Functional viral metagenomics and the next generation of molecular tools

Abstract

The enzymes of bacteriophages and other viruses have been essential research tools since the first days of molecular biology. However, the current repertoire of viral enzymes only hints at their overall potential. The most commonly used enzymes are derived from a surprisingly small number of cultivated viruses, which is remarkable considering the extreme abundance and diversity of viruses revealed over the past decade by metagenomic analysis. To access the treasure trove of enzymes hidden in the global virosphere and develop them for research, therapeutic and diagnostic uses, improvements are needed in our ability to rapidly and efficiently discover, express and characterize viral genes to produce useful proteins. In this paper, we discuss improvements to sampling and cloning methods, functional and genomics-based screens, and expression systems, which should accelerate discovery of new enzymes and other viral proteins for use in research and medicine.

Figure 1

Viral metagenomics and enzyme discovery. Viruses can be enriched from natural environments, such as hot springs (a), by filtration and differential centrifugation. Enrichments are imaged by epifluorescence microscopy (b) to quantify the viral particles and to ensure the absence of contaminating microbial cells. Transmission electron micrographs of viral preparations – as these shown from the Firehole River (c, d, e) and White Creek (f, g, h) areas of Yellowstone National Park – allow determination of viral types based on morphology. These highly enriched viral preparations are then used for construction of libraries that are screened to discover enzymes. Electron microscopy was performed as described [7] by Sue Brumfield and Mark Young, Montana State University. Scale bars represent 200 nm.