Rewiring of of algal metabolisms during viral infection
Phytoplankton underpin ocean biogeochemistry. Changes in species composition and cellular metabolisms of
phytoplankton assemblages reshape the ecosystem processes they mediate, with cascading effects on the carbon exported to the deep ocean and the energy channelled across trophic levels. It is thus crucial to gain a better understanding of their biology. Our knowledge about phytoplankton, based upon a relatively few algal cultures, is being challenged; recent studies have revealed that the metabolic crosstalk occurring naturally between algae and other microbes influences their respective metabolism. Consequently, there is a growing recognition that microbial interactions must be reconsidered in our effort to unravel phytoplankton physiology and ecology. However, and despite this progress, a predominant type of microbial interaction is still being overlooked: viral infection.
Viruses are the most abundant biological entities in the oceans. The formidable number of infection occurring in oceans means that many phytoplankton are under an altered physiological state, overridden by viral genes. However, virtually nothing is known about the physiology of infected phytoplankton and most genes from marine viruses remain functionally uncharacterised. We therefore have an incomplete picture of phytoplankton biology. Our research programme aims to fill this knowledge gap by combining transcriptomics, metabolomics and phenomics to identify the molecular and phenotypic changes induced by infection using a virus-alga model system. These approaches allows us to determine if viruses not only reprogram algal metabolic pathways, but provide novel transient metabolic functions to their host – ‘hidden’ metabolisms. Given the ecological importance of phytoplankton, such physiological amendments in infected cells may have a considerable influence on marine ecosystems. Using this combination of techniques, along with gene functional characterisations, we are currently identifiying molecules, genes and pathways involved with novel metabolic functions in the algal host.
Viral manipulation of host Chromatin in infected algal cells
Genome 3D organisation (i.e., chromatin spatial structure) is central to the regulation of gene expression and
other genomic activities. The exploration of genome 3D organisation via chromosome conformation capture (3C)
and 3C-based high-throughput methods (in particular Hi-C) has revealed the major role of chromosomal conformation in loci function and regulation. Expression of viral genes and modulation of host gene transcriptionare essential for viral replication, and viruses modify their host chromatin to regulate their replication cycle; for instance, the Phycodnaviridae PBCV-1 induces chromatin remodelling in the nucleus of its green algal host.
However, very little is known about the dynamics of virus-host DNA interactions and their role in altering host chromatin structure to modulate gene transcription in order to achieve viral replication. We are investigating this overlooked mechanism for viral manipulation of host algal cells 3C/Hi-C procedures.
Susan Kimmance—Researcher (environmental and experimental virology)
Felix Ciceron—Postdoctoral Researcher (algal synthetic biology)
Victoria Jackson—PhD Student (Arctic microbiology/virology)
Keith Jackson—PhD Student (virology and bioinformatics)
Valerie Williams—Undergraduate Research Assistant (virology)
Tomer Sardjoe—Visiting Student (eDNA bioinformatics)