Nucleic Acids Research Advance Access originally published online on March 17, 2009
Nucleic Acids Research 2009 37(9):2926-2939; doi:10.1093/nar/gkp164
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2009, Vol. 37, No. 9 2926-2939
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Genomics |
Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation
1Department of Biochemistry, 117 Schweitzer Hall, Virtual Institute for Microbial Stress and Survival, University of Missouri-Columbia, Columbia, MO 65211, 2Department of Physical Biosciences, Virtual Institute for Microbial Stress and Survival, Lawrence Berkeley National Lab, 1 Cyclotron Road Mail Stop 978R4121, Berkeley, CA 94720, 3Department of Microbiology, Montana State University, 366 EPS Building, Bozeman, MT 59717 and 4Department of Earth Sciences, Lawrence Berkeley National Lab, 1 Cyclotron Road Mail Stop 70A3317, Berkeley, CA 94720, USA
*To whom correspondence should be addressed. Tel: +1 573 882 9771; Fax: +1 573 882 5635; Email: eliasd{at}missouri.edu
Received October 27, 2008. Revised February 20, 2009. Accepted February 27, 2009.
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.
The authors wish it to be known that, in their opinion, the second and third authors should be regarded as joint Second Authors.