REFERENCES

1. Able K, De Schmertzing H and Peterson J (1963) Classification of microorganisms

of chemical composition: Feasibility of utilizing gas chromatography. J. Bacteriol.

85: 1039-1044.

2. Agbo J.A.C. and Moss M.O. (1979) The isolation and characterization of agarolytic

bacteria from lowland river. J. Gen. Microbiol. 115: 355-368.

3. Alberstsen HM, Abderrahim H, Cann HM, Dausset J, Pasliler DL and Cohen D

(1990) Construction and characterization of a yeast artificial chromosome library

containing seven haploid human genome equivalents. Proc. Nail. Acad. Sci. USA.

87: 4256-4260.

4. Allouch J , Jam M, Helbert W, Barbeyron T, Kloareg B, Henrissat B and Czjzek M

(2003) The three dimensional strucutures of two 13-agarases. J. Biol. Chem. 278:

47171-47180.

5. Allouch J, Helbert W, Henrissat B and Czjzek M (2004) Parallel substrate binding

sites in a 13-agarase suggest a novel mode of action on double helical agarose.

Structure 12: 623-632.

6. Andrykovich G and Marx I (1988) Isolation of a new polysaccharide digesting

bacterium from a salt marsh. Appl. Env. Microbiol. 54: 1061-1062 (1988).

7. Anzai Y, Kim H, Park JY, Wakabayashi H and Oyaizu H (2000) Phylogenetic

affiliation of the Pseudomonads based on 16S rRNA sequence. Int. J. Syst. Evol.

Microbiol. 50: 1563-1589.

8. Aoki T., Araki T. and Kitamikado M (1990) Purification and characterization of a

novel p-agarase from Vibrio sp. AP-2. Eur. J. Biochem. 187: 461-465.

9. Arai C and Arai MK (1956) Studies on the chemical constitution of agar-agar.

XVIII. Isolation of a new crystalline disaccharide by enzymatic hydrolysis of agar-

agar. Bulletin of the Chemical Society of Japan. 29: 3 39-345.

10. Araki C (1956) Structure of agarose constituent of agar-agar. Bull. Chem. 'Soc.

Japan 29: 543.

11. Araki C.K. (1966) Some recent studies on the polysaccharides of agarophytes. In:

Proc 5 th Int. Seaweed Symp. P3 Pregmon, Oxford.

204

12. Armisen R (1991) Agar and Agarose biotechnological applications. Hydrobiologia.

221: 157-166.

13. Bacon, J.S.D. (1979) Factors limiting the action of polysaccharide degrading

enzymes In: Micorbial Polysaccharides and Polysaccharases, (Eds: Beekeley

R.C.W., Gooday G.W. and Ellwood D.C. Academic Press, pp269-284).

14. Bannikova GE, Lopatin SA, Varlamov VP, Kuznetsov BB, Kozina IV,

Miroshinichenko ML, Cherynkh NA, Turova TP and Bonch-Osmolovskaya EA

(2008) The thermophillic bacteria hydrolyzing agar: characterization of

thermostable agarase. Appl. Biochem. Microbiol. 45, 366-371.

15. Barasan P, Hang YD, Barasan N and Worobo RW (2001) Cloning and heterologous

expression of xylanase from Pichia stipitis in Echerichia coli. J. Appl. Microbiol.

90: 248-255.

16. Barbeyron T., Hardion S.L., Cone E., Kloareg B. and Potin P (2001) Zobellia

galactivrorans gen nov., sp. nov., a marine species of Flavobacteriaceae isolated

from a red alga, and classification of (Cytophaga) uligonosa (Zobell and Upham

1944) Reichenback 1989 as Zobellia uliginosa gen nov., comb nov. Int. J. Syst.

Evol. Microbiol. 51: 985-997.

17. Beguin P and Aubert JP (1994) The biological degradation of cellulose. FEMS

Microbiol. Rev. 13: 25-58.

1$. Belas R, (1989) Sequence analysis of the agr A gene encoding I3-agarase from

Pseudomonas atalantica. J. Bact. 171: 602-605.

19. Belas R, Bartlett D and Silverman M (1988) Cloning and gene replacement

mutagenesis of a Pseudomonas atlantica agarase gene. Appl. Env. Microbiol. 54:

30-37.

20. Beleneva IA and Zhukova NV (2006) Bacterial communities of some brown and

red algae from peter the great bay, the sea of Japan. Mikrobiologiya. 75:348-375.

21. Beruto M., Beruto D and Debergh P (1999) Influence of agar on in vitro cultures. I:

Physicochemical properties of agar and agar gelled media. In Vitro Cell Dev. Biol.

Plant. 35: 86-93.

205

22. Bibb MJ, Jones GH, Jospeh R, Buttner MJ and Ward JM (1987) The agarase gene

(dag A) of Streptomyces coelicolor A3(2): Affinity purification and characterization

of the cloned gene product. J. Gen. Microbiol. 133: 2089-2096.

23. Breccia JD, Baigori MD, Castro GR and Sineriz F (1995) Detection of endo-

xylanase activivites in electrophoresis gel with cango red staining. Biotechn. Techn.

9: 145-148.

24. Buddington RK (2001) The use of non digestable oligosaccharides to manage the

gastrointestinal system. Microbial Ecology in Helath and Disease. 13: 9-15.

25. Burtin P (2003) Nutritional value of seaweeds. Electron J. Agric. Food. Chem. 2:

498-503.

26. Buttner MJ, Fearnley IM and Bibb MJ (1987) The agarase gene (dag A) of

Streptomyces coelicolor A3(2): nucleotide sequence and transcriptional analysis.

Mol. Gen. Genet. 209: 101-109).

27. Chen LCM and McCracken I (1993) An antibiotic protocol for preparing axenic

culture of Porphyra lineraris. Botanica Marina. 36: 29-33.

28. Chen N and Yun L (2006) DNA Recovery from Agarose Gels with a Simple

Centrifuge-driven Sephadex Filtration. Forestry Studies in China. 8: 32-34.

29. Chiura HX and Kita-Tsukamoto K (2000) Purification and characterization of a

novel agarase secreted by a marine bacterium Pseudoalteromonas sp. strain CKT1.

Microbes and Environments 15:11-22.

30. Chu, FLE, Webb KL, Hepworth DA and Casey BB (1987) Metamorphosis of

larvae of Crassostrea virginica fed microcapsulated diets. Aquaculture 64:185-199.

31. Cole KD and Akerman B (2000) Enhanced capacity for electrophoretic capture of

plasmid DNA by agarase treatment of agarose gels. Biomolecules. 1: 771-781.

32. Davis CL, Koop K, Muir DG and Robb FT (1983) Bacterial diversity in adjacent

kelp-dominated ecosystems. Mar. Ecol. Prog. Ser. 13: 115-119.

33. Day DF and Yaphe W (1975) Enzymatic hydrolysis of agar: Purification and

characterization of neoagarobiose hydrolase and p-nitrophenyl-a-galactoside

hydrolase. Can. J. Microbiol. 21: 1512-1518.

206

34. Dessouki A.M and Atia K.S, (2002) Immobilization of adenosine deaminase on to

agarose and casein. Biomacromolecules, 3: 432-437.

35. Dipakkore S, Reddy CRK and Jha B (2005) Production and seeding of protoplasts

of Porphyra okhaensis (Bangiales, Rhodophyta) in laboratory culture. J. Appl.

Phycol. 17: 331-337.

36. Dong J, Hashikawa S, Konishi T, Tamaru Y and Araki T (2006) Cloning of the

novel gene encoding I3-agarase C from marine bacterium Virbio sp. strain P0-303

and characterization of the gene product. Appl. Env. Microbiol. 72: 6399-6401.

37. Dong J, Tamaru Y and Araki T (2007) Molecular cloning, expression and

characterization of a 0-agarase gene agaD, from a marine bacterium Vibrio sp.

strain P0-303. Biosci. Biotechnol. Biochem. 71: 38-46.

38. Dretzen G, Bellard M, Sassoni-Corsi P and Chambon P (1981) A reliable method

for the recovery of DNA from agarose and acrylamide gels. Anal. Biochem. 112:

295-298.

39. Duckworth M and Yaphe W (1970) Thin layer chromatographic analysis of

enzymic hydrolysates of agar. J. Chromatog 49: 482-487.

40. Duckworth M and Yaphe W (1971a) The structure of agar. Part I. Fractionation of a

complex mixture of polysaccharides. Carbohyd. Res. 16: 189-197.

41. Duckworth M and Yaphe W (1971b) The structure of agar. Part II: The use of

bacterial agarose to elucidate structural features of the charged polysaccharides in

agar. Carbohydr. Res. 16: 435-445.

42. Eder K (1995) Gas chromatographic analysis of fatty acid methyl esters. J.

Chromatogr. B. 671: 113-131.

43. Ekborg NA, Taylor LE, Longmire AG, Henrissat B, Weiner RM and Hutcheson

SW (2006) Genomic and Proteomic Analyses of the Agarolytic System Expressed

by Saccharophagus degradans 2-40. Appl. Environ. Microbiol. 72: 3396-3405.

44. Ensor LA, Stosz SK and Weiner RM (1999) Expression of multiple complex

polysaccharide degrading enzyme systems by marine bacterium strain 2-40. J. Ind.

Microbiol. Biotechnol. 23: 123-126.

207

45. Epifanio CE (1979) Comparison of yeast and algal diets for bivalve mollusks.

Aqualculture. 16: 187-192.

46. Erasmus JH, Cook PA and Coyne VE (1988) The role of bacteria in the digestion of

seaweed by the abalone Haliotis midae. Aquaculture. 155: 377-386.

47. Fan CF and Mei XG (2005) A simple, efficient and economical method for

recovering DNA from agarose gel. Prep. Biochem. Biotechnol. 35, 71-78.

48. Felsenstein J (2006) PHYLIP (Phylogenetic Inference Package) version 3.66.

Department of Genetics, University of Washington, Seattle, USA.

49. Fernandez-Martinez J, Pujalte MJ, Garcia-Martinez J, Mata M, Garry E and

Rodriguez-Valera F (2003) Description of Alcanivorax venustenusis sp. nov. and

reclassification of Fundibacter jadensis DSM 12178T (Burns and Berther-Corti

1999) as Alcanivorax jadensis comb. nov., members of emended genus

Alcanivorax. Int. J. Syst. Evol. Microbiol. 53: 331-338.

50. Fleurence J (1999) The enzymatic degradation of algal cell walls: a useful approach

for improving proteins accessibility? J. Appl. Phycol. 11: 313-314.

51. Forsblom B, Sarkiala-Kessel E and Jousimies-Somer H (2000) Agar-pitting gram

negative rods in the subgingival flora of the dogs. Anaerobe. 6: 163-168 (abstract

only).

52. Fu W, Han B, Duan D, Liu W and Wang C (2008a) Purification and

characterization of agarases from a marine bacterium Vibrio sp F-6. J. Ind.

Microbiol. Biotechnol. DOI 10.1007/s10295-008-0365-2.

53. Fu XT, Lin H and Kim SM (2008b) Purification and characterization of a novel 13-

agarase AgaA34, from Agarivorans albus YKW-34. Appl. Microbiol. Biotechnol.

78: 265:278.

54. Fukasawa S, Dunlap P.V., Baba M and Osumi M (1987) Identification of an agar-

digesting, luminous bacterium. Agric. Biol. Chem. 51: 265-268.

55. Gacesa P and Wusteman FS (1990) Plate assay for simultaneous detection of

alginate lyases and determination of substrate specificity. Appl. Env. Microbiol. 56:

2265-2267.

208

56. GELRITE Gellan gum for microbiological applications: Kelco Application

Bulletin, CD-34, 2007.

57. Geresh S and Arad S (1991) The extracellular polysaccharides of the red

microalgae: chemistry and rheology. Biores. Techn. 38: 195-201.

58. Ghadi SC, Muraleedharan UD and Jawaid S (1997) Screening for agarolytic

bacteria and development of a novel method for in situ detection of agarase. J. Mar.

Biotechnol. 5: 194-200.

59. Gonzalez JM, Mayer F, Moran MA, Hodson RE and Whitman WB (1997)

Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense

gen. nov., two marine bacteria from a lignin rich pulp mill waste enrichment

community Int. J. Syst. Bacteriol. 47, 369-376.

60. Gonzalez JM, Whitman WB, Hodson RE and Moran MA (1996) Identifying

numerically abundant culturable bacteria from complex communities: an example

from a lignin enrichment culture. App. Environ. Microbiol. 62: 4433-4440.

61. Green DR and Reed JC (1998) Mitochondria and apoptosis. Science. 281: 1309-

1312.

62. Groleau D and Yaphe W (1977) Enzymatic hydrolysis of agar: Purification and

characterization ofil-neoagarotetraose hydrolase from Pseudomonas atlantica. Can.

J. Microbiol. 23: 672-679.

63. Ha JC, Kim GT, Kim SK, Oh TK, Yu JH and Kong IS (1997) (3-agarase from

Pseudomonas W7: Purification of the recombinant enzyme from Escherichia coli

and the effects of salt on its activity. Biotechnol. Appl Biochem. 26: 1-6.

64. Hatada Y, Ohta Y and Horikoshi K (2006) Hyperproduction and application of a-

agarase to enzymatic enhancement of antioxidant activity of porphyran. J. Agri.

Food Chem. 54: 9895-9900.

65. Hendricks CW, Doyle JD and Hugley B (1995) A new solid medium for

enumerating cellulose utilizing bacteria in soil. Appl. Environ. Microbiol. 61: 2016-

201 . 9.

209

66. Hitchens AP and Leikind MC (1939) The introduction of agar-agar into

bacteriology. J. Bacteriol. 37: 485-493.

67. Hjerten S (1952) A new method of preparation of agarose for gel electrophoresis.

Biochem. Biophys. Acta. 62: 445-449.

68. Hodgson DA and Chater KF (1981) A chromosomal locus controlling extracellular

agarase production by Streptomyces coelicolor A3(2) and inactivation by

chromosomal integration of plasmid SCP1. J. Gen. Microbiol. 124: 339-348.

69. Hosoda A and Sakai M (2006) Isolation of Asticcacaulis sp. SA7, a novel agar-

degrading Alphaproteobacterium. Biosci. Biotech. Biochem. 70: 722-725.

70. Hosoda A, Sakai M and Kanazawa S (2003) Isolation and characterization of agar-

degrading Paenibacillus spp associated with the rhizosphere of spinach. Biosci.

Biotech. Biochem. 67: 1048-1055.

71. Howard B, Ekborg N, Weiner RM and Hutcheson SW (2003) Detection and

characterization of chitinases and other chitin-modifying enzymes. J. Ind.

Microbiol. Biotechnol. 30: 627-635.

72. Huleihel M, Ishanu V, Tal J and Arad S (2001) Antiviral effect of red microalgal

polysaccharides on Herpes simplex and Varicella zoster viruses. J. Appl. Phycol.

13: 127-134.

73. Hunger W and Claus D (1978) Reisolation and growth conditions of Bacillus agar-

exedens. Antonie van Leeuwenhoek 44: 105-113.

74. Isiegas C, Parro V and Mellado RP (2002) Streptomyces lividans as a host for the

production and secretion of Escherichia coli TEM 13-lactamase Lett. Appl.

Microbiol. 28: 321 — 326

75. Ivanova EP, Sawabe T, Gorshkova NM, Svetashev VI, Mikhailov VV, Nicolau DV

and Christen R (2001) Shewanella japonica sp. nov. Int. J. Syst. Evol. Microbiol.

51: 1027-1033.

76. Jam M, Flament D, Allouch J, Potin P, Thion L, Kloareg B, Czjzek M, Helbert W,

Michel G and Barbeyron T (2005) The endo-P-agarases AgaA and AgaB from the

marine bacterium Zobellia galactivorans: two paralogue enzymes with different

molecular organizations and catalytic behaviours. Biochem. J. 385: 703-713. 210

77. Jannasch HW (1967) Enrichment of aquatic bacteria in continuous culture. Arch.

Microbiol. 59: 165-173.

78. Jean W, Sheih WY and Liu TY (2006) Thalassomonas agarivorans sp. nov., a

marine agarolytic bacterium isolated from shallow coastal water of An-Ping

Harbour, Taiwan and embedded description of the genus Thalassomonas. Int. J.

Syst. Evol. Microbiol. 56: 1245-1250.

79. Jedrzejas MJ (2000) Structural and function comparison of polysaccharide

degrading enzymes. Critical Rev. Biochem. Mol. Biol. 35: 221-251.

80. Jouberty Y and Fleurence J (2005) DNA Isolation Protocol for Seaweeds. Plant

Mol. Biol. Rep. 23: 197a-197g.

81. Kang NY, Choi YL, Cho YS, Kim BK, Jeon BS, Cha JY, Kim CH and Lee YC

(2003) Cloning, expression and characterization of a (3-agarase gene from a marine

bacterium, Pseudomonas sp. SK38. Biotechnol. Lett. 25: 1165-1170.

82. Karawita R, Siriwardhana N, Lee KW, Heo MS, Yeo IK, Lee YD and Jeon YJ

(2005) Reactive oxygen species scavenging, metal chelation, reducing power and

lipid peroxidation inhibition properties of different solvent fractions from Hizikia

fusiformis. Eur. Food Res. Technol. 220: 363-371.

83. Karrafa L, Fekette E, Gamuaf C, Szentirmai A, Kubick CP and Seiboth B (2006)

D-galactose induces cellulose gene expression in Hypocrea jecoria at low growth

rates. Microbiology. 152: 1507-1514.

84. Khambaty Y, Mody K and Jha B (2008) Purification, characterization and

application of a novel extracellular agarase from a marine Bacillus megatrium.

Biotech. Bioprocess. Eng. 13: 584-591.

85. Kim BJ, Kim HJ, Ha SD, Hwang SH, Byun DS, Lee TH and Kong JY (1999)

Purification and characterization of 13-agarase from marine bacterium Bacillus

cereus ASK202. Biotechnol. Lett. 21: 1011-1015.

86. Kirimura K, Masuda N, IwasakiY, Nakagawa H, Kobayashi R and Usami S

(1999) Purification and characterization of a novel beta-agarase from an

alkalophilic bacterium, Alteromonas sp. E-1. J. Biosci. 87,436-441

211

87. Kloareg B and Quatrano RS (1988) Structure of the cell walls of marine algae and

ecophysiological functions of the matrix polysaccharides. Oceanogr. Mar. Biol.

Annu. Rev. 26: 259-315.

88. Kluepfer D (1988) Screening for prokaryotes for cellulose and hemicellulose

degrading enzymes. In: Methods in Enzymology (Eds: Wood W.A. and Kellogg

S.T.) Vol.160, Academic Press, New York.

89. Kobayashi R, Takisada M, Suzuki T, Kirimura K and Usami S (1997)

Neoagarobiose as a novel moisturizer with whitening effect. Biosci. Biotechnol.

B io chem. 61: 162-163.

90. Kong J, Hwang S, Kim B, Bae S and Kim J (1997) Cloning and expression of an

agarase gene from a marine bacterium Pseudomonas sp W7. Biotechnol. Lett. 10:

23-26.

91. Kong JY (2001) Production and functional properties of agarooligosaccharides.

Proceedings of symposium on scientific study and industrialization of health food.

Health food society of Taiwan, Taipai. 60-81.

92. Kosugi A, Murashima K and Doi RH (2001) Characterization of xylanolytic

enzymes in Clostridium cellulovorans: expression of xylanase activity dependent

on growth substrances. Appl. Environ. Microbiol. 183: 7037-7043.

93. Kurasawa T, Yachi M, Suto M, Kamagata Y, Takao S and Tomita S (1992)

Induction of cellulose by gentiobiose and its sulfur containing analog in Penicillium

purpurogenum. Appl. Env. Microbiol. 58: 106-110.

94. Kurita K (2006) Chitin and chitosan: Functional biopolymers from marine

crustaceans. Mar. Biotechnol. 8: 203-226.

95. Kwakman JHJM and Postma PW (1994) Glucose kinase has a regulatory role in

carbon catabolite repression in Streptomyces coelicolor. J. Bacteriol. 176: 2694-

2698.

96. Lahaye M and Rochas C (1991) Chemical structure and physic-chemical properties

of agar. Hydrobiologia. 221/222: 137.

212

97. Lakshmikanth M, Manohar S, Souche Y and Lalitha J (2006a) Optimization of

culture conditions for the production of agarases from newly isolated Pseudomonas

aeuroginosa AG LSL-11. World. J. Microbiol. Biotechnol. DOI:10.1007/s11274-

006-9068-z.

98. Lakshmikanth• M, Manohar S, Souche Y and Lalitha J (2006b) Extracellular 13-

agarase LSL-1 producing neoagarobiose from a newly isolated agar-liquefying soil

bacterium, Acinetobacter sp., AG LSL-1. World J. Microbiol. Biotechnol.

DOI:10.1007/s11274-006-9147-z.

99. Lavilla-Pitogo CR (1992) Agar digesting bacteria associated with 'rotten thallus

syndrome' of Gracilaria sp. Aquaculture. 102: 1-7.

100. Lay HD and Whithers SG (1999) Mutagenesis of glycosidases. Ann. Rev.

Biochem.68: 487-522.

101. Lee DG, Jang MK, Lee OH, Kim NY, Ju SA and Lee SH (2008) Over-production

of a glycoside hydrolase family 50 [3-agarase from Agarivorans sp. JA-1 in Bacillus

subtilis and the whitening effect of its product. Biotechnol. Lett. 30:911-918.

102. Lee DG, Park GT, Kim NY, Lee EJ, Jang MK, Shin YG, Park GS, Kim TM, Lee

JH, Lee JH, Kim SJ and Lee SH (2006) Cloning, expression, and characterization

of a glycoside hydrolysate family 50 0-agarase from a marine Agarivorans isolate.

Biotechnol. Lett. 28: 1925-1932.

103. Lee SB, Park JH, Yoon SC, Kim JM and Kong IS (2000) Sequence analysis of a 13-

agarase gene (pajA) from Pseudomonas sp. isolated from marine environment. J

Biosci Bioeng 89: 485-488.

104. Leon 0, Quintana L, Peruzzo G and Slebe JC (1992) Purification and Properties of

an Extracellular Agarase from Alteromonas sp. Strain C-1. Appl Environ

Microbiol. 58: 4060-4063.

105. Lesser MP (2006) Oxidative stress in marine environments: Biochemistry and

Physiological ecology. Ann Rev. Physiol. 68: 253-278.

213

106. Li X and Roseman S (2004) The chitinolytic cascade in Vibrios is regulated by

chitin oligosaccharides and a two component chitin catabolic sensor/kinase. 101,

627-631.

107. Li X, Dong X, Zhao C, Chen Z and Chen F (2003) Isolation and some properties of

cellulose-degrading Vibrio sp. LX-3 with agar-liquefying ability from soil. World J.

Microbiol. Biotechnol. 19: 375-379.

108. Li Z, Xinzhi L, Feng H, Cuiping MA, Wengong YU (2007) Purification and

refolding of a novel 13-agarase from inclusion body of E. coli. J. Ocean. Univ. Chin.

6: 80-84.

109. Loewenberg JR and Chapman CM (2004) Sophorose metabolism and cellulose

induction. Arch. Microbiol. 113: 61-64.

110. Lowry OH, Rosebrough NJ, Farr AL, Randall RJ (1951) Protein measurement with

the folin phenol reagent. J. Biol. Chem. 193: 265-275.

111. Ma C, Lu X, Shi C, Li J, Gu Y, Ma Y, Chu Y, Han F, Gong Q and Yu W (2007)

Molecular cloning and characterization of a novel f3-agarase, AgaB from marine

Pseudoalteromonas sp. CY24. J Biol Chem 282: 3747-3754.

112. Malmqvist M (1978) Purification and characterization of two different agarose-

degrading enzymes. Biochem. Biophys. Acta. Protein Strucutre. 537: 31-43.

113. Mann KH (1988) Prsoduction and use of detritus in various fresh water, esturine

and coastal marine ecosystems. Limnol Oceanogr 33: 910-930.

114. Matsuhashi T (1998) Agar In: Polysaccharides: Strucutural diversity and functional

versality. Ed: Severial Dumitriu.

115. Meskiene R, Casaite V, Marcinkeviciene L, Bachmatova I and Meskys R (2003)

Cloning and analysis of agarase-encoding gene from Paenibacillus sp. Biologija. 1:

55-57.

116. Michel G, Nayvall-Collen P, Barbeyron T, Czjzek M and Helbert W (2006)

Bioconversion of red seaweed galactans: a focus on bacterial agarases and

carrageenases. Appl. Microbiol. Biotechnol. 71: 23-33.

214

117. Michen G, Chantalat L, Duee E, Barbeyron T, Henrissat B, Kloareg B and

Dideberg 0 (2001) The ic-carrageenase of P.carrageenovora features a tunnel

shaped active site: A novel insight in the evolution of clan-B glycoside hydrolases.

Structure. 9: 513-525.

118. Miller GL (1960) Measurement of carboxymethyl cellulase activity. Anal.

Biochem. 1: 127-132.

119. Miyazaki K, Hirase T, Kojima Y and Flint HJ (2005) Medium-to large sized

xylooligosaccharides are responsible for xylanse induction in Prevotella bryantii

B I 4. Microbiology. 151: 4121-4125.

120. Miyazaki M, Nogi Y, Ohta Y, Hatada Y, Fujiwara Y, Ito S, Horikoshi K. (2008)

Microbulbifer agarilyticus sp.nov. and Microbulbifer thermotolerans sp.nov., agar-

degrading bacteria isolated from deep-sea sediment. Int. J. Syst. Evol. Microbiol.

58: 1128-1133.

121. Morrice LM, McLean MW, Long WF and Williamson FB (1983a) Porphyran

primary structure. Eur. J. Biochem. 133: 673-684.

122. Morrice LM, McLean MW, Williamson FB and Long WF (1983b)13-agarases I and

II from Pseudomonas atlantica. Eur. J. Biochem. 135: 553-558.

123. Naganuma T and Horikoshi K (1994) Cellular fatty acids of marine agarolytic

gliding bacteria. System Appl. Microbiol. 17: 125-127.

124. Nagao A T, Hahn-Zoric M, Wadsworth C, Gustafsson B, Ulanova M, Hanson L

125. Nedashkovskaya OI, Kim SB, Vancanneyt M, Shin DS, Lysenko AM, Shevchenko

LS, Krasokhin VB, Mikhailov VV, Swings J, Bae KS (2006) Salegentibacter

agarivorans sp. nov., a novel marine bacterium of the family Flavobacteriaceae

isolated from the sponge Artemisina sp. Int J Syst Evol Microbiol. 56: 883-887.

126. Nisizawa T, Suzuki H and Nisizawa K (1971) Denovo synthesis of cellulase

induced by sophorose in Trichoderma viride cells. J. Biochem. 70: 387-393.

127. O'Sullivan AC (1997) Cellulose: the structure slowly unravels. Cellulose. 4: 173-

207.

215

128. Ohata Y and Hatada Y (2006) A novel enzyme X-carrageenase isolated from a deep

sea bacterium. J. Biochem 140: 475-481.

129. Ohta Y and Hatada Y (2006) A novel enzyme X-carrageenase, isolated from a deep

sea bacterium. J. Biochem. 140: 475-481.

130. Ohta Y, Hatada Y, Ito S, Horikoshi K (2005) High-level expression of a

neoagarobiose-producing 13-agarase gene from Agarivorans sp. JAMB-Al 1 in

Bacillus subtilis and enzymic properties of the recombinant enzyme. Biotechnol.

Appl. Biochem. 41: 183-191.

131. Ohta Y, Hatada Y, Miyazaki M, Nogi Y, Ito S and Horikoshi K (2005) Purification

and characterization of a novel a-agarase from a Thalassamonas sp. Curr.

Microbiol. 50: 212-216.

132. Ohta Y, Hatada Y, Nogi Y, Li Z, Ito S and Horikoshi K (2004) Cloning, expression

and characterization of a glycoside hydrolase family 86 13-agarase from a deep-sea

Microbulbifer-like isolate. Appl. Microbiol. Biotechnol. 66: 266-275.

133. Ohta Y, Hatada Y, Nogi Y, Li Z, Ito S and Horikoshi K (2004) Cloning, expression

and characterization of a glycoside hydrolase family 86 f3-agarase from a deep sea

Microbulbifer-like isolate. Appl Microbiol Biotechnol 66: 266-275.

134. Ohta Y, Hatada Y, Nogi Y, Miyazaki M, Li Z, Akita M , Hidaka Y, Goda S, Ito S

and Horikoshi K (2004) Enzymatic properties and nucleotide and amino acid

sequences of a thermostable 13-agarase from a novel species of deep-sea

Microbulbifer. Appl. Microbiol. Biotechnol. DOI: 10.1007/s00253-004-11573-y.

135. Ohta Y, Hatada Y, Nogi Y, Miyazaki M, Li Z, Akita M, Hidaka Y, Goda S, Ito S

and Horikoshi K (2004) Enzymatic properties and nucleotide and amino acid

sequences of a thermostable 0-agarase from a novel species of deep-sea

Microbulbifer. Appl. Microbiol. Biotechnol. 64: 505-514.

136. Ohta Y, Nogi Y, Miyazaki M, Li Z, Hatada Y, Ito S and Horikoshi K. (2004)

Enzymatic properties and nucleotide and amino acid sequences of a thermostable p-

agarase from the novel marine isolate JAMB-A94. Biosci. Biotech. Biochem. 68:

1073-1081.

216

137. Ohta Y, Hatada Y, Nogi Y Miyazaki M, Li Z, Akita M ,Hidaka Y, Goda S, Ito

S and Horikosh K (2004) Enzymatic properties and nucleotide and amino acid

sequences of a thermostable 13-agarase from a novel species of deep-sea

Microbulbifer. Appl. Microbiol. Biotechnol. 64: 505-514.

138. Osumi Y, Kawai M, Amano H, Noda H (1998) Effect of oligosaccharides from

porphyran on in vitro digestions, utilizations by various intestinal bacteria, and

levels of serum lipids in mice. Nippon. Suisan. Gakkaishi. 64: 98-104.

139. Ouyang X, Yu W, Wang Q, He J and Liu Q (2006) Rapid recovery of DNA from

agarose gel slice using a microwave. J. Rapid Methods Automation in

Microbiology. 14: 389-394.

140. Oyaizu H and Komaguta K (1983) Grouping of Pseudomonas species on the basis

of cellular fatty acid composition and the quinine system with special reference to

the existence of 3-hydroxy fatty acids. J. Gen. Appl. Microbiol. 29: 17-40.

141. Pakuski JD and Benner R (1994) Abundance and distribution of carbohydrates in

the ocean. Limnol Oceanogr. 39: 930-940.

142. Peberdy JF (1985) Mycolytic enzymes. In: Fungal protoplasts. Applications in

biochemistry and genetics (Eds: Peberdy JF and Ferenczy L) pp: 31-44. Marcel

Deker, New York.

143. Polne-Fuller M and Gibor A (1987) Microorganisms as digesters of seaweed cell

walls. Hydrobiologia. 151 / 152: 405-409.

144. Potin P, Richard C, Rochas C and Kloareg B (1993) Purification and

characterization of the a-agarase from Alteromonas agarlyticus (cataldi) comb.

Nov., strain GJ1B. Eur. J. Biochem. 214: 599-607.

145. Provosoli L (1971) Media and prospects for cultivation of marine algae. In: selected

papers in phycology. (Eds: Rosowski and Parker B) University of Nerbraska,

Lincoln, Nebraska.pp599-644.

146. Quatrano RS and Cladwell BA (1978) Isolation of a unique marine bacterium

capable of growth on wide of polysaccharides from macroalgae. Appl. Environ.

Microbiol. 36:979-981.

217

147. Rees DA (1969) Structure, conformation, mechanism in the formation of

polysaccharide gels and networks. Advances Carbohyd. Chem. Biochem. 24: 267-

332.

148. Rees DA (1972) Shapely Polysaccharides. The Eighth Colworth Medal Lecture.

Biochem. J. 126: 257-273.

149. Rees GN, Rainey FA, Harfoot CG (1976) Characterization of a novel obligate

anaerobe that ferments agar. Arch. Microbiol. 42: 81-94.

150. Renn DW (1984) Agar and Agarose: Indispensible partners in biotechnology. Ind

Eng Chem Prod Res Dev 23: 17-21.

151. Resmi (1993) Agarase production from by marine bacteria for protoplast isolation

from red algae. M.Sc Thesis, Cochin University of Science and Technology, India.

152. Roberfroid M and Slavin J (2000) Nondigestable oligosaccharides. Crit. Rev. Food.

Sci. Nutr. 40: 461-480.

153. Rocha de Souza MC, Marques CT, Dore CMG, Ferreira da Silva FR, Rocha HAO

and Leite EL (2007) Antioxidant activities of sulfated polysaccharides from brown

and red seaweeds. J. Appl. Phycol. 19:153-160.

154. Rochas C (1991) Chemical structure and physico-chemical properties of agar.

Hydrobiologia. 221: 137-148.

155. Rochas C, Potin P and Kloareg B (1994) NMR spectroscopic investigation of

agarose oligomers produced by an alpha agarase. Carbohydr. Res. 253: 69-77.

156. Romanenko LA, Zhukova NV, Rohde M, Lysenko AM, Mikhailov VV and

Stackebrandt E (2003) Pseudoalteromonas agarivorans sp. nov., a novel marine

agarolytic bacteriuni. Int. J. Syst. Evol. Microbiol. 53: 125-131.

157. Ruijssenaars HJ and Hartmans S (2001) Plate screening methods for the detection

of polysaccharase producing microorganisms. Appl. Microbiol. Biotechnol. 55:

143-149.

158. Ryu SK, Cho SJ, Park SR, Lim WJ, Kim MK, Hong SY, Bae DW, Park YW, Kim

BK, Kim H and Yun HD (2001) Cloning of the cel9A gene and characterization of

218

its gene product from marine bacterium Pseudomonas sp. SK-38. Appl. Microbiol.

Biotechnol. 57: 138-145.

159. Salyers AA, Reeves A and D'Elia J (1996) Solving the problem of how to eat

something as big as yourself: diverse bacterial strategies for degrading

polysaccharides J. Ind. Microbiol. 17: 470-476.

160. Sampietro AR and Sampietro MAV (1971) Characterization of the agarolytic

system ofAgarbacterium pastinator. Biochemica. Biophysica. Acta. 244: 65-76.

161. Sasser M (2006) Bacterial identification by gas chromatographic analysis of fatty

acid methyl esters (GC-FAME). MIDI Technical Note 101.

162. Schroeder DC, Jaffer MA and Coyne VE (2003) Investigation of the role of a p(1 -

4) agarase produced by Pseudoalteromonas gracilis B9 in eliciting disease

symptoms in the red alga Gracilaria gracilis. Microbiology 149: 2919-2929.

163. Seiboth B, Hartl L, Salovuori N, Lanthaler K, Robson GD, Vehmaanpera J, Penttial

ME, Kubicek CP (2005) Role of the Bga-1 encoded extracellular 13-galactosidase of

Hypocrea jecorina in cellulose induction by lactose. Appl. Env. Microbiol. 71: 851-

857.

164. Shi YL, Lu, XZ and Yu WG (2008) A new (3-agarase from marine bacterium

Janthinobacterium sp. SY12. World. J. Microbiol. Biotechnol. 24: 2659-2664.

165. Shieh WY and Jean WD (1998)-Alterococcus agarolyticus, gen. nov., sp.nov., a

halophilic thermophilic bacterium capable of agar degradation. Can. J. Microbiol.

44: 637-645.

166. Shieh WY, Lie TY, Lin SY, Jean WD and Chen J (2008) Simiduia agarivorans

gen. nov., sp. nov., a marine, agarolytic bacterium isolated from shallow coastal

water from Keelung, Taiwan. Int. J. Syst. Evol. Microbiol. 58: 895-900.

167. Shively JM, English RM, Baker SH and Cannon GC (2001) Carbon cycling: the

prokaryotic contribution. Curr. Opinion. Microbiol. 4: 301-306.

168. Shungu D, Valiant M, Tutlane V, Weinberg E, Weissberger B, Koupal L,

Gadebusch H and Stapley E (1983) GELRITE as an agar substitute in

bacteriological mecia. Appl. Environ. Microbiol. 46: 840-845.

219

169. Siddantha AK (2005) Chemical investigation and value addition of seaweeds.

Indian Hydrobiology. 7: 29-34.

170. Simbert RM and Krieg NR (1994) Phenotypic characterization In: Methods for

general and molecular bacteriology, Ed: Gerhardt F, pp. 607-654, American Society

for Microbiology, Washington D.C.

171. Skjak-Barek G and Martinsen A (1991) Applications of some algal polysaccharides

in Biotechnology. In: Seaweed resources in Europe: Uses and potential (Eds: Guiry

MD and Blunden G) pp 219-257, Wiley and Sons, New York.

172. Skjak-Barek G, Larsen B and Grasdalen H (1985) The role of 0-acetyl groups in

the biosynthesis of alginate by Azotobacter vinelandii. Carbohydr. Res. 145: 169-

174.

173. Soo-Cheol Y, Lee JH, Alm SH, Lee EM, Park EM and Kong IS (2003) Purification

and comparison of properties of the C-terminus truncated agarase of Pseudomonas

sp. W7. J. Microbiol. Biotechnol. 13: 767-772.

174. Stanier RY (1941) Studies on agar digesting bacteria. J. Bacteriol. 42: 527-555.

175. Stanley NF (1995) Agars In: Food polysaccharides and their applications. Ed:

Stephen A.M. Marcel Derker Inc, NY., USA.

176. Subramaniyan S and Prema P (2002) Biotechnology of microbial xylanses-

Enzymology, Molecular biology and application. Crit. Rev. Biotehnol. 22: 33-64.

177. Sugano Y, Nagae H, Inagaki K, Yamamoto T, Terada I and Yamazaki Y (1995)

Production and characteristics of some new 13-agarases from a marine bacterium,

Vibrio sp. strain JT0107. J. Ferment. Bioeng. 79: 549-554.

178. Sugano Y, Tereda I, Arita M, Noma M and Matsumoto T (1993) Purification and

characterization of a new agarase from a marine bacterium Vibrio sp. strain JT0107.

Appl. Environ. Microbiol. 59: 1549-1554.

179. Suzuki H, Sawai Y, Suzuki T and Kawai K (2003) Purification and characterization

of extracellular I3-agarase from Bacillus sp. MK03. J. Biosci. Bioeng. 95: 328-334.

220

180. Suzuki H, Sawai Y, Suzuki T, Kawai K (2002) Purification and characterization of

an extracellular a-neoagarooligosaccharide hydrolase from Bacillus sp. MK03. J.

Biosci. Bioeng. 93: 456-463.

181. Swartz MN and Gordon N (1958) Agarase from an agar-digesting bacterium. J.

Bacteriol. 77: 403-409.

182. Tabak HF and Flavell RA (1978) A method for the recovery of DNA from agarose

gels. Nucleic Acid Res. 5: 2321-2332.

183. Tanaka T, Yan. L and Burgess JG (2003) Microbulbifer arenaceous sp. nov., a new

endolithic bacterium isolated from the inside of red sand stone. Curr. Microbiol. 47:

412-416.

184. Tang SK, Wang Y, Cai M, Lou K, Mao PH, Jin X, Jiang CL, Xu LH and Li WJ

(2008) Microbulbifer halophilus sp. nov., a moderately halophilic bacterium from

north west china. Int. J. Syst. Evol. Microbiol. 58, 2036-2040.

185. Teather RM and Wood PJ (1982) Use of Congo red-polysaccharide interactions in

enumeration and characterization of cellulolytic bacteria from bovine rumen. Appl.

Environ. Microbiol. 43: 777-780.

186. Tellez CM and Cole KD (2000) Preparative electrochromatography of proteins in

various types of porous media. 21: 1001-1009.

187. Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: improving the

sensitivity of progressive multiple sequence alignment through sequence weighting,

positions-specific gap penalties and weight matrix choice. Nucleic Acid Res. 22,

4673-4680.

188. Thuring RWJ, Sanders JPM and Borst P (1975) A freeze squeeze method for

recovering long DNA from agarose gels. Anal. Biochem. 66: 213-220.

189. Toncheva-Panova T and Ivanova J (1997) A bacterial pathogen of Rhodella

reticulata. J. Appl. Microbiol. 83: 707-711.

190. Toussaint G, Ding LH, Jaffi -in MY, Hassairi I and Nonus M (2000) Recovery of a-

agarase enzyme from fermentation broths by membrane cross flow filtration.

Separation Science and Technology. 35: 795-809.

221

191. Tseng CK (1944) Agar: A valuable seaweed product. Scientific Monthly. 58: 24-

32.

192. Uchida M (1996) Formation of single cell detritus densely covered with bacteria

during experimental degradation of Laminaria japonica thalli. Fisheries sci. 62:

731-736.

193. Uetanabaro AP, Wahrenburg C, Hunger W, Pukall R, Sproer C, Stackebrandt E, de

Canhos VP, Claus D and Fritze D (2003) Paenibacillus agarexedens sp. nov., and

Paenibacillus agaridevorans sp. nov. Int. J. Syst. Evol. Microbiol. 53: 1051-1057.

194. Vallin C, Ramos A, Pimienta E, Rodriguez R, Hernandez T, Hernandez I, Sol RD,

Rosabal G, Mellaert LV and Anne J (2006) Streptomyces as host for recombinant

production of Mycobacterium tuberculosis proteins. Tuberculosis. 86: 198-202.

195. Van De Velde F, Knusten SH, Usov AI, Rollemma HS and Cerezo AS (2002) 'H

and 13C high resolution NMR spectroscopy of carrageenans: applications in

research and industry. Trends. Food. Sci. Technol. 13: 73-92.

196. Van Der Meulen HJ, Harder W and Veldkamp H (1976) Isolation and

characterization of Cytophaga flevensis sp. nov., a new agarolytic flexibacterium,

Antonie van Leewenhoek. 40: 329-346 (Abstract only).

197. Venkateswaran K and Natarajan R (1980) Distribution of agarolytic bacteria in

Portonovo coastal waters. Indian J. Mar. Sci. 9: 216-218.

198. Vera J, Alvarez R, Murano E, Slebe JC, and Leon 0 (1998) Identification of a

marine agrolytic Pseudoalteromonas isolate and characterization of its extracellular

agarase. Appl. Environ. Microbiol. 64: 4378-4383.

199. Viera MP, Gomez Pinchetti JL, Courtois de Vicose G, Bilbao A, Sua'rez A,

Haroun RJ and Izquierdo MS (2005) Aquaculture. 248: 75-82.

200. Vivian L, Yip Yand Withers SG (2004) Nature's mechanism for the degradation of

oligosaccharides. Org . Biomol. Chem. 2: 2707-2713.

201. Vogelstein B and Gillespie D (1979) Preparative and analytical purification of

DNA from agarose. Proc. Natl. Acad. Sci. 76: 615-619.

222

202. Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE and Streit WR (2003)

Prospecting for Novel Biocatalysts in a Soil Metagenome. Appl. Environ.

Microbiol. 69: 6235-6242.

203. Waksman SA and Bavendamm W (1931) On the decomposition of agar-agar by an

aerobic bacterium. J. Bact. 22: 91-102.

204. Wang J Jiang X, Mou H and H Guan H (2004) Anti-oxidation of agar

oligosaccharides produced by agarase from a marine bacterium, Journal of Applied

Phyco logy Vol-16, 333-340.

205. Wang J, Mou H, Jiang X and Guan H (2006) Characterization of a novel I3-agarase

from marine Alteromonas sp. SY37-12 and its degrading products. Appl. Microbiol.

Biotechnol. DOI: 10.1007/s00253-005-0207-3.

206. Wang P, JKiang X, Jiang Y, Hu X, Mou X, Li M and Guan H (2007) In vitro

antioxidative activities of three marine oligosaccharides. Natural Product Research.

21: 646-657.

207. Wang SC, Wang Y, Xu XW, Zhand DS, Wu YH and Wu M (2009) Microbulbifer

donghaiensis sp. nov., isolated from marine sediments of the west china sea. Int J

Syst Evol Microbiol 59: 545-549.

208. Weiner R, Chakravorthy D and Whiteland L (1998) The architecture of degradative

complex polysaccharide enzyme arrays in a marine bacterium has implications for

bioremediation. In "New developments in marine biotechnology," eds, Gal, L and

Halvorson, Plenum Press, New York, pp.171-176 (1998).

209. Welch DF (1991) Application of cellular fatty acid analysis. Clin. Microbiol. Rev.

4: 422-438.

210. Whiteland LA, Stosz SK and Weiner RM (2001) Characterization of the agarase

system of a multiple carbohydrate degrading marine bacterium. Cytobios. 106

Suppl 1:99-117.

211. Wong KKY, Tan LUL and Saddler JN (1988) Multiplicity of 13-1,4-xylanase in

microorganisms: functions and applications. Microbiol. Rev. 52: 305-317.

223

212. Wong TY, Preston LA and 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.

213. Wu SC, Wen TN and Pan CL (2004) Preparation of algal oligosaccharide mixtures

by bacterial agarases and their Antioxidative properties. Fisheries Sci. 71: 1149-

1159.

214. Xue CH, Fang Y, Lin H, Chen L, Li ZJ, Deng D and Lu CX (2001) Chemical

characters and antioxidative properties of sulfated polysaccharides from Laminaria

japonica . J. Appl. Phycol. 13: 67-70.

215. Yamura I, Matsumoto T, Funatsu M, Shigeiri H and Shibata T (1991) Purification

and some properties of agarase from Psedumonas sp. PT-5. Agric. Biol. Chem. 55:

2531-2536.

216. Yeong HY, Khalid N and Phang SM (2007) Protoplast isolation and regeneration

from Gracialria changii (Gracilariales, Rhodophyta) J. Appl. Phycol. DOI:

10.1007/s10811-007-9249-5.

217. Yi KW and Shin IS (2006) Isolation of marine bacterium decomposing sea tangle

(Laminaria japonica) to single cell detritus. Korean J. Food Sci. Technol. 38: 237-

240.

218. Yoon JH, Kim H, Kang KH, Oh TK and Park YH (2003a) Transfer of

Pseudomonas elongate Humm 1946 to the genus Microbulbifer as Microbulbifer

elongatus comb. nov. Int. J. Syst. Evol. Microbiol. 53: 1357-136.

219. Yoon JH, Kim IG, Oh TK and Park YH (2004) Microbulbifer maritimus sp. nov.,

isolated from an intertidal sediment from the yellow sea, Korea. Int. J. Syst. Evol.

Microbiol. 54: 1111-1116.

220. Yoon JH, Kim IG, Shin DY, Kang KH and Park YH (2003b) Microbulbifer

salipaludis sp. nov., a moderate halophile isolated from a Korean salt marsh. Int. J.

Syst. Evol. Microbiol. 53, 53-57.

221. Yoshizawa Y, Ametani A, Tsunehiro J, Nomura K, Itoh M, Fukui F, Kaminogawa

S, (1995) Macrophage stimulation activity of the polysaccharide fraction from a

224

marine algae (Porphyra yezoensis): structure—function relationships and improved

solubility Biosci, Biotechnol. Biochem. 59:1933-1937.

222. Yoshizawa Y, Enomoto A, Todoh H, Ametani A, Kaminogawa S (1996) Activation

of murine macrophages by polysaccharide fractions from marine algae (Porphyra

yezoensis). Biosci. Biotechnol. Biochem. 57:1862-1866.

223. Yukihisa A and Yuto K (2006) Preparation of recombinant polysaccharide-

degrading enzymes from the marine bacterium, Pseudomonas sp. ND137 for the

production of protoplasts of Porphyra yezoensis. Eur. J. Phycol. 41:321-328.

224. Zhang W and Sun L (2007) Cloning characterization and molecular application of a

beta-agarase gene from Vibrio sp. strain V134. Appl. Env. Microbiol. 73: 2825-

2831.

225. Zhao X, Xue CH, Li ZJ, Cai YP, Liu HY and Qi HT (2004) Antioxidant and

hepatoprotective activities of low molecular weight sulfated polysaccharide from

Laminaria japonica. J. Appl. Phycol 16: 111-115.

226. Zhong Z, Toukdarian A, Helinski D, Knauf V, Sykes S, Wilkinson JE, O'Bryne C,

Shea T, DeLoughery C, Caspi R (2001) Sequence analysis of a 101-kilobase

plasmid required for agar degradation by a Microscilla isolate. Appl. Environ.

Microbiol. 67:5771-5779.

225