Directed evolution of poly[(R)-3-hydroxybutyrate] depolymerase using cell surface display system: Functional importance of asparagine at position 285

Applied Microbiology and Biotechnology

Volumn 97, Issue 11, 2013, Pages 4859-4871

  Tan, Liu Tzea ^a,b   Hiraishi, Tomohiro ^a   Sudesh, Kumar ^b   Maeda, Mizuo ^a  

^a RIKEN   (Japan)

^b SCHOOL OF PHYSICS   (Malaysia)

Author keywords

Cell surface display; Directed evolution; PHB depolymerase; Poly (R) 3 hydroxybutyrate (PHB)

Indexed keywords

CELL SURFACE DISPLAYS; DEGRADATION EFFICIENCY; DIRECTED EVOLUTION; ENZYME CONCENTRATIONS; ESCHERICHIA COLI CELLS; PHB DEPOLYMERASE; POLY[-3-HYDROXYBUTYRATE]; SUBSTRATE RECOGNITION;

AMINO ACIDS; CELL MEMBRANES; DEGRADATION; DISPLAY DEVICES; ESCHERICHIA COLI; ESTERIFICATION; ESTERS; GENES; HYDROLYSIS;

ENZYMES;

ASPARAGINE; PETROCHEMICAL AGENT; POLY(3 HYDROXYBUTYRATE)DEPOLYMERASE; UNCLASSIFIED DRUG;

BACTERIUM; CATALYSIS; ENZYME ACTIVITY; HYDROLYSIS; MUTATION; POLYMERASE CHAIN REACTION; PROTEIN; SUBSTRATE;

AMINO ACID SUBSTITUTION; ARTICLE; CELL SURFACE DISPLAY; DEGRADATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME SPECIFICITY; ESCHERICHIA COLI; GENE MUTATION; HYDROLYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROTEIN EXPRESSION;

ASPARAGINE; CARBOXYLIC ESTER HYDROLASES; CATALYTIC DOMAIN; CELL SURFACE DISPLAY TECHNIQUES; DIRECTED MOLECULAR EVOLUTION; ESCHERICHIA COLI; GENE EXPRESSION; MEMBRANE PROTEINS; MUTAGENESIS; POLYMERASE CHAIN REACTION; RALSTONIA PICKETTII; RECOMBINANT PROTEINS;

ESCHERICHIA COLI; RALSTONIA PICKETTII;

EID: 84878018083     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-012-4366-8     Document Type: Article

References (37)

1. Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics 22:195-201
2. Bachmann BM, Seebach D (1999) Investigation of the enzymatic cleavage of diastereomeric oligo(3-hydroxybutanoates) containing two to eight HB units. A model for the stereoselectivity of PHB depolymerase from Alcaligenes faecalis T1. Macromolecules 32:1777-1784
3. Benkert P, Biasini M, Schwede T (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27:343-350
4. Berg OG, Cajal Y, Butterfoss GL, Grey RL, Alsina MA, Yu BZ, Jain MK (1998) Interfacial activation of triglyceride lipase from Thermomyces (Humicola) lanuginosa: kinetic parameters and a basis for control of the lid. Biochemistry 37:6615-6627
5. Bloom JD, Meyer MM, Meinhold P, Otey CR, Macmillan D, Arnold FH (2005) Evolving strategies for enzyme engineering. Curr Opin Struc Biol 15:447-452
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
7. Chen GQ (2009) A microbial polyhydroxyalkanoates (PHA) based bio- and materials industry. Chem Soc Rev 38:2434-2446
8. Fan Y, Nishida H, Mori T, Shirai Y, Endo T (2004) Thermal degradation of poly(l-lactide): effect of alkali earth metal oxides for selective l,l-lactide formation. Polymer 45:1197-1205
9. Fan Y, Fang W, Xiao Y, Yang X, Zhang Y, Bidochka MJ, Pei Y (2007) Directed evolution for increased chitinase activity. Appl Microbiol Biotechnol 76:135-139
10. Hiraishi T, Taguchi S (2009) Enzyme-catalyzed synthesis and degradation of biopolymers. Mini-Rev Org Chem 6:44-54
11. Hiraishi T, Ohura T, Ito S, Kasuya K, Doi Y (2000) Function of the catalytic domain of poly(3-hydroxybutyrate) depolymerase from Pseudomonas stutzeri. Biomacromolecules 1:320-324
12. Hiraishi T, Hirahara Y, Doi Y, Maeda M, Taguchi S (2006) Effects of mutations in the substrate-binding domain of poly[(R)-3-hydroxybutyrate] (PHB) depolymerase from Ralstonia pickettii T1 on PHB degradation. Appl Environ Microbiol 72:7331-7338
13. Hiraishi T, Komiya N, Maeda M (2010a) Y443F mutation in the substrate-binding domain of extracellular PHB depolymerase enhances its PHB adsorption and disruption abilities. Polym Degrad Stabil 95:1370-1374
14. Hiraishi T, Komiya N, Matsumoto N, Abe H, Fujita M, Maeda M (2010b) Degradation and adsorption characteristics of PHB depolymerase as revealed by kinetics of mutant enzymes with amino acid substitution in substrate-binding domain. Biomacromolecules 11:113-119
15. Hiraishi T, Yamashita K, Sakono M, Nakanishi J, Tan LT, Sudesh K, Abe H, Maeda M (2012) Display of functionally active PHB depolymerase on Escherichia coli cell surface. Macromol Biosci 12:218-224
16. Hisano T, Kasuya K, Tezuka Y, Ishii N, Kobayashi T, Shiraki M, Oroudjev E, Hansma H, Iwata T, Doi Y, Saito T, Miki K (2006) The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters. J Mol Biol 356:993-1004
17. Jendrossek D, Handrick R (2002) Microbial degradation of polyhydroxyalkanoates. Annu Rev Microbiol 56:403-432
18. Jendrossek D, Schirmer A, Schlegel HG (1996) Biodegradation of polyhydroxyalkanoic acids. Appl Microbiol Biotechnol 46:451-463
19. Johannes TW, Zhao H (2006) Directed evolution of enzymes and biosynthetic pathways. Curr Opin Microbiol 9:261-267
20. Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009) The SWISS-MODEL repository and associated resources. Nucl Acids Res 37:387-392
21. Kumar A, Gross RA, Jendrossek D (2000) Poly(3-hydroxybutyrate) depolymerase from Pseudomonas lemoignei: catalysis of esterification in organic media. J Org Chem 65:7800-7806
22. Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685
23. Lin L, Meng X, Liu P, Hong Y, Wu G, Huang X, Li C, Dong J, Xiao L, Liu Z (2009) Improved catalytic efficiency of endo-β-1,4-glucanase from Bacillus subtilis BME-15 by directed evolution. Appl Microbiol Biotechnol 82:671-679
24. Mukai K, Yamada K, Doi Y (1993) Kinetics and mechanism of heterogeneous hydrolysis of poly[(R)-3-hydroxybutyrate] film by PHA depolymerases. Int J Biol Macromol 15:361-366
25. Olsen M, Iverson B, Georgiou G (2000) High-throughput screening of enzyme libraries. Curr Opin Biotechnol 11:331-337
26. Otten LG, Quax WJ (2005) Directed evolution: selecting today's biocatalysts. Biomol Eng 22:1-9
27. Papageorgiou AC, Hermawan S, Singh CB, Jendrossek D (2008) Structural basis of poly(3-hydroxybutyrate) hydrolysis by PhaZ7 depolymerase from Paucimonas lemoignei. J Mol Biol 382:1184-1194
28. Peitsch MC (1995) Protein modeling by e-mail bio/technology. Nat Biotechnol 13:658-660
29. Samuelson P, Gunneriusson E, Nygren PA, Stahl S (2002) Display of proteins on bacteria. J Biotechnol 96:129-154
30. Scandola M, Focarete ML, Frisoni G (1998) Simple kinetic model for the heterogeneous enzymatic hydrolysis of natural poly(3-hydroxybutyrate). Macromolecules 31:3846-3851
31. Suzuki Y, Ohura T, Kasuya K, Toshima K, Doi Y, Matsumura S (2000) Ring-opening polymerization of β-butyrolactone using PHB depolymerase. Chem Lett 4:318-319
32. Suzuki Y, Taguchi S, Saito T, Toshima K, Matsumura S, Doi Y (2001) Involvement of catalytic amino acid residues in enzyme-catalyzed polymerization for the synthesis of polyesters. Biomacromolecules 2:541-544
33. Tokiwa Y, Jarerat A (2004) Biodegradation of poly(l-lactide). Biotechnol Lett 26:771-777
34. Verlinden RAJ, Hill DJ, Kenward MA, Williams CD, Radecka IJ (2007) Bacterial synthesis of biodegradable polyhydroxyalkanoates. Appl Microbiol 102:1437-1449
35. Zhao H, Zha W (2006) In vitro 'sexual' evolution through the PCR-based staggered extension process (StEP). Nat Protoc 1:1865-1871
36. Zhao H, Giver L, Shao Z, Affholter JA, Arnold FH (1998) Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16:258-261
37. Zhao H, Chockalingam K, Chen Z (2002) Directed evolution of enzymes and pathways for industrial biocatalysis. Curr Opin Biotechnol 13:104-110