Identification of a New Agar-hydrolyzing Bacterium Vibrio sp. S4 from the Seawater of Jeju Island and the Biochemical Characterization of Thermostable Agarose |
Lee, Chang-Ro
(Department of Biological Science, Myongji University)
Chi, Won-Jae (Biological and Genetic Resource Assessment Division, National Institute of Biological Resource) Bae, Chang-Hwan (Biological and Genetic Resource Assessment Division, National Institute of Biological Resource) Hong, Soon-Kwang (Department of Biological Science, Myongji University) |
1 | Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang A, Miller W, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein data base. |
2 | Ben-Haim Y, Thompson FL, Thompson CC, Cnockaert MC, Hoste B, Swings J, et al. 2003. Vibrio coralliilyticus sp. nov., a temperature-dependent pathogen of the coral Pocillopora damicornis. Int. J. Syst. Evol. Microbiol. 53: 309-315. DOI |
3 | Chi WJ, Chang YK, Hong SK. 2012. Agar degradation by microorganisms and agar-degrading enzymes. Appl. Microbiol. Biotechnol. 94: 917-930. DOI |
4 | Chi WJ, Lee CR, Dugerjonjuu S, Park JS, Kang DK, Hong SK. 2015. Biochemical characterization of a novel iron-dependent GH16 -agarase, AgaH92, from an agarolytic bacterium Pseudoalteromonas sp. H9. FEMS Microbiol. Lett. 362(7) doi: 10.1093/femsle/fnv035. DOI |
5 | Chi WJ, Park JS, Kang DK, Hong SK. 2014. Production and characterization of a novel thermostable extracellular agarase from Pseudoalteromonas hodoensis newly isolated from the West Sea of South Korea. Appl. Biochem. Biotechnol. 173: 1703-1716. DOI |
6 | Chimetto LA, Cleenwerck I, Moreira APB, Brocchi M, Willems A, Vos PD, et al. 2011. Vibrio variabilis sp. nov. and Vibrio marinus sp. nov., isolated from Palythoa caribaeorum. Int. J. Syst. Evol. Microbiol. Doi:10.1099/ijs.0.026997-0. DOI |
7 | Chun J, Lee JH, Jung YY, Kim MJ, Kim SI, Kim BK, et al. 2007. ExTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57: 2259-2261. DOI |
8 | Cui F, Dong S, Shi X, Zhao X, Zhang XH. 2014. Overexpression and characterization of a novel thermostable -agarase YM01-3, from marine bacterium Catenovulum agarivorans YM01(T). Mar. Drugs 12: 2731-2747. DOI |
9 | Ohta Y, Hatada Y, Nogi Y, Miyazaki M, Li Z, Akita M, et al. 2004. Enzymatic properties and nucleotide and amino acid sequences of a thermostable beta-agarase from a novel species of deep-sea Microbulbifer. Appl. Microbiol. Biotechnol. 64: 505-514. DOI |
10 | Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425. |
11 | Sasser M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Inc., Newark, DE, USA. |
12 | Suzuki MT, Giovannoni SJ. 1996. Bias caused by template annealing in the amplification of mixture of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62: 625-630. |
13 | Takagi E, Hatada Y, Akita M, Ohta Y, Yokoi G, Miyazaki T, et al. 2015. Crystal structure of the catalytic domain of a GH16 -agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94. Biosci. Biotechnol. Biochem. 79: 625-632. DOI |
14 | Temuujin U, Chi WJ, Lee SY, Chang YK, Hong SK. 2011. Overexpression and biochemical characterization of DagA from Streptomyces coelicolor A3(2): an endo-type -agarase producing neoagarotetraose and neoagarohexaose. Appl. Microbiol. Biotechnol. 92: 749-759. DOI |
15 | Thompson FL, Li Y, Gomez-Gil B, Thompson CC, Hoste B, Vandemeulebroecke K, et al. 2003. Vibrio neptunius sp. nov., Vibrio brasiliensis sp. nov. and Vibrio xuii sp. nov., isolated from the marine aquaculture environment (bivalves, fish, rotifers and shrimps). Int. J. Syst. Evol. Microbiol. 53: 245-252. DOI |
16 | Kimura M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, UK. |
17 | Duckworth M, Yaphe W. 1971. Structure of agar. I. Fractionation of a complex mixture of polysaccharides. Carbohydr. Res. 16: 189-197. DOI |
18 | Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41: 95-98. |
19 | Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G. 2010. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464: 908-912. DOI |
20 | Knutsen SH, Myslabodski DE, Larsen B, Usov AI. 1994. A modified system of nomenclature for red algal galactans. Botanica Marina 37: 163-169. |
21 | Li J, Sha Y, Seswita-Zilda D, Hu Q, He P. 2014. Purification and characterization of thermostable agarase from Bacillus sp. BI-3, a thermophilic bacterium isolated from hot spring. J. Microbiol. Biotechnol. 24: 19-25. DOI |
22 | Mesbah M, Premachandran U, Whitman WB. 1989. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int. J. Syst. Bacteriol. 39: 159-167. DOI |
23 | Miller GL. 1959. Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal. Chem. 31: 426-428. DOI |
24 | Miller L, Berger T. 1985. Bacterial identification by gas chromatography of whole cell fatty acid. Hewlett-Packard Application note. pp. 228-241. |
25 | Yun EJ, Lee S, Kim JH, Kim BB, Kim HT, Lee SH, et al. 2013. Enzymatic production of 3,6-anhydro-L-galactose from agarose and its purification and in vitro skin whitening and anti-inflammatory activities. Appl. Microbiol. Biotechnol. 97: 2961-2970. DOI |
26 | Thomson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. DOI |
27 | Usov AI. 1998. Structural analysis of red seaweed galactans of agar and carrageenan groups. Food Hydrocolloids 12: 301-308. DOI |
28 | Xiao TF, Kim SM. 2010. Agarase: Review of major sources, categories, purification method, enzyme characterization and applications. Mar. Drugs 8: 200-218. DOI |