Biotechnology Letters

, Volume 39, Issue 4, pp 577–587

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

  • Amélie Dukunde
  • Dominik Schneider
  • Mingji Lu
  • Silja Brady
  • Rolf Daniel
Original Research Paper
  • 274 Downloads

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.

Keywords

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

Supplementary material

10529_2016_2282_MOESM1_ESM.docx (1.3 mb)
Supplementary material 1 (DOCX 1333 kb)

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 25:3389–3402CrossRefPubMedPubMedCentralGoogle Scholar
  2. Arpigny JL, Jaeger K-E (1999) Bacterial lipolytic enzymes: classification and properties. Biochem J 343:177–183CrossRefPubMedPubMedCentralGoogle Scholar
  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 38:329–336CrossRefGoogle Scholar
  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 45:3–12PubMedGoogle Scholar
  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 40:191–200CrossRefPubMedGoogle Scholar
  6. Bornscheuer UT (2002) Microbial carboxyl esterases: classification, properties and application in biocatalysis. FEMS Microbiol Rev 26:73–81CrossRefPubMedGoogle Scholar
  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:e32041CrossRefPubMedPubMedCentralGoogle Scholar
  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 7:47CrossRefPubMedPubMedCentralGoogle Scholar
  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 8:1–18CrossRefGoogle Scholar
  10. de Castro AP, Fernandes GdaR, Franco OL (2014) Insights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes. Front Microbiol 5:1–9CrossRefGoogle Scholar
  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 314:507–518CrossRefPubMedGoogle Scholar
  12. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797CrossRefPubMedPubMedCentralGoogle Scholar
  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 3:34–47CrossRefGoogle Scholar
  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 571–607CrossRefGoogle Scholar
  15. Hotta Y, Ezaki S, Atomi H, Imanaka T (2002) Extremely stable and versatile carboxylesterase from a hyperthermophilic archaeon. Appl Environ Microbiol 68:3925–3931CrossRefPubMedPubMedCentralGoogle Scholar
  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 115:571–575CrossRefGoogle Scholar
  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 10:395–401CrossRefGoogle Scholar
  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 10:41CrossRefPubMedPubMedCentralGoogle Scholar
  19. Kovacic F, Mandrysch A, Poojari C et al (2016) Structural features determining thermal adaptation of esterases. Protein Eng Des Sel 29:65–76CrossRefPubMedGoogle Scholar
  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 72:7406–7409CrossRefPubMedPubMedCentralGoogle Scholar
  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–D429CrossRefPubMedGoogle Scholar
  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 274:2832–2842CrossRefPubMedGoogle Scholar
  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 289:19031–19041CrossRefPubMedPubMedCentralGoogle Scholar
  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 290:1118–11198Google Scholar
  25. López-López O, Cerdán ME, González Siso MI (2014) New extremophilic lipases and esterases from metagenomics. Curr Protein Pept Sci 15:445–455CrossRefPubMedPubMedCentralGoogle Scholar
  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 4:1026–1031CrossRefGoogle Scholar
  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 7:184–191CrossRefPubMedPubMedCentralGoogle Scholar
  28. Mattos C, Ringe D (2001) Proteins in organic solvents. Curr Opin Struct Biol 11:761–764CrossRefPubMedGoogle Scholar
  29. Metin K, Ateslier ZBB, Basbulbul G, Biyik HH (2006) Characterization of esterase activity in Geobacillus sp. HBB-4. J Basic Microbiol 46:400–409CrossRefPubMedGoogle Scholar
  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 3:3358PubMedGoogle Scholar
  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 78:188–201CrossRefPubMedGoogle Scholar
  32. Nardini M, Dijkstra BW (1999) α/β hydrolase fold enzymes: the family keeps growing. Curr Opin Struct Biol 9:732–737CrossRefPubMedGoogle Scholar
  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 82:367–375CrossRefPubMedGoogle Scholar
  34. Ogino H, Ishikawa H (2001) Enzymes which are stable in the presence of organic solvents. J Biosci Bioeng 91:109–116CrossRefPubMedGoogle Scholar
  35. Østerlund T (2001) Structure-function relationships of hormone-sensitive lipase. Eur J Biochem 268:1899–1907CrossRefPubMedGoogle Scholar
  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 10:95CrossRefPubMedPubMedCentralGoogle Scholar
  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 11:65CrossRefPubMedPubMedCentralGoogle Scholar
  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 71:817–825CrossRefPubMedPubMedCentralGoogle Scholar
  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 72:3021–3025CrossRefPubMedPubMedCentralGoogle Scholar
  40. Robert X, Gouet P (2014) Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 42:W320–W324CrossRefPubMedPubMedCentralGoogle Scholar
  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:e0126651CrossRefPubMedPubMedCentralGoogle Scholar
  42. Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5:725–738CrossRefPubMedPubMedCentralGoogle Scholar
  43. Sellek GA, Chaudhuri JB (1999) Biocatalysis in organic media using enzymes from extremophiles. Enzyme Microb Technol 25:471–482CrossRefGoogle Scholar
  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 11:72CrossRefPubMedPubMedCentralGoogle Scholar
  45. Sharma A, Radha Kishan KV (2011) Serine protease inhibitor mediated peptide bond re-synthesis in diverse protein molecules. FEBS Lett 585:3465–3470CrossRefPubMedGoogle Scholar
  46. Sharma A, Kawarabayasi Y, Satyanarayana T (2012) Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications. Extremophiles 16:1–19CrossRefPubMedGoogle Scholar
  47. Suzuki Y, Miyamoto K, Ohta H (2004) A novel thermostable esterase from the thermoacidophilic archaeon Sulfolobus tokodaii strain 7. FEMS Microbiol Lett 236:97–102CrossRefPubMedGoogle Scholar
  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 309:215–226CrossRefPubMedGoogle Scholar
  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 76:6751–6759CrossRefPubMedPubMedCentralGoogle Scholar
  50. Wilson MC, Mori T, Rückert C et al (2014) An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 506:58–62CrossRefPubMedGoogle Scholar
  51. Xin L, Hui-Ying Y (2013) Purification and characterization of an extracellular esterase from a moderately halophilic bacterium. BMC Biotechnol 13:108CrossRefPubMedPubMedCentralGoogle Scholar
  52. Yang J, Zhang Y (2015) I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res 43:W174–W181CrossRefPubMedPubMedCentralGoogle Scholar
  53. Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinform 9:40CrossRefGoogle Scholar
  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 80:6870–6878CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and GeneticsGeorg-August University GöttingenGöttingenGermany
  2. 2.Bayer AGET-TD-UP Biochemistry & BiocatalysisLeverkusenGermany

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