Skip to main content
Log in

Isolation and characterization of a thermostable esterase from a metagenomic library

  • Biocatalysis
  • Published:
Journal of Industrial Microbiology & Biotechnology

Abstract

A novel esterase gene was isolated by functional screening of a metagenomic library prepared from an activated sludge sample. The gene (est-XG2) consists of 1,506 bp with GC content of 74.8 %, and encodes a protein of 501 amino acids with a molecular mass of 53 kDa. Sequence alignment revealed that Est-XG2 shows a maximum amino acid identity (47 %) with the carboxylesterase from Thermaerobacter marianensis DSM 12885 (YP_004101478). The catalytic triad of Est-XG2 was predicted to be Ser192-Glu313-His412 with Ser192 in a conserved pentapeptide (GXSXG), and further confirmed by site-directed mutagenesis. Phylogenetic analysis suggested Est-XG2 belongs to the bacterial lipase/esterase family VII. The recombinant Est-XG2, expressed and purified from Escherichia coli, preferred to hydrolyze short and medium length p-nitrophenyl esters with the best substrate being p-nitrophenyl acetate (K m and k cat of 0.33 mM and 36.21 s−1, respectively). The purified enzyme also had the ability to cleave sterically hindered esters of tertiary alcohols. Biochemical characterization of Est-XG2 revealed that it is a thermophilic esterase that exhibits optimum activity at pH 8.5 and 70 °C. Est-XG2 had moderate tolerance to organic solvents and surfactants. The unique properties of Est-XG2, high thermostability and stability in the presence of organic solvents, may render it a potential candidate for industrial applications.

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.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped blast and PSI-blast: a new generation of protein database search programs. Nucl Aci Res 25:3389–3402

    Article  CAS  Google Scholar 

  2. Arpigny JL, Jaeger KE (1999) Bacterial lipolytic enzymes: classification and properties. Biochem J 343:177–183

    Article  PubMed  CAS  Google Scholar 

  3. Bassegoda A, Fillat A, Pastor FIJ, Diaz P (2013) Special Rhodococcus sp. CR-53 esterase Est 4 contains a GGG(A)X-oxyanion hole conferring activity for the kinetic resolution of tertiary alcohols. Appl Microbiol Biotechnol. doi:10.1007/s00253-012-4676-x

    PubMed  Google Scholar 

  4. Biver S, Vandenbol M (2013) Characterization of three new carboxylic ester hydrolases isolated by functional screening of a forest soil metagenomic library. J Ind Microbiol Biotechnol 40:191–200

    Article  PubMed  CAS  Google Scholar 

  5. Boczar BA, Forney LJ, Begley WM, Larson RJ, Federle TW (2001) Characterization and distribution of esterase activity in activated sludge. Wat Res 35:4208–4216

    Article  CAS  Google Scholar 

  6. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254

    Article  PubMed  CAS  Google Scholar 

  7. Choi YJ, Miguez CB, Lee BH (2004) Characterization and heterologous gene expression of a novel esterase from Lactobacillus casei CL96. Appl Environ Microbiol 70:3213–3221

    Article  PubMed  CAS  Google Scholar 

  8. Chow J, Kovacic F, Dall AY, Krauss U, Fersini F, Schmeisser C, Lauinger B, Bongen P, Pietruszka J, Schmidt M, Menyes I, Bornscheuer UT, Eckstein M, Thum O, Liese A, Mueller-Dieckmann J, Jaeger KE, Streit WR (2012) The metagenome-derived enzymes LipS and LipT increase the diversity of known lipases. PLoS One 7:e47665

    Article  PubMed  CAS  Google Scholar 

  9. Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3:470–478

    Article  PubMed  CAS  Google Scholar 

  10. Ewis HE, Abdelal AT, Lu CD (2004) Molecular cloning and characterization of two thermostable carboxyl esterases from Geobacillus stearothermophilus. Gene 329:187–195

    Article  PubMed  CAS  Google Scholar 

  11. Fischer M, Pleiss J (2003) The lipase engineering database: a navigation and analysis tool for protein families. Nucl Aci Res 31:319–321

    Article  CAS  Google Scholar 

  12. Gouet P, Courcelle E, Stuart DI, Métoz F (1999) ESPript: analysis of multiple sequence alignments in postscript. Bioinformatics 15:305–308

    Article  PubMed  CAS  Google Scholar 

  13. Gutiérrez A, Del Río J, Martínez A (2009) Microbial and enzymatic control of pitch in the pulp and paper industry. Appl Microbiol Biotechnol 82:1005–1018

    Article  PubMed  Google Scholar 

  14. Hotta Y, Ezaki S, Atomi H, Imanaka T (2002) Extremely stable and versatile carboxylesterase from a hyperthermophilic archaeon. Appl Environ Microbiol 68:3925–3931

    Article  PubMed  CAS  Google Scholar 

  15. Hu Y, Fu C, Huang Y, Yin Y, Cheng G, Lei F, Lu N, Li J, Ashforth EJ, Zhang L, Zhu B (2010) Novel lipolytic genes from the microbial metagenomic library of the South China Sea marine sediment. FEMS Microbiol Ecol 72:228–237

    Article  PubMed  CAS  Google Scholar 

  16. Jaeger KE, Eggert T (2002) Lipases for biotechnology. Curr Opin Biotechnol 13:390–397

    Article  PubMed  CAS  Google Scholar 

  17. Jin P, Pei X, Du P, Yin X, Xiong X, Wu H, Zhou X, Wang Q (2012) Overexpression and characterization of a new organic solvent-tolerant esterase derived from soil metagenomic DNA. Biores Technol 116:234–240

    Article  CAS  Google Scholar 

  18. Kim YJ, Choi GS, Kim SB, Yoon GS, Kim YS, Ryu YW (2006) Screening and characterization of a novel esterase from a metagenomic library. Prot Exp Purif 45:315–323

    Article  CAS  Google Scholar 

  19. Krsek M, Wellington EMH (1999) Comparison of different methods for the isolation and purification of total community DNA from soil. J Microbiol Meth 39:1–16

    Article  CAS  Google Scholar 

  20. Li J, Zhang K, Han W (2010) Cloning and biochemical characterization of a novel lipolytic gene from activated sludge metagenome, and its gene product. Microb Cell Fact 9:83

    Article  Google Scholar 

  21. Liaw RB, Cheng MP, Wu MC, Lee CY (2010) Use of metagenomic approaches to isolate lipolytic genes from activated sludge. Biores Technol 101:8323–8329

    Article  CAS  Google Scholar 

  22. Liu P, Ewis HE, Tai PC, Lu CD, Weber IT (2007) Crystal structure of the Geobacillus stearothermophilus carboxylesterase Est 55 and its activation of prodrug CPT-11. J Mol Biol 367:212–223

    Article  PubMed  CAS  Google Scholar 

  23. Min-A K, Kim HS, Oh JY, Song BK, Song JK (2009) Gene cloning, expression, and characterization of a new carboxylesterase from Serratia sp. SES-01: comparison with Escherichia coli BioHe enzyme. J Microbiol Biotechnol 19:147–154

    Article  Google Scholar 

  24. Nielsen H, Engelbrecht J, Brunak S, von Heijne G (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Prot Eng 10:1–6

    Article  CAS  Google Scholar 

  25. Park HJ, Jeon JH, Kang SG, Lee JH, Lee SA, Kim HK (2007) Functional expression and refolding of new alkaline esterase, EM2L8 from deep-sea sediment metagenome. Prot Exp Purif 52:340–347

    Article  CAS  Google Scholar 

  26. Potterton E, Briggs P, Turkenburg M, Dodson E (2003) A graphical user interface to the CCP4 program suite. Acta Crystallogr D 59:1131–1137

    Article  PubMed  Google Scholar 

  27. Ranjan R, Grover A, Kapardar RK, Sharma R (2005) Isolation of novel lipolytic genes from uncultured bacteria of pond water. Biochem Biophys Res Commun 335:57–65

    Article  PubMed  CAS  Google Scholar 

  28. Rao L, Xue Y, Zheng Y, Lu JR, Ma Y (2013) A novel alkaliphilic Bacillus esterase belongs to the 13th bacterial lipolytic enzyme family. PLoS One 8:e60645

    Article  PubMed  CAS  Google Scholar 

  29. Rees HC, Grant S, Jones B, Grant WD, Heaphy S (2003) Detecting cellulase and esterase enzyme activities encoded by novel genes present in environmental DNA libraries. Extremophiles 7:415–421

    Article  PubMed  CAS  Google Scholar 

  30. Rhee JK, Ahn DG, Kim YG, Oh JW (2005) New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl Environ Microbiol 71:817–825

    Article  PubMed  CAS  Google Scholar 

  31. Rogalska E, Nury S, Douchet I, Verger R (1997) Microbial lipases: structures, function and industrial applications. Biochem Soc Trans 25:161–164

    PubMed  CAS  Google Scholar 

  32. Roh C, Villatte F, Kim BG, Schmid RD (2006) Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples. Appl Biochem Biotechnol 134:97–112

    Article  PubMed  CAS  Google Scholar 

  33. Sang SL, Li G, Hu XP, Liu YH (2011) Molecular cloning, overexpression and characterization of a novel feruloyl esterase from a soil metagenomic library. J Mol Microbiol Biotechnol 20:196–203

    Article  PubMed  CAS  Google Scholar 

  34. Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucl Aci Res 31:3381–3385

    Article  CAS  Google Scholar 

  35. Sharma PK, Capalash N, Kaur J (2007) An improved method for single step purification of metagenomic DNA. Mol Biotechnol 36:61–63

    Article  PubMed  CAS  Google Scholar 

  36. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  PubMed  CAS  Google Scholar 

  37. Tao W, Lee MH, Wu J, Kim NH, Lee SW (2011) Isolation and characterization of a family VII esterase derived from alluvial soil metagenomic library. J Microbiol 49:178–185

    Article  PubMed  CAS  Google Scholar 

  38. Thompson G, Forster C (2003) Bulking in activated sludge plants treating paper mill wastewaters. Wat Res 37:2636–2644

    Article  CAS  Google Scholar 

  39. Tirawongsaroj P, Sriprang R, Harnpicharnchai P, Thongaram T, Champreda V, Tanapongpipat S, Pootanakit K, Eurwilaichitr L (2008) Novel thermophilic and thermostable lipolytic enzymes from a Thailand hot spring metagenomic library. J Biotechnol 133:42–49

    Article  PubMed  CAS  Google Scholar 

  40. Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors acknowledge the financial support of the National Natural Science Foundation of P. R. China (NSFC) (nos. 31070089, 31170078, and J1103514), the National High Technology Research and Development Program of P. R. China (863 Program) (no. 2011AA02A204), the Natural Science Foundation of Hubei Province (2009CDA046), and the Innovation Foundation of Shenzhen Government (JCYJ20120831111657864).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yunjun Yan.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Shao, H., Xu, L. & Yan, Y. Isolation and characterization of a thermostable esterase from a metagenomic library. J Ind Microbiol Biotechnol 40, 1211–1222 (2013). https://doi.org/10.1007/s10295-013-1317-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10295-013-1317-z

Keywords

Navigation