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

Journal Article · Tue Mar 17 04:00:00 EDT 2009 · Nucleic Acids Research, 37(9):2926-2939

DOI:https://doi.org/10.1093/nar/gkp164· OSTI ID:958446

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

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.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 958446
• Journal Information: Nucleic Acids Research, 37(9):2926-2939, Journal Name: Nucleic Acids Research, 37(9):2926-2939 Journal Issue: 9 Vol. 37; ISSN 0305-1048; ISSN NARHAD
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
DESULFOVIBRIO
Environmental Molecular Sciences Laboratory
FUNCTIONALS
GENES
PROTEINS
STRESSES