Directed evolution of the transcriptional regulator DntR: Isolation of mutants with improved DNT-response

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Lönneborg, Rosa ^a   Varga, Edina ^a   Brzezinski, Peter ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

2,4 DINITROTOLUENE; DNTR PROTEIN; GREEN FLUORESCENT PROTEIN; REGULATOR PROTEIN; UNCLASSIFIED DRUG; 2,4-DINITROTOLUENE; BACTERIAL PROTEIN; NITROBENZENE DERIVATIVE;

AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; DIRECTED EVOLUTION; EVOLUTION; FLUORESCENCE ACTIVATED CELL SORTING; GENETIC ENGINEERING; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; LIGAND BINDING; LIMIT OF DETECTION; MUTAGENESIS; PROTEIN EXPRESSION; PROTEIN STRUCTURE; TRANSCRIPTION REGULATION; WILD TYPE; CHEMISTRY; FLOW CYTOMETRY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PROTEIN SECONDARY STRUCTURE;

BACTERIA (MICROORGANISMS);

BACTERIAL PROTEINS; DINITROBENZENES; EVOLUTION, MOLECULAR; FLOW CYTOMETRY; PROTEIN STRUCTURE, SECONDARY;

EID: 84856020198     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0029994     Document Type: Article

References (31)

1. Jenkins TF, Leggett DC, Miyares PH, Walsh ME, Ranney TA, et al. (2001) Chemical signatures of TNT-filled land mines. Talanta 54: 501-513.
2. Galvao TC, Mencia M, de Lorenzo V, (2007) Emergence of novel functions in transcriptional regulators by regression to stem protein types. Mol Microbiol 65: 907-919.
3. Radhika V, Proikas-Cezanne T, Jayaraman M, Onesime D, Ha JH, et al. (2007) Chemical sensing of DNT by engineered olfactory yeast strain. Nat Chem Biol 3: 325-330.
4. Nagatomo K, Kawaguchi T, Miura N, Toko K, Matsumoto K, (2009) Development of a sensitive surface plasmon resonance immunosensor for detection of 2,4-dinitrotoluene with a novel oligo (ethylene glycol)-based sensor surface. Talanta 79: 1142-1148.
5. Jaworski JW, Raorane D, Huh JH, Majumdar A, Lee SW, (2008) Evolutionary screening of biomimetic coatings for selective detection of explosives. Langmuir 24: 4938-4943.
6. Pellinen T, Huovinen T, Karp M, (2004) A cell-free biosensor for the detection of transcriptional inducers using firefly luciferase as a reporter. Anal Biochem 330: 52-57.
7. Stocker J, Balluch D, Gsell M, Harms H, Feliciano J, et al. (2003) Development of a set of simple bacterial biosensors for quantitative and rapid measurements of arsenite and arsenate in potable water. Environ Sci Technol 37: 4743-4750.
8. Spain JC, (1995) Biodegradation of nitroaromatic compounds. Annu Rev Microbiol 49: 523-555.
9. Crawford RL, (1995) The Microbiology and Treatment of Nitroaromatic Compounds. Current Opinion in Biotechnology 6: 329-336.
10. Johnson GR, Spain JC, (2003) Evolution of catabolic pathways for synthetic compounds: bacterial pathways for degradation of 2,4-dinitrotoluene and nitrobenzene. Appl Microbiol Biotechnol 62: 110-123.
11. Spanggord RJ, Spain JC, Nishino SF, Mortelmans KE, (1991) Biodegradation of 2,4-dinitrotoluene by a Pseudomonas sp. Appl Environ Microbiol 57: 3200-3205.
12. Johnson GR, Jain RK, Spain JC, (2002) Origins of the 2,4-dinitrotoluene pathway. J Bacteriol 184: 4219-4232.
13. Lönneborg R, Smirnova I, Dian C, Leonard GA, Brzezinski P, (2007) In vivo and in vitro investigation of transcriptional regulation by DntR. J Mol Biol 372: 571-582.
14. Schell MA, (1985) Transcriptional control of the nah and sal hydrocarbon-degradation operons by the nahR gene product. Gene 36: 301-309.
15. Jones RM, Britt-Compton B, Williams PA, (2003) The naphthalene catabolic (nag) genes of Ralstonia sp. strain U2 are an operon that is regulated by NagR, a LysR-type transcriptional regulator. J Bacteriol 185: 5847-5853.
16. Lessner DJ, Parales RE, Narayan S, Gibson DT, (2003) Expression of the nitroarene dioxygenase genes in Comamonas sp. strain JS765 and Acidovorax sp. strain JS42 is induced by multiple aromatic compounds. J Bacteriol 185: 3895-3904.
17. Ju KS, Parales JV, Parales RE, (2009) Reconstructing the evolutionary history of nitrotoluene detection in the transcriptional regulator NtdR. Mol Microbiol 74: 826-843.
18. Smirnova IA, Dian C, Leonard GA, McSweeney S, Birse D, et al. (2004) Development of a bacterial biosensor for nitrotoluenes: the crystal structure of the transcriptional regulator DntR. J Mol Biol 340: 405-418.
19. Ezezika OC, Haddad S, Clark TJ, Neidle EL, Momany C, (2007) Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator. J Mol Biol 367: 616-629.
20. Devesse L, Smirnova I, Lonneborg R, Kapp U, Brzezinski P, et al. Crystal structures of DntR inducer binding domains in complex with salicylate offer insights into the activation of LysR-type transcriptional regulators. Mol Microbiol 81: 354-367.
21. Galvao TC, de Lorenzo V, (2006) Transcriptional regulators a la carte: engineering new effector specificities in bacterial regulatory proteins. Curr Opin Biotechnol 17: 34-42.
22. Scholz O, Kostner M, Reich M, Gastiger S, Hillen W, (2003) Teaching TetR to recognize a new inducer. J Mol Biol 329: 217-227.
23. Tang SY, Fazelinia H, Cirino PC, (2008) AraC regulatory protein mutants with altered effector specificity. J Am Chem Soc 130: 5267-5271.
24. Jensen RA, (1976) Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30: 409-425.
25. Tokuriki N, Tawfik DS, (2009) Protein dynamism and evolvability. Science 324: 203-207.
26. Bloom JD, Arnold FH, (2009) In the light of directed evolution: pathways of adaptive protein evolution. Proc Natl Acad Sci U S A 106 (Suppl 1): 9995-10000.
27. Cormack BP, Valdivia RH, Falkow S, (1996) FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173: 33-38.
28. Lönneborg R, (2011) In search of a biosensor for DNT detection: studies of inducer response and specificity Stockholm Stockholm University.
29. Ruangprasert A, Craven SH, Neidle EL, Momany C, (2010) Full-Length Structures of BenM and Two Variants Reveal Different Oligomerization Schemes for LysR-Type Transcriptional Regulators. J Mol Biol 404: 568-586.
30. Huang WE, Wang H, Zheng H, Huang L, Singer AC, et al. (2005) Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate. Environ Microbiol 7: 1339-1348.
31. Shin HJ, (2010) Development of highly-sensitive microbial biosensors by mutation of the nahR regulatory gene. J Biotechnol 150: 246-250.