Proteogenomic mapping of bovine respiratory disease pathogens
Reddy, J. S., Buza, T., Ramkumar , R., Edelmann, M. J., Watt, J. M., Lawrence, M. L., & Nanduri, B. (2013). Proteogenomic mapping of bovine respiratory disease pathogens . MCBIOS X: The 10th Anniversary: Discovery in a Sea of Data . University of Missouri, Columbia, MO: MidSouth Computational Biology and Bioinformatics Society (MCBIOS) . 10(1), 100.
Experimental structural annotation (identification and demarcation of functional elements within a geno me) approaches validate gene models in newly sequenced genomes that are based on computational prediction. Transcriptome sequencing, tiling arrays and proteomics are expression based approaches for genome structural annotation. A major proportion of proteins described in the genome are often designated as ‘hypothetical/predicted’. Confirming the expression of these proteins constitutes experimental validation of their existence and enhances the structural annotation. Here we describe proteogenomic annotation of three bacterial pathogens Mannheimia haemolytica, Pasteurella multocida and Histophilus somni that are causative agents of Bovine respiratory disease (BRD) in cattle. Total proteins were isolated from mid-log phase of growth in vitro from three replicate cultures. 2D LC ESI LCQ MS/MS analysis was conducted to identify proteins expressed in these three pathogens under experimental conditions. Mass spectra and tandem mass spectra were matched to the genome sequence translated in six reading frames, and peptides were identified using a randomized decoy database strategy. Peptides identified at 5% FDR were mapped on to the genome using the proteogenomic mapping tool at AgBase. The results were loaded onto Artemis genome annotation tool for further evaluation. We undertook a comparative genomics approach to validate gene models in these important veterinary pathogens.