ArticlePLoS genetics2021
Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.
Article in PLoS genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 42 citations in OpenAlex.
- Symbiotic peptides modulate rhizobial physiology without terminal differentiation.Science advances · 2026Article
- Phage Display Derived Antibodies Against Antimicrobial Peptide FsPDF2 Reveal Stress Response in European Beech.Plant biotechnology journal · 2026Article
- Extended Shine-Dalgarno motifs govern translation initiation in Staphylococcus aureus.Nature communications · 2026Article
- Proteome characterization of single gene deletion mutants lacking zinc finger µ-proteins inmicroLife · 2026Article
- CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.microLife · 2026Article
- De novo origin of numerous microproteins in enterobacteria.Nucleic acids research · 2025Article
- Article
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni.Nature communications · 2025Article
- The hidden bacterial microproteome.Molecular cell · 2025Article
- Large-scale proteogenomics characterization of microproteins in Mycobacterium tuberculosis.Scientific reports · 2024Article
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
- A survey of experimental and computational identification of small proteins.Briefings in bioinformatics · 2024Review
- Proteins à la carte: riboproteogenomic exploration of bacterial N-terminal proteoform expression.mBio · 2024Article
- RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes.Nucleic acids research · 2024Article
- Ribosome profiling reveals the fine-tuned response ofmSystems · 2023Article
- StORF-Reporter: finding genes between genes.Nucleic acids research · 2023Article
- Small proteins in Gram-positive bacteria.FEMS microbiology reviews · 2023Article
- Revealing the small proteome ofmicroLife · 2023Article
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Protein extracts from S. aureus were subjected to different experimental workflows for protein digestion and prefractionation and measured with highly sensitive mass spectrometers. In total, 175 proteins with up to 100 aa (SP100) were identified. Out of these 24 (ranging from 9 to 99 aa) were novel and not contained in the used genome annotation.144 SP100 are highly conserved and were found in at least 50% of the publicly available S. aureus genomes, while 127 are additionally conserved in other staphylococci. Almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids.
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