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Abstract

Introduction

Protocol

Representative Results

Discussion

Acknowledgements

Materials

References

Biochemistry

Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition

Published: October 3rd, 2018

DOI:

10.3791/58307

1Department of Chemistry, Wesleyan University

Here we present a protocol for anaerobic protein purification, anaerobic protein concentration, and subsequent kinetic characterization using an oxygen electrode system. The method is illustrated using the enzyme DesB, a dioxygenase enzyme which is more stable and active when purified and stored in an anaerobic environment.

Oxygen-sensitive proteins, including those enzymes which utilize oxygen as a substrate, can have reduced stability when purified using traditional aerobic purification methods. This manuscript illustrates the technical details involved in the anaerobic purification process, including the preparation of buffers and reagents, the methods for column chromatography in a glove box, and the desalting of the protein prior to kinetics. Also described are the methods for preparing and using an oxygen electrode to perform kinetic characterization of an oxygen-utilizing enzyme. These methods are illustrated using the dioxygenase enzyme DesB, a gallate dioxygenase from the bacterium Sphingobium sp. strain SYK-6.

Enzymes that utilize iron or other metals to activate oxygen are often susceptible to inactivation during the purification process because of their removal from the reducing environment of a cell. Therefore, these proteins must be used as cell lysates, be subjected to external reducing agents, or be purified anaerobically to ensure that they have optimal enzymatic activity1,2,3,4. For those enzymes that are oxygen-sensitive (specifically iron-containing enzymes), performing all the purification and characterization steps while maintaining an....

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1. General Materials and Methods

  1. Prepare all the required media as described in Table 1. Autoclave at 120 ˚C for 15 min. Sterile filter the SOC solution, after the addition of MgCl2 and glucose, by passing it through a 0.2 µm filter. Adjust the pH of the Miller's Lysogeny Broth (LB media) solution prior to autoclaving. Supplement the LB-Amp media solution after autoclaving with sterile solutions of 0.2 mM L-cysteine, then 0.1 mM ferrous ammonium sulfate to enhance pro.......

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Shown is the SDS-PAGE gel analysis of individual fractions from purification of the DesB-maltose binding protein (MBP) fusion construct (Figure 3). The gel reveals that the protein is pure (MW = 91.22 kDa), except for the presence of DesB (MW = 49.22 kDa) and MBP protein domain (42 kDa) cleaved from each other. Fractions E2 and E3 were selected for concentration (step 4.2).

Reproducible results from.......

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The critical steps in obtaining active, purified DesB protein involve the forming and maintaining of the reduced Fe(II) active site in the enzyme. As such, correct performance of the induction, purification, concentration, and desalting steps are essential to successfully obtaining active enzyme. Inducing protein expression in the presence of 1 mM ferrous ammonium sulfate ensures that Fe(II) is correctly incorporated into the active site of DesB. This method is inspired by studies like those with amidohydrolase metalloen.......

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We would like to thank Dr. Camille Keller of Wesleyan University for technical support. Special thanks to Professor Lindsay D. Eltis and Jenna K. Capyk from the University of British Columbia, as well as Christian Whitman from the University of Texas at Austin, for their advice regarding anaerobic protein purification methods and the use of an O2-sensitive electrode.

....

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Name Company Catalog Number Comments
Isopropyl β-D-1-thiogalactopyranodise Gold Bio Technologies I2481C50
Coomassie Brilliant Blue R-250 Bio-Rad 161-0400
Ammonium persulfate Bio-Rad 161-0700
30% Acrylamide Bio-Rad 161-0158
N,N'tetramethyl-ethylenediamine Bio-Rad 161-0801
Amylose Resin High Flow New England Biolabs E8022S
BL21 (DE3) competent Escherichia coli cells New England Biolabs C2527I
L-cysteine Sigma Aldrich C7352
gallic acid Sigma Aldrich G7384
4-nitrocatechol Sigma Aldrich N15553
Ferrous ammonium sulfate Mallinckrodt 5064
Sodium dithionite Alfa Aesar 33381-22
wheaton serum bottles Fisher Scientific 06-406G
25 mm Acrodisc PF Syringe Filter with Supor Membrane Pall Corportation 4187
400 mL Amicon Stirred Cell Concentrator EMD Millipore UFSC40001
76 mm Millipore Ultracel 10 kDa cutoff reconsituted cellulose membrane filter EMD Millipore PLGC07610
DL-dithiothreitol Gold Bio Technologies DTT50
Sephadex G-25 coarse desalting gal column GE Healthcare 17-0033-01
2 mL Crimp-Top Vials Fisher Scientific 03-391-38
Oxygraph Plus Electrode Control Unit Hansatech Instruments OXYG1 Plus
Oxygen Eletrode Chamber Hansatech Instruments DW1
Electrode Disc Hansatech Instruments S1
PTFE (0.0125 mmX25mm) 30m reel Hansatech Instruments S4
Electrode cleaning Kit Hansatech Instruments S16
Spacer paper Zig Zag available at any gas station
He-series Dri-Lab glove box Vacuum/Atmospheres Company
HE-493 Dri-Train Vacuum/Atmospheres Company
Double-Ended Micro-Tapered Stainless Steel Spatula Fisher Scientific 21-401-10
DWK Life Sciences Kimble Kontes Flex Column Economy Column Fisher Scientific k420400-1530
10 μL, Model 701 N SYR, Cemented NDL 26s ga, 2 in, point stlye 2 syringe Hamilton 80300
DWK Life Sciences Kimble Kontes Flex Column Economy Column Fisher Scientific K420401-1505
Emulsiflex-C5 high-pressure homogenizer Avestin
B-PER Complete Bacterial Protein Extraction Reagent Thermo Fisher Scientific 89821
Lysozyme from chicken egg white Sigma Aldrich 12650-88-3
Sodium dodecyl sulfate Thermo Fisher Scientific 151-21-3
ampicillin Sigma Aldrich 7177-48-2
Tryptone Fisher Scientific BP-1421-500
Yeast extract Fisher Scientific BP1422-2
Sodium Chloride Fisher Scientific S271-10
Potassium Chloride Fisher Scientific P217-3
Magnesium Chloride Fisher Scientific M33-500
Dextrose Fisher Scientific D16-3
Sodium Hydroxide Fisher Scientific S318-1
Tris hydrochloride Fisher Scientific BP153-500
Maltose Fisher Scientific BP684-500
Glycine Fisher Scientific G46-500

  1. Awaya, J. D., Walton, C., Borthakur, D. The pydA-pydB fusion gene produces an active dioxygenase-hydrolase that degrades 3-hydroxy-4-pyridone, an intermediate of mimosine metabolism. Applied Microbiology and Biotechnology. 75 (3), 583-588 (2007).
  2. Barry, K. P., Taylor, E. A. Characterizing the Promiscuity of LigAB, a Lignin Catabolite Degrading Extradiol Dioxygenase from Sphingomonas paucimobilis SYK-6. Biochemistry. 52 (38), 6724-6736 (2013).
  3. Colabroy, K. L., Smith, I. R., Vlahos, A. H. S., Markham, A. J., Jakubik, M. E. Defining a kinetic mechanism for l-DOPA 2,3 dioxygenase, a single-domain type I extradiol dioxygenase from Streptomyces lincolnensis. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1844 (3), 607-614 (2014).
  4. Imsand, E. M., Njeri, C. W., Ellis, H. R. Addition of an external electron donor to in vitro assays of cysteine dioxygenase precludes the need for exogenous iron. Archives of Biochemistry and Biophysics. 521 (1), 10-17 (2012).
  5. Tsai, C. -. L., Tainer, J. A., David, S. S. . Methods in Enzymology. 599, 157-196 (2018).
  6. Kuchenreuther, J. M., et al. High-Yield Expression of Heterologous [FeFe] Hydrogenases in Escherichia coli. Public Library of Science ONE. 5 (11), e15491 (2010).
  7. Dupuy, J., et al. Crystallization and preliminary X-ray diffraction data for the aconitase form of human iron-regulatory protein 1. Acta Crystallographica Section F. 61 (5), 482-485 (2005).
  8. Fan, L., et al. XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations. Cell. 133 (5), 789-800 (2008).
  9. Vaillancourt, F. H., Bolin, J. T., Eltis, L. D. The ins and outs of ring-cleaving dioxygenases. Critical Reviews in Biochemistry and Molecular Biology. 41, 241-267 (2006).
  10. Sugimoto, K., et al. Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6. Public Library of Science ONE. 9 (3), e92249 (2014).
  11. Lewis-Ballester, A., et al. Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1. Nature Communications. 8, (2017).
  12. Lipscomb, J. D., Hoffman, B. M. Allosteric control of O-2 reactivity in Rieske oxygenases. Structure. 13 (5), 684-685 (2005).
  13. Mccray, J. A., Brady, F. O. Allosteric Control of Transient Kinetics of Carbon Monoxide-L-Tryptoohan-2,3-Dioxygenase Complex-Formation. Federation Proceedings. 32 (3), 469 (1973).
  14. Pearson, J. T., Siu, S., Meininger, D. P., Wienkers, L. C., Rock, D. A. In Vitro Modulation of Cytochrome P450 Reductase Supported Indoleamine 2,3-Dioxygenase Activity by Allosteric Effectors Cytochrome b(5) and Methylene Blue. Biochemistry. 49 (12), 2647-2656 (2010).
  15. Walsh, H. A., Daya, S. Inhibition of hepatic tryptophan-2,3-dioxygenase: Superior potency of melatonin over serotonin. Journal of Pineal Research. 23 (1), 20-23 (1997).
  16. Barry, K. P., et al. Exploring allosteric activation of LigAB from Sphingobium sp strain SYK-6 through kinetics, mutagenesis and computational studies. Archives of Biochemistry and Biophysics. 567, 35-45 (2015).
  17. Reynolds, M. F., et al. 4-Nitrocatechol as a probe of a Mn(II)-dependent extradiol-cleaving catechol dioxygenase (MndD): comparison with relevant Fe(II) and Mn(II) model complexes. Journal of Biological Inorganic Chemistry. 8 (3), 263-272 (2003).
  18. Tyson, C. A. 4-Nitrocatechol as a colorimetric probe for non-heme iron dioxygenases. Journal of Biological Chemistry. 250 (5), 1765-1770 (1975).
  19. Kasai, D., Masai, E., Miyauchi, K., Katayama, Y., Fukuda, M. Characterization of the gallate dioxygenase gene: Three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6. Journal of Bacteriology. 187 (15), 5067-5074 (2005).
  20. Billings, A. F., et al. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. Standards in Genomic Sciences. 10 (1), 106 (2015).
  21. Brown, M. E., Chang, M. C. Y. Exploring bacterial lignin degradation. Current Opinion in Chemical Biology. 19, 1-7 (2014).
  22. Bugg, T. D. H., Ahmad, M., Hardiman, E. M., Rahmanpour, R. Pathways for degradation of lignin in bacteria and fungi. Natural Product Reports. 28 (12), 1883-1896 (2011).
  23. Clarkson, S. M., et al. Construction and Optimization of a Heterologous Pathway for Protocatechuate Catabolism in Escherichia coli Enables Bioconversion of Model Aromatic Compounds. Applied and Environmental Microbiology. 83 (18), (2017).
  24. de Gonzalo, G., Colpa, D. I., Habib, M. H. M., Fraaije, M. W. Bacterial enzymes involved in lignin degradation. Journal of Biotechnology. 236, 110-119 (2016).
  25. Falade, A. O., Eyisi, O. A. L., Mabinya, L. V., Nwodo, U. U., Okoh, A. I. Peroxidase production and ligninolytic potentials of fresh water bacteria Raoultella ornithinolytica and Ensifer adhaerens. Biotechnology Reports. 16, 12-17 (2017).
  26. Gall, D. L., Ralph, J., Donohue, T. J., Noguera, D. R. A Group of Sequence-Related Sphingomonad Enzymes Catalyzes Cleavage of β-Aryl Ether Linkages in Lignin β-Guaiacyl and β-Syringyl Ether Dimers. Environmental Science & Technology. 48 (20), 12454-12463 (2014).
  27. Li, J., Yuan, H., Yang, J. Bacteria and lignin degradation. Frontiers of Biology in China. 4 (1), 29-38 (2009).
  28. Masai, E., Katayama, Y., Nishikawa, S., Fukuda, M. Characterization of Sphingomonas paucimobilis SYK-6 genes involved in degradation of lignin-related compounds. Journal of Industrial Microbiology & Biotechnology. 23, 364-373 (1999).
  29. Morales, L. T., González-García, L. N., Orozco, M. C., Restrepo, S., Vives, M. J. The genomic study of an environmental isolate of Scedosporium apiospermum shows its metabolic potential to degrade hydrocarbons. Standards in Genomic Sciences. 12 (1), 71 (2017).
  30. Shettigar, M., et al. Isolation of the (+)-Pinoresinol-Mineralizing Pseudomonas sp. Strain SG-MS2 and Elucidation of Its Catabolic Pathway. Applied and Environmental Microbiology. 84 (4), (2018).
  31. Shi, Y., et al. Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8. Biotechnology for Biofuels. 6 (1), 1 (2013).
  32. Varman, A. M., et al. Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization. Proceedings of the National Academy of Sciences. 113 (40), E5802-E5811 (2016).
  33. Wu, W., et al. Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals. Scientific Reports. 7 (1), 8420 (2017).
  34. Koehntop, K. D., Emerson, J. P., Que, L. The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes. Journal of Biological Inorganic Chemistry. 10 (2), 87-93 (2005).
  35. Lipscomb, J. D. Mechanism of extradiol aromatic ring-cleaving dioxygenases. Current Opinion in Structural Biology. 18 (6), 644-649 (2008).
  36. Machonkin, T. E., Doerner, A. E. Substrate specificity of Sphingobium chlorophenolicum 2,6-dichlorohydroquinone 1,2-dioxygenase. Biochemistry. 50, 8899-8913 (2011).
  37. Suzuki, T., Kawamichi, H., Imai, K. Amino Acid Sequence, Spectral, Oxygen-Binding, and Autoxidation Properties of Indoleamine Dioxygenase-Like Myoglobin from the Gastropod Mollusc Turbo cornutus. Journal of Protein Chemistry. 17 (8), 817-826 (1998).
  38. Vaillancourt, F. H., Labbe, G., Drouin, N. M., Fortin, P. D., Eltis, L. D. The Mechanism-based Inactivation of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase by Catecholic Substrates. Journal of Biological Chemistry. 277 (3), 2019-2027 (2002).
  39. Sugimoto, K., et al. Crystallization and preliminary crystallographic analysis of gallate dioxygenase DesB from Sphingobium sp. SYK-6. Acta Crystallographica Section F. 65 (11), 1171-1174 (2009).
  40. Gallagher, S. R. SDS‐Polyacrylamide Gel Electrophoresis (SDS-PAGE). Current Protocols in Essential Laboratory Techniques. 6 (1), 7.3.1-7.3.28 (2012).
  41. Xiang, D. F., et al. Function Discovery and Structural Characterization of a Methylphosphonate Esterase. Biochemistry. 54 (18), 2919-2930 (2015).
  42. Vladimirova, A., et al. Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase. Journal of the American Chemical Society. 138 (3), 826-836 (2016).
  43. Korczynska, M., et al. Functional Annotation and Structural Characterization of a Novel Lactonase Hydrolyzing d-Xylono-1,4-lactone-5-phosphate and l-Arabino-1,4-lactone-5-phosphate. Biochemistry. 53 (28), 4727-4738 (2014).
  44. Netto, L. E. S., Stadtman, E. R. The Iron-Catalyzed Oxidation of Dithiothreitol Is a Biphasic Process: Hydrogen Peroxide Is Involved in the Initiation of a Free Radical Chain of Reactions. Archives of Biochemistry and Biophysics. 333 (1), 233-242 (1996).
  45. Arciero, D. M., Orville, A. M., Lipscomb, J. D. Protocatechuate 4,5-Dioxygenase from Pseudomonas testosteroni. Methods in Enzymology. 188, 89-95 (1990).
  46. Harpel, M. R., Lipscomb, J. D. Gentisate 1,2-dioxygenase from pseudomonas. Purification, characterization, and comparison of the enzymes from Pseudomonas testosteroni and Pseudomonas acidovorans. Journal of Biological Chemistry. 265 (11), 6301-6311 (1990).
  47. Ishida, T., Tanaka, H., Horiike, K. Quantitative structure-activity relationship for the cleavage of C3/C4-substituted catechols by a prototypal extradiol catechol dioxygenase with broad substrate specificity. Journal of Biochemistry. 135 (6), 721-730 (2004).
  48. Vaillancourt, F. H., Han, S., Fortin, P. D., Bolin, J. T., Eltis, L. D. Molecular Basis for the Stabilization and Inhibition of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase by t-Butanol. Journal of Biological Chemistry. 273 (52), 34887-34895 (1998).
  49. Veldhuizen, E. J. A., et al. Steady-state kinetics and inhibition of anaerobically purified human homogentisate 1,2-dioxygenase. Biochemical Journal. 386, 305-314 (2005).
  50. Wolgel, S. A., et al. Purification and Characterization of Protocatechuate 2,3-Dioxygenase from Bacillus macerans: a New Extradiol Catecholic Dioxygenase. Journal of Bacteriology. 175 (14), 4414-4426 (1993).

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