ArticleEnvironmental microbiology2013
How many signal peptides are there in bacteria?
Article in Environmental microbiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- De Novo Sequencing of Peptides from Tandem Mass Spectra and Applications in Proteogenomics.Methods in molecular biology (Clifton, N.J.) · 2025Article
- SignalP: The Evolution of a Web Server.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Extracellular secretion of a cutinase with polyester-degrading potential by E. coli using a novel signal peptide from Amycolatopsis mediterranei.World journal of microbiology & biotechnology · 2022Article
- The Role of Formyl Peptide Receptors in Permanent and Low-Grade Inflammation:International journal of molecular sciences · 2021Review
- Homogeneous Cytochrome 579 Is an Octamer That Reacts Too Slowly With Soluble Iron to Be the Initial Iron Oxidase in the Respiratory Chain ofFrontiers in microbiology · 2021Article
- Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences.Frontiers in genetics · 2020Review
- Enzymatic Labeling of Bacterial Proteins for Super-resolution Imaging in Live Cells.ACS central science · 2019Article
- Export of a Vibrio parahaemolyticus toxin by the Sec and type III secretion machineries in tandem.Nature microbiology · 2019Article
- A comprehensive in silico characterization of bacterial signal peptides for the excretory production of3 Biotech · 2018Article
- Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.Genome biology and evolution · 2018Article
- A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea.BMC bioinformatics · 2015Article
- The human transmembrane proteome.Biology direct · 2015Article
- Proteogenomic analysis and global discovery of posttranslational modifications in prokaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.Journal of proteome research · 2014Article
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Authors and funding
6 authors.
Funding
Abstract
Over the last 5 years proteogenomics (using mass spectroscopy to identify proteins predicted from genomic sequences) has emerged as a promising approach to the high-throughput identification of protein N-termini, which remains a problem in genome annotation. Comparison of the experimentally determined N-termini with those predicted by sequence analysis tools allows identification of the signal peptides and therefore conclusions on the cytoplasmic or extracytoplasmic (periplasmic or extracellular) localization of the respective proteins. We present here the results of a proteogenomic study of the signal peptides in Escherichia coli K-12 and compare its results with the available experimental data and predictions by such software tools as SignalP and Phobius. A single proteogenomics experiment recovered more than a third of all signal peptides that had been experimentally determined during the past three decades and confirmed at least 31 additional signal peptides, mostly in the known exported proteins, which had been previously predicted but not validated. The filtering of putative signal peptides for the peptide length and the presence of an eight-residue hydrophobic patch and a typical signal peptidase cleavage site proved sufficient to eliminate the false-positive hits. Surprisingly, the results of this proteogenomics study, as well as a re-analysis of the E. coli genome with the latest version of SignalP program, show that the fraction of proteins containing signal peptides is only about 10%, or half of previous estimates.
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