Properties of probiotic bacteria explored by proteomic approaches

Current Opinion in Microbiology

Volumn 15, Issue 3, 2012, Pages 381-389

  van de Guchte, Maarten ^a   Chaze, Thibault ^a   Jan, Gwénaël ^b   Mistou, Michel Yves ^a  

^a UMR1319 MICALIS   (France)

^b UMR1253   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROBIOTIC AGENT;

BACTERIAL STRAIN; BIFIDOBACTERIUM ANIMALIS; BIFIDOBACTERIUM BIFIDUM; BIFIDOBACTERIUM LONGUM; COMPUTER MODEL; ENTERITIS; ESCHERICHIA COLI; HEALTH PROMOTION; HUMAN; IMMUNOMODULATION; LACTOBACILLUS ACIDOPHILUS; LACTOBACILLUS CASEI; LACTOBACILLUS JOHNSONII; LACTOBACILLUS PLANTARUM; LACTOBACILLUS RHAMNOSUS; LACTOCOCCUS LACTIS; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROPIONIBACTERIUM FREUDENREICHII; PROTEOMICS; REVIEW; TANDEM MASS SPECTROMETRY;

ANIMALS; BACTERIA; BACTERIAL PROTEINS; COMPUTER SIMULATION; HUMANS; PROBIOTICS; PROTEOMICS;

ANIMALIA; BACTERIA (MICROORGANISMS);

EID: 84864033436     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2012.04.003     Document Type: Review

References (74)

1. WHO: Guidelines for the Evaluation of Probiotics in Food: Joint FAO/WHO Working Group meeting, London Ontario, Canada, 30 April-1 May 2002. http://www.who.int/foodsafety/publications/fs_management/probiotics2/en/.
2. Kok J., Buist G., Zomer A.L., van Hijum S.A., Kuipers O.P. Comparative and functional genomics of lactococci. FEMS Microbiol Rev 2005, 29:411-433.
3. Bermudez-Humaran L.G., Kharrat P., Chatel J.M., Langella P. Lactococci and lactobacilli as mucosal delivery vectors for therapeutic proteins and DNA vaccines. Microb Cell Fact 2011, 10(Suppl. 1):S4.
4. Ventura M., Turroni F., Canchaya C., Vaughan E.E., O'Toole P.W., van Sinderen D. Microbial diversity in the human intestine and novel insights from metagenomics. Front Biosci 2009, 14:3214-3221.
5. Fernandez A., Ogawa J., Penaud S., Boudebbouze S., Ehrlich D., van de Guchte M., Maguin E. Rerouting of pyruvate metabolism during acid adaptation in Lactobacillus bulgaricus. Proteomics 2008, 8:3154-3163.
6. Koponen J., Laakso K., Koskenniemi K., Kankainen M., Savijoki K., Nyman T.A., de Vos W.M., Tynkkynen S., Kalkkinen N., Varmanen P. Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG. J Proteomics 2011, 75:1357-1374.
7. Lee K., Lee H.G., Pi K., Choi Y.J. The effect of low pH on protein expression by the probiotic bacterium Lactobacillus reuteri. Proteomics 2008, 8:1624-1630.
8. Budin-Verneuil A., Pichereau V., Auffray Y., Ehrlich D., Maguin E. Proteome phenotyping of acid stress-resistant mutants of Lactococcus lactis MG1363. Proteomics 2007, 7:2038-2046.
9. Ashida N., Yanagihara S., Shinoda T., Yamamoto N. Characterization of adhesive molecule with affinity to Caco-2 cells in Lactobacillus acidophilus by proteome analysis. J Biosci Bioeng 2011, 112:333-337.
10. Beganovic J., Guillot A., van de Guchte M., Jouan A., Gitton C., Loux V., Roy K., Huet S., Monod H., Monnet V. Characterization of the insoluble proteome of Lactococcus lactis by SDS-PAGE LC-MS/MS leads to the identification of new markers of adaptation of the bacteria to the mouse digestive tract. J Proteome Res 2010, 9:677-688.
11. Bergonzelli G.E., Granato D., Pridmore R.D., Marvin-Guy L.F., Donnicola D., Corthesy-Theulaz I.E. GroEL of Lactobacillus johnsonii La1 (NCC 533) is cell surface associated: potential role in interactions with the host and the gastric pathogen Helicobacter pylori. Infect Immun 2006, 74:425-434.
12. Koskenniemi K., Koponen J., Kankainen M., Savijoki K., Tynkkynen S., de Vos W.M., Kalkkinen N., Varmanen P. Proteome analysis of Lactobacillus rhamnosus GG using 2-D DIGE and mass spectrometry shows differential protein production in laboratory and industrial-type growth media. J Proteome Res 2009, 8:4993-5007.
13. Majumder A., Sultan A., Jersie-Christensen R.R., Ejby M., Schmidt B.G., Lahtinen S.J., Jacobsen S., Svensson B. Proteome reference map of Lactobacillus acidophilus NCFM and quantitative proteomics towards understanding the prebiotic action of lactitol. Proteomics 2011, 11:3470-3481.
14. Wu R., Wang W., Yu D., Zhang W., Li Y., Sun Z., Wu J., Meng H., Zhang H. Proteomics analysis of Lactobacillus casei Zhang, a new probiotic bacterium isolated from traditional home-made koumiss in Inner Mongolia of China. Mol Cell Proteomics 2009, 8:2321-2338.
15. Leitner A., Sturm M., Lindner W. Tools for analyzing the phosphoproteome and other phosphorylated biomolecules: a review. Anal Chim Acta 2011, 703:19-30.
16. Soufi B., Gnad F., Jensen P.R., Petranovic D., Mann M., Mijakovic I., Macek B. The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins. Proteomics 2008, 8:3486-3493.
17. Mijakovic I., Macek B. Impact of phosphoproteomics on studies of bacterial physiology. FEMS Microbiol Rev 2011.
18. Hamon E., Horvatovich P., Bisch M., Bringel F., Marchioni E., Aoude-Werner D., Ennahar S. Investigation of biomarkers of bile tolerance in Lactobacillus casei using comparative proteomics. J Proteome Res 2012, 11:109-118.
19. Hamon E., Horvatovich P., Izquierdo E., Bringel F., Marchioni E., Aoude-Werner D., Ennahar S. Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance. BMC Microbiol 2011, 11:63.
20. Koskenniemi K., Laakso K., Koponen J., Kankainen M., Greco D., Auvinen P., Savijoki K., Nyman T.A., Surakka A., Salusjarvi T., et al. Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. Mol Cell Proteomics 2010, 10. M110 002741.
21. Leverrier P., Dimova D., Pichereau V., Auffray Y., Boyaval P., Jan G. Susceptibility and adaptive response to bile salts in Propionibacterium freudenreichii: physiological and proteomic analysis. Appl Environ Microbiol 2003, 69:3809-3818.
22. Sanchez B., Champomier-Verges M.C., Stuer-Lauridsen B., Ruas-Madiedo P., Anglade P., Baraige F., de los Reyes-Gavilan C.G., Johansen E., Zagorec M., Margolles A. Adaptation and response of Bifidobacterium animalis subsp. lactis to bile: a proteomic and physiological approach. Appl Environ Microbiol 2007, 73:6757-6767.
23. Wu R., Zhang W., Sun T., Wu J., Yue X., Meng H., Zhang H. Proteomic analysis of responses of a new probiotic bacterium Lactobacillus casei Zhang to low acid stress. Int J Food Microbiol 2011, 147:181-187.
24. Roy K., Anba J., Corthier G., Rigottier-Gois L., Monnet V., Mistou M.Y. Metabolic adaptation of Lactococcus lactis in the digestive tract: the example of response to lactose. J Mol Microbiol Biotechnol 2008, 14:137-144.
25. Roy K., Meyrand M., Corthier G., Monnet V., Mistou M.Y. Proteomic investigation of the adaptation of Lactococcus lactis to the mouse digestive tract. Proteomics 2008, 8:1661-1676.
26. Yuan J., Wang B., Sun Z., Bo X., Yuan X., He X., Zhao H., Du X., Wang F., Jiang Z., et al. Analysis of host-inducing proteome changes in bifidobacterium longum NCC2705 grown in vivo. J Proteome Res 2008, 7:375-385.
27. Sanchez B., Champomier-Verges M.C., Anglade P., Baraige F., de Los Reyes-Gavilan C.G., Margolles A., Zagorec M. Proteomic analysis of global changes in protein expression during bile salt exposure of Bifidobacterium longum NCIMB 8809. J Bacteriol 2005, 187:5799-5808.
28. Sanchez B., Noriega L., Ruas-Madiedo P., de los Reyes-Gavilan C.G., Margolles A. Acquired resistance to bile increases fructose-6-phosphate phosphoketolase activity in Bifidobacterium. FEMS Microbiol Lett 2004, 235:35-41.
29. Lan A., Bruneau A., Bensaada M., Philippe C., Bellaud P., Rabot S., Jan G. Increased induction of apoptosis by Propionibacterium freudenreichii TL133 in colonic mucosal crypts of human microbiota-associated rats treated with 1,2-dimethylhydrazine. Br J Nutr 2008, 100:1251-1259.
30. Yu N.Y., Wagner J.R., Laird M.R., Melli G., Rey S., Lo R., Dao P., Sahinalp S.C., Ester M., Foster L.J., et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 2010, 26:1608-1615.
31. Barinov A., Loux V., Hammani A., Nicolas P., Langella P., Ehrlich D., Maguin E., van de Guchte M. Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria. Proteomics 2009, 9:61-73.
32. Bendtsen J.D., Nielsen H., von Heijne G., Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340:783-795.
33. Hunter S., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bork P., Das U., Daugherty L., Duquenne L., et al. InterPro: the integrative protein signature database. Nucleic Acids Res 2009, 37:D211-D215.
34. Eddy S.R. Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
35. Marraffini L.A., Dedent A.C., Schneewind O. Sortases and the art of anchoring proteins to the envelopes of gram-positive bacteria. Microbiol Mol Biol Rev 2006, 70:192-221.
36. Konstantinov S.R., Smidt H., de Vos W.M., Bruijns S.C., Singh S.K., Valence F., Molle D., Lortal S., Altermann E., Klaenhammer T.R., et al. S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions. Proc Natl Acad Sci USA 2008, 105:19474-19479.
37. Henderson B., Martin A. Bacterial virulence in the moonlight: multitasking bacterial moonlighting proteins are virulence determinants in infectious disease. Infect Immun 2011, 79:3476-3491.
38. Baranova I.N., Vishnyakova T.G., Bocharov A.V., Leelahavanichkul A., Kurlander R., Chen Z., Souza A.C., Yuen P.S., Star R.A., Csako G., et al. Class B scavenger receptor types I and II and CD36 mediate bacterial recognition and proinflammatory signaling induced by Escherichia coli, lipopolysaccharide, and cytosolic chaperonin 60. J Immunol 2012, 188:1371-1380.
39. Savijoki K., Lietzen N., Kankainen M., Alatossava T., Koskenniemi K., Varmanen P., Nyman T.A. Comparative proteome cataloging of Lactobacillus rhamnosus strains GG and Lc705. J Proteome Res 2011, 10:3460-3473.
40. Gilad O., Svensson B., Viborg A.H., Stuer-Lauridsen B., Jacobsen S. The extracellular proteome of Bifidobacterium animalis subsp. lactis BB-12 reveals proteins with putative roles in probiotic effects. Proteomics 2011, 11:2503-2514.
41. Gilad O., Hjerno K., Osterlund E.C., Margolles A., Svensson B., Stuer-Lauridsen B., Moller A.L., Jacobsen S. Insights into physiological traits of Bifidobacterium animalis subsp. lactis BB-12 through membrane proteome analysis. J Proteomics 2011, 75:1190-1200.
42. Candela M., Centanni M., Fiori J., Biagi E., Turroni S., Orrico C., Bergmann S., Hammerschmidt S., Brigidi P. DnaK from Bifidobacterium animalis subsp. lactis is a surface-exposed human plasminogen receptor upregulated in response to bile salts. Microbiology 2010, 156:1609-1618.
43. Ruiz L., Coute Y., Sanchez B., de los Reyes-Gavilan C.G., Sanchez J.C., Margolles A. The cell-envelope proteome of Bifidobacterium longum in an in vitro bile environment. Microbiology 2009, 155:957-967.
44. Guglielmetti S., Tamagnini I., Mora D., Minuzzo M., Scarafoni A., Arioli S., Hellman J., Karp M., Parini C. Implication of an outer surface lipoprotein in adhesion of Bifidobacterium bifidum to Caco-2 cells. Appl Environ Microbiol 2008, 74:4695-4702.
45. Ton-That H., Marraffini L.A., Schneewind O. Protein sorting to the cell wall envelope of Gram-positive bacteria. Biochim Biophys Acta 2004, 1694:269-278.
46. Dramsi S., Trieu-Cuot P., Bierne H. Sorting sortases: a nomenclature proposal for the various sortases of Gram-positive bacteria. Res Microbiol 2005, 156:289-297.
47. Lofling J., Vimberg V., Battig P., Henriques-Normark B. Cellular interactions by LPxTG-anchored pneumococcal adhesins and their streptococcal homologues. Cell Microbiol 2011, 13:186-197.
48. Dieye Y., Oxaran V., Ledue-Clier F., Alkhalaf W., Buist G., Juillard V., Lee C.W., Piard J.C. Functionality of sortase A in Lactococcus lactis. Appl Environ Microbiol 2010, 76:7332-7337.
49. Berlec A., Zadravec P., Jevnikar Z., Strukelj B. Identification of candidate carrier proteins for surface display on Lactococcus lactis by theoretical and experimental analyses of the surface proteome. Appl Environ Microbiol 2011, 77:1292-1300.
50. Iwasaki M., Miwa S., Ikegami T., Tomita M., Tanaka N., Ishihama Y. One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. Anal Chem 2010, 82:2616-2620.
51. Valot B., Langella O., Nano E., Zivy M. MassChroQ: a versatile tool for mass spectrometry quantification. Proteomics 2011, 11:3572-3577.
52. Mueller L.N., Brusniak M.Y., Mani D.R., Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res 2008, 7:51-61.
53. Dreisbach A., van Dijl J.M., Buist G. The cell surface proteome of Staphylococcus aureus. Proteomics 2011, 11:3154-3168.
54. Doro F., Liberatori S., Rodriguez-Ortega M.J., Rinaudo C.D., Rosini R., Mora M., Scarselli M., Altindis E., D'Aurizio R., Stella M., et al. Surfome analysis as a fast track to vaccine discovery: identification of a novel protective antigen for Group B Streptococcus hypervirulent strain COH1. Mol Cell Proteomics 2009, 8:1728-1737.
55. Guandalini S. Probiotics for prevention and treatment of diarrhea. J Clin Gastroenterol 2011, 45(Suppl.):S149-S153.
56. Wallace T.C., Guarner F., Madsen K., Cabana M.D., Gibson G., Hentges E., Sanders M.E. Human gut microbiota and its relationship to health and disease. Nutr Rev 2011, 69:392-403.
57. Hamon E., Horvatovich P., Bisch M., Bringel F., Marchioni E., Aoude-Werner D., Ennahar S. Investigation of biomarkers of bile tolerance in Lactobacillus casei using comparative proteomics. J Proteome Res 2011, 11:109-118.
58. Zhang W., Yu D., Sun Z., Wu R., Chen X., Chen W., Meng H., Hu S., Zhang H. Complete genome sequence of Lactobacillus casei Zhang, a new probiotic strain isolated from traditional homemade koumiss in Inner Mongolia, China. J Bacteriol 2010, 192:5268-5269.
59. Wu R., Sun Z., Wu J., Meng H., Zhang H. Effect of bile salts stress on protein synthesis of Lactobacillus casei Zhang revealed by 2-dimensional gel electrophoresis. J Dairy Sci 2010, 93:3858-3868.
60. Marco M.L., de Vries M.C., Wels M., Molenaar D., Mangell P., Ahrne S., de Vos W.M., Vaughan E.E., Kleerebezem M. Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice. ISME J 2010, 4:1481-1484.
61. Ruiz L., Sanchez B., de Los Reyes-Gavilan C.G., Gueimonde M., Margolles A. Coculture of Bifidobacterium longum and Bifidobacterium breve alters their protein expression profiles and enzymatic activities. Int J Food Microbiol 2009, 133:148-153.
62. Gorg A., Weiss W., Dunn M.J. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004, 4:3665-3685.
63. Wittig I., Schagger H. Native electrophoretic techniques to identify protein-protein interactions. Proteomics 2009, 9:5214-5223.
64. Alban A., David S.O., Bjorkesten L., Andersson C., Sloge E., Lewis S., Currie I. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 2003, 3:36-44.
65. Marouga R., David S., Hawkins E. The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 2005, 382:669-678.
66. Roe M.R., Griffin T.J. Gel-free mass spectrometry-based high throughput proteomics: tools for studying biological response of proteins and proteomes. Proteomics 2006, 6:4678-4687.
67. Domon B., Aebersold R. Mass spectrometry and protein analysis. Science 2006, 312:212-217.
68. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376.
69. Kruger M., Moser M., Ussar S., Thievessen I., Luber C.A. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 2008, 134:353.
70. Mann M. Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 2006, 7:952-958.
71. Carvalho P.C., Hewel J., Barbosa V.C., Yates J.R. Identifying differences in protein expression levels by spectral counting and feature selection. Genet Mol Res 2008, 7:342-356.
72. Neilson K.A., Ali N.A., Muralidharan S., Mirzaei M., Mariani M., Assadourian G., Lee A., van Sluyter S.C., Haynes P.A. Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011, 11:535-553.
73. Solis N., Cordwell S.J. Current methodologies for proteomics of bacterial surface-exposed and cell envelope proteins. Proteomics 2011, 11:3169-3189.
74. Righetti P.G., Castagna A., Antonioli P., Boschetti E. Prefractionation techniques in proteome analysis: the mining tools of the third millennium. Electrophoresis 2005, 26:297-319.