Misleading messengers? Interpreting baculovirus transcriptional array profiles

Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus

In this study, two long-read sequencing (LRS) techniques, MinION from Oxford Nanopore Technologies and Sequel from the Pacific Biosciences, were used for the transcriptional characterization of a prototype baculovirus, Autographa californica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, and thereby distinguish between transcript isoforms, mono- and polycistronic RNAs, and overlapping transcripts. Altogether, we detected 875 transcript species, of which 759 were novel and 116 were annotated previously. These RNA molecules include 41 novel putative protein coding transcripts [each containing 5'-truncated in-frame open reading frames (ORFs), 14 monocistronic transcripts, 99 polygenic RNAs, 101 non-coding RNAs, and 504 untranslated region isoforms. This work also identified novel replication origin-associated transcripts, upstream ORFs, cis-regulatory sequences and poly(A) sites. We also detected RNA methylation in 99 viral genes and RNA hyper-editing in the longer 5'-UTR transcript isoform of the canonical ORF 19 transcript.

Third-generation Sequencing Reveals Extensive Polycistronism and Transcriptional Overlapping in a Baculovirus

The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is an insect-pathogen baculovirus. In this study, we applied the Oxford Nanopore Technologies platform for the analysis of the polyadenylated fraction of the viral transcriptome using both cDNA and direct RNA sequencing methods. We identified and annotated altogether 132 novel transcripts and transcript isoforms, including 4 coding and 4 non-coding RNA molecules, 47 length variants, 5 splice isoforms, as well as 23 polycistronic and 49 complex transcripts. All of the identified novel protein-coding genes were 5'-truncated forms of longer host genes. In this work, we demonstrated that in the case of transcript start site isoforms, the promoters and the initiator sequence of the longer and shorter variants belong to the same kinetic class. Long-read sequencing also revealed a complex meshwork of transcriptional overlaps, the function of which needs to be clarified. Additionally, we developed bioinformatics methods to improve the transcript annotation and to eliminate the non-specific transcription reads generated by template switching and false priming.

Modularity and evolutionary constraints in a baculovirus gene regulatory network

BACKGROUND

The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. The Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression.

RESULTS

We observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization.

CONCLUSIONS

Albeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks.

The transcriptome of the baculovirus Autographa californica multiple nucleopolyhedrovirus in Trichoplusia ni cells

Baculoviruses are important insect pathogens that have been developed as protein expression vectors in insect cells and as transduction vectors for mammalian cells. They have large double-stranded DNA genomes containing approximately 156 tightly spaced genes, and they present significant challenges for transcriptome analysis. In this study, we report the first comprehensive analysis of AcMNPV transcription over the course of infection in Trichoplusia ni cells, by a combination of strand-specific RNA sequencing (RNA-Seq) and deep sequencing of 5' capped transcription start sites and 3' polyadenylation sites. We identified four clusters of genes associated with distinctive patterns of mRNA accumulation through the AcMNPV infection cycle. A total of 218 transcription start sites (TSS) and 120 polyadenylation sites (PAS) were mapped. Only 29 TSS were associated with a canonical TATA box, and 14 initiated within or near the previously identified CAGT initiator motif. The majority of viral transcripts (126) initiated within the baculovirus late promoter motif (TAAG), and late transcripts initiated precisely at the second position of the motif. Analysis of 3' ends showed that 92 (77%) of the 3' PAS were located within 30 nucleotides (nt) downstream of a consensus termination signal (AAUAAA or AUUAAA). A conserved U-rich region was found approximately 2 to 10 nt downstream of the PAS for 58 transcripts. Twelve splicing events and an unexpectedly large number of antisense RNAs were identified, revealing new details of possible regulatory mechanisms controlling AcMNPV gene expression. Combined, these data provide an emerging global picture of the organization and regulation of AcMNPV transcription through the infection cycle.

Characterization of the open reading frame 7a from Bombyx mori nucleopolyhedrovirus

The open reading frame 7a of the Bombyx mori nucleopolyhedrovirus (BmNPV orf7a, Bm7a) encodes a predicted polypeptide consisting of 53 amino acid residues. While this polypeptide's homologues were found in certain baculoviruses, its function has not yet been studied. A protein structural assay revealed that the polypeptide expressed from this gene contained a predicted signal peptide at its N-terminus. To investigate the expression of Bm7a, 3'rapid amplification of cDNA ends was used to detect its transcript. A series of recombinant viruses were also constructed to analyze the cellular localization of the Bm7a products. The results indicated that the Bm7a gene is co-transcribed with bv/odv-e26 and orf9. The function of BM7a was studied by using fused enhanced green fluorescence protein (eGFP) as a visual marker to trace the localization of the protein during infection. Fluorescence was observed in the cellular membrane of the infected cells by confocal microscopy. Western blot analysis using an eGFP-antibody also showed that the BM7a-eGFP fusion protein was present in the budded virions (BVs). These data implied that BM7a is a component of the BV. In this work, we identified the function of the Bm7a gene and suggested that it may play a role in BV packaging.

Co-expression vs. co-infection using baculovirus expression vectors in insect cell culture: Benefits and drawbacks

The baculovirus expression vector system (BEVS) is a versatile and powerful platform for protein expression in insect cells. With the ability to approach similar post-translational modifications as in mammalian cells, the BEVS offers a number of advantages including high levels of expression as well as an inherent safety during manufacture and of the final product. Many BEVS products include proteins and protein complexes that require expression from more than one gene. This review examines the expression strategies that have been used to this end and focuses on the distinguishing features between those that make use of single polycistronic baculovirus (co-expression) and those that use multiple monocistronic baculoviruses (co-infection). Three major areas in which researchers have been able to take advantage of co-expression/co-infection are addressed, including compound structure-function studies, insect cell functionality augmentation, and VLP production. The core of the review discusses the parameters of interest for co-infection and co-expression with time of infection (TOI) and multiplicity of infection (MOI) highlighted for the former and the choice of promoter for the latter. In addition, an overview of modeling approaches is presented, with a suggested trajectory for future exploration. The review concludes with an examination of the gaps that still remain in co-expression/co-infection knowledge and practice.

Characterization of an Autographa californica multiple nucleopolyhedrovirus mutant lacking the ac39(p43) gene

Open reading frame 39 [orf39(p43)] of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) is present in 10 isolates of the Alphabaculovirus genus. It is highly conserved in sequence and genomic location in the Group I but much less conserved in the Group II viruses. To investigate the potential role of p43 in AcMNPV infection, we constructed and characterized a p43 knockout mutant. The results showed that the p43 region was expressed as RNA from 3h post infection to at least 24h post infection, and its expression pattern was identical to the expression profile of its neighbouring gene, p47. P47 is an essential core gene component of the baculovirus RNA polymerase. The deletion of the p43 region was confirmed by PCR analysis of bacmid DNA and by RT-PCR analysis of RNA purified from p43 knockout infected cells. The results supported the hypothesis that a large transcript, initiating upstream of p47, includes the p43 ORF. Analyses of protein synthesis in p43 knockout infected cells clearly demonstrated that there were no obvious differences in the timing or amount of expression of P47, LEF-3, or VP39. Growth curves showed that infectious budded virus production and occlusion body formation were also not affected by the p43 knockout. We conclude that orf39(p43) is not essential for virus replication in cell culture.

Mass identification of transcriptional units expressed from the Bombyx mori nucleopolyhedrovirus genome

In order to identify the transcriptional units expressed from an entire nucleopolyhedrovirus (NPV) genome during infection, we constructed a full-length-enriched cDNA library from Bombyx mori NPV (BmNPV)-infected BmN cells. We randomly sequenced 11,520 clones from both ends to obtain a total of 4679 BmNPV-derived transcriptional units. The data revealed a number of novel transcripts, including putative non-coding RNAs, most of which are expressed from recognized baculovirus early or late promoter motifs. These findings provide new insights into the complex transcriptional regulation of an NPV genome and suggest roles for as-yet-uncharacterized transcripts.