Synthetic Auxotrophs with Ligand-Dependent Essential Genes for a BL21(DE3) Biosafety Strain

ACS Synthetic Biology

Volumn 4, Issue 12, 2015, Pages 1279-1286

  Lopez, Gabriel ^a   Anderson, J Christopher ^a  

^a University of California at Berkeley   (United States)

Author keywords

biosafety; biosensor; ligand dependent essential gene; penicillin technique; protein engineering; synthetic auxotroph

Indexed keywords

BENZOTHIAZOLE;

ARTICLE; AUXOTROPHY; BIOSAFETY; COMBINATORIAL LIBRARY; CRYSTAL STRUCTURE; ENZYME ENGINEERING; ESCHERICHIA COLI; ESSENTIAL GENE; GENE LIBRARY; LIMIT OF DETECTION; MICROBIAL GENETICS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN FUNCTION; SEQUENCE ANALYSIS; TRANSGENIC ORGANISM; BACTERIAL GENE; GENETIC ENGINEERING; GENETICS; METABOLISM; PROCEDURES;

ESCHERICHIA COLI; GENES, BACTERIAL; GENETIC ENGINEERING;

EID: 84952801889     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.5b00085     Document Type: Article

References (27)

1. Schallmey, M., Frunzke, J., Eggeling, L., and Marienhagen, J. (2014) Looking for the pick of the bunch: High-throughput screening of producing microorganisms with biosensors Curr. Opin. Biotechnol. 26, 148-154 10.1016/j.copbio.2014.01.005
2. Michener, J. K., Thodey, K., Liang, J. C., and Smolke, C. D. (2012) Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways Metab. Eng. 14 (3) 212-222 10.1016/j.ymben.2011.09.004
3. Raman, S., Taylor, N., Genuth, N., Fields, S., and Church, G. M. (2014) Engineering allostery Trends Genet. 30 (12) 521-528 10.1016/j.tig.2014.09.004
4. Tang, S. Y. and Cirino, P. C. (2011) Design and application of a mevalonate-responsive regulatory protein Angew. Chem., Int. Ed. 50 (5) 1084-1086
5. Hillson, N. J., Hu, P., Andersen, G. L., and Shapiro, L. (2007) Caulobacter crescentus as a whole-cell uranium biosensor Appl. Environ. Microbiol. 73 (23) 7615-7621
6. Mandell, D. J., Lajoie, J. M., Mee, M. T., Takeuchi, R., Kuznetsov, G., Norville, J. E., Gregg, C. J., Stoddard, B. L., and Church, G. M. (2015) Biocontainment of genetically modified organisms by synthetic protein design Nature 518 (7537) 55-60 10.1038/nature14121
7. Rovner, A. J., Haimovich, A. D., Katz, S. R., Li, Z., Grome, M. W., Gassaway, B. M., Amiram, M., Patel, J. R., Gallagher, R. R., Rinehart, J., and Isaacs, F. J. (2015) Recoded organisms engineered to depend on synthetic amino acids Nature 518 (7537) 89-93 10.1038/nature14095
8. Horowitz, N. H. (1991) Fifty years ago: The neurospora revolution Genetics 127 (4) 631-635
9. Beadle, G. W. and Tatum, E. L. (1941) Genetic control of biochemical reactions in neurospora Proc. Natl. Acad. Sci. U. S. A. 27 (11) 499-506
10. Woodward, R., Stokes, L., Larsen, A., and Foster, J. (1943) A neurospora assay for pyridoxine J. Biol. Chem. 150, 17-24
11. Mitchell, H. K. and Houlahan, M. B. (1946) Neurospora. IV. A temperature-sensitive riboflavinless mutant Am. J. Bot. 33 (1) 31-35
12. Metzger, D., Clifford, J., Chiba, H., and Chambon, P. (1995) Conditional site-specific recombination in mammalian cells using a ligand-dependent chimeric Cre recombinase Proc. Natl. Acad. Sci. U. S. A. 92 (15) 6991-6995
13. Tucker, C. L. and Fields, S. (2001) A yeast sensor of ligand binding Nat. Biotechnol. 19 (11) 1042-1046
14. Deckert, K., Budiardjo, S. J., Brunner, L. C., Lovell, S., and Karanicolas, J. (2012) Designing allosteric control into enzymes by chemical rescue of structure J. Am. Chem. Soc. 134 (24) 10055-10060
15. Davis, B. D. (1949) Isolation of biochemically deficient mutants of bacteria by penicillin J. Am. Chem. Soc. 35 (1) 1-10
16. Marisch, K., Bayer, K., Cserjan-Puschmann, M., Luchner, M., and Striedner, G. (2013) Evaluation of three industrial Escherichia coli strains in fed-batch cultivations during high-level SOD protein production Microb. Cell Fact. 12 (58) 1-11
17. Baba, T., Ara, T., Hasegawa, M., Yuki, T., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., and Mori, H. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Mol. Syst. Biol. 10.1038/msb4100050
18. Guo, Z., Zhou, D., and Schultz, P. (2000) Designing small-molecule switches for protein-protein interactions Science 288 (5473) 2042-2045
19. Lederberg, J. and Lederberg, E. M. (1952) Replica plating and indirect selection of bacterial mutants J. Bacteriol. 63 (3) 399-406
20. Stanbury, P. F., Whitaker, A., and Hall, S. J. (2013) Principles of Fermentation Technology, Elsevier Science, Amsterdam.
21. Li, G. and Young, K. D. (2013) Indole production by the tryptophanase TnaA in Escherichia coli is determined by the amount of exogenous tryptophan Microbiology 159 (2) 402-410
22. Douthwaite, B., Keatinge, J. D. H., and Park, J. R. (2001) Why promising technologies fail: The neglected role of user innovation during adoption Resour. Policy 30 (5) 819-836
23. Ellis, H. M., Yu, D., DiTizio, T., and Court, D. L. (2001) High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides Proc. Natl. Acad. Sci. U. S. A. 98 (12) 6742-6746
24. Peng, Z., Richardson, S., Robinson, D., Deutsch, S., and Cheng, J. (2014) Genome editing in Escherichia coli with Cas9 and synthetic CRISPRs. DOE JGI User Meeting, March 1820, 2014, Walnut Creek, CA.
25. Datta, S., Costantino, N., and Court, D. L. (2006) A set of recombineering plasmids for gram-negative bacteria Gene 379, 109-115
26. Esvelt, K. M., Mali, P., Braff, J. L., Moosburner, M., Yaung, S. J., and Church, G. M. (2013) Orthogonal Cas9 proteins for RNA-guided gene regulation and editing Nat. Methods 10 (11) 1116-1121
27. Datsenko, K. and Wanner, B. L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products Proc. Natl. Acad. Sci. U. S. A. 97 (12) 6640-6645