Phage phenomics: Physiological approaches to characterize novel viral proteins

Savannah E. Sanchez, Daniel A. Cuevas, Jason E. Rostron, Tiffany Y. Liang, Cullen G. Pivaroff, Matthew R. Haynes, Jim Nulton, Ben Felts, Barbara A. Bailey, Peter Salamon, Robert A. Edwards, Alex B. Burgin, Anca M. Segall, Forest Rohwer

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)

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.

Original languageEnglish
Article numbere52854
Number of pages18
JournalJournal of Visualized Experiments
VolumeJune 2015
Issue number100
DOIs
Publication statusPublished - 11 Jun 2015
Externally publishedYes

Bibliographical note

Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License

Keywords

  • Continuous culture
  • Immunology
  • Issue 100
  • Metabolomics
  • Multi-phenotype assay plates (MAPs)
  • Phage
  • Phenomics
  • Viral metagenome

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