title: How many signal peptides are there in bacteria?
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.
authors.affiliation: Technische Universität München, Department of Genome-Oriented Bioinformatics, 85354, Freising, Germany.
authors.forename: Dmitry N
authors.initials: DN
authors.lastname: Ivankov
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Payne
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Galperin
authors.forename: Stefano
authors.initials: S
authors.lastname: Bonissone
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
authors.forename: Dmitrij
authors.initials: D
authors.lastname: Frishman
mesh_terms: D001483:Base Sequence; D048168:Escherichia coli K12 / Q000737:chemistry*; D013058:Mass Spectrometry; D008565:Membrane Proteins / Q000032:analysis; D010449:Peptide Mapping; D010455:Peptides / Q000032:analysis* / Q000145:classification; D021382:Protein Sorting Signals; D011506:Proteins / Q000032:analysis / Q000145:classification; D020543:Proteome; D017421:Sequence Analysis; D012697:Serine Endopeptidases / Q000032:analysis; D012984:Software
chemical_list: D008565:Membrane Proteins; D010455:Peptides; D021382:Protein Sorting Signals; D011506:Proteins; D020543:Proteome; D012697:Serine Endopeptidases; C026515:type I signal peptidase
references.citation: J Mol Biol. 1985 Jul 5;184(1):99-105
references.pmid: 4032478
references.citation: mBio. 2012 Nov 20;3(6):
references.pmid: 23169999
references.citation: Science. 1997 Sep 5;277(5331):1453-62
references.pmid: 9278503
references.citation: J Mol Biol. 2004 Jul 16;340(4):783-95
references.pmid: 15223320
references.citation: PLoS Comput Biol. 2008 Nov;4(11):e1000213
references.pmid: 18989393
references.citation: Protein Eng. 1997 Jan;10(1):1-6
references.pmid: 9051728
references.citation: BMC Microbiol. 2005 Jun 14;5:35
references.pmid: 15955239
references.citation: Nat Biotechnol. 2003 May;21(5):566-9
references.pmid: 12665801
references.citation: Science. 2010 Jan 1;327(5961):81-4
references.pmid: 20044574
references.citation: BMC Microbiol. 2005 Oct 07;5:58
references.pmid: 16212653
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W429-32
references.pmid: 17483518
references.citation: Protein Eng. 1999 Jan;12(1):3-9
references.pmid: 10065704
references.citation: Nucleic Acids Res. 2006 Jan 05;34(1):1-9
references.pmid: 16397293
references.citation: Nat Protoc. 2011 Jul 14;6(8):1130-41
references.pmid: 21799483
references.citation: Proc Int Conf Intell Syst Mol Biol. 1998;6:122-30
references.pmid: 9783217
references.citation: J Proteome Res. 2010 May 7;9(5):2148-59
references.pmid: 20218729
references.citation: Antimicrob Agents Chemother. 2007 Oct;51(10):3650-8
references.pmid: 17664315
references.citation: Nucleic Acids Res. 1998 Jun 15;26(12):2941-7
references.pmid: 9611239
references.citation: J Membr Biol. 1990 May;115(3):195-201
references.pmid: 2197415
references.citation: J Proteome Res. 2008 Aug;7(8):3354-63
references.pmid: 18597511
references.citation: BMC Genomics. 2010 Aug 05;11:460
references.pmid: 20687929
references.citation: Tuberculosis (Edinb). 2012 Jul;92(4):291-2
references.pmid: 22484109
references.citation: J Proteome Res. 2009 May;8(5):2241-52
references.pmid: 19231891
references.citation: Nat Methods. 2011 Sep 29;8(10):785-6
references.pmid: 21959131
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5
references.pmid: 22121212
references.citation: Chem Rev. 2002 Dec;102(12):4549-80
references.pmid: 12475201
references.citation: J Mol Biol. 2004 May 14;338(5):1027-36
references.pmid: 15111065
references.citation: BMC Genomics. 2010 Oct 19;11:584
references.pmid: 20959013
references.citation: Biochem Biophys Res Commun. 2007 Nov 16;363(2):297-303
references.pmid: 17880924
references.citation: BMC Bioinformatics. 2005 Oct 13;6:249
references.pmid: 16221310
references.citation: Bioinformatics. 2003 Dec 12;19(18):2498-9
references.pmid: 14668245
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5
references.pmid: 22102590
references.citation: Mol Syst Biol. 2010 Jul;6:390
references.pmid: 20664636
references.citation: Mol Cell Proteomics. 2005 Aug;4(8):1205-9
references.pmid: 15911532
references.citation: Electrophoresis. 1997 Aug;18(8):1259-313
references.pmid: 9298646
references.citation: J Biol Chem. 1988 Aug 25;263(24):11948-53
references.pmid: 3042786
references.citation: Int J Neural Syst. 1997 Oct-Dec;8(5-6):581-99
references.pmid: 10065837
references.citation: J Proteome Res. 2007 Jun;6(6):2195-204
references.pmid: 17444671
references.citation: PLoS One. 2011;6(11):e27587
references.pmid: 22114679
references.citation: Bioinformatics. 2008 Oct 1;24(19):2172-6
references.pmid: 18697773
references.citation: Genome Res. 2007 Sep;17(9):1362-77
references.pmid: 17690205
references.citation: Anal Chem. 2005 Jul 15;77(14):4626-39
references.pmid: 16013882
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D613-24
references.pmid: 23197660
references.citation: J Biol Chem. 2003 Aug 22;278(34):31473-8
references.pmid: 12805383
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W375-9
references.pmid: 15215414