Engineering an Acinetobacter regulon for biosensing and high-throughput enzyme screening in E. coli via flow cytometry

Nucleic Acids Research

Volumn 42, Issue 12, 2014, Pages 8150-8160

  Jha, Ramesh K ^a   Kern, Theresa L ^a   Fox, David T ^a   Strauss, Charlie E M ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2,3 DIHYDROXYBENZOIC ACID; BACTERIAL ENZYME; DEHYDROSHIKIMATE DEHYDRATASE; GREEN FLUORESCENT PROTEIN; UNCLASSIFIED DRUG;

ADP1 GENE; ARTICLE; BACTERIAL GENE; CELL SELECTION; CONTROLLED STUDY; ENZYME ACTIVITY; ESCHERICHIA COLI; FLOW CYTOMETER; FLOW CYTOMETRY; FLUORESCENCE ACTIVATED CELL SORTING; GENE LIBRARY; GENE SEQUENCE; GENETIC ENGINEERING; HIGH THROUGHPUT SCREENING; NONHUMAN; PCAU GENE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; REGULON;

ACINETOBACTER; BACTERIAL PROTEINS; BIOSENSING TECHNIQUES; CELL SEPARATION; ENZYME ASSAYS; ESCHERICHIA COLI; FLOW CYTOMETRY; FLUORESCENT DYES; GENE LIBRARY; GENES, REPORTER; GENETIC ENGINEERING; GREEN FLUORESCENT PROTEINS; HYDRO-LYASES; HYDROXYBENZOATES; PROMOTER REGIONS, GENETIC; REGULON; TRANS-ACTIVATORS;

EID: 84903977635     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku444     Document Type: Article

References (28)

1. Daunert, S., Barrett, G., Feliciano, J.S., Shetty, R.S., Shrestha, S., Smith-Spencer, W. (2000) Genetically engineered whole-cell sensing systems: coupling biological recognition with reporter genes. Chem. Rev., 100, 2705-2738.
2. Gu, M.B., Mitchell, R.J., Kim, B.C. (2004) Whole-cell-based biosensors for environmental biomonitoring and application. In: Zhong, J.-J. (ed). Biomanufacturing Advances in Biochemical Engineering.Springer, Berlin Heidelberg, pp. 269-305.
3. Van der Meer, J.R., Belkin, S. (2010) Where microbiology meets microengineering: design and applications of reporter bacteria. Nat. Rev. Microbiol., 8, 511-522.
4. Dietrich, J.A., McKee, A.E., Keasling, J.D. (2010) High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu. Rev. Biochem., 79, 563-590.
5. Van Sint Fiet, S., Van Beilen, J.B., Witholt, B. (2006) Selection of biocatalysts for chemical synthesis. Proc. Natl. Acad. Sci. U. S. A., 103, 1693-1698.
6. Mohn, W.W., Garmendia, J., Galvao, T.C., de Lorenzo, V. (2006) Surveying biotransformations with a la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacZ-based phenotypes. Environ. Microbiol., 8, 546-555.
7. Uchiyama, T., Miyazaki, K. (2010) Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes. Appl. Environ. Microbiol., 76, 7029-7035.
8. Van Rossum, T., Kengen, S.W.M., van der Oost, J. (2013) Reporter-based screening and selection of enzymes. FEBS J., 280, 2979-2996.
9. Steele, H.L., Jaeger, K.-E., Daniel, R., Streit, W.R. (2009) Advances in recovery of novel biocatalysts from metagenomes. J. Mol. Microbiol. Biotechnol., 16, 25-37.
10. Dietrich, J.A., Shis, D.L., Alikhani, A., Keasling, J.D. (2013) Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. ACS Synth. Biol., 2, 47-58.
11. Zhang, F., Carothers, J.M., Keasling, J.D. (2012) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat. Biotechnol., 30, 354-359.
12. Tang, S.-Y., Qian, S., Akinterinwa, O., Frei, C.S., Gredell, J.A., Cirino, P.C. (2013) Screening for enhanced triacetic acid lactone production by recombinant Escherichia coli expressing a designed triacetic acid lactone reporter. J. Am. Chem. Soc., 135, 10099-10103.
13. Yang, G., Withers, S.G. (2009) Ultrahigh-throughput FACS-based screening for directed enzyme evolution. Chem. Bio. Chem., 10, 2704-2715.
14. Kok, R.G., D'Argenio, D.A., Ornston, L.N. (1998) Mutation analysis of PobR and PcaU, closely related transcriptional activators in Acinetobacter. J. Bacteriol., 180, 5058-5069.
15. Koppisch, A., Fox, D., Hotta, K., Welsh, J. (2011) Production of industrially relevant compounds in prokaryotic organisms. US Patent application #13/018, 066, United States.
16. Fox, D.T., Hotta, K., Kim, C.-Y., Koppisch, A.T. (2008) The Missing Link in Petrobactin Biosynthesis: asbF Encodes a (')-3-Dehydroshikimate Dehydratase . Biochemistry (Mosc.), 47, 12251-12253.
17. Molina-Henares, A.J., Krell, T., Eugenia Guazzaroni, M., Segura, A., Ramos, J.L. (2006) Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors. FEMS Microbiol. Rev., 30, 157-186.
18. Stemmer, W.P., Crameri, A., Ha, K.D., Brennan, T.M., Heyneker, H.L. (1995) Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene, 164, 49-53.
19. Pfleger, B.F., Kim, Y., Nusca, T.D., Maltseva, N., Lee, J.Y., Rath, C.M., Scaglione, J.B., Janes, B.K., Anderson, E.C., Bergman, N.H. et al. (2008) Structural and functional analysis of AsbF: origin of the stealth 3, 4-dihydroxybenzoic acid subunit for petrobactin biosynthesis. Proc. Natl. Acad. Sci., 105, 17133-17138.
20. Varadarajan, N., Cantor, J.R., Georgiou, G., Iverson, B.L. (2009) Construction and flow cytometric screening of targeted enzyme libraries. Nat. Protoc., 4, 893-901.
21. D'Angelo, S., Glanville, J., Ferrara, F., Naranjo, L., Gleasner, C.D., Shen, X., Bradbury, A.R., Kiss, C. (2013) The antibody mining toolbox: an open source tool for the rapid analysis of antibody repertoires. mAbs, 6, 41-53.
22. Gerischer, U., Segura, A., Ornston, L.N. (1998) PcaU, a transcriptional activator of genes for protocatechuate utilization in Acinetobacter. J. Bacteriol., 180, 1512-1524.
23. Ross, W., Aiyar, S.E., Salomon, J., Gourse, R.L. (1998) Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J. Bacteriol., 180, 5375-5383.
24. Blazeck, J., Alper, H.S. (2013) Promoter engineering: recent advances in controlling transcription at the most fundamental level. Biotechnol. J., 8, 46-58.
25. Alper, H., Fischer, C., Nevoigt, E., Stephanopoulos, G. (2005) Tuning genetic control through promoter engineering. Proc. Natl. Acad. Sci. U. S. A., 102, 12678-12683.
26. Kalosakas, G., Rasmussen, K.A., Bishop, A.R., Choi, C.H., Usheva, A. (2004) Sequence-specific thermal fluctuations identify start sites for DNA transcription. Europhys. Lett. EPL, 68, 127-133.
27. Alexandrov, B., Voulgarakis, N.K., Rasmussen, K.A., Usheva, A., Bishop, A.R. (2009) Pre-melting dynamics of DNA and its relation to specific functions. J. Phys. Condens. Matter, 21, 034107.
28. Radzicka, A., Wolfenden, R. (1995) A proficient enzyme. Science, 267, 90-93.