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N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana

Patrick Willems (UGent) , Elvis Ndah (UGent) , Veronique Jonckheere (UGent) , Simon Stael (UGent) , Adriaan Sticker (UGent) , Lennart Martens (UGent) , Frank Van Breusegem (UGent) , Kris Gevaert (UGent) and Petra Van Damme (UGent)
(2017) MOLECULAR & CELLULAR PROTEOMICS. 16(6). p.1064-1080
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Biotechnology for a sustainable economy (Bio-Economy)
Abstract
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well-and poorly-annotated genomes.
Keywords
FRACTIONAL DIAGONAL CHROMATOGRAPHY, MULTIPLE SEARCH ENGINES, MASS-SPECTROMETRY, GENOME ANNOTATION, PROVIDES EVIDENCE, PROTEIN, PEPTIDES, PROTEOGENOMICS, SEQUENCE, IDENTIFICATION

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Citation

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Chicago
Willems, Patrick, Elvis Ndah, Veronique Jonckheere, Simon Stael, Adriaan Sticker, Lennart Martens, Frank Van Breusegem, Kris Gevaert, and Petra Van Damme. 2017. “N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis Thaliana.” Molecular & Cellular Proteomics 16 (6): 1064–1080.
APA
Willems, Patrick, Ndah, E., Jonckheere, V., Stael, S., Sticker, A., Martens, L., Van Breusegem, F., et al. (2017). N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana. MOLECULAR & CELLULAR PROTEOMICS, 16(6), 1064–1080.
Vancouver
1.
Willems P, Ndah E, Jonckheere V, Stael S, Sticker A, Martens L, et al. N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana. MOLECULAR & CELLULAR PROTEOMICS. 2017;16(6):1064–80.
MLA
Willems, Patrick, Elvis Ndah, Veronique Jonckheere, et al. “N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis Thaliana.” MOLECULAR & CELLULAR PROTEOMICS 16.6 (2017): 1064–1080. Print.
@article{8524752,
  abstract     = {Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well-and poorly-annotated genomes.},
  articleno    = {M116.066662},
  author       = {Willems, Patrick and Ndah, Elvis and Jonckheere, Veronique and Stael, Simon and Sticker, Adriaan and Martens, Lennart and Van Breusegem, Frank and Gevaert, Kris and Van Damme, Petra},
  issn         = {1535-9476},
  journal      = {MOLECULAR \& CELLULAR PROTEOMICS},
  language     = {eng},
  number       = {6},
  pages        = {M116.066662:1064--M116.066662:1080},
  title        = {N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1074/mcp.m116.066662},
  volume       = {16},
  year         = {2017},
}

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