Congratulations to Fadi Al Naji who recently completed the minor corrections to his PhD. thesis entitled “Isolation and analysis of recombinants from mixed virus infections of poliovirus using next generation sequencing (NGS) and bioinformatics“. Fadi was registered in the School of Life Sciences, University of Warwick and remained there to complete his studies after the rest of the Evanslab moved to St. Andrews. His external examiner was Professor Glyn Stanway, University of Essex (on the left below). Fadi is the good-looking one in the middle.
Just back from the excellent Europic 2016 meeting in Switzerland where Kirsten Bentley “knocked their socks off” with a talk on her recent analysis of the role of sequence identity and RNA structure in genetic recombination in enteroviruses.
Here’s what our friends in the Cameron and Vignuzzi labs tweeted …
With thanks to Caroline, Urs and Laurent for running a great meeting …
The fidelity of the virus polymerase influences the rate of genetic recombination between viruses coinfecting the same cell. We used cell-based and new, biochemically-defined, assays to demonstrate that the viral polymerase is necessary and sufficient for the strand-transfer event of RNA virus recombination. Furthermore, the fidelity of the polymerase is critical in determining the efficiency with which recombination occurs; low fidelity polymerases exhibit high recombination rates, and vice versa.
The paper is published in Nucleic Acids Research:
Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination
Andrew Woodman; Jamie J. Arnold; Craig E. Cameron; David J. Evans
Nucleic Acids Research 2016; doi: 10.1093/nar/gkw567
Genetic recombination in single-strand, positive-sense RNA viruses is a poorly understand mechanism responsible for generating extensive genetic change and novel phenotypes. By moving a critical cis-acting replication element (CRE) from the polyprotein coding region to the 3′ non-coding region we have further developed a cell-based assay (the 3′CRE-REP assay) to yield recombinants throughout the non-structural coding region of poliovirus from dually transfected cells. We have additionally developed a defined biochemical assay in which the only protein present is the poliovirus RNA dependent RNA polymerase (RdRp), which recapitulates the strand transfer events of the recombination process. We have used both assays to investigate the role of the polymerase fidelity and nucleotide turnover rates in recombination. Our results, of both poliovirus intertypic and intratypic recombination in the CRE-REP assay and using a range of polymerase variants in the biochemical assay, demonstrate that RdRp fidelity is a fundamental determinant of recombination frequency. High fidelity polymerases exhibit reduced recombination and low fidelity polymerases exhibit increased recombination in both assays. These studies provide the basis for the analysis of poliovirus recombination throughout the non-structural region of the virus genome and provide a defined biochemical assay to further dissect this important evolutionary process.
One of our colonies in the bee shed swarmed last week. The swarm ended up clustering around the entrance to the hive it had ‘escaped’ from. It was captured and rehoused successfully. The swarm in the picture is up to 5cm deep in places and probably contains 10-15,000 worker bees … and a single queen bee.
Swarming is the natural way that a honey bee colony ‘reproduces’. The old queen and all of the older foragers leave the hive to establish a new colony. The remaining workers raise a new queen from an egg or young larva in the original hive, so generating two colonies from one. Swarming usually occurs in late Spring or early Summer.
Not as unconnected as you might think. The most numerous photosynthetic organisms on earth – the cyanobacteria – are infected by viruses (cyanhophages). Some of these cyanhophages carry components of the photosynthetic machinery and are thought to contribute to host cell photosynthesis. In a recent study on which we collaborated we show that virus-infected cyanobacteria are inhibited in their ability to fix CO2 (in contrast to uninfected cyanobacteria) whereas photosynthetic electron transport is unaltered. The cyanhophages therefore redirect photosynthesis to support phage development.
These results also have implications for our understanding of global warming. The reduction in CO2 fixation in the marine environment, as a consequence of these cyanophage infections, may be as much as 10%. The global warming calculations are based on assumptions of carbon fixation levels being directly linked to photosynthetic activity. We show that that this is incorrect and that CO2 fixation is likely overestimated in marine environments.
The full abstract of the manuscript “Viruses Inhibit CO2 Fixation in the Most Abundant Phototrophs on Earth” by Puxty et al., is shown below.
Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most numerous photosynthetic organisms on our planet. With a global population size of 3.6 × 1027, they are responsible for approximately 10% of global primary production. Viruses that infect Prochlorococcus and Synechococcus (cyanophages) can be readily isolated from ocean waters and frequently outnumber their cyanobacterial hosts. Ultimately, cyanophage-induced lysis of infected cells results in the release of fixed carbon into the dissolved organic matter pool. What is less well known is the functioning of photosynthesis during the relatively long latent periods of many cyanophages. Remarkably, the genomes of many cyanophage isolates contain genes involved in photosynthetic electron transport (PET) as well as central carbon metabolism, suggesting that cyanophages may play an active role in photosynthesis. However, cyanophage-encoded gene products are hypothesized to maintain or even supplement PET for energy generation while sacrificing wasteful CO2 fixation during infection. Yet this paradigm has not been rigorously tested. Here, we measured the ability of viral-infected Synechococcus cells to fix CO2 as well as maintain PET. We compared two cyanophage isolates that share different complements of PET and central carbon metabolism genes. We demonstrate cyanophage-dependent inhibition of CO2 fixation early in the infection cycle. In contrast, PET is maintained throughout infection. Our data suggest a generalized strategy among marine cyanophages to redirect photosynthesis to support phage development, which has important implications for estimates of global primary production.
Puxty, R.J., Millard, A.D., Evans, D.J. and Scanlan, D.J. (2016) Current Biology http://dx.doi.org/10.1016/j.cub.2016.04.036
We now have signs informing passers-by that our research apiary is now operational and has resident bees.
I enjoyed speaking at the Scottish Beekeepers November meeting in Perth last Saturday. This was the first of several specifically Scottish outreach-type events I’m doing over the next few months and it was a great opportunity to meet people I’ve corresponded with online – often via the highly informative SBAi forum – or who my research group are already collaborating with.
I’m delighted to be talking at the Hampshire Beekeepers Association autumn convention at Sparsholt College this weekend. This is the first of several ‘winter talks’ to BKAs about our research on deformed wing virus and Varroa. Time permitting I hope to discuss some forthcoming studies on coordinated Varroa control that we’re doing with Alan Bowman (Aberdeen) and Fiona Highet (SASA) and that will shortly be featured in the Scottish Beekeeper. I was invited to talk at this event before accepting a post in St. Andrews … it’s a long way to travel. However, one of the advantages of flying to these events is I can’t be tempted by too many goodies from the trade stands 😉
Late last week, in the dark and rain, the first two honeybee colonies were installed in the bee house on our research apiary. The warm(ish) and dry environment will greatly benefit our research by helping us harvest larvae and pupae whatever the weather conditions are outside. In addition, we expect brood rearing by the colony to be extended earlier and later in the season, so enabling us to undertake more extensive studies of the biology of deformed wing virus.
The bee shed has special windows – just about visible in the poor quality cellphone picture – that allows the bees that leave the hive when the roof is removed to ‘escape’ from the shed … they can then re-enter the hive via a tunnel entrance through the shed wall.
We have recently submitted a paper to PeerJ on gene expression changes resulting from deformed wing virus and sacbrood virus infection. A pre-print of this manuscript can be viewed on the PeerJ website.
Manuscript authors and title
2015) Evolutionarily related Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate horizontal or vertical transmission of these viruses. PeerJ PrePrints 3:e1749(
Sacbrood virus (SBV) and deformed wing virus (DWV) are evolutionarily related positive-strand RNA viruses, members of the Iflavirus group, which infect the honeybee Apis mellifera, but have strikingly different levels of virulence when transmitted orally. Honeybee larvae orally infected with SBV usually accumulate high levels of the virus, which halts larval development and causes insect death. In contrast, oral DWV infection at the larval stage usually causes asymptomatic infection with low levels of the virus, although high doses of ingested DWV could lead to DWV replicating to high levels. We investigated effects of DWV and SBV infection on the transcriptome of honeybee larvae and pupae using global RNA-Seq and real-time PCR analysis. This showed that high levels of SBV replication resulted in down-regulation of the genes involved in cuticle and muscle development, together with changes in expression of putative immune-related genes. In particular, honeybee larvae with high levels of SBV replication, with and without high levels of DWV replication, showed concerted up-regulated expression of antimicrobial peptides (AMPs), and down-regulated expression of the prophenoloxidase activating enzyme (PPAE) together with up-regulation of the expression of a putative serpin, which could lead to the suppression of the melanisation pathway. The effects of high SBV levels on expression of these immune genes were unlikely to be a consequence of SBV-induced developmental changes, because similar effects were observed in the honeybee pupae infected by injection. We suggest that the effects of SBV infection on the honeybee immunity could be an adaptation to horizontal transmission of the virus. Up-regulation of the expression of AMP genes in the SBV-infected brood may contribute to protection of the SBV virus particles in dead larvae from bacterial degradation. Suppression of the melanisation may also reduce the loss of infectivity of SBV in the larvae. Therefore it is possible that activation of AMP expression and suppression of melanisation could increase ability of SBV to be transmitted horizontally via cannibalization route. We observed no changes of AMPs and the melanisation pathway genes expression in the orally infected larvae with high levels of DWV replication alone. In the injected pupae, high levels of DWV alone did not alter expression of the tested melanisation pathway genes, but resulted in up-regulation of the AMPs, which could be contributed to the effect of DWV on the regulation of AMP expression in response to wounding. We suggest that the effects of single DWV infection on the expression of these immune-related genes could reflect evolutionary adaptations of DWV to vertical transmission. Up-regulation of AMPs is costly and suppression of melanisation may increase susceptibility to infections, therefore these changes may have negative impact on honeybee survival and, consequently, of the survival of DWV.