1
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Sajid S, Salas LH, Rafiq M, Lund T, Jørgensen MG, Honoré B, Christensen LP, Hansen PR, Franzyk H, Mirza O, Prabhala BK. Physiological response in E. coli to YdgR overexpression depends on whether the protein has an intact function. Biochem Biophys Res Commun 2023; 661:42-49. [PMID: 37087797 DOI: 10.1016/j.bbrc.2023.04.032] [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: 03/30/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/25/2023]
Abstract
Membrane transport proteins are essential for the transport of a wide variety of molecules across the cell membrane to maintain cellular homeostasis. Generally, these transport proteins can be overexpressed in a suitable host (bacteria, yeast, or mammalian cells), and it is well documented that overexpression of membrane proteins alters the global metabolomic and proteomic profiles of the host cells. In the present study, we investigated the physiological consequences of overexpression of a membrane transport protein YdgR that belongs to the POT/PTR family from E. coli by using the lab strain BL21 (DE3)pLysS in its functional and attenuated mutant YdgR-E33Q. We found significant differences between the omics (metabolomics and proteomics) profiles of the cells expressing functional YdgR as compared to cells expressing attenuated YdgR, e.g., upregulation of several uncharacterized y-proteins and enzymes involved in the metabolism of peptides and amino acids. Furthermore, molecular network analysis suggested a relatively higher presence of proline-containing tripeptides in cells expressing functional YdgR. We envisage that an in-depth investigation of physiological alterations due to protein over-expression may be used for the deorphanization of the y-gene transportome.
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Affiliation(s)
- Salvia Sajid
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark; Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Lilia Hernandez Salas
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 10.1, DK-4000, Roskilde, Denmark
| | - Maria Rafiq
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Torben Lund
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 10.1, DK-4000, Roskilde, Denmark
| | - Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Bent Honoré
- Department of Biomedicine, Aarhus University, Nordre Ringgade 1, 8000, Aarhus C, Denmark
| | - Lars Porskjær Christensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Bala Krishna Prabhala
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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2
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Bleffert F, Granzin J, Caliskan M, Schott-Verdugo SN, Siebers M, Thiele B, Rahme L, Felgner S, Dörmann P, Gohlke H, Batra-Safferling R, Jaeger KE, Kovacic F. Structural, mechanistic, and physiological insights into phospholipase A-mediated membrane phospholipid degradation in Pseudomonas aeruginosa. eLife 2022; 11:e72824. [PMID: 35536643 PMCID: PMC9132575 DOI: 10.7554/elife.72824] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
Cells steadily adapt their membrane glycerophospholipid (GPL) composition to changing environmental and developmental conditions. While the regulation of membrane homeostasis via GPL synthesis in bacteria has been studied in detail, the mechanisms underlying the controlled degradation of endogenous GPLs remain unknown. Thus far, the function of intracellular phospholipases A (PLAs) in GPL remodeling (Lands cycle) in bacteria is not clearly established. Here, we identified the first cytoplasmic membrane-bound phospholipase A1 (PlaF) from Pseudomonas aeruginosa, which might be involved in the Lands cycle. PlaF is an important virulence factor, as the P. aeruginosa ΔplaF mutant showed strongly attenuated virulence in Galleria mellonella and macrophages. We present a 2.0-Å-resolution crystal structure of PlaF, the first structure that reveals homodimerization of a single-pass transmembrane (TM) full-length protein. PlaF dimerization, mediated solely through the intermolecular interactions of TM and juxtamembrane regions, inhibits its activity. The dimerization site and the catalytic sites are linked by an intricate ligand-mediated interaction network, which might explain the product (fatty acid) feedback inhibition observed with the purified PlaF protein. We used molecular dynamics simulations and configurational free energy computations to suggest a model of PlaF activation through a coupled monomerization and tilting of the monomer in the membrane, which constrains the active site cavity into contact with the GPL substrates. Thus, these data show the importance of the PlaF-mediated GPL remodeling pathway for virulence and could pave the way for the development of novel therapeutics targeting PlaF.
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Affiliation(s)
- Florian Bleffert
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbHJülichGermany
| | - Joachim Granzin
- Institute of Biological Information Processing - Structural Biochemistry (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbHJülichGermany
| | - Muttalip Caliskan
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbHJülichGermany
| | - Stephan N Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University DüsseldorfDuesseldorfGermany
- Centro de Bioinformática y Simulación Molecular (CBSM), Faculty of Engineering, University of TalcaTalcaChile
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbHJülichGermany
| | - Meike Siebers
- Institute of Molecular Physiology, and Biotechnology of Plants (IMBIO), University of BonnBonnGermany
- Institute for Plant Genetics, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Björn Thiele
- Institute of Bio- and Geosciences, Plant Sciences (IBG-2), and Agrosphere (IBG-3), Forschungszentrum Jülich GmbHJülichGermany
| | - Laurence Rahme
- Department of Microbiology, and Immunobiology, Harvard Medical SchoolBostonUnited States
| | - Sebastian Felgner
- Department of Molecular Bacteriology, Helmholtz Centre for Infection ResearchBraunschweigGermany
| | - Peter Dörmann
- Institute of Molecular Physiology, and Biotechnology of Plants (IMBIO), University of BonnBonnGermany
| | - Holger Gohlke
- Institute of Biological Information Processing - Structural Biochemistry (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbHJülichGermany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University DüsseldorfDuesseldorfGermany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbHJülichGermany
| | - Renu Batra-Safferling
- Institute of Biological Information Processing - Structural Biochemistry (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbHJülichGermany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbHJülichGermany
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbHJülichGermany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbHJülichGermany
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3
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Ledsgaard L, Ljungars A, Rimbault C, Sørensen CV, Tulika T, Wade J, Wouters Y, McCafferty J, Laustsen AH. Advances in antibody phage display technology. Drug Discov Today 2022; 27:2151-2169. [PMID: 35550436 DOI: 10.1016/j.drudis.2022.05.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/24/2022] [Accepted: 05/04/2022] [Indexed: 01/06/2023]
Abstract
Phage display technology can be used for the discovery of antibodies for research, diagnostic, and therapeutic purposes. In this review, we present and discuss key parameters that can be optimized when performing phage display selection campaigns, including the use of different antibody formats and advanced strategies for antigen presentation, such as immobilization, liposomes, nanodiscs, virus-like particles, and whole cells. Furthermore, we provide insights into selection strategies that can be used for the discovery of antibodies with complex binding requirements, such as targeting a specific epitope, cross-reactivity, or pH-dependent binding. Lastly, we provide a description of specialized phage display libraries for the discovery of bispecific antibodies and pH-sensitive antibodies. Together, these methods can be used to improve antibody discovery campaigns against all types of antigen. Teaser: This review provides an overview of the different strategies that can be exploited to improve the success rate of antibody phage display discovery campaigns, addressing key parameters, such as antigen presentation, selection methodologies, and specialized libraries.
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Affiliation(s)
- Line Ledsgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Charlotte Rimbault
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Christoffer V Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Tulika Tulika
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Jack Wade
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Yessica Wouters
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - John McCafferty
- Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, CB2 0QQ, UK; Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
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4
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Di Cesare M, Diagne AM, Bourgey B, Jault JM, Orelle C. Functional Overexpression of Membrane Proteins in E. coli: The Good, the Bad, and the Ugly. Methods Mol Biol 2022; 2507:41-58. [PMID: 35773576 DOI: 10.1007/978-1-0716-2368-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Overexpression of properly folded membrane proteins is a mandatory step for their functional and structural characterization. One of the most used expression systems for the production of proteins is Escherichia coli. Many advantageous strains combined with T7 expression systems have been developed over the years. Recently, we showed that the choice of the strain is critical for the functionality of membrane proteins, even when the proteins are successfully incorporated in the membrane (Mathieu et al. Sci Rep. 2019; 9(1):2654). Notably, the amount and/or activity of the T7-RNA polymerase, which drives the transcription of the genes of interest, may indirectly affect the folding and functionality of overexpressed membrane proteins. Moreover, we reported a general trend in which mild detergents mainly extract the population of active membrane proteins, whereas a harsher detergent like Fos-choline 12 could solubilize them irrespectively of their functionality. Based on these observations, we provide some guidelines to optimize the quality of membrane proteins overexpressed in E. coli.
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Affiliation(s)
- Margot Di Cesare
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Aissatou Maty Diagne
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Benjamin Bourgey
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France.
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/University of Lyon, Lyon, France.
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5
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Royes J, Talbot P, Le Bon C, Moncoq K, Uzan M, Zito F, Miroux B. Membrane Protein Production in Escherichia coli: Protocols and Rules. Methods Mol Biol 2022; 2507:19-39. [PMID: 35773575 DOI: 10.1007/978-1-0716-2368-8_2] [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] [Indexed: 06/15/2023]
Abstract
Despite recent progresses in the use of eukaryotic expression system, production of membrane proteins for structural studies still relies on microbial expression systems. In this review, we provide protocols to achieve high level expression of membrane proteins in Escherichia coli, especially using the T7 RNA polymerase based expression system. From the design of the construct, the choice of the appropriate vector-host combination, the assessment of the bacterial fitness, to the selection of bacterial mutant adapted to the production of the target membrane protein, the chapter covers all necessary methods for a rapid optimization of a specific target membrane protein. In addition, we provide a protocol for membrane protein solubilization based on our recent analysis of the Protein Data Bank.
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Affiliation(s)
- Jordi Royes
- Laboratoire de Colloïdes et Matériaux Divisés École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris 10, Paris, France
| | - Pauline Talbot
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Christel Le Bon
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Karine Moncoq
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Marc Uzan
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Francesca Zito
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Bruno Miroux
- Université Paris Cité, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France.
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6
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Laydevant F, Mahabadi M, Llido P, Bourgouin JP, Caron L, Arnold AA, Marcotte I, Warschawski DE. Growth-phase dependence of bacterial membrane lipid profile and labeling for in-cell solid-state NMR applications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1864:183819. [PMID: 34800428 DOI: 10.1016/j.bbamem.2021.183819] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/31/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
Cell labeling is a preliminary step in multiple biophysical approaches, including the solid-state nuclear magnetic resonance (NMR) study of bacteria in vivo. Deuterium solid-state NMR has been used in the past years to probe bacterial membranes and their interactions with antimicrobial peptides, following a standard labeling protocol. Recent results from our laboratory on a slow-growing bacterium has shown the need to optimize this protocol, especially the bacterial growth time before harvest and the concentration of exogenous labeled fatty acids to be used for both Escherichia coli and Bacillus subtilis. It is also essential for the protocol to remain harmless to cells while providing optimal labeling. We have therefore developed a fast and facile approach to monitor the lipid composition of bacterial membranes under various growth conditions, combining solution 31P NMR and GCMS. Using this approach, the optimized labeling conditions of Escherichia coli and Bacillus subtilis with deuterated palmitic acid were determined. Our results show a modification of B. subtilis phospholipid profile as a function of the growth stage, as opposed to E. coli. Our protocol recommends low concentrations of exogenous palmitic acid in the growth medium, and bacteria harvest after the exponential phase.
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Affiliation(s)
- Florent Laydevant
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Mahsa Mahabadi
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Pierre Llido
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Jean-Philippe Bourgouin
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Laurence Caron
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Alexandre A Arnold
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada.
| | - Dror E Warschawski
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal H3C 3P8, Canada; Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, École normale supérieure, PSL University, 75005 Paris, France.
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7
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Kleetz J, Vasilopoulos G, Czolkoss S, Aktas M, Narberhaus F. Recombinant and endogenous ways to produce methylated phospholipids in Escherichia coli. Appl Microbiol Biotechnol 2021; 105:8837-8851. [PMID: 34709431 PMCID: PMC8590670 DOI: 10.1007/s00253-021-11654-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 10/31/2022]
Abstract
Escherichia coli is the daily workhorse in molecular biology research labs and an important platform microorganism in white biotechnology. Its cytoplasmic membrane is primarily composed of the phospholipids phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and cardiolipin (CL). As in most other bacteria, the typical eukaryotic phosphatidylcholine (PC) is not a regular component of the E. coli membrane. PC is known to act as a substrate in various metabolic or catabolic reactions, to affect protein folding and membrane insertion, and to activate proteins that originate from eukaryotic environments. Options to manipulate the E. coli membrane to include non-native lipids such as PC might make it an even more powerful and versatile tool for biotechnology and protein biochemistry. This article outlines different strategies how E. coli can be engineered to produce PC and other methylated PE derivatives. Several of these approaches rely on the ectopic expression of genes from natural PC-producing organisms. These include PC synthases, lysolipid acyltransferases, and several phospholipid N-methyltransferases with diverse substrate and product preferences. In addition, we show that E. coli has the capacity to produce PC by its own enzyme repertoire provided that appropriate precursors are supplied. Screening of the E. coli Keio knockout collection revealed the lysophospholipid transporter LplT to be responsible for the uptake of lyso-PC, which is then further acylated to PC by the acyltransferase-acyl carrier protein synthetase Aas. Overall, our study shows that the membrane composition of the most routinely used model bacterium can readily be tailored on demand.Key points• Escherichia coli can be engineered to produce non-native methylated PE derivatives.• These lipids can be produced by foreign and endogenous proteins.• Modification of E. coli membrane offers potential for biotechnology and research.
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Affiliation(s)
- Julia Kleetz
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Georgios Vasilopoulos
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Simon Czolkoss
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Meriyem Aktas
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Franz Narberhaus
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany.
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8
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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9
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Ferraz L, Sauer M, Sousa MJ, Branduardi P. The Plasma Membrane at the Cornerstone Between Flexibility and Adaptability: Implications for Saccharomyces cerevisiae as a Cell Factory. Front Microbiol 2021; 12:715891. [PMID: 34434179 PMCID: PMC8381377 DOI: 10.3389/fmicb.2021.715891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
In the last decade, microbial-based biotechnological processes are paving the way toward sustainability as they implemented the use of renewable feedstocks. Nonetheless, the viability and competitiveness of these processes are often limited due to harsh conditions such as: the presence of feedstock-derived inhibitors including weak acids, non-uniform nature of the substrates, osmotic pressure, high temperature, extreme pH. These factors are detrimental for microbial cell factories as a whole, but more specifically the impact on the cell’s membrane is often overlooked. The plasma membrane is a complex system involved in major biological processes, including establishing and maintaining transmembrane gradients, controlling uptake and secretion, intercellular and intracellular communication, cell to cell recognition and cell’s physical protection. Therefore, when designing strategies for the development of versatile, robust and efficient cell factories ready to tackle the harshness of industrial processes while delivering high values of yield, titer and productivity, the plasma membrane has to be considered. Plasma membrane composition comprises diverse macromolecules and it is not constant, as cells adapt it according to the surrounding environment. Remarkably, membrane-specific traits are emerging properties of the system and therefore it is not trivial to predict which membrane composition is advantageous under certain conditions. This review includes an overview of membrane engineering strategies applied to Saccharomyces cerevisiae to enhance its fitness under industrially relevant conditions as well as strategies to increase microbial production of the metabolites of interest.
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Affiliation(s)
- Luís Ferraz
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria João Sousa
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
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10
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Preisler SS, Wiuf AD, Friis M, Kjaergaard L, Hurd M, Becares ER, Nurup CN, Bjoerkskov FB, Szathmáry Z, Gourdon PE, Calloe K, Klaerke DA, Gotfryd K, Pedersen PA. Saccharomyces cerevisiae as a superior host for overproduction of prokaryotic integral membrane proteins. Curr Res Struct Biol 2021; 3:51-71. [PMID: 34235486 PMCID: PMC8244417 DOI: 10.1016/j.crstbi.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/02/2023] Open
Abstract
Integral membrane proteins (IMPs) constitute ~30% of all proteins encoded by the genome of any organism and Escherichia coli remains the first-choice host for recombinant production of prokaryotic IMPs. However, the expression levels of prokaryotic IMPs delivered by this bacterium are often low and overproduced targets often accumulate in inclusion bodies. The targets are therefore often discarded to avoid an additional and inconvenient refolding step in the purification protocol. Here we compared expression of five prokaryotic (bacterial and archaeal) IMP families in E. coli and Saccharomyces cerevisiae. We demonstrate that our S. cerevisiae-based production platform is superior in expression of four investigated IMPs, overall being able to deliver high quantities of active target proteins. Surprisingly, in case of the family of zinc transporters (Zrt/Irt-like proteins, ZIPs), S. cerevisiae rescued protein expression that was undetectable in E. coli. We also demonstrate the effect of localization of the fusion tag on expression yield and sample quality in detergent micelles. Lastly, we present a road map to achieve the most efficient expression of prokaryotic IMPs in our yeast platform. Our findings demonstrate the great potential of S. cerevisiae as host for high-throughput recombinant overproduction of bacterial and archaeal IMPs for downstream biophysical characterization. S. cerevisiae is superior to E. coli in expressing correctly folded and active IMPs. S. cerevisiae completely rescues the expression of the family of zinc transporters. Localization of the fusion tag affects expression yields and protein quality. We provide a roadmap to efficient expression of prokaryotic IMPs in S. cerevisiae.
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Affiliation(s)
- Sarah Spruce Preisler
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Anders Drabaek Wiuf
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Marc Friis
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Lasse Kjaergaard
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Molly Hurd
- University of Copenhagen, Department of Veterinary and Animal Sciences, Dyrlaegevej 100, Frederiksberg, DK, 1870, Denmark
| | - Eva Ramos Becares
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Casper Normann Nurup
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | | | - Zsófia Szathmáry
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
| | - Pontus Emanuel Gourdon
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Kirstine Calloe
- University of Copenhagen, Department of Veterinary and Animal Sciences, Dyrlaegevej 100, Frederiksberg, DK, 1870, Denmark
| | - Dan A Klaerke
- University of Copenhagen, Department of Veterinary and Animal Sciences, Dyrlaegevej 100, Frederiksberg, DK, 1870, Denmark
| | - Kamil Gotfryd
- Membrane Protein Structural Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7-9, DK 2200, Copenhagen N, Denmark
| | - Per Amstrup Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, OE, Denmark
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11
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Decembrino D, Ricklefs E, Wohlgemuth S, Girhard M, Schullehner K, Jach G, Urlacher VB. Assembly of Plant Enzymes in E. coli for the Production of the Valuable (-)-Podophyllotoxin Precursor (-)-Pluviatolide. ACS Synth Biol 2020; 9:3091-3103. [PMID: 33095000 DOI: 10.1021/acssynbio.0c00354] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lignans are plant secondary metabolites with a wide range of reported health-promoting bioactivities. Traditional routes toward these natural products involve, among others, the extraction from plant sources and chemical synthesis. However, the availability of the sources and the complex chemical structures of lignans often limit the feasibility of these approaches. In this work, we introduce a newly assembled biosynthetic route in E. coli for the efficient conversion of the common higher-lignan precursor (+)-pinoresinol to the noncommercially available (-)-pluviatolide via three intermediates. (-)-Pluviatolide is considered a crossroad compound in lignan biosynthesis, because the methylenedioxy bridge in its structure, resulting from the oxidation of (-)-matairesinol, channels the biosynthetic pathway toward the microtubule depolymerizer (-)-podophyllotoxin. This oxidation reaction is catalyzed with high regio- and enantioselectivity by a cytochrome P450 monooxygenase from Sinopodophyllum hexandrum (CYP719A23), which was expressed and optimized regarding redox partners in E. coli. Pinoresinol-lariciresinol reductase from Forsythia intermedia (FiPLR), secoisolariciresinol dehydrogenase from Podophyllum pleianthum (PpSDH), and CYP719A23 were coexpressed together with a suitable NADPH-dependent reductase to ensure P450 activity, allowing for four sequential biotransformations without intermediate isolation. By using an E. coli strain coexpressing the enzymes originating from four plants, (+)-pinoresinol was efficiently converted, allowing the isolation of enantiopure (-)-pluviatolide at a concentration of 137 mg/L (ee ≥99% with 76% isolated yield).
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Affiliation(s)
- Davide Decembrino
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Esther Ricklefs
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Stefan Wohlgemuth
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Marco Girhard
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Katrin Schullehner
- Phytowelt Green Technologies GmbH, Kölsumer Weg 33, 41334 Nettetal, Germany
| | - Guido Jach
- Phytowelt Green Technologies GmbH, Kölsumer Weg 33, 41334 Nettetal, Germany
| | - Vlada B. Urlacher
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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12
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Royes J, Biou V, Dautin N, Tribet C, Miroux B. Inducible intracellular membranes: molecular aspects and emerging applications. Microb Cell Fact 2020; 19:176. [PMID: 32887610 PMCID: PMC7650269 DOI: 10.1186/s12934-020-01433-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/27/2020] [Indexed: 02/08/2023] Open
Abstract
Membrane remodeling and phospholipid biosynthesis are normally tightly regulated to maintain the shape and function of cells. Indeed, different physiological mechanisms ensure a precise coordination between de novo phospholipid biosynthesis and modulation of membrane morphology. Interestingly, the overproduction of certain membrane proteins hijack these regulation networks, leading to the formation of impressive intracellular membrane structures in both prokaryotic and eukaryotic cells. The proteins triggering an abnormal accumulation of membrane structures inside the cells (or membrane proliferation) share two major common features: (1) they promote the formation of highly curved membrane domains and (2) they lead to an enrichment in anionic, cone-shaped phospholipids (cardiolipin or phosphatidic acid) in the newly formed membranes. Taking into account the available examples of membrane proliferation upon protein overproduction, together with the latest biochemical, biophysical and structural data, we explore the relationship between protein synthesis and membrane biogenesis. We propose a mechanism for the formation of these non-physiological intracellular membranes that shares similarities with natural inner membrane structures found in α-proteobacteria, mitochondria and some viruses-infected cells, pointing towards a conserved feature through evolution. We hope that the information discussed in this review will give a better grasp of the biophysical mechanisms behind physiological and induced intracellular membrane proliferation, and inspire new applications, either for academia (high-yield membrane protein production and nanovesicle production) or industry (biofuel production and vaccine preparation).
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Affiliation(s)
- Jorge Royes
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France. .,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France. .,Département de Chimie, École Normale Supérieure, PASTEUR, PSL University, CNRS, Sorbonne Université, 24 Rue Lhomond, 75005, Paris, France.
| | - Valérie Biou
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France
| | - Nathalie Dautin
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France
| | - Christophe Tribet
- Département de Chimie, École Normale Supérieure, PASTEUR, PSL University, CNRS, Sorbonne Université, 24 Rue Lhomond, 75005, Paris, France
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France. .,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France.
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