Directed evolution of the 5'-untranslated region of the phoA gene in Escherichia coli simultaneously yields a stronger promoter and a stronger Shine-Dalgarno sequence

Biotechnology Journal

Volumn 1, Issue 11, 2006, Pages 1275-1282

  Huang, Xu ^a,b   Zhang, Xian En ^a   Zhou, Ya Feng ^a   Zhang, Zhi Ping ^a   Cass, Anthony E G ^c  

^a WUHAN INSTITUTE OF VIROLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

5' Untranslated region; Directed evolution; E. Coli alkaline phosphatase; Error prone PCR

Indexed keywords

ACTIVITY ASSAYS; ALKALINE PHOSPHATASE; AMINO ACID SUBSTITUTION; CELLULAR ENZYMES; CELLULAR LEVELS; CODING SEQUENCES; DIRECTED EVOLUTION; E. COLI; ERROR PRONE PCR; RANDOM MUTAGENESIS; REGULATORY SEQUENCES; SEQUENCE ANALYSIS; UNTRANSLATED REGIONS;

AMINO ACIDS; ENZYME ACTIVITY; GENES; PHOSPHATASES;

ESCHERICHIA COLI;

ALKALINE PHOSPHATASE; MESSENGER RNA; OLIGONUCLEOTIDE; PHOA ALKALINE PHOSPHATASE;

5' UNTRANSLATED REGION; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; CONFORMATION; DIRECTED MOLECULAR EVOLUTION; GENETIC PROCEDURES; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPERON; PLASMID; REGULATORY SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY;

5' UNTRANSLATED REGIONS; ALKALINE PHOSPHATASE; BASE SEQUENCE; DIRECTED MOLECULAR EVOLUTION; GENETIC TECHNIQUES; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; OPERON; PLASMIDS; REGULATORY SEQUENCES, NUCLEIC ACID; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 39049179484     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.200600091     Document Type: Article

References (42)

1. Stemmer, W. P., DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 1994, 91, 10747-10751.
2. Arnold, F. H., Directed evolution: Creating biocatalysts for the future. Chem. Eng. Sci. 1996, 51, 5091-5102.
3. Roodveldt, C., Aharoni, A., Tawfik, D. S., Directed evolution of proteins for heterologous expression and stability. Curr. Opin. Struct. Biol. 2005, 15, 50-56.
4. Kolkman, J. A., Stemmer, W. P., Directed evolution of proteins by exon shuffling. Nat. Biotechnol. 2001, 19, 423-428.
5. Bloom, J. D., Meyer, M. M., Meinhold, P., Otey, C. R., et al., Evolving strategies for enzyme engineering. Curr. Opin. Struct. Biol. 2005, 15, 447-452.
6. Neylon, C., Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: Library construction methods for directed evolution. Nucleic Acids Res. 2004, 32, 1448-1459.
7. Kagiya, G., Ogawa, R., Hatashita, M., Takagi, K., et al., Generation of a strong promoter for Escherichia coli from eukaryotic genome DNA. J. Biotechnol. 2005, 115, 239-248.
8. Remans, T., Grof, C. P., Ebert, P. R., Schenk, P. M., Functional promoter analysis using an approach based on an in vitro evolution strategy. Biotechniques 2005, 38, 209-216.
9. Zhelyabovskaya, O. B., Berlin, Y. A., Birikh, K. R., Artificial genetic selection for an efficient translation initiation site for expression of human RACK1 gene in Escherichia coli. Nucleic Acids Res. 2004, 32, e52.
10. Schwartz, J. H., Lipmann, F., Phosphate incorporation into alkaline phosphatase of E. coli. Proc. Natl. Acad. Sci. USA 1961, 47, 1996-2005.
11. Bradshaw, R. A., Cancedda, F., Ericsson, L. H., Neumann, P. A., et al., Amino acid sequence of Escherichia coli alkaline phosphatase. Proc. Natl. Acad. Sci. USA 1981, 78, 3473-3477.
12. Chang, C. N., Kuang, W. J., Chen, E. Y., Nucleotide sequence of the alkaline phosphatase gene of Escherichia coli. Gene 1986, 44, 121-125.
13. Stec, B., Holtz, K. M., Kantrowitz, E. R., A revised mechanism for the alkaline phosphatase reaction involving three metal ions. J. Mol. Biol. 2000, 299, 1303-1311.
14. Xu, H. F., Zhang, X. E., Zhang, Z. P., Zhang, Y. M., et al., Directed evolution of E. coli alkaline phosphatase towards higher catalytic activity. Biocat. Biotrans. 2003, 21, 41-47.
15. Wang, S. H., Zhang, J. B., Zhang, Z. P., Zhou, Y. F., et al., Construction of single chain variable fragment (ScFv) and BiScFv-alkaline phosphatase fusion protein for detection of Bacillus anthracis. Anal. Chem. 2006, 78, 997-1004.
16. Deng, J. Y., Zhang, X. E., Mang, Y., Zhang, Z. P., et al., Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism. Biosens. Bioelectron. 2004, 19, 1277-1283.
17. Wang, S. H., Wen, J. K., Zhou, Y. F., Zhang, Z. P., et al., Identification and characterization of Bacillus anthracis by multiplex PCR on DNA chip. Biosens. Bioelectron. 2004, 20, 807-813.
18. Wen, J. K., Zhang, X. E., Cheng, Z., Liu, H., et al., A visual DNA chip for simultaneous detection of hepatitis B virus, hepatitis C virus and human immunodeficiency virus type-1. Biosens. Bioelectron. 2004, 19, 685-692.
19. Pierce, J. J., Turner, C., Keshavarz-Moore, E., Dunnill, P., Factors determining more efficient large-scale release of a periplasmic enzyme from E. coli using lysozyme. J. Biotechnol. 1997, 58, 1-11.
20. Branlant, G., Branlant, C., Nucleotide sequence of the Escherichia coli gap gene. Different evolutionary behavior of the NAD+-binding domain and of the catalytic domain of D-glyceraldehyde-3-phosphate dehydrogenase. Eur. J. Biochem. 1985, 150, 61-66.
21. Nelson, K., Whittam, T. S., Selander, R. K., Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. Proc. Natl. Acad. Sci. USA 1991, 88, 6667-6671.
22. Jellen-Ritter, A. S., Kern, W. V., Enhanced expression of the multidrug efflux pumps AcrAB and AcrEF associated with insertion element transposition in Escherichia coli mutants selected with a fluoroquinolone. Antimicrob. Agents Chemother. 2001, 45, 1467-1472.
23. Shine, J., Dalgarno, L., The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites. Proc. Natl. Acad. Sci. USA 1974, 71, 1342-1346.
24. Steitz, J. A., Jakes, K., How ribosomes select initiator regions in mRNA: Base pair formation between the 3' terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proc. Natl. Acad. Sci. USA 1975, 72, 4734-4738.
25. Jacob, W. F., Santer, M., Dahlberg, A. E., A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins. Proc. Natl. Acad. Sci. USA 1987, 84, 4757-4761.
26. de Smit, M. H., van Duin, J., Translational initiation on structured messengers. Another role for the Shine-Dalgarno interaction. J. Mol. Biol. 1994, 235, 173-184.
27. Komarova, A. V., Tchufistova, L. S., Supina, E. V., Boni, I. V., Protein S1 counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation. RNA 2002, 8, 1137-1147.
28. Weyens, G., Charlier, D., Roovers, M., Pierard, A., et al., On the role of the Shine-Dalgarno sequence in determining the efficiency of translation initiation at a weak start codon in the car operon of Escherichia coli K12. J. Mol. Biol. 1988, 204, 1045-1048.
29. Munson, L. M., Stormo, G. D., Niece, R. L., Reznikoff, W. S., LacZ translation initiation mutations. J. Mol. Biol. 1984, 177, 663-683.
30. Kikuchi, Y., Yoda, K., Yamasaki, M., Tamura, G., The nucleotide sequence of the promoter and the amino-terminal region of alkaline phosphatase structural gene (phoA) of Escherichia coli. Nucleic Acids Res. 1981, 9, 5671-5678.
31. Shuttleworth, H., Taylor, J., Minton, N., Sequence of the gene for alkaline phosphatase from Escherichia coli JM83. Nucleic Acids Res. 1986, 14, 8689.
32. de Smit, M. H., van Duin, J., Secondary structure of the ribosome binding site determines translational efficiency: A quantitative analysis. Proc. Natl. Acad. Sci. USA 1990, 87, 7668-7672.
33. McCarthy, J. E., Gualerzi, C., Translational control of prokaryotic gene expression. Trends Genet. 1990, 6, 78-85.
34. de Smit, M. H., van Duin, J., Control of translation by mRNA secondary structure in Escherichia coli. A quantitative analysis of literature data. J. Mol. Biol. 1994, 244, 144-150.
35. de Smit, M. H., van Duin, J., Translational standby sites: How ribosomes may deal with the rapid folding kinetics of mRNA. J. Mol. Biol. 2003, 331, 737-743.
36. Ivanovski, G., Gubensek, F., Pungercar, J., mRNA secondary structure can greatly affect production of recombinant phospholipase A(2) toxins in bacteria. Toxicon 2002, 40, 543-549.
37. Punginelli, C., Ize, B., Stanley, N. R., Stewart, V., et al., mRNA secondary structure modulates translation of Tat-dependent formate dehydrogenase N. J. Bacteriol. 2004, 186, 6311-6315.
38. Voges, D., Watzele, M., Nemetz, C., Wizemann, S., et al., Analyzing and enhancing mRNA translational efficiency in an Escherichia coli in vitro expression system. Biochem. Biophys. Res. Commun. 2004, 318, 601-614.
39. Cebe, R., Geiser, M., Rapid and easy thermodynamic optimization of the 5'-end of mRNA dramatically increases the level of wild type protein expression in Escherichia coli. Protein Expr. Purif. 2005, 45, 374-380.
40. Kozak, M., Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 2005, 361, 13-37.
41. Hall, M. N., Gabay, J., Debarbouille, M., Schwartz, M., A role for mRNA secondary structure in the control of translation initiation. Nature 1982, 295, 616-618.
42. Jia, M., Li, Y., The relationship among gene expression, folding free energy and codon usage bias in Escherichia coli. FEBS Lett. 2005, 579, 5333-5337.