Keynote Presentation: Squeezing out understanding from sequences: Genome to Phenome Connections in Viruses of Microbes

Enigmatic and often vilified, viruses are now known to play important and possibly indispensable roles in the biology and ecology of cellular organisms. Evidence of viral impacts are everywhere. Animal and plant genomes are littered with genes of viral origin. Ecosystems contain large numbers of viruses, an estimated global population of 10e31 individuals, dwarfing co-occurring microbial abundances. Most viruses observed within ecosystems infect microbes. During infection, viruses can alter the phenome of host cells in ways that change the population biology of microbial communities and the flow of nutrients and energy within ecosystems. While we have a high-level view of viral impacts, the details are largely a mystery. These details matter as viral impacts on ecosystems are the net result of hundreds or thousands of interacting populations of viruses and microbial hosts. The mechanistic underpinnings of viral effects on ecosystems can only be fully appreciated through a greater understanding of the phenomic features of viral-host interaction networks. Genomic data have shown that viral genetic diversity is vast and largely unknown. Often less than half of the genes within a dsDNA viral genome can be assigned a function based on homology. This situation is worse for viral metagenomes (viromes). Predicting important phenomic features of an unknown virus based on genomic information alone is not currently possible.  However, we have identified three genes — DNA polymerase A, ribonucleotide reductase (RNRs), and chaperonins — which appear to demonstrate particularly strong links to the phenomic characteristics of viruses of microbes (VoMs).  Mutations within PolA appear to be predictive of whether a virus has a lytic or lysogenic life cycle and polA genes seem to be critical in determining the broader suite of genes involved in viral genome replication.  The class and sub-group of RNR genes carried by a virus appear to predict the environmental conditions most favorable to lytic viral production.  The propensity of a virus to carry chaperonin genes may predict its genome size and its capability for altering, more generally, the protein folding machinery within infected cells.  Viral chaperonins within viromes have also demonstrated the existence of unknown viruses infecting marine archaeal populations.  Ultimately, uncovering genome to phenome links within ecologically-important VoM-host systems will improve the predictive utility of viral genomic and metagenomic data for advancing scientific understanding on the role of viruses within ecosystems.

Learning Objectives:

1. Give examples of how viral infection influences ecosystem processes

2. How might the biochemistry of a replication enzyme inform us about the biology of a virus

3. Why are metagenome data critical to building genome to phenome hypotheses for viruses