Thermostable DNA ligase-mediated PCR production of circular plasmid (PPCP) and its application in directed evolution via in situ error-prone PCR

DNA Research

Volumn 20, Issue 4, 2013, Pages 375-382

  Le, Yilin ^a   Chen, Huayou ^a   Zagursky, Robert ^b   Wu, J H David ^b   Shao, Weilan ^a  

^a JIANGSU UNIVERSITY   (China)

^b University of Rochester   (United States)

Author keywords

amplification of circular plasmids; directed evolution; error prone PCR; random mutagenesis libraries; thermostable DNA ligase

Indexed keywords

CELLULASE; CIRCULAR DNA; DNA FRAGMENT; PLASMID DNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; TAQ POLYMERASE; XYLAN ENDO 1,3 BETA XYLOSIDASE;

5' UNTRANSLATED REGION; AGAR GEL ELECTROPHORESIS; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; CELL DENSITY; DNA FLANKING REGION; DNA LIBRARY; DNA SEQUENCE; DNA STRAND; ELECTROPORATION; ENZYME ACTIVITY; ENZYME SYNTHESIS; ESCHERICHIA COLI; EXPRESSION VECTOR; GENE AMPLIFICATION; MOLECULAR CLONING; MUTAGENESIS; NONHUMAN; POLYMERASE CHAIN REACTION; THERMOSTABILITY; THERMOTOGA MARITIMA;

AMPLIFICATION OF CIRCULAR PLASMIDS; DIRECTED EVOLUTION; ERROR-PRONE PCR; RANDOM MUTAGENESIS LIBRARIES; THERMOSTABLE DNA LIGASE;

ASCOMYCOTA; BACTERIAL PROTEINS; CELLULASES; DIRECTED MOLECULAR EVOLUTION; DNA LIGASES; DNA PRIMERS; ENDO-1,4-BETA XYLANASES; ESCHERICHIA COLI; FUNGAL PROTEINS; GENE LIBRARY; HOT TEMPERATURE; MUTAGENESIS; PLASMIDS; POLYMERASE CHAIN REACTION; TAQ POLYMERASE; THERMOTOGA MARITIMA;

EID: 84884173394     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst016     Document Type: Article

References (25)

1. Chirumamilla, R.R., Muralidhar, R., Marchant, R. and Nigam, P. 2001, Improving the quality of industrially important enzymes by directed evolution, Mol. Cell Biochem., 224, 159-68.
2. Cherry, J.R. and Fidantsef, A.L. 2003,Directed evolution of industrial enzymes: an update, Curr.Opin. Biotechnol., 14, 438-43.
3. Eijsink, V.G.H., Gaseidnes, S., Borchert, T.V. and van den Burg, B. 2005, Directed evolution of enzyme stability, Biomol. Eng., 22, 21-30.
4. Yuan, L., Kurek, I., English, J. and Keenan, R. 2005, Laboratory-directed protein evolution, Microbiol. Mol. Biol. Rev., 69, 373-92.
5. Otten, L.G. and Quax, W.J. 2005, Directed evolution: selecting today's biocatalysts, Biomol. Eng., 22, 1-9.
6. Olsen, M., Iverson, B. and Georgiou, G. 2000, Highthroughput screening of enzyme libraries, Curr. Opin. Biotechnol., 11, 331-7.
7. Lutz, S. and Patrick,W.M. 2004, Novel methods for directed evolution of enzymes: quality, not quantity, Curr. Opin. Biotechnol., 15, 291-7.
8. Ling, M.M. and Robinson, B.H. 1997, Approaches to DNA mutagenesis: an overview, Anal. Biochem., 254, 157-78.
9. Cadwell, R.C. and Joyce, G.F. 1992, Randomization of genes by PCR mutagenesis, PCR Methods Appl., 2, 28-33.
10. Hemsley, A., Arnheim, N., Toney, M.D., Cortopassi, G. and Galas, D.J. 1989,A simplemethod for site-directed mutagenesis using thepolymerasechain reaction, NucleicAcids Res., 17, 6545-51.
11. Matsumura, I.andRowe, L.A. 2005,Whole plasmid mutagenic PCR for directed protein evolution, Biomol. Eng.,22, 73-9.
12. Miyazaki, K. 2011,MEGAWHOPcloning: a method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids, Meth. Enzymol., 498, 399-406.
13. Miyazaki, K. and Takenouchi, M. 2002, Creating random mutagenesis libraries using megaprimer PCR of whole plasmid, Biotechniques, 33, 1033-8.
14. Le, Y., Peng, J., Pei, J., Li, H., Duan, Z. and Shao, W. 2010, Properties of an NAD+-dependent DNA ligase from the hyperthermophile Thermotoga maritima and its application in PCR amplification of long DNA fragments, Enzyme Microb. Technol., 46, 113-7.
15. Jiang, Y., Zhou, Q., Wu, K., Li, X.Q. and Shao, W.L. 2006, A highly efficient method for liquid and solid cultivation of the anaerobic hyperthermophilic eubacterium Thermotoga maritime, FEMS Microbiol. Lett., 259, 254-9.
16. Wu, H., Pei, J., Jiang, Y., Song, X. and Shao, W. 2010, pHsh vectors, a novel expression system of Escherichia coli for the large-scale production of recombinant enzymes, Biotechnol. Lett., 32, 795-801.
17. Yin, E., Le, Y., Pei, J., Shao,W. and Yang, Q. 2008, High-level expression of the xylanase fromThermomyces lanuginosus in Escherichia coli, World J. Microbiol. Biotechnol., 24, 275-80.
18. Lever, M. 1972, A new reaction for colorimetric determination of carbohydrates, Anal. Biochem., 47, 273-9.
19. Hu, G. 1993,DNApolymerase-catalyzed addition of nontemplated extra nucleotides to the 30 end of a DNA fragment, DNA Cell Biol., 12, 763-70.
20. Nakaniwa, T., Tada, T., Takao, M., Sakai, T. and Nishimur, K. 2004, An in vitro evaluation of a thermostable pectate lyase by using error-prone PCR, J. Mol. Catal. B Enzym., 27, 127-31.
21. Zhang, J.H., Dawes, G. and Stemmer, W.P.C. 1997, Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening, Proc. Natl Acad. Sci. USA, 94, 4504-9.
22. Kim, M.-S. and Lei, X.G. 2008, Enhancing thermostability of Escherichia coli phytase AppA2 by error-prone PCR, Appl. Microbiol. Biotechnol., 79, 69-75.
23. Shen, B. 2002, PCR approaches to DNA mutagenesis and recombination. An overview, Methods Mol. Biol., 192, 167-74.
24. Tobias, A.V. 2003, Preparing libraries in Escherichia coli, Methods Mol. Biol., 231, 11-6.
25. Wei, D., Li, M., Zhang, X. and Xing, L. 2004, An improvement of the site-directed mutagenesis method by combination of megaprimer, one-side PCR and DpnI treatment, Anal. Biochem., 331, 401-3.