Label-free quantitative proteomics of two Bifidobacterium longum strains

Journal of Proteomics

Volumn 72, Issue 5, 2009, Pages 771-784

  Guillaume, Elisabeth ^a   Berger, Bernard ^a   Affolter, Michael ^a   Kussmann, Martin ^a  

^a NESTLÉ RESEARCH CENTER   (Switzerland)

Author keywords

Bifidobacteria; DeCyder MS; Heat shock tolerance; Label free quantification

Indexed keywords

BACTERIAL PROTEIN;

ARTICLE; BACTERIAL STRAIN; BIFIDOBACTERIUM LONGUM; CONTROLLED STUDY; ELECTROSPRAY MASS SPECTROMETRY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; PROTEOMICS; QUANTITATIVE ANALYSIS;

BIFIDOBACTERIUM; CALIBRATION; CHROMATOGRAPHY, LIQUID; CYTOSINE; DATABASES, PROTEIN; GENOME, BACTERIAL; GUANINE; HOT TEMPERATURE; MASS SPECTROMETRY; PROTEOME; PROTEOMICS; SOFTWARE; SPECIES SPECIFICITY; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

BIFIDOBACTERIUM LONGUM; POSIBACTERIA;

EID: 67649503203     PISSN: 18743919     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jprot.2009.03.004     Document Type: Article

References (64)

1. Fooks L.J., and Gibson G.R. Probiotics as modulators of the gut flora. Br J Nutr 88 Suppl 1 (2002) S39-S49
2. Kailasapathy K., and Chin J. Survival and therapeutic potential of probiotic organisms with reference to Lactobacillus acidophilus and Bifidobacterium spp. Immunol Cell Biol 78 (2000) 80-88
3. Lammers K.M., Brigidi P., Vitali B., Gionchetti P., Rizzello F., Caramelli E., et al. Immunomodulatory effects of probiotic bacteria DNA: IL-1 and IL-10 response in human peripheral blood mononuclear cells. FEMS Immunol Med Microbiol 38 (2003) 165-172
4. Salminen S., and Gueimonde M. Human studies on probiotics: what is scientifically proven. J Food Sci 69 (2004) M137-M140
5. Vitali B., Wasinger V., Brigidi P., and Guilhaus M. A proteomic view of Bifidobacterium infantis generated by multi-dimensional chromatography coupled with tandem mass spectrometry. Proteomics 5 (2005) 1859-1867
6. Yuan J., Zhu L., Liu X., Li T., Zhang Y., Ying T., et al. A proteome reference map and proteomic analysis of Bifidobacterium longum NCC2705. Mol. Cell Proteomics 5 (2006) 1105-1118
7. Yuan J., Wang B., Sun Z., Bo X., Yuan X., He X., et al. Analysis of host-inducing proteome changes in Bifidobacterium longum NCC2705 grown in vivo. J Proteome Res 7 (2008) 375-385
8. Sanchez B., Ruiz L., de los Reyes-Gavilan C.G., and Margolles A. Proteomics of stress response in Bifidobacterium. Front Biosci 13 (2008) 6905-6919
9. Schmidt G., and Zink R. Basic features of the stress response in three species of bifidobacteria: B. longum, B. adolescentis, and B. breve. Int J Food Microbiol 55 (2000) 41-45
10. Ventura M., Canchaya C., Zink R., Fitzgerald G.F., and van Sinderen D. Characterization of the groEL and groES loci in Bifidobacterium breve UCC 2003: genetic, transcriptional, and phylogenetic analyses. Appl Environ Microbiol 70 (2004) 6197-6209
11. Ventura M., Zink R., Fitzgerald G.F., and van Sinderen D. Gene structure and transcriptional organization of the dnaK operon of Bifidobacterium breve UCC 2003 and application of the operon in bifidobacterial tracing. Appl Environ Microbiol 71 (2005) 487-500
12. Ventura M., Kenny J.G., Zhang Z., Fitzgerald G.F., and van Sinderen D. The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction. Microbiology 151 (2005) 2861-2872
13. Rezzonico E., Lariani S., Barretto C., Cuanoud G., Giliberti G., Delley M., et al. Global transcriptome analysis of the heat shock response of Bifidobacterium longum. FEMS Microbiol Lett 271 (2007) 136-145
14. Marvin-Guy L.F., Parche S., Wagniere S., Moulin J., Zink R., Kussmann M., et al. Rapid identification of stress-related fingerprint from whole bacterial cells of Bifidobacterium lactis using matrix assisted laser desorption/ionization mass spectrometry. J Am Soc Mass Spectrom 15 (2004) 1222-1227
15. Savijoki K., Suokko A., Palva A., Valmu L., Kalkkinen N., and Varmanen P. Effect of heat-shock and bile salts on protein synthesis of Bifidobacterium longum revealed by [35S]methionine labelling and two-dimensional gel electrophoresis. FEMS Microbiol Lett 248 (2005) 207-215
16. Sanchez B., Champomier-Verges M.C., Anglade P., Baraige F., de Los Reyes-Gavilan C.G., Margolles A., et al. Proteomic analysis of global changes in protein expression during bile salt exposure of Bifidobacterium longum NCIMB 8809. J Bacteriol 187 (2005) 5799-5808
17. Gorg A., Weiss W., and Dunn M.J. Current two-dimensional electrophoresis technology for proteomics. Proteomics 4 (2004) 3665-3685
18. Nesvizhskii A.I., and Aebersold R. Interpretation of shotgun proteomic data. Mol Cell Proteomics 4 (2005) 1419-1440
19. Wolters D.A., Washburn M.P., and Yates J.R. An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73 (2001) 5683-5690
20. Julka S., and Regnier F. Quantification in proteomics through stable isotope coding: a review. J Proteome Res 3 (2004) 350-363
21. Liu H.B., Sadygov R.G., and Yates III J.R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76 (2004) 4193-4201
22. Old W.M., Meyer-Arendt K., Aveline-Wolf L., Pierce K.G., Mendoza A., Sevinsky J.R., et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4 (2005) 1487-1502
23. Mueller L.N., Brusniak M.Y., Mani D.R., and Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res 7 (2008) 51-61
24. America A.H., and Cordewener J.H. Comparative LC-MS: a landscape of peaks and valleys. Proteomics 8 (2008) 731-749
25. Mann M. Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 7 (2006) 952-958
26. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17 (1999) 994-999
27. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3 (2004) 1154-1169
28. Roesli C., Elia G., and Neri D. Two-dimensional mass spectrometric mapping. Curr Opin Chem Biol 10 (2006) 35-41
29. Listgarten J., and Emili A. Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 4 (2005) 419-434
30. Zimmer J.S., Monroe M.E., Qian W.J., and Smith R.D. Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom Rev 25 (2006) 450-482
31. Silva J.C., Denny R., Dorschel C., Gorenstein M.V., Li G.Z., Richardson K., et al. Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale. Mol Cell Proteomics 5 (2006) 589-607
32. Johansson C., Samskog J., Sundstrom L., Wadensten H., Bjorkesten L., and Flensburg J. Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data. Proteomics 6 (2006) 4475-4485
33. Schell M.A., Karmirantzou M., Snel B., Vilanova D., Berger B., Pessi G., et al. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U.S.A 99 (2002) 14422-14427
34. Berger B, Moine D, Mansourian R, Arigoni F. Natural selection and molecular characterization of Bifidobacterium longum heat-shock tolerant mutants. submitted.
35. Vitali B., Wasinger V., Brigidi P., and Guilhaus M. A proteomic view of Bifidobacterium infantis generated by multi-dimensional chromatography coupled with tandem mass spectrometry. Proteomics 5 (2005) 1859-1867
36. Pedrioli P.G., Eng J.K., Hubley R., Vogelzang M., Deutsch E.W., Raught B., et al. A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol 22 (2004) 1459-1466
37. Wang G., Wu W.W., Zeng W., Chou C.L., and Shen R.F. Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: reproducibility, linearity, and application with complex proteomes. J. Proteome. Res 5 (2006) 1214-1223
38. Johansson C., Samskog J., Sundstrom L., Wadensten H., Bjorkesten L., and Flensburg J. Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data. Proteomics 6 (2006) 4475-4485
39. Vitali B., Wasinger V., Brigidi P., and Guilhaus M. A proteomic view of Bifidobacterium infantis generated by multi-dimensional chromatography coupled with tandem mass spectrometry. Proteomics 5 (2005) 1859-1867
40. Yuan J., Zhu L., Liu X., Li T., Zhang Y., Ying T., et al. A proteome reference map and proteomic analysis of Bifidobacterium longum NCC2705. Mol Cell Proteomics 5 (2006) 1105-1118
41. Goshe M.B., and Smith R.D. Stable isotope-coded proteomic mass spectrometry. Curr Opin Biotechnol 14 (2003) 101-109
42. Panchaud A., Hansson J., Affolter M., Rhlid R.B., Piu S., Moreillon P., et al. ANIBAL-stable-isotope-based quantitative proteomics by ANIline and Benzoic acid labeling of amino and carboxylic groups. Mol Cell Proteomics 7 (2008) 800-812
43. Skold K., Svensson M., Kaplan A., Bjorkesten L., Astrom J., and Andren P.E. A neuroproteomic approach to targeting neuropeptides in the brain. Proteomics 2 (2002) 447-454
44. Svensson M., Skold K., Svenningsson P., and Andren P.E. Peptidomics-based discovery of novel neuropeptides. J Proteome Res 2 (2003) 213-219
45. Tammen H., Schulte I., Hess R., Menzel C., Kellmann M., Mohring T., et al. Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display. Proteomics 5 (2005) 3414-3422
46. Li X.J., Pedrioli P.G., Eng J., Martin D., Yi E.C., Lee H., et al. A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal Chem 76 (2004) 3856-3860
47. Palagi P.M., Walther D., Quadroni M., Catherinet S., Burgess J., Zimmermann-Ivol C.G., et al. MSight: an image analysis software for liquid chromatography-mass spectrometry. Proteomics 5 (2005) 2381-2384
48. Katajamaa M., and Oresic M. Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics 6 (2005) 179
49. Leptos K.C., Sarracino D.A., Jaffe J.D., Krastins B., and Church G.M. MapQuant: open-source software for large-scale protein quantification. Proteomics 6 (2006) 1770-1782
50. Li X.J., Yi E.C., Kemp C.J., Zhang H., and Aebersold R. A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol Cell Proteom 4 (Sep 2005) 1328 1340
51. Bellew M., Coram M., Fitzgibbon M., Igra M., Randolph T., Wang P., et al. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 22 (2006) 1902-1909
52. Mueller L.N., Rinner O., Schmidt A., Letarte S., Bodenmiller B., Brusniak M.Y., et al. SuperHirn-a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 7 (2007) 3470-3480
53. Wittke S., Fliser D., Haubitz M., Bartel S., Krebs R., Hausadel F., et al. Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers. J Chromatogr A 1013 (2003) 173-181
54. Wang W., Zhou H., Lin H., Roy S., Shaler T.A., Hill L.R., et al. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 75 (2003) 4818-4826
55. Tammen H., Kreipe H., Hess R., Kellmann M., Lehmann U., Pich A., et al. Expression profiling of breast cancer cells by differential peptide display. Breast Cancer Res Treat 79 (2003) 83-93
56. Radulovic D., Jelveh S., Ryu S., Hamilton T.G., Foss E., Mao Y., et al. Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 3 (2004) 984-997
57. Anderson T.J., Tchernyshyov I., Diez R., Cole R.N., Geman D., Dang C.V., et al. Discovering robust protein biomarkers for disease from relative expression reversals in 2-D DIGE data. Proteomics 7 (2007) 1197-1207
58. Johansson C., Samskog J., Sundstrom L., Wadensten H., Bjorkesten L., and Flensburg J. Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data. Proteomics 6 (2006) 4475-4485
59. Ventura M., Canchaya C., Zink R., Fitzgerald G.F., and van Sinderen D. Characterization of the groEL and groES loci in Bifidobacterium breve UCC 2003: genetic, transcriptional, and phylogenetic analyses. Appl Environ Microbiol 70 (2004) 6197-6209
60. Bucca G., Ferina G., Puglia A.M., and Smith C.P. The dnaK operon of Streptomyces coelicolor encodes a novel heat-shock protein which binds to the promoter region of the operon. Mol Microbiol 17 (1995) 663-674
61. Bucca G., Hindle Z., and Smith C.P. Regulation of the dnaK operon of Streptomyces coelicolor A3(2) is governed by HspR, an autoregulatory repressor protein. J Bacteriol 179 (1997) 5999-6004
62. Grandvalet C., Servant P., and Mazodier P. Disruption of hspR, the repressor gene of the dnaK operon in Streptomyces albus G. Mol Microbiol 23 (1997) 77-84
63. Bucca G., Brassington A.M., Schonfeld H.J., and Smith C.P. The HspR regulon of Streptomyces coelicolor: a role for the DnaK chaperone as a transcriptional co-repressordagger. Mol Microbiol 38 (2000) 1093-1103
64. Bucca G., Brassington A.M., Hotchkiss G., Mersinias V., and Smith C.P. Negative feedback regulation of dnaK, clpB and lon expression by the DnaK chaperone machine in Streptomyces coelicolor, identified by transcriptome and in vivo DnaK-depletion analysis. Mol Microbiol 50 (2003) 153-166