1
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Yang L, Wagner T, Mechaly A, Boyko A, Bruch EM, Megrian D, Gubellini F, Alzari PM, Bellinzoni M. High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Nat Commun 2023; 14:4851. [PMID: 37563123 PMCID: PMC10415282 DOI: 10.1038/s41467-023-40253-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/19/2023] [Indexed: 08/12/2023] Open
Abstract
Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), actinobacteria rely on a two-in-one protein (OdhA) in which both the oxidative decarboxylation and succinyl transferase steps are carried out by the same polypeptide. Here we describe high-resolution cryo-EM and crystallographic snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that assembles into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the signalling protein OdhI.
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Affiliation(s)
- Lu Yang
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Wuhan Institute of Biological Products Co. Ltd., Wuhan, 430207, PR China
| | - Tristan Wagner
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, D-28359, Bremen, Germany
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, Plateforme de Cristallographie, F-75015, Paris, France
| | - Alexandra Boyko
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- BostonGene, Yerevan, Armenia
| | - Eduardo M Bruch
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Sanofi, In vitro Biology, Integrated Drug Discovery, 350 Water St, Cambridge, MA, 02141, USA
| | - Daniela Megrian
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Francesca Gubellini
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Pedro M Alzari
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France.
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2
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Abreu C, Ortega C, Olivero-Deibe N, Carrión F, Gaete-Argel A, Valiente-Echeverría F, Soto-Rifo R, Milan Bonotto R, Marcello A, Pantano S. Customizably designed multibodies neutralize SARS-CoV-2 in a variant-insensitive manner. Front Immunol 2023; 14:1226880. [PMID: 37638023 PMCID: PMC10447908 DOI: 10.3389/fimmu.2023.1226880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/20/2023] [Indexed: 08/29/2023] Open
Abstract
The COVID-19 pandemic evolves constantly, requiring adaptable solutions to combat emerging SARS-CoV-2 variants. To address this, we created a pentameric scaffold based on a mammalian protein, which can be customized with up to 10 protein binding modules. This molecular scaffold spans roughly 20 nm and can simultaneously neutralize SARS-CoV-2 Spike proteins from one or multiple viral particles. Using only two different modules targeting the Spike's RBD domain, this construct outcompetes human antibodies from vaccinated individuals' serum and blocks in vitro cell attachment and pseudotyped virus entry. Additionally, the multibodies inhibit viral replication at low picomolar concentrations, regardless of the variant. This customizable multibody can be easily produced in procaryote systems, providing a new avenue for therapeutic development and detection devices, and contributing to preparedness against rapidly evolving pathogens.
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Affiliation(s)
| | | | | | | | - Aracelly Gaete-Argel
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Rafaela Milan Bonotto
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Alessandro Marcello
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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3
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Margenat M, Betancour G, Irving V, Costábile A, García-Cedrés T, Portela MM, Carrión F, Herrera FE, Villarino A. Characteristics of Mycobacterium tuberculosis PtpA interaction and activity on the alpha subunit of human mitochondrial trifunctional protein, a key enzyme of lipid metabolism. Front Cell Infect Microbiol 2023; 13:1095060. [PMID: 37424790 PMCID: PMC10325834 DOI: 10.3389/fcimb.2023.1095060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/29/2023] [Indexed: 07/11/2023] Open
Abstract
During Mycobacterium tuberculosis (Mtb) infection, the virulence factor PtpA belonging to the protein tyrosine phosphatase family is delivered into the cytosol of the macrophage. PtpA interacts with numerous eukaryotic proteins modulating phagosome maturation, innate immune response, apoptosis, and potentially host-lipid metabolism, as previously reported by our group. In vitro, the human trifunctional protein enzyme (hTFP) is a bona fide PtpA substrate, a key enzyme of mitochondrial β-oxidation of long-chain fatty acids, containing two alpha and two beta subunits arranged in a tetramer structure. Interestingly, it has been described that the alpha subunit of hTFP (ECHA, hTFPα) is no longer detected in mitochondria during macrophage infection with the virulent Mtb H37Rv. To better understand if PtpA could be the bacterial factor responsible for this effect, in the present work, we studied in-depth the PtpA activity and interaction with hTFPα. With this aim, we performed docking and in vitro dephosphorylation assays defining the P-Tyr-271 as the potential target of mycobacterial PtpA, a residue located in the helix-10 of hTFPα, previously described as relevant for its mitochondrial membrane localization and activity. Phylogenetic analysis showed that Tyr-271 is absent in TFPα of bacteria and is present in more complex eukaryotic organisms. These results suggest that this residue is a specific PtpA target, and its phosphorylation state is a way of regulating its subcellular localization. We also showed that phosphorylation of Tyr-271 can be catalyzed by Jak kinase. In addition, we found by molecular dynamics that PtpA and hTFPα form a stable protein complex through the PtpA active site, and we determined the dissociation equilibrium constant. Finally, a detailed study of PtpA interaction with ubiquitin, a reported PtpA activator, showed that additional factors are required to explain a ubiquitin-mediated activation of PtpA. Altogether, our results provide further evidence supporting that PtpA could be the bacterial factor that dephosphorylates hTFPα during infection, potentially affecting its mitochondrial localization or β-oxidation activity.
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Affiliation(s)
- Mariana Margenat
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Gabriela Betancour
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Vivian Irving
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Alicia Costábile
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Tania García-Cedrés
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - María Magdalena Portela
- Instituto de Biología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo and Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Federico Carrión
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Fernando E. Herrera
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas-Universidad Nacional del Litoral – CONICET, Santa Fe, Argentina
| | - Andrea Villarino
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
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4
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Fló M, Carrión F, Olivero-Deibe N, Bianchi S, Portela M, Rammauro F, Alvarez B, Pritsch O. Kinetics of Bovine leukemia virus aspartic protease reveals its dimerization and conformational change. PLoS One 2022; 17:e0271671. [PMID: 35867649 PMCID: PMC9307154 DOI: 10.1371/journal.pone.0271671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/05/2022] [Indexed: 11/28/2022] Open
Abstract
The retropepsin (PR) of the Bovine leukemia virus (BLV) plays, as in other retroviruses, a crucial role in the transition from the non-infective viral particle to the infective virion by processing the polyprotein Gag. PR is expressed as an immature precursor associated with Gag, after an occasional −1 ribosomal frameshifting event. Self-hydrolysis of PR at specific N- and C-terminal sites releases the monomer that dimerizes giving rise to the active protease. We designed a strategy to express BLV PR in E. coli as a fusion protein with maltose binding protein, with a six-histidine tag at its N-terminal end, and bearing a tobacco etch virus protease hydrolysis site. This allowed us to obtain soluble and mature recombinant PR in relatively good yields, with exactly the same amino acid composition as the native protein. As PR presents relative promiscuity for the hydrolysis sites we designed four fluorogenic peptide substrates based on Förster resonance energy transfer (FRET) in order to characterize the activity of the recombinant enzyme. These substrates opened the way to perform kinetic studies, allowing us to characterize the dimer-monomer equilibrium. Furthermore, we obtained kinetic evidence for the existence of a conformational change that enables the interaction with the substrate. These results constitute a starting point for the elucidation of the kinetic properties of BLV-PR, and may be relevant not only to improve the chemical warfare against this virus but also to better understand other viral PRs.
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Affiliation(s)
- Martín Fló
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail: (OP); (MF)
| | - Federico Carrión
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Sergio Bianchi
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Laboratorio de Biomarcadores Moleculares, Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madelón Portela
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Facultad de Ciencias, Montevideo, Uruguay
| | - Florencia Rammauro
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Otto Pritsch
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail: (OP); (MF)
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Balaban CL, Suárez CA, Boncompain CA, Peressutti-Bacci N, Ceccarelli EA, Morbidoni HR. Evaluation of factors influencing expression and extraction of recombinant bacteriophage endolysins in Escherichia coli. Microb Cell Fact 2022; 21:40. [PMID: 35292023 PMCID: PMC8922839 DOI: 10.1186/s12934-022-01766-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Endolysins are peptidoglycan hydrolases with promising use as environment-friendly antibacterials mainly when used topically. However, in general, endolysin expression is hampered by its low solubility. Thus, a critical point in endolysin industrial production is optimizing their expression, including improvement of solubility and recovery from cell extracts. Results We report the expression of two endolysins encoded in the genome of phages infecting Staphylococcus aureus. Expression was optimized through changes in the concentration of the inducer and growth temperature during the expression. Usually, only 30–40% of the total endolysin was recovered in the soluble fraction. Co-expression of molecular chaperones (DnaK, GroEL) or N-term fusion tags endowed with increased solubility (DsbC, Trx, Sumo) failed to improve that yield substantially. Inclusion of osmolytes (NaCl, CaCl2, mannitol, glycine betaine, glycerol and trehalose) or tensioactives (Triton X-100, Tween 20, Nonidet P-40, CHAPS, N-lauroylsarcosine) in the cell disruption system (in the absence of any molecular chaperone) gave meager improvements excepted by N-lauroylsarcosine which increased recovery to 54% of the total endolysin content. Conclusion This is the first attempt to systematically analyze methods for increasing yields of recombinant endolysins. We herein show that neither solubility tags nor molecular chaperones co-expression are effective to that end, while induction temperature, (His)6-tag location and lysis buffer additives (e.g.N-lauroylsarcosine), are sensible strategies to obtain higher levels of soluble S. aureus endolysins. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01766-9.
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Affiliation(s)
- Cecilia Lucía Balaban
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Cristian Alejandro Suárez
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carina Andrea Boncompain
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Natalia Peressutti-Bacci
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Eduardo Augusto Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Héctor Ricardo Morbidoni
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina.
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6
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Aversa-Marnai M, Castellano M, Quartiani I, Conijesky D, Perretta A, Villarino A, Silva-Álvarez V, Ferreira AM. Different response of Acipenser gueldenstaedtii CRP/SAP and SAA to bacterial challenge and chronic thermal stress sheds light on the innate immune system of sturgeons. FISH & SHELLFISH IMMUNOLOGY 2022; 121:404-417. [PMID: 34971737 DOI: 10.1016/j.fsi.2021.12.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Sturgeons are chondrostean fish critically endangered due to anthropogenic loss and degradation of natural habitat and overfishing for meat and caviar production. Consequently, sturgeon aquaculture has extensively developed lately, being Russian sturgeon (Acipenser gueldenstaedtii) the second most important species reared for caviar production. However, Russian sturgeon aquaculture in subtropical countries, such as Uruguay, confronts difficulties because fish have to endure excessive summertime warm temperatures, which weaken their innate defences facilitating opportunistic infections. To address this problem, we look for identifying putative acute phase proteins (APPs), which might be robust serum biomarkers of both infection and chronic thermal stress, applied to monitoring Russian sturgeon health status in farms. We focused on the C-Reactive Protein/Serum Amyloid P (CRP/SAP) pentraxin since the pentraxin family includes well-known APPs, better characterised in mammals than fish. We identified A.gueldenstaedtii CRP/SAP (AgCRP/SAP), as a member of the universal CRP/SAP pentraxin sub-family, and studied AgCRP/SAP involvement in sturgeon response to bacterial challenge and chronic thermal stress, in comparison with A. gueldenstaedtii Serum Amyloid A (AgSAA), a previously described positive APP. Results showed that AgCRP/SAP is a constitutive serum component that remained constant upon Aeromonas hydrophila challenge and chronic thermal stress. Contrastingly, serum AgSAA was subjected to regulation by bacterial and thermal stress challenges, showing a 50-fold increase and 3-fold decline in serum levels, respectively. Overall, results highlight the potential value of AgSAA, but not of AgCRP/SAP, as a biomarker of bacterial infection and the need to continue searching for robust chronic thermal stress biomarkers in sturgeons.
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Affiliation(s)
- Marcio Aversa-Marnai
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay
| | - Mauricio Castellano
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay; Sección Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de la República, CP 11400, Montevideo, Uruguay
| | - Ignacio Quartiani
- Unidad de Patología, Biología y Cultivo de Organismos Acuáticos, Departamento de Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad de la República, CP 11300, Montevideo, Uruguay
| | | | - Alejandro Perretta
- Unidad de Patología, Biología y Cultivo de Organismos Acuáticos, Departamento de Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad de la República, CP 11300, Montevideo, Uruguay
| | - Andrea Villarino
- Sección Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de la República, CP 11400, Montevideo, Uruguay
| | - Valeria Silva-Álvarez
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay.
| | - Ana María Ferreira
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay.
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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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8
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Rizza JD, Ortega C, Carrión F, Fló M, Correa A. Production, purification and characterization of a double-tagged TEV protease. Protein Expr Purif 2021; 191:106021. [PMID: 34798273 DOI: 10.1016/j.pep.2021.106021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/04/2021] [Accepted: 11/12/2021] [Indexed: 10/19/2022]
Abstract
Many recombinant proteins are products of great value in biomedical and industrial fields. The use of solubility and affinity tags are commonly used to increase yields and facilitate the purification process. However, it is of paramount importance in several applications to remove the fusion tag from the final product. In this regard, the Tobacco Etch Virus protease (TEV) is one of the most widely used for tag removal. The presence in the TEV of the same tag to be removed facilitates the separation of TEV and the tag from the cleaved recombinant protein in a single purification step. We generated a double-tagged (StrepTagII and HisTag) TEV variant with reported mutations that improve the activity, the expression yield in E.coli, and that decrease the auto-proteolysis. This TEV can be easily purified by two consecutive affinity chromatography steps with high yields and purity. The cleavage reaction can be done to almost completeness in as fast as 15 min at room temperature and the removal of the protease and tags is performed in a single purification step, independent of the previous presence of a StrepTagII or a HisTag on the target.
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Affiliation(s)
| | - Claudia Ortega
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Uruguay
| | | | - Martín Fló
- Immunovirology Unit, Institut Pasteur de Montevideo, Uruguay; Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Uruguay.
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Uruguay.
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9
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Aguilar Lucero D, Cantoia A, Ceccarelli EA, Rosano GL. Starting a new recombinant protein production project in Escherichia coli. Methods Enzymol 2021; 659:3-18. [PMID: 34752291 DOI: 10.1016/bs.mie.2021.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
One of the goals in recombinant protein production in Escherichia coli is to maximize productivity. High volumetric and specific yields can be reached after careful selection of expression strains and optimization of cultivation parameters. In this chapter, we review the many tools available to make the most out of this versatile microbial cell factory. Useful guidelines and options for troubleshooting production are presented.
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Affiliation(s)
- Dianela Aguilar Lucero
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Alejo Cantoia
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Eduardo A Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Germán L Rosano
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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10
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Cantoia A, Aguilar Lucero D, Ceccarelli EA, Rosano GL. From the notebook to recombinant protein production in Escherichia coli: Design of expression vectors and gene cloning. Methods Enzymol 2021; 659:19-35. [PMID: 34752286 DOI: 10.1016/bs.mie.2021.07.008] [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: 01/04/2023]
Abstract
Research in recombinant protein expression in microorganism hosts spans half a century. The field has evolved from mostly trial-and-error approaches to more rational strategies, including careful design of the expression vectors and the coding sequence for the protein of interest. It is important to reflect on many aspects about vector construction, such as codon usage, integration site, coding sequence mutagenesis and many others. In this chapter, we overview methods and considerations to generate a suitable construct and anticipate possible experimental roadblocks.
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Affiliation(s)
- Alejo Cantoia
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Dianela Aguilar Lucero
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Eduardo A Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Germán L Rosano
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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Aguilar Lucero D, Cantoia A, Sánchez-López C, Binolfi A, Mogk A, Ceccarelli EA, Rosano GL. Structural features of the plant N-recognin ClpS1 and sequence determinants in its targets that govern substrate selection. FEBS Lett 2021; 595:1525-1541. [PMID: 33792910 DOI: 10.1002/1873-3468.14081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022]
Abstract
In the N-degron pathway of protein degradation of Escherichia coli, the N-recognin ClpS identifies substrates bearing N-terminal phenylalanine, tyrosine, tryptophan, or leucine and delivers them to the caseinolytic protease (Clp). Chloroplasts contain the Clp system, but whether chloroplastic ClpS1 adheres to the same constraints is unknown. Moreover, the structural underpinnings of substrate recognition are not completely defined. We show that ClpS1 recognizes canonical residues of the E. coli N-degron pathway. The residue in second position influences recognition (especially in N-terminal ends starting with leucine). N-terminal acetylation abrogates recognition. ClpF, a ClpS1-interacting partner, does not alter its specificity. Substrate binding provokes local remodeling of residues in the substrate-binding cavity of ClpS1. Our work strongly supports the existence of a chloroplastic N-degron pathway.
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Affiliation(s)
- Dianela Aguilar Lucero
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina
| | - Alejo Cantoia
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina
| | - Carolina Sánchez-López
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina
| | - Andrés Binolfi
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Rosario, Argentina
| | - Axel Mogk
- DKFZ-ZMBH Alliance, Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Germany
| | - Eduardo A Ceccarelli
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina
| | - Germán L Rosano
- CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, Argentina
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12
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Serum amyloid A is a positive acute phase protein in Russian sturgeon challenged with Aeromonas hydrophila. Sci Rep 2020; 10:22162. [PMID: 33335147 PMCID: PMC7746741 DOI: 10.1038/s41598-020-79065-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/02/2020] [Indexed: 11/23/2022] Open
Abstract
The immune system of sturgeons, one of the most ancient and economically valuable fish worldwide, is poorly understood. The lack of molecular tools and data about infection biomarkers hinders the possibility to monitor sturgeon health during farming and detect infection outbreaks. To tackle this issue, we mined publicly available transcriptomic datasets and identified putative positive acute-phase proteins (APPs) of Russian sturgeons that could be induced by a bacterial infection and monitored using non-invasive methods. Teleost literature compelled us to focus on five promising candidates: hepcidin, a warm acclimation associated hemopexin, intelectin, serum amyloid A protein (SAA) and serotransferrin. Among them, SAA was the most upregulated protein at the mRNA level in the liver of sturgeons challenged with heat-inactivated or live Aeromonas hydrophila. To assess whether this upregulation yielded increasing SAA levels in circulation, we developed an in-house ELISA to quantify SAA levels in sturgeon serum. Circulating SAA rose upon bacterial challenge and positively correlated with hepatic saa expression. This is the first time serum SAA has been quantified in an Actinopterygii fish. Since APPs vary across different fish species, our work sheds light on sturgeon acute-phase response, revealing that SAA is a positive APP with potential value as infection biomarker.
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13
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Parcerisa IL, Rosano GL, Ceccarelli EA. Biochemical characterization of ClpB3, a chloroplastic disaggregase from Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2020; 104:451-465. [PMID: 32803477 DOI: 10.1007/s11103-020-01050-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
The first biochemical characterization of a chloroplastic disaggregase is reported (Arabidopsis thaliana ClpB3). ClpB3 oligomerizes into active hexamers that resolubilize aggregated substrates using ATP and without the aid of partners. Disaggregases from the Hsp100/Clp family are a type of molecular chaperones involved in disassembling protein aggregates. Plant cells are uniquely endowed with ClpB proteins in the cytosol, mitochondria and chloroplasts. Chloroplastic ClpB proteins have been implicated in key processes like the unfolded protein response; however, they have not been studied in detail. In this study, we explored the biochemical properties of a chloroplastic ClpB disaggregase, in particular, ClpB3 from A. thaliana. ClpB3 was produced recombinantly in Escherichia coli and affinity-purified to near homogeneity. ClpB3 forms a hexameric complex in the presence of MgATP and displays intrinsic ATPase activity. We demonstrate that ClpB3 has ATPase activity in a wide range of pH and temperature values and is particularly resistant to heat. ClpB3 specifically targets unstructured polypeptides and mediates the reactivation of heat-denatured model substrates without the aid of the Hsp70 system. Overall, this work represents the first in-depth biochemical description of a ClpB protein from plants and strongly supports its role as the putative disaggregase chaperone in chloroplasts.
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Affiliation(s)
- Ivana L Parcerisa
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000, Rosario, Argentina
| | - Germán L Rosano
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000, Rosario, Argentina.
| | - Eduardo A Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000, Rosario, Argentina
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14
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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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15
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Rosano GL, Morales ES, Ceccarelli EA. New tools for recombinant protein production in Escherichia coli: A 5-year update. Protein Sci 2019; 28:1412-1422. [PMID: 31219641 DOI: 10.1002/pro.3668] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 06/10/2019] [Indexed: 12/11/2022]
Abstract
The production of proteins in sufficient amounts is key for their study or use as biotherapeutic agents. Escherichia coli is the host of choice for recombinant protein production given its fast growth, easy manipulation, and cost-effectiveness. As such, its protein production capabilities are continuously being improved. Also, the associated tools (such as plasmids and cultivation conditions) are subject of ongoing research to optimize product yield. In this work, we review the latest advances in recombinant protein production in E. coli.
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Affiliation(s)
- Germán L Rosano
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Enrique S Morales
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Eduardo A Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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16
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Ortega C, Abreu C, Oppezzo P, Correa A. Overview of High-Throughput Cloning Methods for the Post-genomic Era. Methods Mol Biol 2019; 2025:3-32. [PMID: 31267446 DOI: 10.1007/978-1-4939-9624-7_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The advent of new DNA sequencing technologies leads to a dramatic increase in the number of available genome sequences and therefore of target genes with potential for functional analysis. The insertion of these sequences into proper expression vectors requires a simple an efficient cloning method. In addition, when expressing a target protein, quite often it is necessary to evaluate different DNA constructs to achieve a soluble and homogeneous expression of the target with satisfactory yields. The development of new molecular methods made possible the cloning of a huge number of DNA sequences in a high-throughput manner, necessary for meeting the increasing demands for soluble protein expression and characterization. In this chapter several molecular methods suitable for high-throughput cloning are reviewed.
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Affiliation(s)
- Claudia Ortega
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Cecilia Abreu
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Molecular, Cellular and Animal Technology Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Oppezzo
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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17
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Ortega C, Prieto D, Abreu C, Oppezzo P, Correa A. Multi-Compartment and Multi-Host Vector Suite for Recombinant Protein Expression and Purification. Front Microbiol 2018; 9:1384. [PMID: 29997597 PMCID: PMC6030378 DOI: 10.3389/fmicb.2018.01384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/06/2018] [Indexed: 11/13/2022] Open
Abstract
Recombinant protein expression has become an invaluable tool in basic and applied research. The accumulated knowledge in this field allowed the expression of thousands of protein targets in a soluble, pure, and homogeneous state, essential for biochemical and structural analyses. A lot of progress has been achieved in the last decades, where challenging proteins were expressed in a soluble manner after evaluating different parameters such as host, strain, and fusion partner or promoter strength, among others. In this regard, we have previously developed a vector suite that allows the evaluation of different promoters and solubility enhancer-proteins, through an easy and efficient cloning strategy. Nonetheless, the proper expression of many targets remains elusive, requiring, for example, the addition of complex post-translation modifications and/or passage through specialized compartments. In order to overcome the limitations found when working with a single subcellular localization and a single host type, we herein expanded our previously developed vector suite to include the evaluation of recombinant protein expression in different cell compartments and cell hosts. In addition, these vectors also allow the assessment of alternative purification strategies for the improvement of target protein yields.
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Affiliation(s)
- Claudia Ortega
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Daniel Prieto
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Department of Developmental Neurobiology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Cecilia Abreu
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Oppezzo
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
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18
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Lu J, Zhao Y, Zhang J. High-level expression of Aerococcus viridans pyruvate oxidase in Escherichia coli by optimization of vectors and induction conditions. Lett Appl Microbiol 2018; 67:262-269. [PMID: 29856486 DOI: 10.1111/lam.13013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/15/2018] [Accepted: 05/28/2018] [Indexed: 01/24/2023]
Abstract
Pyruvate oxidase is an important enzyme used as a reagent in kits and biochemical analyses; however, the yield of pyruvate oxidase from wild microbial strains is low. In this study, high-level expression of Aerococcus viridans pyruvate oxidase was achieved in recombinant Escherichia coli by optimizing the expression system and induction conditions. Three recombinant pET vectors were constructed for pyruvate oxidase expression in E. coli. The isopropyl-β-d-thiogalactoside (IPTG) concentration and induction temperature were optimized, with the result that the highest pyruvate oxidase yield (4106·9 U l-1 ) of the recombinant E. colipET28a-pod was obtained under conditions of 25°C, 0·5 mmol l-1 IPTG, 0·5 OD600 , after 24 h of induction, which was 34·2 times the yield achieved with the wild-type strain. The soluble pyruvate oxidase contributed 99·6% of the total pyruvate oxidase expressed. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrates that a highly soluble pyruvate oxidase can be obtained in recombinant Escherichia coli by optimizing vectors and induction conditions. The pyruvate oxidase yield achieved is the highest reported so far, which provides a convenient and cost-saving way to produce pyruvate oxidase. This research promotes pyruvate oxidase application in the pharmaceutical and biochemical industries.
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Affiliation(s)
- J Lu
- Institute of Food Science and Engineering, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Y Zhao
- Institute of Food Science and Engineering, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - J Zhang
- Institute of Food Science and Engineering, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
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19
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Castilla A, Panizza P, Rodríguez D, Bonino L, Díaz P, Irazoqui G, Rodríguez Giordano S. A novel thermophilic and halophilic esterase from Janibacter sp. R02, the first member of a new lipase family (Family XVII). Enzyme Microb Technol 2017; 98:86-95. [DOI: 10.1016/j.enzmictec.2016.12.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/24/2016] [Accepted: 12/31/2016] [Indexed: 01/12/2023]
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20
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Bjerga GEK, Williamson AK. Cold shock induction of recombinant Arctic environmental genes. BMC Biotechnol 2015; 15:78. [PMID: 26286037 PMCID: PMC4544801 DOI: 10.1186/s12896-015-0185-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/24/2015] [Indexed: 11/16/2022] Open
Abstract
Background Heterologous expression of psychrophilic enzymes in E. coli is particularly challenging due to their intrinsic instability. The low stability is regarded as a consequence of adaptation that allow them to function at low temperatures. Recombinant production presents a significant barrier to their exploitation for commercial applications in industry. Methods As part of an enzyme discovery project we have investigated the utility of a cold-shock inducible promoter for low-temperature expression of five diverse genes derived from the metagenomes of marine Arctic sediments. After evaluation of their production, we further optimized for soluble production by building a vector suite from which the environmental genes could be expressed as fusions with solubility tags. Results We found that the low-temperature optimized system produced high expression levels for all putatively cold-active proteins, as well as reducing host toxicity for several candidates. As a proof of concept, activity assays with one of the candidates, a putative chitinase, showed that functional protein was obtained using the low-temperature optimized vector suite. Conclusions We conclude that a cold-shock inducible system is advantageous for the heterologous expression of psychrophilic proteins, and may also be useful for expression of toxic mesophilic and thermophilic proteins where properties of the proteins are deleterious to the host cell growth. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0185-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gro Elin Kjæreng Bjerga
- Norstruct, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway. .,Centre for Applied Biotechnology, Uni Research AS, Thormøhlensgt. 55, N-5008, Bergen, Norway.
| | - Adele Kim Williamson
- Norstruct, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway.
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21
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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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22
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Rosano GL, Ceccarelli EA. Recombinant protein expression in microbial systems. Front Microbiol 2014; 5:341. [PMID: 25071752 PMCID: PMC4085539 DOI: 10.3389/fmicb.2014.00341] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 06/19/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Germán L Rosano
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
| | - Eduardo A Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
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23
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Correa A, Pacheco S, Mechaly AE, Obal G, Béhar G, Mouratou B, Oppezzo P, Alzari PM, Pecorari F. Potent and specific inhibition of glycosidases by small artificial binding proteins (affitins). PLoS One 2014; 9:e97438. [PMID: 24823716 PMCID: PMC4019568 DOI: 10.1371/journal.pone.0097438] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 04/17/2014] [Indexed: 01/05/2023] Open
Abstract
Glycosidases are associated with various human diseases. The development of efficient and specific inhibitors may provide powerful tools to modulate their activity. However, achieving high selectivity is a major challenge given that glycosidases with different functions can have similar enzymatic mechanisms and active-site architectures. As an alternative approach to small-chemical compounds, proteinaceous inhibitors might provide a better specificity by involving a larger surface area of interaction. We report here the design and characterization of proteinaceous inhibitors that specifically target endoglycosidases representative of the two major mechanistic classes; retaining and inverting glycosidases. These inhibitors consist of artificial affinity proteins, Affitins, selected against the thermophilic CelD from Clostridium thermocellum and lysozyme from hen egg. They were obtained from libraries of Sac7d variants, which involve either the randomization of a surface or the randomization of a surface and an artificially-extended loop. Glycosidase binders exhibited affinities in the nanomolar range with no cross-recognition, with efficient inhibition of lysozyme (Ki = 45 nM) and CelD (Ki = 95 and 111 nM), high expression yields in Escherichia coli, solubility, and thermal stabilities up to 81.1°C. The crystal structures of glycosidase-Affitin complexes validate our library designs. We observed that Affitins prevented substrate access by two modes of binding; covering or penetrating the catalytic site via the extended loop. In addition, Affitins formed salt-bridges with residues essential for enzymatic activity. These results lead us to propose the use of Affitins as versatile selective glycosidase inhibitors and, potentially, as enzymatic inhibitors in general.
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Affiliation(s)
- Agustín Correa
- Institut Pasteur de Montevideo, Recombinant Protein Unit, Montevideo, Uruguay
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
| | - Sabino Pacheco
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
| | - Ariel E. Mechaly
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
| | - Gonzalo Obal
- Institut Pasteur de Montevideo, Protein Biophysics Unit, Montevideo, Uruguay
| | - Ghislaine Béhar
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
| | - Barbara Mouratou
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
| | - Pablo Oppezzo
- Institut Pasteur de Montevideo, Recombinant Protein Unit, Montevideo, Uruguay
| | - Pedro M. Alzari
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France
| | - Frédéric Pecorari
- INSERM UMR 892 - CRCNA, Nantes, France
- CNRS UMR 6299, Nantes, France
- University of Nantes, Nantes, France
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24
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Affiliation(s)
- Germán L Rosano
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
| | - Eduardo A Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
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