied in relation to nucleocapsid transportation, apoptosis, and heat shock responses, but is still poorly understood regarding responses involved in pro-survival pathways, DNA damage pathways, protein degradation, translation, signaling pathways, RNAi pathways, and importantly metabolic pathways for energy, nucleotide and amino acid production. We discuss how the two genome-scale transcriptomic tools can be applied for studying such pathways and suggest that proteomics and metabolomics can produce complementary findings to transcriptomic studies.
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Affiliation(s)
- Quan Nguyen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia.
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Baculovirus VP1054 is an acquired cellular PURα, a nucleic acid-binding protein specific for GGN repeats. J Virol 2013; 87:8465-80. [PMID: 23720732 DOI: 10.1128/jvi.00068-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Baculovirus VP1054 protein is a structural component of both of the virion types budded virus (BV) and occlusion-derived virus (ODV), but its exact role in virion morphogenesis is poorly defined. In this paper, we reveal sequence and functional similarity between the baculovirus protein VP1054 and the cellular purine-rich element binding protein PUR-alpha (PURα). The data strongly suggest that gene transfer has occurred from a host to an ancestral baculovirus. Deletion of the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) vp1054 gene completely prevented viral cell-to-cell spread. Electron microscopy data showed that assembly of progeny nucleocapsids is dramatically reduced in the absence of VP1054. More precisely, VP1054 is required for proper viral DNA encapsidation, as deduced from the formation of numerous electron-lucent capsid-like tubules. Complementary searching identified the presence of genetic elements composed of repeated GGN trinucleotide motifs in baculovirus genomes, the target sequence for PURα proteins. Interestingly, these GGN-rich sequences are disproportionally distributed in baculoviral genomes and mostly occurred in proximity to the gene for the major occlusion body protein polyhedrin. We further demonstrate that the VP1054 protein specifically recognizes these GGN-rich islands, which at the same time encode crucial proline-rich domains in p78/83, an essential gene adjacent to the polyhedrin gene in the AcMNPV genome. While some viruses, like human immunodeficiency virus type 1 (HIV-1) and human JC virus (JCV), utilize host PURα protein, baculoviruses encode the PURα-like protein VP1054, which is crucial for viral progeny production.
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Complex dynamics of defective interfering baculoviruses during serial passage in insect cells. J Biol Phys 2013; 39:327-42. [DOI: 10.1007/s10867-013-9317-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/28/2013] [Indexed: 11/26/2022] Open
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Vijayachandran LS, Thimiri Govinda Raj DB, Edelweiss E, Gupta K, Maier J, Gordeliy V, Fitzgerald DJ, Berger I. Gene gymnastics: Synthetic biology for baculovirus expression vector system engineering. Bioengineered 2013; 4:279-87. [PMID: 23328086 DOI: 10.4161/bioe.22966] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Most essential activities in eukaryotic cells are catalyzed by large multiprotein assemblies containing up to ten or more interlocking subunits. The vast majority of these protein complexes are not easily accessible for high resolution studies aimed at unlocking their mechanisms, due to their low cellular abundance and high heterogeneity. Recombinant overproduction can resolve this bottleneck and baculovirus expression vector systems (BEVS) have emerged as particularly powerful tools for the provision of eukaryotic multiprotein complexes in high quality and quantity. Recently, synthetic biology approaches have begun to make their mark in improving existing BEVS reagents by de novo design of streamlined transfer plasmids and by engineering the baculovirus genome. Here we present OmniBac, comprising new custom designed reagents that further facilitate the integration of heterologous genes into the baculovirus genome for multiprotein expression. Based on comparative genome analysis and data mining, we herein present a blueprint to custom design and engineer the entire baculovirus genome for optimized production properties using a bottom-up synthetic biology approach.
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Affiliation(s)
- Lakshmi S Vijayachandran
- European Molecular Biology Laboratory (EMBL); Grenoble Outstation and Unit of Virus Host-Cell Interactions (UVHCI); UJF-EMBL-CNRS, UMR 5233; Grenoble, France; Institut de Biologie Structurale (IBS); UMR5075 CEA-CNRS-Université Joseph Fourier; Grenoble, France; Information Services to Life Science (IStLS); Oberndorf am Neckar, Germany; Geneva Biotech; Geneva, Switzerland
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