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Bacterial riboproteogenomics : the era of N-terminal proteoform existence revealed

Daria Fijalkowska (UGent) , Igor Fijalkowski (UGent) , Patrick Willems (UGent) and Petra Van Damme (UGent)
(2020) FEMS MICROBIOLOGY REVIEWS. 44(4). p.418-431
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  • PROPHECY (PROPHECY: Translational control in infection biology: riboproteogenomics of bacterial pathogens)
Abstract
With the rapid increase in the number of sequenced prokaryotic genomes, relying on automated gene annotation became a necessity. Multiple lines of evidence, however, suggest that current bacterial genome annotations may contain inconsistencies and are incomplete, even for so-called well-annotated genomes. We here discuss underexplored sources of protein diversity and new methodologies for high-throughput genome re-annotation. The expression of multiple molecular forms of proteins (proteoforms) from a single gene, particularly driven by alternative translation initiation, is gaining interest as a prominent contributor to bacterial protein diversity. In consequence, riboproteogenomic pipelines were proposed to comprehensively capture proteoform expression in prokaryotes by the complementary use of (positional) proteomics and the direct readout of translated genomic regions using ribosome profiling. To complement these discoveries, tailored strategies are required for the functional characterization of newly discovered bacterial proteoforms.
Keywords
Microbiology, Infectious Diseases, riboproteogenomics, N-terminal protein biology, N-terminal proteoforms, (alternative) translation initiation, bacterial genome annotation, riboproteogenomics, N-terminal proteoforms, TRANSLATIONAL INITIATION SITES, PROKARYOTIC GENOME ANNOTATION, ESCHERICHIA-COLI, PROTEOGENOMIC ANALYSIS, MASS-SPECTROMETRY, SECRETION SYSTEM, WIDE ANALYSIS, START SITES, IDENTIFICATION, PROTEOMICS

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Citation

Please use this url to cite or link to this publication:

MLA
Fijalkowska, Daria, et al. “Bacterial Riboproteogenomics : The Era of N-Terminal Proteoform Existence Revealed.” FEMS MICROBIOLOGY REVIEWS, vol. 44, no. 4, 2020, pp. 418–31, doi:10.1093/femsre/fuaa013.
APA
Fijalkowska, D., Fijalkowski, I., Willems, P., & Van Damme, P. (2020). Bacterial riboproteogenomics : the era of N-terminal proteoform existence revealed. FEMS MICROBIOLOGY REVIEWS, 44(4), 418–431. https://doi.org/10.1093/femsre/fuaa013
Chicago author-date
Fijalkowska, Daria, Igor Fijalkowski, Patrick Willems, and Petra Van Damme. 2020. “Bacterial Riboproteogenomics : The Era of N-Terminal Proteoform Existence Revealed.” FEMS MICROBIOLOGY REVIEWS 44 (4): 418–31. https://doi.org/10.1093/femsre/fuaa013.
Chicago author-date (all authors)
Fijalkowska, Daria, Igor Fijalkowski, Patrick Willems, and Petra Van Damme. 2020. “Bacterial Riboproteogenomics : The Era of N-Terminal Proteoform Existence Revealed.” FEMS MICROBIOLOGY REVIEWS 44 (4): 418–431. doi:10.1093/femsre/fuaa013.
Vancouver
1.
Fijalkowska D, Fijalkowski I, Willems P, Van Damme P. Bacterial riboproteogenomics : the era of N-terminal proteoform existence revealed. FEMS MICROBIOLOGY REVIEWS. 2020;44(4):418–31.
IEEE
[1]
D. Fijalkowska, I. Fijalkowski, P. Willems, and P. Van Damme, “Bacterial riboproteogenomics : the era of N-terminal proteoform existence revealed,” FEMS MICROBIOLOGY REVIEWS, vol. 44, no. 4, pp. 418–431, 2020.
@article{8661734,
  abstract     = {{With the rapid increase in the number of sequenced prokaryotic genomes, relying on automated gene annotation became a necessity. Multiple lines of evidence, however, suggest that current bacterial genome annotations may contain inconsistencies and are incomplete, even for so-called well-annotated genomes. We here discuss underexplored sources of protein diversity and new methodologies for high-throughput genome re-annotation. The expression of multiple molecular forms of proteins (proteoforms) from a single gene, particularly driven by alternative translation initiation, is gaining interest as a prominent contributor to bacterial protein diversity. In consequence, riboproteogenomic pipelines were proposed to comprehensively capture proteoform expression in prokaryotes by the complementary use of (positional) proteomics and the direct readout of translated genomic regions using ribosome profiling. To complement these discoveries, tailored strategies are required for the functional characterization of newly discovered bacterial proteoforms.}},
  author       = {{Fijalkowska, Daria and Fijalkowski, Igor and Willems, Patrick and Van Damme, Petra}},
  issn         = {{0168-6445}},
  journal      = {{FEMS MICROBIOLOGY REVIEWS}},
  keywords     = {{Microbiology,Infectious Diseases,riboproteogenomics,N-terminal protein biology,N-terminal proteoforms,(alternative) translation initiation,bacterial genome annotation,riboproteogenomics,N-terminal proteoforms,TRANSLATIONAL INITIATION SITES,PROKARYOTIC GENOME ANNOTATION,ESCHERICHIA-COLI,PROTEOGENOMIC ANALYSIS,MASS-SPECTROMETRY,SECRETION SYSTEM,WIDE ANALYSIS,START SITES,IDENTIFICATION,PROTEOMICS}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{418--431}},
  title        = {{Bacterial riboproteogenomics : the era of N-terminal proteoform existence revealed}},
  url          = {{http://doi.org/10.1093/femsre/fuaa013}},
  volume       = {{44}},
  year         = {{2020}},
}

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