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Chapter 16 : Proteomic Approaches To Study Lactic Acid Bacteria

Authors: David P. A. Cohen1, Elaine E. Vaughan2, Willem M. de Vos3, Erwin G. Zoetendal4
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Affiliations: 1: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands; 2: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands; 3: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands; 4: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
Content Type: Monograph
Publication Year: 2008

Category: Clinical Microbiology

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Abstract:

Biology aims to describe, understand, and predict the functionality of living cells, tissues, organisms, and ecosystems. High-throughput approaches that allow simultaneous investigation of more than one parameter will ultimately lead to better understanding of the organism’s behavior. Examples of such high-throughput approaches are genomics, transcriptomics, proteomics, and metabolomics. This chapter focuses on the application of proteomics in microbiological research in which special attention is given to the lactic acid bacteria (LAB). Proteomics has been used to investigate the functionality of LAB during preparation or fermentation of foods or their responses towards certain stress conditions (e.g., bile salts and acid) that these organisms encounter during passage through the human gastrointestinal tract. Proteomic approaches make it possible to gain insights into the relative abundance of proteins under certain conditions, and this knowledge may help predict which proteins of LAB are involved in survival under harsh conditions. Following an introduction regarding recent developments in proteomics, the chapter describes major findings obtained by studying the proteomes of LAB, especially under physiological stress conditions. It highlights the major results that were obtained by studying the proteomes of LAB under various conditions. Two separate proteomic research strategies have been applied frequently to LAB. These approaches include the construction of protein reference maps, systematic indexing of proteins, and analyses of bacterial stress responses culminating in induced changes in different proteomes.

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16

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Proteomic Approaches To Study Lactic Acid Bacteria
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Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
/content/10.1128/9781555815462.ch16.ch16fig01
Figure 1
The gel-based proteomic method can be divided into two main parts, separation of protein complexes and identification of individual proteins. The separation of proteins in mixtures is based on the protein’s isoelectric point and its molecular weight. Identification of the proteins is commonly achieved using MALDI-TOF MS and mass fingerprinting prior to database searching.
10.1128/9781555815462/ch16fig1_thmb.gif
10.1128/9781555815462/ch16fig1.gif
Image of Figure 1
Figure 1

The gel-based proteomic method can be divided into two main parts, separation of protein complexes and identification of individual proteins. The separation of proteins in mixtures is based on the protein’s isoelectric point and its molecular weight. Identification of the proteins is commonly achieved using MALDI-TOF MS and mass fingerprinting prior to database searching.

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
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Figure 2
A schematic overview of stress responses in LAB (based on , and ). Proteins within the dashed circles are associated with several stress responses visualized by two-dimensional gel electrophoresis. DnaK and GroES/EL are induced during specific stress challenges, while Clp is a general stress protein. The third group consists of proteins found to be differentially regulated during stress, changing the metabolism of the bacterium towards adaptation to the stress inducer.
10.1128/9781555815462/ch16fig2_thmb.gif
10.1128/9781555815462/ch16fig2.gif
Image of Figure 2
Figure 2

A schematic overview of stress responses in LAB (based on , and ). Proteins within the dashed circles are associated with several stress responses visualized by two-dimensional gel electrophoresis. DnaK and GroES/EL are induced during specific stress challenges, while Clp is a general stress protein. The third group consists of proteins found to be differentially regulated during stress, changing the metabolism of the bacterium towards adaptation to the stress inducer.

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
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Figure 3
A schematic diagram combines metagenomic and metaproteomic data sets in order to address gut functionality of LAB. With metagenomics, identification of bacterial genes is feasible. Protein predictions of active genes by metagenomics will facilitate protein identification by metaproteomics.
10.1128/9781555815462/ch16fig3_thmb.gif
10.1128/9781555815462/ch16fig3.gif
Image of Figure 3
Figure 3

A schematic diagram combines metagenomic and metaproteomic data sets in order to address gut functionality of LAB. With metagenomics, identification of bacterial genes is feasible. Protein predictions of active genes by metagenomics will facilitate protein identification by metaproteomics.

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
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References

/content/book/10.1128/9781555815462.ch16
1. Aebersold, R. H.,, J. Leavitt,, R. A. Saavedra,, L. E. Hood, and, S. B. H. Kent. 1987. Internal amino acid sequence analysis of proteins separated by one- or two-dimensional gel electrophoresis after in situ protease digestion on nitrocellulose. Proc. Natl. Acad. Sci. USA 84: 6970– 6974.
2. Aebersold, R. H.,, G. Pipes,, L. E. Hood, and, S. B. H. Kent. 1988. N-terminal and internal sequence determination of microgram amounts of proteins separated by isoelectric focusing in immobilized pH gradients. Electrophoresis 9: 520– 530.
3. Alonso, J. C.,, K. Shirahige, and, N. Ogasawara. 1990. Molecular cloning, genetic characterization and DNA sequence analysis of the recM region of Bacillus subtilis. Nucleic Acids Res. 18: 6771– 6777.
4. Altermann, E.,, W. M. Russell,, M. A. Azcarate-Peril,, R. Barrangou,, B. L. Buck,, O. McAuliffe,, N. Souther,, A. Dobson,, T. Duong,, M. Callanan,, S. Lick,, A. Hamrick,, R. Cano, and, T. R. Klaenhammer. 2005. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc. Natl. Acad. Sci. USA 102: 3906– 3912.
5. Anastasiou, R.,, P. Leverrier,, I. Krestas,, A. Rouault,, G. Kalantzopoulos,, P. Boyaval,, E. Tsakalidou,, and G. Jan. 2006. Changes in protein synthesis during thermal adaptation of Propionibacterium freudenreichii subsp. shermanii. Int. J. Food Microbiol. 108: 301– 314.
6. Andersen, J. S., and, M. Mann. 2000. Functional genomics by mass spectrometry. FEBS Lett. 480: 25– 31.
7. Anderson, L. B.,, M. Maderia,, A. J. A. Ouellette,, C. Putnam-Evans,, L. Higgins,, T. Krick,, M. J. MacCoss,, H. Lim,, J. R. Yates III, and, B. A. Barry. 2002. Posttranslational modifications in the CP43 subunit of photosystem II. Proc. Natl. Acad. Sci. USA 99: 14676– 14681.
8. Anglade, P.,, E. Demey,, V. Labas,, J.-P. L. Caer, and, J.-F. Chich. 2000. Towards a proteomic map of Lactococcus lactis NCDO 763. Electrophoresis 21: 2546– 2549.
9. Barber, M.,, R. S. Bordoli,, R. D. Sedgwick, and, A. N. Tyler. 1981. Fast atom bombardment of solids as an ion source in mass spectrometry. Nature 293: 270– 275.
10. Bernstein, C.,, H. Bernstein,, C. M. Payne,, S. E. Beard,, and J. Schneider. 1999. Bile salt activation of stress response promoters in Escherichia coli. Curr. Microbiol. 39: 68– 72.
11. Bonestroo, M. H.,, B. J., M. Kusters,, J. C. De Wit, and, F. M. Rombouts. 1992. Glucose and sucrose fermenting capacity of homofermentative lactic acid bacteria used as starters in fermented salads. Int. J. Food Microbiol. 15:365.
12. Bron, P. A.,, D. Molenaar,, W. M. Vos, and, M. Kleerebezem. 2006. DNA micro-array-based identification of bile-responsive genes in Lactobacillus plantarum. J. Appl. Microbiol. 100: 728– 738.
13. Budin-Verneuil, A.,, V. Pichereau,, Y. Auffray,, D. S. Ehrlich, and, E. Maguin. 2005. Proteomic characterization of the acid tolerance response in Lactococcus lactis MG1363. Proteomics 5: 4794– 4807.
14. Cha, B.,, M. Blades, and, D. J. Douglas. 2000. An interface with a linear quadrupole ion guide for an electrospray-ion trap mass spectrometer system. Anal. Chem. 72: 5647– 5654.
15. Chervaux, C.,, S. D. Ehrlich, and, E. Maguin. 2000. Physiological study of Lactobacillus delbrueckii subsp. bulgaricus strains in a novel chemically defined medium. Appl. Environ. Microbiol. 66: 5306– 5311.
16. Cohen, D. P. A.,, J. Renes,, F. G. Bouwman,, E. G. Zoetendal,, E. Mariman,, W. M. de Vos, and, E. E. Vaughan. 2006. Proteomic analysis of log to stationary growth phase Lacto-bacillus plantarum cells and a 2-DE database. Proteomics 6: 6485– 6493.
17. De Angelis, M., R. Di Cagno,, C. Huet,, C. Crecchio,, P. F. Fox,, and M. Gobbetti. 2004. Heat shock response in Lactobacillus plantarum. Appl. Environ. Microbiol. 70: 1336– 1346.
18. de Vries, M. C. 2006. Analyzing Global Gene Expression of Lactobacillus plantarum in the Human Gastro-Intestinal Tract. Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
19. Di Cagno, R.,, M. De Angelis,, A. Limitone,, P. F. Fox, and, M. Gobbetti. 2006. Response of Lactobacillus helveticus PR4 to heat stress during propagation in cheese whey with a gradient of decreasing temperatures. Appl. Environ. Microbiol. 72: 4503– 4514.
20. Drews, O.,, G. Reil,, H. Parlar, and, A. Görg. 2004. Setting up standards and a reference map for the alkaline proteome of the Gram-positive bacterium Lactococcus lactis. Proteomics 4: 1293– 1304.
21. Drews, O.,, W. Weiss,, G. Reil,, H. Parlar,, R. Wait,, and A. Görg. 2002. High pressure effects step-wise altered protein expression in Lactobacillus sanfranciscensis. Proteomics 2: 765– 774.
22. Enan, G.,, A. A. El-Essawy,, M. Uyttendaele, and, J. Debevere. 1996. Antibacterial activity of Lactobacillus plantarum UG1 isolated from dry sausage: characterization, production and bactericidal action of plantaricin UG1. Int. J. Food Micro-biol. 30:189.
23. Eng, J. K.,, A. L. McCormack, and, J. R. Yates III. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5: 976– 989.
24. Ercolini, D.,, P. J. Hill, and, C. E. R. Dodd. 2003. Bacterial community structure and location in Stilton cheese. Appl. Environ. Microbiol. 69: 3540– 3548.
25. Feder, M. E., and, J.-C. Walser. 2005. The biological limitations of transcriptomics in elucidating stress and stress responses. J. Evol. Biol. 18: 901– 910.
26. Fenn, J. B.,, M. Mann,, C. K. Meng,, S. F. Wong, and, C. M. Whitehouse. 1989. Electrospray ionization for mass spectrometry of large biomolecules. Science 246: 64– 71.
27. Finegold, S. M.,, V. L. Sutter,, J. D. Boyle,, and K. Shimada. 1970. The normal flora of ileostomy and transverse colostomy effluents. J. Infect. Dis. 122:376.
28. Fraenkel-Conrat, H. 1994. Early days of protein chemistry. FASEB J. 8: 452– 453.
29. Frees, D.,, F. K. Vogensen, and, H. Ingmer. 2003. Identification of proteins induced at low pH in Lactococcus lactis. Int. J. Food Microbiol. 87: 293– 300.
30. Friedrich, T., and, D. Scheide. 2000. The respiratory complex I of bacteria, archaea and eukarya and its module common with membrane-bound multisubunit hydrogenases. FEBS Lett. 479: 1– 5.
31. Gill, S. R.,, M. Pop,, R. T. DeBoy,, P. B. Eckburg,, P. J. Turnbaugh,, B. S. Samuel,, J. I. Gordon,, D. A. Relman,, C. M. Fraser-Liggett, and, K. E. Nelson. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312: 1355– 1359.
32. Gitton, C.,, M. Meyrand,, J. Wang,, C. Caron,, A. Trubuil,, A. Guillot,, and M.-Y. Mistou. 2005. Proteomic signature of Lactococcus lactis NCDO763 cultivated in milk. Appl. Environ. Microbiol. 71: 7152– 7163.
33. Graves, P. R., and, T. A. J. Haystead. 2002. Molecular biologist’s guide to proteomics. Microbiol. Mol. Biol. Rev. 66: 39– 63.
34. Grus, F. H.,, V. N. Podust,, K. Bruns,, K. Lackner,, S. Fu,, E. A. Dalmasso,, A. Wirthlin,, and N. Pfeiffer. 2005. SELDITOF-MS protein chip array profiling of tears from patients with dry eye. Investig Ophthalmol. Vis. Sci. 46: 863– 876.
35. Gygi, S. P.,, Y. Rochon,, B. R. Franza, and, R. Aebersold. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19: 1720– 1730.
36. Hartke, A., S. Bouché,, J.-C. Giard,, A. Benachour,, P. Boutibonnes,, and Y. Auffray. 1996. The lactic acid stress response of Lactococcus lactis subsp. lactis. Curr. Microbiol. 33: 194– 199.
37. Hartke, A.,, J. Frère,, P. Boutibonnes, and, Y. Auffray. 1997. Differential induction of the chaperonin GroEL and the co-chaperonin GroES by heat, acid, and UV-irradiation in Lactococcus lactis subsp. lactis. Curr. Microbiol. 34: 23– 26.
38. Henzel, W. J.,, C. Watanabe, and, J. T. Stults. 2003. Protein identification: the origins of peptide mass fingerprinting. J. Am. Soc. Mass Spectrom. 14: 931– 942.
39. Hooper, L. V., and, J. I. Gordon. 2001. Commensal host-bacterial relationships in the gut. Science 292: 1115– 1118.
40. Hörmann, S.,, C. Scheyhing,, J. Behr,, M. Pavlovic,, M. Ehrmann, and, R. F. Vogel. 2006. Comparative proteome approach to characterize the high-pressure stress response of Lactobacillus sanfranciscensis DSM 20451T. Proteomics 6: 1878– 1885.
41. Hu, Q.,, R. J. Noll,, H. Li,, A. Makarov,, M. Hardman, and, R. G. Cooks. 2005. The Orbitrap: a new mass spectrometer. J. Mass Spectrom. 40: 430– 443.
42. Inagaki, N., and, K. Katsuta. 2004. Large gel two-dimensional electrophoresis: improving recovery of cellular proteome. Curr. Proteomics 1: 35– 39.
43. Jan, G.,, P. Leverrier,, V. Pichereau, and, P. Boyaval. 2001. Changes in protein synthesis and morphology during acid adaptation of Propionibacterium freudenreichii. Appl. Environ. Microbiol. 67: 2029– 2036.
44. Jensen, O. N. 2006. Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell Biol. 7: 391– 403.
45. Jensen, P. R., and, K. Hammer. 1993. Minimal requirements for exponential growth of Lactococcus lactis. Appl. Environ. Microbiol. 59: 4363– 4366.
46. Jin, L.-T.,, S.-Y. Hwang,, G.-S. Yoo, and, J.-K. Choi. 2006. A mass spectrometry compatible silver staining method for protein incorporating a new silver sensitizer in sodium dodecyl sulfate-polyacrylamide electrophoresis gels. Proteomics 6: 2334– 2337.
47. Jones, B. V., and, J. R. Marchesi. 2007. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat. Methods 4: 55– 61.
48. Kan, J.,, T. E. Hanson,, J. M. Ginter,, K. Wang,, and F. Chen. 2005. Metaproteomics analysis of Chesapeake Bay microbial communities. Saline Syst. 1:7.
49. Kanehisa, M., and, S. Goto. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28: 27– 30.
50. Klaassens, E. S., W. M. De Vos, and, E. E. Vaughan. 2007. Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl. Environ. Microbiol. 73: 1388– 1392.
51. Koistinen, K. M.,, C. Plumed-Ferrer,, S. J. Lehesranta,, S. O. Karenlampi,, and A. Von Wright. 2007. Comparison of growth-phase-dependent cytosolic proteomes of two Lacto-bacillus plantarum strains used in food and feed fermentations. FEMS Microbiol. Lett. 273: 12– 21.
52. Krutchinsky, A. N.,, M. Kalkum, and, B. T. Chait. 2001. Automatic identification of proteins with a MALDI-Quadrupole Ion Trap mass spectrometer. Anal. Chem. 73: 5066– 5077.
53. Kurokawa, K.,, T. Itoh,, T. Kuwahara,, K. Oshima,, H. Toh,, A. Toyoda,, H. Takami,, H. Morita,, V. K. Sharma,, T. P. Srivastava,, T. D. Taylor,, H. Noguchi,, H. Mori,, Y. Ogura,, D. S. Ehrlich,, K. Itoh,, T. Takagi,, Y. Sakaki,, T. Hayashi,, and M. Hattori. 2007. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14: 169– 181.
54. Lahm, H.-W., and, H. Langen. 2000. Mass spectrometry: a tool for the identification of proteins separated by gels. Electrophoresis 21: 2105– 2114.
55. Larsen, N.,, M. Boye,, H. Siegumfeldt, and, M. Jakobsen. 2006. Differential expression of proteins and genes in the lag phase of Lactococcus lactis subsp. lactis grown in synthetic medium and reconstituted skim milk. Appl. Environ. Micro-biol. 72: 1173– 1179.
56. Leverrier, P.,, D. Dimova,, V. Pichereau,, Y. Auffray,, P. Boyaval,, and G. Jan. 2003. Susceptibility and adaptive response to bile salts in Propionibacterium freudenreichii: physiological and proteomic analysis. Appl. Environ. Microbiol. 69: 3809– 3818.
57. Leverrier, P.,, J. P. C. Vissers,, A. Rouault,, P. Boyaval, and, G. Jan. 2004. Mass spectrometry proteomic analysis of stress adaptation reveals both common and distinct response pathways in Propionibacterium freudenreichii. Arch. Microbiol. 181: 215– 230.
58. Lim, E. M.,, S. D. Ehrlich, and, E. Maguin. 2000. Identification of stress-inducible proteins in Lactobacillus delbrueckii subsp. bulgaricus. Electrophoresis 21: 2557– 2561.
59. Makarov, A.,, E. Denisov,, A. Kholomeev,, W. Balschun,, O. Lange,, K. Strupat,, and S. Horning. 2006. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem. 78: 2113– 2120.
60. Makarova, K.,, A. Slesarev,, Y. Wolf,, A. Sorokin,, B. Mirkin,, E. Koonin,, A. Pavlov,, N. Pavlova,, V. Karamychev,, N. Polouchine,, V. Shakhova,, I. Grigoriev,, Y. Lou,, D. Rohksar,, S. Lucas,, K. Huang,, D. M. Goodstein,, T. Hawkins,, V. Plengvidhya,, D. Welker,, J. Hughes,, Y. Goh,, A. Benson,, K. Baldwin,, J. H. Lee,, I. Diaz-Muniz,, B. Dosti,, V. Smeianov,, W. Wechter,, R. Barabote,, G. Lorca,, E. Altermann,, R. Barrangou,, B. Ganesan,, Y. Xie,, H. Rawsthorne,, D. Tamir,, C. Parker,, F. Breidt,, J. Broadbent,, R. Hutkins,, D. O’Sullivan,, J. Steele,, G. Unlu,, M. Saier,, T. Klaenhammer,, P. Richardson,, S. Kozyavkin,, B. Weimer,, and D. Mills. 2006. Comparative genomics of the lactic acid bacteria. Proc. Natl. Acad. Sci. USA 103: 15611– 15616.
61. Manichanh, C.,, L. Rigottier-Gois,, E. Bonnaud,, K. Gloux,, E. Pelletier,, L. Frangeul,, R. Nalin,, C. Jarrin,, P. Chardon,, P. Marteau,, J. Roca,, and J. Dore. 2006. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55: 205– 211.
62. Mann, M.,, R. C. Hendrickson, and, A. Pandey. 2001. Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70: 437– 473.
63. Marceau, A.,, M. Zagorec,, S. Chaillou, T. Méra, and, M.-C. Champomier-Vergès. 2004. Evidence for involvement of at least six proteins in adaptation of Lactobacillus sakei to cold temperatures and addition of NaCl. Appl. Environ. Microbiol. 70: 7260– 7268.
64. Marshall, A. G.,, C. L. Hendrickson, and, G. S. Jackson. 1998. Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev. 17: 1– 35.
65. Martin, S. E.,, J. Shabanowitz,, D. F. Hunt, and, J. A. Marto. 2000. Subfemtomole MS and MS/MS peptide sequence analysis using Nano-HPLC Micro-ESI Fourier Transform Ion Cyclotron Resonance mass spectrometry. Anal. Chem. 72: 4266– 4274.
66. Matsui, N. M.,, D. M. Smith,, K. R. Clauser,, J. Fichmann,, L. E. Andrews,, C. M. Sullivan,, A. L. Burlingame, and, L. B. Epstein. 1997. Immobilized pH gradient two-dimensional gel electrophoresis and mass spectrometric identification of cytokine-regulated proteins in ME-180 cervical carcinoma cells. Electrophoresis 18: 409– 417.
67. Molin, G. 2001. Probiotics in foods not containing milk or milk constituents, with special reference to Lactobacillus plantarum 299v. Am. J. Clin. Nutr. 73(2 Suppl.): 380S–385S.
68. Nyström, T., and, F. C. Neidhardt. 1994. Expression and role of the universal stress protein, UspA, of Escherichia coli during growth arrest. Mol. Microbiol. 11: 537– 544.
69. O’Farrell, P. H. 1975. High resolution two-dimensional electrophoresis of proteins. J. Biochem. 250: 4007– 4021.
70. O’Sullivan, E., and, S. Condon. 1997. Intracellular pH is a major factor in the induction of tolerance to acid and other stresses in Lactococcus lactis. Appl. Environ. Microbiol. 63: 4210– 4215.
71. Patterson, S. D., and, R. H. Aebersold. 2003. Proteomics: the first decade and beyond. Nat. Genet. 33: 311– 323.
72. Peng, J., and, S. P. Gygi. 2001. Proteomics: the move to mixtures. J. Mass Spectrom. 36: 1083– 1091.
73. Pessione, E.,, R. Mazzoli,, M. G. Giuffrida,, C. Lamberti,, E. Garcia-Moruno,, C. Barello,, A. Conti,, and C. Giunta. 2005. A proteomic approach to studying biogenic amine producing lactic acid bacteria. Proteomics 5: 687– 698.
74. Pieterse, B.,, R. J. Leer,, F. H. J. Schuren, and, M. J. van der Werf. 2005. Unravelling the multiple effects of lactic acid stress on Lactobacillus plantarum by transcription profiling. Microbiology 151: 3881– 3894.
75. Rajilić-Stojanović, M. 2007. Diversity of the Human Gastrointestinal Microbiota: Novel Perspectives from High Throughput Analyses. Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
76. Ram, R. J.,, N. C. VerBerkmoes,, M. P. Thelen,, G. W. Tyson,, B. J. Baker,, R. C. Blake II,, M. Shah,, R. L. Hettich,, and J. Banfield. 2005. Community proteomics of a natural microbial biofilm. Science 308: 1915– 1920.
77. Regula, J. T.,, B. Ueberle,, G. Boguth,, A. Görg,, M. Schnölzer,, R. Herrmann,, and R. Frank. 2000. Towards a two-dimensional proteome map of Mycoplasma pneumoniae. Electrophoresis 21: 3765– 3780.
78. Roe, M. R., and, T. J. Griffin. 2006. Gel-free mass spectrometry-based high throughput proteomics: tools for studying biological response of proteins and proteomes. Proteomics 6: 4678– 4687.
79. Romero, R.,, J. Espinoza,, F. Gotsch,, J. P. Kusanovic,, L. A. Friel,, O. Erez,, S. Mazaki-Tovi,, N. G. Than,, S. Hassan,, and G. Tromp. 2006. The use of high-dimensional biology (genomics, transcriptomics, proteomics, and metabolomics) to understand the preterm parturition syndrome. BJOG 113(Suppl. 3): 118– 135.
80. Schauder, S.,, K. Shokat,, M. G. Surette, and, B. L. Bassler. 2001. The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum-sensing signal molecule. Mol. Microbiol. 41: 463– 476.
81. Singh, O. V., and, N. S. Nagaraj. 2006. Transcriptomics, proteomics and interactomics: unique approaches to track the insights of bioremediation. Brief. Funct. Genomic. Proteomic. 4: 355– 362.
82. Spano, G.,, L. Beneduce,, C. Perrotta, and, S. Massa. 2005. Cloning and characterization of the hsp 18.55 gene, a new member of the small heat shock gene family isolated from wine Lactobacillus plantarum. Res. Microbiol. 156: 219– 224.
83. Strange, K. 2005. The end of “naive reductionism”: rise of systems biology or renaissance of physiology? Am. J. Physiol. Cell Physiol. 288:C968–C974.
84. Takats, Z.,, J. M. Wiseman,, B. Gologan, and, R. G. Cooks. 2004. Mass spectrometry sampling under ambient conditions with desorption electrospray ionization. Science 306: 471– 473.
85. Tanaka, K.,, H. Waki,, Y. Ido,, S. Akita,, Y. Yoshida,, T. Yoshida,, and T. Matsuo. 1988. Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 2: 151– 153.
86. Tang, N.,, P. Tornatore, and, S. R. Weinberger. 2004. Current developments in SELDI affinity technology. Mass Spectrom. Rev. 23: 34– 44.
87. Tlaskalova-Hogenova, H.,, R. Stepankova,, T. Hudcovic,, L. Tuckova,, B. Cukrowska,, R. Lodinova-Zadnikova,, H. Kozakova,, P. Rossmann,, J. Bartova,, D. Sokol,, D. Funda,, D. Borovska,, Z. Rehakova,, J. Sinkora,, J. Hofman,, P. Drastich,, and A. Kokesova. 2004. Commensal bacteria (normal microflora), mucosal immunity and chronic inflammatory and autoimmune diseases. Immunol. Lett. 15: 97– 108.
88. Ünlü, M.,, M. E. Morgan, and, J. S. Minden. 1997. Difference gel electrophoresis. A single gel method for detecting changes in protein extracts. Electrophoresis 18: 2071– 2077.
89. van de Guchte, M.,, P. Serror,, C. Chervaux,, T. Smokvina,, S. D. Ehrlich,, and E. Maguin. 2002. Stress responses in lactic acid bacteria. Antonie Leeuwenhoek 82: 187– 216.
90. Vaughan, E. E.,, M. C. de Vries,, E. G. Zoetendal,, K. Ben-Amor,, A. D. L. Akkermans, and, W. M. de Vos. 2002. The intestinal LABs. Antonie Leeuwenhoek 82: 341– 352.
91. Vido, K.,, H. Diemer,, A. Van Dorsselaer,, E. Leize,, V. Juillard,, A. Gruss,, and P. Gaudu. 2005. Roles of thioredoxin reductase during the aerobic life of Lactococcus lactis. J. Bacteriol. 187: 601– 610.
92. Wayne, F. P. 2000. A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 21: 1123– 1144.
93. Westermeier, R., and, R. Marouga. 2005. Protein detection methods in proteomics research. Biosci. Rep. 25: 19– 32.
94. Wilmes, P., and, P. L. Bond. 2004. The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to mixed community of prokaryotic microorganisms. Environ. Microbiol. 6: 911– 920.
95. Wollnik, H. 1993. Time-of-flight mass analyzers. Mass Spectrom. Rev. 12: 89– 114.
96. Wouters, J. A.,, H. H. Kamphuis,, J. Hugenholtz,, O. P. Kuipers,, W. M. de Vos,, and T. Abee. 2000. Changes in glycolytic activity of Lactococcus lactis induced by low temperature. Appl. Environ. Microbiol. 66: 3686– 3691.
97. Yoon, K. Y.,, E. E. Woodams, and, Y. D. Hang. 2006. Production of probiotic cabbage juice by lactic acid bacteria. Bioresour. Technol. 97: 1427– 1430.
98. Zhou, J., and, D. K. Thompson. 2002. Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol. 13: 204– 207.

Tables

Proteomic Approaches To Study Lactic Acid Bacteria
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Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
/content/10.1128/9781555815462.ch16.ch16table01
Table 1
Methods used to visualize proteins by two-dimensional gel electrophoresis
Generic image for table
Table 1

Methods used to visualize proteins by two-dimensional gel electrophoresis

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
/content/10.1128/9781555815462.ch16.ch16table02
Table 2
Ionization methods and available mass spectrometers commonly used in proteomics studies
Generic image for table
Table 2

Ionization methods and available mass spectrometers commonly used in proteomics studies

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
/content/10.1128/9781555815462.ch16.ch16table03
Table 3
Proteome reference map of lactic acid bacteria
Generic image for table
Table 3

Proteome reference map of lactic acid bacteria

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
/content/10.1128/9781555815462.ch16.ch16table04
Table 4
Proteins produced by LAB as responses to different stress challenges
Generic image for table
Table 4

Proteins produced by LAB as responses to different stress challenges

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16

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