Interactions between proteins and humic substances affect protein identification by mass spectrometry

Biology and Fertility of Soils

Volumn 50, Issue 3, 2014, Pages 447-454

  Arenella, Mariarita ^a   Giagnoni, Laura ^a   Masciandaro, Grazia ^b   Ceccanti, Brunello ^b   Nannipieri, Paolo ^a   Renella, Giancarlo ^a  

^a UNIVERSITY OF FLORENCE   (Italy)

^b CNR   (Italy)

Author keywords

Humic substances; Mass spectrometry; Proteins in soil; Soil proteomics

Indexed keywords

ELECTROKINESIS; ENZYME ACTIVITY; HUMIC SUBSTANCE; MASS SPECTROMETRY; PROTEIN; PROTEOMICS; SOIL ANALYSIS; SOIL ORGANIC MATTER;

EID: 84897496489     PISSN: 01782762     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00374-013-0860-0     Document Type: Article

References (41)

1. Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 13: 198-207.
2. Bremner JM (1951) A review of recent work on soil organic matter. J Soil Sci 2: 67-82.
3. Calamai L, Lozzi I, Ristori GG, Fusi P, Stotzky G (2000) Interaction of catalase with montmorillonite homoionic to cations with different hydrophobicity: effect on bound enzyme activity. Soil Biol Biochem 32: 815-823.
4. Chourey K, Jansson J, VerBerkmoes N, Shah M, Chavarria KL, Tom LM, Brodie EL, Hettich RL (2010) Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome Res 9: 6615-6622.
5. Dani FR, Michelucci E, Francese S, Mastrobuoni G, Cappellozza S, La Marca G, Niccolini A, Felicioli A, Moneti G, Pelosi P (2011) Odorant-binding proteins and chemosensory proteins in pheromone detection and release in the Silkmoth Bombyx mori. Chem Senses 36: 335-344.
6. Daniel JM, Friess SD, Rajagopalan S, Wendt S, Zenobi R (2002) Quantitative determination of noncovalent binding interactions using soft ionization mass spectrometry. Int J Mass Spectrom 216: 1-27.
7. De Kruif CG, Weinbreck F, De Vries R (2004) Complex coacervation of proteins and anionic polysaccharides. Curr Opin Colloid Interface Sci 9: 340-349.
8. Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Martin L, Nesvizhskii AI, Aebersold R (2010) A guided tour of the Trans-Proteomic Pipeline. Proteomics 10: 1150-1159.
9. Ding F, Diao JX, Yang XL, Sun Y (2011) Structural analysis and binding domain of albumin complexes with natural dietary supplement humic acid. J Lumin 131: 2244-2251.
10. Giagnoni L, Magherini F, Landi L, Taghavi S, Modesti A, Bini L, Nannipieri P, van der Lelie D, Renella G (2011) Extraction of microbial proteome from soil: potential and limitations assessed through a model study. Eur J Soil Sci 62: 74-81.
11. Giagnoni L, Magherini F, Landi L, Taghavi S, van der Lelie D, Puglia M, Bianchi L, Bini L, Nannipieri P, Renella G, Modesti A (2012) Soil solid phases effects on the proteomic analysis of Cupriavidus metallidurans CH34. Biol Fertil Soils 48: 425-433.
12. Haynes CA, Norde WJ (1995) Structures and stabilities of adsorbed proteins. J Colloid Interface Sci 169: 313-328.
13. Hsu PH, Hatcher PG (2005) New evidence for covalent coupling of peptides to humic acids based on 2D NMR spectroscopy: a means for preservation. Geochim Cosmochim Acta 69: 4521-4533.
14. Keller M, Hettich R (2009) Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol Mol Biol Rev 73: 62-70.
15. Kim KH, Brown KM, Harris PV, Langston JA, Cherry JR (2007) A proteomics strategy to discover β-glucosidases from Aspergillus fumigatus with two-dimensional page in-gel activity assay and tandem mass spectrometry. J Proteome Res 6: 4749-4757.
16. Krause F (2006) Detection and analysis of protein-protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (membrane) protein complexes and supercomplexes. Electrophoresis 27: 2759-2781.
17. Kyte J, Doolittle RA (1982) Simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
18. Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 15: 680-685.
19. Li XJ, Pedrioli PA, Eng J, Martin D, Yi EC, Lee H, Aebersold RA (2004) Tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal Chem 76: 3856-3860.
20. Mayaudon J (1986) The role of carbohydrates in the free enzymes in soil. In: Fuschman CH (ed) Peat and water. Elsevier, London, pp 263-309.
21. Nannipieri P (2006) Role of stabilized enzymes in microbial ecology and enzyme extraction from soil with potential applications in nucleic acids and proteins in soils. In: Smalla K, Nannipieri P (eds) Nucleic acids and proteins in soil. Soil Biology, Springer, Berlin, pp 75-94.
22. Nannipieri P, Sequi P, Fusi P (1996) Humus and enzyme activity. In: Piccolo A (ed) Humic substances in terrestrial ecosystem. Elsevier, Amsterdam, pp 293-323.
23. Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Eur J Soil Sci 54: 655-670.
24. Nebbioso A, Piccolo A, Spiteller M (2010) Limitations of electrospray ionization in the analysis of a heterogeneous mixture of naturally occurring hydrophilic and hydrophobic compounds. Rapid Commun Mass Spectrom 24: 3163-3170.
25. Norde W (1996) Driving forces for protein adsorption at solid surfaces. Macromol Symp 103: 5-18.
26. Ogawa M, Nishio T, Minoura K, Uozumi T, Wada M, Hashimoto N, Kawachi R, Oku T (2006) Physical and kinetic properties of the family 3 beta-glucosidase from Aspergillus niger which is important for cellulose breakdown. J Appl Glycosci 53: 13-16.
27. Perkins DN, Pappin DJC, Creasy DM, Cottrel JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-3567.
28. Piccolo A (2001) The supramolecular structure of humic substances. Soil Sci 166: 810-832.
29. Pramanik BN, Bartner PL, Mirza UA, Liu YH, Ganguly AK (1998) Electrospray ionization mass spectrometry for the study of non-covalent complexes: an emerging technology. J Mass Spectrom 33: 911-920.
30. Preston GW, Radford SE, Ashcroft AE, Wilson A (2012) Covalent cross-linking within supramolecular peptide structures. Anal Chem 84: 6790-6797.
31. 31P NMR study of the adsorption of bovine serum albumin on montmorillonite using phosphate and the paramagnetic cation Mn2+: modification of conformation with pH. J Colloid Interface Sci 148: 343-352.
32. Renella G, Landi L, Nannipieri P (2002) Hydrolase activity during and after the chloroform fumigation of soils as affected by protease activity. Soil Biol Biochem 34: 51-60.
33. Renella G, Giagnoni L, Arenella M, Nannipieri P (2014) Soil proteomics. In: Nannipieri P, Pietramellara G, Renella G (eds) Omics in soil science. Horizon Scientific and Caister Academic, Norwich, in press.
34. Revault M, Quiquampoix H, Baron MH, Noinville S (2005) Fate of prions in soil: trapped conformation of full-length ovine prion protein induced by adsorption on clays. BBA-Gen Subj 1724: 367-374.
35. Schulze WH, Gleixner G, Kaiser K, Guggenberger G, Mann M, Schulze ED (2005) A proteomic fingerprint of dissolved organic carbon and soil particles. Oecologia 142: 335-343.
36. Swift RG (1996) Organic matter characterization. In: Sparks DL, Page AL, Helmke PA, Loeppert RH, Soltanpour PN, Tabatabai MA, Johnston CT, Summer ME (eds) Methods of soil analysis. Part 3. Chemical methods. American Society of Agronomy, Soil Science Society of America, Madison, pp 1011-1069.
37. Tan WF, Koopal LK, Weng LP, van Riemsdijk WH, Norde W (2008) Humic acid protein complexation. Geochim Cosmochim Acta 72: 2090-2099.
38. Tomaszewski JE, Schwarzenbach RP, Sander M (2011) Protein encapsulation by humic substances. Environ Sci Technol 45: 6003-6010.
39. Wang H-B, Zhang Z-X, Li H, He H-B, Fang C-X, Zhang A-J, Li Q-S, Chen R-S, Guo X-K, Lin H-F, Wu L-K, Lin S, Chen T, Lin R-Y, Peng X-X, Lin W-X (2011) Characterization of metaproteomics in crop rhizospheric soil. J Proteome Res 10: 932-940.
40. Wu L, Wang H, Zhang Z, Lin R, Zhang Z, Lin W (2011) Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil. Plos One 6: e20611.
41. Zang X, van Heemst JDH, Dria KJ, Hatcher PG (2000) Encapsulation of protein in humic acid from a histosol as an explanation for the occurrence of organic nitrogen in soil and sediment. Org Geochem 31: 679-695.