Phage phenomics: Physiological approaches to characterize novel viral proteins
Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysis by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Thus, representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.
- San Diego State Univ., San Diego, CA (United States)
- San Diego State Univ., San Diego, CA (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
- Broad Institute, Cambridge, MA (United States)
- Publication Date:
- OSTI Identifier:
- Grant/Contract Number:
- Accepted Manuscript
- Journal Name:
- Journal of Visualized Experiments
- Additional Journal Information:
- Journal Issue: 100; Journal ID: ISSN 1940-087X
- MyJoVE Corp.
- Research Org:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org:
- Country of Publication:
- United States
- 59 BASIC BIOLOGICAL SCIENCES
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