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J Vis Exp. 2015 Jun 11;(100):e52854. doi: 10.3791/52854.

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins.

Author information

1
Department of Biology, San Diego State University; sanchez.s.elizabeth@gmail.com.
2
Computational Science Research Center, San Diego State University.
3
Department of Biology, San Diego State University.
4
Bioinformatics and Medical Informatics Research Center, San Diego State University.
5
Department of Mathematics and Statistics, San Diego State University.
6
Department of Biology, San Diego State University; Department of Computer Science, San Diego State University; Mathematics and Computer Science Division, Argonne National Laboratory.
7
SPARC Committee, Broad Institute.

Abstract

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). 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.

PMID:
26132888
PMCID:
PMC4544906
DOI:
10.3791/52854
[Indexed for MEDLINE]
Free PMC Article

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