A water-soluble DsbB variant that catalyzes disulfide bond formation in vivo

Escherichia coli DsbB is a transmembrane enzyme that catalyzes the re-oxidation of the periplasmic oxidase DsbA by ubiquinone. Here, we sought to convert membrane-bound DsbB into a water-soluble biocatalyst by leveraging a previously described method for in vivo solubilization of integral membrane proteins (IMPs). When solubilized DsbB variants were co-expressed with an export-defective copy of DsbA in the cytoplasm of wild-type E. coli cells, artificial oxidation pathways were created that efficiently catalyzed de novo disulfide bond formation in a range of substrate proteins and in a manner that depended on both DsbA and quinone. Hence, DsbB solubilization was achieved with preservation of both catalytic activity and substrate specificity. Moreover, given the generality of the solubilization technique, the results presented here should pave the way for unlocking the biocatalytic potential of other membrane-bound enzymes whose utility has been limited by poor stability of IMPs outside of their native lipid bilayer context.

[1]  Alan Wise,et al.  Target validation of G-protein coupled receptors. , 2002, Drug discovery today.

[2]  J. Beckwith,et al.  Roles of thiol-redox pathways in bacteria. , 2001, Annual review of microbiology.

[3]  H. Mori,et al.  Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.

[4]  Cristen B. Peterson,et al.  Efficient expression of full-length antibodies in the cytoplasm of engineered bacteria , 2015, Nature Communications.

[5]  L. Pollack,et al.  Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy , 2015, Nature Communications.

[6]  J. Walker,et al.  Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. , 1996, Journal of molecular biology.

[7]  J. Beckwith,et al.  The Nonconsecutive Disulfide Bond of Escherichia coli Phytase (AppA) Renders It Dependent on the Protein-disulfide Isomerase, DsbC* , 2005, Journal of Biological Chemistry.

[8]  Koreaki Ito,et al.  Paradoxical redox properties of DsbB and DsbA in the protein disulfide‐introducing reaction cascade , 2002, The EMBO journal.

[9]  D. Langosch,et al.  Role of GxxxG Motifs in Transmembrane Domain Interactions. , 2015, Biochemistry.

[10]  Jeffery G. Saven,et al.  Computational design of water-soluble analogues of the potassium channel KcsA , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[11]  G. Heijne,et al.  Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms , 1998, Protein science : a publication of the Protein Society.

[12]  P. Martineau,et al.  Expression of an antibody fragment at high levels in the bacterial cytoplasm. , 1998, Journal of molecular biology.

[13]  Jason T Boock,et al.  The ribosomal exit tunnel as a target for optimizing protein expression in Escherichia coli , 2011, Biotechnology journal.

[14]  J. Beckwith,et al.  Two cysteines in each periplasmic domain of the membrane protein DsbB are required for its function in protein disulfide bond formation. , 1994, The EMBO journal.

[15]  W. Wackernagel,et al.  Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. , 1995, Gene.

[16]  Maxim V. Petoukhov,et al.  Small Angle X-Ray Scattering Studies of Mitochondrial Glutaminase C Reveal Extended Flexible Regions, and Link Oligomeric State with Enzyme Activity , 2013, PloS one.

[17]  Samuel Wagner,et al.  Rationalizing membrane protein overexpression. , 2006, Trends in biotechnology.

[18]  Z. Derewenda,et al.  Overcoming expression and purification problems of RhoGDI using a family of "parallel" expression vectors. , 1999, Protein expression and purification.

[19]  Koreaki Ito,et al.  Roles of Disulfide Bonds in Bacterial Alkaline Phosphatase* , 1997, The Journal of Biological Chemistry.

[20]  David Eisenberg,et al.  GXXXG and AXXXA: Common α-Helical Interaction Motifs in Proteins, Particularly in Extremophiles† , 2002 .

[21]  Dmitri I Svergun,et al.  Applications of small-angle X-ray scattering to biomacromolecular solutions. , 2013, The international journal of biochemistry & cell biology.

[22]  Dmitri I. Svergun,et al.  Determination of the regularization parameter in indirect-transform methods using perceptual criteria , 1992 .

[23]  F. Baneyx,et al.  Recombinant protein folding and misfolding in Escherichia coli , 2004, Nature Biotechnology.

[24]  M. Gerstein,et al.  Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. , 2000, Journal of molecular biology.

[25]  Feras Hatahet,et al.  Disruption of reducing pathways is not essential for efficient disulfide bond formation in the cytoplasm of E. coli , 2010, Microbial cell factories.

[26]  David Eisenberg,et al.  GXXXG and AXXXA: common alpha-helical interaction motifs in proteins, particularly in extremophiles. , 2002, Biochemistry.

[27]  Y. Yang,et al.  Methods for Structural and Functional Analyses of Intramembrane Prenyltransferases in the UbiA Superfamily. , 2017, Methods in enzymology.

[28]  John A Tainer,et al.  Accurate SAXS profile computation and its assessment by contrast variation experiments. , 2013, Biophysical journal.

[29]  P. Curnow Membrane proteins in nanotechnology. , 2009, Biochemical Society transactions.

[30]  A. Hopkins,et al.  The druggable genome , 2002, Nature Reviews Drug Discovery.

[31]  Lydia M. Contreras-Martinez,et al.  Intracellular ribosome display via SecM translation arrest as a selection for antibodies with enhanced cytosolic stability. , 2007, Journal of molecular biology.

[32]  G von Heijne,et al.  Membrane proteins: from sequence to structure. , 1990, Protein engineering.

[33]  C. Tribet,et al.  Amphipols: polymers that keep membrane proteins soluble in aqueous solutions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[34]  O. Gursky,et al.  Thermal unfolding of human high-density apolipoprotein A-1: implications for a lipid-free molten globular state. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[35]  G. Privé,et al.  Lipopeptide detergents designed for the structural study of membrane proteins , 2003, Nature Biotechnology.

[36]  Dmitri I Svergun,et al.  Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS). , 2013, Current opinion in structural biology.

[37]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.

[38]  J. Beckwith,et al.  Evidence that the pathway of disulfide bond formation in Escherichia coli involves interactions between the cysteines of DsbB and DsbA. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Satoshi Murakami,et al.  Crystal Structure of the DsbB-DsbA Complex Reveals a Mechanism of Disulfide Bond Generation , 2006, Cell.

[40]  Paul H. Bessette,et al.  Efficient folding of proteins with multiple disulfide bonds in the Escherichia coli cytoplasm. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Paul H. Bessette,et al.  Effect of Sequences of the Active-Site Dipeptides of DsbA and DsbC on In Vivo Folding of Multidisulfide Proteins inEscherichia coli , 2001, Journal of bacteriology.

[42]  Tae-Joon Jeon,et al.  Transmembrane glycine zippers: physiological and pathological roles in membrane proteins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Mingshan Li,et al.  Nanodiscs separate chemoreceptor oligomeric states and reveal their signaling properties. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[44]  C. Emrich,et al.  SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm , 2012, Microbial Cell Factories.

[45]  Dmitri I. Svergun,et al.  Electronic Reprint Applied Crystallography Dammif, a Program for Rapid Ab-initio Shape Determination in Small-angle Scattering Applied Crystallography Dammif, a Program for Rapid Ab-initio Shape Determination in Small-angle Scattering , 2022 .

[46]  Feras Hatahet,et al.  Topological plasticity of enzymes involved in disulfide bond formation allows catalysis in either the periplasm or the cytoplasm. , 2013, Journal of molecular biology.

[47]  A. Rawlings,et al.  Membrane proteins: always an insoluble problem? , 2016, Biochemical Society transactions.

[48]  P. Loll Membrane protein structural biology: the high throughput challenge. , 2003, Journal of structural biology.

[49]  J. Beckwith,et al.  Identification of a protein required for disulfide bond formation in vivo , 1991, Cell.

[50]  D. Belin,et al.  Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter , 1995, Journal of bacteriology.

[51]  Andrej Sali,et al.  FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles , 2016, Nucleic Acids Res..

[52]  Koreaki Ito,et al.  Reactivities of Quinone-free DsbB from Escherichia coli* , 2005, Journal of Biological Chemistry.

[53]  L. Rajendran,et al.  Subcellular targeting strategies for drug design and delivery , 2010, Nature Reviews Drug Discovery.

[54]  C. Tate Practical considerations of membrane protein instability during purification and crystallisation. , 2010, Methods in molecular biology.