Identifying new PCR targets for pathogenic bacteria using top-down LC/MS protein discovery

Journal of Biomolecular Techniques

Volumn 16, Issue 2, 2005, Pages 134-142

  Williams, Tracie L ^a   Monday, Steven R ^a   Feng, Peter C H ^a   Musser, Steven M ^a  

^a CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

Author keywords

Biomarkers; LC MS; Mass spectrometry

Indexed keywords

BACTERIAL PROTEIN;

ARTICLE; ENTEROBACTER INFECTION; ESCHERICHIA COLI K 12; ESCHERICHIA COLI O157; GENETICS; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLISM; MICROBIOLOGY; PATHOGENICITY; POLYMERASE CHAIN REACTION; PROTEOMICS;

BACTERIAL PROTEINS; CHROMATOGRAPHY, LIQUID; ESCHERICHIA COLI INFECTIONS; ESCHERICHIA COLI K12; ESCHERICHIA COLI O157; HUMANS; MASS SPECTROMETRY; POLYMERASE CHAIN REACTION; PROTEOMICS;

EID: 27744583099     PISSN: 15240215     EISSN: 19434731     Source Type: Journal    
DOI: None     Document Type: Article

References (30)

1. Nataro JP, Kaper, JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev 1998;11(1):142-201.
2. Paton JC, Paton AW. Pathogenesis and diagnosis of Shiga toxin-producing Escherichia coli infections. Clin Microbiol Rev 1998;11(3):450-479.
3. Johnson RP, Clarke RC, Wilson JB, et al. Growing concern and recent outbreaks involving non-0157:H7 serotypes of verotoxigenic Escherichia coli. J Food Prot 1996;59:1112-1122.
4. Monday SR, Whittam TS, Feng PC. Genetic and evolutionary analysis of mutations in the gusA gene that cause the absence of beta-glucuronidase activity in Escherichia coli 0157:H7. J Infect Dis 2001;184(7): 918-921.
5. Tominaga A, Mahmoud MA, Mukaihara T, Enomoto M. Molecular characterization of intact, but cryptic, fla-gellin genes in the genus Shigella. Mol Microbiol 1994; 12(2):277-285.
6. Monday SR, Minnich SA, Feng PC. A 12-base-pair deletion in the flagellar master control gene flhC causes nonmotility of the pathogenic German sorbitol-fermenting Escherichia coli 0157:H- strains. J Bacteriol 2004;186(8):2319-2327.
7. Cordwell SJ, Nouwens AS, Walsh BJ. Comparative proteomics of bacterial pathogens. Proteomics 2001;1(4): 461-472.
8. Li C, Chen Z, Xiao Z, et al. Comparative proteomics analysis of human lung squamous carcinoma. Biochem Biophys Res Commun 2003;309(1):253-260.
9. Ge Y, El-Naggar M, Sze SK, et al. Top down characterization of secreted proteins from Mycobacterium tuberculosis by electron capture dissociation mass spectrometry. J Am Soc Mass Spectrom 2003;14(3):253-261.
10. Ge Y, Lawhorn BG, ElNaggar M, et al. Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J Am Chem Soc 2002;124(4):672-678.
11. Kettman JR, Frey JR, Lefkovits I. Proteome, transcriptome and genome: Top down or bottom up analysis? Biomol Eng 2001;18(5):207-212.
12. Hamler RL, Zhu K, Buchanan NS, et al. A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification. Proteomics 2004;4(3): 562-577.
13. Wu CC, MacCoss MJ. Shotgun proteomics: Tools for the analysis of complex biological systems. Curr Opin Mol Ther 2002;4(3):242-250.
14. Bodnar WM, Blackburn RK, Krise JM, Moseley MA. Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage. J Am Soc Mass Spectrom 2003;14(9):971-979.
15. McDonald WH, Yates JR, 3rd. Shotgun proteomics and biomarker discovery. Dis Markers 2002;18(2):99-105.
16. Griffin T J, Han DK, Gygi SP, et al. Toward a highthroughput approach to quantitative proteomic analysis: Expression-dependent protein identification by mass spectrometry. J Am Soc Mass Spectrom 2001; 12(12):1238-1246.
17. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH. Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999;17(10):994-999.
18. Chakraborty A, Regnier FE. Global internal standard technology for comparative proteomics. J Chromatogr A 2002;949(1/2):173-184.
19. Ji J, Chakraborty A, Geng M, et al. Strategy for qualitative and quantitative analysis in proteomics based on signature peptides. J Chromatogr B Biomed Sci Appl 2000;745(1):197-210.
20. Regnier FE, Riggs L, Zhang R, et al. Comparative proteomics based on stable isotope labeling and affinity selection. J Mass Spectrom 2002;37(2):133-145.
21. Williams TL, Leopold P, Musser S. Automated postprocessing of electrospray LC/MS data for profiling protein expression in bacteria. Anal Chem 2002;74(22):5807-5813.
22. Williams TL, Musser SM, Nordstrom JL, DePaola A, Monday SR. Identification of a protein biomarker unique to the pandemic 03:K6 clone of Vibrio parahaemolyticus. J Clin Microbiol 2004;42(4):1657-1665.
23. Karch H, Bielaszewska M. Sorbitol-fermenting Shiga toxin-producing Escherichia coli 0157:H(-) strains: Epidemiology, phenotypic and molecular characteristics, and microbiological diagnosis. J Clin Microbiol 2001;39(6):2043-2049.
24. Feng P, Dey M, Abe A, Takeda T. Isogenic strain of Escherichia coli 0157:H7 that has lost both Shiga toxin 1 and 2 genes. Clin Diagn Lab Immunol 2001;8(4): 711-717.
25. Feng P, Weagant SD, Monday SR. Genetic analysis for virulence factors in Escherichia coli 0104:H21 that was implicated in an outbreak of hemorrhagic colitis. J Clin Microbiol 2001;39(1):24-28.
26. Feng P, Monday SR. Multiplex PCR for detection of trait and virulence factors in enterohemorrhagic Escherichia coli serotypes. Mol Cell Probes 2000;14(6):333-337.
27. Feng P, Lampel KA, Karch H, Whittam TS. Genotypic and phenotypic changes in the emergence of Escherichia coli 0157:H7. J Infect Dis 1998;177(6):1750-1753.
28. Nesic D, Hsu Y, Stebbins CE. Assembly and function of a bacterial genotoxin. Nature 2004;429(6990):429-433.
29. Haghjoo E, Galan JE. Salmonella typhi encodes a functional cytolethal distending toxin that is delivered into host cells by a bacterial-internalization pathway. Proc Natl Acad Sci U S A 2004;101(13):4614-4619.
30. Williams TL, Callahan JH, Monday SR, Feng PC, Musser SM. Relative quantitation of intact proteins of bacterial cell extracts using coextracted proteins as internal standards. Anal Chem 2004;76(4):1002-1007.