New extremophilic Lipases and esterases from metagenomics

Current Protein and Peptide Science

Volumn 15, Issue 5, 2014, Pages 445-455

  López López, Olalla ^a   Cerdán, Maria E ^a   González Siso, Maria I ^a  

^a UNIVERSITY OF A CORUÑA   (Spain)

Author keywords

Extremophiles; Industrial biocatalysts; Lipases and esterases; Lipolytic enzymes classification; Metagenomics; Nonculturable microorganisms

Indexed keywords

DNA; ESTERASE; TRIACYLGLYCEROL LIPASE;

ARTICLE; BIOCATALYST; DNA EXTRACTION; ENANTIOSELECTIVITY; ENZYME ACTIVITY; ENZYME STABILITY; EXTREMOPHILE; MARINE ENVIRONMENT; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROORGANISM; NONHUMAN; PATHOGENESIS; PH; PHYSICAL CHEMISTRY; SALT TOLERANCE; TEMPERATURE; VIRULENCE; CHEMISTRY; ENVIRONMENT; GENETICS; METABOLISM; PROCEDURES;

ENVIRONMENT; ESTERASES; LIPASE; METAGENOMICS;

EID: 84904506321     PISSN: 13892037     EISSN: 18755550     Source Type: Journal    
DOI: 10.2174/1389203715666140228153801     Document Type: Article

References (77)

1. Bornscheuer, U.T. Microbial carboxyl esterases: classification, properties and application in biocatalysis. FEMS Microbiol. Rev., 2002, 26(1), 73-81.
2. Jaeger, K.E.; Dijkstra, B.W.; Reetz, M.T. Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu. Rev. Microbiol., 1999, 53, 315-351.
3. Gupta, R.; Gupta, N.; Rathi, P. Bacterial lipases: an overview of production, purification and biochemical properties. Appl. Microbiol. Biotechnol., 2004, 64(6), 763-781.
4. Arpigny, J.L.; Jaeger, K.E. Bacterial lipolytic enzymes: classification and properties. Biochem. J., 1999, 343, 177-183.
5. Lee, M.H.; Lee, C.H.; Oh, T.K.; Song, J.K.; Yoon, J.H. 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., 2006, 72(11), 7406-7409.
6. Chu, X.; He, H.; Guo, C.; Sun, B. Identification of two novel esterases from a marine metagenomic library derived from South China Sea. Appl. Microbiol. Biotechnol., 2008, 80(4), 615-625.
7. Kim, E.Y.; Oh, K.H.; Lee, M.H.; Kang, C.H.; Oh, T.K.; Yoon, J.H. Novel cold-adapted alkaline lipase from an intertidal flat metagenome and proposal for a new family of bacterial lipases. Appl. Environ. Microbiol, 2009, 75(1), 257-260.
8. Wu, C.; Sun, B. Identification of novel esterase from metagenomic library of Yangtze river. J. Microbiol. Biotechnol., 2009, 19(2), 187-193.
9. Fu, C.; Hu, Y.; Xie, F.; Guo, H.; Ashforth, E.J.; Polyak, S.W.; Zhu, B.; Zhang, L. Molecular cloning and characterization of a new cold-active esterase from a deep-sea metagenomic library. Appl. Microbiol. Biotechnol., 2011, 90(3), 961-970.
10. Verger, R. Interfacial activation' of lipases: facts and artifacts. Tibtech., 1997, 15, 32-38.
11. Jaeger, K.E.; Eggert, T. Lipases for biotechnology. Curr. Opin. Biotechnol., 2002, 13(4), 390-397.
12. Haki, G.D.; Rakshit, S.K. Developments in industrially important thermostable enzymes: a review. Bioresour. Technol., 2003, 89(1), 17-34.
13. Joseph, B.; Ramteke, P.W.; Thomas, G.; Shrivastava, N. Standard review cold-active microbial lipases: a versatile tool for industrial applications. Biotechnol. Mol. Biol. Rev., 2007, 2(2), 39-48.
14. Demirjian, D.C.; Morís-Varas, F.; Cassidy, C.S. Enzymes from extremophiles. Curr. Opin. Chem. Biol., 2001, 5(2), 144-151.
15. Niehaus, F.; Bertoldo, C.; Kähler, M.; Antranikian, G. Extremophiles as a source of novel enzymes for industrial application. Appl. Microbiol. Biotechnol., 1999, 51, 711-729.
16. Cho, A.R.; Yoo, S.K.; Kim, E.J. Cloning, sequencing and expression in Escherichia coli of a thermophilic lipase from Bacillus thermoleovorans ID-1. FEMS Microbiol. Lett., 2000, 186(2), 235-238.
17. Feller, G. Molecular adaptations to cold in psychrophilic enzymes. Cell. Mol. Life. Sci., 2003, 60(4), 648-662.
18. Hårdeman, F.; Sjöling, S. Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment. FEMS Microbiol. Ecol., 2007, 59(2), 524-534.
19. Ko, K.C.; Rim, S.O.; Han, Y.; Shin, B.S.; Kim, G.J.; Choi, J.H.; Song, J.J. Identification and characterization of a novel coldadapted esterase from a metagenomic library of mountain soil. J. Ind. Microbiol. Biotechnol., 2012, 39(5), 681-689.
20. Ghanem, A.; Aboul-Enein, H.Y. Application of lipases in kinetic resolution of racemates. Chirality, 2005, 17(1), 1-15.
21. Yang, Z.; Pan, W. Ionic liquids: Green solvents for nonaqueous biocatalysis. Enzyme Microb. Technol., 2005, 37, 19-28.
22. van Rantwijk, F.; Sheldon, R.A. Biocatalysis in ionic liquids. Chem. Rev., 2007, 107(6), 2757-2785.
23. Oren A. Industrial and environmental applications of halophilic microorganisms. Environ. Technol., 2010, 31(8-9), 825-834.
24. DasSarma, S.; DasSarma, P. Halophiles. eLS, 2012. Reference available from: http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a00003 94.pub3/abstract
25. Kourist, R.; Domínguez de María, P.; Bornscheuer, U.T. Enzymatic synthesis of optically active tertiary alcohols: expanding the biocatalysis toolbox. Chembiochem., 2008, 9(4), 491-498.
26. CBS Genome Atlas Database: http://www.cbs.dtu.dk/services/GenomeAtlas-3.0/. (Accesed September 5, 2012)
27. Henne, A.; Brüggemann, H.; Raasch, C.; Wiezer, A.; Hartsch, T.; Liesegang, H.; Johann, A.; Lienard, T.; Gohl, O.; Martinez-Arias, R.; Jacobi, C.; Starkuviene, V.; Schlenczeck, S.; Dencker, S.; Huber, R.; Klenk, H.P.; Kramer, W.; Merkl, R.; Gottschalk, G.; Fritz, H.J. The genome sequence of the extreme thermophile. Thermus thermophilus. Nat. Biotechnol., 2004, 22(5), 547-553.
28. López-López, O.; Fuciños, P.; Pastrana, L.; Rúa, M.L.; Cerdán, M.E.; González-Siso, M.I. Heterologous expression of an esterase from Thermus thermophilus HB27 in Saccharomyces cerevisiae. J. Biotechnol., 2010, 145(3), 226-232.
29. Amann, R.I.; Ludwig, W.; Schleifer, K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev., 1995, 59(1), 143-169.
30. Handelsman, J.; Rondon, M.R.; Brady, S.F.; Clardy, J.; Goodman, R.M. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol., 1998, 5(10), R245-R249.
31. Streit, W.R.; Schmitz, R.A. Metagenomics: the key to the uncultured microbes. Curr. Opin. Microbiol., 2004, 7(5), 492-498.
32. Simon, C.; Daniel, R. Metagenomic analyses: past and future trends. Appl. Environ. Microbiol., 2011, 77(4), 1153-1161.
33. The Genomes OnLine Database (GOLD). http://www.genomesonline.org/cgi-bin/GOLD/index.cgi). (Accessed September 5, 2012).
34. Bell, P.J.; Sunna, A.; Gibbs, M.D.; Curach, N.C.; Nevalainen, H.; Bergquist, P.L. Prospecting for novel lipase genes using PCR. Microbiology, 2002, 148(Pt 8), 2283-2291.
35. Gabor, E.M.; Alkema, W.B.L.; Janssen, D.B. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ. Microbiol., 2004, 6(9), 879-886.
36. Craig, J.W.; Chang, F.Y.; Kim, J.H.; Obiajulu, S.C.; Brady, S.F. Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse proteobacteria. Appl. Environ. Microbiol., 2010, 76(5), 1633-1641.
37. Lussier, F.X.; Chambenoit, O.; Côté, A.; Hupé, J.F.; Denis, F.; Juteau, P.; Beaudet, R.; Shareck, F. Construction and functional screening of a metagenomic library using a T7 RNA polymerasebased expression cosmid vector. J. Ind. Microbiol. Biotechnol., 2011, 38(9), 1321-1328.
38. Angelov, A.; Mientus, M.; Liebl, S.; Liebl, W. A two-host fosmid system for functional screening of (meta)genomic libraries from extreme thermophiles. Syst. Appl. Microbiol., 2009, 32(3), 177-185.
39. Handelsman, J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev., 2004, 68(4), 669-685.
40. Wang, Q.; Wu, H.; Wang, A.; Du, P.; Pei, X.; Li, H.; Yin, X.; Huang, L.; Xiong, X. Prospecting metagenomic enzyme subfamily genes for DNA family shuffling by a novel PCR-based approach. J. Biol. Chem., 2010, 285(53), 41509-41516.
41. Lawrence, R.C.; Fryer, T.F.; Reiter, B. Rapid method for the quantitative estimation of microbial lipases. Nature (London), 1967, 213, 1264-1265.
42. Kouker, G.; Jaeger K.E. Specific and sensitive plate assay for bacterial lipases. Appl. Environ. Microbiol., 1987, 53(1), 211-213.
43. Park, S.Y.; Shin, H.J.; Kim, G.J. Screening and identification of a novel esterase EstPE from a metagenomic DNA library. J. Microbiol., 2011, 49(1), 7-14.
44. Ferrer, M.; Golyshina, O.V.; Chernikova, T.N.; Khachane, A.N.; Martins Dos Santos, V.A.; Yakimov, M.M.; Timmis, K.N.; Golyshin, P.N. Microbial enzymes mined from the Urania deep-sea hypersaline anoxic basin. Chem. Biol., 2005, 12(8), 895-904.
45. Okamura, Y.; Kimura, T.; Yokouchi, H.; Meneses-Osorio, M.; Katoh, M.; Matsunaga, T.; Takeyama, H. Isolation and characterization of a GDSL esterase from the metagenome of a marine sponge-associated bacteria. Mar. Biotechnol. (NY), 2010, 12(4), 395-402.
46. Wang, B.; Tang, X.; Ren, G.; Liu, J.; Yu, H. A new highthroughput screening method for determining active and enantioselective hydrolases. Biochem. Eng. J., 2009, 46(3), 345-349.
47. Lämmle, K.; Zipper, H.; Breuer, M.; Hauer, B.; Buta, C.; Brunner, H.; Rupp, S. Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning. J. Biotechnol., 2007, 127(4), 575-592.
48. Meilleur, C.; Hupé, J.F.; Juteau, P.; Shareck, F. Isolation and characterization of a new alkali-thermostable lipase cloned from a metagenomic library. J. Ind. Microbiol. Biotechnol., 2009, 36(6), 853-861.
49. Côté, A.; Shareck, F. Expression and characterization of a novel heterologous moderately thermostable lipase derived from metagenomics in Streptomyces lividans. J. Ind. Microbiol. Biotechnol., 2010, 37(9), 883-891.
50. Sharma, P.K.; Singh, K.; Singh, R.; Capalash, N.; Ali, A.; Mohammad, O.; Kaur, J. Characterization of a thermostable lipase showing loss of secondary structure at ambient temperature. Mol. Biol. Rep., 2012, 39(3), 2795-2804.
51. Rhee, J.K.; Ahn, D.G.; Kim, Y.G.; Oh, J.W. New thermophilic and thermostable esterase with sequence similarity to the hormonesensitive lipase family, cloned from a metagenomic library. Appl. Environ. Microbiol, 2005, 71(2), 817-825.
52. Tirawongsaroj, P.; Sriprang, R.; Harnpichamchai, P.; Thongaram, T.; Champreda, V.; Tanapongpipat, S.; Pootanakit, K.; Eurwilaichitr, L. Novel thermophilic and thermostable lipolytic enzymes from a Thailand hot spring metagenomic library. J. Biotechnol, 2008, 133, 42-49.
53. Sharma, P.K.; Kumar, R.; Kumar, R.; Mohammad, O.; Singh, R.; Kaur, J. Engineering of a metagenome derived lipase toward thermal tolerance: effect of asparagine to lysine mutation on the protein surface. Gene, 2012, 491(2), 264-271.
54. Kim, Y.H.; Kwon, E.J.; Kim, S.K.; Jeong, Y.S.; Kim, J.; Yun, H.D.; Kim, H. Molecular cloning and characterization of a novel family VIII alkaline esterase from a compost metagenomic library. Biochem. Biophys. Res. Commun., 2010, 393(1), 45-49.
55. Kang, C.H.; Oh, K.H.; Lee, M.H.; Oh, T.K.; Kim, B.H.; Yoon, J. A novel family VII esterase with industrial potential from compost metagenomic library. Microb. Cell. Fact., 2011, 10, 41.
56. Wei, P.; Bai, L.; Song, W.; Hao, G. Characterization of two soil metagenome-derived lipases with high specificity for p-nitrophenyl palmitate. Arch. Microbiol., 2009, 191, 233-240.
57. Elend, C.; Schmeisser, C.; Hoebenreich, H.; Steele, H.L.; Streit, W.R. Isolation and characterization of a metagenome-derived and cold-active lipase with high stereospecificity for (R)-ibuprofen esters. J. Biotechnol., 2007, 130(4), 370-377.
58. Fan, X.; Liu, X.; Wang, K.; Wang, S.; Huang, R.; Liu, Y. Highly soluble expression and molecular characterization of an organic solvent-stable and thermotolerant lipase originating from the metagenome. J. Mol. Catal. B: Enzym., 2011, 72(3-4), 319-326.
59. Yuhong, Z.; Shi, P.; Liu, W.; Meng, K.; Bai, Y.; Wang, G.; Zhan, Z.; Yao, B. Lipase diversity in glacier soil based on analysis of metagenomic DNA fragments and cell culture. J. Microbiol. Biotechnol., 2009, 19(9), 888-897.
60. Berlemont, R.; Pipers, D.; Delsaute, M.; Angiono, F.; Feller, G.; Galleni, M.; Power, P. Exploring the Antarctic soil metagenome as a source of novel cold-adapted enzymes and genetic mobile elements. Rev. Argent. Microbiol., 2011, 43(2), 94-103.
61. Yu, E.Y.; Kwon, M.A.; Lee, M.; Oh, J.Y.; Choi, J.E.; Lee, J.Y.; Song, B.K.; Hahm, D.H.; Song, J.K. Isolation and characterization of cold-active family VIII esterases from an arctic soil metagenome. Appl. Microbiol. Biotechnol., 2011, 90(2), 573-581.
62. Park, H.J.; Jeon, J.H.; Kang, S.G.; Lee, J.H.; Lee, S.A.; Kim, H.K. Functional expression and refolding of new alkaline esterase, EM2L8 from deep-sea sediment metagenome. Protein Expr. Purif., 2007, 52(2), 340-347.
63. Hu, X.P.; Heath, C.; Taylor, M.P.; Tuffin, M.; Cowan, D. A novel, extremely alkaliphilic and cold-active esterase from Antarctic desert soil. Extremophiles, 2012, 16(1), 79-86.
64. Heath, C.; Hu, X.P.; Cary, S.C.; Cowan, D. Identification of a novel alkaliphilic esterase active at low temperatures by screening a metagenomic library from Antarctic desert soil. Appl. Environ. Microbiol., 2009, 75(13), 4657-4659.
65. Faoro, H.; Glogauer, A.; Couto, G.H.; de Souza, E.M.; Rigo, L.U.; Cruz, L.M.; Monteiro, R.A.; de Oliveira Pedrosa, F. Characterization of a new Acidobacteria-derived moderately thermostable lipase from a Brazilian Atlantic Forest soil metagenome. FEMS Microbiol. Ecol., 2012, 81(2), 386-394.
66. Faoro, H.; Glogauer, A.; Souza, E.M.; Rigo, L.U.; Cruz, L.M.; Monteiro, R.A.; Pedrosa, F.O. Identification of a new lipase family in the Brazilian Atlantic Forest soil metagenome. Environ. Microbiol. Rep., 2011, 3(6), 750-755.
67. Kennedy, J.; O'Leary, N.D.; Kiran, G.S.; Morrissey, J.P.; O'Gara, F.; Selvin, J.; Dobson, A.D. Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems. J. Appl. Microbiol., 2011, 111(4), 787-99.
68. Jeon, J.H.; Lee, H.S.; Kim, J.T.; Kim, S.J.; Choi, S.H.; Kang, S.G.; Lee, J.H. Identification of a new subfamily of salt-tolerant esterases from a metagenomic library of tidal flat sediment. Appl. Microbiol. Biotechnol., 2012, 93(2), 623-631.
69. Beloqui, A.; Polaina, J.; Vieites, J.M.; Reyes-Duarte, D.; Torres, R.; Golyshina, O.V.; Chernikova, T.N.; Waliczek, A.; Aharoni, A.; Yakimov, M.M.; Timmis, K.N.; Golyshin, P.N.; Ferrer, M. Novel hybrid esterase-haloacid dehalogenase enzyme. Chembiochem., 2010, 11(14), 1975-1978.
70. Jeon, J.H.; Kim, J.T.; Kang, S.G.; Lee, J.H.; Kim, S.J. Characterization and its potential application of two esterases derived from the arctic sediment metagenome. Mar. Biotechnol. (NY), 2009, 11(3), 307-316.
71. Jeon, J.H.; Kim, J.T.; Kim, Y.J.; Kim, H.K.; Lee, H.S.; Kang, S.G.; Kim, S.J.; Lee, J.H. Cloning and characterization of a new coldactive lipase from a deep-sea sediment metagenome. Appl. Microbiol. Biotechnol., 2009, 81(5), 865-874.
72. Jeon, J.H.; Kim, J.T.M; Lee, H.S.; Kim, S.J.; Kang, S.G.; Choi, S.H.; Lee, J.H. Novel lipolytic enzymes identified from metagenomic library of deep-sea sediment, Evid. Based Complement. Alternat. Med., 2011, 2011, Article ID 271419, 9 pages. Reference available from: http://www.hindawi.com/journals/ecam/ 2011/271419/
73. Hu, Y.; Fu C.; Huang, Y.; Yin, Y.; Cheng, G.; Lei, F.; Lu, N.; Li, J.; Ashforth, E.J.; Zhang, L.; Zhu, B. Novel lipolytic genes from the microbial metagenomic library of the South China Sea marine sediment. FEMS Microbiol. Ecol., 2010, 72(2), 228-237.
74. Selvin, J.; Kennedy, J.; Lejon, D.P.; Kiran, S.; Dobson, A.D. Isolation identification and biochemical characterization of a novel halotolerant lipase from the metagenome of the marine sponge Haliclona simulans. Microb. Cell. Fact., 2012, 11(1), 72.
75. Yung, P.Y.; Burke, C.; Lewis, M; Kjelleberg, S.; Thomas, T. Novel antibacterial proteins from the microbial communities associated with the sponge Cymbastela concentrica and the green alga Ulva australis. Appl. Environ. Microbiol., 2011, 77(4), 1512-1515.
76. Roh, C.; Villatte, F. Isolation of a low-temperature adapted lipolytic enzyme from uncultivated micro-organism. J. Appl. Microbiol., 2008, 105(1), 116-123.
77. Morohoshi, T.; Oikawa, M.; Sato, S.; Kikuchi, N.; Kato, N.; Ikeda, T. Isolation and characterization of novel lipases from a metagenomic library of the microbial community in the pitcher fluid of the carnivorous plant Nepenthes hybrida. J. Biosci. Bioeng., 2011, 112(4), 315-320.