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3 Biotech

, 8:445 | Cite as

Recombinant β-agarases: insights into molecular, biochemical, and physiochemical characteristics

  • Sneeha Veerakumar
  • Ramesh Pathy Manian
Review Article
  • 53 Downloads

Abstract

Agarases (agarose 4-glycanohydrolase; EC 3.2.1.81) are class of enzymes that belong to glycoside hydrolase (GH) family capable of hydrolyzing agar. Their classification depends on hydrolysis pattern and product formation. Among all the agarases, β-agarases and the oligosaccharides formed by its action have fascinated quite a lot of industries. Ample of β-agarase genes have been endowed from marine sources such as algae, sea water, and marine sediments, and the expression of these genes into suitable host gives rise to recombinant β-agarases. These recombinant β-agarases have wide range of industrial applications due to its improved catalytic efficiency and stability in tough environments with ease of production on large scale. In this review, we have perused different types of recombinant β-agarases in consort with their molecular, physiochemical, and kinetic properties in detail and the significant features of those agarases are spotlighted. From the literature reviewed after 2010, we have found that the recombinant β-agarases belonged to the families GH16, GH39, GH50, GH86, and GH118. Among that, GH39, GH50, and GH86 belonged to clan GH-A, while the GH16 family belonged to clan GH-B. It was observed that GH16 is the largest polyspecific glycoside hydrolase family with ample number of β-agarases and the families GH50 and GH118 were found to be monospecific with only β-agarase activity. And, out of 84 non-catalytic carbohydrate-binding modules (CBMs), only CBM6 and CBM13 were professed in β-agarases. We witnessed a larger heterogeneity in molecular, physiochemical, and catalytic characteristics of the recombinant β-agarases including molecular mass: 32–132 kDa, optimum pH: 4.5–9, optimum temperature 16–60 °C, KM: 0.68–59.8 mg/ml, and Vmax: 0.781–11,400 U/mg. Owing to this extensive range of heterogeneity, they have lion’s share in the multibillion dollar enzyme market. This review provides a holistic insight to a few aspects of recombinant β-agarases which can be referred by the upcoming explorers to this area.

Keywords

Recombinant β-agarases Glycoside hydrolase Molecular characteristics Physiochemical properties Kinetic properties 

Notes

Acknowledgements

The authors are very thankful to the management of VIT for providing the necessary infrastructure to carry out this work.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest for this article.

References

  1. AGBO JA, MOSS MO (1979) The isolation and characterization of agarolytic bacteria from a lowland river. Microbiology 115(2):355–368Google Scholar
  2. Alkotaini B, Han NS, Kim BS (2016) Enhanced catalytic efficiency of endo-β-agarase I by fusion of carbohydrate-binding modules for agar prehydrolysis. Enzyme Microb Technol 93:142–149PubMedCrossRefGoogle Scholar
  3. Allouch J, Jam M, Helbert W, Barbeyron T, Kloareg B, Henrissat B, Czjzek M (2003) The three-dimensional structures of two β-agarases. J Biol Chem 278(47):47171–47180PubMedCrossRefGoogle Scholar
  4. Allouch J, Helbert W, Henrissat B, Czjzek M (2004) Parallel substrate binding sites in a β-agarase suggest a novel mode of action on double-helical agarose. Structure 12(4):623–632PubMedCrossRefGoogle Scholar
  5. An K, Shi X, Cui F, Cheng J, Liu N, Zhao X, Zhang XH (2018) Characterization and overexpression of a glycosyl hydrolase family 16 beta-agarase YM01-1 from marine bacterium Catenovulum agarivorans YM01T. Protein Expr Purif 143:1–8PubMedCrossRefGoogle Scholar
  6. Carbohydrate active enzyme database (2018). http://www.cazy.org/. Accessed 1 Oct 2018
  7. Carlsson J, Malmqvist M (1977) Effects of bacterial agarase on agarose gel in cell culture. In Vitro 13(7):417–422PubMedCrossRefGoogle Scholar
  8. Chen XL, Hou YP, Jin M, Zeng RY, Lin HT (2016) Expression and characterization of a novel thermo stable and pH-stable β-agarase from deep-sea bacterium Flammeovirga sp. OC4. J Agric Food Chem 64(38):7251–7258PubMedCrossRefGoogle Scholar
  9. Chi WJ, Seo YB, Chang YK, Lee SY, Hong SK (2014) Cloning, expression, and biochemical characterization of a novel GH16 β-agarase AgaG1 from Alteromonas sp. GNUM-. Appl Microbiol Biotechnol 98(10):4545–4555PubMedCrossRefGoogle Scholar
  10. Chi WJ, Lee CR, Dugerjonjuu S, Park JS, Kang DK, Hong SK (2015a) Biochemical characterization of a novel iron-dependent GH16 β-agarase, AgaH92, from an agarolytic bacterium Pseudoalteromonas sp. H9. FEMS Microbiol Lett 362(7):1–7Google Scholar
  11. Chi WJ, Park JS, Chang YK, Hong SK (2015b) Cloning, expression, and biochemical characterization of a GH16 β-agarase AgaH71 from Pseudoalteromonas hodoensis H7. Appl Biochem Biotechnol 175(2):733–747PubMedCrossRefGoogle Scholar
  12. Cui F, Dong S, Shi X, Zhao X, Zhang XH (2014) Overexpression and characterization of a novel thermo stable β-Agarase YM01-3, from marine bacterium Catenovulum agarivorans YM01T. Mar Drugs 12(5):2731–2747PubMedPubMedCentralCrossRefGoogle Scholar
  13. Di W, Qu W, Zeng R (2018) Cloning, expression, and characterization of thermal-stable and pH-stable agarase from mangrove sediments. J Basic Microbiol 58(4):302–309PubMedCrossRefGoogle Scholar
  14. Dong Q, Ruan L, Shi H (2016) A β-agarase with high pH stability from Flammeovirga sp. SJP92. Carbohydr Res 432:1–8PubMedCrossRefGoogle Scholar
  15. Ekborg NA, Taylor LE, Longmire AG, Henrissat B, Weiner RM, Hutcheson SW (2006) Genomic and proteomic analyses of the agarolytic system expressed by Saccharophagus degradans 2-40. Appl Environ Microbiol 72(5):3396–3405PubMedPubMedCentralCrossRefGoogle Scholar
  16. Fu XT, Kim SM (2010) Agarase: review of major sources, categories, purification method, enzyme characteristics and applications. Mar Drugs 8(1):200–218PubMedPubMedCentralCrossRefGoogle Scholar
  17. Fu XT, Pan CH, Lin H, Kim SM (2009) Gene cloning, expression, and characterization of a beta-agarase, agaB34, from Agarivorans albus YKW-34. J Microbiol Biotechnol 19(3):257–264PubMedGoogle Scholar
  18. Gebler J, Gilkes NR, Claeyssens M, Wilson DB, Béguin P, Wakarchuk WW, Kilburn DG, Miller RC, Warren RA, Withers SG (1992) Stereoselective hydrolysis catalyzed by related beta-1, 4-glucanases and beta-1, 4-xylanases. J Biol Chem 267(18):12559–12561PubMedGoogle Scholar
  19. Giles K (2014) Insight into the functionality of an unusual glycoside hydrolase from family 50 (Doctoral dissertation)Google Scholar
  20. Ha SC, Lee S, Lee J, Kim HT, Ko HJ, Kim KH, Choi IG (2011) Crystal structure of a key enzyme in the agarolytic pathway, α-neoagarobiose hydrolase from Saccharophagus degradans 2-40. Biochem Biophys Res Commun 412(2):238–244PubMedCrossRefGoogle Scholar
  21. Hehemann JH (2009) Structural and functional organisation of the agarolytic enzyme system of the marine flavobacterium Zobellia galactanivorans. Doctoral dissertation, Paris 6Google Scholar
  22. Hehemann JH, Correc G, Thomas F, Bernard T, Barbeyron T, Jam M, Helbert W, Michel G, Czjzek M (2012) Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans. J Biol Chem 287:30571–30584PubMedPubMedCentralCrossRefGoogle Scholar
  23. Henrissat B, Bairoch A (1996) Updating the sequence-based classification of glycosyl hydrolases. Biochem J 316(Pt 2):695PubMedPubMedCentralCrossRefGoogle Scholar
  24. Hong SJ, Lee JH, Kim EJ, Yang HJ, Park JS, Hong SK (2017) Anti-obesity and anti-diabetic effect of neoagarooligosaccharides on high-fat diet-induced obesity in mice. Mar drugs 15(4):90PubMedCentralCrossRefGoogle Scholar
  25. Hou Y, Chen X, Chan Z, Zeng R (2015) Expression and characterization of a thermo stable and pH-stable β-agarase encoded by a new gene from Flammeovirga pacifica WPAGA1. Process Biochem 50(7):1068–1075CrossRefGoogle Scholar
  26. Hsu PH, Wei CH, Lu WJ, Shen F, Pan CL, Lin HT (2015) Extracellular production of a novel endo-β-agarase AgaA from Pseudomonas vesicularis MA103 that cleaves agarose into neoagarotetraose and neoagarohexaose. Int J Mol Sci 16(3):5590–5603PubMedPubMedCentralCrossRefGoogle Scholar
  27. Jang MK, Lee DG, Kim NY, Yu KH, Jang HJ, Lee SW, Lee YJ, Lee SH (2009) Purification and characterization of neoagarotetraose from hydrolyzed agar. J Microbiol Biotechnol 19(10):1197–1200PubMedGoogle Scholar
  28. Jung S, Jeong BC, Hong SK, Lee CR (2017a) Cloning, expression, and biochemical characterization of a novel acidic GH16 β-Agarase, AgaJ11, from Gayadomonas joobiniege G7. Appl Biochem Biotechnol 181(3):961–971PubMedCrossRefGoogle Scholar
  29. Jung S, Lee CR, Chi WJ, Bae CH, Hong SK (2017b) Biochemical characterization of a novel cold-adapted GH39 β-agarase, AgaJ9, from an agar-degrading marine bacterium Gayadomonas joobiniege G. Appl Microbiol Biotechnol 101(5):1965–1974PubMedCrossRefGoogle Scholar
  30. Kim HT, Lee S, Lee D, Kim HS, Bang WG, Kim KH, Choi IG (2010) Overexpression and molecular characterization of Aga50D from Saccharophagus degradans 2-40: an exo-type β-agarase producing neoagarobiose. Appl Microbiol Biotechnol 86(1):227–234PubMedCrossRefGoogle Scholar
  31. Kim JH, Yun EJ, Seo N, Yu S, Kim DH, Cho KM, An HJ, Kim JH, Choi IG, Kim KH (2017) Enzymatic liquefaction of agarose above the sol–gel transition temperature using a thermo stable endo-type β-agarase, Aga16B. Appl Microbiol Biotechnol 101(3):1111–1120PubMedCrossRefGoogle Scholar
  32. Kim SW, Kim YW, Hong CH, Lyo IW, Lim HD, Kim GJ, Shin HJ (2018) Recombinant agarase increases the production of reducing sugars from HCl-treated Gracilaria verrucosa, a red algae. Algal Res 31:517–524CrossRefGoogle Scholar
  33. Lakshmikanth M, Manohar S, Souche Y, Lalitha J (2006) Extracellular β-agarase LSL-1 producing neoagarobiose from a newly isolated agar-liquefying soil bacterium, Acinetobacter sp., AG LSL-1. World J Microbiol Biotechnol 22(10):1087–1094CrossRefGoogle Scholar
  34. Lee DG, Jeon MJ, Lee SH (2012) Cloning, expression, and characterization of a glycoside hydrolase family 118 beta-agarase from Agarivorans sp. JA-1. J Microbiol Biotechnol 22(12):1692–1697PubMedCrossRefGoogle Scholar
  35. Lee Y, Oh C, De Zoysa M, Kim H, Wickramaarachchi WD, Whang I, Kang DH, Lee J (2013) Molecular cloning, overexpression, and enzymatic characterization of glycosyl hydrolase family 16 β-agarase from marine bacterium Saccharophagus sp. AG21 in Escherichia coli. J Microbiol Biotechnol 23(7):913–922PubMedCrossRefGoogle Scholar
  36. Lee YR, Jung S, Chi WJ, Bae CH, Jeong BC, Hong SK, Lee CR (2018) Biochemical characterization of a novel GH86 β-agarase producing neoagarohexaose from Gayadomonas joobiniege G7. J Microbiol Biotechnol 28(2):284–292PubMedCrossRefGoogle Scholar
  37. Li G, Sun M, Wu J, Ye M, Ge X, Wei W, Li H, Hu F (2015) Identification and biochemical characterization of a novel endo-type β-agarase AgaW from Cohnella sp. strain LGH. Appl Microbiol Biotechnol 99(23):10019–10029PubMedCrossRefGoogle Scholar
  38. Liang SS, Chen YP, Chen YH, Chiu SH, Liaw LL (2014) Characterization and overexpression of a novel β-agarase from Thalassomonas agarivorans. J Appl Microbiol 116(3):563–572PubMedCrossRefGoogle Scholar
  39. Liao L, Xu XW, Jiang XW, Cao Y, Yi N, Huo YY, Wu YH, Zhu XF, Zhang XQ, Wu M (2011) Cloning, expression, and characterization of a new β-agarase from Vibrio sp. strain CN41. Appl Environ Microbiol 77(19):7077–7079PubMedPubMedCentralCrossRefGoogle Scholar
  40. Lin B, Lu G, Zheng Y, Xie W, Li S, Hu Z (2012) Gene cloning, expression and characterization of a neoagarotetraose-producing β-agarase from the marine bacterium Agarivorans sp. HZ105. World J Microbiol Biotechnol 28(4):1691–1697PubMedCrossRefGoogle Scholar
  41. Lin B, Liu Y, Lu G, Zhao M, Hu Z (2017) An agarase of glycoside hydrolase family 16 from marine bacterium Aquimarina agarilytica ZC1. FEMS Microbiol Lett 364(4):1–6CrossRefGoogle Scholar
  42. Liu N, Mao X, Du Z, Mu B, Wei D (2014a) Cloning and characterization of a novel neoagarotetraose-forming-β-agarase, AgWH50A from Agarivorans gilvus WH0801. Carbohydr Res 388:147–151PubMedCrossRefGoogle Scholar
  43. Liu N, Mao X, Yang M, Mu B, Wei D (2014b) Gene cloning, expression and characterization of a new β-agarase, AgWH50C, producing neoagarobiose from Agarivorans gilvus WH0801. World J Microbiol Biotechnol 30(6):1691–1698PubMedCrossRefGoogle Scholar
  44. Lu X, Chu Y, Wu Q, Gu Y, Han F, Yu W (2009) Cloning, expression and characterization of a new agarase-encoding gene from marine Pseudoalteromonas sp. Biotechnol Lett 31(10):1565–1570PubMedCrossRefGoogle Scholar
  45. Oh C, Nikapitiya C, Lee Y, Whang I, Kang DH, Heo SJ, Choi YU, Lee J (2010a) Molecular cloning, characterization and enzymatic properties of a novel βeta-agarase from a marine isolate Pseudoalteromonas sp. AG52. Braz J Microbiol 41(4):876–889PubMedPubMedCentralCrossRefGoogle Scholar
  46. Oh C, Nikapitiya C, Lee Y, Whang I, Kim SJ, Kang DH, Lee J (2010b) Cloning, purification and biochemical characterization of beta agarase from the marine bacterium Pseudoalteromonas sp. AG4. J Ind Microbiol Biotechnol 37(5):483–494PubMedCrossRefGoogle Scholar
  47. Ohta Y, Nogi Y, Miyazaki M, Li Z, Hatada Y, ITO S, Horikoshi K (2004) Enzymatic properties and nucleotide and amino acid sequences of a thermostable β-agarase from the novel marine isolate, JAMB-A94. Biosci Biotechnol Biochem 68(5):1073–1081PubMedCrossRefGoogle Scholar
  48. Osamu A, Inoue T, Kubo H, Minami K, Nakamura M, Iwai M, Moriyama H, Yanagisawa M, Nakasaki K (2012) Cloning of agarase gene from non-marine agarolytic bacterium Cellvibrio sp. J Microbiol Biotechnol 22(9):1237–1244CrossRefGoogle Scholar
  49. Pluvinage B, Hehemann JH, Boraston AB (2013) Substrate recognition and hydrolysis by a family 50 exo-β-agarase, Aga50D, from the marine bacterium Saccharophagus degradans. J Biol Chem 288(39):28078–28088PubMedPubMedCentralCrossRefGoogle Scholar
  50. Rajagopalan KV, Fridovich I, Handler P (1961) Competitive inhibition of enzyme activity by urea. J Biol Chem 236:1059–1065PubMedGoogle Scholar
  51. Ramos KR, Valdehuesa KN, Nisola GM, Lee WK, Chung WJ (2018) Identification and characterization of a thermo stable endolytic β-agarase Aga2 from a newly isolated marine agarolytic bacteria Cellulophaga omnivescoria W5C. New Biotechnol 40:261–267CrossRefGoogle Scholar
  52. Seo YB, Lu Y, Chi WJ, Park HR, Jeong KJ, Hong SK, Chang YK (2014) Heterologous expression of a newly screened β-agarase from Alteromonas sp. GNUM1 in Escherichia coli and its application for agarose degradation. Process Biochem 49(3):430–436CrossRefGoogle Scholar
  53. Su Q, Jin T, Yu Y, Yang M, Mou H, Li L (2017) Extracellular expression of a novel β-agarase from Microbulbifer sp. Q7, isolated from the gut of sea cucumber. AMB Express 7(1):220PubMedPubMedCentralCrossRefGoogle Scholar
  54. Sugano Y, Terada I, Arita M, Noma M, Matsumoto T (1993) Purification and characterization of a new agarase from a marine bacterium, Vibrio sp. strain JT0107. Appl Environ Microbiol 59(5):1549–1554PubMedPubMedCentralGoogle Scholar
  55. Takagi E, Hatada Y, Akita M, Ohta Y, Yokoi G, Miyazaki T, Nishikawa A, Tonozuka T (2015) Crystal structure of the catalytic domain of a GH16 β-agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94. Biosci Biotechnol Biochem 79(4):625–632PubMedCrossRefGoogle Scholar
  56. Tawara M, Sakatoku A, Tiodjio RE, Tanaka D, Nakamura S (2015) Cloning and characterization of a novel agarase from a newly isolated bacterium Simiduia sp. strain TM-2 able to degrade various seaweeds. Appl Biochem Biotechnol 177(3):610–623PubMedCrossRefGoogle Scholar
  57. 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 β-agarase producing neoagarotetraose and neoagarohexaose. Appl Microbiol Biotechnol 92(4):749–759PubMedCrossRefGoogle Scholar
  58. Temuujin U, Chi WJ, Chang YK, Hong SK (2012) Identification and biochemical characterization of Sco3487 from Streptomyces coelicolor A3 (2), an exo-and endo-type β-agarase-producing neoagarobiose. J Bacteriol 194(1):142–149PubMedPubMedCentralCrossRefGoogle Scholar
  59. Xiao A, Xiao Q, Lin Y, Ni H, Zhu Y, Cai H (2017) Efficient immobilization of agarase using carboxyl-functionalized magnetic nanoparticles as support. Electron J Biotechnol 25:13–20CrossRefGoogle Scholar
  60. Xie W, Lin B, Zhou Z, Lu G, Lun J, Xia C, Li S, Hu Z (2013) Characterization of a novel β-agarase from an agar-degrading bacterium Catenovulum sp. X3. Appl Microbiol Biotechnol 97(11):4907–4915PubMedCrossRefGoogle Scholar
  61. Xu XQ, Su BM, Xie JS, Li RK, Yang J, Lin J, Ye XY (2018) Preparation of bioactive neoagaroligosaccharides through hydrolysis of Gracilaria lemaneiformis agar: a comparative study. Food Chem 240:330–337PubMedCrossRefGoogle Scholar
  62. Yang JI, Chen LC, Shih YY, Hsieh C, Chen CY, Chen WM, Chen CC (2011) Cloning and characterization of β-agarase AgaYT from Flammeovirga yaeyamensis strain YT. J Biosci Bioeng 112(3):225–232PubMedCrossRefGoogle Scholar
  63. Yun EJ, Yu S, Kim KH (2017) Current knowledge on agarolytic enzymes and the industrial potential of agar-derived sugars. Appl Microbiol Biotechnol 101(14):5581–5589PubMedCrossRefGoogle Scholar
  64. Zhu Y, Zhao R, Xiao A, Li L, Jiang Z, Chen F, Ni H (2016) Characterization of an alkaline β-agarase from Stenotrophomonas sp. NTa and the enzymatic hydrolysates. Int J Biol Macromol 86:525–534PubMedCrossRefGoogle Scholar

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© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biotechnology, School of Bio Sciences and TechnologyVellore Institute of Technology (VIT)VelloreIndia

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