Putative Alginate Assimilation Process of the Marine Bacterium Saccharophagus degradans 2-40 Based on Quantitative Proteomic Analysis

Marine Biotechnology

Volumn 18, Issue 1, 2016, Pages 15-23

  Takagi, Toshiyuki ^a,b,c   Morisaka, Hironobu ^a,b   Aburaya, Shunsuke ^a,b   Tatsukami, Yohei ^a,b,c   Kuroda, Kouichi ^a,b   Ueda, Mitsuyoshi ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c JAPAN SOCIETY FOR THE PROMOTION OF SCIENCE   (Japan)

Author keywords

4 Deoxy l erythro 5 hexoseulose uronic acid reductase; Alginate; Marine bacterium; Quantitative proteomic analysis; Saccharophagus degradans

Indexed keywords

BACTERIA; CARBON; CARBOXYLIC ACIDS; COLUMN CHROMATOGRAPHY; DEHYDROGENATION; ENZYME ACTIVITY; ENZYMES; GENES; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PROTEINS; TRANSCRIPTION;

CARBOHYDRATE METABOLISM; CARBON SOURCE; LIQUID CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY; MARINE BACTERIUM; MONOLITHIC SILICA; QUANTITATIVE PROTEOMIC ANALYSIS; SACCHAROPHAGUS DEGRADANS; URONIC ACIDS;

ALGINATE;

ALGINATE; BACTERIUM; ENZYME ACTIVITY; GENETIC ANALYSIS; METABOLISM; POLYSACCHARIDE; PROTEOMICS; QUANTITATIVE ANALYSIS;

BACTERIA (MICROORGANISMS); SACCHAROPHAGUS DEGRADANS; SACCHAROPHAGUS DEGRADANS 2-40;

ALGINIC ACID; BACTERIAL PROTEIN; GLUCURONIC ACID; HEXURONIC ACID; PROTEOME;

AQUATIC SPECIES; CHEMISTRY; GAMMAPROTEOBACTERIA; METABOLISM; PHYSIOLOGY; SIGNAL TRANSDUCTION;

ALGINATES; AQUATIC ORGANISMS; BACTERIAL PROTEINS; GAMMAPROTEOBACTERIA; GLUCURONIC ACID; HEXURONIC ACIDS; PROTEOME; SIGNAL TRANSDUCTION;

EID: 84953352153     PISSN: 14362228     EISSN: 14362236     Source Type: Journal    
DOI: 10.1007/s10126-015-9667-3     Document Type: Article

References (29)

1. Aoki W, Tatsukami Y, Kitahara N, Matsui K, Morisaka H, Kuroda K, Ueda M (2013) Elucidation of potentially virulent factors of Candida albicans during serum adaptation by using quantitative time-course proteomics. J Proteomics 91:417–429
2. Braun V (1995) Energy-coupled transport and signal transduction through the gram-negative outer membrane via TonB-ExbB-ExbD-dependent receptor proteins. FEMS Microbiol Rev 16:295–307
3. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37:D233–D238
4. Demirbas A (2010) Use of algae as biofuel sources. Energy Convers Manag 51:2738–2749
5. Enquist-Newman M, Faust AM, Bravo DD, Santos CN, Raisner RM, Hanel A, Sarvabhowman P, Le C, Regitsky DD, Cooper SR, Peereboom L, Clark A, Martinez Y, Goldsmith J, Cho MY, Donohoue PD, Luo L, Lamberson B, Tamrakar P, Kim EJ, Villari JL, Gill A, Tripathi SA, Karamchedu P, Paredes CJ, Rajgarhia V, Kotlar HK, Bailey RB, Miller DJ, Ohler NL, Swimmer C, Yoshikuni Y (2014) Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform. Nature 505:239–243
6. Esaka K, Aburaya S, Morisaka H, Kuroda K, Ueda M (2015) Exoproteomic analysis of Clostridium cellulovorans in natural soft-biomass degradation. AMB Express 5:2
7. Garron ML, Cygler M (2010) Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology 20:1547–1573
8. Gray KA, Zhao L, Emptage M (2006) Bioethanol. Curr Opin Chem Biol 10:141–146
9. Hutcheson SW, Zhang H, Suvorov M (2011) Carbohydrase systems of Saccharophagus degradans degrading marine complex polysaccharides. Mar Drugs 9:645–665
10. Izu H, Adachi O, Yamada M (1997) Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli. J Mol Biol 267:778–793
11. Kabisch A, Otto A, Konig S, Becher D, Albrecht D, Schuler M, Teeling H, Amann RI, Schweder T (2014) Functional characterization of polysaccharide utilization loci in the marine bacteroidetes ‘Gramella forsetii’ KT0803. ISME J 8:1492–1502
12. Kavanagh KL, Jornvall H, Persson B, Oppermann U (2008) Medium- and short-chain dehydrogenase/reductase gene and protein families: the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes. Cell Mol Life Sci 65:3895–3906
13. Kim HT, Ko H-J, Kim N, Kim D, Lee D (2012a) Characterization of a recombinant endo-type alginate lyase (Alg7D) from Saccharophagus degradans. Biotechnol Lett 34:1087–1092
14. Kim HT, Chung JH, Wang D, Lee J, Woo HC, Choi IG, Kim KH (2012b) Depolymerization of alginate into a monomeric sugar acid using Alg17C, an exo-oligoalginate lyase cloned from Saccharophagus degradans 2-40. Appl Microbiol Biotechnol 93:2233–2239
15. Koebnik R (2005) TonB-dependent trans-envelope signalling: the exception or the rule? Trends Microbiol 13:343–347
16. Matsui K, Bae J, Esaka K, Morisaka H, Kuroda K, Ueda M (2013) Exoproteome profiles of Clostridium cellulovorans grown on various carbon sources. Appl Environ Microbiol 79:6576–6584
17. Morisaka H, Matsui K, Tatsukami Y, Kuroda K, Miyake H, Tamaru Y, Ueda M (2012) Profile of native cellulosomal proteins of Clostridium cellulovorans adapted to various carbon sources. AMB Express 2:37
18. Ross AB, Jones JM, Kubacki ML, Bridgeman T (2008) Classification of macroalgae as fuel and its thermochemical behaviour. Bioresour Technol 99:6494–6504
19. Sato T, Imanaka H, Rashid N, Fukui T, Atomi H, Imanaka T (2004) Genetic evidence identifying the true gluconeogenic fructose-1,6-bisphosphatase in Thermococcus kodakaraensis and other hyperthermophiles. J Bacteriol 186:5799–5807
20. Schurig H, Beaucamp N, Ostendorp R, Jaenicke R, Adler E, Knowles JR (1995) Phosphoglycerate kinase and triosephosphate isomerase from the hyperthermophilic bacterium Thermotoga maritima form a covalent bifunctional enzyme complex. EMBO J 14:442–451
21. Takagi T, Yokoi T, Shibata T, Morisaka H, Kuroda K, Ueda M (2015) Engineered yeast whole-cell biocatalyst for direct degradation of alginate from macroalgae and production of non-commercialized useful monosaccharide from alginate. Appl Microbiol Biotechnol. doi:10.1007/s00253-015-7035-x
22. Takase R, Ochiai A, Mikami B, Hashimoto W, Murata K (2010) Molecular identification of unsaturated uronate reductase prerequisite for alginate metabolism in Sphingomonas sp. A1. Biochim Biophys Acta 1804:1925–1936
23. Tang K, Jiao N, Liu K, Zhang Y, Li S (2012) Distribution and functions of TonB-dependent transporters in marine bacteria and environments: implications for dissolved organic matter utilization. PLoS One 7:e41204
24. Taylor AL, Trotter CD (1967) Revised linkage map of Escherichia coli. Bacteriol Rev 31:332–353
25. van Staalduinen LM, Jia Z (2014) Post-translational hydroxylation by 2OG/Fe(II)-dependent oxygenases as a novel regulatory mechanism in bacteria. Front Microbiol 5:798
26. Wang da M, Kim HT, Yun EJ, Kim do H, Park YC, Woo HC, Kim KH (2014) Optimal production of 4-deoxy-l-erythro-5-hexoseulose uronic acid from alginate for brown macro algae saccharification by combining endo- and exo-type alginate lyases. Bioprocess Biosyst Eng 37:2105–2111
27. Wargacki AJ, Leonard E, Win MN, Regitsky DD, Santos CN, Kim PB, Cooper SR, Raisner RM, Herman A, Sivitz AB, Lakshmanaswamy A, Kashiyama Y, Baker D, Yoshikuni Y (2012) An engineered microbial platform for direct biofuel production from brown macroalgae. Science 335:308–313
28. T. PLoS Genet 4(5):e1000087
29. Wong TY, Preston LA, Schiller NL (2000) ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications. Annu Rev Microbiol 54:289–340