Global metabolite profiling of agarose degradation by Saccharophagus degradans 2-40

New Biotechnology

Volumn 27, Issue 2, 2010, Pages 156-168

  Shin, Min Hye ^a   Lee, Do Yup ^b   Wohlgemuth, Gert ^b   Choi, In Geol ^a   Fiehn, Oliver ^b   Kim, Kyoung Heon ^a  

^a Korea University   (South Korea)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGAROSE; CARBON SOURCE; CATABOLIC PATHWAY; EXPRESSION PROFILE; MAIN COMPONENT; MARINE RED ALGA; METABOLITE PROFILES; METABOLITE PROFILING; PLANT CELL WALL; SACCHAROPHAGUS DEGRADANS;

ALGAE; AMINO ACIDS; BIOCHEMISTRY; BIOMOLECULES; CELLULOSE; DEGRADATION; FATTY ACIDS; FINANCIAL DATA PROCESSING; GLUCOSE; GLYCEROL; METABOLISM; METABOLITES; ORGANIC ACIDS; PLANT CELL CULTURE; POLYSACCHARIDES;

PRINCIPAL COMPONENT ANALYSIS;

AGAROSE; AMINO ACID; CARBON; CELLULOSE; FATTY ACID; GALACTOSE; GLUCOSE; GLYCEROL; GLYCEROL DERIVATIVE; NUCLEOTIDE; POLYSACCHARIDE; BACTERIAL PROTEIN; PROTEOME; SEPHAROSE;

ARTICLE; BACTERIAL CELL; BACTERIAL STRAIN; CARBON SOURCE; CELL GROWTH; CONTROLLED STUDY; ENZYME ANALYSIS; ENZYME DEGRADATION; ENZYME METABOLISM; GAS CHROMATOGRAPHY; GENE EXPRESSION PROFILING; GENETIC DATABASE; MARINE BACTERIUM; NONHUMAN; NUCLEOTIDE METABOLISM; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SACCHAROPHAGUS DEGRADANS; SIGNAL TRANSDUCTION; TIME OF FLIGHT MASS SPECTROMETRY; ALTEROMONADACEAE; METABOLISM; PEPTIDE MAPPING; PROCEDURES;

ALTEROMONADACEAE; BACTERIAL PROTEINS; GENE EXPRESSION PROFILING; PEPTIDE MAPPING; PROTEOME; SEPHAROSE;

ALGAE; AMINO ACIDS; BIOCHEMISTRY; CELLULOSE; DEGRADATION; FATTY ACIDS; GLUCOSE; GLYCEROL; METABOLISM; ORGANIC ACIDS; POLYSACCHARIDES;

RHODOPHYTA; SACCHAROPHAGUS DEGRADANS; SACCHAROPHAGUS DEGRADANS 2-40;

EID: 77952239598     PISSN: 18716784     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.nbt.2010.02.023     Document Type: Article

References (75)

1. Fu X.T., et al. Purification and characterization of a novel β-agarase AgaA34, from Agarivorans albus YKW-34. Appl. Microbiol. Biotechnol. 78 (2008) 265-273
2. 13C-N.M.R.-spectroscopic investigation of agarose oligomers. Carbohydr. Res. 148 (1986) 199-207
3. Wang J., et al. Anti-oxidation of agar oligosaccharides produced by agarase from a marine bacterium. J. Appl. Phycol. 16 (2004) 333-340
4. Weinberger F., et al. Structure-activity relationships of oligoagar elicitors toward Gracilaria conferta (Rhodophyta). J. Phycol. 37 (2001) 418-426
5. Gross M. Algal biofuel hopes. Curr. Biol. 18 (2008) R46-R47
6. Horn S.J., et al. Ethanol production from seaweed extract. J. Ind. Microbiol. Biotechnol. 25 (2000) 249-254
7. Aizawa, M. et al., (2007) Seaweed bioethanol production in Japan - the Ocean Sunrise Project. Oceans 2007, Vancouver, BC, Canada, September 29-October 4, 2007.
8. Jensen A. Present and future needs for algae and algal products. Hydrobiologia 260/261 (1993) 15-23
9. 2 remediation: a review. J. Appl. Phycol. 6 (1994) 45-60
10. Craigie J. Cell walls. In: Cole K.M., and Sheath R.G. (Eds). Biology of the Red Algae (1990), Cambridge University Press 221-257
11. Michel G., et al. Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases. Appl. Microbiol. Biotechnol. 71 (2006) 23-33
12. 13C-nmr spectroscopy. Carbohydr. Res. 54 (1977) C7-C10
13. Ma C., et al. Molecular cloning and characterization of a novel β-agarase AgaB, from marine Pseudoalteromonas sp. CY24. J. Biol. Chem. 282 (2007) 3747-3754
14. Lee D.-G., et al. Over-production of a glycoside hydrolase family 50 β-agarase from Agarivorans sp. JA-1 in Bacillus subtilis and the whitening effect of its product. Biotechnol. Lett. 30 (2008) 911-918
15. Ohta Y., et al. High-level expression of a neoagarobiose-producing β-agarase gene from Agarivorans sp. JAMB-AII in Bacillus subtilis and enzymic properties of the recombinant enzyme. Biotechnol. Appl. Biochem. 41 (2005) 183-191
16. Lee D.-G., et al. Cloning, expression, and characterization of a glycoside hydrolase family 50 β-agarase from a marine Agarivorans isolate. Biotechnol. Lett. 28 (2006) 1925-1932
17. Vera J., et al. Identification of a marine agarolytic Pseudoalteromonas isolate and characterization of its extracellular agarase. Appl. Environ. Microbiol. 64 (1998) 4378-4383
18. Ekborg N.A., et al. Genomic and proteomic analyses of the agarolytic system expressed by Saccharophagus degradans 2-40. Appl. Environ. Microbiol. 72 (2006) 3396-3405
19. T. PLoS Genet. 4 (2008) e1000087
20. Whitehead L.A., et al. Characterization of the agarase system of a multiple carbohydrate degrading marine bacterium. Cytobios 106 suppl. 1 (2001) 99-117
21. Servín-González L., et al. Transcriptional regulation of the four promoters of the agarase gene (dagA) of Streptomyces coelicolor A3(2). Microbiology-UK 140 (1994) 2555-2565
22. Parro V., and Mellado R.P. Effect of glucose on agarase overproduction by Streptomyces. Gene 145 (1994) 49-55
23. Parro V., et al. Effects of phosphate limitation on agarase production by Streptomyces lividans TK21. FEMS Microbiol. Lett. 158 (1998) 107-113
24. Dong J., et al. Molecular cloning, expression, and characterization of a β-agarase gene, agaD, from a marine bacterium, Vibrio sp. strain PO-303. Biosci. Biotechnol. Biochem. 71 (2007) 38-46
25. Dong J., et al. Cloning of the novel gene encoding β-agarase C from a marine bacterium Vibrio sp. strain PO-303, and characterization of the gene product. Appl. Environ. Microbiol. 72 (2006) 6399-6401
26. Sugano Y., et al. Cloning and sequencing of agaA, a unique agarase 0107 gene from a marine bacterium, Vibrio sp. strain JT0107. Appl. Environ. Microbiol. 59 (1993) 3750-3756
27. Dong J., et al. A unique β-agarase, AgaA, from a marine bacterium, Vibrio sp. strain PO-303. Appl. Microbiol. Biotechnol. 74 (2007) 1248-1255
28. Zhang W.-W., and Sun L. Cloning, characterization, and molecular application of a beta-agarase gene from Vibrio sp. strain V134. Appl. Environ. Microbiol. 73 (2007) 2825-2831
29. Andrykovitch G., and Marx I. Isolation of a new polysaccharide-digesting bacterium from a salt marsh. Appl. Environ. Microbiol. 54 (1988) 1061-1062
30. Ekborg N.A., et al. Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides. Int. J. Syst. Evol. Microbiol. 55 (2005) 1545-1549
31. T. J. Bacteriol. 188 (2006) 3849-3861
32. Matsuzaki F., et al. Proteomic and metabolomic analyses of the white-rot fungus Phanerochaete chrysosporium exposed to exogenous benzoic acid. J. Proteome Res. 7 (2008) 2342-2350
33. Oldiges M., et al. Metabolomics: current state and evolving methodologies and tools. Appl. Microbiol. Biotechnol. 76 (2007) 495-511
34. Vijayendran C., et al. Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling. Genome Biol. 9 (2008) R72
35. van der Werf M.J., et al. Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources. Mol. Biosyst. 4 (2008) 315-327
36. Pope G.A., et al. Metabolic footprinting as a tool for discriminating between brewing yeasts. Yeast 24 (2007) 667-679
37. Mashego M.R., et al. Microbial metabolomics: past, present and future methodologies. Biotechnol. Lett. 29 (2007) 1-16
38. Shin M.H., et al. Global metabolic profiling of plant cell wall polysaccharide degradation by Saccharophagus degradans. Biotechnol. Bioeng. 105 (2010) 477-488
39. Ensor L.A., et al. Expression of multiple complex polysaccharide-degrading enzyme systems by marine bacterium strain 2-40. J. Ind. Microbiol. Biotechnol. 23 (1999) 123-126
40. Desvaux M., et al. Cellulose catabolism by Clostridium cellulolyticum growing in batch culture on defined medium. Appl. Environ. Microbiol. 66 (2000) 2461-2470
41. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
42. Lee D.Y., and Fiehn O. High quality metabolomic data for Chlamydomonas reinhardtii. Plant Methods 4 (2008) 7
43. Miller G.L. Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal. Chem. 31 (1959) 426-428
44. Xiao Z., et al. Microplate-based filter paper assay to measure total cellulase activity. Biotechnol. Bioeng. 88 (2004) 832-837
45. Fiehn O., et al. Quality control for plant metabolomics: reporting MSI-compliant studies. Plant J. 53 (2008) 691-704
46. Denkert C., et al. Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol. Cancer 7 (2008) 72
47. Want E.J., et al. Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry. Anal. Chem. 78 (2006) 743-752
48. Rabinowitz J.D., and Kimball E. Acidic acetonitrile for cellular metabolome extraction from Escherichia coli. Anal. Chem. 79 (2007) 6167-6173
49. Mach R.L., et al. Carbon catabolite repression of xylanase I (xyn1) gene expression in Trichoderma reesei. Mol. Microbiol. 21 (1996) 1273-1281
50. Paulsen I.T. Carbon metabolism and its regulation in Streptomyces and other high GC Gram-positive bacteria. Res. Microbiol. 147 (1996) 535-541
51. Sugano Y., et al. Purification and characterization of a novel enzyme, α-neoagarooligosaccharide hydrolase (α-NAOS hydrolase), from a marine bacterium, Vibrio sp. strain JT0107. J. Bacteriol. 176 (1994) 6812-6818
52. Suzuki H., et al. Purification and characterization of an extracellular α-neoagarooligosaccharide hydrolase from Bacillus sp. MK03. J. Biosci. Bioeng. 93 (2002) 456-463
53. Yu S. The anhydrofructose pathway of glycogen catabolism. IUBMB Life 60 (2008) 798-809
54. Yu S., and Fiskesund R. The anhydrofructose pathway and its possible role in stress response and signaling. Biochim. Biophys. Acta-Gen. Subj. 1760 (2006) 1314-1322
55. Kühn A., et al. Catabolism of 1,5-anhydro-d-fructose in Sinorhizobium morelense S-30.7.5: discovery, characterization, and overexpression of a new 1,5-anhydro-d-fructose reductase and its application in sugar analysis and rare sugar synthesis. Appl. Environ. Microbiol. 72 (2006) 1248-1257
56. Sakuma M., et al. Purification and some properties of a hepatic NADPH-dependent reductase that specifically acts on 1,5-anhydro-d-fructose. J. Biochem. 123 (1998) 189-193
57. LeBlanc D.J., and Mortlock R.P. Metabolism of d-arabinose: a new pathway in Escherichia coli. J. Bacteriol. 106 (1971) 90-96
58. Menavuvu B.T., et al. Novel substrate specificity of d-arabinose isomerase from Klebsiella pneumoniae and its application to production of d-altrose from d-psicose. J. Biosci. Bioeng. 102 (2006) 436-441
59. Elsinghorst E.A., and Mortlock R.P. Molecular cloning of the Escherichia coli B l-fucose-d-arabinose gene cluster. J. Bacteriol. 176 (1994) 7223-7232
60. Thomas T.D., et al. Galactose fermentation by Streptococcus lactis and Streptococcus cremoris: pathways, products, and regulation. J. Bacteriol. 144 (1980) 672-682
61. Stephanopoulos G.N., et al. Metabolic Engineering; Principles and Methodologies (1998), Academic Press
62. De Ley J., and Doudoroff M. The metabolism of d-galactose in Pseudomonas saccharophila. J. Biol. Chem. 227 (1957) 745-757
63. Bond D.R., et al. The diversion of lactose carbon through the tagatose pathway reduces the intracellular fructose 1,6-bisphosphate and growth rate of Streptococcus bovis. Appl. Microbiol. Biotechnol. 49 (1998) 600-605
64. Crow V.L., et al. Plasmid linkage of the d-tagatose 6-phosphate pathway in Streptococcus lactis: effect on lactose and galactose metabolism. J. Bacteriol. 153 (1983) 76-83
65. Arias A., and Cervenansky C. Galactose metabolism in Rhizobium meliloti L5-30. J. Bacteriol. 167 (1986) 1092-1094
66. Wong T.Y., and Yao X.-T. The DeLey-Doudoroff pathway of galactose metabolism in Azotobacter vinelandii. Appl. Environ. Microbiol. 60 (1994) 2065-2068
67. Berka T.R., and Lessie T.G. Enzymes related to galactose utilization in Pseudomonas cepacia. Curr. Microbiol. 11 (1984) 43-48
68. Sussman I., and Avron M. Characterization and partial purification of dl-glycerol-1-phosphatase from Dunaliella salina. Biochim. Biophys. Acta 661 (1981) 199-204
69. Albertyn J., et al. Purification and characterization of glycerol-3-phosphate dehydrogenase of Saccharomyces cerevisiae. FEBS Lett. 308 (1992) 130-132
70. Qi Q., et al. Pyruvate dehydrogenase complex and acetyl-CoA carboxylase in pea root plastids: their characterization and role in modulating glycolytic carbon flow to fatty acid biosynthesis. J. Exp. Bot. 47 (1996) 1889-1896
71. Seker T., et al. Analysis of acyl CoA ester intermediates of the mevalonate pathway in Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 67 (2005) 119-124
72. Jin S., et al. Metabolic flux distributions in recombinant Saccharomyces cerevisiae during foreign protein production. J. Biotechnol. 54 (1997) 161-174
73. Rolfes R.J. Regulation of purine nucleotide biosynthesis: in yeast and beyond. Biochem. Soc. Trans. 34 (2006) 786-790
74. Dawes S.S., and Mizrahi V. DNA metabolism in Mycobacterium leprae. Lepr. Rev. 72 (2001) 408-414
75. Berg J.M., et al. Biochemistry (2002), W.H. Freeman and Company