title: Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation.
abstract: Hypothetical (HyP) and conserved HyP genes account for >30% of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved HyP (9.5%) along with 887 HyP genes (24.4%). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 HyP and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC-MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. One thousand two hundred and twelve of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations.
authors.affiliation: Department of Biochemistry, Virtual Institute for Microbial Stress and Survival, University of Missouri-Columbia, Columbia, MO 65211, USA. eliasd@missouri.edu
authors.forename: Dwayne A
authors.initials: DA
authors.lastname: Elias
authors.forename: Aindrila
authors.initials: A
authors.lastname: Mukhopadhyay
authors.forename: Marcin P
authors.initials: MP
authors.lastname: Joachimiak
authors.forename: Elliott C
authors.initials: EC
authors.lastname: Drury
authors.forename: Alyssa M
authors.initials: AM
authors.lastname: Redding
authors.forename: Huei-Che B
authors.initials: HC
authors.lastname: Yen
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Fields
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
authors.forename: Jay D
authors.initials: JD
authors.lastname: Keasling
authors.forename: Judy D
authors.initials: JD
authors.lastname: Wall
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D016969:Desulfovibrio vulgaris / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D012097:Repressor Proteins / Q000378:metabolism; D017384:Sequence Deletion; D013312:Stress, Physiological
chemical_list: D001426:Bacterial Proteins; D012097:Repressor Proteins; C068477:ferric uptake regulating proteins, bacterial