Bacterial Pathogens and their Pan-Proteome - From Next-Generation Sequencing to Target Identification

Bacterial Pathogens and their Pan-Proteome - From Next-Generation Sequencing to Target Identification

Andreas Ströhlein^1,2, Hon Q. Tran¹, Antje Krause², Paul M. Selzer¹

1) Intervet Innovation GmbH, Zur Propstei, Schwabenheim, Germany

2) Fachhochschule Bingen, Berlinstraße 109, Bingen am Rhein, Germany

Bovine respiratory disease (BRD), also known as shipping fever, causes an immense economic loss to the cattle industry. The cause of BRD is multi-factorial. Known factors are viruses, bacteria, and environmental stress such as transportation of the cattle. The severity of BRD is induced by bacteria of the Pasteurellaceae: Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni [Melnikow et al., 2008]. Next-generation sequencing allows the application of the pan-proteome concept for proteome wide drug target identification. A pan-proteome consists of (i) strain-specific proteins, (ii) proteins shared by all given organisms (core proteome), and (iii) proteins shared by only a subset of the organisms [D’Auria et al., 2010]. Four genomes from BRD case isolates were sequenced (2 x M. haemolytica, 2 x P. multocida). The H. somni 2336 genome sequence is publicly available. Here we describe the bioinformatic workflow starting from the assembly of the sequence, followed by sequence annotation, and finally the calculation of the pan-proteome. For sequence assembly and functional annotation a fully automated tool was implemented using the software PipelinePilot (Accelrys Inc.). The pan-proteome was calculated on the basis of the five BRD-relevant proteome datasets. It is supposed that BRD-specific virulence factors can be found in the core proteome. Nonetheless, other clusters of orthologous proteins could offer valuable clues to species-specific virulence factors as well. This work analyzes the pan-proteome of BRD-relevant pathogens which enables us to learn more about proteins relevant to BRD.