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Small Proteins Can No Longer Be Ignored
Open accessAbstract
Small proteins, here defined as proteins of 50 amino acids or fewer in the absence of processing, have traditionally been overlooked due to challenges in their annotation and biochemical detection. In the past several years, however, increasing numbers of small proteins have been identified either through the realization that mutations in intergenic regions are actually within unannotated small protein genes or through the discovery that some small, regulatory RNAs encode small proteins. These insights, together with comparative sequence analysis, indicate that tens if not hundreds of small proteins are synthesized in a given organism. This review summarizes what has been learned about the functions of several of these bacterial small proteins, most of which act at the membrane, illustrating the astonishing range of processes in which these small proteins act and suggesting several general conclusions. Important questions for future studies of these overlooked proteins are also discussed.
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“However, growing experimental evidence in mycobacteria and other prokaryotes has shown that many sproteins are functional, requiring a rethinking of gene definitions (71–75).”
From Mycobacterium smegmatis: The Vanguard of Mycobacterial Research (2023) · cites this paper as [71]
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A proteogenomics workflow to uncover the world of small proteins in Staphylococcus aureusPreprint
Fuchs, S., Kucklick, M., Lehmann, E., Beckmann, A., Wilkens, M., Kolte, B. S., Mustafayeva, A., Ludwig, T., Diwo, M., Wissing, J. B., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.25.114132 · Cited by 2
De novo birth of functional, human-specific microproteinsPreprint
Vakirlis, N., Duggan, K. M., & McLysaght, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.01.462744 · Cited by 2
Cornet, L., Cleenwerck, I., Praet, J., Léonard, R. R., Vereecken, N. J., Michez, D., Smagghe, G. J., Baurain, D., & Vandamme, P. A. R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.10.472130 · Cited by 2
The GndA microprotein promotes cell growth during heat shock in Escherichia coliPreprint
Mohsen, J. J., Bertolotti, N. R., Jiang, K., Mohsen, M. G., DeRosa, C. M., Dewani, N., Quinto, L. B., Dabdoub, G., Erkalo, B., Landajuela, A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.29.601336 · Cited by 2
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Harnessing toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs
Troian, E. A., Barth, V. C., Chauhan, U., Zheng, H., Zhao, C., Zeng, J., Husson, R. N., & Woychik, N. A. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag252 · Cited by 1
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The conserved small protein SniP3 is a regulator of primary metabolism in cyanobacteria
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Discovering Elusive Small Genes
Brocchieri, L. (2016) · Journal of Phylogenetics & Evolutionary Biology · doi:10.4172/2329-9002.1000e120 · Cited by 1
Structure–activity relationship of biological macromolecules
Chung, A. S. M. T., Teo, Y. K., Cheng, W. T., & Tan, J. B. L. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-85759-8.00002-6 · Cited by 1
Ventroux, M., & Noirot-Gros, M.-F. (2022) · Microbiology · doi:10.1099/mic.0.001268 · Cited by 1
Analyzing domain features of small proteins using a machine‐learning method
Ding, S., Liao, H., Huang, F., Chen, L., Guo, W., Feng, K., Huang, T., & Cai, Y. (2024) · PROTEOMICS · doi:10.1002/pmic.202300302 · Cited by 1
Metadata
- Authors
- Storz, G., Wolf, Y. I., & Ramamurthi, K. S.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Storz, Gisela
- Ramamurthi, Kumaran S.
- Venue
- Annual Review of Biochemistry
- Publisher
- Annual Reviews
- Published
- 2014-06-02
- Volume
- 83
- Issue
- 1
- Pages
- 753-777
- ISSN
- 0066-4154 (ISSN-L)
- 1545-4509
- PMC
- PMC4166647
- OpenAlex
- W2121350645
- Cited by
- 359
- References
- 108
- Citations by year
- 2026: 19 · 2025: 27 · 2024: 32 · 2023: 37 · 2022: 22 · 2021: 46 · 2020: 41 · 2019: 29 · 2018: 38 · 2017: 28 · 2016: 24 · 2015: 11 · 2014: 4
- FWCI
- 2.96
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Annual Review of Biochemistry (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (Z99 LM999999)
- National Cancer Institute (ZIABC011211)
- National Institute of Child Health and Human Development
- U.S. National Library of Medicine
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (ZIAHD008855)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Keywords
- small proteins, small regulatory RNAs, protein annotation, membrane proteins, sequence comparison, protein function
- MeSH terms
- Amino Acids, Animals, Bacillus subtilis, Bacterial Proteins, Bacteriophages, Cell Division, Codon, Drosophila, Escherichia coli, Protein Kinases, Proteins, Ribosomes, RNA, Signal Transduction, Open Reading Frames, Computational Biology
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