Category Archives: In press

Viruses and global warming paper in Current Biology

Current Biology

Current Biology

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

Tuplin et al., 2015

Recently published

Tuplin, A., Struthers, M., Cook, J., Bentley., K and Evans, D.J. (2015) Inhibition of HCV translation by disrupting the structure and interactions of the viral CRE and 3′ X-tail. Nucl. Acids Res. doi: 10.1093/nar/gkv142

Abstract

A phylogenetically conserved RNA structure within the NS5B coding region of hepatitis C virus functions as a cis-replicating element (CRE). Integrity of this CRE, designated SL9266 (alternatively 5BSL3.2), is critical for genome replication. SL9266 forms the core of an extended pseudoknot, designated SL9266/PK, involving long distance RNA–RNA interactions between unpaired loops of SL9266 and distal regions of the genome. Previous studies demonstrated that SL9266/PK is dynamic, with ‘open’ and ‘closed’ conformations predicted to have distinct functions during virus replication. Using a combination of site-directed mutagenesis and locked nucleic acids (LNA) complementary to defined domains of SL9266 and its interacting regions, we have explored the influence of this structure on genome translation and replication. We demonstrate that LNAs which block formation of the closed conformation inhibit genome translation. Inhibition was at least partly independent of the initiation mechanism, whether driven by homologous or heterologous internal ribosome entry sites or from a capped message. Provision of SL9266/PK in trans relieved translational inhibition, and mutational analysis implied a mechanism in which the closed conformation recruits a cellular factor that would otherwise suppresses translation. We propose that SL9266/PK functions as a temporal switch, modulating the mutually incompatible processes of translation and replication.

 

Wood et al., 2014

Recently accepted for publication

Wood et al., (2014) MosaicSolver: a tool for determining recombinants of viral genomes from pileup data. Nucleic Acids Research (in press)

Abstract

Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, changes in tropism and possibly transmission across species barriers. Determining whether recombination has occurred and the specific recombination points is thus of major importance in understanding emerging diseases and pathogenesis. This paper describes a method for determining recombinant mosaics (and their proportions) originating from two parent genomes, using high-throughput sequence data. The method involves setting the problem geometrically and the use of appropriately constrained quadratic programming. Recombinants of the honeybee deformed wing virus and the Varroa destructor virus-1 are inferred to illustrate the method, using siRNAs and sequence data sampling the viral genome population (cDNA library). Matlab software (MosaicSolver) is available.

Witteveldt et al., 2013

Recently accepted for publication

Witteveldt, J. et al., (2013) The influence of viral RNA secondary structure on interactions with innate host cell defences. Nucleic Acids Research. December 2013

Abstract

RNA viruses infecting vertebrates differ fundamentally in their ability to establish persistent infections with markedly different patterns of transmission, disease mechanisms and evolutionary relationships with their hosts. Although interactions with host innate and adaptive responses are complex and persistence mechanisms likely multi-factorial, we previously observed associations between bioinformatically predicted RNA secondary formation in genomes of positive-stranded RNA viruses with their in vivo fitness and persistence. To analyse this interactions functionally, we transfected fibroblasts with non-replicating, non-translated RNA transcripts from RNA viral genomes with differing degrees of genome-scale ordered RNA structure (GORS). Single-stranded RNA transcripts induced interferon-β mediated though RIG-I and PKR activation, the latter associated with rapid induction of antiviral stress granules. A striking inverse correlation was observed between induction of both cellular responses with transcript RNA structure formation that was independent of both nucleotide composition and sequence length. The consistent inability of cells to recognize RNA transcripts possessing GORS extended to downstream differences from unstructured transcripts in expression of TNF-α, other interferon-stimulated genes and induction of apoptosis. This functional association provides novel insights into interactions between virus and host early after infection and provides evidence for a novel mechanism for evading intrinsic and innate immune responses.