A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Shao, Wenguang ^a   Zhang, Min ^a   Lam, Henry ^a   Lau, Stanley C K ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ALGORITHM; ANIMAL; CLASSIFICATION; DNA FINGERPRINTING; DNA SEQUENCE; ESCHERICHIA COLI; FECES; GENETICS; ISOLATION AND PURIFICATION; LIQUID CHROMATOGRAPHY; MICROBIOLOGY; MOLECULAR TYPING; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROCEDURES; PROTEOMICS; TANDEM MASS SPECTROMETRY;

ALGORITHMS; ANIMALS; BASE SEQUENCE; CHROMATOGRAPHY, LIQUID; DNA FINGERPRINTING; DNA, BACTERIAL; ESCHERICHIA COLI; FECES; MOLECULAR TYPING; POLYMERASE CHAIN REACTION; PROTEOMICS; SEQUENCE ANALYSIS, DNA; TANDEM MASS SPECTROMETRY;

EID: 84942437080     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep14337     Document Type: Article

References (65)

1. Vaneechoutte, M. DNA fngerprinting techniques for microorganisms. Mol Biotechnol 6, 115-142 (1996).
2. Karlsson, R. et al. Strain-level typing and identifcation of bacteria using mass spectrometry-based proteomics. J Proteome Res 11, 2710-2720 (2012).
3. Conway, G. C., Smole, S. C., Sarracino, D. A., Arbeit, R. D. & Leopold, P. E. Phyloproteomics: species identifcation of Enterobacteriaceae using matrix-assisted laser desorption/ionization time-of-fight mass spectrometry. J Mol Microbiol Biotech 3, 103-112 (2001).
4. Sandrin, T. R., Goldstein, J. E. & Schumaker, S. MALDI TOF MS profling of bacteria at the strain level: a review. Mass Spectrom Rev 32, 188-217 (2013).
5. Wolters, D. A., Washburn, M. P. & Yates, J. R. An automated multidimensional protein identifcation technology for shotgun proteomics. Anal Chem 73, 5683-5690 (2001).
6. Yates III, J. R. A century of mass spectrometry: from atoms to proteomes. Nat Methods 8, 633-637 (2011).
7. Jabbour, R. E. et al. Double-blind characterization of non-genome-sequenced bacteria by mass spectrometry-based proteomics. Appl Environ Microbiol 76, 3637-3644 (2010).
8. Kooken, J., Fox, K., Fox, A. & Wunschel, D. Reprint of "Assessment of marker proteins identifed in whole cell extracts for bacterial speciation using liquid chromatography electrospray ionization tandem mass spectrometry". Mol Cell Probe 28, 58-64 (2014).
9. Jabbour, R. E. et al. Identifcation of Yersinia pestis and Escherichia coli strains by whole cell and outer membrane protein extracts with mass spectrometry-based proteomics. J Proteome Res 9, 3647-3655 (2010).
10. McDonald, W. H. & Yates, J. R. Shotgun proteomics and biomarker discovery. Dis Markers 18, 99-105 (2002).
11. Denef, V. J. et al. Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol 11, 313-325 (2009).
12. Hettich, R. L., Pan, C., Chourey, K. & Giannone, R. J. Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem 85, 4203-4214 (2013).
13. Nesvizhskii, A. I. Proteogenomics: concepts, applications and computational strategies. Nat Methods 11, 1114-1125 (2014).
14. Lapierre, P. & Gogarten, J. P. Estimating the size of the bacterial pan-genome. Trends Genet 25, 107-110 (2009).
15. Önder, Ö., Shao, W., Kemps, B. D., Lam, H. & Brisson, D. Identifying sources of tick blood meals using unidentifed tandem mass spectral libraries. Nat Commun 4, 1746 (2013).
16. O'Brien, C. L. & Gordon, D. M. Efect of diet and gut dynamics on the establishment and persistence of Escherichia coli. Microbiol 157, 1375-1384 (2011).
17. Ishii, S. & Sadowsky, M. J. Escherichia coli in the environment: implications for water quality and human health. Microbes Environ 23, 101-108 (2008).
18. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198-207 (2003).
19. Dombek, P. E., Johnson, L. K., Zimmerley, S. T. & Sadowsky, M. J. Use of repetitive DNA sequences and the PCR to diferentiate Escherichia coli isolates from human and animal sources. Appl Environ Microbiol 66, 2572-2577 (2000).
20. Carson, C. A., Shear, B. L., Ellersieck, M. R. & Schnell, J. D. Comparison of ribotyping and repetitive extragenic palindromic-PCR for identifcation of fecal Escherichia coli from humans and animals. Appl Environ Microbiol 69, 1836-1839 (2003).
21. Ho, B. & Tam, T.-Y. Enumeration of E. coli in environmental waters and wastewater using a chromogenic medium. Water science and technology 35, 409-413 (1997).
22. Horakova, K., Mlejnkova, H. & Mlejnek, P. Specifc detection of Escherichia coli isolated from water samples using polymerase chain reaction targeting four genes: cytochrome bd complex, lactose permease, β-d-glucuronidase, and β-d-galactosidase. J Appl Microbiol 105, 970-976 (2008).
23. Sabat, G., Rose, P., Hickey, W. & Harkin, J. Selective and sensitive method for PCR amplifcation of Escherichia coli 16S rRNA genes in soil. Appl Environ Microbiol 66, 844-849 (2000).
24. Kessner, D., Chambers, M., Burke, R., Agus, D. & Mallick, P. ProteoWizard: open source sofware for rapid proteomics tools development. Bioinformatics 24, 2534-2536 (2008).
25. Lam, H. et al. Development and validation of a spectral library searching method for peptide identifcation from MS/MS. Proteomics 7, 655-667 (2007).
26. Elias, J. E. & Gygi, S. P. Target-decoy search strategy for increased confdence in large-scale protein identifcations by mass spectrometry. Nat Methods 4, 207-214 (2007).
27. Geer, L. Y. et al. Open mass spectrometry search algorithm. J Proteome Res 3, 958-964 (2004).
28. Craig, R. & Beavis, R. C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467 (2004).
29. Shteynberg, D. et al. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identifcation rates and error estimates. Mol Cell Proteomics 10, M111. 007690 (2011).
30. Deutsch, E. W. et al. A guided tour of the Trans-Proteomic Pipeline. Proteomics 10, 1150-1159 (2010).
31. Mohapatra, B. R., Broersma, K. & Mazumder, A. Comparison of fve rep-PCR genomic fngerprinting methods for diferentiation of fecal Escherichia coli from humans, poultry and wild birds. FEMS Microbiol Lett 277, 98-106 (2007).
32. Team, R. C. (ISBN 3-900051-07-0. R Foundation for Statistical Computing. Vienna, Austria, 2013. 2005).
33. Paradis, E., Claude, J. & Strimmer, K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289-290 (2004).
34. Lê Cao, K.-A., González, I. & Déjean, S. integrOmics: an R package to unravel relationships between two omics datasets. Bioinformatics 25, 2855-2856 (2009).
35. Stoeckel, D. M. & Harwood, V. J. Performance, design, and analysis in microbial source tracking studies. Appl Environ Microbiol 73, 2405-2415 (2007).
36. Barker, M. & Rayens, W. Partial least squares for discrimination. J Chemometr 17, 166-173 (2003).
37. Mørtz, E. et al. Sequence tag identifcation of intact proteins by matching tanden mass spectral data against sequence data bases. P Natl Acad Sci USA 93, 8264-8267 (1996).
38. Tabb, D. L., Ma, Z.-Q., Martin, D. B., Ham, A.-J. L. & Chambers, M. C. DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res 7, 3838-3846 (2008).
39. Ma, B. et al. PEAKS: powerful sofware for peptide de novo sequencing by tandem mass spectrometry. Rapdi Commun Mass Sp 17, 2337-2342 (2003).
40. Vizcaíno, J. A. et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 32, 223-226 (2014).
41. Gordienko, E. N., Kazanov, M. D. & Gelfand, M. S. Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica. J Bacteriol 195, 2786-2792 (2013).
42. Haegeman, B. & Weitz, J. S. A neutral theory of genome evolution and the frequency distribution of genes. BMC genomics 13, 196 (2012).
43. Touchon, M. et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5, e1000344 (2009).
44. Kaas, R. S., Friis, C., Ussery, D. W. & Aarestrup, F. M. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC genomics 13, 577 (2012).
45. Rasko, D. A. et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190, 6881-6893 (2008).
46. Ochman, H. & Selander, R. K. Standard reference strains of Escherichia coli from natural populations. J Bacteriol 157, 690-693 (1984).
47. Tenaillon, O., Skurnik, D., Picard, B. & Denamur, E. The population genetics of commensal Escherichia coli. Nat Rev Microbiol 8, 207-217 (2010).
48. Versalovic, J., Koeuth, T. & Lupski, R. Distribution of repetitive DNA sequences in eubacteria and application to fnerpriting of bacterial enomes. Nucleic Acids Res 19, 6823-6831 (1991).
49. Tobes, R. & Ramos, J. L. REP code: defning bacterial identity in extragenic space. Environ Microbiol 7, 225-228 (2005).
50. Cohan, F. M. & Koeppel, A. F. The origins of ecological diversity in prokaryotes. Curr Biol 18, R1024-R1034 (2008).
51. Guttman, D. S. & Dykhuizen, D. E. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 266, 1380 (1994).
52. Desjardins, P., Picard, B., Kaltenböck, B., Elion, J. & Denamurl, E. Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplifed polymorphic DNA and restriction-fragment-length polymorphism. J Mol Evol 41, 440-448 (1995).
53. Mott, J. & Smith, A. in Microbial Source Tracking: Methods, Applications, and Case Studies 31-59 (Springer, 2011).
54. Lo, I. et al. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446, 537-541 (2007).
55. Fagerquist, C. K. et al. Top-Down Proteomic Identifcation of Shiga Toxin 2 Subtypes from Shiga Toxin-Producing Escherichia coli by Matrix-Assisted Laser Desorption Ionization-Tandem Time of Flight Mass Spectrometry. Appl Environ Microbiol 80, 2928-2940 (2014).
56. Ruelle, V., Moualij, B. E., Zorzi, W., Ledent, P. & Pauw, E. D. Rapid identifcation of environmental bacterial strains by matrix-assisted laser desorption/ionization time-of-fight mass spectrometry. Rapdi Commun Mass Sp 18, 2013-2019 (2004).
57. Siegrist, T. J. et al. Discrimination and characterization of environmental strains of Escherichia coli by matrix-assisted laser desorption/ionization time-of-fight mass spectrometry (MALDI-TOF-MS). J Microbiol Meth 68, 554-562 (2007).
58. Cohen, D. P. et al. Proteomic analysis of log to stationary growth phase Lactobacillus plantarum cells and a 2-DE database. Proteomics 6, 6485-6493 (2006).
59. Li, Z., Nimtz, M. & Rinas, U. The metabolic potential of Escherichia coli BL21 in defned and rich medium. Microb Cell Fact 13, 45 (2014).
60. Nyström, T. Stationary-phase physiology. Annu. Rev. Microbiol. 58, 161-181 (2004).
61. Maiden, M. C. et al. Multilocus sequence typing: a portable approach to the identifcation of clones within populations of pathogenic microorganisms. P Natl Acad Sci USA 95, 3140-3145 (1998).
62. Larsen, M. V. et al. Multilocus sequence typing of total genome sequenced bacteria. Journal of clinical microbiology, JCM. 06094-06011 (2012).
63. Hall, B. G., Ehrlich, G. D. & Hu, F. Z. Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing. Microbiol 156, 1060-1068 (2010).
64. Harris, S. R. et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327, 469-474 (2010).
65. Lange, V., Picotti, P., Domon, B. & Aebersold, R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 4, 222 (2008).