Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol

  1. Sébastien Gallien1,8,
  2. Emmanuel Perrodou2,3,4,5,
  3. Christine Carapito1,
  4. Caroline Deshayes6,7,
  5. Jean-Marc Reyrat6,7,
  6. Alain Van Dorsselaer1,
  7. Olivier Poch2,3,4,5,
  8. Christine Schaeffer1 and
  9. Odile Lecompte2,3,4,5
  1. 1 Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, ULP, CNRS, UMR7178, 67 087 Strasbourg, France;
  2. 2 Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), F-67400 Illkirch, France;
  3. 3 INSERM, U596, F-67400 Illkirch, France;
  4. 4 CNRS, UMR7104, F-67400 Illkirch, France;
  5. 5 Faculté des Sciences de la Vie, Université Louis Pasteur, F-67000 Strasbourg, France;
  6. 6 Faculté de Médecine René Descartes, Université Paris Descartes, Paris Cedex 15, F-75730, France;
  7. 7 INSERM, U570, Unité de Pathogénie des Infections Systémiques, Paris Cedex 15, F-75730, France

Abstract

The progress in sequencing technologies irrigates biology with an ever-increasing number of genome sequences. In most cases, the gene repertoire is predicted in silico and conceptually translated into proteins. As recently highlighted, the predicted genes exhibit frequent errors, particularly in start codons, with a serious impact on subsequent biological studies. A new “ortho-proteogenomic” approach is presented here for the annotation refinement of multiple genomes at once. It combines comparative genomics with an original proteomic protocol that allows the characterization of both N-terminal and internal peptides in a single experiment. This strategy was applied to the Mycobacterium genus with Mycobacterium smegmatis as the reference, and identified 946 distinct proteins, including 443 characterized N termini. These experimental data allowed the correction of 19% of the characterized start codons, the identification of 29 proteins missed during the annotation process, and the curation, thanks to comparative genomics, of 4328 sequences of 16 other Mycobacterium proteomes.

Footnotes

  • ↵8 Corresponding author.

    ↵E-mail sgallien{at}chimie.u-strasbg.fr; fax 33-3-90-24-27-81.

  • [Supplemental material is available online at www.genome.org.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.081901.108.

    • Received June 5, 2008.
    • Accepted October 2, 2008.
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  1. Published in Advance October 27, 2008, doi: 10.1101/gr.081901.108 Genome Res. 19: 128-135 Copyright © 2009, Cold Spring Harbor Laboratory Press

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