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Exposing the small protein load of bacterial life

Laure Simoens (UGent) , Igor Fijalkowski (UGent) and Petra Van Damme (UGent)
(2023) FEMS MICROBIOLOGY REVIEWS. 47(6).
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Abstract
The ever-growing repertoire of genomic techniques continues to expand our understanding of the true diversity and richness of prokaryotic genomes. Riboproteogenomics laid the foundation for dynamic studies of previously overlooked genomic elements. Most strikingly, bacterial genomes were revealed to harbor robust repertoires of small open reading frames (sORFs) encoding a diverse and broadly expressed range of small proteins, or sORF-encoded polypeptides (SEPs). In recent years, continuous efforts led to great improvements in the annotation and characterization of such proteins, yet many challenges remain to fully comprehend the pervasive nature of small proteins and their impact on bacterial biology. In this work, we review the recent developments in the dynamic field of bacterial genome reannotation, catalog the important biological roles carried out by small proteins and identify challenges obstructing the way to full understanding of these elusive proteins. As small proteins represent an underexplored source of knowledge for improving our understanding of bacterial biology, this review reports on recent technical advancements and remaining challenges in bacterial small ORF (sORF) annotation and the detection and characterization of their encoded SEPs (sORF-encoded polypeptides).
Keywords
Infectious Diseases, Microbiology, small ORF (sORF), small ORF-encoded polypeptide (SEP), riboproteogenomics, genome (re)annotation, bacterial pathogens, proteomics, ESCHERICHIA-COLI, IN-VIVO, IDENTIFICATION, ANNOTATION, POLYPEPTIDE, TRANSLATION, REPOSITORY, SORFS.ORG, REVEALS, TAG

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MLA
Simoens, Laure, et al. “Exposing the Small Protein Load of Bacterial Life.” FEMS MICROBIOLOGY REVIEWS, vol. 47, no. 6, 2023, doi:10.1093/femsre/fuad063.
APA
Simoens, L., Fijalkowski, I., & Van Damme, P. (2023). Exposing the small protein load of bacterial life. FEMS MICROBIOLOGY REVIEWS, 47(6). https://doi.org/10.1093/femsre/fuad063
Chicago author-date
Simoens, Laure, Igor Fijalkowski, and Petra Van Damme. 2023. “Exposing the Small Protein Load of Bacterial Life.” FEMS MICROBIOLOGY REVIEWS 47 (6). https://doi.org/10.1093/femsre/fuad063.
Chicago author-date (all authors)
Simoens, Laure, Igor Fijalkowski, and Petra Van Damme. 2023. “Exposing the Small Protein Load of Bacterial Life.” FEMS MICROBIOLOGY REVIEWS 47 (6). doi:10.1093/femsre/fuad063.
Vancouver
1.
Simoens L, Fijalkowski I, Van Damme P. Exposing the small protein load of bacterial life. FEMS MICROBIOLOGY REVIEWS. 2023;47(6).
IEEE
[1]
L. Simoens, I. Fijalkowski, and P. Van Damme, “Exposing the small protein load of bacterial life,” FEMS MICROBIOLOGY REVIEWS, vol. 47, no. 6, 2023.
@article{01HHMKQ8C2CF6WK9XQ0TMP0KQ9,
  abstract     = {{The ever-growing repertoire of genomic techniques continues to expand our understanding of the true diversity and richness of prokaryotic genomes. Riboproteogenomics laid the foundation for dynamic studies of previously overlooked genomic elements. Most strikingly, bacterial genomes were revealed to harbor robust repertoires of small open reading frames (sORFs) encoding a diverse and broadly expressed range of small proteins, or sORF-encoded polypeptides (SEPs). In recent years, continuous efforts led to great improvements in the annotation and characterization of such proteins, yet many challenges remain to fully comprehend the pervasive nature of small proteins and their impact on bacterial biology. In this work, we review the recent developments in the dynamic field of bacterial genome reannotation, catalog the important biological roles carried out by small proteins and identify challenges obstructing the way to full understanding of these elusive proteins.
As small proteins represent an underexplored source of knowledge for improving our understanding of bacterial biology, this review reports on recent technical advancements and remaining challenges in bacterial small ORF (sORF) annotation and the detection and characterization of their encoded SEPs (sORF-encoded polypeptides).}},
  articleno    = {{fuad063}},
  author       = {{Simoens, Laure and Fijalkowski, Igor and Van Damme, Petra}},
  issn         = {{0168-6445}},
  journal      = {{FEMS MICROBIOLOGY REVIEWS}},
  keywords     = {{Infectious Diseases,Microbiology,small ORF (sORF),small ORF-encoded polypeptide (SEP),riboproteogenomics,genome (re)annotation,bacterial pathogens,proteomics,ESCHERICHIA-COLI,IN-VIVO,IDENTIFICATION,ANNOTATION,POLYPEPTIDE,TRANSLATION,REPOSITORY,SORFS.ORG,REVEALS,TAG}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{13}},
  title        = {{Exposing the small protein load of bacterial life}},
  url          = {{http://doi.org/10.1093/femsre/fuad063}},
  volume       = {{47}},
  year         = {{2023}},
}
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