The dynamics of the flavin, NADPH, and active site loops determine the mechanism of activation of class B flavin-dependent monooxygenases.

Flavin-dependent monooxygenases (FMOs) constitute a diverse enzyme family that catalyzes crucial hydroxylation, epoxidation, and Baeyer-Villiger reactions across various metabolic pathways in all domains of life. Due to the intricate nature of this enzyme family's mechanisms, some aspects of their functioning remain unknown. Here, we present the results of molecular dynamics computations, supplemented by a bioinformatics analysis, that clarify the early stages of their catalytic cycle. We have elucidated the intricate binding mechanism of NADPH and L-Orn to a class B monooxygenase, the ornithine hydroxylase from Aspergillus $$ Aspergillus $$ fumigatus $$ fumigatus $$ known as SidA. Our investigation involved a comprehensive characterization of the conformational changes associated with the FAD (Flavin Adenine Dinucleotide) cofactor, transitioning from the out to the in position. Furthermore, we explored the rotational dynamics of the nicotinamide ring of NADPH, shedding light on its role in facilitating FAD reduction, supported by experimental evidence. Finally, we also analyzed the extent of conservation of two Tyr-loops that play critical roles in the process.

PluriBAC: A Versatile Baculovirus-Based Modular System to Express Heterologous Genes in Different Biotechnological Platforms.

Baculoviruses are insect-specific pathogens widely used in biotechnology. In particular, the Autographa californica nucleopolyhedrovirus (AcMNPV) has been exploited as a platform for bio-inputs production. This is why the improvement of the technologies used for the production of recombinant baculoviruses takes on particular relevance. To achieve this goal, we developed a highly versatile baculoviral transfer vector generation system called PluriBAC. The PluriBAC system consists of three insert entry levels using Golden Gate assembly technology. The wide availability of vectors and sticky ends allows enough versatility to combine more than four different promoters, genes of interest, and terminator sequences. Here, we report not only the rational design of the PluriBAC system but also its use for the generation of baculoviral reporter vectors applied to different fields of biotechnology. We demonstrated that recombinant AcMNPV baculoviruses generated with the PluriBAC system were capable of infecting Spodoptera frugiperda larvae. On the other hand, we found that the recombinant budded virions (BV) generated using our system were capable of transducing different types of tumor and normal cells both in vitro and in vivo. Our findings suggest that the PluriBAC system could constitute a versatile tool for the generation of insecticide and gene therapy vectors.

Effects of Mixed Baculovirus Infections in Biological Control: A Comprehensive Historical and Technical Analysis.

Baculoviruses are insect-specific DNA viruses that have been exploited as bioinsecticides for the control of agricultural and forest pests around the world. Mixed infections with two different baculoviruses have been found in nature, infecting the same host. They have been studied to understand the biology of virus interactions, their effects on susceptible insects, and their insecticidal implications. In this work, we summarize and analyze the in vivo baculovirus co-infections reported in the literature, mainly focusing on pest biocontrol applications. We discuss the most common terms used to describe the effects of mixed infections, such as synergism, neutralism, and antagonism, and how to determine them based on host mortality. Frequently, baculovirus co-infections found in nature are caused by a combination of a nucleopolyhedrovirus and a granulovirus. Studies performed with mixed infections indicated that viral dose, larval stage, or the presence of synergistic factors in baculovirus occlusion bodies are important for the type of virus interaction. We also enumerate and discuss technical aspects to take into account in studies on mixed infections, such as statistical procedures, quantification of viral inocula, the selection of instars, and molecular methodologies for an appropriate analysis of baculovirus interaction. Several experimental infections using two different baculoviruses demonstrated increased viral mortality or a synergistic effect on the target larvae compared to single infections. This can be exploited to improve the baculovirus-killing properties of commercial formulations. In this work, we offer a current overview of baculovirus interactions in vivo and discuss their potential applications in pest control strategies.

Genomic diversity in a population of Spodoptera frugiperda nucleopolyhedrovirus.

Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) represents a strong candidate to develop environmental-friendly pesticides against the fall armyworm (Spodoptera frugiperda), a widespread pest that poses a severe threat to different crops around the world. To date, SfMNPV genomic diversity of different isolates has been mainly studied by means of restriction pattern analyses and by sequencing of the egt region. Here, the genomic diversity present inside an isolate of SfMNPV was explored using high-throughput sequencing for the first time. We identified 704 intrahost single nucleotide variants, from which 184 are nonsynonymous mutations distributed among 82 different coding sequences. We detected several structural variants affecting SfMNPV genome, including two previously reported deletions inside the egt region. A comparative analysis between polymorphisms present in different SfMNPV isolates and our intraisolate diversity data suggests that coding regions with higher genetic diversity are associated with oral infectivity or unknown functions. In this context, through molecular evolution studies we provide evidence of diversifying selection acting on sf29, a putative collagenase which could contribute to the oral infectivity of SfMNPV. Overall, our results contribute to deepen our understanding of the coevolution between SfMNPV and the fall armyworm and will be useful to improve the applicability of this virus as a biological control agent.

Identification of a microRNA encoded by Anticarsia gemmatalis multiple nucleopolyhedrovirus.

MicroRNAs are regulatory RNAs that are scarcely described in Baculoviruses. In this work we predicted a microRNA in silico, denominated agmnpv-miR-4, encoded in the genome of Anticarsia gemmatalis Nucleopolyhedrovirus (AgMNPV), which is homologous to the already validated bmnpv-miR-4 from Bombyx mori Nucleopolyhedrovirus (BmNPV). Considering information known for bmnpv-miR-4 such as seed sequence, coding location in the genome and putative target binding, we searched for the coding sequence of agmnpv-miR-4 in AgMNPV genome. A precursor sequence of agmnpv-miR-4 was predicted, and we identified a putative 23 nt mature microRNA, agmnpv-miR-4, coded in the complementary strand of AgMNPV-2D between positions 49,450 and 49,472. We validated agmnpv-miR-4 by Northern blot from HighFive cells and A. gemmatalis larve extracts infected with AgMNPV.

A simplified strategy to package foreign proteins into baculovirus occlusion bodies without engineering the viral genome.

Polyhedron envelope protein (PEP) is the major component of the calyx that surrounds the baculovirus occlusion body (OB). PEP has been associated with the stabilization and resistance of polyhedra in the environment. Due to the abundant levels of PEP in OBs, we decided to use this protein as a fusion partner to redirect foreign proteins to baculovirus polyhedra. In this study we developed a strategy that involves the generation of a monoclonal transformed insect cell line expressing a protein of interest fused to the the Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) N-terminus of PEP that enables the packaging of foreign proteins into the OBs without generating a recombinant baculovirus. This proved to be an efficient platform that could be exploited to improve wild type baculovirus for their use as bioinsecticides without facing the concerns of releasing genetically modified DNA to the environment and bypassing the associated regulatory issues. We demonstrated, using immunological, proteomic and microscopy techniques, that the envelope of AgMNPV OBs can effectively trap chimeric proteins in an infected insect cell line expressing AgMNPV PEP fused to the enhanced green fluorescent protein (eGFP). Furthermore, packaging of chimeric PEP also took place with heterologous OBs such as those of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), another group I alphabaculovirus.

Identificación de un aislamiento argentino de Spodoptera frugiperda granulovirus / Identification of an Argentinean isolate of Spodoptera frugiperda granulovirus

Abstract The fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is an important maize pest. Due to the environmental impact and emergence of resistance caused by chemical pesticides and transgenic events, the use of baculoviruses becomes a safe and useful alternative for its control in integrated pest management strategies. Here we report the identification of a novel isolate of a granulovirus of S. frugiperda native to the central region of Argentina, named SfGV ARG. We observed that larvae infected with SfGV ARG showed a yellowish coloration, swollen body and, in some cases, severe lesions in the last abdominal segments. We confirmed the identity of the isolate by sequencing fragments of the lef-8, lef-9 and granulin genes and by calculating evolutionary distances using the Kimura-2-Parameter model. SfGV ARG DNA restriction pattern allowed to estimate a genome of at least 135 kb.

Resumen La oruga militar tardía, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), es una plaga importante del maíz. Debido al impacto ambiental y a la aparición de resistencia causados por los pesticidas químicos y los eventos transgénicos, el uso de baculovirus resulta una alternativa útil y saludable para su control en estrategias de manejo integrado de plagas. En este trabajo reportamos la identificación de un nuevo aislamiento del granulovirus de la S. frugiperda nativo de la región central de Argentina, SfGV ARG. Se observó que larvas infectadas con SfGV ARG mostraron coloración amarillenta, hinchazón y, en algunos casos, lesiones graves en los últimos segmentos abdominales. Se confirmó la identidad del aislamiento por secuenciación de fragmentos de los genes lef-8, lef-9y granulina, y por cálculo de distancias evolutivas usando el parámetro de Kimura-2. El patrón de restricción generado con el ADN genómico de SfGV ARG permitió estimar un tamaño de genoma de al menos 135 kb.

Identification of an Argentinean isolate of Spodoptera frugiperda granulovirus.

The fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is an important maize pest. Due to the environmental impact and emergence of resistance caused by chemical pesticides and transgenic events, the use of baculoviruses becomes a safe and useful alternative for its control in integrated pest management strategies. Here we report the identification of a novel isolate of a granulovirus of S. frugiperda native to the central region of Argentina, named SfGV ARG. We observed that larvae infected with SfGV ARG showed a yellowish coloration, swollen body and, in some cases, severe lesions in the last abdominal segments. We confirmed the identity of the isolate by sequencing fragments of the lef-8, lef-9 and granulin genes and by calculating evolutionary distances using the Kimura-2-Parameter model. SfGV ARG DNA restriction pattern allowed to estimate a genome of at least 135 kb.

Protein composition of the occlusion bodies of Epinotia aporema granulovirus.

Within family Baculoviridae, members of the Betabaculovirus genus are employed as biocontrol agents against lepidopteran pests, either alone or in combination with selected members of the Alphabaculovirus genus. Epinotia aporema granulovirus (EpapGV) is a fast killing betabaculovirus that infects the bean shoot borer (E. aporema) and is a promising biopesticide. Because occlusion bodies (OBs) play a key role in baculovirus horizontal transmission, we investigated the composition of EpapGV OBs. Using mass spectrometry-based proteomics we could identify 56 proteins that are included in the OBs during the final stages of larval infection. Our data provides experimental validation of several annotated hypothetical coding sequences. Proteogenomic mapping against genomic sequence detected a previously unannotated ac110-like core gene and a putative translation fusion product of ORFs epap48 and epap49. Comparative studies of the proteomes available for the family Baculoviridae highlight the conservation of core gene products as parts of the occluded virion. Two proteins specific for betabaculoviruses (Epap48 and Epap95) are incorporated into OBs. Moreover, quantification based on emPAI values showed that Epap95 is one of the most abundant components of EpapGV OBs.

Genomic analysis of an Argentinean isolate of Spodoptera frugiperda granulovirus reveals that various baculoviruses code for Lef-7 proteins with three F-box domains.

A new isolate of the Spodoptera frugiperda granulovirus, SfGV ARG, was completely sequenced and analyzed. The SfGV ARG genome is 139,812 bp long and encodes 151 putative open reading frames. Of these ORFs, 56 were found in betabaculoviruses, 19 of which are present only in GVs closely related to SfGV. Seven ORFs found homologs in this small GV group and also in noctuid NPVs. ORF066 codes a 74 amino acid protein, overlapped with nudix gene, with several homologs in baculovirus, found by tblastn search. Comparison with the genome of the Colombian isolate SfGV VG008 resulted in SfGV being 1101 bp smaller and lacking a homologue of VG008 ORF084, which codes for Lef-7. However, we found that ORF051 shows remote homology to Lef-7 proteins. Moreover, analysis of ORF051 along with Lef-7 proteins coded by a group of noctuid specific GVs and NPVs indicated that Lef-7 proteins coded by these viruses include three F-box domains in contrast to the single one reported for AcMNPV Lef-7. SfGV ARG genome also contains a split photolyase as a distinct feature not found in VG008. BlastX analysis revealed that a complete photolyase is coded considering a putative frameshift in a poly-A tract, which resembles known slippery sequences involved in programmed ribosome frameshifting.

Genome of Epinotia aporema granulovirus (EpapGV), a polyorganotropic fast killing betabaculovirus with a novel thymidylate kinase gene.

BACKGROUND: Epinotia aporema (Lepidoptera: Tortricidae) is an important pest of legume crops in South America. Epinotia aporema granulovirus (EpapGV) is a baculovirus that causes a polyorganotropic infection in the host larva. Its high pathogenicity and host specificity make EpapGV an excellent candidate to be used as a biological control agent. RESULTS: The genome of Epinotia aporema granulovirus (EpapGV) was sequenced and analyzed. Its circular double-stranded DNA genome is 119,082 bp in length and codes for 133 putative genes. It contains the 31 baculovirus core genes and a set of 19 genes that are GV exclusive. Seventeen ORFs were unique to EpapGV in comparison with other baculoviruses. Of these, 16 found no homologues in GenBank, and one encoded a thymidylate kinase. Analysis of nucleotide sequence repeats revealed the presence of 16 homologous regions (hrs) interspersed throughout the genome. Each hr was characterized by the presence of 1 to 3 clustered imperfect palindromes which are similar to previously described palindromes of tortricid-specific GVs. Also, one of the hrs (hr4) has flanking sequences suggestive of a putative non-hr ori. Interestingly, two more complex hrs were found in opposite loci, dividing the circular dsDNA genome in two halves. Gene synteny maps showed the great colinearity of sequenced GVs, being EpapGV the most dissimilar as it has a 20 kb-long gene block inversion. Phylogenetic study performed with 31 core genes of 58 baculoviral genomes suggests that EpapGV is the baculovirus isolate closest to the putative common ancestor of tortricid specific betabaculoviruses. CONCLUSIONS: This study, along with previous characterization of EpapGV infection, is useful for the better understanding of the pathology caused by this virus and its potential utilization as a bioinsecticide.