Functional Insights into the Adjacent Stem-Loop in Honey Bee Dicistroviruses That Promotes Internal Ribosome Entry Site-Mediated Translation and Viral Infection

Factor-Dependent Internal Ribosome Entry Site and -1 Programmed Frameshifting Signal in the Bemisia-Associated Dicistrovirus 2

The dicistrovirus intergenic (IGR) IRES uses the most streamlined translation initiation mechanism: the IRES recruits ribosomes directly without using protein factors and initiates translation from a non-AUG codon. Several subtypes of dicistroviruses IRES have been identified; typically, the IRESs adopt two -to three overlapping pseudoknots with key stem-loop and unpaired regions that interact with specific domains of the ribosomal 40S and 60S subunits to direct translation. We previously predicted an atypical IGR IRES structure and a potential -1 programmed frameshift (-1 FS) signal within the genome of the whitefly Bemisia-associated dicistrovirus 2 (BaDV-2). Here, using bicistronic reporters, we demonstrate that the predicted BaDV-2 -1 FS signal can drive -1 frameshifting in vitro via a slippery sequence and a downstream stem-loop structure that would direct the translation of the viral RNA-dependent RNA polymerase. Moreover, the predicted BaDV-2 IGR can support IRES translation in vitro but does so through a mechanism that is not typical of known factorless dicistrovirus IGR IRES mechanisms. Using deletion and mutational analyses, the BaDV-2 IGR IRES is mapped within a 140-nucleotide element and initiates translation from an AUG codon. Moreover, the IRES does not bind directly to purified ribosomes and is sensitive to eIF2 and eIF4A inhibitors NSC1198983 and hippuristanol, respectively, indicating an IRES-mediated factor-dependent mechanism. Biophysical characterization suggests the BaDV-2 IGR IRES contains several stem-loops; however, mutational analysis suggests a model whereby the IRES is unstructured or adopts distinct conformations for translation initiation. In summary, we have provided evidence of the first -1 FS frameshifting signal and a novel factor-dependent IRES mechanism in this dicistrovirus family, thus highlighting the diversity of viral RNA-structure strategies to direct viral protein synthesis.

The structure and mechanism of action of a distinct class of dicistrovirus intergenic region IRESs

Internal ribosomal entry sites (IRESs) engage with the eukaryotic translation apparatus to promote end-independent initiation. We identified a conserved class of ∼150 nt long intergenic region (IGR) IRESs in dicistrovirus genomes derived from members of the phyla Arthropoda, Bryozoa, Cnidaria, Echinodermata, Entoprocta, Mollusca and Porifera. These IRESs, exemplified by Wenling picorna-like virus 2, resemble the canonical cricket paralysis virus (CrPV) IGR IRES in comprising two nested pseudoknots (PKII/PKIII) and a 3'-terminal pseudoknot (PKI) that mimics a tRNA anticodon stem-loop base-paired to mRNA. However, they are ∼50 nt shorter than CrPV-like IRESs, and PKIII is an H-type pseudoknot that lacks the SLIV and SLV stem-loops that are primarily responsible for the affinity of CrPV-like IRESs for the 40S ribosomal subunit and that restrict initial binding of PKI to its aminoacyl (A) site. Wenling-class IRESs bound strongly to 80S ribosomes but only weakly to 40S subunits. Whereas CrPV-like IRESs must be translocated from the A site to the peptidyl (P) site by elongation factor 2 for elongation to commence, Wenling-class IRESs bound directly to the P site of 80S ribosomes, and decoding begins without a prior translocation step. A chimeric CrPV clone containing a Wenling-class IRES was infectious, confirming that the IRES functioned in cells.

The hinge region of the Israeli acute paralysis virus internal ribosome entry site directs ribosomal positioning, translational activity and virus infection

All viruses must usurp host ribosomes for viral protein synthesis. Dicistroviruses utilize an InterGenic Region Internal Ribosome Entry Site (IGR IRES) to directly recruit ribosomes and mediate translation initiation from a non-AUG start codon. The IGR IRES adopts a three-pseudoknot structure that is comprised of a ribosome binding domain of pseudoknot II and III (PKII and PKIII), and a tRNA-like anticodon domain (PKI) connected via a short, one to three nucleotide hinge region. Recent cryo-EM structural analysis of the dicistrovirus Taura syndrome virus (TSV) IGR IRES bound to the ribosome suggests that the hinge region may facilitate translocation of the IRES from the ribosomal A to P site. In this study, we provide mechanistic and functional insights into the role of the hinge region in IGR IRES translation. Using the honeybee dicistrovirus, Israeli acute paralysis virus (IAPV), as a model, we demonstrate that mutations of the hinge region resulted in decreased IRES-dependent translation in vitro. Toeprinting primer extension analysis of mutant IRESs bound to purified ribosomes and in rabbit reticulocyte lysates showed defects in the initial ribosome positioning on the IRES. Finally, using a hybrid dicistrovirus clone, mutations in the hinge region of the IAPV IRES resulted in decreased viral yield. Our work reveals an unexpected role of the hinge region of the dicistrovirus IGR IRES coordinating the two independently folded domains of the IRES to properly position the ribosome to start translation. IMPORTANCE Viruses must use the host cell machinery to direct viral protein expression for productive infection. One such mechanism is an internal ribosome entry site which can directly recruit host cell machinery. In this study, we have identified a novel sequence in an IRES that provides insight into the mechanism of viral gene expression. Specifically, this novel sequence promotes viral IRES activity by directly guiding the host cell machinery to start gene expression at a specific site.

A novel cripavirus of an ectoparasitoid wasp increases pupal duration and fecundity of the wasp's Drosophila melanogaster host

We identified a 9332-nucleotide-long novel picornaviral genome sequence in the transcriptome of an agriculturally important parasitoid wasp (Pachycrepoideus vindemmiae (Rondani, 1875)). The genome of the novel virus, Rondani's wasp virus 1 (RoWV-1), contains two long open reading frames encoding a nonstructural and a structural protein, respectively, and is 3'-polyadenylated. Phylogenetic analyses firmly place RoWV-1 into the dicistrovirid genus Cripavirus. We detected RoWV-1 in various tissues and life stages of the parasitoid wasp, with the highest virus load measured in the larval digestive tract. We demonstrate that RoWV-1 is transmitted horizontally from infected to uninfected wasps but not vertically to wasp offspring. Comparison of several important biological parameters between the infected and uninfected wasps indicates that RoWV-1 does not have obvious detrimental effects on wasps. We further demonstrate that RoWV-1 also infects Drosophila melanogaster (Meigen, 1830), the hosts of the pupal ectoparasitoid wasps, and thereby increases its pupal developmental duration and fecundity, but decreases the eclosion rate. Together, these results suggest that RoWV-1 may have a potential benefit to the wasp by increasing not only the number of potential wasp hosts but also the developmental time of the hosts to ensure proper development of wasp offspring.

Resurrection of a Viral Internal Ribosome Entry Site from a 700 Year Old Ancient Northwest Territories Cripavirus

The dicistrovirus intergenic region internal ribosome entry site (IGR IRES) uses an unprecedented, streamlined mechanism whereby the IRES adopts a triple-pseudoknot (PK) structure to directly bind to the conserved core of the ribosome and drive translation from a non-AUG codon. The origin of this IRES mechanism is not known. Previously, a partial fragment of a divergent dicistrovirus RNA genome, named ancient Northwest territories cripavirus (aNCV), was extracted from 700-year-old caribou feces trapped in a subarctic ice patch. The aNCV IGR sequence adopts a secondary structure similar to contemporary IGR IRES structures, however, there are subtle differences including 105 nucleotides upstream of the IRES of unknown function. Using filter binding assays, we showed that the aNCV IRES could bind to purified ribosomes, and toeprinting analysis pinpointed the start site at a GCU alanine codon adjacent to PKI. Using a bicistronic reporter RNA, the aNCV IGR can direct translation in vitro in a PKI-dependent manner. Lastly, a chimeric infectious clone swapping in the aNCV IRES supported translation and virus infection. The characterization and resurrection of a functional IGR IRES from a divergent 700-year-old virus provides a historical framework for the importance of this viral translational mechanism.

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs

Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches.

CSV2018: The 2nd Symposium of the Canadian Society for Virology

The 2nd Symposium of the Canadian Society for Virology (CSV2018) was held in June 2018 in Halifax, Nova Scotia, Canada, as a featured event marking the 200th anniversary of Dalhousie University. CSV2018 attracted 175 attendees from across Canada and around the world, more than double the number that attended the first CSV symposium two years earlier. CSV2018 provided a forum to discuss a wide range of topics in virology including human, veterinary, plant, and microbial pathogens. Invited keynote speakers included David Kelvin (Dalhousie University and Shantou University Medical College) who provided a historical perspective on influenza on the 100th anniversary of the 1918 pandemic; Sylvain Moineau (Université Laval) who described CRISPR-Cas systems and anti-CRISPR proteins in warfare between bacteriophages and their host microbes; and Kate O’Brien (then from Johns Hopkins University, now relocated to the World Health Organization where she is Director of Immunization, Vaccines and Biologicals), who discussed the underlying viral etiology for pneumonia in the developing world, and the evidence for respiratory syncytial virus (RSV) as a primary cause. Reflecting a strong commitment of Canadian virologists to science communication, CSV2018 featured the launch of Halifax’s first annual Soapbox Science event to enable public engagement with female scientists, and the live-taping of the 499th episode of the This Week in Virology (TWIV) podcast, hosted by Vincent Racaniello (Columbia University) and science writer Alan Dove. TWIV featured interviews of CSV co-founders Nathalie Grandvaux (Université de Montréal) and Craig McCormick (Dalhousie University), who discussed the origins and objectives of the new society; Ryan Noyce (University of Alberta), who discussed technical and ethical considerations of synthetic virology; and Kate O’Brien, who discussed vaccines and global health. Finally, because CSV seeks to provide a better future for the next generation of Canadian virologists, the symposium featured a large number of oral and poster presentations from trainees and closed with the awarding of presentation prizes to trainees, followed by a tour of the Halifax Citadel National Historic Site and an evening of entertainment at the historic Alexander Keith’s Brewery.

UGA stop codon readthrough to translate intergenic region of Plautia stali intestine virus does not require RNA structures forming internal ribosomal entry site

The translation of capsid proteins of Plautia stali intestine virus (PSIV), encoded in its second open reading frame (ORF2), is directed by an internal ribosomal entry site (IRES) located in the intergenic region (IGR). Owing to the specific properties of PSIV IGR in terms of nucleotide length and frame organization, capsid proteins are also translated via stop codon readthrough in mammalian cultured cells as an extension of translation from the first ORF (ORF1) and IGR. To delineate stop codon readthrough in PSIV, we determined requirements of cis-acting elements through a molecular genetics approach applied in both cell-free translation systems and cultured cells. Mutants with deletions from the 3' end of IGR revealed that almost none of the sequence of IGR is necessary for readthrough, apart from the 5'-terminal codon CUA. Nucleotide replacement of this CUA trinucleotide or change of the termination codon from UGA severely impaired readthrough. Chemical mapping of the IGR region of the most active 3' deletion mutant indicated that this defined minimal element UGACUA, together with its downstream sequence, adopts a single-stranded conformation. Stimulatory activities of downstream RNA structures identified to date in gammaretrovirus, coltivirus, and alphavirus were not detected in the context of PSIV IGR, despite the presence of structures for IRES. To our knowledge, PSIV IGR is the first example of stop codon readthrough that is solely defined by the local hexamer sequence, even though the sequence is adjacent to an established region of RNA secondary/tertiary structures.

Diverse Factors Affecting Efficiency of RNAi in Honey Bee Viruses

Infection and transmission of honey bee viruses pose a serious threat to the pollination services of crops and wild plants, which plays a vital role in agricultural economy and ecology. RNA interference (RNAi) is an effective defense mechanism against commonly occurring viral infections of animals and plants. However, recent studies indicate that the effects of RNAi on the honey bee can induce additional impacts and might not always be effective in suppressing the virus. Moreover, the RNAi responses differed in relation to the developmental stage of the insect and the target tissue used, even though the same method of delivery was used. These results indicate that further analysis and field experiments should be performed to characterize the varying effectiveness of RNAi-based methods for treating honey bee viral infections. In this review, we provide an overview of the current knowledge and the recent progress in RNAi-based anti-viral treatments for honey bees, focusing in particular highlight the role of the dsRNA-delivery method used and its effect on RNAi efficiency and demonstrate the potential practical value of this tool for controlling the virus. We conclude studying the gene function and disease control of honey bee by RNAi technology requires a complex consideration from physiology, genetics to environment.