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Open Access Research article

Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome

Julie Lamontagne1, Maxime Béland1, Anik Forest1, Alexandra Côté-Martin1, Najib Nassif1, Fadi Tomaki1, Ignacio Moriyón2, Edgardo Moreno3 and Eustache Paramithiotis1*

Author Affiliations

1 Caprion Proteomics Inc., 7150 Alexander-Fleming, Montreal, Quebec, Canada

2 Depto. Microbiología - Edificio de Investigación, Universidad de Navarra, Pamplona, España

3 Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica

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BMC Genomics 2010, 11:300  doi:10.1186/1471-2164-11-300

Published: 12 May 2010

Abstract

Background

Brucellosis is a major bacterial zoonosis affecting domestic livestock and wild mammals, as well as humans around the globe. While conducting proteomics studies to better understand Brucella abortus virulence, we consolidated the proteomic data collected and compared it to publically available genomic data.

Results

The proteomic data was compiled from several independent comparative studies of Brucella abortus that used either outer membrane blebs, cytosols, or whole bacteria grown in media, as well as intracellular bacteria recovered at different times following macrophage infection. We identified a total of 621 bacterial proteins that were differentially expressed in a condition-specific manner. For 305 of these proteins we provide the first experimental evidence of their expression. Using a custom-built protein sequence database, we uncovered 7 annotation errors. We provide experimental evidence of expression of 5 genes that were originally annotated as non-expressed pseudogenes, as well as start site annotation errors for 2 other genes.

Conclusions

An essential element for ensuring correct functional studies is the correspondence between reported genome sequences and subsequent proteomics studies. In this study, we have used proteomics evidence to confirm expression of multiple proteins previously considered to be putative, as well as correct annotation errors in the genome of Brucella abortus strain 2308.