title: Meta-analytic approach to the accurate prediction of secreted virulence effectors in gram-negative bacteria.
abstract: BACKGROUND
  Many pathogens use a type III secretion system to translocate virulence proteins (called effectors) in order to adapt to the host environment. To date, many prediction tools for effector identification have been developed. However, these tools are insufficiently accurate for producing a list of putative effectors that can be applied directly for labor-intensive experimental verification. This also suggests that important features of effectors have yet to be fully characterized.
  
  
  RESULTS
  In this study, we have constructed an accurate approach to predicting secreted virulence effectors from Gram-negative bacteria. This consists of a support vector machine-based discriminant analysis followed by a simple criteria-based filtering. The accuracy was assessed by estimating the average number of true positives in the top-20 ranking in the genome-wide screening. In the validation, 10 sets of 20 training and 20 testing examples were randomly selected from 40 known effectors of Salmonella enterica serovar Typhimurium LT2. On average, the SVM portion of our system predicted 9.7 true positives from 20 testing examples in the top-20 of the prediction. Removal of the N-terminal instability, codon adaptation index and ProtParam indices decreased the score to 7.6, 8.9 and 7.9, respectively. These discrimination features suggested that the following characteristics of effectors had been uncovered: unstable N-terminus, non-optimal codon usage, hydrophilic, and less aliphathic. The secondary filtering process represented by coexpression analysis and domain distribution analysis further refined the average true positive counts to 12.3. We further confirmed that our system can correctly predict known effectors of P. syringae DC3000, strongly indicating its feasibility.
  
  
  CONCLUSIONS
  We have successfully developed an accurate prediction system for screening effectors on a genome-wide scale. We confirmed the accuracy of our system by external validation using known effectors of Salmonella and obtained the accurate list of putative effectors of the organism. The level of accuracy was sufficient to yield candidates for gene-directed experimental verification. Furthermore, new features of effectors were revealed: non-optimal codon usage and instability of the N-terminal region. From these findings, a new working hypothesis is proposed regarding mechanisms controlling the translocation of virulence effectors and determining the substrate specificity encoded in the secretion system.
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Japan. y-sato@faculty.chiba-u.jp
authors.forename: Yoshiharu
authors.initials: Y
authors.lastname: Sato
authors.forename: Akiko
authors.initials: A
authors.lastname: Takaya
authors.forename: Tomoko
authors.initials: T
authors.lastname: Yamamoto
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D058947:Bacterial Secretion Systems; D006090:Gram-Negative Bacteria / Q000737:chemistry / Q000378:metabolism* / Q000472:pathogenicity*; D015201:Meta-Analysis as Topic; D020411:Oligonucleotide Array Sequence Analysis; D021381:Protein Transport; D012984:Software; D060388:Support Vector Machine; D014774:Virulence; D037521:Virulence Factors / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D058947:Bacterial Secretion Systems; D037521:Virulence Factors
references.citation: Infect Immun. 2005 Oct;73(10):6260-71
references.pmid: 16177297
references.citation: Nucleic Acids Res. 1982 Nov 25;10(22):7055-74
references.pmid: 6760125
references.citation: J Bacteriol. 2002 Jan;184(1):224-32
references.pmid: 11741864
references.citation: Infect Immun. 2003 Feb;71(2):690-6
references.pmid: 12540547
references.citation: Brief Bioinform. 2002 Mar;3(1):87-91
references.pmid: 12002227
references.citation: Bioinformatics. 2011 Mar 15;27(6):777-84
references.pmid: 21233168
references.citation: PLoS Genet. 2006 Dec;2(12):e209
references.pmid: 17194219
references.citation: Comput Appl Biosci. 1997 Oct;13(5):555-6
references.pmid: 9367129
references.citation: Infect Disord Drug Targets. 2009 Nov;9(5):518-47
references.pmid: 19594425
references.citation: Methods Mol Biol. 1999;112:531-52
references.pmid: 10027275
references.citation: J Biol Chem. 2010 Feb 26;285(9):6790-800
references.pmid: 20034934
references.citation: Infect Immun. 2011 Jun;79(6):2182-92
references.pmid: 21464085
references.citation: J Bacteriol. 2003 May;185(10):3155-66
references.pmid: 12730176
references.citation: PLoS Pathog. 2009 Apr;5(4):e1000375
references.pmid: 19390620
references.citation: BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S47
references.pmid: 20122221
references.citation: Novartis Found Symp. 2002;247:91-101; discussion 101-3, 119-28, 244-52
references.pmid: 12539951
references.citation: Biochem Biophys Res Commun. 2004 Sep 24;322(3):1038-44
references.pmid: 15336569
references.citation: Bioinformatics. 2000 Apr;16(4):404-5
references.pmid: 10869041
references.citation: Curr Opin Microbiol. 2009 Feb;12(1):53-60
references.pmid: 19168384
references.citation: Nucleic Acids Res. 1987 Feb 11;15(3):1281-95
references.pmid: 3547335
references.citation: Infect Immun. 2011 Jan;79(1):23-32
references.pmid: 20974833
references.citation: Nat Rev Genet. 2010 Jan;11(1):31-46
references.pmid: 19997069
references.citation: Mol Plant Microbe Interact. 2005 Aug;18(8):877-88
references.pmid: 16134900
references.citation: Biosystems. 2006 Sep;85(3):225-30
references.pmid: 16644095
references.citation: Bioinformatics. 2007 Sep 1;23(17):2337-8
references.pmid: 17599940
references.citation: Infect Genet Evol. 2009 Jul;9(4):468-73
references.pmid: 19454277
references.citation: Bioinformatics. 2004 Mar 1;20(4):586-7
references.pmid: 14990457
references.citation: Mol Biosyst. 2010 Dec;6(12):2448-58
references.pmid: 20877914
references.citation: Appl Microbiol Biotechnol. 2010 Mar;86(1):285-93
references.pmid: 20107986
references.citation: Mol Microbiol. 1998 Oct;30(1):175-88
references.pmid: 9786194
references.citation: PLoS Pathog. 2009 Apr;5(4):e1000376
references.pmid: 19390696
references.citation: Mol Microbiol. 2005 Jun;56(6):1636-47
references.pmid: 15916612
references.citation: PLoS Pathog. 2009 Jul;5(7):e1000508
references.pmid: 19593377
references.citation: Proc Natl Acad Sci U S A. 2002 May 28;99(11):7652-7
references.pmid: 12032338
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W563-8
references.pmid: 20507913
references.citation: Infect Immun. 2011 Jan;79(1):33-43
references.pmid: 20974834
references.citation: PLoS One. 2009 Jun 15;4(6):e5917
references.pmid: 19526054
references.citation: J Mol Evol. 1986;24(1-2):28-38
references.pmid: 3104616
references.citation: Protein Sci. 2000 Jun;9(6):1162-76
references.pmid: 10892809
references.citation: BMC Genomics. 2010 Jul 08;11:422
references.pmid: 20615251
references.citation: Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14941-6
references.pmid: 16990433
references.citation: Mol Plant Microbe Interact. 2006 Nov;19(11):1180-92
references.pmid: 17073301
references.citation: Microbiology (Reading). 2008 Jun;154(Pt 6):1570-1583
references.pmid: 18524912
references.citation: J Membr Biol. 2006;214(2):75-90
references.pmid: 17546510