1
|
İncir İ, Kaplan Ö. Escherichia coli as a versatile cell factory: Advances and challenges in recombinant protein production. Protein Expr Purif 2024; 219:106463. [PMID: 38479588 DOI: 10.1016/j.pep.2024.106463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 05/08/2024]
Abstract
E. coli plays a substantial role in recombinant protein production. Its importance increased with the discovery of recombinant DNA technology and the subsequent production of the first recombinant insulin in E. coli. E. coli is a widely used and cost-effective host to produce recombinant proteins. It is also noteworthy that a significant portion of the approved therapeutic proteins have been produced in this organism. Despite these advantages, it has some disadvantages, such as toxicity and lack of eukaryotic post-translational modifications that can lead to the production of misfolded, insoluble, or dysfunctional proteins. This study focused on the challenges and engineering approaches for improved expression and solubility in recombinant protein production in E. coli. In this context, solution strategies such as strain and vector selection, codon usage, mRNA stability, expression conditions, translocation to the periplasmic region and addition of fusion tags in E. coli were discussed.
Collapse
Affiliation(s)
- İbrahim İncir
- Karamanoğlu Mehmetbey University, Kazım Karabekir Vocational School, Department of Medical Services and Techniques, Environmental Health Program Karaman, Turkey.
| | - Özlem Kaplan
- Alanya Alaaddin Keykubat University, Rafet Kayış Faculty of Engineering, Department of Genetics and Bioengineering, Antalya, Turkey.
| |
Collapse
|
2
|
Chen Y, Sewsurn S, Amand S, Kunz C, Pietrancosta N, Calabro K, Buisson D, Mann S. Metabolic Investigation and Auxiliary Enzyme Modelization of the Pyrrocidine Pathway Allow Rationalization of Paracyclophane-Decahydrofluorene Formation. ACS Chem Biol 2024; 19:886-895. [PMID: 38576157 DOI: 10.1021/acschembio.3c00684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Fungal paracyclophane-decahydrofluorene-containing natural products are complex polycyclic metabolites derived from similar hybrid PKS-NRPS pathways. Herein we studied the biosynthesis of pyrrocidines, one representative of this family, by gene inactivation in the producer Sarocladium zeae coupled to thorough metabolic analysis and molecular modeling of key enzymes. We characterized nine pyrrocidines and analogues as well as in mutants a variety of accumulating metabolites with new structures including rare cis-decalin, cytochalasan, and fused 6/15/5 macrocycles. This diversity highlights the extraordinary plasticity of the pyrrocidine biosynthetic gene cluster. From accumulating metabolites, we delineated the scenario of pyrrocidine biosynthesis. The ring A of the decahydrofluorene is installed by PrcB, a membrane-bound cyclizing isomerase, on a PKS-NRPS-derived pyrrolidone precursor. Docking experiments in PrcB allowed us to characterize the active site suggesting a mechanism triggered by arginine-mediated deprotonation at the terminal methyl of the substrate. Next, two integral membrane proteins, PrcD and PrcE, each predicted as a four-helix bundle, perform hydroxylation of the pyrrolidone ring and paracyclophane formation, respectively. Modelization of PrcE highlights a topological homology with vitamin K oxido-reductase and the presence of a disulfide bond. Our results suggest a previously unsuspected coupling mechanism via a transient loss of aromaticity of tyrosine residue to form the strained paracyclophane motif. Finally, the lipocalin-like protein PrcX drives the exo-cycloaddition yielding ring B and C of the decahydrofluorene to afford pyrrocidine A, which is transformed by a reductase PrcI to form pyrrocidine B. These insights will greatly facilitate the microbial production of pyrrocidine analogues by synthetic biology.
Collapse
Affiliation(s)
- Youwei Chen
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Steffi Sewsurn
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Séverine Amand
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Caroline Kunz
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 927, F-75005 Paris, France
| | - Nicolas Pietrancosta
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, PSL University, CNRS, F-75005 Paris, France
- Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, INSERM, CNRS, F-75005 Paris, France
| | - Kevin Calabro
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Didier Buisson
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Stéphane Mann
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| |
Collapse
|
3
|
Jeong H, Kim Y, Lee HS. CdbC: a disulfide bond isomerase involved in the refolding of mycoloyltransferases in Corynebacterium glutamicum cells exposed to oxidative conditions. J Biochem 2024; 175:457-470. [PMID: 38227582 DOI: 10.1093/jb/mvae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 01/18/2024] Open
Abstract
In Corynebacterium glutamicum cells, cdbC, which encodes a protein containing the CysXXCys motif, is regulated by the global redox-responsive regulator OsnR. In this study, we assessed the role of the periplasmic protein CdbC in disulfide bond formation and its involvement in mycomembrane biosynthesis. Purified CdbC efficiently refolded scrambled RNaseA, exhibiting prominent disulfide bond isomerase activity. The transcription of cdbC was decreased in cells grown in the presence of the reductant dithiothreitol (DTT). Moreover, unlike wild-type and cdbC-deleted cells, cdbC-overexpressing (P180-cdbC) cells grown in the presence of DTT exhibited retarded growth, abnormal cell morphology, increased cell surface hydrophobicity and altered mycolic acid composition. P180-cdbC cells cultured in a reducing environment accumulated trehalose monocorynomycolate, indicating mycomembrane deformation. Similarly, a two-hybrid analysis demonstrated the interaction of CdbC with the mycoloyltransferases MytA and MytB. Collectively, our findings suggest that CdbC, a periplasmic disulfide bond isomerase, refolds misfolded MytA and MytB and thereby assists in mycomembrane biosynthesis in cells exposed to oxidative conditions.
Collapse
Affiliation(s)
- Haeri Jeong
- Department of Biotechnology and Bioinformatics, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, Jecheon, 65, Semyeong-ro, Chungbuk 27136, Republic of Korea
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| |
Collapse
|
4
|
Méndez AAE, Argüello JM, Soncini FC, Checa SK. Scs system links copper and redox homeostasis in bacterial pathogens. J Biol Chem 2024; 300:105710. [PMID: 38309504 PMCID: PMC10907172 DOI: 10.1016/j.jbc.2024.105710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
The bacterial envelope is an essential compartment involved in metabolism and metabolites transport, virulence, and stress defense. Its roles become more evident when homeostasis is challenged during host-pathogen interactions. In particular, the presence of free radical groups and excess copper in the periplasm causes noxious reactions, such as sulfhydryl group oxidation leading to enzymatic inactivation and protein denaturation. In response to this, canonical and accessory oxidoreductase systems are induced, performing quality control of thiol groups, and therefore contributing to restoring homeostasis and preserving survival under these conditions. Here, we examine recent advances in the characterization of the Dsb-like, Salmonella-specific Scs system. This system includes the ScsC/ScsB pair of Cu+-binding proteins with thiol-oxidoreductase activity, an alternative ScsB-partner, the membrane-linked ScsD, and a likely associated protein, ScsA, with a role in peroxide resistance. We discuss the acquisition of the scsABCD locus and its integration into a global regulatory pathway directing envelope response to Cu stress during the evolution of pathogens that also harbor the canonical Dsb systems. The evidence suggests that the canonical Dsb systems cannot satisfy the extra demands that the host-pathogen interface imposes to preserve functional thiol groups. This resulted in the acquisition of the Scs system by Salmonella. We propose that the ScsABCD complex evolved to connect Cu and redox stress responses in this pathogen as well as in other bacterial pathogens.
Collapse
Affiliation(s)
- Andrea A E Méndez
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Fernando C Soncini
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Susana K Checa
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina.
| |
Collapse
|
5
|
Pormohammad A, Firrincieli A, Salazar-Alemán DA, Mohammadi M, Hansen D, Cappelletti M, Zannoni D, Zarei M, Turner RJ. Insights into the Synergistic Antibacterial Activity of Silver Nitrate with Potassium Tellurite against Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0062823. [PMID: 37409940 PMCID: PMC10433965 DOI: 10.1128/spectrum.00628-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
The constant, ever-increasing antibiotic resistance crisis leads to the announcement of "urgent, novel antibiotics needed" by the World Health Organization. Our previous works showed a promising synergistic antibacterial activity of silver nitrate with potassium tellurite out of thousands of other metal/metalloid-based antibacterial combinations. The silver-tellurite combined treatment not only is more effective than common antibiotics but also prevents bacterial recovery, decreases the risk of future resistance chance, and decreases the effective concentrations. We demonstrate that the silver-tellurite combination is effective against clinical isolates. Further, this study was conducted to address knowledge gaps in the available data on the antibacterial mechanism of both silver and tellurite, as well as to give insight into how the mixture provides synergism as a combination. Here, we defined the differentially expressed gene profile of Pseudomonas aeruginosa under silver, tellurite, and silver-tellurite combination stress using an RNA sequencing approach to examine the global transcriptional changes in the challenged cultures grown in simulated wound fluid. The study was complemented with metabolomics and biochemistry assays. Both metal ions mainly affected four cellular processes, including sulfur homeostasis, reactive oxygen species response, energy pathways, and the bacterial cell membrane (for silver). Using a Caenorhabditis elegans animal model we showed silver-tellurite has reduced toxicity over individual metal/metalloid salts and provides increased antioxidant properties to the host. This work demonstrates that the addition of tellurite would improve the efficacy of silver in biomedical applications. IMPORTANCE Metals and/or metalloids could represent antimicrobial alternatives for industrial and clinical applications (e.g., surface coatings, livestock, and topical infection control) because of their great properties, such as good stability and long half-life. Silver is the most common antimicrobial metal, but resistance prevalence is high, and it can be toxic to the host above a certain concentration. We found that a silver-tellurite composition has antibacterial synergistic effect and that the combination is beneficial to the host. So, the efficacy and application of silver could increase by adding tellurite in the recommended concentration(s). We used different methods to evaluate the mechanism for how this combination can be so incredibly synergistic, leading to efficacy against antibiotic- and silver-resistant isolates. Our two main findings are that (i) both silver and tellurite mostly target the same pathways and (ii) the coapplication of silver with tellurite tends not to target new pathways but targets the same pathways with an amplified change.
Collapse
Affiliation(s)
- Ali Pormohammad
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
- CCrest Laboratories, Inc., Montreal, Quebec, Canada
| | - Andrea Firrincieli
- Department for Innovation in Biological, Agro-Food and Forest systems, University of Tuscia, Viterbo, Italy
| | - Daniel A. Salazar-Alemán
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Mehdi Mohammadi
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Dave Hansen
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Mohammad Zarei
- Renal Division, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- John B. Little Center for Radiation Sciences, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Raymond J. Turner
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
6
|
Knoke LR, Zimmermann J, Lupilov N, Schneider JF, Celebi B, Morgan B, Leichert LI. The role of glutathione in periplasmic redox homeostasis and oxidative protein folding in Escherichia coli. Redox Biol 2023; 64:102800. [PMID: 37413765 DOI: 10.1016/j.redox.2023.102800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/24/2023] [Indexed: 07/08/2023] Open
Abstract
The thiol redox balance in the periplasm of E. coli depends on the DsbA/B pair for oxidative power and the DsbC/D system as its complement for isomerization of non-native disulfides. While the standard redox potentials of those systems are known, the in vivo "steady state" redox potential imposed onto protein thiol disulfide pairs in the periplasm remains unknown. Here, we used genetically encoded redox probes (roGFP2 and roGFP-iL), targeted to the periplasm, to directly probe the thiol redox homeostasis in this compartment. These probes contain two cysteine residues that are virtually completely reduced in the cytoplasm, but once exported into the periplasm, can form a disulfide bond, a process that can be monitored by fluorescence spectroscopy. Even in the absence of DsbA, roGFP2, exported to the periplasm, was almost fully oxidized, suggesting the presence of an alternative system for the introduction of disulfide bonds into exported proteins. However, the absence of DsbA shifted the steady state periplasmic thiol-redox potential from -228 mV to a more reducing -243 mV and the capacity to re-oxidize periplasmic roGFP2 after a reductive pulse was significantly decreased. Re-oxidation in a DsbA strain could be fully restored by exogenous oxidized glutathione (GSSG), while reduced GSH accelerated re-oxidation of roGFP2 in the WT. In line, a strain devoid of endogenous glutathione showed a more reducing periplasm, and was significantly worse in oxidatively folding PhoA, a native periplasmic protein and substrate of the oxidative folding machinery. PhoA oxidative folding could be enhanced by the addition of exogenous GSSG in the WT and fully restored in a ΔdsbA mutant. Taken together this suggests the presence of an auxiliary, glutathione-dependent thiol-oxidation system in the bacterial periplasm.
Collapse
Affiliation(s)
- Lisa R Knoke
- Ruhr University Bochum, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, Bochum, Germany
| | - Jannik Zimmermann
- Institute of Biochemistry, Centre for Human and Molecular Biology (ZHMB), Saarland University, 66123, Saarbrücken, Germany
| | - Natalie Lupilov
- Ruhr University Bochum, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, Bochum, Germany
| | - Jannis F Schneider
- Ruhr University Bochum, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, Bochum, Germany
| | - Beyzanur Celebi
- Ruhr University Bochum, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, Bochum, Germany
| | - Bruce Morgan
- Institute of Biochemistry, Centre for Human and Molecular Biology (ZHMB), Saarland University, 66123, Saarbrücken, Germany
| | - Lars I Leichert
- Ruhr University Bochum, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, Bochum, Germany.
| |
Collapse
|
7
|
Pecoraro C, Carbone D, Parrino B, Cascioferro S, Diana P. Recent Developments in the Inhibition of Bacterial Adhesion as Promising Anti-Virulence Strategy. Int J Mol Sci 2023; 24:ijms24054872. [PMID: 36902301 PMCID: PMC10002502 DOI: 10.3390/ijms24054872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Infectious diseases caused by antimicrobial-resistant strains have become a serious threat to global health, with a high social and economic impact. Multi-resistant bacteria exhibit various mechanisms at both the cellular and microbial community levels. Among the different strategies proposed to fight antibiotic resistance, we reckon that the inhibition of bacterial adhesion to host surfaces represents one of the most valid approaches, since it hampers bacterial virulence without affecting cell viability. Many different structures and biomolecules involved in the adhesion of Gram-positive and Gram-negative pathogens can be considered valuable targets for the development of promising tools to enrich our arsenal against pathogens.
Collapse
|
8
|
Theoretical Evaluation of Sulfur-Based Reactions as a Model for Biological Antioxidant Defense. Int J Mol Sci 2022; 23:ijms232314515. [PMID: 36498842 PMCID: PMC9741100 DOI: 10.3390/ijms232314515] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Sulfur-containing amino acids, Methionine (Met) and Cysteine (Cys), are very susceptible to Reactive Oxygen Species (ROS). Therefore, sulfur-based reactions regulate many biological processes, playing a key role in maintaining cellular redox homeostasis and modulating intracellular signaling cascades. In oxidative conditions, Met acts as a ROS scavenger, through Met sulfoxide formation, while thiol/disulfide interchange reactions take place between Cys residues as a response to many environmental stimuli. In this work, we apply a QM/MM theoretical-computational approach, which combines quantum-mechanical calculations with classical molecular dynamics simulations to estimate the free energy profile for the above-mentioned reactions in solution. The results obtained, in good agreement with experimental data, show the validity of our approach in modeling sulfur-based reactions, enabling us to study these mechanisms in more complex biological systems.
Collapse
|
9
|
Protein Fusion Strategies for Membrane Protein Stabilization and Crystal Structure Determination. CRYSTALS 2022. [DOI: 10.3390/cryst12081041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Crystal structures of membrane proteins are highly desired for their use in the mechanistic understanding of their functions and the designing of new drugs. However, obtaining the membrane protein structures is difficult. One way to overcome this challenge is with protein fusion methods, which have been successfully used to determine the structures of many membrane proteins, including receptors, enzymes and adhesion molecules. Existing fusion strategies can be categorized into the N or C terminal fusion, the insertion fusion and the termini restraining. The fusions facilitate protein expression, purification, crystallization and phase determination. Successful applications often require further optimization of protein fusion linkers and interactions, whose design can be facilitated by a shared helix strategy and by AlphaFold prediction in the future.
Collapse
|
10
|
Vazulka S, Schiavinato M, Wagenknecht M, Cserjan-Puschmann M, Striedner G. Interaction of Periplasmic Fab Production and Intracellular Redox Balance in Escherichia coli Affects Product Yield. ACS Synth Biol 2022; 11:820-834. [PMID: 35041397 PMCID: PMC8859853 DOI: 10.1021/acssynbio.1c00502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antibody fragments such as Fab's require the formation of disulfide bonds to achieve a proper folding state. During their recombinant, periplasmic expression in Escherichia coli, oxidative folding is mediated by the DsbA/DsbB system in concert with ubiquinone. Thereby, overexpression of Fab's is linked to the respiratory chain, which is not only immensely important for the cell's energy household but also known as a major source of reactive oxygen species. However, the effects of an increased oxidative folding demand and the consequently required electron flux via ubiquinone on the host cell have not been characterized so far. Here, we show that Fab expression in E. coli BL21(DE3) interfered with the intracellular redox balance, thereby negatively impacting host cell performance. Production of four different model Fab's in lab-scale fed-batch cultivations led to increased oxygen consumption rates and strong cell lysis. An RNA sequencing analysis revealed transcription activation of the oxidative stress-responsive soxS gene in the Fab-producing strains. We attributed this to the accumulation of intracellular superoxide, which was measured using flow cytometry. An exogenously supplemented ubiquinone analogue improved Fab yields up to 82%, indicating that partitioning of the quinone pool between aerobic respiration and oxidative folding limited ubiquinone availability and hence disulfide bond formation capacity. Combined, our results provide a more in-depth understanding of the profound effects that periplasmic Fab expression and in particular disulfide bond formation has on the host cell. Thereby, we show new possibilities to elaborate cell engineering and process strategies for improved host cell fitness and process outcome.
Collapse
Affiliation(s)
- Sophie Vazulka
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Matteo Schiavinato
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Martin Wagenknecht
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| |
Collapse
|
11
|
Guérin A, Sulaeman S, Coquet L, Ménard A, Barloy-Hubler F, Dé E, Tresse O. Membrane Proteocomplexome of Campylobacter jejuni Using 2-D Blue Native/SDS-PAGE Combined to Bioinformatics Analysis. Front Microbiol 2020; 11:530906. [PMID: 33329413 PMCID: PMC7717971 DOI: 10.3389/fmicb.2020.530906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 10/14/2020] [Indexed: 12/27/2022] Open
Abstract
Campylobacter is the leading cause of the human bacterial foodborne infections in the developed countries. The perception cues from biotic or abiotic environments by the bacteria are often related to bacterial surface and membrane proteins that mediate the cellular response for the adaptation of Campylobacter jejuni to the environment. These proteins function rarely as a unique entity, they are often organized in functional complexes. In C. jejuni, these complexes are not fully identified and some of them remain unknown. To identify putative functional multi-subunit entities at the membrane subproteome level of C. jejuni, a holistic non a priori method was addressed using two-dimensional blue native/Sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) in strain C. jejuni 81-176. Couples of acrylamide gradient/migration-time, membrane detergent concentration and hand-made strips were optimized to obtain reproducible extraction and separation of intact membrane protein complexes (MPCs). The MPCs were subsequently denatured using SDS-PAGE and each spot from each MPCs was identified by mass spectrometry. Altogether, 21 MPCs could be detected including multi homo-oligomeric and multi hetero-oligomeric complexes distributed in both inner and outer membranes. The function, the conservation and the regulation of the MPCs across C. jejuni strains were inspected by functional and genomic comparison analyses. In this study, relatedness between subunits of two efflux pumps, CmeABC and MacABputC was observed. In addition, a consensus sequence CosR-binding box in promoter regions of MacABputC was present in C. jejuni but not in Campylobacter coli. The MPCs identified in C. jejuni 81-176 membrane are involved in protein folding, molecule trafficking, oxidative phosphorylation, membrane structuration, peptidoglycan biosynthesis, motility and chemotaxis, stress signaling, efflux pumps and virulence.
Collapse
Affiliation(s)
| | | | - Laurent Coquet
- UMR 6270 Laboratoire Polymères Biopolymères Surfaces, UNIROUEN, INSA Rouen, CNRS, Normandie Université, Rouen, France
- UNIROUEN, Plateforme PISSARO, IRIB, Normandie Université, Mont-Saint-Aignan, France
| | - Armelle Ménard
- INSERM, UMR 1053 Bordeaux Research in Translational Oncology, BaRITOn, Bordeaux, France
| | - Frédérique Barloy-Hubler
- UMR 6290, CNRS, Institut de Génétique et Développement de Rennes, University of Rennes, Rennes, France
| | - Emmanuelle Dé
- UMR 6270 Laboratoire Polymères Biopolymères Surfaces, UNIROUEN, INSA Rouen, CNRS, Normandie Université, Rouen, France
| | | |
Collapse
|
12
|
Ren X, Zou L, Holmgren A. Targeting Bacterial Antioxidant Systems for Antibiotics Development. Curr Med Chem 2020; 27:1922-1939. [PMID: 31589114 DOI: 10.2174/0929867326666191007163654] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 09/18/2018] [Accepted: 12/13/2018] [Indexed: 12/15/2022]
Abstract
The emergence of multidrug-resistant bacteria has become an urgent issue in modern medicine which requires novel strategies to develop antibiotics. Recent studies have supported the hypothesis that antibiotic-induced bacterial cell death is mediated by Reactive Oxygen Species (ROS). The hypothesis also highlighted the importance of antioxidant systems, the defense mechanism which contributes to antibiotic resistance. Thioredoxin and glutathione systems are the two major thiol-dependent systems which not only provide antioxidant capacity but also participate in various biological events in bacteria, such as DNA synthesis and protein folding. The biological importance makes them promising targets for novel antibiotics development. Based on the idea, ebselen and auranofin, two bacterial thioredoxin reductase inhibitors, have been found to inhibit the growth of bacteria lacking the GSH efficiently. A recent study combining ebselen and silver exhibited a strong synergistic effect against Multidrug-Resistant (MDR) Gram-negative bacteria which possess both thioredoxin and glutathione systems. These drug-repurposing studies are promising for quick clinical usage due to their well-known profile.
Collapse
Affiliation(s)
- Xiaoyuan Ren
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Lili Zou
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.,Translational Neuroscience & Neural Regeneration and Repair Institute/ Institute of Cell Therapy, The First Hospital of Yichang, Three Gorges University, 443000 Yichang, China
| | - Arne Holmgren
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| |
Collapse
|
13
|
Size-Dependent Antibacterial Activity of Silver Nanoparticle-Loaded Graphene Oxide Nanosheets. NANOMATERIALS 2020; 10:nano10061207. [PMID: 32575669 PMCID: PMC7353109 DOI: 10.3390/nano10061207] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/28/2020] [Accepted: 06/14/2020] [Indexed: 12/19/2022]
Abstract
A series of graphene oxide (GO) suspensions with different particle sizes (<100 nm, ~100 nm, ~1 µm and >1 µm) were successfully fabricated after 0, 30, 60 and 120 min of sonication, respectively. The antibacterial properties of GO suspensions showed that >1 µm GO size resulted in a loss of nearly 50% of bacterial viability, which was higher than treatment by ~100 nm GO size (25%) towards Escherichia coli (E. coli). Complete entrapment of bacteria by the larger GO was observed in transmission electron microscopy (TEM). Silver nanoparticles (Ag NPs) were doped onto GO samples with different lateral sizes to form GO-Ag NP composites. Resulting larger GO-Ag NPs showed higher antibacterial activity than smaller GO-Ag NPs. As observed by Fourier transform infrared spectroscopy (FTIR), the interaction between E. coli and GO occurred mainly at the outer membrane, where membrane amino acids interact with hydroxyl and epoxy groups. The reactive oxygen species (ROS) and the considerable penetration of released Ag+ into the inner bacterial cell membrane result in loss of membrane integrity and damaged morphology. The present work improves the combined action of GO size effect with constant Ag loadings for potential antibacterial activity.
Collapse
|
14
|
Abstract
The formation of disulfide bonds is critical to the folding of many extracytoplasmic proteins in all domains of life. With the discovery in the early 1990s that disulfide bond formation is catalyzed by enzymes, the field of oxidative folding of proteins was born. Escherichia coli played a central role as a model organism for the elucidation of the disulfide bond-forming machinery. Since then, many of the enzymatic players and their mechanisms of forming, breaking, and shuffling disulfide bonds have become understood in greater detail. This article summarizes the discoveries of the past 3 decades, focusing on disulfide bond formation in the periplasm of the model prokaryotic host E. coli.
Collapse
|
15
|
Microcin PDI Inhibits Antibiotic-Resistant Strains of Escherichia coli and Shigella through a Mechanism of Membrane Disruption and Protection by Homotrimer Self-Immunity. Appl Environ Microbiol 2019; 85:AEM.00371-19. [PMID: 30902857 DOI: 10.1128/aem.00371-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/15/2019] [Indexed: 11/20/2022] Open
Abstract
Microcin PDI (MccPDI), a class IIa microcin that is produced by Escherichia coli strains 25 and 284, is known to inhibit foodborne pathogenic enterohemorrhagic E. coli serotypes O157:H7 and O26. Here we demonstrate that MccPDI can inhibit Shigella strains and E. coli isolates that are multidrug resistant, the latter including strains known to cause urinary tract infections in people and companion animals. Two exceptions out of 17 strains were identified. One of the two resistant E. coli isolates (AR0349) has a mutation in a critical amino acid residue that was identified in previous work as a requisite for the MccPDI precursor protein (McpM) to interact with outer membrane porin F (OmpF) on susceptible cells. The second resistant E. coli strain (MAD 96) had no mutations in ompF, but it was PCR positive for two antimicrobial peptides, of which colicin Ia/Ib likely inhibits the MccPDI-producing strain during coculture. Recombinant McpM was still effective against strain MAD 96. In an assessment of how MccPDI affects susceptible strains, results from both an extracellular ATP assay and a nucleic acid staining assay were consistent with membrane damage, while the addition of 200- to 600-Da polyethylene glycol (PEG) to cocultures protected against MccPDI (>600-Da PEG did not provide protection). Further studies using a paraformaldehyde cross-linking experiment and a bacterial two-hybrid assay demonstrated that MccPDI immunity protein (McpI) forms a multimeric complex with itself and presumably protects the producer strain from within the periplasm through an unknown mechanism.IMPORTANCE Microcins represent potential alternatives to conventional antibiotics for human and veterinary medicine. For them to be applied in this manner, however, we need to better understand their spectrum of activity, how these proteins interact with susceptible cells, and how producer cells are protected against the antimicrobial properties of the microcins. For microcin PDI (MccPDI), we report that the spectrum of activity likely includes most E. coli strains due to a conserved binding motif found on an outer membrane protein. Shigella has this motif as well and is susceptible to MccPDI killing via damage to the bacterial membrane. Receptor specificity suggests that these proteins could be used without causing large-scale disruptions to a microbiota, but this also increases the likelihood that resistance can evolve via random mutations. As with conventional antibiotics, good stewardship will be needed to preserve the efficacy of microcins should they be deployed for clinical use.
Collapse
|
16
|
Fu X, Chang Z. Biogenesis, quality control, and structural dynamics of proteins as explored in living cells via site-directed photocrosslinking. Protein Sci 2019; 28:1194-1209. [PMID: 31002747 DOI: 10.1002/pro.3627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023]
Abstract
Protein biogenesis and quality control are essential to maintaining a functional pool of proteins and involve numerous protein factors that dynamically and transiently interact with each other and with the substrate proteins in living cells. Conventional methods are hardly effective for studying dynamic, transient, and weak protein-protein interactions that occur in cells. Herein, we review how the site-directed photocrosslinking approach, which relies on the genetic incorporation of a photoreactive unnatural amino acid into a protein of interest at selected individual amino acid residue positions and the covalent trapping of the interacting proteins upon ultraviolent irradiation, has become a highly efficient way to explore the aspects of protein contacts in living cells. For example, in the past decade, this approach has allowed the profiling of the in vivo substrate proteins of chaperones or proteases under both physiologically optimal and stressful (e.g., acidic) conditions, mapping residues located at protein interfaces, identifying new protein factors involved in the biogenesis of membrane proteins, trapping transiently formed protein complexes, and snapshotting different structural states of a protein. We anticipate that the site-directed photocrosslinking approach will play a fundamental role in dissecting the detailed mechanisms of protein biogenesis, quality control, and dynamics in the future.
Collapse
Affiliation(s)
- Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province, 350117, China
| | - Zengyi Chang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Center for Protein Science, Beijing, 100871, China
| |
Collapse
|
17
|
Membrane protein engineering to the rescue. Biochem Soc Trans 2018; 46:1541-1549. [PMID: 30381335 DOI: 10.1042/bst20180140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023]
Abstract
The inherent hydrophobicity of membrane proteins is a major barrier to membrane protein research and understanding. Their low stability and solubility in aqueous environments coupled with poor expression levels make them a challenging area of research. For many years, the only way of working with membrane proteins was to optimise the environment to suit the protein, through the use of different detergents, solubilising additives, and other adaptations. However, with innovative protein engineering methodologies, the membrane proteins themselves are now being adapted to suit the environment. This mini-review looks at the types of adaptations which are applied to membrane proteins from a variety of different fields, including water solubilising fusion tags, thermostabilising mutation screening, scaffold proteins, stabilising protein chimeras, and isolating water-soluble domains.
Collapse
|
18
|
Mechanical architecture and folding of E. coli type 1 pilus domains. Nat Commun 2018; 9:2758. [PMID: 30013059 PMCID: PMC6048123 DOI: 10.1038/s41467-018-05107-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 05/03/2018] [Indexed: 12/16/2022] Open
Abstract
Uropathogenic Escherichia coli attach to tissues using pili type 1. Each pilus is composed by thousands of coiled FimA domains followed by the domains of the tip fibrillum, FimF-FimG-FimH. The domains are linked by non-covalent β-strands that must resist mechanical forces during attachment. Here, we use single-molecule force spectroscopy to measure the mechanical contribution of each domain to the stability of the pilus and monitor the oxidative folding mechanism of a single Fim domain assisted by periplasmic FimC and the oxidoreductase DsbA. We demonstrate that pilus domains bear high mechanical stability following a hierarchy by which domains close to the tip are weaker than those close to or at the pilus rod. During folding, this remarkable stability is achieved by the intervention of DsbA that not only forms strategic disulfide bonds but also serves as a chaperone assisting the folding of the domains. The pilus type 1 of uropathogenic E. coli must resist mechanical forces to remain attached to the epithelium. Here the authors use single-molecule force spectroscopy to demonstrate a hierarchy of mechanical stability among the pilus domains and show that the oxidoreductase DsbA also acts as a folding chaperone on the domains.
Collapse
|
19
|
Novel Sequence Features of DNA Repair Genes/Proteins from Deinococcus Species Implicated in Protection from Oxidatively Generated Damage. Genes (Basel) 2018. [PMID: 29518000 PMCID: PMC5867870 DOI: 10.3390/genes9030149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Deinococcus species display a high degree of resistance to radiation and desiccation due to their ability to protect critical proteome from oxidatively generated damage; however, the underlying mechanisms are not understood. Comparative analysis of DNA repair proteins reported here has identified 22 conserved signature indels (CSIs) in the proteins UvrA1, UvrC, UvrD, UvsE, MutY, MutM, Nth, RecA, RecD, RecG, RecQ, RecR, RuvC, RadA, PolA, DnaE, LigA, GyrA and GyrB, that are uniquely shared by all/most Deinococcus homologs. Of these CSIs, a 30 amino acid surface-exposed insert in the Deinococcus UvrA1, which distinguishes it from all other UvrA homologs, is of much interest. The uvrA1 gene in Deinococcus also exhibits specific genetic linkage (predicted operonic arrangement) to genes for three other proteins including a novel Deinococcus-specific transmembrane protein (designated dCSP-1) and the proteins DsbA and DsbB, playing central roles in protein disulfide bond formation by oxidation-reduction of CXXC (C represents cysteine, X any other amino acid) motifs. The CXXC motifs provide important targets for oxidation damage and they are present in many DNA repair proteins including five in UvrA, which are part of Zinc-finger elements. A conserved insert specific for Deinococcus is also present in the DsbA protein. Additionally, the uvsE gene in Deinococcus also shows specific linkage to the gene for a membrane-associated protein. To account for these novel observations, a model is proposed where specific interaction of the Deinococcus UvrA1 protein with membrane-bound dCSP-1 enables the UvrA1 to receive electrons from DsbA-DsbB oxido-reductase machinery to ameliorate oxidation damage in the UvrA1 protein.
Collapse
|
20
|
Onder O, Verissimo AF, Khalfaoui-Hassani B, Peters A, Koch HG, Daldal F. Absence of Thiol-Disulfide Oxidoreductase DsbA Impairs cbb3-Type Cytochrome c Oxidase Biogenesis in Rhodobacter capsulatus. Front Microbiol 2017; 8:2576. [PMID: 29312253 PMCID: PMC5742617 DOI: 10.3389/fmicb.2017.02576] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/11/2017] [Indexed: 12/20/2022] Open
Abstract
The thiol-disulfide oxidoreductase DsbA carries out oxidative folding of extra-cytoplasmic proteins by catalyzing the formation of intramolecular disulfide bonds. It has an important role in various cellular functions, including cell division. The purple non-sulfur bacterium Rhodobacter capsulatus mutants lacking DsbA show severe temperature-sensitive and medium-dependent respiratory growth defects. In the presence of oxygen, at normal growth temperature (35°C), DsbA− mutants form colonies on minimal medium, but they do not grow on enriched medium where cells elongate and lyse. At lower temperatures (i.e., 25°C), cells lacking DsbA grow normally in both minimum and enriched media, however, they do not produce the cbb3-type cytochrome c oxidase (cbb3-Cox) on enriched medium. Availability of chemical oxidants (e.g., Cu2+ or a mixture of cysteine and cystine) in the medium becomes critical for growth and cbb3-Cox production in the absence of DsbA. Indeed, addition of Cu2+ to the enriched medium suppresses, and conversely, omission of Cu2+ from the minimal medium induces, growth and cbb3-Cox defects. Alleviation of these defects by addition of redox-active chemicals indicates that absence of DsbA perturbs cellular redox homeostasis required for the production of an active cbb3-Cox, especially in enriched medium where bioavailable Cu2+ is scarce. This is the first report describing that DsbA activity is required for full respiratory capability of R. capsulatus, and in particular, for proper biogenesis of its cbb3-Cox. We propose that absence of DsbA, besides impairing the maturation of the c-type cytochrome subunits, also affects the incorporation of Cu into the catalytic subunit of cbb3-Cox. Defective high affinity Cu acquisition pathway, which includes the MFS-type Cu importer CcoA, and lower production of the c-type cytochrome subunits lead together to improper assembly and degradation of cbb3-Cox.
Collapse
Affiliation(s)
- Ozlem Onder
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Andreia F Verissimo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Annette Peters
- Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Institut für Biochemie und Molekularbiologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Institut für Biochemie und Molekularbiologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
21
|
Mamipour M, Yousefi M, Hasanzadeh M. An overview on molecular chaperones enhancing solubility of expressed recombinant proteins with correct folding. Int J Biol Macromol 2017; 102:367-375. [PMID: 28412337 PMCID: PMC7185796 DOI: 10.1016/j.ijbiomac.2017.04.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/14/2017] [Accepted: 04/06/2017] [Indexed: 02/07/2023]
Abstract
The majority of research topics declared that most of the recombinant proteins have been expressed by Escherichia coli in basic investigations. But the majority of high expressed proteins formed as inactive recombinant proteins that are called inclusion body. To overcome this problem, several methods have been used including suitable promoter, environmental factors, ladder tag to secretion of proteins into the periplasm, gene protein optimization, chemical chaperones and molecular chaperones sets. Co-expression of the interest protein with molecular chaperones is one of the common methods The chaperones are a group of proteins, which are involved in making correct folding of recombinant proteins. Chaperones are divided two groups including; cytoplasmic and periplasmic chaperones. Moreover, periplasmic chaperones and proteases can be manipulated to increase the yields of secreted proteins. In this article, we attempted to review cytoplasmic chaperones such as Hsp families and periplasmic chaperones including; generic chaperones, specialized chaperones, PPIases, and proteins involved in disulfide bond formation.
Collapse
Affiliation(s)
- Mina Mamipour
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammadreza Yousefi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biotechnology, Higher Education Institute of Rab-Rashid, Tabriz, Iran
| | - Mohammad Hasanzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
22
|
Abstract
Cysteine thiols are among the most reactive functional groups in proteins, and their pairing in disulfide linkages is a common post-translational modification in proteins entering the secretory pathway. This modest amino acid alteration, the mere removal of a pair of hydrogen atoms from juxtaposed cysteine residues, contrasts with the substantial changes that characterize most other post-translational reactions. However, the wide variety of proteins that contain disulfides, the profound impact of cross-linking on the behavior of the protein polymer, the numerous and diverse players in intracellular pathways for disulfide formation, and the distinct biological settings in which disulfide bond formation can take place belie the simplicity of the process. Here we lay the groundwork for appreciating the mechanisms and consequences of disulfide bond formation in vivo by reviewing chemical principles underlying cysteine pairing and oxidation. We then show how enzymes tune redox-active cofactors and recruit oxidants to improve the specificity and efficiency of disulfide formation. Finally, we discuss disulfide bond formation in a cellular context and identify important principles that contribute to productive thiol oxidation in complex, crowded, dynamic environments.
Collapse
Affiliation(s)
- Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Colin Thorpe
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| |
Collapse
|
23
|
Verissimo AF, Khalfaoui-Hassani B, Hwang J, Steimle S, Selamoglu N, Sanders C, Khatchikian CE, Daldal F. The thioreduction component CcmG confers efficiency and the heme ligation component CcmH ensures stereo-specificity during cytochrome c maturation. J Biol Chem 2017. [PMID: 28634234 DOI: 10.1074/jbc.m117.794586] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In many Gram-negative bacteria, including Rhodobacter capsulatus, cytochrome c maturation (Ccm) is carried out by a membrane-integral machinery composed of nine proteins (CcmA to I). During this process, the periplasmic thiol-disulfide oxidoreductase DsbA is thought to catalyze the formation of a disulfide bond between the Cys residues at the apocytochrome c heme-binding site (CXXCH). Subsequently, a Ccm-specific thioreductive pathway involving CcmG and CcmH reduces this disulfide bond to allow covalent heme ligation. Currently, the sequence of thioredox reactions occurring between these components and apocytochrome c and the identity of their active Cys residues are unknown. In this work, we first investigated protein-protein interactions among the apocytochrome c, CcmG, and the heme-ligation components CcmF, CcmH, and CcmI. We found that they all interact with each other, forming a CcmFGHI-apocytochrome c complex. Using purified wild-type CcmG, CcmH, and apocytochrome c, as well as their respective Cys mutant variants, we determined the rates of thiol-disulfide exchange reactions between selected pairs of Cys residues from these proteins. We established that CcmG can efficiently reduce the disulfide bond of apocytochrome c and also resolve a mixed disulfide bond formed between apocytochrome c and CcmH. We further show that Cys-45 of CcmH and Cys-34 of apocytochrome c are most likely to form this mixed disulfide bond, which is consistent with the stereo-specificity of the heme-apocytochrome c ligation reaction. We conclude that CcmG confers efficiency, and CcmH ensures stereo-specificity during Ccm and present a comprehensive model for thioreduction reactions that lead to heme-apocytochrome c ligation.
Collapse
Affiliation(s)
- Andreia F Verissimo
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019
| | - Bahia Khalfaoui-Hassani
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019
| | - Josephine Hwang
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019
| | - Stefan Steimle
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019
| | - Nur Selamoglu
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019
| | - Carsten Sanders
- the Department of Physical Sciences, University of Kutztown, Kutztown, Pennsylvania 19530, and
| | - Camilo E Khatchikian
- the Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968
| | - Fevzi Daldal
- From the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6019,
| |
Collapse
|
24
|
Bocian-Ostrzycka KM, Grzeszczuk MJ, Banaś AM, Jastrząb K, Pisarczyk K, Kolarzyk A, Łasica AM, Collet JF, Jagusztyn-Krynicka EK. Engineering of Helicobacter pylori Dimeric Oxidoreductase DsbK (HP0231). Front Microbiol 2016; 7:1158. [PMID: 27507968 PMCID: PMC4960241 DOI: 10.3389/fmicb.2016.01158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/12/2016] [Indexed: 12/16/2022] Open
Abstract
The formation of disulfide bonds that are catalyzed by proteins of the Dsb (disulfide bond) family is crucial for the correct folding of many extracytoplasmic proteins. Thus, this formation plays an essential, pivotal role in the assembly of many virulence factors. The Helicobacter pylori disulfide bond-forming system is uncomplicated compared to the best-characterized Escherichia coli Dsb pathways. It possesses only two extracytoplasmic Dsb proteins named HP0377 and HP0231. As previously shown, HP0377 is a reductase involved in the process of cytochrome c maturation. Additionally, it also possesses disulfide isomerase activity. HP0231 was the first periplasmic dimeric oxidoreductase involved in disulfide generation to be described. Although HP0231 function is critical for oxidative protein folding, its structure resembles that of dimeric EcDsbG, which does not confer this activity. However, the HP0231 catalytic motifs (CXXC and the so-called cis-Pro loop) are identical to that of monomeric EcDsbA. To understand the functioning of HP0231, we decided to study the relations between its sequence, structure and activity through an extensive analysis of various HP0231 point mutants, using in vivo and in vitro strategies. Our work shows the crucial role of the cis-Pro loop, as changing valine to threonine in this motif completely abolishes the protein function in vivo. Functioning of HP0231 is conditioned by the combination of CXXC and the cis-Pro loop, as replacing the HP0231 CXXC motif by the motif from EcDsbG or EcDsbC results in bifunctional protein, at least in E. coli. We also showed that the dimerization domain of HP0231 ensures contact with its substrates. Moreover, the activity of this oxidase is independent on the structure of the catalytic domain. Finally, we showed that HP0231 chaperone activity is independent of its redox function.
Collapse
Affiliation(s)
- Katarzyna M Bocian-Ostrzycka
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Magdalena J Grzeszczuk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Anna M Banaś
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Katarzyna Jastrząb
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Karolina Pisarczyk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Anna Kolarzyk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Anna M Łasica
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Jean-François Collet
- Walloon Excellence in Life Sciences and BiotechnologyBrussels, Belgium; de Duve Institute, Université Catholique de LouvainBrussels, Belgium
| | - Elżbieta K Jagusztyn-Krynicka
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| |
Collapse
|
25
|
Smith RP, Paxman JJ, Scanlon MJ, Heras B. Targeting Bacterial Dsb Proteins for the Development of Anti-Virulence Agents. Molecules 2016; 21:molecules21070811. [PMID: 27438817 PMCID: PMC6273893 DOI: 10.3390/molecules21070811] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 05/21/2016] [Accepted: 05/25/2016] [Indexed: 11/22/2022] Open
Abstract
Recent years have witnessed a dramatic increase in bacterial antimicrobial resistance and a decline in the development of novel antibiotics. New therapeutic strategies are urgently needed to combat the growing threat posed by multidrug resistant bacterial infections. The Dsb disulfide bond forming pathways are potential targets for the development of antimicrobial agents because they play a central role in bacterial pathogenesis. In particular, the DsbA/DsbB system catalyses disulfide bond formation in a wide array of virulence factors, which are essential for many pathogens to establish infections and cause disease. These redox enzymes are well placed as antimicrobial targets because they are taxonomically widespread, share low sequence identity with human proteins, and many years of basic research have provided a deep molecular understanding of these systems in bacteria. In this review, we discuss disulfide bond catalytic pathways in bacteria and their significance in pathogenesis. We also review the use of different approaches to develop inhibitors against Dsb proteins as potential anti-virulence agents, including fragment-based drug discovery, high-throughput screening and other structure-based drug discovery methods.
Collapse
Affiliation(s)
- Roxanne P Smith
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, Vic 3083, Australia.
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, Vic 3083, Australia.
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Royal Parade, Parkville, Vic 3052, Australia.
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, Vic 3083, Australia.
| |
Collapse
|
26
|
Khalfaoui-Hassani B, Verissimo AF, Shroff NP, Ekici S, Trasnea PI, Utz M, Koch HG, Daldal F. Biogenesis of Cytochrome c Complexes: From Insertion of Redox Cofactors to Assembly of Different Subunits. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_27] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
27
|
Bailey JB, Subramanian RH, Churchfield LA, Tezcan FA. Metal-Directed Design of Supramolecular Protein Assemblies. Methods Enzymol 2016; 580:223-50. [PMID: 27586336 PMCID: PMC5131729 DOI: 10.1016/bs.mie.2016.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Owing to their central roles in cellular signaling, construction, and biochemistry, protein-protein interactions (PPIs) and protein self-assembly have become a major focus of molecular design and synthetic biology. In order to circumvent the complexity of constructing extensive noncovalent interfaces, which are typically involved in natural PPIs and protein self-assembly, we have developed two design strategies, metal-directed protein self-assembly (MDPSA) and metal-templated interface redesign (MeTIR). These strategies, inspired by both the proposed evolutionary roles of metals and their prevalence in natural PPIs, take advantage of the favorable properties of metal coordination (bonding strength, directionality, and reversibility) to guide protein self-assembly with minimal design and engineering. Using a small, monomeric protein (cytochrome cb562) as a model building block, we employed MDPSA and MeTIR to create a diverse array of functional supramolecular architectures which range from structurally tunable oligomers to metalloprotein complexes that can properly self-assemble in living cells into novel metalloenzymes. The design principles and strategies outlined herein should be readily applicable to other protein systems with the goal of creating new PPIs and protein assemblies with structures and functions not yet produced by natural evolution.
Collapse
Affiliation(s)
- J B Bailey
- University of California, San Diego, La Jolla, CA, United States
| | - R H Subramanian
- University of California, San Diego, La Jolla, CA, United States
| | - L A Churchfield
- University of California, San Diego, La Jolla, CA, United States
| | - F A Tezcan
- University of California, San Diego, La Jolla, CA, United States.
| |
Collapse
|
28
|
Albesa-Jové D, Comino N, Tersa M, Mohorko E, Urresti S, Dainese E, Chiarelli LR, Pasca MR, Manganelli R, Makarov V, Riccardi G, Svergun DI, Glockshuber R, Guerin ME. The Redox State Regulates the Conformation of Rv2466c to Activate the Antitubercular Prodrug TP053. J Biol Chem 2015; 290:31077-89. [PMID: 26546681 DOI: 10.1074/jbc.m115.677039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 11/06/2022] Open
Abstract
Rv2466c is a key oxidoreductase that mediates the reductive activation of TP053, a thienopyrimidine derivative that kills replicating and non-replicating Mycobacterium tuberculosis, but whose mode of action remains enigmatic. Rv2466c is a homodimer in which each subunit displays a modular architecture comprising a canonical thioredoxin-fold with a Cys(19)-Pro(20)-Trp(21)-Cys(22) motif, and an insertion consisting of a four α-helical bundle and a short α-helical hairpin. Strong evidence is provided for dramatic conformational changes during the Rv2466c redox cycle, which are essential for TP053 activity. Strikingly, a new crystal structure of the reduced form of Rv2466c revealed the binding of a C-terminal extension in α-helical conformation to a pocket next to the active site cysteine pair at the interface between the thioredoxin domain and the helical insertion domain. The ab initio low-resolution envelopes obtained from small angle x-ray scattering showed that the fully reduced form of Rv2466c adopts a "closed" compact conformation in solution, similar to that observed in the crystal structure. In contrast, the oxidized form of Rv2466c displays an "open" conformation, where tertiary structural changes in the α-helical subdomain suffice to account for the observed conformational transitions. Altogether our structural, biochemical, and biophysical data strongly support a model in which the formation of the catalytic disulfide bond upon TP053 reduction triggers local structural changes that open the substrate binding site of Rv2466c allowing the release of the activated, reduced form of TP053. Our studies suggest that similar structural changes might have a functional role in other members of the thioredoxin-fold superfamily.
Collapse
Affiliation(s)
- David Albesa-Jové
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain, the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Natalia Comino
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Montse Tersa
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Elisabeth Mohorko
- the Institute for Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Saioa Urresti
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | | | - Laurent R Chiarelli
- Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Maria Rosalia Pasca
- Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | | | - Vadim Makarov
- the A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia, and
| | - Giovanna Riccardi
- Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Dmitri I Svergun
- the European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, D-22603 Hamburg, Germany
| | - Rudi Glockshuber
- the Institute for Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Marcelo E Guerin
- From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain, the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain,
| |
Collapse
|
29
|
Valero-Ruiz E, González-Sánchez MI, Batchelor-McAuley C, Compton RG. Halogen mediated voltammetric oxidation of biological thiols and disulfides. Analyst 2015; 141:144-9. [PMID: 26539570 DOI: 10.1039/c5an01955a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electrochemical generation of the halides, bromine and iodine, in the presence of biologically relevant organosulfur is demonstrated to result in an analytically useful response. In the case of the iodide/iodine redox couple only the thiol causes an increase in the electrochemical oxidative peak current. Conversely, the formed bromine may catalytically oxidise both thiols and disulfides. Hence, the differing reactivities of the halide ions readily allow discrimination between the closely related thiol and disulphide species. For all of the organosulfur species investigated (glutathione, cysteine and homocysteine) micromolar limits of detection are attainable. In the case of the bromine mediated oxidation this sensitivity at least partially arises from the large catalytic amplification, such that, for each disulphide molecule up to ten electrons may be transferred. Ultimately this bromine oxidation results in the formation of the sulfonate species. For the iodine mediated oxidation of the thiols the oxidation proceeds no further than to the formation of the associated disulfide.
Collapse
Affiliation(s)
- Edelmira Valero-Ruiz
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
| | | | | | | |
Collapse
|
30
|
Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet JF, Jagusztyn-Krynicka EK. Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain. Front Microbiol 2015; 6:1065. [PMID: 26500620 PMCID: PMC4597128 DOI: 10.3389/fmicb.2015.01065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/16/2015] [Indexed: 12/15/2022] Open
Abstract
Helicobacter pylori does not encode the classical DsbA/DsbB oxidoreductases that are crucial for oxidative folding of extracytoplasmic proteins. Instead, this microorganism encodes an untypical two proteins playing a role in disulfide bond formation – periplasmic HP0231, which structure resembles that of EcDsbC/DsbG, and its redox partner, a membrane protein HpDsbI (HP0595) with a β-propeller structure. The aim of presented work was to assess relations between HP0231 structure and function. We showed that HP0231 is most closely related evolutionarily to the catalytic domain of DsbG, even though it possesses a catalytic motif typical for canonical DsbA proteins. Similarly, the highly diverged N-terminal dimerization domain is homologous to the dimerization domain of DsbG. To better understand the functioning of this atypical oxidoreductase, we examined its activity using in vivo and in vitro experiments. We found that HP0231 exhibits oxidizing and chaperone activities but no isomerizing activity, even though H. pylori does not contain a classical DsbC. We also show that HP0231 is not involved in the introduction of disulfide bonds into HcpC (Helicobactercysteine-rich protein C), a protein involved in the modulation of the H. pylori interaction with its host. Additionally, we also constructed a truncated version of HP0231 lacking the dimerization domain, denoted HP0231m, and showed that it acts in Escherichia coli cells in a DsbB-dependent manner. In contrast, HP0231m and classical monomeric EcDsbA (E. coli DsbA protein) were both unable to complement the lack of HP0231 in H. pylori cells, though they exist in oxidized forms. HP0231m is inactive in the insulin reduction assay and possesses high chaperone activity, in contrast to EcDsbA. In conclusion, HP0231 combines oxidative functions characteristic of DsbA proteins and chaperone activity characteristic of DsbC/DsbG, and it lacks isomerization activity.
Collapse
Affiliation(s)
- Katarzyna M Bocian-Ostrzycka
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Anna M Łasica
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology Warsaw, Poland
| | - Stanisław Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology Warsaw, Poland
| | - Magdalena J Grzeszczuk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Karolina Drabik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Aneta M Dobosz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Renata Godlewska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology Warsaw, Poland
| | - Jean-Francois Collet
- de Duve Institute, Université catholique de Louvain (UCL)/Walloon Excellence in Life Sciences and Biotechnology Brussels, Belgium
| | - Elżbieta K Jagusztyn-Krynicka
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| |
Collapse
|
31
|
Abstract
Antibacterial drugs with novel scaffolds and new mechanisms of action are desperately needed to address the growing problem of antibiotic resistance. The periplasmic oxidative folding system in Gram-negative bacteria represents a possible target for anti-virulence antibacterials. By targeting virulence rather than viability, development of resistance and side effects (through killing host native microbiota) might be minimized. Here, we undertook the design of peptidomimetic inhibitors targeting the interaction between the two key enzymes of oxidative folding, DsbA and DsbB, with the ultimate goal of preventing virulence factor assembly. Structures of DsbB - or peptides - complexed with DsbA revealed key interactions with the DsbA active site cysteine, and with a hydrophobic groove adjacent to the active site. The present work aimed to discover peptidomimetics that target the hydrophobic groove to generate non-covalent DsbA inhibitors. The previously reported structure of a Proteus mirabilis DsbA active site cysteine mutant, in a non-covalent complex with the heptapeptide PWATCDS, was used as an in silico template for virtual screening of a peptidomimetic fragment library. The highest scoring fragment compound and nine derivatives were synthesized and evaluated for DsbA binding and inhibition. These experiments discovered peptidomimetic fragments with inhibitory activity at millimolar concentrations. Although only weakly potent relative to larger covalent peptide inhibitors that interact through the active site cysteine, these fragments offer new opportunities as templates to build non-covalent inhibitors. The results suggest that non-covalent peptidomimetics may need to interact with sites beyond the hydrophobic groove in order to produce potent DsbA inhibitors.
Collapse
|
32
|
Bocian-Ostrzycka KM, Grzeszczuk MJ, Dziewit L, Jagusztyn-Krynicka EK. Diversity of the Epsilonproteobacteria Dsb (disulfide bond) systems. Front Microbiol 2015; 6:570. [PMID: 26106374 PMCID: PMC4460558 DOI: 10.3389/fmicb.2015.00570] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/24/2015] [Indexed: 12/20/2022] Open
Abstract
The bacterial proteins of the Dsb family-important components of the post-translational protein modification system-catalyze the formation of disulfide bridges, a process that is crucial for protein structure stabilization and activity. Dsb systems play an essential role in the assembly of many virulence factors. Recent rapid advances in global analysis of bacteria have thrown light on the enormous diversity among bacterial Dsb systems. While the Escherichia coli disulfide bond-forming system is quite well understood, the mechanisms of action of Dsb systems in other bacteria, including members of class Epsilonproteobacteria that contain pathogenic and non-pathogenic bacteria colonizing extremely diverse ecological niches, are poorly characterized. Here we present a review of current knowledge on Epsilonproteobacteria Dsb systems. We have focused on the Dsb systems of Campylobacter spp. and Helicobacter spp. because our knowledge about Dsb proteins of Wolinella and Arcobacter spp. is still scarce and comes mainly from bioinformatic studies. Helicobacter pylori is a common human pathogen that colonizes the gastric epithelium of humans with severe consequences. Campylobacter spp. is a leading cause of zoonotic enteric bacterial infections in most developed and developing nations. We focus on various aspects of the diversity of the Dsb systems and their influence on pathogenicity, particularly because Dsb proteins are considered as potential targets for a new class of anti-virulence drugs to treat human infections by Campylobacter or Helicobacter spp.
Collapse
|
33
|
Santiago AE, Mann BJ, Qin A, Cunningham AL, Cole LE, Grassel C, Vogel SN, Levine MM, Barry EM. Characterization of Francisella tularensis Schu S4 defined mutants as live-attenuated vaccine candidates. Pathog Dis 2015; 73:ftv036. [PMID: 25986219 PMCID: PMC4462183 DOI: 10.1093/femspd/ftv036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2015] [Indexed: 01/11/2023] Open
Abstract
Francisella tularensis (Ft), the etiological agent of tularemia and a Tier 1 select agent, has been previously weaponized and remains a high priority for vaccine development. Ft tularensis (type A) and Ft holarctica (type B) cause most human disease. We selected six attenuating genes from the live vaccine strain (LVS; type B), F. novicida and other intracellular bacteria: FTT0507, FTT0584, FTT0742, FTT1019c (guaA), FTT1043 (mip) and FTT1317c (guaB) and created unmarked deletion mutants of each in the highly human virulent Ft strain Schu S4 (Type A) background. FTT0507, FTT0584, FTT0742 and FTT1043 Schu S4 mutants were not attenuated for virulence in vitro or in vivo. In contrast, Schu S4 gua mutants were unable to replicate in murine macrophages and were attenuated in vivo, with an i.n. LD50 > 105 CFU in C57BL/6 mice. However, the gua mutants failed to protect mice against lethal challenge with WT Schu S4, despite demonstrating partial protection in rabbits in a previous study. These results contrast with the highly protective capacity of LVS gua mutants against a lethal LVS challenge in mice, and underscore differences between these strains and the animal models in which they are evaluated, and therefore have important implications for vaccine development. Mutations in guanine biosynthesis genes, but not in four other hypothetical virulence factors in highly virulent Francisella tularensis strain Schu S4 resulted in attenuation in macrophage replication and mouse virulence.
Collapse
Affiliation(s)
- Araceli E Santiago
- Departments of Pediatrics, University of Virginia Children's Hospital, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Barbara J Mann
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Aiping Qin
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Aimee L Cunningham
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Leah E Cole
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Christen Grassel
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Stefanie N Vogel
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Myron M Levine
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Eileen M Barry
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| |
Collapse
|
34
|
Mia40 Combines Thiol Oxidase and Disulfide Isomerase Activity to Efficiently Catalyze Oxidative Folding in Mitochondria. J Mol Biol 2014; 426:4087-4098. [DOI: 10.1016/j.jmb.2014.10.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 11/21/2022]
|
35
|
Folding energetics and oligomerization of polytopic α-helical transmembrane proteins. Arch Biochem Biophys 2014; 564:281-96. [DOI: 10.1016/j.abb.2014.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/26/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
|
36
|
Rudolph J, Erbse AH, Behlen LS, Copley SD. A radical intermediate in the conversion of pentachlorophenol to tetrachlorohydroquinone by Sphingobium chlorophenolicum. Biochemistry 2014; 53:6539-49. [PMID: 25238136 PMCID: PMC4204890 DOI: 10.1021/bi5010427] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Pentachlorophenol
(PCP) hydroxylase, the first enzyme in the pathway
for degradation of PCP in Sphingobium chlorophenolicum, is an unusually slow flavin-dependent monooxygenase (kcat = 0.02 s–1) that converts PCP to
a highly reactive product, tetrachlorobenzoquinone (TCBQ). Using stopped-flow
spectroscopy, we have shown that the steps up to and including formation
of TCBQ are rapid (5–30 s–1). Before products
can be released from the active site, the strongly oxidizing TCBQ
abstracts an electron from a donor at the active site, possibly a
cysteine residue, resulting in an off-pathway diradical state that
only slowly reverts to an intermediate capable of completing the catalytic
cycle. TCBQ reductase, the second enzyme in the PCP degradation pathway,
rescues this nonproductive complex via two fast sequential one-electron
transfers. These studies demonstrate how adoption of an ancestral
catalytic strategy for conversion of a substrate with different steric
and electronic properties can lead to subtle yet (literally) radical
changes in enzymatic reaction mechanisms.
Collapse
Affiliation(s)
- Johannes Rudolph
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, and ‡Department of Chemistry and Biochemistry, University of Colorado Boulder , Boulder, Colorado 80309, United States
| | | | | | | |
Collapse
|
37
|
Verissimo AF, Daldal F. Cytochrome c biogenesis System I: an intricate process catalyzed by a maturase supercomplex? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:989-98. [PMID: 24631867 DOI: 10.1016/j.bbabio.2014.03.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 11/16/2022]
Abstract
Cytochromes c are ubiquitous heme proteins that are found in most living organisms and are essential for various energy production pathways as well as other cellular processes. Their biosynthesis relies on a complex post-translational process, called cytochrome c biogenesis, responsible for the formation of stereo-specific thioether bonds between the vinyl groups of heme b (protoporphyrin IX-Fe) and the thiol groups of apocytochromes c heme-binding site (C1XXC2H) cysteine residues. In some organisms this process involves up to nine (CcmABCDEFGHI) membrane proteins working together to achieve heme ligation, designated the Cytochrome c maturation (Ccm)-System I. Here, we review recent findings related to the Ccm-System I found in bacteria, archaea and plant mitochondria, with an emphasis on protein interactions between the Ccm components and their substrates (apocytochrome c and heme). We discuss the possibility that the Ccm proteins may form a multi subunit supercomplex (dubbed "Ccm machine"), and based on the currently available data, we present an updated version of a mechanistic model for Ccm. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
Collapse
Affiliation(s)
- Andreia F Verissimo
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6019, USA
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6019, USA.
| |
Collapse
|
38
|
Mia40 targets cysteines in a hydrophobic environment to direct oxidative protein folding in the mitochondria. Nat Commun 2014; 5:3041. [DOI: 10.1038/ncomms4041] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/29/2013] [Indexed: 11/08/2022] Open
|
39
|
Walden PM, McMahon RM, Archbold JK. Membrane Protein Structures for Rational Antimicrobial Drug Design. Aust J Chem 2014. [DOI: 10.1071/ch14333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Antibiotic resistance is a major global health threat. Bacteria have developed novel resistance mechanisms to many of the latest generations of antibiotics and there is an urgent need to develop new therapies to combat these infections. Infections that are caused by multi-drug resistant Gram-negative bacteria result in poor prognosis, prolonged illness, and greater costs for health care. Recent research has pointed to several key bacterial membrane proteins as potential targets for drug and vaccine development. However, determination of the structures of these membrane proteins is not a trivial task. Here we review recent breakthroughs of the structural determination of bacterial membrane proteins and their potential for the future rational design of novel antimicrobial therapies.
Collapse
|
40
|
Israel BA, Kodali VK, Thorpe C. Going through the barrier: coupled disulfide exchange reactions promote efficient catalysis in quiescin sulfhydryl oxidase. J Biol Chem 2013; 289:5274-84. [PMID: 24379406 DOI: 10.1074/jbc.m113.536219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The quiescin sulfhydryl oxidase (QSOX) family of enzymes generates disulfide bonds in peptides and proteins with the reduction of oxygen to hydrogen peroxide. Determination of the potentials of the redox centers in Trypanosoma brucei QSOX provides a context for understanding catalysis by this facile oxidant of protein thiols. The CXXC motif of the thioredoxin domain is comparatively oxidizing (E'0 of -144 mV), consistent with an ability to transfer disulfide bonds to a broad range of thiol substrates. In contrast, the proximal CXXC disulfide in the ERV (essential for respiration and vegetative growth) domain of TbQSOX is strongly reducing (E'0 of -273 mV), representing a major apparent thermodynamic barrier to overall catalysis. Reduction of the oxidizing FAD cofactor (E'0 of -153 mV) is followed by the strongly favorable reduction of molecular oxygen. The role of a mixed disulfide intermediate between thioredoxin and ERV domains was highlighted by rapid reaction studies in which the wild-type CGAC motif in the thioredoxin domain of TbQSOX was replaced by the more oxidizing CPHC or more reducing CGPC sequence. Mixed disulfide bond formation is accompanied by the generation of a charge transfer complex with the flavin cofactor. This provides thermodynamic coupling among the three redox centers of QSOX and avoids the strongly uphill mismatch between the formal potentials of the thioredoxin and ERV disulfides. This work identifies intriguing mechanistic parallels between the eukaryotic QSOX enzymes and the DsbA/B system catalyzing disulfide bond generation in the bacterial periplasm and suggests that the strategy of linked disulfide exchanges may be exploited in other catalysts of oxidative protein folding.
Collapse
Affiliation(s)
- Benjamin A Israel
- From the Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | | | | |
Collapse
|
41
|
Yazawa K, Furusawa H, Okahata Y. Real-time monitoring of intermediates reveals the reaction pathway in the thiol-disulfide exchange between disulfide bond formation protein A (DsbA) and B (DsbB) on a membrane-immobilized quartz crystal microbalance (QCM) system. J Biol Chem 2013; 288:35969-81. [PMID: 24145032 PMCID: PMC3861646 DOI: 10.1074/jbc.m113.519876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/18/2013] [Indexed: 11/06/2022] Open
Abstract
Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone.
Collapse
Affiliation(s)
- Kenjiro Yazawa
- From the Innovative Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, Yamagata 992-8510, Japan and Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroyuki Furusawa
- From the Innovative Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, Yamagata 992-8510, Japan and Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yoshio Okahata
- From the Innovative Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, Yamagata 992-8510, Japan and Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| |
Collapse
|
42
|
Kurth F, Rimmer K, Premkumar L, Mohanty B, Duprez W, Halili MA, Shouldice SR, Heras B, Fairlie DP, Scanlon MJ, Martin JL. Comparative sequence, structure and redox analyses of Klebsiella pneumoniae DsbA show that anti-virulence target DsbA enzymes fall into distinct classes. PLoS One 2013; 8:e80210. [PMID: 24244651 PMCID: PMC3828196 DOI: 10.1371/journal.pone.0080210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 09/30/2013] [Indexed: 12/21/2022] Open
Abstract
Bacterial DsbA enzymes catalyze oxidative folding of virulence factors, and have been identified as targets for antivirulence drugs. However, DsbA enzymes characterized to date exhibit a wide spectrum of redox properties and divergent structural features compared to the prototypical DsbA enzyme of Escherichia coli DsbA (EcDsbA). Nonetheless, sequence analysis shows that DsbAs are more highly conserved than their known substrate virulence factors, highlighting the potential to inhibit virulence across a range of organisms by targeting DsbA. For example, Salmonella enterica typhimurium (SeDsbA, 86 % sequence identity to EcDsbA) shares almost identical structural, surface and redox properties. Using comparative sequence and structure analysis we predicted that five other bacterial DsbAs would share these properties. To confirm this, we characterized Klebsiella pneumoniae DsbA (KpDsbA, 81 % identity to EcDsbA). As expected, the redox properties, structure and surface features (from crystal and NMR data) of KpDsbA were almost identical to those of EcDsbA and SeDsbA. Moreover, KpDsbA and EcDsbA bind peptides derived from their respective DsbBs with almost equal affinity, supporting the notion that compounds designed to inhibit EcDsbA will also inhibit KpDsbA. Taken together, our data show that DsbAs fall into different classes; that DsbAs within a class may be predicted by sequence analysis of binding loops; that DsbAs within a class are able to complement one another in vivo and that compounds designed to inhibit EcDsbA are likely to inhibit DsbAs within the same class.
Collapse
Affiliation(s)
- Fabian Kurth
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Kieran Rimmer
- Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Lakshmanane Premkumar
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Biswaranjan Mohanty
- Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Wilko Duprez
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Maria A. Halili
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Stephen R. Shouldice
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Begoña Heras
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Martin J. Scanlon
- Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre of Excellence for Coherent X-ray Science, Monash University, Parkville, Victoria, Australia
- * E-mail: (JLM); (MJS)
| | - Jennifer L. Martin
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (JLM); (MJS)
| |
Collapse
|
43
|
Premkumar L, Heras B, Duprez W, Walden P, Halili M, Kurth F, Fairlie DP, Martin JL. Rv2969c, essential for optimal growth in Mycobacterium tuberculosis, is a DsbA-like enzyme that interacts with VKOR-derived peptides and has atypical features of DsbA-like disulfide oxidases. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1981-94. [PMID: 24100317 PMCID: PMC3792642 DOI: 10.1107/s0907444913017800] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/28/2013] [Indexed: 12/16/2022]
Abstract
The bacterial disulfide machinery is an attractive molecular target for developing new antibacterials because it is required for the production of multiple virulence factors. The archetypal disulfide oxidase proteins in Escherichia coli (Ec) are DsbA and DsbB, which together form a functional unit: DsbA introduces disulfides into folding proteins and DsbB reoxidizes DsbA to maintain it in the active form. In Mycobacterium tuberculosis (Mtb), no DsbB homologue is encoded but a functionally similar but structurally divergent protein, MtbVKOR, has been identified. Here, the Mtb protein Rv2969c is investigated and it is shown that it is the DsbA-like partner protein of MtbVKOR. It is found that it has the characteristic redox features of a DsbA-like protein: a highly acidic catalytic cysteine, a highly oxidizing potential and a destabilizing active-site disulfide bond. Rv2969c also has peptide-oxidizing activity and recognizes peptide segments derived from the periplasmic loops of MtbVKOR. Unlike the archetypal EcDsbA enzyme, Rv2969c has little or no activity in disulfide-reducing and disulfide-isomerase assays. The crystal structure of Rv2969c reveals a canonical DsbA fold comprising a thioredoxin domain with an embedded helical domain. However, Rv2969c diverges considerably from other DsbAs, including having an additional C-terminal helix (H8) that may restrain the mobility of the catalytic helix H1. The enzyme is also characterized by a very shallow hydrophobic binding surface and a negative electrostatic surface potential surrounding the catalytic cysteine. The structure of Rv2969c was also used to model the structure of a paralogous DsbA-like domain of the Ser/Thr protein kinase PknE. Together, these results show that Rv2969c is a DsbA-like protein with unique properties and a limited substrate-binding specificity.
Collapse
Affiliation(s)
- Lakshmanane Premkumar
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Begoña Heras
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Wilko Duprez
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Patricia Walden
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Maria Halili
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Fabian Kurth
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - David P. Fairlie
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Jennifer L. Martin
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| |
Collapse
|
44
|
Wang L, Li J, Wang X, Liu W, Zhang XC, Li X, Rao Z. Structure analysis of the extracellular domain reveals disulfide bond forming-protein properties of Mycobacterium tuberculosis Rv2969c. Protein Cell 2013; 4:628-40. [PMID: 23828196 DOI: 10.1007/s13238-013-3033-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 05/28/2013] [Indexed: 11/25/2022] Open
Abstract
Disulfide bond-forming (Dsb) protein is a bacterial periplasmic protein that is essential for the correct folding and disulfide bond formation of secreted or cell wallassociated proteins. DsbA introduces disulfide bonds into folding proteins, and is re-oxidized through interaction with its redox partner DsbB. Mycobacterium tuberculosis, a Gram-positive bacterium, expresses a DsbA-like protein ( Rv2969c), an extracellular protein that has its Nterminus anchored in the cell membrane. Since Rv2969c is an essential gene, crucial for disulfide bond formation, research of DsbA may provide a target of a new class of anti-bacterial drugs for treatment of M.tuberculosis infection. In the present work, the crystal structures of the extracellular region of Rv2969c (Mtb DsbA) were determined in both its reduced and oxidized states. The overall structure of Mtb DsbA can be divided into two domains: a classical thioredoxin-like domain with a typical CXXC active site, and an α-helical domain. It largely resembles its Escherichia coli homologue EcDsbA, however, it possesses a truncated binding groove; in addition, its active site is surrounded by an acidic, rather than hydrophobic surface. In our oxidoreductase activity assay, Mtb DsbA exhibited a different substrate specificity when compared to EcDsbA. Moreover, structural analysis revealed a second disulfide bond in Mtb DsbA, which is rare in the previously reported DsbA structures, and is assumed to contribute to the overall stability of Mtb DsbA. To investigate the disulphide formation pathway in M.tuberculosis, we modeled Mtb Vitamin K epoxide reductase (Mtb VKOR), a binding partner of Mtb DsbA, to Mtb DsbA.
Collapse
Affiliation(s)
- Lu Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | | | | | | | | |
Collapse
|
45
|
Tang M, Nesbitt AE, Sperling LJ, Berthold DA, Schwieters CD, Gennis RB, Rienstra CM. Structure of the disulfide bond generating membrane protein DsbB in the lipid bilayer. J Mol Biol 2013; 425:1670-82. [PMID: 23416557 PMCID: PMC3670690 DOI: 10.1016/j.jmb.2013.02.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/11/2013] [Accepted: 02/08/2013] [Indexed: 12/16/2022]
Abstract
The integral membrane protein DsbB in Escherichia coli is responsible for oxidizing the periplasmic protein DsbA, which forms disulfide bonds in substrate proteins. We have developed a high-resolution structural model by combining experimental X-ray and solid-state NMR with molecular dynamics (MD) simulations. We embedded the high-resolution DsbB structure, derived from the joint calculation with X-ray reflections and solid-state NMR restraints, into the lipid bilayer and performed MD simulations to provide a mechanistic view of DsbB function in the membrane. Further, we revealed the membrane topology of DsbB by selective proton spin diffusion experiments, which directly probe the correlations of DsbB with water and lipid acyl chains. NMR data also support the model of a flexible periplasmic loop and an interhelical hydrogen bond between Glu26 and Tyr153.
Collapse
Affiliation(s)
- Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Anna E. Nesbitt
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Lindsay J. Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Charles D. Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert B. Gennis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| |
Collapse
|
46
|
Sperling LJ, Tang M, Berthold DA, Nesbitt AE, Gennis RB, Rienstra CM. Solid-state NMR study of a 41 kDa membrane protein complex DsbA/DsbB. J Phys Chem B 2013; 117:6052-60. [PMID: 23527473 DOI: 10.1021/jp400795d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The disulfide bond generation system in E. coli is led by a periplasmic protein, DsbA, and an integral membrane protein, DsbB. Here we present a solid-state NMR (SSNMR) study of a 41 kDa membrane protein complex DsbA/DsbB precipitated in the presence of native lipids to investigate conformational changes and dynamics that occur upon transient complex formation within the electron transfer pathway. Chemical shift changes in the periplasmic enzyme DsbA in three states (wild type, C33S mutant, and in complex with DsbB) reveal structural and/or dynamic information. We report a 4.9 ppm (15)N chemical shift change observed for Pro31 in the active site between the wild type and C33S mutant of DsbA. Additionally, the Pro31 residue remains elusive in the DsbA/DsbB complex, indicating that the dynamics change drastically in the active site between the three states of DsbA. Using three-dimensional SSNMR spectra, partial (13)C and (15)N de novo chemical shift assignments throughout DsbA in the DsbA/DsbB complex were compared with the shifts from DsbA alone to map site-specific chemical shift perturbations. These results demonstrate that there are further structural and dynamic changes of DsbA in the native membrane observed by SSNMR, beyond the differences between the crystal structures of DsbA and the DsbA/DsbB complex.
Collapse
Affiliation(s)
- Lindsay J Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | | | | | | | | | | |
Collapse
|
47
|
Di Silvio E, Di Matteo A, Malatesta F, Travaglini-Allocatelli C. Recognition and binding of apocytochrome c to P. aeruginosa CcmI, a component of cytochrome c maturation machinery. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1554-61. [PMID: 23648553 DOI: 10.1016/j.bbapap.2013.04.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 01/13/2023]
Abstract
The biogenesis of c-type cytochromes (Cytc) is a process that in Gram-negative bacteria demands the coordinated action of different periplasmic proteins (CcmA-I), whose specific roles are still being investigated. Activities of Ccm proteins span from the chaperoning of heme b in the periplasm to the specific reduction of oxidized apocytochrome (apoCyt) cysteine residues and to chaperoning and recognition of the unfolded apoCyt before covalent attachment of the heme to the cysteine thiols can occur. We present here the functional characterization of the periplasmic domain of CcmI from the pathogen Pseudomonas aeruginosa (Pa-CcmI*). Pa-CcmI* is composed of a TPR domain and a peculiar C-terminal domain. Pa-CcmI* fulfills both the ability to recognize and bind to P. aeruginosa apo-cytochrome c551 (Pa-apoCyt) and a chaperoning activity towards unfolded proteins, as it prevents citrate synthase aggregation in a concentration-dependent manner. Equilibrium and kinetic experiments with Pa-CcmI*, or its isolated domains, with peptides mimicking portions of Pa-apoCyt sequence allow us to quantify the molecular details of the interaction between Pa-apoCyt and Pa-CcmI*. Binding experiments show that the interaction occurs at the level of the TPR domain and that the recognition is mediated mainly by the C-terminal sequence of Pa-apoCyt. The affinity of Pa-CcmI* to full-length Pa-apoCyt or to its C-terminal sequence is in the range expected for a component of a multi-protein complex, whose task is to receive the apoCyt and to deliver it to other components of the apoCyt:heme b ligation protein machinery.
Collapse
Affiliation(s)
- Eva Di Silvio
- Department of Biochemical Sciences, Università di Roma La Sapienza, Roma, Italy
| | | | | | | |
Collapse
|
48
|
Travaglini-Allocatelli C. Protein Machineries Involved in the Attachment of Heme to Cytochrome c: Protein Structures and Molecular Mechanisms. SCIENTIFICA 2013; 2013:505714. [PMID: 24455431 PMCID: PMC3884852 DOI: 10.1155/2013/505714] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 11/24/2013] [Indexed: 05/09/2023]
Abstract
Cytochromes c (Cyt c) are ubiquitous heme-containing proteins, mainly involved in electron transfer processes, whose structure and functions have been and still are intensely studied. Surprisingly, our understanding of the molecular mechanism whereby the heme group is covalently attached to the apoprotein (apoCyt) in the cell is still largely unknown. This posttranslational process, known as Cyt c biogenesis or Cyt c maturation, ensures the stereospecific formation of the thioether bonds between the heme vinyl groups and the cysteine thiols of the apoCyt heme binding motif. To accomplish this task, prokaryotic and eukaryotic cells have evolved distinctive protein machineries composed of different proteins. In this review, the structural and functional properties of the main maturation apparatuses found in gram-negative and gram-positive bacteria and in the mitochondria of eukaryotic cells will be presented, dissecting the Cyt c maturation process into three functional steps: (i) heme translocation and delivery, (ii) apoCyt thioreductive pathway, and (iii) apoCyt chaperoning and heme ligation. Moreover, current hypotheses and open questions about the molecular mechanisms of each of the three steps will be discussed, with special attention to System I, the maturation apparatus found in gram-negative bacteria.
Collapse
Affiliation(s)
- Carlo Travaglini-Allocatelli
- Department of Biochemical Sciences, University of Rome “Sapienza”, P.le A. Moro 5, 00185 Rome, Italy
- *Carlo Travaglini-Allocatelli:
| |
Collapse
|
49
|
Piek S, Kahler CM. A comparison of the endotoxin biosynthesis and protein oxidation pathways in the biogenesis of the outer membrane of Escherichia coli and Neisseria meningitidis. Front Cell Infect Microbiol 2012; 2:162. [PMID: 23267440 PMCID: PMC3526765 DOI: 10.3389/fcimb.2012.00162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 12/01/2012] [Indexed: 01/13/2023] Open
Abstract
The Gram-negative bacterial cell envelope consists of an inner membrane (IM) that surrounds the cytoplasm and an asymmetrical outer-membrane (OM) that forms a protective barrier to the external environment. The OM consists of lipopolysaccahride (LPS), phospholipids, outer membrane proteins (OMPs), and lipoproteins. Oxidative protein folding mediated by periplasmic oxidoreductases is required for the biogenesis of the protein components, mainly constituents of virulence determinants such as pili, flagella, and toxins, of the Gram-negative OM. Recently, periplasmic oxidoreductases have been implicated in LPS biogenesis of Escherichia coli and Neisseria meningitidis. Differences in OM biogenesis, in particular the transport pathways for endotoxin to the OM, the composition and role of the protein oxidation, and isomerization pathways and the regulatory networks that control them have been found in these two Gram-negative species suggesting that although form and function of the OM is conserved, the pathways required for the biosynthesis of the OM and the regulatory circuits that control them have evolved to suit the lifestyle of each organism.
Collapse
Affiliation(s)
- Susannah Piek
- Department of Pathology and Laboratory Medicine, The University of Western Australia Perth, WA, Australia
| | | |
Collapse
|
50
|
Zhou DH, Nieuwkoop AJ, Berthold DA, Comellas G, Sperling LJ, Tang M, Shah GJ, Brea EJ, Lemkau LR, Rienstra CM. Solid-state NMR analysis of membrane proteins and protein aggregates by proton detected spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2012; 54:291-305. [PMID: 22986689 PMCID: PMC3484199 DOI: 10.1007/s10858-012-9672-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 09/05/2012] [Indexed: 05/04/2023]
Abstract
Solid-state NMR has emerged as an important tool for structural biology and chemistry, capable of solving atomic-resolution structures for proteins in membrane-bound and aggregated states. Proton detection methods have been recently realized under fast magic-angle spinning conditions, providing large sensitivity enhancements for efficient examination of uniformly labeled proteins. The first and often most challenging step of protein structure determination by NMR is the site-specific resonance assignment. Here we demonstrate resonance assignments based on high-sensitivity proton-detected three-dimensional experiments for samples of different physical states, including a fully-protonated small protein (GB1, 6 kDa), a deuterated microcrystalline protein (DsbA, 21 kDa), a membrane protein (DsbB, 20 kDa) prepared in a lipid environment, and the extended core of a fibrillar protein (α-synuclein, 14 kDa). In our implementation of these experiments, including CONH, CO(CA)NH, CANH, CA(CO)NH, CBCANH, and CBCA(CO)NH, dipolar-based polarization transfer methods have been chosen for optimal efficiency for relatively high protonation levels (full protonation or 100 % amide proton), fast magic-angle spinning conditions (40 kHz) and moderate proton decoupling power levels. Each H-N pair correlates exclusively to either intra- or inter-residue carbons, but not both, to maximize spectral resolution. Experiment time can be reduced by at least a factor of 10 by using proton detection in comparison to carbon detection. These high-sensitivity experiments are especially important for membrane proteins, which often have rather low expression yield. Proton-detection based experiments are expected to play an important role in accelerating protein structure elucidation by solid-state NMR with the improved sensitivity and resolution.
Collapse
Affiliation(s)
- Donghua H. Zhou
- Department of Physics, Oklahoma State University, Stillwater, OK 74074, USA,
| | - Andrew J. Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
- Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Gemma Comellas
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Lindsay J. Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Gautam J. Shah
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Elliott J. Brea
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Luisel R. Lemkau
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| |
Collapse
|