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:
-
- San Diego State Univ., San Diego, CA (United States)
- (ANL), Argonne, IL (United States)
- Broad Institute, Cambridge, MA (United States)
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1225531
- DOE Contract Number:
- AC02-06CH11357
- Resource Type:
- Multimedia
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; GENOMES; PHAGE; BACTERIA; E-COLI
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., Argonne National Lab., Burgin, Alex B., Segall, Anca M., and Rohwer, Forest. Phage phenomics: Physiological approaches to characterize novel viral proteins. United States: N. p., 2015.
Web.
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., Argonne National Lab., Burgin, Alex B., Segall, Anca M., & Rohwer, Forest. Phage phenomics: Physiological approaches to characterize novel viral proteins. United States.
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., Argonne National Lab., Burgin, Alex B., Segall, Anca M., and Rohwer, Forest. Thu .
"Phage phenomics: Physiological approaches to characterize novel viral proteins". United States. https://www.osti.gov/servlets/purl/1225531.
@article{osti_1225531,
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 Argonne National Lab. 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 = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Thu Jun 11 00:00:00 EDT 2015},
month = {Thu Jun 11 00:00:00 EDT 2015}
}