Mechanistic peptidomics: Factors that dictate specificity in the formation of endogenous peptides in human milk

Molecular and Cellular Proteomics

Volumn 13, Issue 12, 2014, Pages 3343-3351

  Guerrero, Andres ^a   Dallas, David C ^a   Contreras, Stephanie ^a   Chee, Sabrina ^a   Parker, Evan A ^a   Sun, Xin ^a   Dimapasoc, Lauren ^a   Barile, Daniela ^a   German, J Bruce ^a   Lebrilla, Carlito B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA CASEIN; CASEIN KINASE IALPHA; MILK PROTEIN; OSTEOPONTIN; PROTEINASE; SECRETORY COMPONENT; PEPTIDE; PROTEOME;

AMINO ACID SEQUENCE; ARTICLE; BREAST MILK; ENZYME ACTIVITY; ENZYME SPECIFICITY; FEMALE; HUMAN; IN VIVO STUDY; LACTATION; MAMMARY GLAND; MASS SPECTROMETRY; NORMAL HUMAN; PEPTIDOMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN DEGRADATION; PROTEIN HYDROLYSIS; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; PEPTIDE MAPPING;

AMINO ACID SEQUENCE; ENDOPEPTIDASES; FEMALE; HUMANS; MILK PROTEINS; MILK, HUMAN; MOLECULAR SEQUENCE DATA; PEPTIDE MAPPING; PEPTIDES; PROTEOLYSIS; PROTEOME; SUBSTRATE SPECIFICITY;

EID: 84924721660     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M113.036194     Document Type: Article

References (59)

1. Schulz-Knappe, P., Schrader, M., and Zucht, H.-D. (2005) The peptidomics concept. Combinat. Chem. High Throughput Screening 8, 697-704
2. Cunningham, R., Ma, D., and Li, L. (2012) Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery. Front. Biol. 7, 313-335
3. Shen, Y., Liu, T., Tolicì, N., Petritis, B. O., Zhao, R., Moore, R. J., Purvine, S. O., Camp, D. G., and Smith, R. D. (2010) Strategy for degradomicpeptidomic analysis of human blood plasma. J. Proteome Res. 9, 2339-2346
4. Wiltfang, J., Esselmann, H., Smirnov, A., Bibl, M., Cepek, L., Steinacker, P., Mollenhauer, B., Buerger, K., Hampel, H., Paul, S., Neumann, M., Maler, M., Zerr, I., Kornhuber, J., Kretzschmar, H. A., Poser, S., and Otto, M. (2003) β-amyloid peptides in cerebrospinal fluid of patients with Creutzfeldt-Jakob disease. Ann. Neurol. 54, 263-267
5. Huang, C.-M., and Zhu, W. (2009) Profiling human saliva endogenous peptidome via a high throughput MALDI-TOF-TOF mass spectrometry. Combinat. Chem. High Throughput Screening 12, 521-531
6. Messana, I., Cabras, T., Pisano, E., Sanna, M. T., Olianas, A., Manconi, B., Pellegrini, M., Paludetti, G., Scarano, E., Fiorita, A., Agostino, S., Contucci, A. M., Calò, L., Picciotti, P. M., Manni, A., Bennick, A., Vitali, A., Fanali, C., Inzitari, R., and Castagnola, M. (2008) Trafficking and postsecretory events responsible for the formation of secreted human salivary peptides: a proteomics approach. Mol. Cell. Proteomics 7, 911-926
7. Hayakawa, E., Landuyt, B., Baggerman, G., Cuyvers, R., Lavigne, R., Luyten, W., and Schoofs, L. (2013) Peptidomic analysis of human reflex tear fluid. Peptides 42, 63-69
8. Jurgens, M., Appel, A., Heine, G., Neitz, S., Menzel, C., Tammen, H., and Zucht, H.-D. (2005) Towards characterization of the human urinary peptidome. Combinat. Chem. High Throughput Screening 8, 757-765
9. Shen, Y., Tolić, N., Liu, T., Zhao, R., Petritis, B. O., Gritsenko, M. A., Camp, D. G., Moore, R. J., Purvine, S. O., Esteva, F. J., and Smith, R. D. (2010) Blood peptidome-degradome profile of breast cancer. PLoS One 5, e13133
10. Ling, X. B., Mellins, E. D., Sylvester, K. G., and Cohen, H. J. (2010) Urine peptidomics for clinical biomarker discovery. Advances in Clinical Chemistry (Gregory, S. M., Ed), Vol. 51, pp. 181-213, Elsevier, London, UK
11. Wen, Q., Liu, L. Y., Yang, T., Alev, C., Wu, S., Stevenson, D. K., Sheng, G., Butte, A. J., and Ling, X. B. (2013) Peptidomic identification of serum peptides diagnosing preeclampsia. PLoS One 8, e65571
12. Quintana, L. F., Campistol, J. M., Alcolea, M. P., Bañon-Maneus, E., Sol-González, A., and Cutillas, P. R. (2009) Application of label-free quantitative peptidomics for the identification of urinary biomarkers of kidney chronic allograft dysfunction. Mol. Cell. Proteomics 8, 1658-1673
13. Villanueva, J., Martorella, A. J., Lawlor, K., Philip, J., Fleisher, M., Robbins, R. J., and Tempst, P. (2006) Serum peptidome patterns that distinguish metastatic thyroid carcinoma from cancer-free controls are unbiased by gender and age. Mol. Cell. Proteomics 5, 1840-1852
14. Sasaki, K., Takahashi, N., Satoh, M., Yamasaki, M., and Minamino, N.(2010) A peptidomics strategy for discovering endogenous bioactive peptides. J. Proteome Res. 9, 5047-5052
15. Svensson, M., Sköld, K., Svenningsson, P., and Andren, P. E. (2003) Peptidomics-based discovery of novel neuropeptides. J. Proteome Res. 2, 213-219
16. Tamvakopoulos, C. (2007) Mass spectrometry for the quantification of bioactive peptides in biological fluids. Mass Spectrom. Rev. 26, 389-402
17. Bernay, B., Gaillard, M.-C., Guryča, V., Emadali, A., Kuhn, L., Bertrand, A., Detraz, I., Carcenac, C., Savasta, M., Brouillet, E., Garin, J., and Elalouf, J.-M. (2009) Discovering new bioactive neuropeptides in the striatum secretome using in vivo microdialysis and versatile proteomics. Mol. Cell. Proteomics 8, 946-958
18. Villanueva, J., Shaffer, D. R., Philip, J., Chaparro, C. A., Erdjument-Bromage, H., Olshen, A. B., Fleisher, M., Lilja, H., Brogi, E., Boyd, J., Sanchez-Carbayo, M., Holland, E. C., Cordon-Cardo, C., Scher, H. I., and Tempst, P. (2006) Differential exoprotease activities confer tumor-specific serum peptidome patterns. J. Clin. Invest. 116, 271-284
19. Diamandis, E. P. (2006) Peptidomics for cancer diagnosis: present and future. J. Proteome Res. 5, 2079-2082
20. Ferranti, P., Traisci, M. V., Picariello, G., Nasi, A., Boschi, V., Siervo, M., Falconi, C., Chianese, L., and Addeo, F. (2004) Casein proteolysis in human milk: tracing the pattern of casein breakdown and the formation of potential bioactive peptides. J. Dairy Res. 71, 74-87
21. Timmer, J. C., Zhu, W., Pop, C., Regan, T., Snipas, S. J., Eroshkin, A. M., Riedl, S. J., and Salvesen, G. S. (2009) Structural and kinetic determinants of protease substrates. Nat. Struct. Mol. Biol. 16, 1101-1108
22. Hubbard, S. J. (1998) The structural aspects of limited proteolysis of native proteins. Biochim. Biophys. Acta Protein Struct. Mol. Enzymol. 1382, 191-206
23. Novotný;, J., and Bruccoleri, R. E. (1987) Correlation among sites of limited proteolysis, enzyme accessibility and segmental mobility. FEBS Lett. 211, 185-189
24. Kazanov, M. D., Igarashi, Y., Eroshkin, A. M., Cieplak, P., Ratnikov, B., Zhang, Y., Li, Z., Godzik, A., Osterman, A. L., and Smith, J. W. (2011) Structural determinants of limited proteolysis. J. Proteome Res. 10, 3642-3651
25. Seppo, L., Jauhiainen, T., Poussa, T., and Korpela, R. (2003) A fermented milk high in bioactive peptides has a blood pressure-lowering effect in hypertensive subjects. Am. J. Clin. Nutrition 77, 326-330
26. Matar, C., Amiot, J., Savoie, L., and Goulet, J. (1996) The effect of milk fermentation by Lactobacillus helveticus on the release of peptides during in vitro digestion. J. Dairy Sci. 79, 971-979
27. Smacchi, E., and Gobbetti, M. (2000) Bioactive peptides in dairy products: synthesis and interaction with proteolytic enzymes. Food Microbiol. 17, 129-141
28. Argyri, K., Miller, D. D., Glahn, R. P., Zhu, L., and Kapsokefalou, M. (2007) Peptides isolated from in vitro digests of milk enhance iron uptake by caco-2 cells. J. Agric. Food Chem. 55, 10221-10225
29. Ye, A., Cui, J., and Singh, H. (2011) Proteolysis of milk fat globule membrane proteins during in vitro gastric digestion of milk. J. Dairy Sci. 94, 2762-2770
30. Picariello, G., Ferranti, P., Fierro, O., Mamone, G., Caira, S., Di Luccia, A., Monica, S., and Addeo, F. (2010) Peptides surviving the simulated gastrointestinal digestion of milk proteins: biological and toxicological implications. J. Chromatogr. B 878, 295-308
31. Clare, D. A., and Swaisgood, H. E. (2000) Bioactive milk peptides: a prospectus. J. Dairy Sci. 83, 1187-1195
32. Bellamy, W., Takase, M., Wakabayashi, H., Kawase, K., and Tomita, M. (1992) Antibacterial spectrum of lactoferricin B, a potent bactericidal peptide derived from the N-terminal region of bovine lactoferrin. J. Appl. Bacteriol. 73, 472-479
33. Benkerroum, N. (2010) Antimicrobial peptides generated from milk proteins: a survey and prospects for application in the food industry. A review. Int. J. Dairy Technol. 63, 320-338
34. FitzGerald, R. J., Murray, B. A., and Walsh, D. J. (2004) Hypotensive peptides from milk proteins. J. Nutrition 134, 980S-988S
35. Jäkälä, P., and Vapaatalo, H. (2010) Antihypertensive peptides from milk proteins. Pharmaceuticals 3, 251-272
36. Politis, I., and Chronopoulou, R. (2008) Milk peptides and immune response in the neonate. Bioactive Components of Milk (Bösze, Z., Ed), Vol 606, pp. 253-269, Springer, New York
37. Huang, S.-M., Chen, K.-N., Chen, Y.-P., Hong, W.-S., and Chen, M.-J. (2010) Immunomodulatory properties of the milk whey products obtained by enzymatic and microbial hydrolysis. Int. J. Food Sci. Technol. 45, 1061-1067
38. Meisel, H., and FitzGerald, R. J. (2000) Opioid peptides encrypted in intact milk protein sequences. Br. J. Nutrition 84 (Supplement S1), 27-31
39. Christensen, B., Schack, L., Kläning, E., and Sorensen, E. S. (2010) Osteopontin is cleaved at multiple sites close to its integrin-binding motifs in milk and is a novel substrate for plasmin and cathepsin D. J. Biol. Chem. 285, 7929-7937
40. Dallas, D. C., Guerrero, A., Khaldi, N., Castillo, P. A., Martin, W. F., Smilowitz, J. T., Bevins, C. L., Barile, D., German, J. B., and Lebrilla, C. B. (2013) Extensive in vivo human milk peptidomics reveals specific proteolysis yielding protective antimicrobial peptides. J. Proteome Res. 12, 2295-2304
41. Smith, P. K., Krohn, R. I., Hermanson, G. T., Mallia, A. K., Gartner, F. H., Provenzano, M. D., Fujimoto, E. K., Goeke, N. M., Olson, B. J., and Klenk, D. C. (1985) Measurement of protein using bicinchoninic acid. Anal. Biochem. 150, 76-85
42. Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467
43. Molinari, C. E., Casadio, Y. S., Hartmann, B. T., Livk, A., Bringans, S., Arthur, P. G., and Hartmann, P. E. (2012) Proteome mapping of human skim milk proteins in term and preterm milk. J. Proteome Res. 11, 1696-1714
44. Mange, A., Bellet, V., Tuaillon, E., Van de Perre, P., and Solassol, J. (2008) Comprehensive proteomic analysis of the human milk proteome: contribution of protein fractionation. J. Chromatogr. B 876, 252-256
45. Liao, Y., Alvarado, R., Phinney, B., and Lonnerdal, B. (2011) Proteomic characterization of human milk fat globule membrane proteins during a 12 month lactation period. J. Proteome Res. 10, 3530-3541
46. Peng, K., Vucetic, S., Radivojac, P., Brown, C. J., Dunker, A. K., and Obradovic, Z. (2005) Optimizing long intrinsic disorder predictors with protein evolutionary information. J. Bioinformat. Comput. Biol. 03, 35-60
47. Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., and Bairoch, A. (2005) Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook, Humana Press, 571-607
48. Korycha-Dahl, M., Dumas, B. R., Chene, N., and Martal, J. (1983) Plasmin activity in milk. J. Dairy Sci. 66, 704-711
49. Monti, J. C., Mermoud, A. F., and Jollès, P. (1986) Trypsin in human milk. Experientia 42, 39-41
50. Borulf, S., Lindberg, T., and Mansson, M. (1987) Immunoreactive anionic trypsin and anionic elastase in human milk. Acta Pædiatr. 76, 11-15
51. Vetvicka, V., Vagner, J., Baudys, M., Tang, J., Foundling, S. I., and Fusek, M. (1993) Human breast milk contains procathepsin D-detection by specific antibodies. Biochem. Mol. Biol. Int. 30, 921-928
52. Tompa, P. (2002) Intrinsically unstructured proteins. Trends Biochem. Sci. 27, 527-533
53. Kaetzel, C. S. (2005) The polymeric immunoglobulin receptor: bridging innate and adaptive immune responses at mucosal surfaces. Immunol. Rev. 206, 83-99
54. Asher, G., Reuven, N., and Shaul, Y. (2006) 20S proteasomes and protein degradation "by default." Bioessays 28, 844-849
55. Minervini, F., Algaron, F., Rizzello, C. G., Fox, P. F., Monnet, V., and Gobbetti, M. (2003) Angiotensin I-converting-enzyme-inhibitory and antibacterial peptides from Lactobacillus helveticus PR4 proteinase-hydrolyzed caseins of milk from six species. Appl. Environ. Microbiol. 69, 5297-5305
56. Lönnerdal, B. (2013) Bioactive proteins in breast milk. J. Paediatr. Child Health 49, 1-7
57. Lund, S., Giachelli, C., and Scatena, M. (2009) The role of osteopontin in inflammatory processes. J. Cell Commun. Signal. 3, 311-322
58. Koomen, J. M., Li, D., Xiao, L.-c., Liu, T. C., Coombes, K. R., Abbruzzese, J., and Kobayashi, R. (2005) Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J. Proteome Res. 4, 972-981
59. Gelman, J. S., Sironi, J., Castro, L. M., Ferro, E. S., and Fricker, L. D. (2011) Peptidomic analysis of human cell lines. J. Proteome Res. 10, 1583-1592