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Ortega C, Oppezzo P, Correa A. Overcoming the Solubility Problem in E. coli: Available Approaches for Recombinant Protein Production. Methods Mol Biol 2022; 2406:35-64. [PMID: 35089549 DOI: 10.1007/978-1-0716-1859-2_2] [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: 06/14/2023]
Abstract
Despite the importance of recombinant protein production in the academy and industrial fields, many issues concerning the expression of soluble and homogeneous products are still unsolved. Several strategies were developed to overcome these obstacles; however, at present, there is no magic bullet that can be applied for all cases. Indeed, several key expression parameters need to be evaluated for each protein. Among the different hosts for protein expression, Escherichia coli is by far the most widely used. In this chapter, we review many of the different tools employed to circumvent protein insolubility problems.
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Affiliation(s)
- Claudia Ortega
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Oppezzo
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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2
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Zutz A, Hamborg L, Pedersen LE, Kassem MM, Papaleo E, Koza A, Herrgård MJ, Jensen SI, Teilum K, Lindorff-Larsen K, Nielsen AT. A dual-reporter system for investigating and optimizing protein translation and folding in E. coli. Nat Commun 2021; 12:6093. [PMID: 34667164 PMCID: PMC8526717 DOI: 10.1038/s41467-021-26337-1] [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: 01/13/2020] [Accepted: 10/01/2021] [Indexed: 01/29/2023] Open
Abstract
Strategies for investigating and optimizing the expression and folding of proteins for biotechnological and pharmaceutical purposes are in high demand. Here, we describe a dual-reporter biosensor system that simultaneously assesses in vivo protein translation and protein folding, thereby enabling rapid screening of mutant libraries. We have validated the dual-reporter system on five different proteins and find an excellent correlation between reporter signals and the levels of protein expression and solubility of the proteins. We further demonstrate the applicability of the dual-reporter system as a screening assay for deep mutational scanning experiments. The system enables high throughput selection of protein variants with high expression levels and altered protein stability. Next generation sequencing analysis of the resulting libraries of protein variants show a good correlation between computationally predicted and experimentally determined protein stabilities. We furthermore show that the mutational experimental data obtained using this system may be useful for protein structure calculations.
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Affiliation(s)
- Ariane Zutz
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Louise Hamborg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Maher M Kassem
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Elena Papaleo
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Anna Koza
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark.
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Szmitkowska A, Pekárová B, Hejátko J. A High-Throughput Strategy for Recombinant Protein Expression and Solubility Screen in Escherichia coli : A Case of Sensor Histidine Kinase. Methods Mol Biol 2020; 2077:19-36. [PMID: 31707649 DOI: 10.1007/978-1-4939-9884-5_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: 06/10/2023]
Abstract
Determining conditions optimal for host growth, maximal protein yield, and lysis buffer composition is of critical importance for the efficient purification of soluble and well-folded recombinant proteins suitable for functional and/or structural studies. Small-scale optimization of conditions for protein production and stability saves time, labor, and costs. Here we describe a protocol for quick protein production and solubility screen using TissueLyser II system from Qiagen enabling simultaneous processing of 96 protein samples, with application to recombinant proteins encompassing two intracellular domains of ethylene-recognizing sensor histidine kinase ETHYLENE RESPONSE1 (ETR1) from Arabidopsis thaliana. We demonstrate that conditions for expression and cell lysis found in our small-scale screen allow successful large-scale production of pure and functional domains of sensor histidine kinase, providing a strategy potentially transferable to other similar catalytic domains.
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Affiliation(s)
- Agnieszka Szmitkowska
- Central European Institute of Technology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Blanka Pekárová
- Central European Institute of Technology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jan Hejátko
- Central European Institute of Technology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
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Sormanni P, Aprile FA, Vendruscolo M. Third generation antibody discovery methods: in silico rational design. Chem Soc Rev 2018; 47:9137-9157. [PMID: 30298157 DOI: 10.1039/c8cs00523k] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Owing to their outstanding performances in molecular recognition, antibodies are extensively used in research and applications in molecular biology, biotechnology and medicine. Recent advances in experimental and computational methods are making it possible to complement well-established in vivo (first generation) and in vitro (second generation) methods of antibody discovery with novel in silico (third generation) approaches. Here we describe the principles of computational antibody design and review the state of the art in this field. We then present Modular, a method that implements the rational design of antibodies in a modular manner, and describe the opportunities offered by this approach.
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Affiliation(s)
- Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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5
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Zeng Y, Jones AM, Thomas EE, Nassif B, Silberg JJ, Segatori L. A Split Transcriptional Repressor That Links Protein Solubility to an Orthogonal Genetic Circuit. ACS Synth Biol 2018; 7:2126-2138. [PMID: 30089365 PMCID: PMC6858789 DOI: 10.1021/acssynbio.8b00129] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Monitoring the aggregation of proteins within the cellular environment is key to investigating the molecular mechanisms underlying the formation of off-pathway protein assemblies associated with the development of disease and testing therapeutic strategies to prevent the accumulation of non-native conformations. It remains challenging, however, to couple protein aggregation events underlying the cellular pathogenesis of a disease to genetic circuits and monitor their progression in a quantitative fashion using synthetic biology tools. To link the aggregation propensity of a target protein to the expression of an easily detectable reporter, we investigated the use of a transcriptional AND gate system based on complementation of a split transcription factor. We first identified two-fragment tetracycline repressor (TetR) variants that can be regulated via ligand-dependent induction and demonstrated that split TetR variants can function as transcriptional AND gates in both bacteria and mammalian cells. We then adapted split TetR for use as an aggregation sensor. Protein aggregation was detected by monitoring complementation between a larger TetR fragment that serves as a "detector" and a smaller TetR fragment expressed as a fusion to an aggregation-prone protein that serves as a "sensor" of the target protein aggregation status. This split TetR represents a novel genetic component that can be used for a wide range of applications in bacterial as well as mammalian synthetic biology and a much needed cell-based sensor for monitoring a protein's conformational status in complex cellular environments.
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Affiliation(s)
- Yimeng Zeng
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Alicia M. Jones
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Emily E. Thomas
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Barbara Nassif
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Jonathan J. Silberg
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| | - Laura Segatori
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
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The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules. mBio 2016; 7:e01781-15. [PMID: 26814179 PMCID: PMC4742702 DOI: 10.1128/mbio.01781-15] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Gram-positive bacterium Lactococcus lactis, used for the production of cheeses and other fermented dairy products, falls victim frequently to fortuitous infection by tailed phages. The accompanying risk of dairy fermentation failures in industrial facilities has prompted in-depth investigations of these phages. Lactococcal phage Tuc2009 possesses extensive genomic homology to phage TP901-1. However, striking differences in the baseplate-encoding genes stimulated our interest in solving the structure of this host’s adhesion device. We report here the X-ray structures of phage Tuc2009 receptor binding protein (RBP) and of a “tripod” assembly of three baseplate components, BppU, BppA, and BppL (the RBP). These structures made it possible to generate a realistic atomic model of the complete Tuc2009 baseplate that consists of an 84-protein complex: 18 BppU, 12 BppA, and 54 BppL proteins. The RBP head domain possesses a different fold than those of phages p2, TP901-1, and 1358, while the so-called “stem” and “neck” domains share structural features with their equivalents in phage TP901-1. The BppA module interacts strongly with the BppU N-terminal domain. Unlike other characterized lactococcal phages, Tuc2009 baseplate harbors two different carbohydrate recognition sites: one in the bona fide RBP head domain and the other in BppA. These findings represent a major step forward in deciphering the molecular mechanism by which Tuc2009 recognizes its saccharidic receptor(s) on its host. Understanding how siphophages infect Lactococcus lactis is of commercial importance as they cause milk fermentation failures in the dairy industry. In addition, such knowledge is crucial in a general sense in order to understand how viruses recognize their host through protein-glycan interactions. We report here the lactococcal phage Tuc2009 receptor binding protein (RBP) structure as well as that of its baseplate. The RBP head domain has a different fold than those of phages p2, TP901-1, and 1358, while the so-called “stem” and “neck” share the fold characteristics also found in the equivalent baseplate proteins of phage TP901-1. The baseplate structure contains, in contrast to other characterized lactococcal phages, two different carbohydrate binding modules that may bind different motifs of the host’s surface polysaccharide.
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McCabe O, Spinelli S, Farenc C, Labbé M, Tremblay D, Blangy S, Oscarson S, Moineau S, Cambillau C. The targeted recognition of Lactococcus lactis phages to their polysaccharide receptors. Mol Microbiol 2015; 96:875-86. [PMID: 25708888 DOI: 10.1111/mmi.12978] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2015] [Indexed: 01/21/2023]
Abstract
Each phage infects a limited number of bacterial strains through highly specific interactions of the receptor-binding protein (RBP) at the tip of phage tail and the receptor at the bacterial surface. Lactococcus lactis is covered with a thin polysaccharide pellicle (hexasaccharide repeating units), which is used by a subgroup of phages as a receptor. Using L. lactis and phage 1358 as a model, we investigated the interaction between the phage RBP and the pellicle hexasaccharide of the host strain. A core trisaccharide (TriS), derived from the pellicle hexasaccharide repeating unit, was chemically synthesised, and the crystal structure of the RBP/TriS complex was determined. This provided unprecedented structural details of RBP/receptor site-specific binding. The complete hexasaccharide repeating unit was modelled and found to aptly fit the extended binding site. The specificity observed in in vivo phage adhesion assays could be interpreted in view of the reported structure. Therefore, by combining synthetic carbohydrate chemistry, X-ray crystallography and phage plaquing assays, we suggest that phage adsorption results from distinct recognition of the RBP towards the core TriS or the remaining residues of the hexasacchride receptor. This study provides a novel insight into the adsorption process of phages targeting saccharides as their receptors.
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Affiliation(s)
- Orla McCabe
- Centre for Molecular Innovation and Drug Discovery, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin, Ireland
| | - Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Marseille, UMR, 7257, France.,Aix-Marseille University, Campus de Luminy, Case 932, Marseille, 13288, France
| | - Carine Farenc
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Marseille, UMR, 7257, France.,Aix-Marseille University, Campus de Luminy, Case 932, Marseille, 13288, France
| | - Myriam Labbé
- Groupe de recherche en écologie buccale & Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, G1V 0A6, Canada
| | - Denise Tremblay
- Groupe de recherche en écologie buccale & Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, G1V 0A6, Canada
| | - Stéphanie Blangy
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Marseille, UMR, 7257, France.,Aix-Marseille University, Campus de Luminy, Case 932, Marseille, 13288, France
| | - Stefan Oscarson
- Centre for Molecular Innovation and Drug Discovery, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin, Ireland
| | - Sylvain Moineau
- Groupe de recherche en écologie buccale & Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, G1V 0A6, Canada
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Marseille, UMR, 7257, France.,Aix-Marseille University, Campus de Luminy, Case 932, Marseille, 13288, France
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Overcoming the solubility problem in E. coli: available approaches for recombinant protein production. Methods Mol Biol 2015; 1258:27-44. [PMID: 25447857 DOI: 10.1007/978-1-4939-2205-5_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite the importance of recombinant protein production in academy and industrial fields, many issues concerning the expression of soluble and homogeneous product are still unsolved. Although several strategies were developed to overcome these obstacles, at present there is no magic bullet that can be applied for all cases. Indeed, several key expression parameters need to be evaluated for each protein. Among the different hosts for protein expression, Escherichia coli is by far the most widely used. In this chapter, we review many of the different tools employed to circumvent protein insolubility problems.
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9
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Saez NJ, Nozach H, Blemont M, Vincentelli R. High throughput quantitative expression screening and purification applied to recombinant disulfide-rich venom proteins produced in E. coli. J Vis Exp 2014:e51464. [PMID: 25146501 PMCID: PMC4692350 DOI: 10.3791/51464] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli (E. coli) is the most widely used expression system for the production of recombinant proteins for structural and functional studies. However, purifying proteins is sometimes challenging since many proteins are expressed in an insoluble form. When working with difficult or multiple targets it is therefore recommended to use high throughput (HTP) protein expression screening on a small scale (1-4 ml cultures) to quickly identify conditions for soluble expression. To cope with the various structural genomics programs of the lab, a quantitative (within a range of 0.1-100 mg/L culture of recombinant protein) and HTP protein expression screening protocol was implemented and validated on thousands of proteins. The protocols were automated with the use of a liquid handling robot but can also be performed manually without specialized equipment. Disulfide-rich venom proteins are gaining increasing recognition for their potential as therapeutic drug leads. They can be highly potent and selective, but their complex disulfide bond networks make them challenging to produce. As a member of the FP7 European Venomics project (www.venomics.eu), our challenge is to develop successful production strategies with the aim of producing thousands of novel venom proteins for functional characterization. Aided by the redox properties of disulfide bond isomerase DsbC, we adapted our HTP production pipeline for the expression of oxidized, functional venom peptides in the E. coli cytoplasm. The protocols are also applicable to the production of diverse disulfide-rich proteins. Here we demonstrate our pipeline applied to the production of animal venom proteins. With the protocols described herein it is likely that soluble disulfide-rich proteins will be obtained in as little as a week. Even from a small scale, there is the potential to use the purified proteins for validating the oxidation state by mass spectrometry, for characterization in pilot studies, or for sensitive micro-assays.
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Affiliation(s)
- Natalie J Saez
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université
| | - Hervé Nozach
- iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Commissariat à l'énergie atomique et aux énergies alternatives (CEA) Saclay, France
| | - Marilyne Blemont
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université;
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Walther C, Mayer S, Jungbauer A, Dürauer A. Getting ready for PAT: Scale up and inline monitoring of protein refolding of Npro fusion proteins. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.03.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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11
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Molecular insights on the recognition of a Lactococcus lactis cell wall pellicle by the phage 1358 receptor binding protein. J Virol 2014; 88:7005-15. [PMID: 24719416 DOI: 10.1128/jvi.00739-14] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The Gram-positive bacterium Lactococcus lactis is used for the production of cheeses and other fermented dairy products. Accidental infection of L. lactis cells by virulent lactococcal tailed phages is one of the major risks of fermentation failures in industrial dairy factories. Lactococcal phage 1358 possesses a host range limited to a few L. lactis strains and strong genomic similarities to Listeria phages. We report here the X-ray structures of phage 1358 receptor binding protein (RBP) in complex with monosaccharides. Each monomer of its trimeric RBP is formed of two domains: a "shoulder" domain linking the RBP to the rest of the phage and a jelly roll fold "head/host recognition" domain. This domain harbors a saccharide binding crevice located in the middle of a monomer. Crystal structures identified two sites at the RBP surface, ∼8 Å from each other, one accommodating a GlcNAc monosaccharide and the other accommodating a GlcNAc or a glucose 1-phosphate (Glc1P) monosaccharide. GlcNAc and GlcNAc1P are components of the polysaccharide pellicle that we identified at the cell surface of L. lactis SMQ-388, the host of phage 1358. We therefore modeled a galactofuranose (Galf) sugar bridging the two GlcNAc saccharides, suggesting that the trisaccharidic motif GlcNAc-Galf-GlcNAc (or Glc1P) might be common to receptors of genetically distinct lactococcal phages p2, TP091-1, and 1358. Strain specificity might therefore be elicited by steric clashes induced by the remaining components of the pellicle hexasaccharide. Taken together, these results provide a first insight into the molecular mechanism of host receptor recognition by lactococcal phages. IMPORTANCE Siphophages infecting the Gram-positive bacterium Lactococcus lactis are sources of milk fermentation failures in the dairy industry. We report here the structure of the pellicle polysaccharide from L. lactis SMQ-388, the specific host strain of phage 1358. We determined the X-ray structures of the lytic lactococcal phage 1358 receptor binding protein (RBP) in complex with monosaccharides. The positions and nature of monosaccharides bound to the RBP are in agreement with the pellicle structure and suggest a general binding mode of lactococcal phages to their pellicle saccharidic receptor.
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12
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Saez NJ, Vincentelli R. High-throughput expression screening and purification of recombinant proteins in E. coli. Methods Mol Biol 2014; 1091:33-53. [PMID: 24203323 DOI: 10.1007/978-1-62703-691-7_3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The protocols outlined in this chapter allow for the small-scale test expression of a single or multiple proteins concurrently using several expression conditions to identify optimal strategies for producing soluble, stable proteins. The protocols can be performed manually without the need for specialized equipment, or can be translated to robotic platforms. The high-throughput protocols begin with transformation in a 96-well format, followed by small-scale test expression using auto-induction medium in a 24-well format, finishing with purification in a 96-well format. Even from such a small scale, there is the potential to use the purified proteins for characterization in pilot studies, for sensitive micro-assays, or for the quick detection of and differentiation of the expected size and oxidation state of the protein by mass spectrometry.
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Affiliation(s)
- Natalie J Saez
- Architecture et Fonction des Macromolécules Biologiques, Aix Marseille Université, Marseille, France
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13
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Durand E, Zoued A, Spinelli S, Watson PJH, Aschtgen MS, Journet L, Cambillau C, Cascales E. Structural characterization and oligomerization of the TssL protein, a component shared by bacterial type VI and type IVb secretion systems. J Biol Chem 2012; 287:14157-68. [PMID: 22371492 DOI: 10.1074/jbc.m111.338731] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Type VI secretion system (T6SS) is a macromolecular system distributed in Gram-negative bacteria, responsible for the secretion of effector proteins into target cells. The T6SS has a broad versatility as it can target both eukaryotic and prokaryotic cells. It is therefore involved in host pathogenesis or killing neighboring bacterial cells to colonize a new niche. At the architecture level, the T6SS core apparatus is composed of 13 proteins, which assemble in two subcomplexes. One of these subcomplexes, composed of subunits that share structural similarities with bacteriophage tail and baseplate components, is anchored to the cell envelope by the membrane subcomplex. This latter is constituted of at least three proteins, TssL, TssM, and TssJ. The crystal structure of the TssJ outer membrane lipoprotein and its interaction with the inner membrane TssM protein have been recently reported. TssL and TssM share sequence homology and characteristics with two components of the Type IVb secretion system (T4bSS), IcmH/DotU and IcmF, respectively. In this study, we report the crystal structure of the cytoplasmic domain of the TssL inner membrane protein from the enteroaggregative Escherichia coli Sci-1 T6SS. It folds as a hook-like structure composed of two three-helix bundles. Two TssL molecules associate to form a functional complex. Although the TssL trans-membrane segment is the main determinant of self-interaction, contacts between the cytoplasmic domains are required for TssL function. Based on sequence homology and secondary structure prediction, we propose that the TssL structure is the prototype for the members of the TssL and IcmH/DotU families.
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Affiliation(s)
- Eric Durand
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France
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14
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Felisberto-Rodrigues C, Durand E, Aschtgen MS, Blangy S, Ortiz-Lombardia M, Douzi B, Cambillau C, Cascales E. Towards a structural comprehension of bacterial type VI secretion systems: characterization of the TssJ-TssM complex of an Escherichia coli pathovar. PLoS Pathog 2011; 7:e1002386. [PMID: 22102820 PMCID: PMC3213119 DOI: 10.1371/journal.ppat.1002386] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 10/04/2011] [Indexed: 11/24/2022] Open
Abstract
Type VI secretion systems (T6SS) are trans-envelope machines dedicated to the secretion of virulence factors into eukaryotic or prokaryotic cells, therefore required for pathogenesis and/or for competition towards neighboring bacteria. The T6SS apparatus resembles the injection device of bacteriophage T4, and is anchored to the cell envelope through a membrane complex. This membrane complex is composed of the TssL, TssM and TagL inner membrane anchored proteins and of the TssJ outer membrane lipoprotein. Here, we report the crystal structure of the enteroaggregative Escherichia coli Sci1 TssJ lipoprotein, a two four-stranded β-sheets protein that exhibits a transthyretin fold with an additional α-helical domain and a protruding loop. We showed that TssJ contacts TssM through this loop since a loop depleted mutant failed to interact with TssM in vitro or in vivo. Biophysical analysis of TssM and TssJ-TssM interaction suggest a structural model of the membrane-anchored outer shell of T6SS. Collectively, our results provide an improved understanding of T6SS assembly and encourage structure-aided drug design of novel antimicrobials targeting T6SS. Type VI secretion systems (T6SS) are specialized secretion machines responsible for the transport of virulence factors. T6SS are versatile as they are able to target both eukaryotic and prokaryotic cells. They therefore play an important role in pathogenesis by acting directly on the host, as well as eliminating competing bacteria from the niche. At a molecular level, T6SS are composed of a minimum of 13 proteins called core-components, all required for the activity of the secretion system. These core-components can be divided in two groups: soluble proteins having a common evolution history with bacteriophage T4 subunits, and membrane or membrane-associated proteins required for anchoring the bacteriophage-like structure to the envelope. Here, we report the crystal structure of one of the membrane-associated core component, the TssJ lipoprotein. The structure exhibits a transthyretin fold supplemented with additional structural elements. One of these, a loop connecting two beta-strands, is responsible for the interaction of the TssJ lipoprotein with the C-terminal domain of the inner membrane protein TssM. We propose that these two proteins link the two membranes and form a channel accommodating the bacteriophage-like structure. These results provide important new insights to understand the biogenesis of these secretion apparati.
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Affiliation(s)
- Catarina Felisberto-Rodrigues
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille, France
- CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Campus de Luminy, Marseille, France
| | - Eric Durand
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille, France
- CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Campus de Luminy, Marseille, France
| | - Marie-Stéphanie Aschtgen
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, CNRS UPR9027, Aix-Marseille Université, Marseille, France
| | - Stéphanie Blangy
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille, France
- CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Campus de Luminy, Marseille, France
| | - Miguel Ortiz-Lombardia
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille, France
- CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Campus de Luminy, Marseille, France
| | - Badreddine Douzi
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille, France
- CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Campus de Luminy, Marseille, France
| | - Christian Cambillau
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille, France
- CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Campus de Luminy, Marseille, France
- * E-mail: (EC); (CC)
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, CNRS UPR9027, Aix-Marseille Université, Marseille, France
- * E-mail: (EC); (CC)
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15
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Mühle M, Löchelt M, Denner J. Optimisation of expression and purification of the feline and primate foamy virus transmembrane envelope proteins using a 96 deep well screen. Protein Expr Purif 2011; 81:96-105. [PMID: 21964437 DOI: 10.1016/j.pep.2011.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 09/04/2011] [Accepted: 09/13/2011] [Indexed: 12/21/2022]
Abstract
The production of recombinant transmembrane proteins is due to their biochemical properties often troublesome and time consuming. Here the prokaryotic expression and purification of the transmembrane envelope proteins of the feline and primate foamy viruses using a screening assay for optimisation of expression in 96 deep well plates is described. Testing simultaneously various bacterial strains, media, temperatures, inducer concentrations and different transformants, conditions for an about twentyfold increased production were quickly determined. These small scale test conditions could be easily scaled up, allowing purification of milligram amounts of recombinant protein. Proteins with a purity of about 95% were produced using a new purification protocol, they were characterised by gel filtration and circular dichroism and successfully applied in immunological assays screening for foamy virus infection and in immunisation studies. Compared to the previously described protocol (M. Mühle, A. Bleiholder, S. Kolb, J. Hübner, M. Löchelt, J. Denner, Immunological properties of the transmembrane envelope protein of the feline foamy virus and its use for serological screening, Virology 412 (2011) 333-340), proteins with similar characteristics but about thirtyfold increased yields were obtained. The screening and production method presented here can also be applied for the production of transmembrane envelope proteins of other retroviruses, including HIV-1.
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Affiliation(s)
- Michael Mühle
- Robert Koch Institute, Nordufer 20, Berlin 13353, Germany
| | - Martin Löchelt
- German Institute for Cancer Research, Im Neuenheimer Feld 242, Heidelberg 69120, Germany
| | - Joachim Denner
- Robert Koch Institute, Nordufer 20, Berlin 13353, Germany.
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16
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High-throughput protein expression screening and purification in Escherichia coli. Methods 2011; 55:65-72. [DOI: 10.1016/j.ymeth.2011.08.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 07/25/2011] [Accepted: 08/11/2011] [Indexed: 11/18/2022] Open
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17
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Douillard FP, Mahony J, Campanacci V, Cambillau C, van Sinderen D. Construction of two Lactococcus lactis expression vectors combining the Gateway and the NIsin Controlled Expression systems. Plasmid 2011; 66:129-35. [PMID: 21807023 DOI: 10.1016/j.plasmid.2011.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2011] [Revised: 07/11/2011] [Accepted: 07/15/2011] [Indexed: 11/16/2022]
Abstract
Over the last 10 years, the NIsin Controlled Expression (NICE) system has been extensively used in the food-grade bacterium Lactococcus lactis subsp. cremoris to produce homologous and heterologous proteins for academic and biotechnological purposes. Although various L. lactis molecular tools have been developed, no expression vectors harboring the popular Gateway recombination system are currently available for this widely used cloning host. In this study, we constructed two expression vectors that combine the NICE and the Gateway recombination systems and we tested their applicability by recombining and over-expressing genes encoding structural proteins of lactococcal phages Tuc2009 and TP901-1. Over-expressed phage proteins were analyzed by immunoblotting and purified by His-tag affinity chromatography with protein productions yielding 2.8-3.7 mg/l of culture. This therefore is the first description of L. lactis NICE expression vectors which integrate the Gateway cloning technology and which are suitable for the production of sufficient amounts of proteins to facilitate subsequent structural and functional analyses.
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Affiliation(s)
- François P Douillard
- Department of Microbiology, University College Cork, Western Road, Cork, Ireland.
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18
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Correa A, Oppezzo P. Tuning different expression parameters to achieve soluble recombinant proteins in E. coli: advantages of high-throughput screening. Biotechnol J 2011; 6:715-30. [PMID: 21567962 DOI: 10.1002/biot.201100025] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/15/2011] [Accepted: 03/21/2011] [Indexed: 01/04/2023]
Abstract
Proteins are the main reagents for structural, biomedical, and biotechnological studies; however, some important challenges remain concerning protein solubility and stability. Numerous strategies have been developed, with some success, to mitigate these challenges, but a universal strategy is still elusive. Currently, researchers face a plethora of alternatives for the expression of the target protein, which generates a great diversity of conditions to be evaluated. Among these, different promoter strength, diverse expression host and constructs, or special culture conditions have an important role in protein solubility. With the arrival of automated high-throughput screening (HTS) systems, the evaluation of hundreds of different conditions within reasonable cost and time limits is possible. This technology increases the chances to obtain the target protein in a pure, soluble, and stable state. This review focuses on some of the most commonly used strategies for the expression of recombinant proteins in the enterobacterium Escherichia coli, including the use of HTS for the production of soluble proteins.
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Affiliation(s)
- Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
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19
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The Drosophila peptidoglycan-recognition protein LF interacts with peptidoglycan-recognition protein LC to downregulate the Imd pathway. EMBO Rep 2011; 12:327-33. [PMID: 21372849 DOI: 10.1038/embor.2011.19] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 01/03/2011] [Accepted: 01/20/2011] [Indexed: 01/14/2023] Open
Abstract
The peptidoglycan (PGN)-recognition protein LF (PGRP-LF) is a specific negative regulator of the immune deficiency (Imd) pathway in Drosophila. We determine the crystal structure of the two PGRP domains constituting the ectodomain of PGRP-LF at 1.72 and 1.94 Å resolution. The structures show that the LFz and LFw domains do not have a PGN-docking groove that is found in other PGRP domains, and they cannot directly interact with PGN, as confirmed by biochemical-binding assays. By using surface plasmon resonance analysis, we show that the PGRP-LF ectodomain interacts with the PGRP-LCx ectodomain in the absence and presence of tracheal cytotoxin. Our results suggest a mechanism for downregulation of the Imd pathway on the basis of the competition between PRGP-LCa and PGRP-LF to bind to PGRP-LCx.
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20
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Scaltriti E, Launay H, Genois MM, Bron P, Rivetti C, Grolli S, Ploquin M, Campanacci V, Tegoni M, Cambillau C, Moineau S, Masson JY. Lactococcal phage p2 ORF35-Sak3 is an ATPase involved in DNA recombination and AbiK mechanism. Mol Microbiol 2011; 80:102-16. [PMID: 21276096 DOI: 10.1111/j.1365-2958.2011.07561.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Virulent phages of the Siphoviridae family are responsible for milk fermentation failures worldwide. Here, we report the characterization of the product of the early expressed gene orf35 from Lactococcus lactis phage p2 (936 group). ORF35(p2), also named Sak3, is involved in the sensitivity of phage p2 to the antiviral abortive infection mechanism AbiK. The localization of its gene upstream of a gene coding for a single-strand binding protein as well as its membership to a superfamily of single-strand annealing proteins (SSAPs) suggested a possible role in homologous recombination. Electron microscopy showed that purified ORF35(p2) form a hexameric ring-like structure that is often found in proteins with a conserved RecA nucleotide-binding core. Gel shift assays and surface plasmon resonance data demonstrated that ORF35(p2) interacts preferentially with single-stranded DNA with nanomolar affinity. Atomic force microscopy showed also that it preferentially binds to sticky DNA substrates over blunt ends. In addition, in vitro assays demonstrated that ORF35(p2) is able to anneal complementary strands. Sak3 also stimulates Escherichia coli RecA-mediated homologous recombination. Remarkably, Sak3 was shown to possess an ATPase activity that is required for RecA stimulation. Collectively, our results demonstrate that ORF35(p2) is a novel SSAP stimulating homologous recombination.
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Affiliation(s)
- Erika Scaltriti
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités d'Aix-Marseille I & II, Campus de Luminy, case 932, 13288 Marseille cedex 09, France
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21
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Vellaiswamy M, Kowalczewska M, Merhej V, Nappez C, Vincentelli R, Renesto P, Raoult D. Characterization of rickettsial adhesin Adr2 belonging to a new group of adhesins in α-proteobacteria. Microb Pathog 2011; 50:233-42. [PMID: 21288480 DOI: 10.1016/j.micpath.2011.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/17/2011] [Accepted: 01/24/2011] [Indexed: 11/25/2022]
Abstract
BACKGROUND Rickettsia prowazekii is the etiological agent of epidemic typhus and is an obligate intracellular bacterium that grows as a parasite freely within the cytoplasm of a eukaryotic host cell. Previous studies have shown that rOmpA and rOmpB which belong to the family of rickettsial cell surface antigens are involved in vitro in the adhesion of Rickettsiae to epithelial cells. Recently, two putative rickettsial adhesins have been identified using high resolution 2D-PAGE coupled with mass spectrometry. In this study, we further characterize and describe the adhesin Adr2 from R. prowazekii. METHODOLOGY/PRINCIPAL FINDINGS Using an overlay assay coupled with mass spectrometry two adhesins, Adr1 (RP827) and Adr2 (RP828), were identified from the R. prowazekii proteome Recombinant R. prowazekii Adr2 was expressed through fusion with Dsbc in Escherichia coli, purified and concentrated, thus allowing production of specific monoclonal antibodies, as confirmed by western blot assays. Finally, inhibition of rickettsiae-induced cytotoxicity with monoclonal anti-Adr2 antibody has showed a greatest impact on bacterial cell entry at 8 h post-infection (ca50%) and then decreased progressively to attempt 18% of inhibition at day 7. These, correlated to the inhibition of rickettsiae-induced cytotoxicity with monoclonal anti-rOmpB antibody. Thus, Adr2 is sufficient to mediate R. prowazekii entry into the cell at early stage of mammalian cell infection. CONCLUSIONS Our results suggest that R. prowazekii Adr2 could be the main actor promoting the entry of rickettsiae into the host cells. The present study opens the framework for future investigations for better understanding of the Adr2 -mediated mechanisms involved in adhesion/invasion or intracellular survival of R. prowazekii.
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Affiliation(s)
- Manohari Vellaiswamy
- Université de la Méditerranée, Unité des Rickettsies, URMITE CNRS-IRD, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille cedex 05, France
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22
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Kinoshita Y, Tayama T, Kitamura K, Salimullah M, Uchida H, Suzuki M, Husimi Y, Nishigaki K. Novel concept microarray enabling PCR and multistep reactions through pipette-free aperture-to-aperture parallel transfer. BMC Biotechnol 2010; 10:71. [PMID: 20923572 PMCID: PMC2959086 DOI: 10.1186/1472-6750-10-71] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 10/06/2010] [Indexed: 11/15/2022] Open
Abstract
Background The microarray has contributed to developing the omic analysis. However, as it depends basically on the surface reaction, it is hard to perform bulk reactions and sequential multistep reactions. On the other hand, the popular microplate technology, which has a great merit of being able to perform parallel multistep reactions, has come to its limit in increasing the number of wells (currently, up to 9600) and reducing the volume to deal with due to the difficulty in operations. Results Here, we report a novel microarray technology which enables us to explore advanced applications, termed microarray-with-manageable volumes (MMV). The technical essence is in the pipette-free direct parallel transfer from well to well performed by centrifugation, evading the evaporation and adsorption-losses during handling. By developing the MMV plate, accompanying devices and techniques, generation of multiple conditions (256 kinds) and performance of parallel multistep reactions, including PCR and in vitro translation reactions, have been made possible. These were demonstrated by applying the MMV technology to searching lysozyme-crystallizing conditions and selecting peptides aimed for Aβ-binding or cathepsin E-inhibition. Conclusions With the introduction of a novel concept microarray (MMV) technology, parallel and multistep reactions in sub-μL scale have become possible.
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Affiliation(s)
- Yasunori Kinoshita
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
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23
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Genomics and structure/function studies of Rhabdoviridae proteins involved in replication and transcription. Antiviral Res 2010; 87:149-61. [DOI: 10.1016/j.antiviral.2010.02.322] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 02/20/2010] [Indexed: 01/19/2023]
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24
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Groisillier A, Hervé C, Jeudy A, Rebuffet E, Pluchon PF, Chevolot Y, Flament D, Geslin C, Morgado IM, Power D, Branno M, Moreau H, Michel G, Boyen C, Czjzek M. MARINE-EXPRESS: taking advantage of high throughput cloning and expression strategies for the post-genomic analysis of marine organisms. Microb Cell Fact 2010; 9:45. [PMID: 20546566 PMCID: PMC2897777 DOI: 10.1186/1475-2859-9-45] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 06/14/2010] [Indexed: 11/14/2022] Open
Abstract
Background The production of stable and soluble proteins is one of the most important steps prior to structural and functional studies of biological importance. We investigated the parallel production in a medium throughput strategy of genes coding for proteins from various marine organisms, using protocols that involved recombinatorial cloning, protein expression screening and batch purification. This strategy was applied in order to respond to the need for post-genomic validation of the recent success of a large number of marine genomic projects. Indeed, the upcoming challenge is to go beyond the bioinformatic data, since the bias introduced through the genomes of the so called model organisms leads to numerous proteins of unknown function in the still unexplored world of the oceanic organisms. Results We present here the results of expression tests for 192 targets using a 96-well plate format. Genes were PCR amplified and cloned in parallel into expression vectors pFO4 and pGEX-4T-1, in order to express proteins N-terminally fused to a six-histidine-tag and to a GST-tag, respectively. Small-scale expression and purification permitted isolation of 84 soluble proteins and 34 insoluble proteins, which could also be used in refolding assays. Selected examples of proteins expressed and purified to a larger scale are presented. Conclusions The objective of this program was to get around the bottlenecks of soluble, active protein expression and crystallization for post-genomic validation of a number of proteins that come from various marine organisms. Multiplying the constructions, vectors and targets treated in parallel is important for the success of a medium throughput strategy and considerably increases the chances to get rapid access to pure and soluble protein samples, needed for the subsequent biochemical characterizations. Our set up of a medium throughput strategy applied to genes from marine organisms had a mean success rate of 44% soluble protein expression from marine bacteria, archaea as well as eukaryotic organisms. This success rate compares favorably with other protein screening projects, particularly for eukaryotic proteins. Several purified targets have already formed the base for experiments aimed at post-genomic validation.
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Affiliation(s)
- Agnès Groisillier
- UPMC Univ Paris 6, UMR 7139 Végétaux marins et Biomolécules, LIA DIAMS, Station Biologique, Roscoff, France
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Yumerefendi H, Tarendeau F, Mas PJ, Hart DJ. ESPRIT: an automated, library-based method for mapping and soluble expression of protein domains from challenging targets. J Struct Biol 2010; 172:66-74. [PMID: 20206698 DOI: 10.1016/j.jsb.2010.02.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 02/24/2010] [Accepted: 02/28/2010] [Indexed: 01/28/2023]
Abstract
Expression of sufficient quantities of soluble protein for structural biology and other applications is often a very difficult task, especially when multimilligram quantities are required. In order to improve yield, solubility or crystallisability of a protein, it is common to subclone shorter genetic constructs corresponding to single- or multi-domain fragments. However, it is not always clear where domain boundaries are located, especially when working on novel targets with little or no sequence similarity to other proteins. Several methods have been described employing aspects of directed evolution to the recombinant expression of challenging proteins. These combine the construction of a random library of genetic constructs of a target with a screening or selection process to identify solubly expressing protein fragments. Here we review several datasets from the ESPRIT (Expression of Soluble Proteins by Random Incremental Truncation) technology to provide a view on its capabilities. Firstly, we demonstrate how it functions using the well-characterised NF-kappaB p50 transcription factor as a model system. Secondly, application of ESPRIT to the challenging PB2 subunit of influenza polymerase has led to several novel atomic resolution structures; here we present an overview of the screening phase of that project. Thirdly, analysis of the human kinase TBK1 is presented to show how the ESPRIT technology rapidly addresses the compatibility of challenging targets with the Escherichia coli expression system.
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Affiliation(s)
- Hayretin Yumerefendi
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, Grenoble Cedex 9, France
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Campanacci V, Veesler D, Lichière J, Blangy S, Sciara G, Moineau S, van Sinderen D, Bron P, Cambillau C. Solution and electron microscopy characterization of lactococcal phage baseplates expressed in Escherichia coli. J Struct Biol 2010; 172:75-84. [PMID: 20153432 DOI: 10.1016/j.jsb.2010.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 02/04/2010] [Accepted: 02/07/2010] [Indexed: 10/19/2022]
Abstract
We report here the characterization of several large structural protein complexes forming the baseplates (or part of them) of Siphoviridae phages infecting Lactococcus lactis: TP901-1, Tuc2009 and p2. We revisited a "block cloning" expression strategy and extended this approach to genomic fragments encoding proteins whose interacting partners have not yet been clearly identified. Biophysical characterization of some of these complexes using circular dichroism and size exclusion chromatography, coupled with on-line light scattering and refractometry, demonstrated that the over-produced recombinant proteins interact with each other to form large (up to 1.9MDa) and stable baseplate assemblies. Some of these complexes were characterized by electron microscopy confirming their structural homogeneity as well as providing a picture of their overall molecular shapes and symmetry. Finally, using these results, we were able to highlight similarities and differences with the well characterized much larger baseplate of the myophage T4.
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Affiliation(s)
- Valérie Campanacci
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 6098 CNRS and Universités Aix-Marseille I & II, Campus de Luminy, Case 932, Marseille Cedex 09, France.
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Listwan P, Pédelacq JD, Lockard M, Bell C, Terwilliger TC, Waldo GS. The optimization of in vitro high-throughput chemical lysis of Escherichia coli. Application to ACP domain of the polyketide synthase ppsC from Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2010; 11:41-9. [PMID: 20069378 PMCID: PMC2855807 DOI: 10.1007/s10969-009-9077-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 12/30/2009] [Indexed: 11/26/2022]
Abstract
Protein production in Escherichia coli involves high-level expression in a culture, followed by harvesting of the cells and finally their disruption, or lysis, to release the expressed proteins. We compare three high-throughput chemical lysis methods to sonication, using a robotic platform and methodologies developed in our laboratory [1]. Under the same expression conditions, all lysis methods varied in the degree of released soluble proteins. With a set of 96 test proteins, we used our split GFP to quantify the soluble and insoluble protein fractions after lysis. Both the amount of soluble protein and the percentage recovered in the soluble fraction using SoluLyse were well correlated with sonication. Two other methods, Bugbuster and lysozyme, did not correlate well with sonication. Considering the effects of lysis methods on protein solubility is especially important when accurate protein solubility measurements are needed, for example, when testing adjuvants, growth media, temperature, or when establishing the effects of truncation or sequence variation on protein stability.
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Affiliation(s)
- Pawel Listwan
- Bioscience Division, MS-M888, Los Alamos National Laboratory, Bikini Atoll Rd, SM30, Los Alamos, NM 87545, USA.
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Diacovich L, Dumont A, Lafitte D, Soprano E, Guilhon AA, Bignon C, Gorvel JP, Bourne Y, Méresse S. Interaction between the SifA virulence factor and its host target SKIP is essential for Salmonella pathogenesis. J Biol Chem 2009; 284:33151-60. [PMID: 19801640 PMCID: PMC2785157 DOI: 10.1074/jbc.m109.034975] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 09/16/2009] [Indexed: 11/06/2022] Open
Abstract
SifA is a Salmonella effector that is translocated into infected cells by the pathogenicity island 2-encoded type 3 secretion system. SifA is a critical virulence factor. Previous studies demonstrated that, upon translocation, SifA binds the pleckstrin homology motif of the eukaryotic host protein SKIP. In turn, the SifA-SKIP complex regulates the mobilization of the molecular motor kinesin-1 on the bacterial vacuole. SifA exhibits multiple domains containing functional motifs. Here we performed a molecular dissection and a mutational study of SifA to evaluate the relative contribution of the different domains to SifA functions. Biochemical and crystallographic analysis confirmed that the N-terminal domain of SifA is sufficient to interact with the pleckstrin homology domain of SKIP, forming a 1:1 complex with a micromolar dissociation constant. Mutation of the tryptophan residue in the WXXXE motif, which has been proposed to mimic active form of GTPase, deeply affected the stability and the translocation of SifA while mutations of the glutamic residue had no functional impact. A SifA L130D mutant that does not bind SKIP showed a DeltasifA-like phenotype both in infected cells and in the mouse model of infection. We concluded that the WXXXE motif is essential for maintaining the tertiary structure of SifA, the functions of which require the interaction with the eukaryotic protein SKIP.
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Affiliation(s)
- Lautaro Diacovich
- From the
Centre d'Immunologie de Marseille-Luminy, CNRS UMR 6102, INSERM U631, Université de la Méditerranée, Parc Scientifique de Luminy, Case 906, 13288 Marseille Cedex 9
| | - Audrey Dumont
- From the
Centre d'Immunologie de Marseille-Luminy, CNRS UMR 6102, INSERM U631, Université de la Méditerranée, Parc Scientifique de Luminy, Case 906, 13288 Marseille Cedex 9
| | - Daniel Lafitte
- the
Plateau Protéomique Timone, INSERM UMR 911, Aix-Marseille Université, 13288 Marseille, France
| | - Elodie Soprano
- the
Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS Université Aix-Marseille, Parc Scientifique de Luminy, Case 932, 13288 Marseille Cedex 9, and
| | - Aude-Agnès Guilhon
- From the
Centre d'Immunologie de Marseille-Luminy, CNRS UMR 6102, INSERM U631, Université de la Méditerranée, Parc Scientifique de Luminy, Case 906, 13288 Marseille Cedex 9
| | - Christophe Bignon
- the
Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS Université Aix-Marseille, Parc Scientifique de Luminy, Case 932, 13288 Marseille Cedex 9, and
| | - Jean-Pierre Gorvel
- From the
Centre d'Immunologie de Marseille-Luminy, CNRS UMR 6102, INSERM U631, Université de la Méditerranée, Parc Scientifique de Luminy, Case 906, 13288 Marseille Cedex 9
| | - Yves Bourne
- the
Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS Université Aix-Marseille, Parc Scientifique de Luminy, Case 932, 13288 Marseille Cedex 9, and
| | - Stéphane Méresse
- From the
Centre d'Immunologie de Marseille-Luminy, CNRS UMR 6102, INSERM U631, Université de la Méditerranée, Parc Scientifique de Luminy, Case 906, 13288 Marseille Cedex 9
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Alberto F, Navarro D, de Vries R, Asther M, Record E. Technical advance in fungal biotechnology: development of a miniaturized culture method and an automated high-throughput screening. Lett Appl Microbiol 2009; 49:278-82. [DOI: 10.1111/j.1472-765x.2009.02655.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Mammalian G-protein-coupled receptor expression in Escherichia coli: I. High-throughput large-scale production as inclusion bodies. Anal Biochem 2009; 386:147-55. [DOI: 10.1016/j.ab.2008.12.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 11/27/2008] [Accepted: 12/13/2008] [Indexed: 11/20/2022]
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Crystal structure of ORF12 from Lactococcus lactis phage p2 identifies a tape measure protein chaperone. J Bacteriol 2008; 191:728-34. [PMID: 19047351 DOI: 10.1128/jb.01363-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We report here the characterization of the nonstructural protein ORF12 of the virulent lactococcal phage p2, which belongs to the Siphoviridae family. ORF12 was produced as a soluble protein, which forms large oligomers (6- to 15-mers) in solution. Using anti-ORF12 antibodies, we have confirmed that ORF12 is not found in the virion structure but is detected in the second half of the lytic cycle, indicating that it is a late-expressed protein. The structure of ORF12, solved by single anomalous diffraction and refined at 2.9-A resolution, revealed a previously unknown fold as well as the presence of a hydrophobic patch at its surface. Furthermore, crystal packing of ORF12 formed long spirals in which a hydrophobic, continuous crevice was identified. This crevice exhibited a repeated motif of aromatic residues, which coincided with the same repeated motif usually found in tape measure protein (TMP), predicted to form helices. A model of a complex between ORF12 and a repeated motif of the TMP of phage p2 (ORF14) was generated, in which the TMP helix fitted exquisitely in the crevice and the aromatic patches of ORF12. We suggest, therefore, that ORF12 might act as a chaperone for TMP hydrophobic repeats, maintaining TMP in solution during the tail assembly of the lactococcal siphophage p2.
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Listwan P, Terwilliger TC, Waldo GS. Automated, high-throughput platform for protein solubility screening using a split-GFP system. ACTA ACUST UNITED AC 2008; 10:47-55. [PMID: 19039681 DOI: 10.1007/s10969-008-9049-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 11/06/2008] [Indexed: 10/21/2022]
Abstract
Overproduction of soluble and stable proteins for functional and structural studies is a major bottleneck for structural genomics programs and traditional biochemistry laboratories. Many high-payoff proteins that are important in various biological processes are "difficult to handle" as protein reagents in their native form. We have recently made several advances in enabling biochemical technologies for improving protein stability (http://www.lanl.gov/projects/gfp/), allowing stratagems for efficient protein domain trapping, solubility-improving mutations, and finding protein folding partners. In particular split-GFP protein tags are a very powerful tool for detection of stable protein domains. Soluble, stable proteins tagged with the 15 amino acid GFP fragment (amino acids 216-228) can be detected in vivo and in vitro using the engineered GFP 1-10 "detector" fragment (amino acids 1-215). If the small tag is accessible, the detector fragment spontaneously binds resulting in fluorescence. Here, we describe our current and on-going efforts to move this process from the bench (manual sample manipulation) to an automated, high-throughput, liquid-handling platform. We discuss optimization and validation of bacterial culture growth, lysis protocols, protein extraction, and assays of soluble and insoluble protein in multiple 96 well plate format. The optimized liquid-handling protocol can be used for rapid determination of the optimal, compact domains from single ORFS, collections of ORFS, or cDNA libraries.
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Affiliation(s)
- Pawel Listwan
- Bioscience Division, MS-M888, Los Alamos National Laboratory, Bikini Atoll Rd, SM30, Los Alamos, NM 87545, USA
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Busso D, Thierry JC, Moras D. The structural biology and genomics platform in strasbourg: an overview. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2008; 426:523-36. [PMID: 18542888 DOI: 10.1007/978-1-60327-058-8_35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This chapter describes the modules and facilities of the Structural Biology and Genomics Platform (SBGP), Strasbourg, France. The platform consists of three modules (cloning, mini-expression screening; optimization-large scale protein production; characterization, crystallization) with dedicated scientists, and other facilities for purifying recombinant proteins and solving three-dimensional (3D) structures. Strong collaborations have been established with the Integrative Bioinformatics and Genomics group, located in the same institition, for target selection and domains definition. To handle large numbers of samples, classical and new protocols were adapted to automation, increasing reproducibility and reducing error risks as well. Using the platform and its facilities, over 2,000 expression vectors have been constructed and more than 40 novel structures, of mostly human proteins, have been solved.
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Affiliation(s)
- Didier Busso
- Structural Biology and Genomics Platform, IGBMC, CNRS/INSERM/Université Louis Pasteur, Illkirch, France
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Dherbécourt J, Falentin H, Canaan S, Thierry A. A genomic search approach to identify esterases in Propionibacterium freudenreichii involved in the formation of flavour in Emmental cheese. Microb Cell Fact 2008; 7:16. [PMID: 18498642 PMCID: PMC2442053 DOI: 10.1186/1475-2859-7-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Accepted: 05/22/2008] [Indexed: 11/25/2022] Open
Abstract
Background Lipolysis is an important process of cheese ripening that contributes to the formation of flavour. Propionibacterium freudenreichii is the main agent of lipolysis in Emmental cheese; however, the enzymes involved produced by this species have not yet been identified. Lipolysis is performed by esterases (carboxylic ester hydrolases, EC 3.1.1.-) which are able to hydrolyse acylglycerols bearing short, medium and long chain fatty acids. The genome sequence of P. freudenreichii type strain CIP103027T was recently obtained in our laboratory. The aim of this study was to identify as exhaustively as possible the potential esterases in P. freudenreichii that could be involved in the hydrolysis of acylglycerols in Emmental cheese. The proteins identified were produced in a soluble and active form by heterologous expression in Escherichia coli for further study of their activity and specificity of hydrolysed substrates. Results The approach chosen was a genomic search approach that combined and compared four methods based on automatic and manual searches of homology and motifs among P. freudenreichii CIP103027T predicted proteins. Twenty-three putative esterases were identified in this step. Then a selection step permitted to focus the study on the 12 most probable esterases, according to the presence of the GXSXG motif of the α/β hydrolase fold family. The 12 corresponding coding sequences were cloned in expression vectors, containing soluble N-terminal fusion proteins. The best conditions to express each protein in a soluble form were found thanks to an expression screening, using an incomplete factorial experimental design. Eleven out of the 12 proteins were expressed in a soluble form in E. coli and six showed esterase activity on 1-naphthyl acetate and/or propionate, as demonstrated by a zymographic method. Conclusion We were able to demonstrate that our genomic search approach was efficient to identify esterases from the genome of a P. freudenreichii strain, more exhaustively than classical approaches. This study highlights the interest in using the automatic search of motifs, with the manual search of homology to previously characterised enzymes as a complementary method. Only further characterisations would permit the identification of the esterases of P. freudenreichii involved in the lipolysis in Emmental cheese.
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Affiliation(s)
- Julien Dherbécourt
- INRA, Agrocampus Rennes, UMR1253 Science et Technologie du Lait et de l'OEuf, F-35000 Rennes, France.
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Busso D, Stierlé M, Thierry JC, Moras D. A comparison of inoculation methods to simplify recombinant protein expression screening in Escherichia coli. Biotechniques 2008; 44:101-6. [PMID: 18254387 DOI: 10.2144/000112632] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the past five years, Structural Genomics (SG) initiatives have established an automated pipeline for protein production in Escherichia coli to rapidly screen various conditions, resulting in soluble expression of recombinant proteins to aid in carrying out structural studies. However, some steps of the procedure are still extensive and require manual handling. Here, we present a comparative study of one step of the process, E. coli cultivation, using a set of 12 expression vectors encoding for fusion proteins of seven independent target proteins. First, we show that performing E. coli growth in auto-inducible medium (ZYM-5052) results in a comparable protein expression/solubility profile to that obtained when growing cells in classical Luria-Bertani (LB) medium. Second, we show that the transformation mix can be used directly to inoculate a culture, saving time and circumventing the error-prone step of colony picking, without impairing cell growth and the protein expression/solubility profile. Thus, we show that a basic, but nevertheless essential, step of a protein production pipeline, E. coli cultivation, can be simplified to a single event that is fully compatible with complete automation.
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Affiliation(s)
- Didier Busso
- Institut de Génetique et de Biologie Moléculaire et Cellulaire/Centre National de Recherche Scientifique/Institut National de la Santé de la Recherche Médicale, Université Louis Pasteur, Illkirch, France.
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Peleg Y, Unger T. Application of high-throughput methodologies to the expression of recombinant proteins in E. coli. Methods Mol Biol 2008; 426:197-208. [PMID: 18542865 DOI: 10.1007/978-1-60327-058-8_12] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Despite the large body of knowledge accumulated on recombinant protein expression, production, primarily of eukaryotic proteins, remains a challenge. The biggest obstacle is in obtaining large amounts of a given protein in a correctly folded form. Several strategies are being used to increase both yields and solubility. These include expression with fusion proteins, co-expression with molecular chaperones or a protein partner, and use of multiple constructs for each protein. Any given method may help to increase expression and solubility for a given protein, but often more than one rescue strategy should be tried. To perform several different rescue strategies on multiple proteins, high throughout (HTP) methodologies are applied. This chapter presents HTP methodologies for DNA cloning in multiple expression vectors and expression screening to identify clones capable of producing soluble proteins.
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Affiliation(s)
- Yoav Peleg
- Israel Structural Proteomics Center (ISPC), Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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37
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Sciara G, Blangy S, Siponen M, Mc Grath S, van Sinderen D, Tegoni M, Cambillau C, Campanacci V. A topological model of the baseplate of lactococcal phage Tuc2009. J Biol Chem 2007; 283:2716-23. [PMID: 18045876 DOI: 10.1074/jbc.m707533200] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phages infecting Lactococcus lactis, a Gram-positive bacterium, are a recurrent problem in the dairy industry. Despite their economical importance, the knowledge on these phages, belonging mostly to Siphoviridae, lags behind that accumulated for members of Myoviridae. The three-dimensional structures of the receptor-binding proteins (RBP) of three lactococcal phages have been determined recently, illustrating their modular assembly and assigning the nature of their bacterial receptor. These RBPs are attached to the baseplate, a large phage organelle, located at the tip of the tail. Tuc2009 baseplate is formed by the products of 6 open read frames, including the RBP. Because phage binding to its receptor induces DNA release, it has been postulated that the baseplate might be the trigger for DNA injection. We embarked on a structural study of the lactococcal phages baseplate, ultimately to gain insight into the triggering mechanism following receptor binding. Structural features of the Tuc2009 baseplate were established using size exclusion chromatography coupled to on-line UV-visible absorbance, light scattering, and refractive index detection (MALS/UV/RI). Combining the results of this approach with literature data led us to propose a "low resolution" model of Tuc2009 baseplate. This model will serve as a knowledge base to submit relevant complexes to crystallization trials.
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Affiliation(s)
- Giuliano Sciara
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, 163 Avenue de Luminy Case 932, Marseille Cedex 09, France
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Psakis G, Nitschkowski S, Holz C, Kress D, Maestre-Reyna M, Polaczek J, Illing G, Essen LO. Expression screening of integral membrane proteins from Helicobacter pylori 26695. Protein Sci 2007; 16:2667-76. [PMID: 17965189 DOI: 10.1110/ps.073104707] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The efficiency of Helicobacter pylori as a mucosal pathogen is caused by unique soluble and integral membrane proteins, which allow its survival at acidic pH and successful colonization of the gastric environment. With about one-fourth of the H. pylori's proteome comprising integral membrane proteins, the need for solution of their three-dimensional (3D) structures becomes persistent as it can potentially drive the generation of more effective drugs. This study presents a medium-throughput approach for cloning and expression screening of integral membrane proteins from H. pylori (26695) using Escherichia coli as the expression host. One-hundred sixteen H. pylori targets were cloned into two different vector systems and heterologously expressed in E. coli. Eighty-four percent of these proteins displayed medium to high expression. No clear-cut correlation was found between expression levels and number of putative transmembrane spans, predicted functionality, and molecular mass. Nonetheless, expression of transporters and hypothetical proteins < or =40 kDa with two to four transmembrane spans displayed generally high expression levels. To statistically strengthen the quality of the data from the medium-throughput approach, a comparison with data derived from robotic-based methodologies was conducted. Optimization of expression and solubilization conditions for selected targets was also performed. Seventeen targets have been purified and subjected to crystallization so far. Eighteen percent of these targets (2/17) produced crystals under specific sets of crystallization conditions.
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Affiliation(s)
- Georgios Psakis
- Department of Chemistry, Philipps University, Marburg 35032, Germany
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Prodromou C, Savva R, Driscoll PC. DNA fragmentation-based combinatorial approaches to soluble protein expression Part I. Generating DNA fragment libraries. Drug Discov Today 2007; 12:931-8. [PMID: 17993411 DOI: 10.1016/j.drudis.2007.08.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 08/16/2007] [Accepted: 08/21/2007] [Indexed: 11/28/2022]
Abstract
In addressing a new drug discovery target, the generation of tractable protein substrates for functional and structural analyses can represent a significant hurdle. Traditional approaches rely on protein expression trials of multiple variants in various systems, frequently with limited success. The increasing knowledge base derived from genomics and structural proteomics initiatives assists the bioinformatics-led design of these experiments. Nevertheless, for many eukaryotic polypeptides, particularly those with relatively few homologues, the generation of useful protein products can still be a major challenge. This review describes the basis of efforts to forge an alternative 'domain-hunting' paradigm, based upon combinatorial sampling of expression construct libraries derived by fragmentation of the encoding DNA template, namely the methods and considerations in generating fragment length DNA from target genes. An accompanying review focuses upon the expression screening of such combinatorial DNA libraries for the sampling of the corresponding set of protein fragments.
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Affiliation(s)
- Chrisostomos Prodromou
- Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, United Kingdom
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40
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Benoit I, Coutard B, Oubelaid R, Asther M, Bignon C. Expression in Escherichia coli, refolding and crystallization of Aspergillus niger feruloyl esterase A using a serial factorial approach. Protein Expr Purif 2007; 55:166-74. [PMID: 17533138 DOI: 10.1016/j.pep.2007.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 03/23/2007] [Accepted: 04/01/2007] [Indexed: 11/19/2022]
Abstract
Hydrolysis of plant biomass is achieved by the combined action of enzymes secreted by microorganisms and directed against the backbone and the side chains of plant cell wall polysaccharides. Among side chains degrading enzymes, the feruloyl esterase A (FAEA) specifically removes feruloyl residues. Thus, FAEA has potential applications in a wide range of industrial processes such as paper bleaching or bio-ethanol production. To gain insight into FAEA hydrolysis activity, we solved its crystal structure. In this paper, we report how the use of four consecutive factorial approaches (two incomplete factorials, one sparse matrix, and one full factorial) allowed expressing in Escherichia coli, refolding and then crystallizing Aspergillus niger FAEA in 6 weeks. Culture conditions providing the highest expression level were determined using an incomplete factorial approach made of 12 combinations of four E. coli strains, three culture media and three temperatures (full factorial: 36 combinations). Aspergillus niger FAEA was expressed in the form of inclusion bodies. These were dissolved using a chaotropic agent, and the protein was purified by affinity chromatography on Ni column under denaturing conditions. A suitable buffer for refolding the protein eluted from the Ni column was found using a second incomplete factorial approach made of 96 buffers (full factorial: 3840 combinations). After refolding, the enzyme was further purified by gel filtration, and then crystallized following a standard protocol: initial crystallization conditions were found using commercial crystallization screens based on a sparse matrix. Crystals were then optimized using a full factorial screen.
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Affiliation(s)
- Isabelle Benoit
- UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Université de Provence et de la Méditerranée, ESIL, 163 avenue de Luminy CP 925, 13288 Marseille cedex 09, France
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Jenney FE, Adams MWW. The impact of extremophiles on structural genomics (and vice versa). Extremophiles 2007; 12:39-50. [PMID: 17563834 DOI: 10.1007/s00792-007-0087-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 04/19/2007] [Indexed: 11/24/2022]
Abstract
The advent of the complete genome sequences of various organisms in the mid-1990s raised the issue of how one could determine the function of hypothetical proteins. While insight might be obtained from a 3D structure, the chances of being able to predict such a structure is limited for the deduced amino acid sequence of any uncharacterized gene. A template for modeling is required, but there was only a low probability of finding a protein closely-related in sequence with an available structure. Thus, in the late 1990s, an international effort known as structural genomics (SG) was initiated, its primary goal to "fill sequence-structure space" by determining the 3D structures of representatives of all known protein families. This was to be achieved mainly by X-ray crystallography and it was estimated that at least 5,000 new structures would be required. While the proteins (genes) for SG have subsequently been derived from hundreds of different organisms, extremophiles and particularly thermophiles have been specifically targeted due to the increased stability and ease of handling of their proteins, relative to those from mesophiles. This review summarizes the significant impact that extremophiles and proteins derived from them have had on SG projects worldwide. To what extent SG has influenced the field of extremophile research is also discussed.
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Affiliation(s)
- Francis E Jenney
- Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Sciences Complex, Green Street, Athens, GA 30602-7229, USA
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Taussig MJ, Stoevesandt O, Borrebaeck CAK, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dübel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, Hoheisel JD, Joos TO, Kallioniemi O, Koegl M, Koegll M, Konthur Z, Korn B, Kremmer E, Krobitsch S, Landegren U, van der Maarel S, McCafferty J, Muyldermans S, Nygren PA, Palcy S, Plückthun A, Polic B, Przybylski M, Saviranta P, Sawyer A, Sherman DJ, Skerra A, Templin M, Ueffing M, Uhlén M. ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods 2007; 4:13-7. [PMID: 17195019 DOI: 10.1038/nmeth0107-13] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human proteome. Given the huge diversity of the proteome, the scale of the project is potentially immense but nevertheless feasible in the context of a pan-European or even worldwide coordination.
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Affiliation(s)
- Michael J Taussig
- Technology Research Group, The Babraham Institute, Cambridge CB22 3AT, UK.
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Fullerton SWB, Blaschke M, Coutard B, Gebhardt J, Gorbalenya A, Canard B, Tucker PA, Rohayem J. Structural and functional characterization of sapovirus RNA-dependent RNA polymerase. J Virol 2006; 81:1858-71. [PMID: 17121797 PMCID: PMC1797576 DOI: 10.1128/jvi.01462-06] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Sapoviruses are one of the major agents of acute gastroenteritis in childhood. They form a tight genetic cluster (genus) in the Caliciviridae family that regroups both animal and human pathogenic strains. No permissive tissue culture has been developed for human sapovirus, limiting its characterization to surrogate systems. We report here on the first extensive characterization of the key enzyme of replication, the RNA-dependent RNA polymerase (RdRp) associated with the 3D(pol)-like protein. Enzymatically active sapovirus 3D(pol) and its defective mutant were expressed in Escherichia coli and purified. The overall structure of the sapovirus 3D(pol) was determined by X-ray crystallography to 2.32-A resolution. It revealed a right hand fold typical for template-dependent polynucleotide polymerases. The carboxyl terminus is located within the active site cleft, as observed in the RdRp of some (norovirus) but not other (lagovirus) caliciviruses. Sapovirus 3D(pol) prefers Mn(2+) over Mg(2+) but may utilize either as a cofactor in vitro. In a synthetic RNA template-dependent reaction, sapovirus 3D(pol) synthesizes a double-stranded RNA or labels the template 3' terminus by terminal transferase activity. Initiation of RNA synthesis occurs de novo on heteropolymeric templates or in a primer-dependent manner on polyadenylated templates. Strikingly, this mode of initiation of RNA synthesis was also described for norovirus, but not for lagovirus, suggesting structural and functional homologies in the RNA-dependent RNA polymerase of human pathogenic caliciviruses. This first experimental evidence makes sapovirus 3D(pol) an attractive target for developing drugs to control calicivirus infection in humans.
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Ricagno S, Campanacci V, Blangy S, Spinelli S, Tremblay D, Moineau S, Tegoni M, Cambillau C. Crystal structure of the receptor-binding protein head domain from Lactococcus lactis phage bIL170. J Virol 2006; 80:9331-5. [PMID: 16940545 PMCID: PMC1563906 DOI: 10.1128/jvi.01160-06] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis, a gram-positive bacterium widely used by the dairy industry, is subject to lytic phage infections. In the first step of infection, phages recognize the host saccharidic receptor using their receptor binding protein (RBP). Here, we report the 2.30-A-resolution crystal structure of the RBP head domain from phage bIL170. The structure of the head monomer is remarkably close to those of other lactococcal phages, p2 and TP901-1, despite any sequence identity with them. The knowledge of the three-dimensional structures of three RBPs gives a better insight into the module exchanges which have occurred among phages.
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Affiliation(s)
- Stefano Ricagno
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités Aix-Marseille I & II, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France
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Abstract
The rapid assessment of protein solubility is essential for evaluating expressed proteins and protein variants for use as reagents for downstream studies. Solubility screens based on antibody blots are complex and have limited screening capacity. Protein solubility screens using split beta-galactosidase in vivo and in vitro can perturb protein folding. Split GFP used for monitoring protein interactions folds poorly, and to overcome this limitation, we recently developed a protein-tagging system based on self-complementing split GFP derived from an exceptionally well folded variant of GFP termed 'superfolder GFP'. Here we present the step-by-step procedure of the solubility assay using split GFP. A 15-amino-acid GFP fragment, GFP 11, is fused to a test protein. The GFP 1-10 detector fragment is expressed separately. These fragments associate spontaneously to form fluorescent GFP. The fragments are soluble, and the GFP 11 tag has minimal effect on protein solubility and folding. We describe high-throughput protein solubility screens amenable both for in vivo and in vitro formats. The split-GFP system is composed of two vectors used in the same strain: pTET GFP 11 and pET GFP 1-10 (Fig. 1 and Supplementary Note online). The gene encoding the protein of interest is cloned into the pTET GFP 11 vector (resulting in an N-terminal fusion) and transformed into Escherichia coli BL21 (DE3) cells containing the pET GFP 1-10 plasmid. We also describe how this system can be used for selecting soluble proteins from a library of variants (Box 1). The large screening power of the in vivo assay combined with the high accuracy of the in vitro assay point to the efficiency of this two-step split-GFP tool for identifying soluble clones suitable for purification and downstream applications.
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Affiliation(s)
- Stéphanie Cabantous
- Bioscience Division, MS-M888, Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87545, USA
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Schultz T, Martinez L, de Marco A. The evaluation of the factors that cause aggregation during recombinant expression in E. coli is simplified by the employment of an aggregation-sensitive reporter. Microb Cell Fact 2006; 5:28. [PMID: 16948849 PMCID: PMC1564408 DOI: 10.1186/1475-2859-5-28] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 09/01/2006] [Indexed: 11/28/2022] Open
Abstract
Background The yields of soluble recombinant proteins expressed in bacteria are often low due to the tendency of the heterologous proteins to form aggregates. Therefore, aggregation reporters have been envisaged to simplify the comparison among different expression conditions and to speed up the identification of suitable protocols that improve the solubility. The probe we used is composed by an IbpAB promoter specifically activated by protein aggregates fused to a sequence coding the β-galactosidase, the activity of which becomes, therefore, indicative of the aggregation degree. Results The collected data show that the probe is reliable in terms of reproducibility inside a range of experimental conditions and faster and more sensitive than the analysis methods based on SDS-PAGE and successive western blot. The β-galactosidase probe was useful to identify which parameters could influence the aggregation of the model proteins and to set up an optimized expression protocol. The effect of growth temperature, induction modality, co-expression with molecular chaperones and addition of osmolytes on the accumulation of aggregates were evaluated following the β-galactosidase activity. Interestingly, a significant correlation was observed between estimated decreased aggregation and higher yields of soluble protein. We also compared a set of expression vectors with various regulative features and found that the single characteristics, like promoter, copy number or polymerase, were not relevant for controlling the recombinant protein aggregation whilst the crucial factor resulted being the total expression rate of the system. Conclusion The aggregation reporter used in our experiments represents a useful tool to evaluate the different factors that can be modulated to optimize a recombinant expression protocol. Furthermore, the rapid estimation of the aggregation degree enables to discriminate this from other causes responsible for scarce recombinant yields.
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Affiliation(s)
- Tina Schultz
- EMBL Scientific Core Facilities, Meyerhofstr. 1, D-69117, Heidelberg, Germany
| | - Lucia Martinez
- EMBL Scientific Core Facilities, Meyerhofstr. 1, D-69117, Heidelberg, Germany
| | - Ario de Marco
- EMBL Scientific Core Facilities, Meyerhofstr. 1, D-69117, Heidelberg, Germany
- IFOM-IEO Campus, Biochemistry Unit, via Adamello 16, I-20139, Milano, Italy
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Goulet A, Spinelli S, Campanacci V, Porciero S, Blangy S, Garrett RA, van Tilbeurgh H, Leulliot N, Basta T, Prangishvili D, Cambillau C. Crystallization and preliminary X-ray diffraction analysis of protein 14 from Sulfolobus islandicus filamentous virus (SIFV). Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:884-6. [PMID: 16946470 PMCID: PMC2242861 DOI: 10.1107/s1744309106029150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 07/27/2006] [Indexed: 11/10/2022]
Abstract
A large-scale programme has been embarked upon aiming towards the structural determination of conserved proteins from viruses infecting hyperthermophilic archaea. Here, the crystallization of protein 14 from the archaeal virus SIFV is reported. This protein, which contains 111 residues (MW 13 465 Da), was cloned and expressed in Escherichia coli with an N-terminal His(6) tag and purified to homogeneity. The tag was subsequently cleaved and the protein was crystallized using PEG 1000 or PEG 4000 as a precipitant. Large crystals were obtained of the native and the selenomethionine-labelled protein using sitting drops of 100-300 nl. Crystals belong to space group P6(2)22 or P6(4)22, with unit-cell parameters a = b = 68.1, c = 132.4 A. Diffraction data were collected to a maximum acceptable resolution of 2.95 and 3.20 A for the SeMet-labelled and native protein, respectively.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Valérie Campanacci
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Sophie Porciero
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Stéphanie Blangy
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Roger A. Garrett
- Danish Archaea Centre, Institute of Molecular Biology, Copenhagen University, Soelvgade 83H, DK1307 Copenhagen K, Denmark
| | - Herman van Tilbeurgh
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris 11, Bâtiment 430, 91405 Orsay, France
| | - Nicolas Leulliot
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris 11, Bâtiment 430, 91405 Orsay, France
| | - Tamara Basta
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 25 Rue du Dr Roux, 75724 Paris CEDEX 15, France
| | - David Prangishvili
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 25 Rue du Dr Roux, 75724 Paris CEDEX 15, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
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Wu G, Doberstein SK. HTS technologies in biopharmaceutical discovery. Drug Discov Today 2006; 11:718-24. [PMID: 16846799 DOI: 10.1016/j.drudis.2006.06.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 04/07/2006] [Accepted: 06/14/2006] [Indexed: 12/31/2022]
Abstract
The concepts and philosophies of HTS can be productively applied to the discovery of new biopharmaceuticals. It is now possible, comprehensively and systematically, to enumerate, clone, produce and screen all secreted proteins, by building upon knowledge accumulated over the past two decades in HTS, genomics and parallel protein expression technologies. Each of the crucial operational components (comprehensive and high-quality cDNA library construction, proper protein-sequence classification, high-throughput protein production, medically relevant assays, state-of-the-art screening and data management) must be optimized to increase the chances of success. In this review, we draw comparisons between small-molecule and protein screening to illuminate common underlying principles as well as differences between the two operations.
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Affiliation(s)
- Ge Wu
- Five Prime Therapeutics, 1650 Owens St., Suite 200, San Francisco, CA 94158, USA.
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Charbonnier S, Zanier K, Masson M, Travé G. Capturing protein-protein complexes at equilibrium: the holdup comparative chromatographic retention assay. Protein Expr Purif 2006; 50:89-101. [PMID: 16884919 DOI: 10.1016/j.pep.2006.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 06/12/2006] [Accepted: 06/14/2006] [Indexed: 11/28/2022]
Abstract
The popular pulldown chromatographic assay detects complexes mediated by fusion proteins retained on affinity resin. The main limitation of this method is that it does not analyze complexes at equilibrium but after several washing steps. Consequently, fast-dissociating complexes may remain undetected. Here, we present the holdup assay, based on the principle of comparative chromatographic retention which eliminates the use of washing steps. The assay evaluates fractions of free and bound species at equilibrium. We used human papillomavirus oncoprotein E6, an E6-binding peptide and an E6-binding PDZ domain, to test several protocols utilizing pure proteins or expression extracts. The holdup assay is faster and more informative than the pulldown assay. It detects fast-dissociating complexes and it is also suited for evaluating equilibrium constants. It is potentially adaptable for automated determination of affinity constants and high-throughput analysis of interactions between proteins and other proteins, peptides, nucleic acids, or small regulatory molecules.
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Affiliation(s)
- Sebastian Charbonnier
- Equipe Oncoprotéines, UMR CNRS 7175-LC1, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brandt, BP 10413, 67412 Illkirch Cedex, France
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50
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Ricagno S, Coutard B, Grisel S, Brémond N, Dalle K, Tocque F, Campanacci V, Lichière J, Lantez V, Debarnot C, Cambillau C, Canard B, Egloff MP. Crystallization and preliminary X-ray diffraction analysis of Nsp15 from SARS coronavirus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:409-11. [PMID: 16582498 PMCID: PMC2222560 DOI: 10.1107/s1744309106009407] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 03/13/2006] [Indexed: 11/12/2022]
Abstract
The non-structural protein Nsp15 from the aetiological agent of SARS (severe acute respiratory syndrome) has recently been characterized as a uridine-specific endoribonuclease. This enzyme plays an essential role in viral replication and transcription since a mutation in the related H229E human coronavirus nsp15 gene can abolish viral RNA synthesis. SARS full-length Nsp15 (346 amino acids) has been cloned and expressed in Escherichia coli with an N-terminal hexahistidine tag and has been purified to homogeneity. The protein was subsequently crystallized using PEG 8000 or 10 000 as precipitants. Small cubic crystals of the apoenzyme were obtained from 100 nl nanodrops. They belong to space group P4(1)32 or P4(3)32, with unit-cell parameters a = b = c = 166.8 angstroms. Diffraction data were collected to a maximum resolution of 2.7 angstroms.
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Affiliation(s)
- Stéfano Ricagno
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Bruno Coutard
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Sacha Grisel
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Nicolas Brémond
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Karen Dalle
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Fabienne Tocque
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Valérie Campanacci
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Julie Lichière
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Violaine Lantez
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Claire Debarnot
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Christian Cambillau
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Bruno Canard
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Marie-Pierre Egloff
- Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
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