1
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Papadopoulou D, Mavrikaki V, Charalampous F, Tzaferis C, Samiotaki M, Papavasileiou KD, Afantitis A, Karagianni N, Denis MC, Sanchez J, Lane JR, Faidon Brotzakis Z, Skretas G, Georgiadis D, Matralis AN, Kollias G. Discovery of the First-in-Class Inhibitors of Hypoxia Up-Regulated Protein 1 (HYOU1) Suppressing Pathogenic Fibroblast Activation. Angew Chem Int Ed Engl 2024; 63:e202319157. [PMID: 38339863 DOI: 10.1002/anie.202319157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/12/2024]
Abstract
Fibroblasts are key regulators of inflammation, fibrosis, and cancer. Targeting their activation in these complex diseases has emerged as a novel strategy to restore tissue homeostasis. Here, we present a multidisciplinary lead discovery approach to identify and optimize small molecule inhibitors of pathogenic fibroblast activation. The study encompasses medicinal chemistry, molecular phenotyping assays, chemoproteomics, bulk RNA-sequencing analysis, target validation experiments, and chemical absorption, distribution, metabolism, excretion and toxicity (ADMET)/pharmacokinetic (PK)/in vivo evaluation. The parallel synthesis employed for the production of the new benzamide derivatives enabled us to a) pinpoint key structural elements of the scaffold that provide potent fibroblast-deactivating effects in cells, b) discriminate atoms or groups that favor or disfavor a desirable ADMET profile, and c) identify metabolic "hot spots". Furthermore, we report the discovery of the first-in-class inhibitor leads for hypoxia up-regulated protein 1 (HYOU1), a member of the heat shock protein 70 (HSP70) family often associated with cellular stress responses, particularly under hypoxic conditions. Targeting HYOU1 may therefore represent a potentially novel strategy to modulate fibroblast activation and treat chronic inflammatory and fibrotic disorders.
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Affiliation(s)
- Dimitra Papadopoulou
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Vasiliki Mavrikaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Vari, 16672, Athens, Greece
- Department of Chemistry, Laboratory of Organic Chemistry, National and Kapodistrian University of Athens, 15784, Athens, Greece
| | - Filippos Charalampous
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Christos Tzaferis
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Konstantinos D Papavasileiou
- Department of ChemoInformatics, Novamechanics Ltd., 1070, Nicosia, Cyprus
- Department of Chemoinformatics, Novamechanics MIKE, 18545, Piraeus, Greece
- Division of Data Driven Innovation, Entelos Institute, 6059, Larnaca, Cyprus
| | - Antreas Afantitis
- Department of ChemoInformatics, Novamechanics Ltd., 1070, Nicosia, Cyprus
- Department of Chemoinformatics, Novamechanics MIKE, 18545, Piraeus, Greece
- Division of Data Driven Innovation, Entelos Institute, 6059, Larnaca, Cyprus
| | | | | | - Julie Sanchez
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, NG7 2UH, Nottingham, U.K
- Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, NG2 7AG, Midlands, U.K
| | - J Robert Lane
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, NG7 2UH, Nottingham, U.K
- Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, NG2 7AG, Midlands, U.K
| | - Zacharias Faidon Brotzakis
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, U.K
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Georgios Skretas
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635, Athens, Greece
| | - Dimitris Georgiadis
- Department of Chemistry, Laboratory of Organic Chemistry, National and Kapodistrian University of Athens, 15784, Athens, Greece
| | - Alexios N Matralis
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - George Kollias
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece
- Research Institute of New Biotechnologies and Precision Medicine, National and Kapodistrian University of Athens, 11527, Athens, Greece
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2
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Vasilopoulou E, Chroumpi T, Skretas G. Escherichia coli strains with precise domain deletions in the ribonuclease RNase E can achieve greatly enhanced levels of membrane protein production. Protein Sci 2024; 33:e4864. [PMID: 38073126 PMCID: PMC10804669 DOI: 10.1002/pro.4864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 01/26/2024]
Abstract
Escherichia coli is one of the most widely utilized hosts for production of recombinant membrane proteins (MPs). Bacterial MP production, however, is usually accompanied by severe toxicity and low-level volumetric accumulation. In previous work, we had discovered that co-expression of RraA, an inhibitor of the RNA-degrading activity of RNase E, can efficiently suppress the cytotoxicity associated with the MP overexpression process and, simultaneously, enhance significantly the cellular accumulation of membrane-incorporated recombinant MPs in bacteria. Based on this, we constructed the specialized MP-producing E. coli strain SuptoxR, which can achieve dramatically enhanced volumetric yields of well-folded recombinant MPs. Ιn the present work, we have investigated whether domain deletions in the E. coli RNase E, which exhibit reduced ribonucleolytic activity, can result in suppressed MP-induced toxicity and enhanced recombinant MP production, in a manner resembling the conditions of rraA overexpression in E. coli SuptoxR. We have found that some strains encoding specific RNase E truncation variants can achieve significantly enhanced levels of recombinant MP production. Among these, we have found a single RNase E variant strain, which can efficiently suppress MP-induced toxicity and achieve greatly enhanced levels of recombinant MP production for proteins of both prokaryotic and eukaryotic origin. Based on its properties, and in analogy to the original SuptoxR strain, we have termed this strain SuptoxRNE22. E. coli SuptoxRNE22 can perform better than commercially available bacterial strains, which are frequently utilized for recombinant MP production. We anticipate that SuptoxRNE22 will become a widely utilized host for recombinant MP production in bacteria.
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Affiliation(s)
- Eleni Vasilopoulou
- Institute for Bio‐innovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
- Institute of Chemical Biology, National Hellenic Research FoundationAthensGreece
- Department of Biochemistry and BiotechnologyUniversity of ThessalyLarisaGreece
| | - Tania Chroumpi
- Institute of Chemical Biology, National Hellenic Research FoundationAthensGreece
| | - Georgios Skretas
- Institute for Bio‐innovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
- Institute of Chemical Biology, National Hellenic Research FoundationAthensGreece
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3
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Papanikolaou A, Chatzikonstantinou AV, Zarafeta D, Kourkoumelis N, Skretas G, Pavlidis ΙV, Stamatis H. Substrate Specificity of the Highly Thermostable Esterase EstDZ3. Chembiochem 2023; 24:e202200642. [PMID: 36545817 DOI: 10.1002/cbic.202200642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
Esterases are among the most studied enzymes, and their applications expand into several branches of industrial biotechnology. Yet, despite the fact that information on their substrate specificity is crucial for selecting or designing the best fitted biocatalyst for the desired application, it cannot be predicted from their amino acid sequence. In this work, we studied the substrate scope of the newly discovered hydrolytic extremozyme, EstDZ3, against a library of esters with variable carbon chain lengths in an effort to understand the crucial amino acids for the substrate selectivity of this enzyme. EstDZ3 appears to be active against a wide range of esters with high selectivity towards medium- to long-carbon chain vinyl esters. In-silico studies of its 3D structure revealed that the selectivity might arise from the mainly hydrophobic nature of the active site's environment.
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Affiliation(s)
- Angelos Papanikolaou
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110, Ioannina, Greece
| | - Alexandra V Chatzikonstantinou
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110, Ioannina, Greece
| | - Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635, Athens, Greece
| | - Nikolaos Kourkoumelis
- Department of Medical Physics, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635, Athens, Greece.,Institute for Bio-innovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Vari, Greece
| | - Ιoannis V Pavlidis
- Department of Chemistry, University of Crete Voutes, University Campus, 70013, Heraklion, Greece
| | - Haralambos Stamatis
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110, Ioannina, Greece
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4
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Vasilopoulou E, Giannakopoulou A, Kapsalis C, Michou M, Michoglou-Sergiou A, Kolisis FN, Skretas G. Second-Generation Escherichia coli SuptoxR Strains for High-Level Recombinant Membrane Protein Production. ACS Synth Biol 2022; 11:2599-2609. [PMID: 35922033 PMCID: PMC9397408 DOI: 10.1021/acssynbio.1c00598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli is one of the most widely utilized hosts for recombinant protein production, including that of membrane proteins (MPs). We have recently engineered a specialized E. coli strain for enhanced recombinant MP production, termed SuptoxR. By appropriately co-expressing the effector gene rraA, SuptoxR can suppress the high toxicity, which is frequently observed during the MP-overexpression process, and, at the same time, enhance significantly the cellular accumulation of membrane-incorporated and properly folded recombinant MP. The combination of these two beneficial effects results in dramatically enhanced volumetric yields for various prokaryotic and eukaryotic MPs. Here, we engineered second-generation SuptoxR strains with further improved properties, so that they can achieve even higher levels of recombinant MP production. We searched for naturally occurring RraA variants with similar or improved MP toxicity-suppressing and production-promoting effects to that of the native E. coli RraA of the original SuptoxR strain. We found that the RraA proteins from Proteus mirabilis and Providencia stuartii can be even more potent enhancers of MP productivity than the E. coli RraA. By exploiting these two newly identified RraAs, we constructed two second-generation SuptoxR strains, termed SuptoxR2.1 and SuptoxR2.2, whose MP-production capabilities often surpass those of the original SuptoxR significantly. SuptoxR2.1 and SuptoxR2.2 are expected to become widely useful expression hosts for recombinant MP production in bacteria.
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Affiliation(s)
- Eleni Vasilopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Larisa 41500, Greece
| | - Artemis Giannakopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Charalampos Kapsalis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Myrsini Michou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Larisa 41500, Greece
| | | | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15772, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
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5
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Delivoria DC, Skretas G. The Discovery of Peptide Macrocycle Rescuers of Pathogenic Protein Misfolding and Aggregation by Integrating SICLOPPS Technology and Ultrahigh-Throughput Screening in Bacteria. Methods Mol Biol 2022; 2371:215-246. [PMID: 34596851 DOI: 10.1007/978-1-0716-1689-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The phenomenon of protein misfolding and aggregation has been widely associated with numerous human diseases, such as Alzheimer's disease, systemic amyloidosis and type 2 diabetes, the vast majority of which remain incurable. To advance early stage drug discovery against these diseases, investigation of molecular libraries with expanded diversities and ultrahigh-throughput screening methodologies that allow deeper investigation of chemical space are urgently required. Toward this, we describe how Escherichia coli can be engineered so as to enable (1) the production of expanded combinatorial libraries of short, drug-like, head-to-tail cyclic peptides and (2) their simultaneous functional screening for identifying effective inhibitors of protein misfolding and aggregation using a genetic assay that links protein folding and misfolding to cell fluorescence. In this manner, cyclic peptides with the ability to inhibit pathogenic protein misfolding and/or aggregation can be readily selected by flow cytometric cell sorting in an ultrahigh-throughput fashion. This biotechnological approach accelerates significantly the identification of hit/lead molecules with potentially therapeutic properties against devastating diseases.
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Affiliation(s)
- Dafni C Delivoria
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.
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6
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Skretas G, Ventura S. Editorial: Protein Aggregation and Solubility in Microorganisms (Archaea, Bacteria and Unicellular Eukaryotes): Implications and Applications. Front Microbiol 2020; 11:620239. [PMID: 33329506 PMCID: PMC7734127 DOI: 10.3389/fmicb.2020.620239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Salvador Ventura
- Departament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
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7
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Myrtollari K, Katsoulakis N, Zarafeta D, Pavlidis IV, Skretas G, Smonou I. Activity and specificity studies of the new thermostable esterase EstDZ2. Bioorg Chem 2020; 104:104214. [PMID: 32927128 DOI: 10.1016/j.bioorg.2020.104214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/23/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
In this paper, we study the activity and specificity of EstDZ2, a new thermostable carboxyl esterase of unknown function, which was isolated from a metagenome library from a Russian hot spring. The biocatalytic reaction employing EstDZ2 proved to be an efficient method for the hydrolysis of aryl p-, o- or m-substituted esters of butyric acid and esters of secondary alcohols. Docking studies revealed structural features of the enzyme that led to activity differences among the different substrates.
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Affiliation(s)
- Kamela Myrtollari
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece
| | - Nikolaos Katsoulakis
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece
| | - Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Ioannis V Pavlidis
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Ioulia Smonou
- Department of Chemistry, University of Crete, University Campus-Voutes, 70013 Heraklion, Crete, Greece.
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8
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Michou M, Delivoria DC, Skretas G. High-level Production of Recombinant Membrane Proteins Using the Engineered Escherichia coli Strains SuptoxD and SuptoxR. Bio Protoc 2020; 10:e3710. [PMID: 33659374 DOI: 10.21769/bioprotoc.3710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/25/2020] [Accepted: 06/21/2020] [Indexed: 11/02/2022] Open
Abstract
We have previously described the development of two specialized Escherichia coli strains for high-level recombinant membrane protein (MP) production. These engineered strains, termed SuptoxD and SuptoxR, are capable of suppressing the cytotoxicity caused by MP overexpression and of producing greatly enhanced MP yields. Here, we present a Bio-protocol that describes gene overexpression and culturing conditions that maximize the accumulation of membrane-integrated and well-folded recombinant MPs in these strains.
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Affiliation(s)
- Myrsini Michou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Larisa 41500, Greece
| | - Dafni C Delivoria
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
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9
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Michou M, Stergios A, Skretas G. SuptoxD2.0: A second-generation engineered Escherichia coli strain achieving further enhanced levels of recombinant membrane protein production. Biotechnol Bioeng 2020; 117:2434-2445. [PMID: 32383198 DOI: 10.1002/bit.27378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 11/10/2022]
Abstract
The bacterium Escherichia coli is among the most popular hosts for recombinant protein production, including that of membrane proteins (MPs). We have recently generated the specialized MP-producing E. coli strain SuptoxD, which upon co-expression of the effector gene djlA, is capable of alleviating two major bottlenecks in bacterial recombinant MP production: it suppresses the toxicity that frequently accompanies the MP-overexpression process and it markedly increases the cellular accumulation of membrane incorporated and properly folded recombinant MP. Combined, these two positive effects result in dramatically enhanced volumetric yields for various recombinant MPs of both prokaryotic and eukaryotic origin. Based on the observation that djlA is found in the genomes of various pathogenic bacteria, the aim of the present work was to investigate (a) whether other naturally occurring DjlA variants can exert the MP toxicity-suppressing and production-promoting effects similarly to the E. coli DjlA and (b) if we can identify a DjlA variant whose efficiency surpasses that of the E. coli DjlA of SuptoxD. We report that a quite surprisingly broad variety of homologous DjlA proteins exert beneficial effects on recombinant MP when overexpressed in E. coli. Furthermore, we demonstrate that the Salmonella enterica DjlA is an even more potent enhancer of MP productivity compared with the E. coli DjlA of SuptoxD. Based on this, we constructed a second-generation SuptoxD strain, termed SuptoxD2.0, whose MP-production capabilities surpass significantly those of the original SuptoxD, and we anticipate that SuptoxD2.0 will become a broadly utilized expression host for recombinant MP production in bacteria.
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Affiliation(s)
- Myrsini Michou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, Greece
| | - Angelos Stergios
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
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10
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Zarafeta D, Galanopoulou AP, Leni ME, Kaili SI, Chegkazi MS, Chrysina ED, Kolisis FN, Hatzinikolaou DG, Skretas G. XynDZ5: A New Thermostable GH10 Xylanase. Front Microbiol 2020; 11:545. [PMID: 32390953 PMCID: PMC7193231 DOI: 10.3389/fmicb.2020.00545] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
Xylanolytic enzymes have a broad range of applications in industrial biotechnology as biocatalytic components of various processes and products, such as food additives, bakery products, coffee extraction, agricultural silage and functional foods. An increasing market demand has driven the growing interest for the discovery of xylanases with specific industrially relevant characteristics, such as stability at elevated temperatures and in the presence of other denaturing factors, which will facilitate their incorporation into industrial processes. In this work, we report the discovery and biochemical characterization of a new thermostable GH10 xylanase, termed XynDZ5, exhibiting only 26% amino acid sequence identity to the closest characterized xylanolytic enzyme. This new enzyme was discovered in an Icelandic hot spring enrichment culture of a Thermoanaerobacterium species using a recently developed bioinformatic analysis platform. XynDZ5 was produced recombinantly in Escherichia coli, purified and characterized biochemically. This analysis revealed that it acts as an endo-1,4-β-xylanase that performs optimally at 65–75°C and pH 7.5. The enzyme is capable of retaining high levels of catalytic efficiency after several hours of incubation at high temperatures, as well as in the presence of significant concentrations of a range of metal ions and denaturing agents. Interestingly, the XynDZ5 biochemical profile was found to be atypical, as it also exhibits significant exo-activity. Computational modeling of its three-dimensional structure predicted a (β/α)8 TIM barrel fold, which is very frequently encountered among family GH10 enzymes. This modeled structure has provided clues about structural features that may explain aspects of its catalytic performance. Our results suggest that XynDZ5 represents a promising new candidate biocatalyst appropriate for several high-temperature biotechnological applications in the pulp, paper, baking, animal-feed and biofuel industries.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia P Galanopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Evangelia Leni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Stavroula I Kaili
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Magda S Chegkazi
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitris G Hatzinikolaou
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
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11
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Delivoria DC, Chia S, Habchi J, Perni M, Matis I, Papaevgeniou N, Reczko M, Chondrogianni N, Dobson CM, Vendruscolo M, Skretas G. Bacterial production and direct functional screening of expanded molecular libraries for discovering inhibitors of protein aggregation. Sci Adv 2019; 5:eaax5108. [PMID: 31663025 PMCID: PMC6795521 DOI: 10.1126/sciadv.aax5108] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 09/25/2019] [Indexed: 05/17/2023]
Abstract
Protein misfolding and aggregation are associated with a many human disorders, including Alzheimer's and Parkinson's diseases. Toward increasing the effectiveness of early-stage drug discovery for these conditions, we report a bacterial platform that enables the biosynthesis of molecular libraries with expanded diversities and their direct functional screening for discovering protein aggregation inhibitors. We illustrate this approach by performing, what is to our knowledge, the largest functional screen of small-size molecular entities described to date. We generated a combinatorial library of ~200 million drug-like, cyclic peptides and rapidly screened it for aggregation inhibitors against the amyloid-β peptide (Aβ42), linked to Alzheimer's disease. Through this procedure, we identified more than 400 macrocyclic compounds that efficiently reduce Aβ42 aggregation and toxicity in vitro and in vivo. Finally, we applied a combination of deep sequencing and mutagenesis analyses to demonstrate how this system can rapidly determine structure-activity relationships and define consensus motifs required for bioactivity.
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Affiliation(s)
- Dafni C. Delivoria
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece
| | - Sean Chia
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Johnny Habchi
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Ilias Matis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Nikoletta Papaevgeniou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- Faculty of Biology and Pharmacy, Institute of Nutrition, Friedrich Schiller University of Jena, Jena 07743, Germany
| | - Martin Reczko
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center “Alexander Fleming,” Athens 16672, Greece
| | - Niki Chondrogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- Corresponding author.
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12
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Michou M, Kapsalis C, Pliotas C, Skretas G. Optimization of Recombinant Membrane Protein Production in the Engineered Escherichia coli Strains SuptoxD and SuptoxR. ACS Synth Biol 2019; 8:1631-1641. [PMID: 31243979 DOI: 10.1021/acssynbio.9b00120] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins (MPs) execute a wide variety of critical biological functions in all living organisms and constitute approximately half of current targets for drug discovery. As in the case of soluble proteins, the bacterium Escherichia coli has served as a very popular overexpression host for biochemical/structural studies of membrane proteins as well. Bacterial recombinant membrane protein production, however, is typically hampered by poor cellular accumulation and severe toxicity for the host, which leads to low levels of final biomass and minute volumetric yields. In previous work, we generated the engineered E. coli strains SuptoxD and SuptoxR, which upon coexpression of the effector genes djlA or rraA, respectively, can suppress the cytotoxicity caused by MP overexpression and produce enhanced MP yields. Here, we systematically looked for gene overexpression and culturing conditions that maximize the accumulation of membrane-integrated and well-folded recombinant MPs in these strains. We have found that, under optimal conditions, SuptoxD and SuptoxR achieve greatly enhanced recombinant production for a variety of MP, irrespective of their archaeal, eubacterial, or eukaryotic origin. Furthermore, we demonstrate that the use of these engineered strains enables the production of well-folded recombinant MPs of high quality and at high yields, which are suitable for functional and structural studies. We anticipate that SuptoxD and SuptoxR will become broadly utilized expression hosts for recombinant MP production in bacteria.
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Affiliation(s)
- Myrsini Michou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Larisa 41500, Greece
| | - Charalampos Kapsalis
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY169ST, United Kingdom
| | - Christos Pliotas
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY169ST, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
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13
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Koutsandreas T, Ladoukakis E, Pilalis E, Zarafeta D, Kolisis FN, Skretas G, Chatziioannou AA. ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data. Front Genet 2019; 10:469. [PMID: 31178894 PMCID: PMC6543708 DOI: 10.3389/fgene.2019.00469] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/01/2019] [Indexed: 01/27/2023] Open
Abstract
Metagenomic analysis of environmental samples provides deep insight into the enzymatic mixture of the corresponding niches, capable of revealing peptide sequences with novel functional properties exploiting the high performance of next-generation sequencing (NGS) technologies. At the same time due to their ever increasing complexity, there is a compelling need for ever larger computational configurations to ensure proper bioinformatic analysis, and fine annotation. With the aiming to address the challenges of such an endeavor, we have developed a novel web-based application named ANASTASIA (automated nucleotide aminoacid sequences translational plAtform for systemic interpretation and analysis). ANASTASIA provides a rich environment of bioinformatic tools, either publicly available or novel, proprietary algorithms, integrated within numerous automated algorithmic workflows, and which enables versatile data processing tasks for (meta)genomic sequence datasets. ANASTASIA was initially developed in the framework of the European FP7 project HotZyme, whose aim was to perform exhaustive analysis of metagenomes derived from thermal springs around the globe and to discover new enzymes of industrial interest. ANASTASIA has evolved to become a stable and extensible environment for diversified, metagenomic, functional analyses for a range of applications overarching industrial biotechnology to biomedicine, within the frames of the ELIXIR-GR project. As a showcase, we report the successful in silico mining of a novel thermostable esterase termed “EstDZ4” from a metagenomic sample collected from a hot spring located in Krisuvik, Iceland.
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Affiliation(s)
- Theodoros Koutsandreas
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, Athens, Greece
| | - Efthymios Ladoukakis
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Eleftherios Pilalis
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, Athens, Greece
| | - Dimitra Zarafeta
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis A Chatziioannou
- Institute of Chemical Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, Athens, Greece
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14
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Kostelidou K, Matis I, Skretas G. Microbial Genetic Screens for Monitoring Protein Misfolding Associated with Neurodegeneration: Tools for Identifying Disease-Relevant Genes and for Screening Synthetic and Natural Compound Libraries for the Discovery of Potential Therapeutics. Curr Pharm Des 2018; 24:2055-2075. [DOI: 10.2174/1381612824666180515143752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/02/2018] [Accepted: 05/11/2018] [Indexed: 11/22/2022]
Abstract
Neurodegenerative Diseases (ND) are a major threat to the aging population and the lack of a single
preventive or disease-modifying agent only serves to increase their impact. In the past few years, protein misfolding
and the subsequent formation of neurotoxic oligomeric/aggregated protein species have emerged as a unifying
theme underlying the pathology of these complex diseases. Recently developed microbial genetic screens and
selection systems for monitoring ND-associated protein misfolding have allowed the establishment of highthroughput
assays for the identification of cellular factors and processes that are important mediators of NDassociated
proteotoxicities. In addition, such systems have facilitated the discovery of synthetic and natural compounds
with the ability to rescue the misfolding and the associated pathogenic effects of aggregation-prone proteins
associated with NDs. This review outlines such available systems in bacteria and yeast, whose usage will
likely accelerate the pre-clinical discovery process for effective drugs against a variety of NDs with high socioeconomic
impact.
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Affiliation(s)
- Kalliopi Kostelidou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 11635 Athens, Greece
| | - Ilias Matis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 11635 Athens, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 11635 Athens, Greece
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15
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Matis I, Delivoria DC, Mavroidi B, Papaevgeniou N, Panoutsou S, Bellou S, Papavasileiou KD, Linardaki ZI, Stavropoulou AV, Vekrellis K, Boukos N, Kolisis FN, Gonos ES, Margarity M, Papadopoulos MG, Efthimiopoulos S, Pelecanou M, Chondrogianni N, Skretas G. Publisher Correction: An integrated bacterial system for the discovery of chemical rescuers of disease-associated protein misfolding. Nat Biomed Eng 2018; 2:49. [PMID: 31015658 DOI: 10.1038/s41551-017-0164-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this Article originally published, in Fig. 1c-e, on the x axes, the lines labelled 'Aβ42' and 'Aβ42(F19S;L34P)' grouped the data incorrectly; the line labelled Aβ42 should have grouped the data for Random 1-2 and Clones 1-10, and the line labelled Aβ42(F19S;L34P) should have only grouped the data for Random 1-2 on the right end of the plots and blots. These figures have now been corrected in all versions of the Article.
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Affiliation(s)
- Ilias Matis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,School of Chemical Engineering, National Technical University of Athens, 15780, Athens, Greece
| | - Dafni Chrysanthi Delivoria
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,School of Chemical Engineering, National Technical University of Athens, 15780, Athens, Greece
| | - Barbara Mavroidi
- Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310, Athens, Greece
| | - Nikoletta Papaevgeniou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,Faculty of Biology and Pharmacy, Institute of Nutrition, Friedrich Schiller University of Jena, 07743, Jena, Germany
| | - Stefania Panoutsou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,Department of Biology, National and Kapodistrian University of Athens, 15701, Athens, Greece
| | - Stamatia Bellou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece
| | - Konstantinos D Papavasileiou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", 15310, Athens, Greece
| | - Zacharoula I Linardaki
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,Department of Biology, University of Patras, 26504, Patras, Greece
| | | | - Kostas Vekrellis
- Department of Neuroscience, Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Nikos Boukos
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", 15310, Athens, Greece
| | - Fragiskos N Kolisis
- School of Chemical Engineering, National Technical University of Athens, 15780, Athens, Greece
| | - Efstathios S Gonos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,Medical School, Örebro University, 70182, Örebro, Sweden
| | | | - Manthos G Papadopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece
| | - Spiros Efthimiopoulos
- Department of Biology, National and Kapodistrian University of Athens, 15701, Athens, Greece
| | - Maria Pelecanou
- Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310, Athens, Greece
| | - Niki Chondrogianni
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.
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16
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Matis I, Delivoria DC, Mavroidi B, Papaevgeniou N, Panoutsou S, Bellou S, Papavasileiou KD, Linardaki ZI, Stavropoulou AV, Vekrellis K, Boukos N, Kolisis FN, Gonos ES, Margarity M, Papadopoulos MG, Efthimiopoulos S, Pelecanou M, Chondrogianni N, Skretas G. An integrated bacterial system for the discovery of chemical rescuers of disease-associated protein misfolding. Nat Biomed Eng 2017; 1:838-852. [DOI: 10.1038/s41551-017-0144-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/06/2017] [Indexed: 01/31/2023]
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17
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Gialama D, Delivoria DC, Michou M, Giannakopoulou A, Skretas G. Functional Requirements for DjlA- and RraA-Mediated Enhancement of Recombinant Membrane Protein Production in the Engineered Escherichia coli Strains SuptoxD and SuptoxR. J Mol Biol 2017; 429:1800-1816. [PMID: 28501587 DOI: 10.1016/j.jmb.2017.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 04/30/2017] [Accepted: 05/04/2017] [Indexed: 12/17/2022]
Abstract
In previous work, we have generated the engineered Escherichia coli strains SuptoxD and SuptoxR, which upon co-expression of the effector genes djlA or rraA, respectively, are capable of suppressing the cytotoxicity caused by membrane protein (MP) overexpression and of producing dramatically enhanced yields for a variety of recombinant MPs of both prokaryotic and eukaryotic origin. Here, we investigated the functional requirements for DnaJ-like protein A (DjlA)- and regulator of ribonuclease activity A (RraA)-mediated enhancement of recombinant MP production in these strains and show that: (i) DjlA and RraA act independently, that is, the beneficial effects of each protein on recombinant MP production occur through a mechanism that does not involve the other, and in a non-additive manner; (ii) full-length and membrane-bound DjlA is required for exerting its beneficial effects on recombinant MP production in E. coli SuptoxD; (iii) the MP production-promoting properties of DjlA in SuptoxD involve the action of the molecular chaperone DnaK but do not rely on the activation of the regulation of capsular synthesis response, a well-established consequence of djlA overexpression; (iv) the observed RraA-mediated effects in E. coli SuptoxR involve the ribonucleolytic activity of RNase E, but not that of its paralogous ribonuclease RNase G; and (v) DjlA and RraA are unique among similar E. coli proteins in their ability to promote bacterial recombinant MP production. These observations provide important clues about the molecular requirements for suppressed toxicity and enhanced MP accumulation in SuptoxD/SuptoxR and will guide future studies aiming to decipher the exact mechanism of DjlA- and RraA-mediated enhancement of recombinant MP production in these strains.
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Affiliation(s)
- Dimitra Gialama
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece; Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
| | - Dafni Chrysanthi Delivoria
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece; Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
| | - Myrsini Michou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece; Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, 41500, Greece
| | - Artemis Giannakopoulou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece.
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18
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Gialama D, Kostelidou K, Michou M, Delivoria DC, Kolisis FN, Skretas G. Development of Escherichia coli Strains That Withstand Membrane Protein-Induced Toxicity and Achieve High-Level Recombinant Membrane Protein Production. ACS Synth Biol 2017; 6:284-300. [PMID: 27797488 DOI: 10.1021/acssynbio.6b00174] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane proteins perform critical cellular functions in all living organisms and constitute major targets for drug discovery. Escherichia coli has been the most popular overexpression host for membrane protein biochemical/structural studies. Bacterial production of recombinant membrane proteins, however, is typically hampered by poor cellular accumulation and severe toxicity for the host, which leads to low final biomass and minute volumetric yields. In this work, we aimed to rewire the E. coli protein-producing machinery to withstand the toxicity caused by membrane protein overexpression in order to generate engineered bacterial strains with the ability to achieve high-level membrane protein production. To achieve this, we searched for bacterial genes whose coexpression can suppress membrane protein-induced toxicity and identified two highly potent effectors: the membrane-bound DnaK cochaperone DjlA, and the inhibitor of the mRNA-degrading activity of the E. coli RNase E, RraA. E. coli strains coexpressing either djlA or rraA, termed SuptoxD and SuptoxR, respectively, accumulated markedly higher levels of final biomass and produced dramatically enhanced yields for a variety of prokaryotic and eukaryotic recombinant membrane proteins. In all tested cases, either SuptoxD, or SuptoxR, or both, outperformed the capabilities of commercial strains frequently utilized for recombinant membrane protein production purposes.
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Affiliation(s)
- Dimitra Gialama
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
- Laboratory
of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece
| | - Kalliopi Kostelidou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Myrsini Michou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Dafni Chrysanthi Delivoria
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
- Laboratory
of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece
| | - Fragiskos N. Kolisis
- Laboratory
of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens 11635, Greece
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19
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Zarafeta D, Moschidi D, Ladoukakis E, Gavrilov S, Chrysina ED, Chatziioannou A, Kublanov I, Skretas G, Kolisis FN. Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. Sci Rep 2016; 6:38886. [PMID: 27991516 PMCID: PMC5171882 DOI: 10.1038/srep38886] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/14/2016] [Indexed: 11/09/2022] Open
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Evangelia D. Chrysina
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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20
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Zarafeta D, Szabo Z, Moschidi D, Phan H, Chrysina ED, Peng X, Ingham CJ, Kolisis FN, Skretas G. EstDZ3: A New Esterolytic Enzyme Exhibiting Remarkable Thermostability. Front Microbiol 2016; 7:1779. [PMID: 27899916 PMCID: PMC5110521 DOI: 10.3389/fmicb.2016.01779] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/24/2016] [Indexed: 11/25/2022] Open
Abstract
Lipolytic enzymes that retain high levels of catalytic activity when exposed to a variety of denaturing conditions are of high importance for a number of biotechnological applications. In this study, we aimed to identify new lipolytic enzymes, which are highly resistant to prolonged exposure to elevated temperatures. To achieve this, we searched for genes encoding for such proteins in the genomes of a microbial consortium residing in a hot spring located in China. After performing functional genomic screening on a bacterium of the genus Dictyoglomus, which was isolated from this hot spring following in situ enrichment, we identified a new esterolytic enzyme, termed EstDZ3. Detailed biochemical characterization of the recombinant enzyme, revealed that it constitutes a slightly alkalophilic and highly active esterase against esters of fatty acids with short to medium chain lengths. Importantly, EstDZ3 exhibits remarkable thermostability, as it retains high levels of catalytic activity after exposure to temperatures as high as 95°C for several hours. Furthermore, it exhibits very good stability against exposure to high concentrations of a variety of organic solvents. Interestingly, EstDZ3 was found to have very little similarity to previously characterized esterolytic enzymes. Computational modeling of the three-dimensional structure of this new enzyme predicted that it exhibits a typical α/β hydrolase fold that seems to include a “subdomain insertion”, which is similar to the one present in its closest homolog of known function and structure, the cinnamoyl esterase Lj0536 from Lactobacillus johnsonii. As it was found in the case of Lj0536, this structural feature is expected to be an important determinant of the catalytic properties of EstDZ3. The high levels of esterolytic activity of EstDZ3, combined with its remarkable thermostability and good stability against a range of organic solvents and other denaturing agents, render this new enzyme a candidate biocatalyst for high-temperature biotechnological applications.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research FoundationAthens, Greece; Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of AthensAthens, Greece
| | | | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Hien Phan
- Danish Archaea Centre, Department of Biology, Copenhagen University Copenhagen, Denmark
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation Athens, Greece
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, Copenhagen University Copenhagen, Denmark
| | | | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation Athens, Greece
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21
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Zarafeta D, Kissas D, Sayer C, Gudbergsdottir SR, Ladoukakis E, Isupov MN, Chatziioannou A, Peng X, Littlechild JA, Skretas G, Kolisis FN. Discovery and Characterization of a Thermostable and Highly Halotolerant GH5 Cellulase from an Icelandic Hot Spring Isolate. PLoS One 2016; 11:e0146454. [PMID: 26741138 PMCID: PMC4704807 DOI: 10.1371/journal.pone.0146454] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/17/2015] [Indexed: 12/20/2022] Open
Abstract
With the ultimate goal of identifying robust cellulases for industrial biocatalytic conversions, we have isolated and characterized a new thermostable and very halotolerant GH5 cellulase. This new enzyme, termed CelDZ1, was identified by bioinformatic analysis from the genome of a polysaccharide-enrichment culture isolate, initiated from material collected from an Icelandic hot spring. Biochemical characterization of CelDZ1 revealed that it is a glycoside hydrolase with optimal activity at 70°C and pH 5.0 that exhibits good thermostability, high halotolerance at near-saturating salt concentrations, and resistance towards metal ions and other denaturing agents. X-ray crystallography of the new enzyme showed that CelDZ1 is the first reported cellulase structure that lacks the defined sugar-binding 2 subsite and revealed structural features which provide potential explanations of its biochemical characteristics.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitrios Kissas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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22
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Gialama D, Kolisis F, Skretas G. Making life better for Escherichia coli cells that produce toxic membrane proteins. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.1745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Skretas G, Delivoria D, Matis I, Papaevgeniou N, Chondrogianni N. Engineering bacteria for the discovery of potential therapeutic compounds against protein misfolding diseases. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.1640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zarafeta D, Skretas G, Kolisis FN. Discovery of thermostable hydrolytic enzymes of industrial interest by metagenomic screening. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.2043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Skretas G, Kolisis FN. Combinatorial approaches for inverse metabolic engineering applications. Comput Struct Biotechnol J 2013; 3:e201210021. [PMID: 24688681 PMCID: PMC3962077 DOI: 10.5936/csbj.201210021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 02/11/2013] [Accepted: 02/17/2013] [Indexed: 11/22/2022] Open
Abstract
Traditional metabolic engineering analyzes biosynthetic and physiological pathways, identifies bottlenecks, and makes targeted genetic modifications with the ultimate goal of increasing the production of high-value products in living cells. Such efforts have led to the development of a variety of organisms with industrially relevant properties. However, there are a number of cellular phenotypes important for research and the industry for which the rational selection of cellular targets for modification is not easy or possible. In these cases, strain engineering can be alternatively carried out using “inverse metabolic engineering”, an approach that first generates genetic diversity by subjecting a population of cells to a particular mutagenic process, and then utilizes genetic screens or selections to identify the clones exhibiting the desired phenotype. Given the availability of an appropriate screen for a particular property, the success of inverse metabolic engineering efforts usually depends on the level and quality of genetic diversity which can be generated. Here, we review classic and recently developed combinatorial approaches for creating such genetic diversity and discuss the use of these methodologies in inverse metabolic engineering applications.
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Affiliation(s)
- Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens - Zografou Campus, Athens, Greece
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Skretas G, Makino T, Varadarajan N, Pogson M, Georgiou G. Multi-Copy Genes that Enhance the Yield of Mammalian G Protein-Coupled Receptors in Escherichia coli. N Biotechnol 2012. [DOI: 10.1016/j.nbt.2012.08.406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Skretas G, Makino T, Varadarajan N, Pogson M, Georgiou G. Multi-copy genes that enhance the yield of mammalian G protein-coupled receptors in Escherichia coli. Metab Eng 2012; 14:591-602. [PMID: 22609824 DOI: 10.1016/j.ymben.2012.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 04/18/2012] [Accepted: 05/07/2012] [Indexed: 01/01/2023]
Abstract
Low yields of recombinant expression represent a major barrier to the physical characterization of membrane proteins. Here, we have identified genes that globally enhance the production of properly folded G protein-coupled receptors (GPCRs) in Escherichia coli. Libraries of bacterial chromosomal fragments were screened using two separate systems that monitor: (i) elevated fluorescence conferred by enhanced expression of GPCR-GFP fusions and (ii) increased binding of fluorescent ligand in cells producing more active receptor. Three multi-copy hits were isolated by both methods: nagD, encoding the ribonucleotide phosphatase NagD; a fragment of nlpD, encoding a truncation of the predicted lipoprotein NlpD, and the three-gene cluster ptsN-yhbJ-npr, encoding three proteins of the nitrogen phosphotransferase system. Expression of these genes resulted in a 3- to 10-fold increase in the yields of different mammalian GPCRs. Our data is consistent with the hypothesis that the expression of these genes may serve to maintain the integrity of the bacterial periplasm and to provide a favorable environment for proper membrane protein folding, possibly by inducing a fine-tuned stress response and/or via modifying the composition of the bacterial cell envelope.
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Affiliation(s)
- Georgios Skretas
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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Makino T, Skretas G, Georgiou G. Strain engineering for improved expression of recombinant proteins in bacteria. Microb Cell Fact 2011; 10:32. [PMID: 21569582 PMCID: PMC3120638 DOI: 10.1186/1475-2859-10-32] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/14/2011] [Indexed: 01/17/2023] Open
Abstract
Protein expression in Escherichia coli represents the most facile approach for the preparation of non-glycosylated proteins for analytical and preparative purposes. So far, the optimization of recombinant expression has largely remained a matter of trial and error and has relied upon varying parameters, such as expression vector, media composition, growth temperature and chaperone co-expression. Recently several new approaches for the genome-scale engineering of E. coli to enhance recombinant protein expression have been developed. These methodologies now enable the generation of optimized E. coli expression strains in a manner analogous to metabolic engineering for the synthesis of low-molecular-weight compounds. In this review, we provide an overview of strain engineering approaches useful for enhancing the expression of hard-to-produce proteins, including heterologous membrane proteins.
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Affiliation(s)
- Tomohiro Makino
- Department of Chemical Engineering, The University of Texas at Austin, 78712, USA
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Makino T, Skretas G, Kang TH, Georgiou G. Comprehensive engineering of Escherichia coli for enhanced expression of IgG antibodies. Metab Eng 2010; 13:241-51. [PMID: 21130896 DOI: 10.1016/j.ymben.2010.11.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 09/29/2010] [Accepted: 11/15/2010] [Indexed: 01/30/2023]
Abstract
The expression of IgG antibodies in Escherichia coli is of increasing interest for analytical and therapeutic applications. In this work, we describe a comprehensive and systematic approach to the development of a dicistronic expression system for enhanced IgG expression in E. coli encompassing: (i) random mutagenesis and high-throughput screening for the isolation of over-expressing strains using flow cytometry and (ii) optimization of translation initiation via the screening of libraries of synonymous codons in the 5' region of the second cistron (heavy chain). The effects of different promoters and co-expression of molecular chaperones on full-length IgG production were also investigated. The optimized system resulted in reliable expression of fully assembled IgG at yields between 1 and 4 mg/L of shake flask culture for different antibodies.
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Affiliation(s)
- Tomohiro Makino
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712-0231, USA
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Skretas G, Carroll S, DeFrees S, Schwartz MF, Johnson KF, Georgiou G. Expression of active human sialyltransferase ST6GalNAcI in Escherichia coli. Microb Cell Fact 2009; 8:50. [PMID: 19788761 PMCID: PMC2762462 DOI: 10.1186/1475-2859-8-50] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 09/30/2009] [Indexed: 01/07/2023] Open
Abstract
Background The presence of terminal, surface-exposed sialic acid moieties can greatly enhance the in vivo half-life of glycosylated biopharmaceuticals and improve their therapeutic efficacy. Complete and homogeneous sialylation of glycoproteins can be efficiently performed enzymically in vitro but this process requires large amounts of catalytically active sialyltransferases. Furthermore, standard microbial hosts used for large-scale production of recombinant enzymes can only produce small quantities of glycosyltransferases of animal origin, which lack catalytic activity. Results and conclusion In this work, we have expressed the human sialyltransferase ST6GalNAc I (ST6), an enzyme that sialylates O-linked glycoproteins, in Escherichia coli cells. We observed that wild-type bacterial cells are able to produce only very small amounts of soluble ST6 enzyme. We have found, however, that engineered bacterial strains which possess certain types of oxidative cytoplasm or which co-express the molecular chaperones/co-chaperones trigger factor, DnaK/DnaJ, GroEL/GroES, and Skp, can produce greatly enhanced amounts of soluble ST6. Furthermore, we have developed a novel high-throughput assay for the detection of sialyltransferase activity and used it to demonstrate that the bacterially expressed ST6 enzyme is active and able to transfer sialic acid onto a desialylated O-glycoprotein, bovine submaxillary mucin. To the best of our knowledge, this is the first example of expression of active human sialyltransferase in bacteria. This system may be used as a starting point for the evolution of sialyltransferases with better expression characteristics or altered donor/acceptor specificities.
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Affiliation(s)
- Georgios Skretas
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA.
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Skretas G, Georgiou G. Genetic analysis of G protein-coupled receptor expression in Escherichia coli: inhibitory role of DnaJ on the membrane integration of the human central cannabinoid receptor. Biotechnol Bioeng 2009; 102:357-67. [PMID: 18828176 DOI: 10.1002/bit.22097] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The overexpression of G protein-coupled receptors (GPCRs) and of many other heterologous membrane proteins in simple microbial hosts, such as the bacterium Escherichia coli, often results in protein mistargeting, aggregation into inclusion bodies or cytoplasmic degradation. Furthermore, membrane protein production is very frequently accompanied by severe cell toxicity. In this work, we have employed a genetic strategy to isolate E. coli mutants that produce markedly increased amounts of the human central cannabinoid receptor (CB1), a pharmacologically significant GPCR that expresses very poorly in wild-type E. coli. By utilizing a CB1 fusion with the green fluorescent protein (GFP) and fluorescence-activated cell sorting (FACS), we screened an E. coli transposon library and identified an insertion in dnaJ that resulted in a large increase in CB1-GFP fluorescence and a dramatic enhancement in bacterial production of membrane-integrated CB1. Furthermore, the dnaJ::Tn5 inactivation suppressed the severe cytotoxicity associated with CB1 production. This revealed an unexpected inhibitory role of the chaperone/ co-chaperone DnaJ in the protein folding or membrane insertion of bacterially produced CB1. Our strategy can be easily adapted to identify expression bottlenecks for different GPCRs or any other integral membrane protein, provide useful and unanticipated mechanistic insights, and assist in the construction of genetically engineered E. coli strains for efficient heterologous membrane protein production.
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Affiliation(s)
- Georgios Skretas
- Department of Chemical Engineering, University of Texas at Austin, 2500 Speedway, Austin, Texas 78712, USA
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Link AJ, Skretas G, Strauch EM, Chari NS, Georgiou G. Efficient production of membrane-integrated and detergent-soluble G protein-coupled receptors in Escherichia coli. Protein Sci 2008; 17:1857-63. [PMID: 18593817 PMCID: PMC2548370 DOI: 10.1110/ps.035980.108] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 06/19/2008] [Accepted: 06/20/2008] [Indexed: 10/21/2022]
Abstract
G protein-coupled receptors (GPCRs) are notoriously difficult to express, particularly in microbial systems. Using GPCR fusions with the green fluorescent protein (GFP), we conducted studies to identify bacterial host effector genes that result in a general and significant enhancement in the amount of membrane-integrated human GPCRs that can be produced in Escherichia coli. We show that coexpression of the membrane-bound AAA+ protease FtsH greatly enhances the expression yield of four different class I GPCRs, irrespective of the presence of GFP. Using this new expression system, we produced 0.5 and 2 mg/L of detergent-solubilized and purified full-length central cannabinoid receptor (CB1) and bradykinin receptor 2 (BR2) in shake flask cultures, respectively, two proteins that had previously eluded expression in microbial systems.
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MESH Headings
- ATP-Dependent Proteases/biosynthesis
- ATP-Dependent Proteases/genetics
- Cell Membrane/chemistry
- Cell Membrane/metabolism
- Detergents/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/genetics
- Green Fluorescent Proteins/biosynthesis
- Humans
- Protein Engineering
- Receptor, Bradykinin B2/biosynthesis
- Receptor, Bradykinin B2/chemistry
- Receptor, Bradykinin B2/isolation & purification
- Receptor, Cannabinoid, CB1/biosynthesis
- Receptor, Cannabinoid, CB1/chemistry
- Receptor, Cannabinoid, CB1/isolation & purification
- Receptors, G-Protein-Coupled/biosynthesis
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/isolation & purification
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/isolation & purification
- Solubility
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Affiliation(s)
- A James Link
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
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Skretas G, Meligova AK, Villalonga-Barber C, Mitsiou DJ, Alexis MN, Micha-Screttas M, Steele BR, Screttas CG, Wood DW. Engineered Chimeric Enzymes as Tools for Drug Discovery: Generating Reliable Bacterial Screens for the Detection, Discovery, and Assessment of Estrogen Receptor Modulators. J Am Chem Soc 2007; 129:8443-57. [PMID: 17569534 DOI: 10.1021/ja067754j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Engineered protein-based sensors of ligand binding have emerged as attractive tools for the discovery of therapeutic compounds through simple screening systems. We have previously shown that engineered chimeric enzymes, which combine the ligand-binding domains of nuclear hormone receptors with a highly sensitive thymidylate synthase reporter, yield simple sensors that report the presence of hormone-like compounds through changes in bacterial growth. This work describes an optimized estrogen sensor in Escherichia coli with extraordinary reliability in identifying diverse estrogenic compounds and in differentiating between their agonistic/antagonistic pharmacological effects. The ability of this system to assist the discovery of new estrogen-mimicking compounds was validated by screening a small compound library, which led to the identification of two structurally novel estrogen receptor modulators and the accurate prediction of their agonistic/antagonistic biocharacter in human cells. Strong evidence is presented here that the ability of our sensor to detect ligand binding and recognize pharmacologically critical properties arises from allosteric communication between the artificially combined protein domains, where different ligand-induced conformational changes in the receptor are transmitted to the catalytic domain and translated to distinct levels of enzymic efficiency. To the best of our knowledge, this is one of the first examples of an engineered enzyme with the ability to sense multiple receptor conformations and to be either activated or inactivated depending on the nature of the bound effector molecule. Because the proposed mechanism of ligand dependence is not specific to nuclear hormone receptors, we anticipate that our protein engineering strategy will be applicable to the construction of simple sensors for different classes of (therapeutic) binding proteins.
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Affiliation(s)
- Georgios Skretas
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, USA.
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Abstract
Subtype-selective nuclear hormone receptor modulators could potentially allow the development of valuable tissue-specific therapeutics. A simple biosensor that allows subtype-specific nuclear hormone receptor binding to be reflected by the growth phenotype of Escherichia coli cells has been constructed. This system will potentially enable the facile detection or evolution of subtype-selective hormone analogues.
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Affiliation(s)
- Georgios Skretas
- Department of Chemical Engineering, Princeton University, Engineering Quadrangle, Olden St., Princeton, NJ 08544, USA
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Abstract
The nuclear hormone receptors comprise one of the largest classes of protein targets for drug discovery, as their function has been linked to a variety of serious diseases, including several forms of cancer. Identifying novel compounds with the ability to modulate the function of these targets could lead to the development of effective therapeutics. In vivo sensors of ligand binding have emerged as tools that can greatly accelerate the lead identification process, allowing new drugs to be discovered more rapidly and cheaply. In this work, a novel sensor of nuclear hormone binding has been developed in Escherichia coli by constructing a fusion of the ligand-binding domain of the human estrogen receptor with a thymidylate synthase enzyme (TS). Expression of this fusion protein in TS-deficient bacterial cells resulted in growth phenotypes that were dependent on the presence of estrogen. Subsequent replacement of the estrogen receptor with the ligand-binding domain of the human thyroid hormone receptor led to specific thyroid hormone-enhanced growth that was insensitive to estrogen. This biosensor was then challenged with a small library of estrogen and thyroid hormone analogues, and it was observed that levels of cell growth correlate well with ligand-binding affinity. Remarkably, this simple biosensor was able to discriminate between agonistic and antagonistic activities, as combinations of estrogen agonists had an additive impact on cell growth, whereas known estrogen antagonists were found to neutralize agonist effects. This system constitutes a technique for facile selection of lead compounds with potential medical applications.
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Affiliation(s)
- Georgios Skretas
- Department of Chemical Engineering, Princeton University, Engineering Quadrangle, Olden St., Princeton, NJ 08544, USA
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Abstract
Inteins are the protein analogs of self-splicing RNA introns, as they post-translationally excise themselves from a variety of protein hosts. Intein insertion abolishes, in general, the activity of its host protein, which is subsequently restored upon intein excision. These protein elements therefore have the potential to be used as general molecular "switches" for the control of arbitrary target proteins. Based on rational design, an intein-based protein switch has been constructed whose splicing activity is conditionally triggered in vivo by the presence of thyroid hormone or synthetic analogs. This modified intein was used in Escherichia coli to demonstrate that a number of different proteins can be inactivated by intein insertion and then reactivated by the addition of thyroid hormone via ligand-induced splicing. This conditional activation was also found to occur in a dose-dependent manner. Rational protein engineering was then combined with genetic selection to evolve an additional intein whose activity is controlled by the presence of synthetic estrogen ligands. The ability to regulate protein function post-translationally through the use of ligand-controlled intein splicing will most likely find applications in metabolic engineering, drug discovery and delivery, biosensing, molecular computation, as well as many additional areas of biotechnology.
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Affiliation(s)
- Georgios Skretas
- Department of Chemical Engineering, Princeton University, Engineering Quadrangle, Olden St., Princeton, NJ 08544, USA
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