Skip to main content
Log in

A high-molecular-weight, alkaline, and thermostable β-1,4-xylanase of a subseafloor Microcella alkaliphila

  • Original Paper
  • Published:
Extremophiles Aims and scope Submit manuscript

Abstract

An endo β-1,4-xylanase (XynE15) from a culture broth of a deep subseafloor microorganism, Microcella alkaliphila JAM-AC0309, was purified to homogeneity. The molecular mass of XynE15 was approximately 150 kDa as judged by SDS-PAGE. The optimal pH and temperature for hydrolysis of xylan were pH 8 and 65 °C. The enzyme was stable to incubation for 30 min at up to 75 °C, and the half-life at 50 °C was 48 h. XynE15 hydrolyzed arabinoxylan, oat spelt xylan, and birchwood xylan well, but not avicel, carboxymethylcellulose, or arabinan. Xylooligosaccharides were hydrolyzed to mainly xylobiose from higher than xylotetraose. The genome sequencing analysis of strain JAM-AC03039 revealed that XynE15 was composed of 1,319 amino acids with one catalytic domain and three carbohydrate-binding domains belonging to glycoside hydrolase (GH) family 10 and carbohydrate-binding module (CBM) family 4, respectively.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Ali MK, Fukumura M, Sakano K, Karita S, Kimura T, Sakka K, Ohmiya K (1999) Cloning, sequencing, and expression of the gene encoding the Clostridium stercorarium xylanase C in Escherichia coli. Biosci Biotechnol Biochem 63:1596–1604

    Article  CAS  PubMed  Google Scholar 

  • Araki T, Hashikawa S, Morishita T (2000) Cloning, sequencing, and expression in Escherichia coli of the new gene encoding β-1,3-xylanase from a marine bacterium, Vibrio sp. strain XY-214. Appl Environ Microbiol 66:1741–1743

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beg QK, Kapoor M, Mahajan L, Hoondal GS (2001) Microbial xylanases and their industrial applications: a review. Appl Microbiol Biotechnol 56:326–338

    Article  CAS  PubMed  Google Scholar 

  • Cambell JM, Fahey J, Wolf BW (1997) Selected indigestible oligosaccharides affect large bowel mass, cecal and fecal short-chain fatty acids, pH and microflora in rats. J Nutr 12:130–136

    Google Scholar 

  • Chanjuan L, Hong Y, Shao Z, Lin L, Huang X, Liu P, Wu G, Meng X, Liu Z (2009) Novel alkali-stable, cellulase free xylanase from deep-sea Kocuria sp. Mn22. J Microbiol Biotechnol 19:873–880

    Article  PubMed  Google Scholar 

  • Chung YC, Hsu CK, Ko CY, Chan YC (2007) Dietary intake of xylooligosaccharides improves the intestinal microbiota, fecal moisture, and pH value in the elderly. Nutr Res 27:756–761

    Article  CAS  Google Scholar 

  • Collins T, Gerday C, Feller G (2005) Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol Rev 29:3–23

    Article  CAS  PubMed  Google Scholar 

  • Dheeran P, Nandhagopal N, Kumar S, Jaiswal YK, Adhikari DK (2012) A novel thermostable xylanase of Paenibacillus macerans IIPSP3 isolated from the termite gut. J Ind Microbiol Biotechnol 39:851–860

    Article  CAS  PubMed  Google Scholar 

  • Franz J, St J, Rice JD, Preston JF (2006) Paenibacillus sp. strain JDR-2 and xynA1: a novel system for methylglucuronoxylan utilization. Appl Environ Microbiol 72:1496–1506

    Article  Google Scholar 

  • Fukada Y, Koide O, Miura T, Kobayashi T, Inoue A, Horikoshi K (2011) Endo-1,5-α-l-arabinase from a subseafloor Bacillus subtilis: purification, characterization, and nucleotide sequence of its gene. J Appl Glycosci 58:61–66

    Article  CAS  Google Scholar 

  • Gessesse A (1998) Purification and properties of two thermostable alkaline xylanases from an alkaliphilic Bacillus sp. Appl Environ Microbiol 64:3533–3535

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gobinath D, Madhu AN, Prashant G, Srinivasan K, Prapulla SG (2010) Beneficial effect of xylo-oligosaccharides and fructo-oligosaccharides in streptozotocin- induced diabetic rats. Br J Nutr 104:40–47

    Article  CAS  PubMed  Google Scholar 

  • Gupta S, Bhushan B, Hoondal GS (2000) Isolation, purification and characterization of xylanase from Staphylococcus sp. SG-13 and its application in biobleaching of kraft pulp. J Appl Microbiol 88:325–334

    Article  CAS  PubMed  Google Scholar 

  • Horikoshi K (2006) Alkaliphiles: genetic properties and applications of enzymes. Kodansha Ltd, Tokyo, pp 195–205

    Google Scholar 

  • Horton HR, Koshland DE Jr (1965) A highly reactive colored reagent with selectivity for the tryptophan residue in proteins. 2-Hydroxy-5-nitrobenzyl bromide. J Am Chem Soc 87:1126–1132

    Article  CAS  PubMed  Google Scholar 

  • Iriki Y, Suzuki T, Nishizawa K, Miwa T (1960) Xylan of siphonaceous green algae. Nature 187:82–83

    Article  CAS  PubMed  Google Scholar 

  • Ito Y, Tomita T, Roy N, Nakano A, Sugawara-Tomita N, Watanabe S, Okai N, Abe N, Kamio Y (2003) Cloning, expression, and cell surface localization of Paenibacillus sp. strain W-61 xylanase 5, a multidomain xylanase. Appl Environ Microbiol 69:6969–6978

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ito S, Kobayashi T, Hatada Y, Horikoshi K (2005) Enzymes in modern detergents. Methods. Biotechnol 17:151–163

    CAS  Google Scholar 

  • Kapitany RA, Zebrowski EJ (1973) A high resolution PAS stain for polyacrylamide gel electrophoresis. Anal Biochem 56:361–369

    Article  CAS  PubMed  Google Scholar 

  • Kim H, Jung KH, Pack MY (2000) Molecular characterization of xynX, a gene encoding a multidomain xylanase with a thermostabilizing domain from Clostridium thermocellum. Appl Microbiol Biotechnol 54:521–527

    Article  CAS  PubMed  Google Scholar 

  • Kobayashi T, Koide O, Mori K, Shimamura S, Matsuura T, Miura T, Takaki Y, Morono Y, Nunoura T, Imachi H, Inagaki F, Takai K, Horikoshi K (2008) Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula. Extremophiles 12:519–527

    Article  CAS  PubMed  Google Scholar 

  • Kobayashi T, Koide O, Deguchi S, Horikoshi K (2011) Characterization of chitosanase of a deep biosphere Bacillus strain. Biosci Biotechnol Biochem 75:669–673

    Article  CAS  PubMed  Google Scholar 

  • Kobayashi T, Uchimura K, Kubota T, Nunoura T, Deguchi S (2016) Biochemical and genetic characterization of β-1,3 glucanase from a deep subseafloor Laceyella putida. Appl Microbiol Biotechnol 100:203–214

    Article  CAS  PubMed  Google Scholar 

  • Kumar V, Satyanarayana T (2013) Biochemical and thermodynamic characteristics of thermo-alkali-stable xylanase from a novel polyextremophilic Bacillus halodurans TSEV1. Extremophiles 17:797–808

    Article  CAS  PubMed  Google Scholar 

  • Kurata A, Hirose Y, Misawa N, Wakazuki S, Kishimoto N, Kobayashi T (2016) Complete genome sequence of the xylan-degrading subseafloor bacterium Microcella alkaliphila JAM-AC0309. J Biotechnol 221:32–33

    Article  CAS  PubMed  Google Scholar 

  • Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685

    Article  CAS  PubMed  Google Scholar 

  • Lee DS, Lee KH, Cho EJ, Kim HM, Kim CS, Bae HJ (2012) Characterization and pH-dependent substrate specificity of alkalophilic xylanase from Bacillus alcalophilus. J Ind Microbiol Biotechnol 39:1465–1475

    Article  CAS  PubMed  Google Scholar 

  • Liu SY, Gherardini FC, Matuschek M, Bahl H, Wiegel J (1996) Cloning, sequencing, and expression of the gene encoding a large S-layer-associated endoxylanase from Thermoanaerobacterium sp. strain JW/SL-YS 485 in Escherichia coli. J Bacteriol 178:1539–1547

    CAS  PubMed  PubMed Central  Google Scholar 

  • McDowell RH (1967) Chemistry and enzymology of marine algal polysaccharides. Academic Press, London, pp. 88–96, pp. 134–137

  • Meng X, Shao Z, Hong Y, Lin L, Li C, Liu Z (2009) A novel pH-stable, bifunctional xylanase isolated from a deep-sea microorganism, Demequina sp. JK4. J Microbiol Biotechnol 19:1077–1084

    CAS  PubMed  Google Scholar 

  • Menon G, Mody K, Keshri J, Jha B (2010) Isolation, purification, and characterization of haloalkaline xylanase from a marine Bacillus pumilis strain, GESF-1. Biotechnol Bioprocess Eng 15:998–1005

    Article  CAS  Google Scholar 

  • Morris DD, Gibbs MD, Ford M, Thomas J, Bergquist PL (1999) Family 10 and 11 xylanase genes from Caldicellulosiruptor sp. strain Rt69B.1. Extremophiles 3:103–111

    Article  CAS  PubMed  Google Scholar 

  • Okazaki M, Fujikawa S, Matsumoto N (1990) Effect of xylo-oligosaccharide on the growth of bifidobacteria. Bifidobact Microflora 9:77–86

    Article  Google Scholar 

  • Okazaki F, Tamaru Y, Hashikawa S, Li YT, Araki T (2002) Novel carbohydrate-binding module of β-1,3-xylanase from a marine bacterium, Alcaligenes sp. strain XY-234. J Bacteriol 184:2399–2403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roy N, Okai N, Tomita T, Muramoto K, Kamio Y (2000) Purification and some properties of high-molecular-weight xylanases, the xylanases 4 and 5 of Aeromonas caviae W-61. Biosci Biotechnol Biochem 64:408–413

    Article  CAS  PubMed  Google Scholar 

  • Sasaki M, Koide O, Kobayashi T, Usami R, Horikoshi K (2015) A pectate lyase from a deep subseafloor Georgenia muralis with unusual molecular characteristics. Extremophiles 19:119–125

    Article  CAS  PubMed  Google Scholar 

  • Shibasaki H, Uchimura K, Miura T, Kobayashi T, Usami R, Horikoshi K (2014) Highly thermostable and surfactant-activated chitinase from a subseafloor bacterium, Laceyella putida. Appl Microbiol Biotechnol 98:7845–7853

    Article  CAS  PubMed  Google Scholar 

  • Takai K, Abe M, Miyazaki M, Koide O, Nunoura T, Imachi H, Inagaki F, Kobayashi T (2013) Sunxiuqinia faeciviva sp. nov., a novel facultatively anaerobic, organoheterotroph of the Bacteroidetes isolated from deep subseafloor sediment. Int J Syst Evol Microbiol 63:1602–1609

    Article  CAS  PubMed  Google Scholar 

  • Tiago I, Morais PV, da Costa MS, Veríssimo A (2006) Microcella alkaliphila sp. nov., a novel member of the family Microbacteriaceae isolated from a non-saline alkaline ground water, and emended description of the genus Microcella. Int J Syst Evol Microbiol 56:2313–2316

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Jin Y, Wu H, Tian Z, Wu Y, Xie X (2012) A novel, alkali-tolerant thermostable xylanase from Saccharomonospora viridis: direct gene cloning, expression and enzyme characterization. World J Microbiol Biotechnol 28:2741–2748

    Article  CAS  PubMed  Google Scholar 

  • Wu S, Liu B, Zhang X (2006) Characterization of a recombinant thermostable xylanase from deep-sea thermophilic Geobacillus sp. MT-1 in East Pacific. Appl Microbiol Biotechnol 72:1210–1216

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Tohru Kobayashi.

Additional information

Communicated by F. Robb.

K. Kuramochi, K. Uchimura, A. Kurata, T. Kobayashi, Y. Hirose, T. Miura, N. Kishimoto, R. Usami dedicate this paper to the memory of Dr. Koki Horikoshi who died on Mar 16 2016

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PPTX 96 kb)

Supplementary material 2 (PPTX 71 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kuramochi, K., Uchimura, K., Kurata, A. et al. A high-molecular-weight, alkaline, and thermostable β-1,4-xylanase of a subseafloor Microcella alkaliphila . Extremophiles 20, 471–478 (2016). https://doi.org/10.1007/s00792-016-0837-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00792-016-0837-7

Keywords

Navigation