NADPH-dependent reductive biotransformation with Escherichia coli and its pfkA deletion mutant: Influence on global gene expression and role of oxygen supply

Biotechnology and Bioengineering

Volumn 111, Issue 10, 2014, Pages 2067-2075

  Siedler, Solvej ^a   Bringer, Stephanie ^a   Polen, Tino ^a   Bott, Michael ^a  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

DNA microarrays; Escherichia coli; Phosphofructokinase; Reductive whole cell biotransformation; Resting cells; SthA transhydrogenase

Indexed keywords

ACTIVATION ANALYSIS; BIOASSAY; BIOCHIPS; ESCHERICHIA COLI; GENE EXPRESSION; GLUCOSE; NUCLEIC ACIDS;

DNA MICRO-ARRAY; PHOSPHOFRUCTOKINASE; RESTING CELLS; TRANSHYDROGENASES; WHOLE-CELL BIOTRANSFORMATIONS;

BIOCONVERSION;

3 HYDROXYBUTYRIC ACID; 6 PHOSPHOFRUCTOKINASE; ACETOACETIC ACID DERIVATIVE; ALCOHOL DEHYDROGENASE; DISSOLVED OXYGEN; GLUCOSE; NICOTINAMIDE ADENINE DINUCLEOTIDE (PHOSPHATE) TRANSHYDROGENASE; OXYGEN; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; TRANSCRIPTOME; 2-METHYL-3-HYDROXYBUTYRIC ACID; HYDROXYBUTYRIC ACID; METHYL ACETOACETATE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE;

ARTICLE; BACTERIAL STRAIN; BIOREACTOR; BIOTRANSFORMATION; BREATHING RATE; CONTROLLED STUDY; DNA DETERMINATION; DNA MICROARRAY; ESCHERICHIA COLI; GENE EXPRESSION; LACTOBACILLUS BREVIS; METABOLITE; MICROARRAY ANALYSIS; NONHUMAN; OXIDATION; OXIDATIVE STRESS; OXYGEN SUPPLY; OXYGENATION; WHOLE CELL; GENE DELETION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; OXIDATION REDUCTION REACTION;

ESCHERICHIA COLI; LACTOBACILLUS BREVIS;

ACETOACETATES; BIOTRANSFORMATION; ESCHERICHIA COLI; GENE DELETION; GENE EXPRESSION REGULATION, BACTERIAL; GLUCOSE; HYDROXYBUTYRATES; NADP; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDATION-REDUCTION; OXYGEN; PHOSPHOFRUCTOKINASE-1; TRANSCRIPTOME;

EID: 84906786924     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.25271     Document Type: Article

References (46)

1. Akinterinwa O, Cirino PC. 2011. Anaerobic obligatory xylitol production in Escherichia coli strains devoid of native fermentation pathways. Appl Environ Microbiol 77(2):706-709.
2. Boonstra B, French CE, Wainwright I, Bruce NC. 1999. The udhA gene of Escherichia coli encodes a soluble pyridine nucleotide transhydrogenase. J Bacteriol 181(3):1030-1034.
3. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. 2001. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29(4):365-371.
4. Cardinale S, Joachimiak MP, Arkin AP. 2013. Effects of genetic variation on the E. coli host-circuit interface. Cell Rep 4:231-237.
5. Chin JW, Cirino PC. 2011. Improved NADPH supply for xylitol production by engineered Escherichia coli with glycolytic mutations. Biotechnol Prog 27(2):333-341.
6. Cho BK, Knight EM, Palsson BO. 2006. Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology 152(Pt 8):2207-2219.
7. Ernst M, Kaup B, Müller M, Bringer-Meyer S, Sahm H. 2005. Enantioselective reduction of carbonyl compounds by whole-cell biotransformation, combining a formate dehydrogenase and a (R)-specific alcohol dehydrogenase. Appl Microbiol Biotechnol 66(6):629-634.
8. Georgellis D, Kwon O, Lin EC. 2001. Quinones as the redox signal for the Arc two-component system of bacteria. Science 292:2314-2316.
9. Goldberg K, Schroer K, Lütz S, Liese A. 2007. Biocatalytic ketone reduction-A powerful tool for the production of chiral alcohols-part II: Whole-cell reductions. Appl Microbiol Biotechnol 76(2):249-255.
10. Greenberg JT, Monach P, Chou JH, Josephy PD, Demple B. 1990. Positive control of a global antioxidant defense regulon activated by superoxide-generating agents in Escherichia coli. Proc Natl Acad Sci USA 87(16):6181-6185.
11. Green J, Paget MS. 2004. Bacterial redox sensors. Nat Rev Microbiol 2(12):954-966.
12. Griffith KL, Wolf RE Jr. 2004. Genetic evidence for pre-recruitment as the mechanism of transcription activation by SoxS of Escherichia coli: The dominance of DNA binding mutations of SoxS. J Mol Biol 344(1):1-10.
13. Habrych M, Rodriguez S, Stewart JD. 2002. Purification and identification of an Escherichia coli beta-keto ester reductase as 2, 5-diketo-D-gluconate reductase YqhE. Biotechnol Prog 18(2):257-261.
14. Hanahan D, Jessee J, Bloom FR. 1991. Plasmid transformation of Escherichia coli and other bacteria. Methods Enzymol 204:63-113.
15. 1 complex and low pH on global gene expression in Gluconobacter oxydans 621H using DNA microarray technology. J Biotechnol 157(3):359-372.
16. Hidalgo E, Leautaud V, Demple B. 1998. The redox-regulated SoxR protein acts from a single DNA site as a repressor and an allosteric activator. EMBO J 17(9):2629-2636.
17. Ishige T, Honda K, Shimizu S. 2005. Whole organism biocatalysis. Curr Opin Chem Biol 9(2):174-180.
18. Jackson JB. 2003. Proton translocation by transhydrogenase. FEBS Lett 545(1):18-24.
19. Jarboe LR. 2011. YqhD: A broad-substrate range aldehyde reductase with various applications in production of biorenewable fuels and chemicals. Appl Microbiol Biotechnol 89(2):249-257.
20. Jeong H, Barbe V, Lee CH, Vallenet D, Yu DS, Choi SH, Couloux A, Lee SW, Yoon SH, Cattolico L, Hur CG, Park HS, Segurens B, Kim SC, Oh TK, Lenski RE, Studier FW, Daegelen P, Kim JF. 2009. Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol 394(4):644-652.
21. Jeudy S, Monchois V, Maza C, Claverie JM, Abergel C. 2006. Crystal structure of Escherichia coli DkgA, a broad-specificity aldo-keto reductase. Proteins 62(1):302-307.
22. Klig LS, Carey J, Yanofsky C. 1988. trp repressor interactions with the trp aroH and trpR operators. Comparison of repressor binding in vitro and repression in vivo. J Mol Biol 202(4):769-777.
23. Koo MS, Lee JH, Rah SY, Yeo WS, Lee JW, Lee KL, Koh YS, Kang SO, Roe JH. 2003. A reducing system of the superoxide sensor SoxR in Escherichia coli. EMBO J 22(11):2614-2622.
24. Krapp AR, Humbert MV, Carrillo N. 2011. The soxRS response of Escherichia coli can be induced in the absence of oxidative stress and oxygen by modulation of NADPH content. Microbiology 157(Pt 4):957-965.
25. Lamark T, Rokenes TP, McDougall J, Strom AR. 1996. The complex bet promoters of Escherichia coli: Regulation by oxygen (ArcA), choline (BetI), and osmotic stress. J Bacteriol 178(6):1655-1662.
26. Lee C, Kim I, Lee J, Lee KL, Min B, Park C. 2010. Transcriptional activation of the aldehyde reductase YqhD by YqhC and its implication in glyoxal metabolism of Escherichia coli K-12. J Bacteriol 192(16):4205-4214.
27. Liochev SI, Fridovich I. 1992. Fumarase C, the stable fumarase of Escherichia coli, is controlled by the soxRS regulon. Proc Natl Acad Sci USA 89(13):5892-5896.
28. Liu X, De Wulf P. 2004. Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling. J Biol Chem 279(13):12588-12597.
29. Malpica R, Sandoval GR, Rodriguez C, Franco B, Georgellis D. 2006. Signaling by the Arc two-component system provides a link between the redox state of the quinone pool and gene expression. Antioxid Redox Signal 8(5-6):781-795.
30. Neusser T, Polen T, Geissen R, Wagner R. 2010. Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery. BMC Genomics 11:165.
31. Park DM, Akhtar MS, Ansari AZ, Landick R, Kiley PJ. 2013. The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally. PLoS Genet 9(10):e1003839.
32. Polen T, Rittmann D, Wendisch VF, Sahm H. 2003. DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate. Appl Environ Microbiol 69(3):1759-1774.
33. Polen T, Wendisch VF. 2004. Genomewide expression analysis in amino acid-producing bacteria using DNA microarrays. Appl Biochem Biotechnol 118(1-3):215-232.
34. Pomposiello PJ, Bennik MH, Demple B. 2001. Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate. J Bacteriol 183(13):3890-3902.
35. Sarsero JP, Wookey PJ, Pittard AJ. 1991. Regulation of expression of the Escherichia coli K-12 mtr gene by TyrR protein and Trp repressor. J Bacteriol 173(13):4133-4143.
36. Sauer U, Canonaco F, Heri S, Perrenoud A, Fischer E. 2004. The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. J Biol Chem 279(8):6613-6619.
37. Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T. 2010. Interdependence of cell growth and gene expression: Origins and consequences. Science 330(6007):1099-1102.
38. Siedler S, Bringer S, Blank LM, Bott M. 2012. Engineering yield and rate of reductive biotransformation in Escherichia coli by partial cyclization of the pentose phosphate pathway and PTS-independent glucose transport. Appl Microbiol Biotechnol 93(4):1459-1467.
39. Siedler S, Bringer S, Bott M. 2011. Increased NADPH availability in Escherichia coli: Improvement of the product per glucose ratio in reductive whole-cell biotransformation. Appl Microbiol Biotechnol 92(5):929-937.
40. Siedler S, Schendzielorz G, Binder S, Eggeling L, Bringer S, Bott M. 2014. SoxR as a single-cell biosensor for NADPH-consuming enzymes in Escherichia coli. ACS Synth Biol 3(1):41-47.
41. Spiro S, Guest JR. 1991. Adaptive responses to oxygen limitation in Escherichia coli. Trends Biochem Sci 16(8):310-314.
42. Studier FW, Daegelen P, Lenski RE, Maslov S, Kim JF. 2009. Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes. J Mol Biol 394(4):653-680.
43. Tan I. 2006. Applications of whole cell biotransformations for the production of chiral alcohols. PhD thesis, University of Bonn, Bonn, Germany.
44. Tsaneva IR, Weiss B. 1990. soxR, a locus governing a superoxide response regulon in Escherichia coli K-12. J Bacteriol 172(8):4197-4205.
45. Turner PC, Miller EN, Jarboe LR, Baggett CL, Shanmugam KT, Ingram LO. 2011. YqhC regulates transcription of the adjacent Escherichia coli genes yqhD and dkgA that are involved in furfural tolerance. J Ind Microbiol Biotechnol 38:431-439.
46. Yum DY, Lee BY, Pan JG. 1999. Identification of the yqhE and yafB genes encoding two 2, 5-diketo-D-gluconate reductases in Escherichia coli. Appl Environ Microbiol 65(8):3341-3346.