Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

Journal Article · Mon Oct 27 04:00:00 EDT 2008 · Nucleic Acids Research

OSTI ID:960285

Elias, Dwayne A; Mukhopadhyay, Aindrila; Joachimiak, Marcin P; Drury, Elliott C; Redding, Alyssa M; Yen, Huei-Che B; Fields, Matthew W; Hazen, Terry C; Arkin, Adam P; Keasling, Jay D; Wall, Judy D

Hypothetical and conserved hypothetical genes account for>30percent of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved hypothetical (9.5percent) along with 887 hypothetical genes (24.4percent). 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 hypothetical 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. 1212 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.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: Physical Biosciences Division
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 960285
• Report Number(s): LBNL-1888E
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research; ISSN 0305-1048; ISSN NARHAD
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
DESULFOVIBRIO
FUNCTIONALS
GENES
MUTANTS
PROTEINS
STRESSES
expression profiling
hypothetical genes
improved functional annotation