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Title: Phage phenomics: Physiological approaches to characterize novel viral proteins

Journal Article · · Journal of Visualized Experiments
DOI:https://doi.org/10.3791/52854· OSTI ID:1224998
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  1. San Diego State Univ., San Diego, CA (United States)
  2. San Diego State Univ., San Diego, CA (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
  3. Broad Institute, Cambridge, MA (United States)
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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.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1224998
Journal Information:
Journal of Visualized Experiments, Journal Issue: 100; ISSN 1940-087X
Publisher:
MyJoVE Corp.Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 8 works
Citation information provided by
Web of Science

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Cited By (2)

Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics journal April 2017
From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model journal June 2016

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