Advertisement

Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

A novel, versatile family IV carboxylesterase exhibits high stability and activity in a broad pH spectrum

  • 563 Accesses

  • 8 Citations

Abstract

Objectives

To investigate the properties of a novel metagenome-derived member of the hormone-sensitive lipase family of lipolytic enzymes.

Results

A forest soil metagenome-derived gene encoding an esterase (Est06) belonging to the hormone-sensitive lipase family of lipolytic enzymes was subcloned, heterologously expressed and characterized. Est06 is a polypeptide of 295 amino acids with a molecular mass of 31 kDa. The deduced protein sequence shares 61% similarity with a hypothetical protein from the marine symbiont Candidatus Entotheonella sp. TSY1. Purified Est06 exhibited high affinity for acyl esters with short-chain fatty acids, and showed optimum activity with p-nitrophenyl valerate (C5). Maximum enzymatic activity was at 50 °C and pH 7. Est06 exhibited high stability at moderate temperatures by retaining all of its catalytic activity below 30 °C over 13 days. Additionally, Est06 displayed high stability between pH 5 and 9. Esterase activity was not inhibited by metal ions or detergents, although organic solvents decreased activity.

Conclusions

The combination of Est06 properties place it among novel biocatalysts that have potential for industrial use including low temperature applications.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  1. Altschul SF, Madden TL, Schäffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 25:3389–3402

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

  3. Ayna Ç, Kolcuoğlu Y, Öz F et al (2013) Purification and characterization of a pH and heat stable esterase from Geobacillus sp. TF17. Turk J Biochem 38:329–336

  4. Berlemont R, Spee O, Delsaute M et al (2013) Novel organic solvent-tolerant esterase isolated by metagenomics: insights into the lipase/esterase classification. Rev Argent Microbiol 45:3–12

  5. 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

  6. Bornscheuer UT (2002) Microbial carboxyl esterases: classification, properties and application in biocatalysis. FEMS Microbiol Rev 26:73–81

  7. Brault G, Shareck F, Hurtubise Y et al (2012) Isolation and characterization of EstC, a new cold-active esterase from Streptomyces coelicolor A3(2). PLoS ONE 7:e32041

  8. Byun J-S, Rhee J-K, Kim ND et al (2007) Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties. BMC Struct Biol 7:47

  9. Charbonneau DM, Beauregard M (2013) Role of key salt bridges in thermostability of G. thermodenitrificans EstGtA2: distinctive patterns within the new bacterial lipolytic enzyme Family XV. PLoS ONE 8:1–18

  10. de Castro AP, Fernandes GdaR, Franco OL (2014) Insights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes. Front Microbiol 5:1–9

  11. De Simone G, Menchise V, Manco G et al (2001) The crystal structure of a hyper-thermophilic carboxylesterase from the archaeon Archaeoglobus fulgidus. J Mol Biol 314:507–518

  12. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

  13. Facchin S, Diniz Alves PD, De Faria Siqueira F et al (2013) Biodiversity and secretion of enzymes with potential utility in wastewater treatment. Open J Ecol 3:34–47

  14. Gasteiger E, Hoogland C, Gattiker A et al (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Humana Press Inc., Totowa, pp 571–607

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

  16. Hriscu M, Chiş L, Toşa M, Irimie FD (2013) pH-profiling of thermoactive lipases and esterases: caveats and further notes. Eur J Lipid Sci Technol 115:571–575

  17. Kademi A, Aït-Abdelkader N, Fakhreddine L, Baratti JC (2000) Characterization of a new thermostable esterase from the moderate thermophilic bacterium Bacillus circulans. J Mol Catal B Enzym 10:395–401

  18. Kang C-H, Oh K-H, Lee M-H et al (2011) A novel family VII esterase with industrial potential from compost metagenomic library. Microb Cell Fact 10:41

  19. Kovacic F, Mandrysch A, Poojari C et al (2016) Structural features determining thermal adaptation of esterases. Protein Eng Des Sel 29:65–76

  20. Lee M-H, Lee C-H, Oh T-K et al (2006) Isolation and characterization of a novel lipase from a metagenomic library of tidal flat sediments: evidence for a new family of bacterial lipases. Appl Environ Microbiol 72:7406–7409

  21. Lenfant N, Hotelier T, Velluet E et al (2013) ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions. Nucleic Acid Res 41:D423–D429

  22. Levisson M, van der Oost J, Kengen SWM (2007) Characterization and structural modeling of a new type of thermostable esterase from Thermotoga maritima. FEBS J 274:2832–2842

  23. Li PY, Ji P, Li CY et al (2014) Structural basis for dimerization and catalysis of a novel sterase from the GTSAG motif subfamily of the bacterial hormone-sensitive lipase family. J Biol Chem 289:19031–19041

  24. Li P-Y, Chen X-L, Ji P et al (2015) Interdomain hydrophobic interactions modulate the thermostability of microbial esterases from the hormone-sensitive lipase family. J Biol Chem 290:1118–11198

  25. López-López O, Cerdán ME, González Siso MI (2014) New extremophilic lipases and esterases from metagenomics. Curr Protein Pept Sci 15:445–455

  26. Ma B-D, Kong X-D, Yu H-L et al (2014) Increased catalyst productivity in α-hydroxy acids resolution by esterase mutation and substrate modification. ACS Catal 4:1026–1031

  27. Martínez-Martínez M, Lores I, Peña-García C et al (2014) Biochemical studies on a versatile esterase that is most catalytically active with polyaromatic esters. Microb Biotechnol 7:184–191

  28. Mattos C, Ringe D (2001) Proteins in organic solvents. Curr Opin Struct Biol 11:761–764

  29. Metin K, Ateslier ZBB, Basbulbul G, Biyik HH (2006) Characterization of esterase activity in Geobacillus sp. HBB-4. J Basic Microbiol 46:400–409

  30. Mohamed YM, Ghazy MA, Sayed A et al (2013) Isolation and characterization of a heavy metal-resistant, thermophilic esterase from a Red Sea brine pool. Sci Rep 3:3358

  31. Nacke H, Will C, Herzog S et al (2011) Identification of novel lipolytic genes and gene families by screening of metagenomic libraries derived from soil samples of the German Biodiversity Exploratories. FEMS Microbiol Ecol 78:188–201

  32. Nardini M, Dijkstra BW (1999) α/β hydrolase fold enzymes: the family keeps growing. Curr Opin Struct Biol 9:732–737

  33. Novototskaya-Vlasova K, Petrovskaya L, Yakimov S, Gilichinsky D (2012) Cloning, purification, and characterization of a cold-adapted esterase produced by Psychrobacter cryohalolentis K5T from Siberian cryopeg. FEMS Microbiol Ecol 82:367–375

  34. Ogino H, Ishikawa H (2001) Enzymes which are stable in the presence of organic solvents. J Biosci Bioeng 91:109–116

  35. Østerlund T (2001) Structure-function relationships of hormone-sensitive lipase. Eur J Biochem 268:1899–1907

  36. Peng Q, Zhang X, Shang M et al (2011) A novel esterase gene cloned from a metagenomic library from neritic sediments of the South China Sea. Microb Cell Fact 10:95

  37. Phrommao E, Yongsawatdigul J, Rodtong S, Yamabhai M (2011) A novel subtilase with NaCl-activated and oxidant-stable activity from Virgibacillus sp. SK37. BMC Biotechnol 11:65

  38. Rhee J-K, Ahn D-G, Kim Y-G, Oh J-W (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

  39. Rhee J-K, Kim D-Y, Ahn D-G et al (2006) Analysis of the thermostability determinants of hyperthermophilic esterase EstE1 based on its predicted three-dimensional structure. Appl Environ Microbiol 72:3021–3025

  40. Robert X, Gouet P (2014) Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 42:W320–W324

  41. Rodríguez MC, Loaces I, Amarelle V et al (2015) Est10: a novel alkaline esterase isolated from bovine rumen belonging to the new family XV of lipolytic enzymes. PLoS ONE 10:e0126651

  42. Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5:725–738

  43. Sellek GA, Chaudhuri JB (1999) Biocatalysis in organic media using enzymes from extremophiles. Enzyme Microb Technol 25:471–482

  44. Selvin J, Kennedy J, Lejon DPH et al (2012) Isolation identification and biochemical characterization of a novel halo-tolerant lipase from the metagenome of the marine sponge Haliclona simulans. Microb Cell Fact 11:72

  45. Sharma A, Radha Kishan KV (2011) Serine protease inhibitor mediated peptide bond re-synthesis in diverse protein molecules. FEBS Lett 585:3465–3470

  46. Sharma A, Kawarabayasi Y, Satyanarayana T (2012) Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications. Extremophiles 16:1–19

  47. Suzuki Y, Miyamoto K, Ohta H (2004) A novel thermostable esterase from the thermoacidophilic archaeon Sulfolobus tokodaii strain 7. FEMS Microbiol Lett 236:97–102

  48. van Pouderoyen G, Eggert T, Jaeger K-E, Dijkstra BW (2001) The crystal structure of Bacillus subtilis lipase: a minimal α/β hydrolase fold enzyme. J Mol Biol 309:215–226

  49. Will C, Thürmer A, Wollherr A et al (2010) Horizon-specific bacterial community composition of german grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl Environ Microbiol 76:6751–6759

  50. Wilson MC, Mori T, Rückert C et al (2014) An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 506:58–62

  51. Xin L, Hui-Ying Y (2013) Purification and characterization of an extracellular esterase from a moderately halophilic bacterium. BMC Biotechnol 13:108

  52. Yang J, Zhang Y (2015) I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res 43:W174–W181

  53. Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinform 9:40

  54. Zhang X-Y, Fan X, Qiu Y-J et al (2014) Newly identified thermostable esterase from Sulfobacillus acidophilus: properties and performance in phthalate ester degradation. Appl Environ Microbiol 80:6870–6878

Download references

Acknowledgements

We thank the DFG (German Science Foundation) for funding this work in the context of the graduate school ‘Die Bedeutung der Biodiversität für Stoffkreisläufe und biotische Interaktionen in temperaten Laubwäldern (GRK 1086)’. We thank Dr. Heiko Nacke for providing the lipolytic clone pLE06 used in this work, as well as Florian Jung and Jörn Lindemann for providing technical assistance.

Supporting information

Supplementary Table 1—Amino acid sequence similarities between Est06 and related lipolytic proteins.

Supplementary Table 2—The effect of water-miscible organic solvents on the stability of Est06.

Supplementary Figure 1—Maps of plasmids for cloning and expression of the lipolytic gene est06.

Supplementary Figure 2—Predicted tertiary structure of esterase Est06.

Author information

Correspondence to Rolf Daniel.

Ethics declarations

Conflict of interest

The authors declare no conflict of interest exists.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 1333 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Dukunde, A., Schneider, D., Lu, M. et al. A novel, versatile family IV carboxylesterase exhibits high stability and activity in a broad pH spectrum. Biotechnol Lett 39, 577–587 (2017). https://doi.org/10.1007/s10529-016-2282-1

Download citation

Keywords

  • Carboxylesterases
  • Esterase
  • Family IV esterase
  • Hormone-sensitive lipase family
  • Soil metagenome