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). 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.affiliation: Department of Biology, San Diego State University; sanchez.s.elizabeth@gmail.com.
authors.forename: Savannah E
authors.initials: SE
authors.lastname: Sanchez
authors.affiliation: Computational Science Research Center, San Diego State University.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Cuevas
authors.affiliation: Department of Biology, San Diego State University.
authors.forename: Jason E
authors.initials: JE
authors.lastname: Rostron
authors.affiliation: Bioinformatics and Medical Informatics Research Center, San Diego State University.
authors.forename: Tiffany Y
authors.initials: TY
authors.lastname: Liang
authors.affiliation: Department of Biology, San Diego State University.
authors.forename: Cullen G
authors.initials: CG
authors.lastname: Pivaroff
authors.affiliation: Department of Biology, San Diego State University.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Haynes
authors.affiliation: Department of Mathematics and Statistics, San Diego State University.
authors.forename: Jim
authors.initials: J
authors.lastname: Nulton
authors.affiliation: Department of Mathematics and Statistics, San Diego State University.
authors.forename: Ben
authors.initials: B
authors.lastname: Felts
authors.affiliation: Department of Mathematics and Statistics, San Diego State University.
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Bailey
authors.affiliation: Department of Mathematics and Statistics, San Diego State University.
authors.forename: Peter
authors.initials: P
authors.lastname: Salamon
authors.affiliation: Department of Biology, San Diego State University; Department of Computer Science, San Diego State University; Mathematics and Computer Science Division, Argonne National Laboratory.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.affiliation: SPARC Committee, Broad Institute.
authors.forename: Alex B
authors.initials: AB
authors.lastname: Burgin
authors.affiliation: Department of Biology, San Diego State University.
authors.forename: Anca M
authors.initials: AM
authors.lastname: Segall
authors.affiliation: Department of Biology, San Diego State University.
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
mesh_terms: D001435:Bacteriophages / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism / Q000821:virology*; D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D014764:Viral Proteins / Q000096:biosynthesis / Q000235:genetics*
chemical_list: D014764:Viral Proteins