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Detection of the pH-dependent Activity of Escherichia coli Chaperone HdeB In Vitro and In Vivo

Published: October 23rd, 2016



1Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 2Howard Hughes Medical Institute, University of Michigan

This study describes biophysical, biochemical and molecular techniques to characterize the chaperone activity of Escherichia coli HdeB under acidic pH conditions. These methods have been successfully applied for other acid-protective chaperones such as HdeA and can be modified to work for other chaperones and stress conditions.

Bacteria are frequently exposed to environmental changes, such as alterations in pH, temperature, redox status, light exposure or mechanical force. Many of these conditions cause protein unfolding in the cell and have detrimental impact on the survival of the organism. A group of unrelated, stress-specific molecular chaperones have been shown to play essential roles in the survival of these stress conditions. While fully folded and chaperone-inactive before stress, these proteins rapidly unfold and become chaperone-active under specific stress conditions. Once activated, these conditionally disordered chaperones bind to a large number of different aggregation-prone proteins, prevent their aggregation and either directly or indirectly facilitate protein refolding upon return to non-stress conditions. The primary approach for gaining a more detailed understanding about the mechanism of their activation and client recognition involves the purification and subsequent characterization of these proteins using in vitro chaperone assays. Follow-up in vivo stress assays are absolutely essential to independently confirm the obtained in vitro results.

This protocol describes in vitro and in vivo methods to characterize the chaperone activity of E. coli HdeB, an acid-activated chaperone. Light scattering measurements were used as a convenient read-out for HdeB's capacity to prevent acid-induced aggregation of an established model client protein, MDH, in vitro. Analytical ultracentrifugation experiments were applied to reveal complex formation between HdeB and its client protein LDH, to shed light into the fate of client proteins upon their return to non-stress conditions. Enzymatic activity assays of the client proteins were conducted to monitor the effects of HdeB on pH-induced client inactivation and reactivation. Finally, survival studies were used to monitor the influence of HdeB's chaperone function in vivo.

A common natural environment in which microbial pathogens experience acid-induced protein unfolding conditions is the mammalian stomach (pH range 1-4), whose acidic pH serves as an effective barrier against food-borne pathogens 1. Protein unfolding and aggregation, which is caused by amino acid side chain protonation, affects biological processes, damages cellular structures and eventually causes cell death 1,2. Since the pH of the bacterial periplasm equilibrates almost instantaneously with the environmental pH due to the free diffusion of protons through the porous outer membrane, periplasmic and inner membrane proteins of Gram-negative bacteri....

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1. Expression and Purification of Periplasmic HdeB

NOTE: HdeB was expressed in E. coli cells harboring the plasmid pTrc-hdeB10, and purified from the periplasm upon polymyxin lysis.

  1. Prepare an overnight culture of E. coli cells harboring the plasmid pTrc-hdeB 10 in 30 ml LB containing 200 µg/ml ampicillin (LBAmp). Inoculate four 1 L cultures of LBAmp and grow them at 37 °C and 200 rpm until O.D.600nm of.......

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HdeA and HdeB are homologous E. coli proteins, known to protect periplasmic proteins against acid stress conditions 10. Our work revealed that similar to HdeA, HdeB also functions as an acid activated molecular chaperone. However, in contrast to HdeA, HdeB functions at a pH that is still potentially bactericidal, but significantly higher than the pH optimum of HdeA 6,9,10,22. To investigate the pH optimum of HdeB's chaperone activity in vitro, n.......

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In order to study the mechanism of activation and chaperone function of HdeB, large quantities of HdeB have to be expressed and purified. A number of expression vector systems are available for the production of high levels of a target protein, including pTrc or pBAD vectors, both of which were used in this study. The promoters are readily accessible for E. coli RNA polymerase and thus allow strongly upregulated expression of HdeB in any E. coli strain. This aspect is especially relevant for in vivo.......

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We thank Dr. Claudia Cremers for her helpful advice on chaperone assays. Ken Wan is acknowledged for his technical assistance in HdeB purification. This work was supported by the Howard Hughes Medical Institute (to J.C.A.B.) and the National Institutes of Health grant RO1 GM102829 to J.C.A.B. and U.J. J.-U. D. is supported by a postdoctoral research fellowship provided by the German Research Foundation (DFG).


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Name Company Catalog Number Comments
NEB10-beta E. coli cells New England Biolabs C3019I
Ampicillin Gold Biotechnology A-301-3
LB Broth mix, Lennox LAB Express 3003
IPTG Gold Biotechnology I2481C50
Sodium chloride Fisher Scientific S271-10
Tris Amresco 0826-5kg
EDTA Fisher Scientific BP120-500
Polymyxin B sulfate  ICN Biomedicals Inc. 100565
0.2 UM pore sterile Syringe Filter Corning 431218
HiTrap Q HP (CV 5 ml) GE Healthcare Life Sciences 17-1153-01
Mini-Protean TGX, 15% Bio-Rad 4561046
Malate dehydrogenase (MDH) Roche 10127914001
Potassium phosphate (Monobasic) Fisher Scientific BP362-500
Potassium phosphate (Dibasic) Fisher Scientific BP363-1
F-4500 fluorescence spectrophotometer Hitachi FL25
Oxaloacetate Sigma O4126-5G
NADH Sigma  N8129-100MG
Sodium phosphate monobasic Sigma  S9390-2.5KG
Sodium phosphate dibasic Sigma  S397-500
Lactate dehydrogenase (LDH) Roche 10127230001
Beckman Proteome Lab XL-I analytical Ultracentrifuge Beckman Coulter 392764
Centerpiece, 12 mm, Epon Charcoal-filled Beckman Coulter 306493
AN-50 Ti Rotor, Analytical, 8-Place Beckman Coulter 363782
Wizard Plus Miniprep Kit Promega A1470 used for plasmid purification (Protocol 5.1)
L-arabinose Gold Biotechnology A-300-500
Glycine DOT Scientific Inc DSG36050-1000
Fluorescence Cell cuvette Hellma Analytics 119004F-10-40
Oligonucleotides Invitrogen
Phusion High-Fidelity DNA polymerase New England Biolabs M0530S
dNTP set Invitrogen 10297018
Hydrochloric Acid Fisher Scientific A144-212
Sodium Hydroxide Fisher Scientific BP359-500
Amicon Ultra 15 mL 3K NMWL Millipore UFC900324
Centrifuge Avanti J-26XPI Beckman Coulter 393127
Varian Cary 50 spectrophotometer Agilent Tech
Spectra/Por 1 Dialysis Membrane MWCO: 6 kDa Spectrum Laboratories 132650
Amicon Ultra Centrifugal Filter Units 30K Millipore UFC803024
SDS Fisher Scientific bp166-500
Veriti 96-Well Thermal Cycler Thermo Fisher 4375786

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