Chapter 33 : Bioprospecting for Industrial Enzymes: Importance of Integrated Technology Platforms for Successful Biocatalyst Development

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Bioprospecting for Industrial Enzymes: Importance of Integrated Technology Platforms for Successful Biocatalyst Development, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817770/9781555812676_Chap33-1.gif /docserver/preview/fulltext/10.1128/9781555817770/9781555812676_Chap33-2.gif


This chapter focuses on the discovery of enzymes from natural environments and on optimization of enzymes by protein engineering and directed molecular evolution to develop products that show optimal performance in their target application. Screening large numbers of culturable microbes is considered one of the most successful and efficient means of finding novel biological compounds such as biocatalysts, and this classical route of screening will continue to be applied with success in the future. Once the best performing candidates have been selected by primary and secondary screening, genes from the top candidates are cloned and expressed by a variety of different methods. Cloning and expression represent essential steps in the production of industrial enzymes today. Industrial applications utilizing enzymes as biocatalysts often put extreme demands on the properties of the enzymes due to the very harsh conditions often applied under such processes. Enzyme properties other than the protein stability-related parameters are important in a functional biocatalyst. There is no guarantee that the enzymatic answer to an industrial process can necessarily be isolated from nature, as such a guarantee would demand that survival of an organism would depend on an enzyme functional under the conditions relevant for that particular application. Two approaches for improving natural proteins in the laboratory have traditionally been taken, rational protein engineering and directed molecular evolution. Each of these two approaches is described separately; however, the borderline between the technologies has become less distinct in recent years.

Citation: Schafer T, Borchert T. 2004. Bioprospecting for Industrial Enzymes: Importance of Integrated Technology Platforms for Successful Biocatalyst Development, p 375-390. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch33

Key Concept Ranking

Bacteria and Archaea
Microbial Ecology
Aspergillus nidulans
Bacillus subtilis
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Number of gene sequences submitted to public databases from 1982 to 2000. Data were taken directly from the National Center for Biotechnology Information (NCBI) homepage (http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html).

Citation: Schafer T, Borchert T. 2004. Bioprospecting for Industrial Enzymes: Importance of Integrated Technology Platforms for Successful Biocatalyst Development, p 375-390. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch33
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

The codon cube shows the correlation between the amino acid and the encoding codons in the DNA represented by the three nucleotides along the , and axes.

Citation: Schafer T, Borchert T. 2004. Bioprospecting for Industrial Enzymes: Importance of Integrated Technology Platforms for Successful Biocatalyst Development, p 375-390. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch33
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Amann, R.,, J. Snaidr,, M. Wagner,, W. Ludwig,, and K. H. Schlerfeu. 1996. In situ visualization of high genetic diversity microbial community. J. Bacteriol. 178:34963500.
2. Ando, H.,, M. Adachi,, K. Umeda,, A. Matsuura,, M. Nonaka,, R. Uchio,, H. Tanaka, and M. Motoki. 1989. Purification and characteristics of a novel transglutaminase derived from microorganisms. Agric. Biol. Chem. 53:26132617.
3. Archer, D. B. 1994. Enzyme production by recombinant Aspergillus. Bioprocess Technol. 19:373393.
4. Archer, D. B., and J. F. Peberdy. 1997. The molecular biology of secreted enzyme production by fungi. Crit. Rev. Biotechnol. 17:273306.
5. Beier, L.,, A. Svendsen,, C. Andersen,, T. P. Frandsen,, T. V. Borchert,, J. R. Cherry. 2000. Conversion of the maltogenic a-amylase Novamyl into a CGTase. Protein Eng. 13:509513.
6. Bisgaard-Frantzen, H.,, A. Svendsen,, B. Norman,, S. Pedersen,, S. Kjaerulff,, H. Outtrup,, and T. V. Borchert. 1999. Development of industrially important alpha-amylases. J. Appl. Glycosci. 46:199206.
7. Brady, S. F.,, C. J. Chao,, J. Handelsman,, and J. Clardy. 2001. Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org. Lett. 3:19811984.
8. Brunger, A. T.,, and E. D. Laue. 2000. Biophysical methods. New approaches to study macromolecular structure and function. Curr. Opin. Struct. Biol. 10:557.
9. Bryan, P. 2000. Protein engineering of subtilisins. Biochem. Biophys. Acta-Protein Struct. Mol Enzymol. 1553:203222.
10. Bull, A. T.,, M. Goodfellow,, and J. H. Slate. 1992. Biodiversity as a source of innovation in biotechnology. Ann. Rev Microbiol 46:219252.
11. Bull, A. T.,, A. C. Ward,, and M. Goodfellow. 2000. Search and discovery strategies for biotechnology: the paradigm shift. Microbiol. Mol. Biol. Rev. 64:573606.
12. Bult, C. J.,, O. White,, G. J. Olsen,, L. X. Zhou,, R. D. Fleischmann,, G. G. Sutton,, J. A. Blake,, L. M. Fitzgerald,, R. A. Clayton,, J. D. Gocayne,, A. R. Kerlavage,, B. A. Dougherty,, J. F. Tomb,, M. D. Adams,, C. I. Reich,, R. Overbeek,, E. F. Kirkness,, K. G. Weinstock,, J. M. Merrick,, A. Glodek,, J. L. Scott,, N. S. M. Geoghagen,, J. F. Weidman,, J. L. Fuhrmann,, D. Nguyen,, T. R. Utterback,, J. M. Kelley,, J. D. Peterson,, P. W. Sadow,, M. C. Hanna,, M. D. Cotton,, K. M. Roberts,, M. A. Hurst,, B. P. Kaine,, M. Borodovsky,, H. P. Klenk,, C. M. Fraser,, H. O. Smith,, C. R. Woese,, and J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon, methanococcus-jannaschii. Science 273:10581073.
13. Callebaut, I.,, G. Labesse,, P. Durand,, A. Poupon,, L. Canard,, J. Chomilier,, B. Henrissat,, and J. P. Mornor. 1997. Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives. Cell. Mol. Life Sci. 53:621645.
14. Cedrone, F.,, A. Menez, and E. Quemeneur. 2000. Tailoring new enzyme functions by rational redesign. Curr. Opin. Struct. Biol. 10:405410.
15. Cheetham, P. S. J. 1998. What makes a good biocatalyst? J. Biotechnol. 66:310.
16. Cherry, J. R.,, M. H. Lamsa,, P. Schneider,, J. Vind,, A. Svendsen,, A. Jones,, and A. H. Pedersen. 1999. Directed evolution of a fungal peroxidase. Nat. Biotechnol. 17:379384.
17. Coco, W. M.,, W. E. Levinson,, M. J. Crist,, H. J. Hektor,, A. Darzins,, P. T. Pienkos,, C. H. Squires,, and D. J. Monticello. 2001. DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat. Biotechnol. 19:354359.
18. Cottrell, M. T.,, J. A. Moore,, and D. L. Kirchman. 1999. Chitinases from uncultivated marine microorganisms. Appl. Environ. Microbiol. 65:25532557.
19. Crameri, A.,, S. A. Raillard,, E. Bermudez,, and W. P. Stemmer. 1998. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391:288291.
20. Dalbøge, H.,, and L. Lange. 1998. Using molecular techniques to identify new microbial biocatalysts. Trends Biotechnol. 16:265272.
21. Dalbøge, H.,, Th. Sandal,, S. Kauppinen,, and B. Diderichsen. August 2001. Method of providing a hybrid polypeptide exhibiting an activity of interest. U.S. Patent 6,270,968.
22. Demirjian, D. C.,, F. Moris-Varas,, and C. S. Cassidy. 2001. Enzymes from extremophiles. Curr. Opin. Chem. Biol. 5:144151.
23. Diderichsen, B.,, and L. Christiansen. 1988. Cloning of a maltogenic alpha-amylase from Bacillus stearothermophilus. FEMS Microbiol. Lett. 56:5360.
24. Duffner, F.,, R. Wilting,, and K. Schnorr. 2001. Signal sequence trapping. Patent application W00177315-A1.
25. Dunn-Coleman, N.,, and R. Prade. 1998. Toward a global filamentous fungus genome sequencing effort. Nat. Biotechnol. 16:5.
26. Durick, K.,, J. Mendlein, and K. C. Xanthopoulos. 1999. Hunting with traps: genome-wide strategies for gene discovery and functional analysis. Genome Res. 9:10191025.
27. Encheva, P.,, W. Liebl,, A. Joham,, T. Hartsch,, and M. R. Strevt. 2001. Direct cloning from enrichment cultures, a reliable strategy for isolation of complete opérons and genes from microbiol consortua. Appl. Environ. Microbiol. 67:8999.
28. Fabret, C.,, S. Poncet,, S. Danielsen,, T. Borchert,, S. D., Ehrlich,, and L. Janniero. 2000. Efficient gene targeted random mutagenesis in genetically stable Escherichia coli strains. Nucleic Acids Res. 28:21 e95 15.
29. Felse, P. A.,, and T. Panda. 2000. Production of microbial chitinases: a revisit. Bioprocess Eng. 23:127134.
30. Franco, C. M. M.,, and N. C.. McClura. 1998. Isolation of microorganisms for biotechnological application. J. Microbiol. Biotechnol. 8:101110.
31. Godfrey, T.,, and S. I. West,. 1996. Introduction to industrial enzymes, p. 18. In T. Godfrey, and S. I. West, (ed.), Industrial Enzymology, 2nd ed. Macmillan Press Inc., London, United Kingdom.
32. Gordon, J., 1999. Intellectual property, p. 309320. In A. L. Demain, and J. E. Davies (ed.), Manual of Industrial Microbiology and Biotechnology. ASM Press, Washington, D.C.
33. Greener, A.,, M. Callahan,, and B. Jerpseth. 1996. An efficient random mutagenesis technique using an E. coli mutator strain. Methods Mol. Biol. 57:375385.
34. Hallberg, K. B.,, and D. B. Johnson. 2001. Biodiversity of acidophilic prokaryotes. Adv. Appl. Microbiol. 49:3784.
35. Handelsman, J.,, M. R. Rondon,, S. F. Brady,, J. Clardy,, and R. M. Goodman. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. (London) 5:R245R249.
36. Hanes, J.,, and A. S. Plückthun. 1997. In vitro selection and evolution of functional proteins by using ribosome display. Proc. Natl. Acad. Sci. USA 94:49374942.
37. Hansson, T.,, C., Oostenbrink,, and W. F. Gunsteren. 2002. Molecular dynamics simulations. Curr. Opin. Struct. Biol. 12:190196.
38. Hartley, B. S.,, N., Hanlon,, R. J. Jackson,, and M. Rangarajan. 2000. Glucose isomerase: insights into protein engineering for increased thermostability. Biochem. Biophys. Acta Protein Struct. Mol. Enzymol. 1553:294335.
39. Hawksworth, D. L. 2001. The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycolog. Res. 105:14221432.
40. Henne, A.,, R. Daniel,, R. A. Schmitz,, and G. Gottschall. 1999. Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4- hydroxybutyrate. Appl. Environ. Microbiol. 65:39013907.
41. Henne, A.,, R. A. Schmitz,, M. Bomeke,, G. Gottschalk,, and R. Daniel. 2000. Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl. Environ. Microbiol. 66:31133116.
42. Henrissat, B.,, and P. Borla. 1996. On the classification of modular proteins. Protein Eng. 9:725726.
43. Henrissat, B.,, and A. Romeu. 1995. Families, superfamilies and subfamilies of glycosyl hydrolases. Biochem. J. 311:350351.
44. Hirose, I.,, K. Sano,, I. Shioda,, M. Kumano,, K. Nakamura,, and K. Yamano. 2000. Proteome analysis of Bacillus subtilis extracellular proteins: a two-dimensional protein electrophoretic study. Microbiology 146:6575.
45. Honig, B.,, and A. Nicholls. 1995. Classical electrostatics in biology and chemistry. Science 268:11441149.
46. Hugenholtz, P.,, and N. R. Pace. 1996. Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol. 14:190197.
47. Joo, H.,, A. Arisawa,, Z. L., Lin,, and F. H. Arnold. 1999. A high-throughput digital imaging screen for the discovery and directed evolution of oxygenases. Chem. Biol. 6:699706.
48. Kirk, O.,, T. V. Borchert,, and C. C. Fuglsang. 2002. Industrial enzyme applications. Curr. Opin. Biotechnol. 13:345351.
49. Kongsbak, L.,, K. S. Jørgensen,, C. T. Jørgensen,, T. L. Husum,, S. Ernst,, and S. Møller. 1999. A fluorescence polarisation screening method. Novo Nordisk A/S, patent application W09945143-A2.
50. Kunst, F.,, N. Ogasawara,, I. Moszer,, A. M. Albertini,, G. Alloni,, V. Azevedo,, M. G. Bertero,, P. Bessifres,, A. Bolotin,, S. Borchert,, R. Borriss,, L. Boursier,, A. Brans,, M. Braun,, S. C. Brignell,, S. Bron,, S. Brouillet,, C. V. Bruschi,, B. Caldweil,, V. Capuano,, N. M. Carter,, S. K. Choi,, J. J. Codani,, I. P. Connerton,, and A. Danchir. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390: 249256.
51. Kuske, C. R.,, S. M., Barns,, and J. D. Busch. 1997. Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl. Environ. Microbiol. 63:36143621.
52. Lassen, S. F.,, J. Breinholt,, P. R. Ostergaard,, R. Brugger,, A. Bischoff,, M. Wyss,, and C. C. Fuglsang. 2001. Expression, gene cloning, and characterization of five novel phytases from four basidiomycete fungi: Peniophora lycii, Agrocybe pediades, a Ceriporia sp., and Trametes pubescens. Appl. Environ. Microbiol. 67:47014707.
53. Li, W. Z.,, and A. Godzila. 2002. Discovering new genes with advanced homology detection. Trends Biotechnol. 20:315316.
54. Liberman, D. F.,, R. Fink,, and F. Schaefer,. 1999. Biosafety and biotechnology, p. 300308. In A. L. Demain, and J. E. Davies (ed.), Manual of Industrial Microbiology and Biotechnology. ASM Press, Washington, D.C.
55. Liesack, W.,, and E. Stackebrandt. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174:50725078.
56. Lorenz, P.,, and C. Schleper. 2002. Metagenome—a challenging source of enzyme discovery. J. Mol. Catal. 19-20C:1319.
57. Majernik, A.,, G. Gottschalk,, and R. Daniel. 2001. Screening of environmental DNA libraries for the presence of genes conferring Na+(L+)/H+ antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products. Bacteriol. 183:66456653.
58. McCoy, M. 2000. Novozymes emerges. Chem. Eng. News 19:2325.
59. Meeuwsen, P. J. A.,, J. P. Vincken,, G. Beldman,, and A. G. J. Voragen. 2000. A universal assay for screening expression libraries for carbohydrases. J. Biosci. Bioeng. 89:107109.
60. Merlin, C.,, S. McAteer,, and M. Masters. 2002. Tools for characterization of Escherichia coli genes of unknown function. J. Bacteriol. 184:45734581.
61. Naki, D.,, C. Paech,, G. Ganshaw,, and V. Schellenberger. 1998. Selection of a subtilisin-hyperproducing Bacillus in a highly structured environment. Appl. Microbiol. Biotechnol. 49: 290294.
62. Nelson, W. N. 1991. Modern Techniques for Rapid Microbiological Analysis. VCH Publishers Inc., Deerfield Beach, Fla.
63. Ness, J. E.,, M. Welch,, L. Giver,, M. Bueno,, J. R. Cherry,, T. V. Borchert,, W. P. C. Stemmer,, and J. Minshull. 1999. DNA shuffling of subgenomic sequences of subtilisin. Nat. Biotechnol. 17:893896.
64. Nielsen, J. E.,, and T. V. Borchert. 2000. Protein engineering of bacterial alpha-amylases. Biochem. Biophys. Acta Protein Struct. Mol. Enzymol. 1553:253274.
65. O'Neil, K. T.,, and R. H. Hoes. 1995. Phage display: protein engineering by directed evolution. Curr. Opin. Struct. Biol. 5:443449.
66. OECD (Organisation for Economic Co-operation andDevelopment). 1998. Biotechnology for Clean Industrial Products and Processes: Towards Industrial Sustainability. OECD, Paris, France.
67. OECD (Organisation for Economic Co-operation and Development). 2001. The Application of Biotechnology to Industrial Sustainability. OECD, Paris, France.
68. Ogawa, J.,, and S. Shimizs. 2002. Industrial microbial enzymes: their discovery by screening and use in large-scale production of useful chemicals in Japan. Curr. Opin. Biotechnol. 13: 367375.
69. Ogram, A. 2000. Soil molecular microbial ecology at age 20: methodological challenges for the future. Soil Biol. Biochem. 32:14991504.
70. Ohnishi, J.,, S. Mitsuhashi,, M. Hayashi,, S. Ando,, H. Yokoi,, K. Ochiai,, and M. Ikeda. 2002. A novel methodology employing Corynebacterium glutamicum genome information to generate a new L-lysine-producing mutant. Appl. Microbiol. Biotechnol. 58:217223.
71. Olsen, G. J.,, and C. R. Woese. 1997. Archaeal genomics: an overview. Cell 89:991994.
72. Olsen, G. J.,, D. J. Lane,, S. J. Giovannoni,, N. R. Pace,, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337365.
73. Ostermeier, M.,, J. H. Shim,, and S. J. Benkovic. 1999. A combinatorial approach to hybrid enzymes independent of DNA homology. Nat. Biotechnol. 17:12051209.
74. Pandey, A.,, G. Szakacs,, C. R. Soccol,, J. A. Rodriguez-Leon,, and V. T. Soccol. 2001. Production, purification and properties of microbial phytases. Bioresource Technol. 77:203214.
75. Precigou, S.,, P. Goulas,, and R. Duran. 2001. Rapid and specific identification of nitrile hydratase (NHase)-encoding genes in soil samples by polymerase chain reaction. FEMS MicrobioL Lett. 204:155161.
76. Preisig, C.,, and G. Byng. 2001. Applications of mass spectrometry in screening for new biocataiysts. J. Mol. Catal. B 11:733741.
77. Psenner, R.,, and B. Sattler. 1998. Microbial communities—life at the freezing-point. Science 280:20732074.
78. Radford, A.,, and J. H. Parish. 1997. The genome and genes of Neurospora crassa. Fungal Genet. Biol. 21:258266.
79. Reisman, H. B., 1999. Economics, p. 273288. In A. L. Demain, and J. E. Davis (ed), Manual of Industrial Microbiology and Biotechnology. ASM Press, Washington, D.C.
80. Rondon, M. R.,, R. M. Goodman,, and J. Handelsman. 1999. The Earth's bounty: assessing and accessing soil microbial diversity. Trends Biotechnol. 17:403409.
81. Rondon, M. R.,, P. R. August,, A. D. Bettermann,, S. F. Brady,, T. H. Grossman,, M. R. Liles,, K. A. Loiacono,, B. A. Lynch,, I. A. Mac-Neil,, C. Minor,, C. L. Tiong,, M. Gilman,, M. S. Osburne,, J. Clardy,, J. Handelsman,, and R. M. Goodman. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:25412547.
82. Rosteek, P. R.,, B. S. DeHoff,, F. H. Norris,, and P. K. Rockey,. 1999. Bacterial genomics and genome informatics, p. 495500. In A. L. Demain, and J. E. Davies (ed.), Manual of Industrial Microbiology and Biotechnology. ASM Press, Washington, D.C.
83. Rothschild, L. J.,, and R. I. Mancinelli. 2001. Life in extreme environments. Nature 409:10921101.
84. Ruijssenaars, H. J.,, and S. Hartmans. 2001. Plate screening methods for the detection of polysaccharase-producing microorganisms. Appl. Microbiol. Biotechnol. 55:143149.
85. Sambrock, J.,, and D. W. Russel. 2001. Molecular Cloning, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
86. Sanchez, D. O.,, R. O. Zandomeni,, S. Cravero,, R. E. Verdun,, E. Pierrou,, P. Faccio,, G. Diaz,, S. Lanzavecchia,, F. Aguero,, A. C. C. Frasch,, S. G. E. Andersson,, O. L. Rossetti,, O. Grau,, and R. A. Ugalda. 2001. Gene discovery through genomic sequencing of Brucella abortus. Infect. Immun. 69:865868.
87. Sandal, Th.,, C. Sjoholm,, T. Schaefer,, L. Lange,, and F. Duffner. 2000. Method for generating a gene library. Novo Nordisk A/S, (patent), W0200024882-A1.
88. Sattler, B.,, H. Puxbaum,, and R. Psenner. 2001. Bacterial growth in supercooled cloud droplets. Geophys. Res. Lett. 28:239242.
89. Sauer, J.,, B. W. Sigurdskjold,, U. Christensen,, T. P. Frandsen,, E. Mirgorodskaya,, M. Harrison,, P. Roepstorff,, and B. Svensson. 2000. Glucoamylase: structure/function relationships, and protein engineering. Biochem. Biophys. Acta Protein Struct. Mol. Enzymol. 1543:275293.
90. Schaefer, T.,, O. Kirk,, T. V. Borchert,, C. C. Fuglsang,, S. Pedersen,, S. Salmon,, H. S. Olsen,, R. Deinhammer,, and H. Lind,. 2002. Enzymes for technical applications. In A. Steinbuechel (ed) Biopolymers. Wiley VCH, New York, N.Y.
91. Schellenberger, V. 1997. Compartmentalization method for screening microorganisms. Genencore International Inc., patent 87/37036.
92. Schmidt, T. M.,, E. F. DeLong,, and N. R. Pace. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:43714378.
93. Schülein, M. 2000. Protein engineering of cellulases. Biochem. Biophys. Acta-Protein Struct. Mol. Enzymol. 1553:239252.
94. Schülein, M.,, L. N. Andersen,, S. F. Lassen,, L. Lange,, S. Kauppinen,, R. Nielsen,, O. Ihara,, and S. Takagi. 1996. Novel Endoglucanases. U.S. patent 6,001,639.
95. Short, J. M. 1997. Recombinant approaches for accessing biodiversity. Nat. Biotechnol. 15:13221323.
96. Short, J. M.,, and M. Keller. 2001. High-throughput screening for novel enzymes. U.S. patent 6,174, 673 Bl.
97. Sieber, V.,, C. A. Martinez,, and F. A. Arnold. 2001. Libraries of hybrid proteins from distantly related sequences. Nat. Biotechnol. 19:456460.
98. Smith, M. 1985. In vitro mutagenesis. Annu. Rev. Genet. 19:423462.
99. Stahl, D. A.,, D. J. Lane,, G. J. Olsen,, and N. R. Pace. 1985. Characterization of a Yellowstone USA hot spring microbial community by 5S ribosomal RNA sequences. Appl. Environ. Microbiol. 49:13791384.
100. Stähl, S.,, and M. Uhlep. 1997. Bacterial surface display. Trend of Biotechnol. 15:185192.
101. Steffan, R. J.,, J. Goksoyr,, A. K. Bej,, and R. M. Atlas. 1988. Recovery of DNA from soils and sediments. Appl. Environ. Microbiol. 54:29082915.
102. Steipe, B. 1999. Evolutionary approaches to protein engineering. Curr. Top. Microbiol. Immun. 243:5586.
103. Stemmer, W. P. 1994a. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91:1074710751.
104. Stemmer, W. P. 1994b. Rapid evolution of a protein by in vitro DNA shuffling. Nature 370:389391.
105. Suzuki, Y. 1989. A general principle of increasing protein thermostability. Proc. Jpn. Acad. 65:146148.
106. Svendsen, A. 2000. Lipase protein engineering. Biochem. Biophys. Acta Protein Struct. Mol. Enzymol. 1553:223238.
107. Takai, K.,, H. Hirayama,, Y. Sakihama,, F. Inagaki,, Y. Yamato,, and K. Horikoshi. 2002. Isolation and metabolic characteristics of previously uncultured members of the order Aquificales in a subsurface gold mine. Appl. Environ. Microbiol. 68:30463054.
108. Tiedje, J. M.,, and J. L. Stein,. 1999. Microbial diversity: strategies for its recovery, p. 682692. In A. L. Demain, and J. E. Davies (ed.), Manual of Industrial Microbiology and Biotechnology. ASM Press, Washington, D.C.
109. Tobin, M. B.,, C. Gustafsson,, and G. W. Huisman. 2000. Directed evolution: the "rational" basis for "irrational" design. Curr. Opin. Struct. Biol. 10:421427.
110. Torsvik, V. L. 1980. Isolation of bacterial DNA from soil. Soil Biol. Biochem. 12:1522.
111. Torsvik, V.,, F. L. Daae,, R. Sandaa,, and L. Ovreas. 1998. Novel techniques for analysing microbial diversity in natural and perturbed environments. J. Biotechnol. 64:5362.
112. Torsvik, V.,, J. Goksoyr,, and F. L. Daao. 1990. High diversity in DNA of soil bacterial. Appl. Environ. Microbiol. 56:782787.
113. Torsvik, V.,, L. Ovreas,, and T. F. Thingstad. 2002. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296:10641066.
114. van Beilen, J. B.,, and Z. Li. 2002. Enzyme technology: an overview. Curr. Opin. Biotechnol. 13:338344.
115. Van den Burg, B.,, G. Vriend,, O. R. Veltman,, G. Venema,, and V. G. H. Eijsink. 1998. Engineering an enzyme to resist boiling. Proc. Natl. Acad. Sci. USA 95:20562060.
116. van der Veen, B. A.,, J. C. M. Uitdehaag,, B. W. Dijkstra,, L. Dijkhuizen. 2000. Engineering of cyclodextrin glycosyltransferase reaction and product specificity. Biochem. Biophys. Acta 1543:336360.
117. Voigt, C. A.,, S. Kauffman,, and Z. G. Wang. 2001. Rational evolutionary design: the theory of in vitro protein evolution. Adv. Protein Chem. 55:79160.
118. Waive, M.,, V. Shejval,, C. Sonawane,, M. Rahalkar,, A. Matapurkar,, Y. Shouche,, M. Patole,, N. Phadnis,, A. Champhenkar,, K. Damie,, S. Karandikar,, V. Kshirsagar,, and M. Jog. 2000. The "K" selected oligophilic bacteria: a key to uncultured diversity?. Curr. Sci. (Bangalore) 78:15351542.
119. Widner, B.,, M. Thomas,, D. Sternberg,, D. Lammon,, R. Behr,, and A. Sloma. 2000. Development of marker-free strains of Bacillus subtilis capable of secreting high levels of industrial enzymes. J. Ind. Microbiol. Biotechnol. 25:204212.
120. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221271.
121. Wölke, J.,, and D. Ullmann. 2001. Miniaturized HTS technologies—uHTS. Drug Discovery Today 6:637646.
122. Zagulski, M.,, C. J. Herbert,, and J. Rytka. 1998. Sequencing and functional analysis of the yeast genome. Ada Biochim. Polon. 45:627643.
123. Zhao, H.,, L. Giver,, Z. Shao,, J. A. Affholter,, and F. H. Arnold. 1998. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol. 16:258261.


Generic image for table
Table 1

Screening of metagenomics libraries: summary of described results

Citation: Schafer T, Borchert T. 2004. Bioprospecting for Industrial Enzymes: Importance of Integrated Technology Platforms for Successful Biocatalyst Development, p 375-390. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch33
Generic image for table
Table 2

Size of theoretical libraries encoding all combinations of the 20 amino acids in the specified number of positions

Citation: Schafer T, Borchert T. 2004. Bioprospecting for Industrial Enzymes: Importance of Integrated Technology Platforms for Successful Biocatalyst Development, p 375-390. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch33

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error