The effect of chemical structure on the hydrolysis of tetrapeptides along a river-to-ocean transect: AVFA and SWGA

Marine Chemistry

Volumn 119, Issue 1-4, 2010, Pages 108-120

  Liu, Zhanfei ^a   Kobiela, Megan E ^a   McKee, Georgina A ^a   Tang, Tiantian ^b   Lee, Cindy ^b   Mulholland, Margaret R ^c   Hatcher, Patrick G ^a  

^a OLD DOMINION UNIVERSITY   (United States)

^b STONY BROOK UNIVERSITY   (United States)

^c Old Dominion University   (United States)

Author keywords

Chesapeake Bay; DON cycling; Glycosylation; James River; Lag time; Peptide amide; Peptide hydrolysis; Tetrapeptide

Indexed keywords

CARBOXYLIC ACID; ENVIRONMENTAL EFFECT; ENZYME; HYDROLYSIS; INHIBITION; MEMBRANE; NUTRIENT CYCLING; OLIGOTROPHIC ENVIRONMENT; PEPTIDE; PRESERVATION; SALINITY;

ATLANTIC COAST [EUROPE]; CHESAPEAKE BAY; JAMES RIVER; UNITED STATES; VIRGINIA;

EID: 77950515982     PISSN: 03044203     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.marchem.2010.01.005     Document Type: Article

References (72)

1. Aluwihare L.I., Repeta D.J., Pantoja S., and Johnson C.G. Two chemically distinct pools of organic nitrogen accumulate in the ocean. Science 308 (2005) 1007-1010
2. Aluwihare L.I., and Meador T. Chemical composition of marine dissolved organic nitrogen. In: Capone D., et al. (Ed). Nitrogen in the Marine Environment (2008), Academic, New York
3. Arnosti C. Substrate specificity in polysaccharide hydrolysis: contrasts between bottom water and sediments. Limnol. Oceanogr. 45 (2000) 1112-1119
4. Arnosti C. Functional differences between Arctic seawater and sedimentary microbial communities: contrasts in microbial hydrolysis of complex substrates. FEMS Microbiol. Ecol. 66 (2008) 343-351
5. Arnosti C., and Repeta D.J. Oligosaccharide degradation by anaerobic marine bacteria: characterization of an experimental system to study polymer degradation in sediments. Limnol. Oceangr. 39 (1994) 1865-1877
6. Azam F., and Malfatti F. Microbial structuring of marine ecosystems. Nat. Rev. Microbiol. 5 (2007) 782-791
7. Barrett A.J., Rawlings N.D., and Woessner J.F. Handbook of proteolytic enzymes. 2nd ed (2004), Elsevier Academic Press
8. Billen, G., 1991. Protein degradation in aquatic environments In: Chróst, R. J. (Ed.), Microbial Enzymes in Aquatic Environments. Springer, New York.
9. Bronk D.A. Dynamics of DON. In: Hansell D.A., and Carlson C.A. (Eds). Biogeochemistry of Marine Dissolved Organic Matter (2002), Academic Press 153-247
10. Chan W.C., and White P.D. Fmoc Solid Phase Peptide Synthesis: A Practical Approach (2000), Oxford University Press
11. Cottrell M.T., and Kirchman D.L. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl. Environ. Microb. 66 (2000) 1692-1697
12. Crump B.C., Hopkinson C.S., Sogin M.L., and Hobbie J.E. Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl. Environ. Microb. 70 (2004) 1494-1505
13. Ding Y.-X., Chin W.-C., Rodriguez A., Hung C.-C., Santschi P.H., and Verdugo P. Amphiphilic exopolymers from Sagittula stellata induce DOM self-assembly and formation of marine microgels. Mar. Chem. 112 (2008) 11-19
14. Ferguson R.L., Buckley E.N., and Palumbo A.V. Response of marine bacterioplankton to differential filtration and confinement. Appl. Environ. Microb. 47 (1984) 49-55
15. Filippino K.C., Bernhardt P.W., and Mulholland M.R. Nutrient dynamics and primary productivity in the Chesapeake Bay outflow plume during 2005 and 2006. Estuar. Coast 32 (2009) 410-424
16. Fuhrman J. Close coupling between release and uptake of dissolved free amino acids in seawater studied by an isotope-dilution approach. Mar. Ecol. Prog. Ser. 37 (1987) 45-52
17. Hashimoto S., Fujiwara K., Fuwa K., and Saino T. Distribution and characteristics of carboxypeptidase activity in pond, river, and seawaters in the vicinity of Tokyo. Limnol. Oceanogr. 30 (1985) 631-645
18. Hedges J.I., Baldock J.A., Gelinas Y., Lee C., Peterson M., and Wakeham S.G. Evidence for non-selective preservation of organic matter in sinking marine particles. Nature 409 (2001) 801-804
19. Hollibaugh J.T., and Azam F. Microbial-degradation of dissolved proteins in seawater. Limnol. Oceanogr. 28 (1983) 1104-1116
20. Hoppe H.G. Significance of exoenzymatic activities in the ecology of brackish water-measurements by means of methylumbelliferyl substrates. Mar. Ecol. Prog. Ser. 11 (1983) 299-308
21. Hoppe H.G. Significance of exoenzymatic activities in the ecology of brackish water-measurements by means of methylumbelliferyl substractes. Mar. Ecol. Prog. Ser. 11 (1983) 299-308
22. Hsu P.H., and Hatcher P.G. New evidence for covalent coupling of peptides to humic acids based on 2D NMR spectroscopy: a means for preservation. Geochim. Cosmochim. Acta 69 (2005) 4521-4533
23. Imperiali B., and Rickert K.W. Conformational implications of asparagine-linked glycosylation. Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 97-101
24. Keil R.G., and Kirchman D.L. Dissolved combined amino acids: chemical form and utilization by marine bacteria. Limnol. Oceanogr. 38 (1993) 1256-1270
25. Kirchman D.L., Dittel A.I., Findlay S.E.G., and Fischer D. Changes in bacteria activity and community structure in response to dissolved organic matter in the Hudson River, New York. Aquat. Microb. Ecol. 35 (2004) 243-257
26. Kirchman D.L., Dittel A.I., Malmstrom R.R., and Cottrell M.T. Biogeography of major bacterial groups in the Delaware estuary. Limnol. Oceanogr. 50 (2005) 1697-1706
27. Knicker H., and Hatcher P.G. Survival of protein in an organic-rich sediment: possible protection by encapsulation in organic matter. Naturwissenschaften 84 (1997) 231-234
28. Kulathila R., Merkler K.A., and Merkler D.J. Enzymatic formation of C-terminal amides. Nat. Prod. Rep. 16 (1999) 145-154
29. Kuznetsova M., and Lee C. Enhanced extracellular enzymatic peptide hydrolysis in the sea-surface microlayer. Mar. Chem. 73 (2001) 319-332
30. Kuznetsova M., and Lee C. Dissolved free and combined amino acids in nearshore seawater, sea surface microlayers and foams: influence of extracellular hydrolysis. Aquat. Sci. 64 (2002) 252-268
31. Kuznetsova M., Lee C., and Aller J. Characterization of the proteinaceous matter in marine aerosols. Mar. Chem. 96 (2005) 359-377
32. Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982) 105-132
33. Lee C., Hedges J.I., Wakeham S.G., and Zhu N. Effectiveness of various treatments in retarding microbial activity in sediment trap material and their effects on the collection of swimmers. Limnol. Oceanogr. 37 (1992) 117-130
34. Lee C., Wakeham S.G., and Hedges J.I. Composition and flux of particulate amino acids and chloropigments in equatorial Pacific seawater and sediments. Deep-Sea Res. 47 (2000) 1535-1568
35. Lemke T.L., and Williams D.A. Foye's Principle of Medicinal Chemistry. 6 ed. (2007), Lippincott Williams and Wilkins
36. Liu Z.F., and Lee C. Drying effects on sorption capacity of coastal sediment: The importance of architecture and polarity of organic matter. Geochim. Cosmochim. Acta 70 (2006) 3313-3324
37. Liu Z.F., and Lee C. The role of organic matter in the sorption capacity of marine sediments. Mar. Chem. 105 (2007) 240-257
38. Liu Z.F., Lee C., and Wakeham S.G. Effects of mercuric chloride and protease inhibitors on degradation of particulate organic matter from the diatom Thalassiosira pseudonana. Org. Geochem. 37 (2006) 1003-1018
39. Liu Z.F., Lee C., and Aller R.C. Drying effects on decomposition of salt marsh sediment and on lysine sorption. J. Mar. Res. 66 (2008) 665-689
40. McCarthy M., Hedges J.I., and Benner R. Major biochemical composition of dissolved high molecular weight organic matter in seawater. Mar. Chem. 55 (1996) 281-297
41. McCarthy M., Pratum T., Hedges J.I., and Benner R. Chemical composition of dissolved organic nitrogen in the ocean. Nature 390 (1997) 150-154
42. Mulholland M.R., and Lomas M.W. Nitrogen uptake and assimilation. In: Capone D., et al. (Ed). Nitrogen in the Marine Environment (2008), Academic, New York
43. Mulholland M.R., and Lee C. Peptide hydrolysis and dipeptide uptake in cultures and natural communities dominated by phytoplankton mixotrophs. Limnol. Oceanogr. 54 (2009) 856-868
44. Mulholland M.R., Lee C., and Glibert P.M. Extracellular enzyme activity and uptake of carbon and nitrogen along an estuarine salinity and nutrient gradient. Mar. Ecol. Prog. Ser. 258 (2003) 3-17
45. Nagata T., and Kirchman D.L. Bacterial degradation of protein adsorbed to model submicron particles in seawater. Mar. Ecol. Prog. Ser. 132 (1996) 241-248
46. Nikaido H., and Saier M.H. Transport proteins in bacteria-common themes in their design. Science 258 (1992) 936-942
47. Obayashi Y., and Suzuki S. Proteolytic enzymes in coastal surface seawater: significant activity of endopeptidases and exopeptidases. Limnol. Oceanogr. 50 (2005) 722-726
48. Pantoja S., and Lee C. Peptide decomposition by extracellular hydrolysis in coastal seawater and salt marsh sediment. Mar. Chem. 63 (1999) 273-291
49. Pantoja S., Lee C., and Marecek J.F. Hydrolysis of peptides in seawater and sediment. Mar. Chem. 57 (1997) 25-40
50. Parsons T.R., Maita Y., and Lalli C.M. A Manual of Chemical and Biological Methods for Seawater Analysis. 1st ed. (1984), Pergamon Press
51. Powell M.J., Sutton J.N., del Castillo C.E., and Timperman A.I. Marine proteomics: generation of sequence tags for dissolved proteins in seawater using tandem mass spectrometry. Mar. Chem. 95 (2005) 183-198
52. Roth L.C., and Harvey H.R. Intact protein modification and degradation in estuarine environments. Mar. Chem. 102 (2006) 33-45
53. Saijo S., and Tanoue E. Chemical forms and dynamics of amino acid-containing particulate organic matter in Pacific surface waters. Deep-Sea Res. 52 (2005) 1865-1884
54. Selje N., and Simon M. Composition and dynamics of particle-associated and free-living bacterial communities in the Weser estuary, Germany. Aquat. Microb. Ecol. 30 (2003) 221-237
55. Shafer M.M., Hoffmann S.R., Overdier J.T., and Armstrong D.E. Physical and kinetic speciation of copper and zinc in three geochemically contrasting marine estuaries. Environ. Sci. Technol. 38 (2004) 3810-3819
56. Sleighter R.L., Mckee G.A., Liu Z.F., and Hatcher P.G. Naturally present fatty acids as internal calibrants for Fourier transform mass spectra of dissolved organic matter. Limnol. Oceanogr. Meth. 6 (2008) 246-253
57. Stevenson, F.J., 1994. Humus chemistry: genesis, composition, reactions. Wiley, New York.
58. Solorzano L. Determination of ammonia in natural waters by the phenolhypochlorite method. Limnol. Oceanogr. 14 (1969) 799-801
59. Somville M., and Billen G. A method for determining exoproteolytic activity in natural waters. Limnol. Oceanogr. 28 (1983) 190-193
60. Tanoue E. Detection of dissolved protein molecules in oceanic waters. Mar. Chem. 51 (1995) 239-252
61. Tanoue E., Ishii M., and Midorikawa T. Discrete dissolved and particulate proteins in oceanic waters. Limnol. Oceanogr. 41 (1996) 1334-1343
62. Troussellier M., Schafer H., Batailler N., Bernard L., Courties C., Lebaron P., Muyzer G., Servais P., and Vives-Rego J. Bacterial activity and genetic richness along an estuarine gradient (Rhone River plume, France). Aquat. Microb. Ecol. 28 (2002) 13-24
63. Valderrama J.C. The simultaneous analysis of total nitrogen and total phosphorus in natural waters. Mar. Chem. 10 (1981) 109-122
64. Verdugo P., Alldredge A.L., Azam F., Kirchman D.L., Passow U., and Santschi P.H. The oceanic gel phase: a bridge in the DOM-POM continuum. Mar. Chem. 92 (2004) 67-85
65. Vuljanic T., Bergquist K.E., Clausen H., Roy S., and Kihlberg J. Piperidine is preferred to morpholine for Fmoc cleavage in solid phase glycopeptide synthesis as exemplified by preparation of glycopeptides related to HIV gp120 and mucins. Tetrahedron 52 (1996) 7983-8000
66. Wang X.C., and Lee C. Adsorption and desorption of aliphatic amines, amino acids and acetate by clay minerals and marine sediments. Mar. Chem. 44 (1993) 1-23
67. Weber E.J., Spidle D.L., and Thorn K.A. Covalent binding of aniline to humic substances.1. Kinetic studies. Environ. Sci. Technol. 30 (1996) 2755-2763
68. Weiss M.S., Abele U., Weckesser J., Welte W., Schiltz E., and Schulz G.E. Molecular architecture and electrostatic properties of a bacterial porin. Science 254 (1991) 1627-1630
69. Welschmeyer N.A. Fluorometric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments. Limnol. Oceanogr. 39 (1994) 1985-1992
70. Westrich J.T., and Berner R.A. The role of sedimentary organic matter in bacterial sulfate reduction: The G model tested. Limnol. Oceanogr. 29 (1984) 236-249
71. Wu W.G., Pasternack L., Huang D.H., Koeller K.M., Lin C.C., Seitz O., and Wong C.H. Structural study on O-glycopeptides: glycosylation-induced conformational changes of O-GlcNAc, O-LacNAc, O-sialyl-LacNAc, and O-sialyl-lewis-X peptides of the mucin domain of MAdCAM-1. J. Am. Chem. Soc. 121 (1999) 2409-2417
72. Yamada N., and Tanoue E. Detection and partial characterization of dissolved glycoproteins in oceanic waters. Limnol. Oceanogr. 48 (2003) 1037-1048