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

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). 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.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [3];  [1];  [1]
+ Show Author Affiliations
  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)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1224998
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Visualized Experiments
Additional Journal Information:
Journal Issue: 100; Journal ID: ISSN 1940-087X
Publisher:
MyJoVE Corp.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Sanchez, Savannah E., Cuevas, Daniel A., Rostron, Jason E., Liang, Tiffany Y., Pivaroff, Cullen G., Haynes, Matthew R., Nulton, Jim, Felts, Ben, Bailey, Barbara A., Salamon, Peter, Edwards, Robert A., Burgin, Alex B., Segall, Anca M., and Rohwer, Forest. Phage phenomics: Physiological approaches to characterize novel viral proteins. United States: N. p., 2015. Web. doi:10.3791/52854.
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Sanchez, Savannah E., Cuevas, Daniel A., Rostron, Jason E., Liang, Tiffany Y., Pivaroff, Cullen G., Haynes, Matthew R., Nulton, Jim, Felts, Ben, Bailey, Barbara A., Salamon, Peter, Edwards, Robert A., Burgin, Alex B., Segall, Anca M., & Rohwer, Forest. Phage phenomics: Physiological approaches to characterize novel viral proteins. United States. https://doi.org/10.3791/52854
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Sanchez, Savannah E., Cuevas, Daniel A., Rostron, Jason E., Liang, Tiffany Y., Pivaroff, Cullen G., Haynes, Matthew R., Nulton, Jim, Felts, Ben, Bailey, Barbara A., Salamon, Peter, Edwards, Robert A., Burgin, Alex B., Segall, Anca M., and Rohwer, Forest. Thu . "Phage phenomics: Physiological approaches to characterize novel viral proteins". United States. https://doi.org/10.3791/52854. https://www.osti.gov/servlets/purl/1224998.
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@article{osti_1224998,
title = {Phage phenomics: Physiological approaches to characterize novel viral proteins},
author = {Sanchez, Savannah E. and Cuevas, Daniel A. and Rostron, Jason E. and Liang, Tiffany Y. and Pivaroff, Cullen G. and Haynes, Matthew R. and Nulton, Jim and Felts, Ben and Bailey, Barbara A. and Salamon, Peter and Edwards, Robert A. and Burgin, Alex B. and Segall, Anca M. and Rohwer, Forest},
abstractNote = {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.},
doi = {10.3791/52854},
journal = {Journal of Visualized Experiments},
number = 100,
volume = ,
place = {United States},
year = {Thu Jun 11 00:00:00 EDT 2015},
month = {Thu Jun 11 00:00:00 EDT 2015}
}
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https://doi.org/10.3791/52854
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    Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics
    journal, April 2017

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    From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model
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    • DOI: 10.3389/fmicb.2016.00907

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