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.

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

“…Stress-specific responses include the upregulation of the hcp gene (encoding hydroxylamine reductase) during nitrite stress, the Na + /H + antiporter gene (nhaC2) in alkalinity stress, and genes involved in exopolysaccharide biosynthesis in biofilms during growth on a steel surface 73 . However, much of the divergence in stress responses is attributable to changes in the expression of a large number of genes with unknown functions, many of which genes are unique to SRMs 74 . Thus, a refined understanding of the specificity of stress responses warrants efforts to characterize these genes of unknown functions.…”

Substrate-Dependent Regulation of Carbon Catabolism in Marine Sulfate-Reducing <i>Desulfobacterium autotrophicum</i> HRM2

“…to oxygen or heat shock [Chhabra et al, 2006]. Moreover, the genome annotation status was improved by expression of (conserved) hypothetical genes [Elias et al, 2009], and the central metabolism was studied by flux analysis [Tang et al, 2007]. With sulfate-reducing bacteria other than Desulfovibrio spp., research has rarely advanced from the physiological to the molecular level.…”

The Anaerobe-Specific Orange Protein Complex of Desulfovibrio vulgaris Hildenborough Is Encoded by Two Divergent Operons Coregulated by σ 54 and a Cognate Transcriptional Regulator

“…So far, more than 20 complete genomes of SRM are available. The analysis of the genome of the deltaproteobacterium Desulfovibrio vulgaris Hildenborough revealed that 34% of it encodes hypothetical and conserved hypothetical proteins of unknown function (19,27). Among them, several are conserved in anaerobes, suggesting that they serve critical cellular functions in the anaerobic way of life of D. vulgaris Hildenborough and other SRM.…”