Autographa californica baculoviruses with large genomic deletions are rapidly generated in infected insect cells

Enhancement of exogenous protein stability in AcMNPV by overexpressing lef5 gene during passaging

The baculovirus insect cell expression system is pivotal for exogenous protein expression. However, serial passages of baculovirus in insect cells often result in defective virus generation and a rapid decline in exogenous protein expression, limiting its wider application. Previous studies have shown that the expression of the late expression factor 5 (lef5) from other baculoviruses can enhance the stability of exogenous genes in Autographa californica multiple nucleopolyhedrovirus (AcMNPV). In this study, we engineered diverse recombinant strains of AcMNPV to express the enhanced green fluorescent protein (eGFP) and enterovirus 71 virus-like particles (EV71-VLPs), co-expressed with the P1 and 3CD proteins of EV71. We investigated the influence of lef5 overexpression, regulated by various promoters, on the stability of exogenous genes and their protein expressions. Notably, lef5 overexpression significantly improved the stability of eGFP and EV71-P1 gene and protein expressions during serial passages in Sf9 cells. Specifically, the lef5 overexpression driven by the op166 promoter was more beneficial for enhancing the expression stability of complex exogenous proteins, such as EV71-VLPs. This study underscores the importance of lef5 overexpression in maintaining the stability of exogenous gene expression in baculovirus systems, particularly for producing complex proteins such as VLPs of enterovirus. KEY POINTS: • The overexpression of lef5 stabilizes exogenous gene expression in the baculovirus system. • Promoter choice affects lef5-mediated gene expression stability. • The overexpression of lef5 is crucial for producing complex proteins like EV71-VLPs.

Adapting Next-Generation Sequencing to in Process CRISPR-Cas9 Genome Editing of Recombinant AcMNPV Vectors: From Shotgun to Tiled-Amplicon Sequencing

The alphabaculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is the most commonly used virus in the Baculovirus Expression Vector System (BEVS) and has been utilized for the production of many human and veterinary biologics. AcMNPV has a large dsDNA genome that remains understudied, and relatively unmodified from the wild-type, especially considering how extensively utilized it is as an expression vector. Previously, our group utilized CRISPR-Cas9 genome engineering that revealed phenotypic changes when baculovirus genes are targeted using either co-expressed sgRNA or transfected sgRNA into a stable insect cell line that produced the Cas9 protein. Here, we describe a pipeline to sequence the recombinant AcMNPV expression vectors using shotgun sequencing, provide a set of primers for tiled-amplicon sequencing, show that untargeted baculovirus vector genomes remain relatively unchanged when amplified in Sf9-Cas9 cells, and confirm that AcMNPV gp64 gene disruption can minimize baculovirus contamination in cell cultures. Our findings provide a robust baseline for analyzing in process genome editing of baculoviruses.

Unveiling the new chapter in nanobody engineering: advances in traditional construction and AI-driven optimization

Nanobodies (Nbs), miniature antibodies consisting solely of the variable region of heavy chains, exhibit unique properties such as small size, high stability, and strong specificity, making them highly promising for disease diagnosis and treatment. The engineering production of Nbs has evolved into a mature process, involving library construction, screening, and expression purification. Different library types, including immune, naïve, and synthetic/semi-synthetic libraries, offer diverse options for various applications, while display platforms like phage display, cell surface display, and non-surface display provide efficient screening of target Nbs. Recent advancements in artificial intelligence (AI) have opened new avenues in Nb engineering. AI's exceptional performance in protein structure prediction and molecular interaction simulation has introduced novel perspectives and tools for Nb design and optimization. Integrating AI with traditional experimental methods is anticipated to enhance the efficiency and precision of Nb development, expediting the transition from basic research to clinical applications. This review comprehensively examines the latest progress in Nb engineering, emphasizing library construction strategies, display platform technologies, and AI applications. It evaluates the strengths and weaknesses of various libraries and display platforms and explores the potential and challenges of AI in predicting Nb structure, antigen-antibody interactions, and optimizing physicochemical properties.

Baculovirus Genetic Diversity and Population Structure

Baculoviruses can naturally regulate lepidopteran populations and are used as biological insecticides. The genetic diversity of these viruses affects their survival and efficacy in pest control. For nucleopolyhedroviruses, occlusion-derived virions and the occlusion body facilitate the transmission of groups of genomes, whereas this is not the case for granuloviruses. We review the evidence for baculovirus genetic diversity in the environment, in the host insect, and in occlusion bodies and virions. Coinfection allows defective genotypes to persist through complementation and results in the pseudotyping of virus progeny that can influence their transmissibility and insecticidal properties. Genetic diversity has marked implications for the development of pest resistance to virus insecticides. We conclude that future research is warranted on the physical segregation of genomes during virus replication and on the independent action of virions during infection. We also identify opportunities for studies on the transmission of genetic diversity and host resistance to viruses.

A robust and flexible baculovirus-insect cell system for AAV vector production with improved yield, capsid ratios and potency

Manufacturing of adeno-associated viruses (AAV) for gene and cell therapy applications has increased significantly and spurred development of improved mammalian and insect cell-based production systems. We developed a baculovirus-based insect cell production system-the SGMO Helper-with a novel gene architecture and greater flexibility to modulate the expression level and content of individual Rep and Cap proteins. In addition, we incorporated modifications to the AAV6 capsid sequence that improves yield, capsid integrity, and potency. Production of recombinant AAV 6 (rAAV6) using the SGMO Helper had improved yields compared to the Bac-RepCap helper from the Kotin lab. SGMO Helper-derived rAAV6 is resistant to a previously described proteolytic cleavage unique to baculovirus-insect cell production systems and has improved capsid ratios and potency, in vitro and in vivo, compared with rAAV6 produced using Bac-RepCap. Next-generation sequencing sequence analysis demonstrated that the SGMO Helper is stable over six serial passages and rAAV6 capsids contain comparable amounts of non-vector genome DNA as rAAV6 produced using Bac-RepCap. AAV production using the SGMO Helper is scalable using bioreactors and has improved yield, capsid ratio, and in vitro potency. Our studies demonstrate that the SGMO Helper is an improved platform for AAV manufacturing to enable delivery of cutting-edge gene and cell therapies.

Architecture of the baculovirus nucleocapsid revealed by cryo-EM

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.

Insecticidal Traits of Variants in a Genotypically Diverse Natural Isolate of Anticarsia Gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV)

Outbreaks of Anticarsia gemmatalis (Hübner, 1818) (Lepidoptera: Erebidae), a major pest of soybean, can be controlled below economic thresholds with methods that do not involve the application of synthetic insecticides. Formulations based on natural isolates of the Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) (Baculoviridae: Alphabaculovirus) played a significant role in integrated pest management programs in the early 2000s, but a new generation of chemical insecticides and transgenic soybean have displaced AgMNPV-based products over the past decade. However, the marked genotypic variability present among and within alphabaculovirus isolates suggests that highly insecticidal genotypic variants can be isolated and used to reduce virus production costs or overcome isolate-dependent host resistance. This study aimed to select novel variants of AgMNPV with suitable insecticidal traits that could complement the existing AgMNPV active ingredients. Three distinct AgMNPV isolates were compared using their restriction endonuclease profile and in terms of their occlusion body (OB) pathogenicity. One isolate was selected (AgABB51) from which eighteen genotypic variants were plaque purified and characterized in terms of their insecticidal properties. The five most pathogenic variants varied in OB pathogenicity, although none of them was faster-killing or had higher OB production characteristics than the wild-type isolate. We conclude that the AgABB51 wild-type isolates appear to be genotypically structured for fast speed of kill and high OB production, both of which would favor horizontal transmission. Interactions among the component variants are likely to influence this insecticidal phenotype.

The Magic Staff: A Comprehensive Overview of Baculovirus-Based Technologies Applied to Human and Animal Health

Baculoviruses are enveloped, insect-specific viruses with large double-stranded DNA genomes. Among all the baculovirus species, Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is the most studied. Due to its characteristics regarding biosafety, narrow host range and the availability of different platforms for modifying its genome, AcMNPV has become a powerful biotechnological tool. In this review, we will address the most widespread technological applications of baculoviruses. We will begin by summarizing their natural cycle both in larvae and in cell culture and how it can be exploited. Secondly, we will explore the different baculovirus-based protein expression systems (BEVS) and their multiple applications in the pharmaceutical and biotechnological industry. We will focus particularly on the production of vaccines, many of which are either currently commercialized or in advanced stages of development (e.g., Novavax, COVID-19 vaccine). In addition, recombinant baculoviruses can be used as efficient gene transduction and protein expression vectors in vertebrate cells (e.g., BacMam). Finally, we will extensively describe various gene therapy strategies based on baculoviruses applied to the treatment of different diseases. The main objective of this work is to provide an extensive up-to-date summary of the different biotechnological applications of baculoviruses, emphasizing the genetic modification strategies used in each field.

Spatially Segregated Transmission of Co-Occluded Baculoviruses Limits Virus-Virus Interactions Mediated by Cellular Coinfection during Primary Infection

The occlusion bodies (OBs) of certain alphabaculoviruses are polyhedrin-rich structures that mediate the collective transmission of tens of viral particles to the same insect host. In addition, in multiple nucleopolyhedroviruses, occlusion-derived virions (ODVs) form nucleocapsid aggregates that are delivered to the same host cell. It has been suggested that, by favoring coinfection, this transmission mode promotes evolutionarily stable interactions between different baculovirus variants. To quantify the joint transmission of different variants, we obtained OBs from cells coinfected with two viral constructs, each encoding a different fluorescent reporter, and used them for inoculating Spodoptera exigua larvae. The microscopy analysis of midguts revealed that the two reporter genes were typically segregated into different infection foci, suggesting that ODVs show limited ability to promote the co-transmission of different virus variants to the same host cell. However, a polyhedrin-deficient mutant underwent inter-host transmission by exploiting the OBs of a fully functional virus and re-acquired the lost gene through recombination, demonstrating cellular coinfection. Our results suggest that viral spatial segregation during transmission and primary infection limits interactions between different baculovirus variants, but that these interactions still occur within the cells of infected insects later in infection.

Human and Insect Cell-Produced Recombinant Adeno-Associated Viruses Show Differences in Genome Heterogeneity

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.

Innovations in the Insect Cell Expression System for Industrial Recombinant Vaccine Antigen Production

The insect cell expression system has previously been proposed as the preferred biosecurity strategy for production of any vaccine, particularly for future influenza pandemic vaccines. The development and regulatory risk for new vaccine candidates is shortened as the platform is already in use for the manufacturing of the FDA-licensed seasonal recombinant influenza vaccine Flublok^®. Large-scale production capacity is in place and could be used to produce other antigens as well. However, as demonstrated by the 2019 SARS-CoV-2 pandemic the insect cell expression system has limitations that need to be addressed to ensure that recombinant antigens will indeed play a role in combating future pandemics. The greatest challenge may be the ability to produce an adequate quantity of purified antigen in an accelerated manner. This review summarizes recent innovations in technology areas important for enhancing recombinant-protein production levels and shortening development timelines. Opportunities for increasing product concentrations through vector development, cell line engineering, or bioprocessing and for shortening timelines through standardization of manufacturing processes will be presented.

Baculoviruses in Gene Therapy and Personalized Medicine

This review will outline the role of baculoviruses in gene therapy and future potential in personalized medicine. Baculoviruses are a safe, non-toxic, non-integrative vector with a large cloning capacity. Baculoviruses are also a highly adaptable, low-cost vector with a broad tissue and host tropism due to their ability to infect both quiescent and proliferating cells. Moreover, they only replicate in insect cells, not mammalian cells, improving their biosafety. The beneficial properties of baculoviruses make it an attractive option for gene delivery. The use of baculoviruses in gene therapy has advanced significantly, contributing to vaccine production, anti-cancer therapies and regenerative medicine. Currently, baculoviruses are primarily used for recombinant protein production and vaccines.  This review will also discuss methods to optimize baculoviruses protein production and mammalian cell entry, limitations and potential for gene therapy and personalized medicine. Limitations such as transient gene expression, complement activation and virus fragility are discussed in details as they can be overcome through further genetic modifications and other methods. This review concludes that baculoviruses are an excllent candidate for gene therapy, personalized medicine and other biotherapeutic applications.

Relocation of the attTn7 Transgene Insertion Site in Bacmid DNA Enhances Baculovirus Genome Stability and Recombinant Protein Expression in Insect Cells

Baculovirus expression vectors are successfully used for the commercial production of complex (glyco)proteins in eukaryotic cells. The genome engineering of single-copy baculovirus infectious clones (bacmids) in E. coli has been valuable in the study of baculovirus biology, but bacmids are not yet widely applied as expression vectors. An important limitation of first-generation bacmids for large-scale protein production is the rapid loss of gene of interest (GOI) expression. The instability is caused by the mini-F replicon in the bacmid backbone, which is non-essential for baculovirus replication in insect cells, and carries the adjacent GOI in between attTn7 transposition sites. In this paper, we test the hypothesis that relocation of the attTn7 transgene insertion site away from the mini-F replicon prevents deletion of the GOI, thereby resulting in higher and prolonged recombinant protein expression levels. We applied lambda red genome engineering combined with SacB counterselection to generate a series of bacmids with relocated attTn7 sites and tested their performance by comparing the relative expression levels of different GOIs. We conclude that GOI expression from the odv-e56 (pif-5) locus results in higher overall expression levels and is more stable over serial passages compared to the original bacmid. Finally, we evaluated this improved next-generation bacmid during a bioreactor scale-up of Sf9 insect cells in suspension to produce enveloped chikungunya virus-like particles as a model vaccine.

Production of Baculovirus and Stem Cells for Baculovirus-Mediated Gene Transfer into Human Mesenchymal Stem Cells

The discovery of the genome-editing tool CRISPR-Cas9 is revolutionizing the world of gene therapy and will extend the gene therapy product pipeline. While applying gene therapy products, the main difficulty is an efficient and effective transfer of the nucleic acids carrying the relevant information to their target destination, the nucleus of the cells. Baculoviruses have shown to be very suitable transport vehicles for this task due to, inter alia, their ability to transduce mammalian/human cells without being pathogenic. This property allows the usage of baculovirus-transduced cells as cell therapy products, thus, combining the advantages of gene and cell therapy. To make such pharmaceuticals available for patients, a successful production and purification is necessary. In this chapter, we describe the generation of a pseudotyped baculovirus vector, followed by downstream processing using depth and tangential-flow filtration. This vector is used subsequently to transduce human mesenchymal stem cells. The production of the cells and the subsequent transduction process are illustrated.

Baculovirus Expression and Functional Analysis of Vpa2 Proteins from Bacillus thuringiensis

The mode of action underlying the insecticidal activity of the Bacillus thuringiensis (Bt) binary pesticidal protein Vpa1/Vpa2 is uncertain. In this study, three recombinant baculoviruses were constructed using Bac-to-Bac technology to express Vpa2Ac1 and two novel Vpa2-like genes, Vpa2-like1 and Vpa2-like2, under the baculovirus p10 promoter in transfected Sf9 cells. Pairwise amino acid analyses revealed a higher percentage of identity and a lower number of gaps between Vpa2Ac1 and Vpa2-like2 than to Vpa2-like1. Moreover, Vpa2-like1 lacked the conserved Ser-Thr-Ser motif, involved in NAD binding, and the (F/Y)xx(Q/E)xE consensus sequence, characteristic of the ARTT toxin family involved in actin polymerization. Vpa2Ac1, Vpa2-like1 and Vpa2-like2 transcripts and proteins were detected in Sf9 culture cells, but the signals of Vpa2Ac1 and Vpa2-like2 were weak and decreased over time. Sf9 cells infected by a recombinant bacmid expressing Vpa2-like1 showed typical circular morphology and produced viral occlusion bodies (OBs) at the same level as the control virus. However, expression of Vpa2Ac1 and Vpa2-like2 induced cell polarization, similar to that produced by the microfilament-destabilizing agent cytochalasin D and OBs were not produced. The presence of filament disrupting agents, such as nicotinamide and nocodazole, during transfection prevented cell polarization and OB production was observed. We conclude that Vpa2Ac1 and Vpa2-like2 proteins likely possess ADP-ribosyltransferase activity that modulated actin polarization, whereas Vpa2-like1 is not a typical Vpa2 protein. Vpa2-like2 has now been designated Vpa2Ca1 (accession number AAO86513) by the Bacillus thuringiensis delta-endotoxin nomenclature committee.

Baculovirus-Derived Vectors for Immunization and Therapeutic Applications

Baculoviruses are arthropod-specific, enveloped viruses with circular, supercoiled double-stranded deoxyribonucleic acid genomes. While many viruses are studied to seek solutions for their adverse impact on human, veterinary, and plant health, the study of baculoviruses was stimulated initially by their potential utility to control insect pests. Later, the utility of baculovirus as gene expression vectors was evidenced leading to numerous applications. Several strategies are employed to obtain recombinant viruses that express large quantities of heterologous proteins. A major step forward was the development of bacmid technology (the construction of bacterial artificial chromosomes containing the genome of the baculovirus) which allows the manipulation of the baculovirus genome in bacteria. With this technology, foreign genes can be introduced into the bacmid by homologous and site-directed recombination or by transposition. Baculoviruses have been used to explore fundamental questions in molecular biology such as the nature of programmed cell-death. Moreover, the ability of baculoviruses to transduce mammalian cells led to the consideration of their use as gene-therapy and vaccine vectors. Strategies for genetic engineering of baculoviruses have been developed to meet the requirements of new application areas. Display of foreign proteins on the surface of virions or in nucleocapsid structures, the assembly of expressed proteins to form virus-like particles or protein complexes have been explored and validated as vaccines. The aim of this chapter is to update the areas of application of the baculoviruses in protein expression, alternative vaccine designs and gene therapy of infectious diseases and genetic disorders. Finally, we review the baculovirus-derived products on the market and in the pipeline for biomedical and veterinary use.

On the stability of sequences inserted into viral genomes

Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Many of these engineered viruses are viable and express heterologous proteins at high levels, but the inserted sequences often prove to be unstable over time and are rapidly lost, limiting heterologous protein expression. Although virologists are aware that inserted sequences can be unstable, processes leading to insert instability are rarely considered from an evolutionary perspective. Here, we review experimental work on the stability of inserted sequences over a broad range of viruses, and we present some theoretical considerations concerning insert stability. Different virus genome organizations strongly impact insert stability, and factors such as the position of insertion can have a strong effect. In addition, we argue that insert stability not only depends on the characteristics of a particular genome, but that it will also depend on the host environment and the demography of a virus population. The interplay between all factors affecting stability is complex, which makes it challenging to develop a general model to predict the stability of genomic insertions. We highlight key questions and future directions, finding that insert stability is a surprisingly complex problem and that there is need for mechanism-based, predictive models. Combining theoretical models with experimental tests for stability under varying conditions can lead to improved engineering of viral modified genomes, which is a valuable tool for understanding genome evolution as well as for biotechnological applications, such as gene therapy.

Expression- and genomic-level changes during passage of four baculoviruses derived from bacmids in permissive insect cell lines

The baculovirus-based bacmid expression vector system has been widely used for protein production in basic research and biotechnological laboratories. Since the first construction of the Autographa californica multiple nucleopolyhedrovirus bacmid (AcBacmid), three more bacmids have been created from Bombyx mori nucleopolyhedrovirus (BmBacmid), Spodoptera exigua nucleopolyhedrovirus (SeBacmid) and Helicoverpa armigera nucleopolyhedrovirus (HaBacmid). Each of these bacmid-derived viruses replicates efficiently in a range of specific and permissive cell types. Here, we investigated the relative stability of each virus derived from the bacmid during passage in permissive cell lines through assessment of their expression level and genome structure changes. Using two different reporters, the expression levels of the viruses from the AcBacmid-Sf9, AcBacmid-Tn5, BmBacmid-BmN and SeBacmid-SeE1 bacmid-cell systems were significantly reduced after five passages of the viruses, whereas the reductions were not detected in the AcBacmid-Sf21 and HaBacmid-HzAM1 systems. Pulse field gel electrophoresis (PFGE) and restriction fragment length polymorphism (RFLP) analysis of viral DNA isolated from passaged viruses from the AcBacmid-Sf21 and HaBacmid-HzAM1 systems showed no major genomic changes. In contrast, the genomes from passaged viruses in the AcBacmid-Tn5 and AcBacmid-Sf9 systems displayed reduced genome size and various mutations at individual loci, including genotypes missing one at least or more viral RNA polymerase subunits and fp25k. These genotypic changes were correlated with reduced protein expression. RFLP analysis of viral DNA from passaged viruses in the BmBacmid-BmN and SeBacmid-SeE1 systems exhibited changes in genome size, including excision of particular EcoRI fragments containing the mini-F replicon. Collectively, our data suggest that the viruses from the AcBacmid-Sf21 and HaBacmid-HzAM1 bacmid-cell systems are better for large-scale protein expression in continuous culture. Further study is needed to investigate the mechanism(s) behind the protein expression reduction in these bacmid-derived virus/cell systems.

Remarkably efficient production of a highly insecticidal Chrysodeixis chalcites nucleopolyhedrovirus (ChchNPV) isolate in its homologous host

BACKGROUND

A Chrysodeixis chalcites nucleopolyhedrovirus from the Canary Islands (ChchNPV-TF1) has proved to be effective for control of Chrysodeixis chalcites on banana crops. Commercialization of this virus as a bioinsecticide requires an efficient production system.

RESULTS

The sixth instar (L₆ ) was the most suitable for virus production, producing 1.80 × 10¹¹ occlusion bodies (OB)/larva and showed a lower prevalence of cannibalism (5.4%) than fourth (L₄ ) or fifth (L₅ ) instars. Inoculation of L₆ at 24 h post molting produced six times more OB (5.72 × 10¹¹ OB/larva) than recently molted L₆ larvae (1.00 × 10¹¹ OB/larva). No significant differences were recorded in mean time to death (165-175 h) or OB production per larva (3.75 × 10¹¹ to 5.97 × 10¹¹ ) or per mg larval weight (1.30 × 10¹¹ to 2.11 × 10⁹ ), in larvae inoculated with a range of inoculum concentrations (LC₅₀ -LC₉₀ ). Groups of infected L₆ larvae reared at a density of 150 larvae/container produced a greater total number of OBs (8.07 × 10¹³ OB/container) than lower densities (25, 50 and 100 OB/container), and a similar number to containers with 200 inoculated larvae (8.43 × 10¹³ OB/container).

CONCLUSION

The processes described here allow efficient production of sufficient OBs to treat ∼ 40 ha of banana crops using the insects from a single container. © 2018 Society of Chemical Industry.

Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses

Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate-the rate at which deletions removing the insertion occur-and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness.

MultiBac: from protein complex structures to synthetic viral nanosystems

The MultiBac baculovirus/insect cell expression vector system was conceived as a user-friendly, modular tool-kit for producing multiprotein complexes for structural biology applications. MultiBac has allowed the structure and function of many molecular machines to be elucidated, including previously inaccessible high-value drug targets. More recently, MultiBac developments have shifted to customized baculoviral genomes that are tailored for a range of applications, including synthesizing artificial proteins by genetic code expansion. We review some of these developments, including the ongoing rewiring of the MultiBac system for mammalian applications, notably CRISPR/Cas9-mediated gene editing.

The Autographa californica Multiple Nucleopolyhedrovirus ac83 Gene Contains a cis-Acting Element That Is Essential for Nucleocapsid Assembly

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.

Trade-offs and mixed infections in an obligate-killing insect pathogen

Natural populations of pathogens are frequently composed of numerous interacting strains. Understanding what maintains this diversity remains a key focus of research in disease ecology. In addition, within-host pathogen dynamics can have a strong impact on both infection outcome and the evolution of pathogen virulence, and thus, understanding the impact of pathogen diversity is important for disease management. We compared eight genetically distinguishable variants from Spodoptera exempta nucleopolyhedrovirus (SpexNPV) isolated from the African armyworm, Spodoptera exempta. NPVs are obligate killers, and the vast majority of transmission stages are not released until after the host has died. The NPV variants differed significantly in their virulence and could be clustered into two groups based on their dose-response curves. They also differed in their speed of kill and productivity (transmission potential) for S. exempta. The mixed-genotype wild-type (WT) SpexNPV, from which each variant was isolated, was significantly more virulent than any individual variant and its mean mortality rate was within the fastest group of individual variants. However, the WT virus produced fewer new infectious stages than any single variant, which might reflect competition among the variants. A survival analysis, combining the mortality and speed of kill data, confirmed the superiority of the genetically mixed WT virus over any single variant. Spodoptera exempta larvae infected with WT SpexNPV were predicted to die 2·7 and 1·9 times faster than insects infected with isolates from either of the two clusters of genotypes. Theory suggests that there are likely to be trade-offs between pathogen fitness traits. Across all larvae, there was a negative linear relationship between virus yield and speed of kill, such that more rapid host death carried the cost of producing fewer transmission stages. We also found a near-significant relationship for the same trend at the intervariant level. However, there was no evidence for a significant relationship between the induced level of mortality and transmission potential (virus yield) or speed of kill.

Evaluation of the Insecticidal Efficacy of Wild Type and Recombinant Baculoviruses

A considerable amount of work has been undertaken to genetically enhance the efficacy of baculovirus insecticides. Following construction of a genetically altered baculovirus, laboratory bioassays are used to quantify various parameters of insecticidal activity such as the median lethal concentration (or dose) required to kill 50 % of infected larvae (LC50 or LD50), median survival of larvae infected (ST50), and feeding damage incurred by infected larvae. In this chapter, protocols are described for a variety of bioassays and the corresponding data analyses for assessment of the insecticidal activity of baculovirus insecticides.

Manufacturing of AcMNPV baculovirus vectors to enable gene therapy trials

Over the past two decades, baculoviruses have become workhorse research tools for transient transgene expression. Although they have not yet been used directly as a gene therapy vector in the clinical setting, numerous preclinical studies have suggested the highly promising potential of baculovirus as a delivery vector for a variety of therapeutic applications including vaccination, tissue engineering, and cancer treatment. As such, there is growing interest in using baculoviruses as human gene therapy vectors, which has led to advances in baculovirus bioprocessing methods. This review provides an overview of the current approaches for scaled-up amplification, concentration, purification, and formulation of AcMNPV baculoviruses, and highlights the key regulatory requirements that must be met before gene therapy clinical trials can be initiated.

Development of a recombination system for the generation of occlusion positive genetically modified Anticarsia gemmatalis multiple nucleopolyhedrovirus

Anticarsia gemmatalis is an important pest in legume crops in South America and it has been successfully controlled using Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV) in subtropical climate zones. Nevertheless, in temperate climates its speed of kill is too slow. Taking this into account, genetic modification of AgMNPV could lead to improvements of its biopesticidal properties. Here we report the generation of a two-component system that allows the production of recombinant AgMNPV. This system is based on a parental AgMNPV in which the polyhedrin gene (polh) was replaced by a bacterial β-galactosidase (lacZ) gene flanked by two target sites for the homing endonuclease I-PpoI. Co-transfection of insect cells with linearized (I-PpoI-digested) parental genome and a transfer vector allowed the restitution of polh and the expression of a heterologous gene upon homologous recombination, with a low background of non-recombinant AgMNPV. The system was validated by constructing a recombinant occlusion-positive (polh⁺) AgMNPV expressing the green fluorescent protein gene (gfp). This recombinant virus infected larvae normally per os and led to the expression of GFP in cell culture as well as in A. gemmatalis larvae. These results demonstrate that the system is an efficient method for the generation of recombinant AgMNPV expressing heterologous genes, which can be used for manifold purposes, including biotechnological and pharmaceutical applications and the production of orally infectious recombinants with improved biopesticidal properties.

The production of multiprotein complexes in insect cells using the baculovirus expression system

The production of a homogeneous protein sample in sufficient quantities is an essential prerequisite not only for structural investigations but represents also a rate-limiting step for many functional studies. In the cell, a large fraction of eukaryotic proteins exists as large multicomponent assemblies with many subunits, which act in concert to catalyze specific activities. Many of these complexes cannot be obtained from endogenous source material, so recombinant expression and reconstitution are then required to overcome this bottleneck. This chapter describes current strategies and protocols for the efficient production of multiprotein complexes in large quantities and of high quality, using the baculovirus/insect cell expression system.

Experimental evolution of pseudogenization and gene loss in a plant RNA virus

Viruses have evolved highly streamlined genomes and a variety of mechanisms to compress them, suggesting that genome size is under strong selection. Horizontal gene transfer has, on the other hand, played an important role in virus evolution. However, evolution cannot integrate initially nonfunctional sequences into the viral genome if they are rapidly purged by selection. Here we report on the experimental evolution of pseudogenization in virus genomes using a plant RNA virus expressing a heterologous gene. When long 9-week passages were performed, the added gene was lost in all lineages, whereas viruses with large genomic deletions were fixed in only two out of ten 3-week lineages and none in 1-week lineages. Illumina next-generation sequencing revealed considerable convergent evolution in the 9- and 3-week lineages with genomic deletions. Genome size was correlated to within-host competitive fitness, although there was no correlation with virus accumulation or virulence. Within-host competitive fitness of the 3-week virus lineages without genomic deletions was higher than for the 1-week lineages. Our results show that the strength of selection for a reduced genome size and the rate of pseudogenization depend on demographic conditions. Moreover, for the 3-week passage condition, we observed increases in within-host fitness, whereas selection was not strong enough to quickly remove the nonfunctional heterologous gene. These results suggest a demographically determined "sweet spot" might exist, where heterologous insertions are not immediately lost while evolution can act to integrate them into the viral genome.

Deletion genotypes reduce occlusion body potency but increase occlusion body production in a Colombian Spodoptera frugiperda nucleopolyhedrovirus population

A Colombian field isolate (SfCOL-wt) of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) is a mixture of different genotypes. To evaluate the insecticidal properties of the different genotypic variants, 83 plaque purified virus were characterized. Ten distinct genotypes were identified (named A through J). SfCOL-A was the most prevalent (71±2%; mean ± SE) showing a PstI restriction profile indistinguishable to that of SfCOL-wt. The remaining nine genotypes presented genomic deletions of 3.8 - 21.8 Kb located mainly between nucleotides 11,436 and 33,883 in the reference genome SfMNPV-B, affecting the region between open reading frames (ORFs) sf20 and sf33. The insecticidal activity of each genotype from SfCOL-wt and several mixtures of genotypes was compared to that of SfCOL-wt. The potency of SfCOL-A occlusion bodies (OBs) was 4.4-fold higher than SfCOL-wt OBs, whereas the speed of kill of SfCOL-A was similar to that of SfCOL-wt. Deletion genotype OBs were similarly or less potent than SfCOL-wt but six deletion genotypes were faster killing than SfCOL-wt. The potency of genotype mixtures co-occluded within OBs were consistently reduced in two-genotype mixtures involving equal proportions of SfCOL-A and one of three deletion genotypes (SfCOL-C, -D or -F). Speed of kill and OB production were improved only when the certain genotype mixtures were co-occluded, although OB production was higher in the SfCOL-wt isolate than in any of the component genotypes, or mixtures thereof. Deleted genotypes reduced OB potency but increased OB production of the SfCOL-wt population, which is structured to maximize the production of OBs in each infected host.

Gene gymnastics: Synthetic biology for baculovirus expression vector system engineering

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.

Evolution and the microbial control of insects

Insect pathogens can be utilized in a variety of pest management approaches, from inundative release to augmentation and classical biological control, and microevolution and the consideration of evolutionary principles can potentially influence the success of all these strategies. Considerable diversity exists in natural entomopathogen populations and this diversity can be either beneficial or detrimental for pest suppression, depending on the pathogen and its mode of competition, and this should be considered in the selection of isolates for biological control. Target hosts can exhibit considerable variation in their susceptibility to entomopathogens, and cases of field-evolved resistance have been documented for Bacillus thuringiensis and baculoviruses. Strong selection, limited pathogen diversity, reduced gene flow, and host plant chemistry are linked to cases of resistance and should be considered when developing resistance management strategies. Pre- and post-release monitoring of microbial control programs have received little attention; however, to date there have been no reports of host-range evolution or long-term negative effects on nontarget hosts. Comparative analyses of pathogen population structure, virulence, and host resistance over time are required to elucidate the evolutionary dynamics of microbial control systems.

Production of baculovirus defective interfering particles during serial passage is delayed by removing transposon target sites in fp25k

Accumulation of baculovirus defective interfering particle (DIP) and few polyhedra (FP) mutants is a major limitation to continuous large-scale baculovirus production in insect-cell culture. Although overcoming these mutations would result in a cheaper platform for producing baculovirus biopesticides, little is known regarding the mechanism of FP and DIP formation. This issue was addressed by comparing DIP production of wild-type (WT) Autographa californica multiple nucleopolyhedrovirus (AcMNPV) with that of a recombinant AcMNPV (denoted Ac-FPm) containing a modified fp25k gene with altered transposon insertion sites that prevented transposon-mediated production of the FP phenotype. In addition to a reduction in the incidence of the FP phenotype, DIP formation was delayed on passaging of Ac-FPm compared with WT AcMNPV. Specifically, the yield of DIP DNA in Ac-FPm was significantly lower than in WT AcMNPV up to passage 16, thereby demonstrating that modifying the transposon insertion sites increases the genomic stability of AcMNPV. A critical component of this investigation was the optimization of a systematic method based on the use of pulsed-field gel electrophoresis (PFGE) to characterize extracellular virus DNA. Specifically, PFGE was used to detect defective genomes, determine defective genome sizes and quantify the amount of defective genome within a heterogeneous genome population of passaged virus.

Multigene expression of protein complexes by iterative modification of genomic Bacmid DNA

Background

Many cellular multi-protein complexes are naturally present in cells at low abundance. Baculovirus expression offers one approach to produce milligram quantities of correctly folded and processed eukaryotic protein complexes. However, current strategies suffer from the need to produce large transfer vectors, and the use of repeated promoter sequences in baculovirus, which itself produces proteins that promote homologous recombination. One possible solution to these problems is to construct baculovirus genomes that express each protein in a complex from a separate locus within the viral DNA. However current methods for selecting such recombinant genomes are too inefficient to routinely modify the virus in this way.

Results

This paper reports a method which combines the lambda red and bacteriophage P1 Cre-recombinase systems to efficiently generate baculoviruses in which protein complexes are expressed from multiple, single-locus insertions of foreign genes. This method is based on an 88 fold improvement in the selection of recombinant viruses generated by red recombination techniques through use of a bipartite selection cassette. Using this system, seven new genetic loci were identified in the AcMNPV genome suitable for the high level expression of recombinant proteins. These loci were used to allow the recovery two recombinant virus-like particles with potential biotechnological applications (influenza A virus HA/M1 particles and bluetongue virus VP2/VP3/VP5/VP7 particles) and the mammalian chaperone and cancer drug target CCT (16 subunits formed from 8 proteins).

Conclusion

1. Use of bipartite selections can significantly improve selection of modified bacterial artificial chromosomes carrying baculovirus DNA. Furthermore this approach is sufficiently robust to allow routine modification of the virus genome. 2. In addition to the commonly used p10 and polyhedrin loci, the ctx, egt, 39k, orf51, gp37, iap2 and odv-e56 loci in AcMNPV are all suitable for the high level expression of heterologous genes. 3. Two protein, four protein and eight protein complexes including virus-like particles and cellular chaperone complexes can be produced using the new approach.

Establishment of an insect cell clone that harbours a partial baculoviral genome and is resistant to homologous virus infection

After serially undiluted passage of Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV), persistently infected Se301 cells were established. A cell strain, in which no polyhedra or viral particles were observed, was cloned and designated P8-Se301-C1. The P8-Se301-C1 cells are morphologically similar to but grow slower than Se301 cells and they can homologously interfere with SeMNPV. PCR analysis showed that SeMNPV ie-0 and polyhedrin genes were present but DNA polymerase and orf67 genes were absent in P8-Se301-C1, suggesting that the cells harbour incomplete SeMNPV genomes. Dot-blot analysis demonstrated that 0.32+/-0.16 ng SeMNPV DNA was present in 1.25 x 10(5) P8-Se301-C1 cells. A quantitative real-time PCR assay showed that there were 13.2+/-4.3 copies of the SeMNPV polyhedrin gene in each cell. Nested RT-PCR demonstrated the presence of SeMNPV polyhedrin transcripts in P8-Se301-C1 cells. The fact that P8-Se301-C1 cells carry low levels of partial viral genome but do not produce viral progeny suggests a latent-like viral infection in the cells.

E. coli and insect cell expression, automated purification and quantitative analysis

The production of recombinant proteins usually involves the exploration of a wide variety of expression and purification methodologies in the pursuit of a strategy tailored to a particular protein. The methods applied are reliant on exploiting individual differences between expression systems or the variations in specific protein properties. These bespoke strategies have not lent themselves to high-throughput methodologies. Ultimately the development of robust generic methods capable of simplifying and stabilizing the process, allowing automation, was necessary to increase throughput. This chapter describes a series of high-throughput methods used to express, purify, and quantify recombinant protein produced in E. coli or insect cells.

Accumulation of few-polyhedra mutants upon serial passage of Anticarsia gemmatalis multiple nucleopolyhedrovirus in cell culture

Anticarsia gemmatalis nucleopolyhedrovirus (AgMNPV) has been widely used to control the velvetbean caterpillar, Anticarsia gemmatalis, in Brazil. To date, AgMNPV has been produced by larval infection and, due to in vivo production limitations and the continuing high demand for the biopesticide, attempts should be made to develop in vitro production of this virus. In order to investigate the effects caused by serial passage of AgMNPV in cell culture, we carried out a total of ten passages and analyzed the morphological and the genomic changes of the virus. After six passages, the many-polyhedra (MP) phenotype started to switch to the few-polyhedra (FP) phenotype which rapidly accumulated in the virus population. Ultrastructural analysis showed typical signs of FP mutant formation such as decrease in the number of polyhedra per cell, polyhedra aberrant morphology and low numbers of virions occluded in the protein matrix. Also enhanced BV production was observed from the fifth passage indicating that FP mutants were becoming predominant in comparison to the wild type virus. Restriction endonuclease analysis of the viral DNA revealed that lower and higher passages had similar profiles indicating that there were no large insertions or deletions or rearrangements in their genomes and indicating the generation of FP mutants instead of defective interfering viruses.

The origins of replication of granuloviruses

The genomes of eight granuloviruses (GVs), have been analyzed for the presence of homologous regions (hrs) that may act as origins of replication. Thirteen 74-76-bp palindromes within 11 hrs have previously been identified in the Cydia pomonella GV (CpGV) genome and found to replicate in an infection-dependent DNA replication assay. We report a further palindrome within one of the hrs, which was found to replicate, bringing the total to 14 palindromes. We also report imperfect palindromes, with similar 13-bp end sequences to the CpGV palindromes, within the Adoxophyes orana GV, Cryptophlebia leucotreta GV (CrleGV), Choristoneura occidentalis GV and Phthorimaea operculella GV genomes. No hrs were detected in Agrotis segetum GV, and no additional hrs or palindromes, other than those published, were detected in the Plutella xylostella GV and Xestia c-nigrum GV genomes. Several putative hrs from the GVs were tested for replication in C. pomonella cells using a CpGV-dependent replication assay. Two CrleGV hrs were found to replicate at a low level.

Low multiplicity of infection in vivo results in purifying selection against baculovirus deletion mutants

The in vivo fate of Autographa californica multiple nucleopolyhedrovirus deletion mutants originating from serial passage in cell culture was investigated by passaging a population enriched in these mutants in insect larvae. The infectivity of polyhedra and occlusion-derived virion content per polyhedron were restored within two passages in vivo. The frequency of occurrence of deletion mutants was determined by real-time PCR. The frequency of the non-homologous region origin (non-HR ori) of DNA replication was reduced to wild-type levels within two passages. The frequency of the polyhedrin gene did not increase and remained below wild-type levels. A low m.o.i. during the initial infection in insect larvae, causing strong purifying selection for autonomously replicating viruses, could explain these observations. The same virus population used in vivo was also passaged once at a different m.o.i. in cell culture. A similar effect (i.e. lower non-HR ori frequency) was observed at low m.o.i. only, indicating that m.o.i. was the key selective condition.