Identification and characterization of a new true lipase isolated through metagenomic approach

Microbial Cell Factories

Volumn 10, Issue , 2011, Pages

  Glogauer, Arnaldo ^a   Martini, Viviane P ^a   Faoro, Helisson ^a   Couto, Gustavo H ^a   Müller Santos, Marcelo ^a   Monteiro, Rose A ^a   Mitchell, David A ^a   de Souza, Emanuel M ^a   Pedrosa, Fabio O ^a   Krieger, Nadia ^a  

^a FEDERAL UNIVERSITY OF PARANÁ   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

AGAR; BACTERIAL ENZYME; CALCIUM ION; CHAPERONE; FAT; LIPC12 PROTEIN; LONG CHAIN TRIACYLGLYCEROL; OLIVE OIL; TRIACYLGLYCEROL LIPASE; TRIBUTYRIN; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; RECOMBINANT PROTEIN;

ARTICLE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ISOLATION; ENZYME STABILITY; ESCHERICHIA COLI; METAGENOMICS; NONHUMAN; PH; PROTEIN FOLDING; SOIL; SOIL POLLUTION; THERMOSTABILITY; WASTE WATER TREATMENT PLANT; YERSINIA ENTEROCOLITICA; AMINO ACID SEQUENCE; BIOSYNTHESIS; CHEMISTRY; CLASSIFICATION; ENZYME SPECIFICITY; ENZYMOLOGY; GENE LIBRARY; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; PHYLOGENY; PROTEIN STABILITY; SEQUENCE ALIGNMENT; STEREOISOMERISM; TEMPERATURE;

BACTERIA (MICROORGANISMS); PROKARYOTA; SUIDAE; YERSINIA ENTEROCOLITICA;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; GENE LIBRARY; HYDROGEN-ION CONCENTRATION; LIPASE; METAGENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STABILITY; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; STEREOISOMERISM; SUBSTRATE SPECIFICITY; TEMPERATURE; YERSINIA ENTEROCOLITICA;

EID: 79960563626     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-10-54     Document Type: Article

References (75)

1. Jaeger KE, Dijkstra BW, Reetz MT. Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu Rev Microbiol 1999, 53:315-351. 10.1146/annurev.micro.53.1.315, 10547694.
2. Jaeger KE, Eggert T. Lipases for biotechnology. Curr Opin Biotechnol 2002, 13:390-397. 10.1016/S0958-1669(02)00341-5, 12323363.
3. Gupta R, Gupta N, Rathi P. Bacterial lipases: an overview of production, purification and biochemical properties. Appl Microbiol Biotechnol 2004, 64:763-781. 10.1007/s00253-004-1568-8, 14966663.
4. Hasan F, Shah AA, Hameed A. Industrial applications of microbial lipases. Enzyme Microb Technol 2006, 39:235-251.
5. Shu Z-Y, Jiang H, Lin R-F, Jiang Y-M, Lin L, Huang J-Z. Technical methods to improve yield, activity and stability in the development of microbial lipases. J Mol Catal B: Enzym 2010, 62:1-8.
6. Xiao M, Mathew S, Obbard JP. Biodiesel fuel production via transesterification of oils using lipase biocatalyst. GCB Bioenergy 2009, 1:115-125.
7. Bajaj A, Lohan P, Jha PN, Mehrotra R. Biodiesel production through lipase catalyzed transesterification: an overview. J Mol Catal B: Enzym 2010, 62:9-14.
8. Bisen PS, Sanodiya BS, Thakur GS, Baghel RK, Prasad G. Biodiesel production with special emphasis on lipase-catalyzed transesterification. Biotechnol Lett 2010, 32:1019-1030. 10.1007/s10529-010-0275-z, 20401680.
9. Xu XB. Production of specific-structured triacylglycerols by lipase-catalyzed reactions: a review. Eur J Lipid Sci Technol 2000, 102:287-303.
10. Hayes DG. Enzyme-catalyzed modification of oilseed materials to produce eco-friendly products. J Am Oil Chem Soc 2004, 81:1077-1103.
11. Hasan F, Shah AA, Javed S, Hameed A. Enzymes used in detergents: lipases. Afr J Biotechnol 2010, 9:4836-4844.
12. Houde A, Kademi A, Leblanc D. Lipases and their industrial applications - an overview. Appl Biochem Biotechnol 2004, 118:155-170. 10.1385/ABAB:118:1-3:155, 15304746.
13. Jaeger KE, Eggert T, Eipper A, Reetz MT. Directed evolution and the creation of enantioselective biocatalysts. Appl Microbiol Biotechnol 2001, 55:519-530. 10.1007/s002530100643, 11414315.
14. Liu DN, Trodler P, Eiben S, Koschorreck K, Muller M, Pleiss J, Maurer SC, Branneby C, Schmid RD, Hauer B. Rational design of Pseudozyma antarctica lipase B yielding a general esterification catalyst. ChemBioChem 2010, 11:789-795. 10.1002/cbic.200900776, 20209560.
15. Syren PO, Lindgren E, Hoeffken HW, Branneby C, Maurer S, Hauer B, Hult K. Increased activity of enzymatic transacylation of acrylates through rational design of lipases. J Mol Catal B: Enzym 2010, 65:3-10.
16. Steele HL, Jaeger KE, Daniel R, Streit WR. Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol Biotechnol 2009, 16:25-37. 10.1159/000142892, 18957860.
17. 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, 127:575-592. 10.1016/j.jbiotec.2006.07.036, 16963141.
18. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 2000, 66:2541-2547. 10.1128/AEM.66.6.2541-2547.2000, 110579, 10831436.
19. Henne A, Schmitz RA, Bomeke M, Gottschalk G, Daniel R. Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl Environ Microbiol 2000, 66:3113-3116. 10.1128/AEM.66.7.3113-3116.2000, 92121, 10877816.
20. Yun J, Ryu S. Screening for novel enzymes from metagenome and SIGEX, as a way to improve it. Microb Cell Fact 2005, 4:8. 10.1186/1475-2859-4-8, 1079935, 15790425.
21. Lorenz P, Eck J. Metagenomics and industrial applications. Nat Rev Microbiol 2005, 3:510-516. 10.1038/nrmicro1161, 15931168.
22. Kakirde KS, Parsley LC, Liles MR. Size does matter: application-driven approaches for soil metagenomics. Soil Biol Biochem 2010, 42:1911-1923. 10.1016/j.soilbio.2010.07.021, 21076656.
23. Kennedy J, Marchesi JR, Dobson ADW. Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Fact 2008, 7:27. 10.1186/1475-2859-7-27, 2538500, 18717988.
24. Jiang C, Wu L-L, Zhao G-C, Shen P-H, Jin K, Hao Z-Y, Li S-X, Ma G-F, Luo F-F, Hu G-Q, Kang W-L, Qin X-M, Bi Y-L, Tang X-L, Wu B. Identification and characterization of a novel fumarase gene by metagenome expression cloning from marine microorganisms. Microb Cell Fact 2010, 9:91. 10.1186/1475-2859-9-91, 3002918, 21092234.
25. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 1998, 5:R245-R249. 10.1016/S1074-5521(98)90108-9, 9818143.
26. Simon C, Daniel R. Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 2009, 85:265-276. 10.1007/s00253-009-2233-z, 2773367, 19760178.
27. Uchiyama T, Miyazaki K. Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 2009, 20:616-622. 10.1016/j.copbio.2009.09.010, 19850467.
28. Liaw R-B, Cheng M-P, Wu M-C, Lee C-Y. Use of metagenomic approaches to isolate lipolytic genes from activated sludge. Bioresour Technol 2010, 101:8323-8329. 10.1016/j.biortech.2010.05.091, 20639117.
29. Li G, Wang K, Liu Y. Molecular cloning and characterization of a novel pyrethroid-hydrolyzing esterase originating from the Metagenome. Microb Cell Fact 2008, 7:38. 10.1186/1475-2859-7-38, 2657102, 19116015.
30. Zhang T, Han WJ, Liu ZP. Gene cloning and characterization of a novel esterase from activated sludge metagenome. Microb Cell Fact 2009, 8:67. 10.1186/1475-2859-8-67, 20028524.
31. Li JG, Zhang KG, Han WJ. Cloning and biochemical characterization of a novel lipolytic gene from activated sludge metagenome, and its gene product. Microb Cell Fact 2010, 9:83. 10.1186/1475-2859-9-83, 2987919, 21054894.
32. Jiang ZB, Wang HP, Ma YS, Wei DZ. Characterization of two novel lipase genes isolated directly from environmental sample. Appl Microbiol Biotechnol 2006, 70:327-332. 10.1007/s00253-005-0065-z, 16003556.
33. Lee MH, Lee CH, Oh TK, Song JK, Yoon JH. 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, 72:7406-7409. 10.1128/AEM.01157-06, 1636159, 16950897.
34. Elend C, Schmeisser C, Hoebenreich H, Steele HL, Streit WR. Isolation and characterization of a metagenome-derived and cold-active lipase with high stereospecificity for (R)-ibuprofen esters. J Biotechnol 2007, 130:370-377. 10.1016/j.jbiotec.2007.05.015, 17601620.
35. Jeon JH, Kim JT, Kim YJ, Kim HK, Lee HS, Kang SG, Kim SJ, Lee JH. Cloning and characterization of a new cold-active lipase from a deep-sea sediment metagenome. Appl Microbiol Biotechnol 2009, 81:865-874. 10.1007/s00253-008-1656-2, 18773201.
36. Liu KL, Wang JQ, Bu DP, Zhao SG, McSweeney C, Yu P, Li D. Isolation and biochemical characterization of two lipases from a metagenomic library of China Holstein cow rumen. Biochem Biophys Res Commun 2009, 385:605-611. 10.1016/j.bbrc.2009.05.110, 19486892.
37. Meilleur C, Hupé JF, Juteau P, Shareck F. Isolation and characterization of a new alkali-thermostable lipase cloned from a metagenomic library. J Ind Microbiol Biotechnol 2009, 36:853-861. 10.1007/s10295-009-0562-7, 19333634.
38. Tirawongsaroj P, Sriprang R, Harnpicharnchai 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.
39. Arpigny JL, Jendrossek D, Jaeger KE. A novel heat-stable lipolytic enzyme from Sulfolobus acidocaldarius DSM 639 displaying similarity to polyhydroxyalkanoate depolymerases. Fems Microbiol Lett 1998, 167:69-73. 10.1111/j.1574-6968.1998.tb13209.x, 9785454.
40. Elend C, Schmeisser C, Leggewie C, Babiak P, Carballeira JD, Steele HL, Reymond JL, Jaeger KE, Streit WR. Isolation and biochemical characterization of two novel metagenome-derived esterases. Appl Environ Microbiol 2006, 72:3637-3645. 10.1128/AEM.72.5.3637-3645.2006, 1472341, 16672512.
41. Ollis DL, Shea E, Cygler M, Dijkstra B, Frolow F. The α/β hydrolase fold. Protein Eng 1992, 5:197. 10.1093/protein/5.3.197, 1409539.
42. Arpigny JL, Jaeger KE. Bacterial lipolytic enzymes: classification and properties. Biochem J 1999, 343 Pt 1:177-183. 1220539, 10493927.
43. Nardini M, Lang DA, Liebeton K, Jaeger KE, Dijkstra BW. Crystal structure of Pseudomonas aeruginosa lipase in the open conformation. The prototype for family I.1 of bacterial lipases. J Biol Chem 2000, 275:31219-31225.
44. Hasan F, Shah AA, Hameed A. Methods for detection and characterization of lipases: a comprehensive review. Biotechnol Adv 2009, 27:782-798. 10.1016/j.biotechadv.2009.06.001, 19539743.
45. Grochulski P, Li Y, Schrag JD, Bouthillier F, Smith P. Insights into interfacial activation from an open structure of Candida rugosa lipase. J Biol Chem 1993, 268:12843.
46. Colton IJ, Ahmed SN, Kazlauskas RJ. A 2-propanol treatment increases the enantioselectivity of Candida rugosa lipase toward esters of chiral carboxylic-acids. J Org Chem 1995, 60:212-217.
47. Eichler J. Biotechnological uses of archaeal extremozymes. Biotechnol Adv 2001, 19:261-278. 10.1016/S0734-9750(01)00061-1, 14538076.
48. Scopes RK. Protein purification: priciples and practice 1994, New York: Springer-Verlag.
49. Rajendhran J, Gunasekaran P. Strategies for accessing soil metagenome for desired applications. Biotechnol Adv 2008, 26:576-590. 10.1016/j.biotechadv.2008.08.002, 18786627.
50. Gabor EM, de Vries EJ, Janssen DB. Efficient recovery of environmental DNA for expression cloning by indirect extraction methods. Fems Microbiol Ecol 2003, 44:153-163. 10.1016/S0168-6496(02)00462-2, 19719633.
51. Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 2004, 38:525-552. 10.1146/annurev.genet.38.072902.091216, 15568985.
52. Daniel R. The metagenomics of soil. Nat Rev Microbiol 2005, 3:470-478. 10.1038/nrmicro1160, 15931165.
53. Kimura N. Metagenomics: access to unculturable microbes in the environment. Microbes Environ 2006, 21:201-215.
54. Nini L, Sarda L, Comeau L-C, Boitard E, Dubès J-P, Chahinian H. Lipase-catalysed hydrolysis of short-chain substrates in solution and in emulsion: a kinetic study. Biochim Biophys Acta, Mol Cell Biol Lipids 2001, 1534:34-44.
55. Sharma R, Chisti Y, Banerjee UC. Production, purification, characterization, and applications of lipases. Biotechnol Adv 2001, 19:627-662. 10.1016/S0734-9750(01)00086-6, 14550014.
56. 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, 59:524-534. 10.1111/j.1574-6941.2006.00206.x, 17328767.
57. Sambrook J, Maniatis T, Fritsch EF. Molecular cloning: a laboratory manual 1989, Cold Spring Harbor: Cold Spring Harbor Laboratory Press.
58. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo LYG, Helberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko R, Tatusov L, Tatusova TA, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008, 36:D13-21. 2238880, 18045790.
59. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
60. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305:567-580. 10.1006/jmbi.2000.4315, 11152613.
61. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340:783-795. 10.1016/j.jmb.2004.05.028, 15223320.
62. Hirokawa T, Boon-Chieng S, Mitaku S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 1998, 14:378-379. 10.1093/bioinformatics/14.4.378, 9632836.
63. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook 2005, 571-607. Totowa: Humana Press, Walker JM.
64. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
65. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24:1596-1599. 10.1093/molbev/msm092, 17488738.
66. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K. Current protocols in molecular biology 2003, New York: John Wiley & Sons.
67. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970, 227:680-685. 10.1038/227680a0, 5432063.
68. Oh B, Kim H, Lee J, Kang S, Oh T. Staphylococcus haemolyticus lipase: biochemical properties, substrate specificity and gene cloning. FEMS Microbiol Lett 1999, 179:385-392. 10.1111/j.1574-6968.1999.tb08753.x, 10518741.
69. Westermeier R, Naven T. Proteomics in practice: a laboratory manual of proteome analysis 2002, Chichester: Wiley-VCH.
70. Winkler UK, Stuckmann M. Glycogen, hyaluronate, and some other polysaccharides greatly enhance the formation of exolipase by Serratia marcescens. J Bacteriol 1979, 138:663-670. 218088, 222724.
71. Rhee JK, Ahn DG, Kim YG, Oh JW. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl Environ Microbiol 2005, 71:817-825. 10.1128/AEM.71.2.817-825.2005, 546692, 15691936.
72. Somers NA, Kazlauskas RJ. Mapping the substrate selectivity and enantioselectivity of esterases from thermophiles. Tetrahedron-Asymmetry 2004, 15:2991-3004.
73. Mateos JC, Ruiz K, Rodriguez JA, Cordova J, Baratti J. Mapping substrate selectivity of lipases from thermophilic fungi. J Mol Catal B: Enzym 2007, 49:104-112.
74. Janes LE, Kazlauskas RJ. Quick E. A Fast Spectrophotometric Method to Measure the Enantioselectivity of Hydrolases. J Org Chem 1997, 62:4560-4561.
75. Tiss A, Carriere F, Verger R. Effects of gum arabic on lipase interfacial binding and activity. Anal Biochem 2001, 294:36-43. 10.1006/abio.2001.5095, 11412003.