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Karim JA, Lambert NA, Pioszak AA. Time- and cost-efficient bacterial expression and purification of potato apyrase. Protein Expr Purif 2023; 203:106215. [PMID: 36535546 PMCID: PMC9807108 DOI: 10.1016/j.pep.2022.106215] [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: 10/27/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Apyrase from potato (Solanum tuberosum) is a divalent metal ion-dependent enzyme that catalyzes the hydrolysis of nucleoside di- and tri-phosphates with broad substrate specificity. The enzyme is widely used to manipulate nucleotide levels such as in the G protein-coupled receptor (GPCR) field where it is used to deplete guanine nucleotides to stabilize nucleotide-free ternary agonist-GPCR-G protein complexes. Potato apyrase is available commercially as the native enzyme purified from potatoes or as a recombinant protein, but these are prohibitively expensive for some research applications. Here, we report a relatively simple method for the bacterial production of soluble, active potato apyrase. Apyrase has several disulfide bonds, so we co-expressed the enzyme bearing a C-terminal (His)6 tag with the E. coli disulfide isomerase DsbC at low temperature (18 °C) in the oxidizing cytoplasm of E. coli Origami B (DE3). This allowed low level production of soluble apyrase. A two-step purification procedure involving Ni-affinity followed by Cibacron Blue-affinity chromatography yielded highly purified apyrase at a level of ∼0.5 mg per L of bacterial culture. The purified enzyme was functional for ATP hydrolysis in an ATPase assay and for GTP/GDP hydrolysis in a GPCR-G protein coupling assay. This methodology enables the time- and cost-efficient production of recombinant apyrase for various research applications.
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Affiliation(s)
- Jordan A Karim
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Augen A Pioszak
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
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2
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Talaei A, Mazaheri S, Bayat E, Bakhshandeh B, Sabzalinejad M, Damough S, Mahboudi F, Nematollahi L, Talebkhan Y. Production of Soluble and Functional Anti-TNF-α Fab' Fragment in Cytoplasm of E. coli: Investigating the Effect of Process Conditions on Cellular Biomass and Protein Yield Using Response Surface Methodology. Protein J 2021; 40:786-798. [PMID: 34023982 DOI: 10.1007/s10930-021-09996-3] [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] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
With the increasing dominance of monoclonal antibodies (mAbs) in the biopharmaceutical industry and smaller antibody fragments bringing notable advantages over full-length antibodies, it is of considerable significance to choose the most suitable production system. Although mammalian expression system has been the preferred choice in recent years for mAbs production, E. coli could be the favorable host for non-glycosylated small antibody fragments due to the emergence of new engineered E. coli strains capable of forming disulfide-bonds in their cytoplasm.In this study, non-glycosylated anti-TNF-α Fab' moiety of Certolizumab pegol, produced by periplasmic expression in E. coli in previous studies, was produced in the cytoplasm of E. coli SHuffle strain. The results indicated that it is biologically functional by testing the antigen-binding activity via indirect ELISA and inhibition of TNF-α induced cytotoxicity using MTT test. Major factors affecting protein production and, optimized culture conditions were examined by analyzing growth characteristics and patterns of expression in 24 h of post-induction cultivation and, optimization of culture conditions by response surface methodology considering temperature, time of induction and concentration of inducer in small (tube) and shake-flask scale. Based on the results, temperature had the most significant influence on functional protein yield while exerting different impacts in small and shake-flask scales, which indicated that cultivation volume is also an important factor that should be taken into account in optimization process. Furthermore, richness of medium and slower cellular growth rate improved specific cellular yield of functional protein by having a positive effect on the solubility of Fab' antibody.
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Affiliation(s)
- Andisheh Talaei
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Somayeh Mazaheri
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Elham Bayat
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Behnaz Bakhshandeh
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Shadi Damough
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Leila Nematollahi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Yeganeh Talebkhan
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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3
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Pellegrini O, Gilet L, Trinquier A, Tolcan A, Allouche D, Durand S, Braun F, Condon C. Assay of Bacillus subtilis Ribonuclease Activity In Vitro. Methods Mol Biol 2021; 2209:403-424. [PMID: 33201483 DOI: 10.1007/978-1-0716-0935-4_25] [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: 06/11/2023]
Abstract
Ribonucleases can cleave RNAs internally in endoribonucleolytic mode or remove one nucleotide at a time from either the 5' or 3' end through exoribonuclease action. To show direct implication of an RNase in a specific pathway of RNA maturation or decay requires the setting up of in vitro assays with purified enzymes and substrates. This chapter complements Chapter 24 on assays of ribonuclease action in vivo by providing detailed protocols for the assay of B. subtilis RNases with prepared substrates in vitro.
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Affiliation(s)
- Olivier Pellegrini
- Expression Génétique Microbienne, UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Laetitia Gilet
- Expression Génétique Microbienne, UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Aude Trinquier
- Expression Génétique Microbienne, UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Anastasia Tolcan
- Expression Génétique Microbienne, UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Delphine Allouche
- Expression Génétique Microbienne, UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Sylvain Durand
- Expression Génétique Microbienne, UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Frédérique Braun
- Expression Génétique Microbienne, UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Ciarán Condon
- Expression Génétique Microbienne, UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France.
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4
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Crystal Structures of [Fe]-Hydrogenase from Methanolacinia paynteri Suggest a Path of the FeGP-Cofactor Incorporation Process. INORGANICS 2020. [DOI: 10.3390/inorganics8090050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
[Fe]-hydrogenase (Hmd) catalyzes the reversible heterolytic cleavage of H2, and hydride transfer to methenyl-tetrahydromethanopterin (methenyl-H4MPT+). The iron-guanylylpyridinol (FeGP) cofactor, the prosthetic group of Hmd, can be extracted from the holoenzyme and inserted back into the protein. Here, we report the crystal structure of an asymmetric homodimer of Hmd from Methanolacinia paynteri (pHmd), which was composed of one monomer in the open conformation with the FeGP cofactor (holo-form) and a second monomer in the closed conformation without the cofactor (apo-form). In addition, we report the symmetric pHmd-homodimer structure in complex with guanosine monophosphate (GMP) or guanylylpyridinol (GP), in which each ligand was bound to the protein, where the GMP moiety of the FeGP-cofactor is bound in the holo-form. Binding of GMP and GP modified the local protein structure but did not induce the open conformation. The amino-group of the Lys150 appears to interact with the 2-hydroxy group of pyridinol ring in the pHmd–GP complex, which is not the case in the structure of the pHmd–FeGP complex. Lys150Ala mutation decreased the reconstitution rate of the active enzyme with the FeGP cofactor at the physiological pH. These results suggest that Lys150 might be involved in the FeGP-cofactor incorporation into the Hmd protein in vivo.
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5
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Efficient development and expression of scFv recombinant proteins against PD-L1 surface domain and potency in cancer therapy. Cytotechnology 2019; 71:705-722. [PMID: 31098772 DOI: 10.1007/s10616-019-00316-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/29/2019] [Indexed: 12/25/2022] Open
Abstract
PD-L1 is a 40 kDa trans-membrane protein of B7 family and an important T cell regulator. Binding of PD-L1 and PD-1 inhibits proliferation and activation of T cell results cell exhaustion. This phenomenon can be reversed by blocking PD-L1/PD-1 interactions with single chain variables fragment (scFv) fusion proteins and by direct inhibition of tumor cells with drug conjugates. The human phage-displayed scFv library was utilized to generate scFv against the PD-L1 antigen by affinity bio-panning. The positive clones were selected by continuous transfection of bacterial cells and sequence analysis. The binding affinity and specificity of the scFv and antibody fragments were determined by using surface plasmon resonance biosensor, western blot analysis, and immunofluorescence assay. After three rounds of panning selection, about 30% of clones have a binding affinity with targeted PD-L1 antigen. Eight positive clones with accurate sequences were isolated and analyzed for binding affinity with PD-L1 antigen. Three of those with accurate sequences and binding affinity were selected for the recombinant formation and soluble expression by Escherichia coli host machinery. The highly positive recombinant clones with the exact orientation of FR and CDR domains were developed and can be used as a drug carrier tools in ADC formation or direct inhibition of immune checkpoint in cancer immunotherapy. The conjugate achieved its initial potency and need efficient improvement to enhance direct tumor suppression and bio-therapeutics strategies enrichment.
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Alam CM, Jain G, Kausar A, Singh AK, Mandal B, Varma A, Sharfuddin C, Chakraborty S. Dicer 1 of Candida albicans cleaves plant viral dsRNA in vitro and provides tolerance in plants against virus infection. Virusdisease 2019; 30:237-244. [PMID: 31179362 DOI: 10.1007/s13337-019-00520-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/13/2019] [Indexed: 11/25/2022] Open
Abstract
Most of the viral diseases of plants are caused by RNA viruses which drastically reduce crop yield. In order to generate resistance against RNA viruses infecting plants, we isolated the dicer 1 protein (CaDcr1), a member of RNAse III family (enzyme that cleaves double stranded RNA) from an opportunistic fungus Candida albicans. In vitro analysis revealed that the CaDcr1 cleaved dsRNA of the coat protein gene of cucumber mosaic virus (genus Cucumovirus, family Bromoviridae). Furthermore, we developed transgenic tobacco plants (Nicotiana tabacum cv. Xanthi) over-expressing expressing CaDcr1 by Agrobacterium mediated transformation. Transgenic tobacco lines were able to suppress infection of an Indian isolate of potato virus X (genus Potexvirus, family Alphaflexiviridae). The present study demonstrates that CaDcr1 can cleave double stranded replicative intermediate and provide tolerance to plant against RNA viruses.
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Affiliation(s)
- Chaudhary Mashhood Alam
- 1Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
- 2Department of Botany, Patna University, Patna, Bihar 600005 India
| | - Garima Jain
- 1Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Aarzoo Kausar
- 1Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Ashish Kumar Singh
- 1Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Bikash Mandal
- 3Advanced Centre of Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Anupam Varma
- 3Advanced Centre of Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | | | - Supriya Chakraborty
- 1Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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7
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Homburg C, Bommer M, Wuttge S, Hobe C, Beck S, Dobbek H, Deutscher J, Licht A, Schneider E. Inducer exclusion in Firmicutes: insights into the regulation of a carbohydrate ATP binding cassette transporter from Lactobacillus casei BL23 by the signal transducing protein P-Ser46-HPr. Mol Microbiol 2017; 105:25-45. [PMID: 28370477 DOI: 10.1111/mmi.13680] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2017] [Indexed: 12/24/2022]
Abstract
Catabolite repression is a mechanism that enables bacteria to control carbon utilization. As part of this global regulatory network, components of the phosphoenolpyruvate:carbohydrate phosphotransferase system inhibit the uptake of less favorable sugars when a preferred carbon source such as glucose is available. This process is termed inducer exclusion. In bacteria belonging to the phylum Firmicutes, HPr, phosphorylated at serine 46 (P-Ser46-HPr) is the key player but its mode of action is elusive. To address this question at the level of purified protein components, we have chosen a homolog of the Escherichia coli maltose/maltodextrin ATP-binding cassette transporter from Lactobacillus casei (MalE1-MalF1G1K12 ) as a model system. We show that the solute binding protein, MalE1, binds linear and cyclic maltodextrins but not maltose. Crystal structures of MalE1 complexed with these sugars provide a clue why maltose is not a substrate. P-Ser46-HPr inhibited MalE1/maltotetraose-stimulated ATPase activity of the transporter incorporated in proteoliposomes. Furthermore, cross-linking experiments revealed that P-Ser46-HPr contacts the nucleotide-binding subunit, MalK1, in proximity to the Walker A motif. However, P-Ser46-HPr did not block binding of ATP to MalK1. Together, our findings provide first biochemical evidence that P-Ser-HPr arrests the transport cycle by preventing ATP hydrolysis at the MalK1 subunits of the transporter.
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Affiliation(s)
- Constanze Homburg
- Institut für Biologie/Physiologie der Mikroorganismen, Humboldt-Universität zu Berlin, Berlin, D-10099, Germany
| | - Martin Bommer
- Institut für Biologie/Strukturbiologie und Biochemie, Humboldt-Universität zu Berlin, Berlin, D-10099, Germany
| | - Steven Wuttge
- Institut für Biologie/Physiologie der Mikroorganismen, Humboldt-Universität zu Berlin, Berlin, D-10099, Germany
| | - Carolin Hobe
- Institut für Biologie/Physiologie der Mikroorganismen, Humboldt-Universität zu Berlin, Berlin, D-10099, Germany
| | - Sebastian Beck
- Institut für Chemie/Angewandte Analytik und Umweltchemie, Humboldt-Universität zu Berlin, Berlin, D-10099, Germany
| | - Holger Dobbek
- Institut für Biologie/Strukturbiologie und Biochemie, Humboldt-Universität zu Berlin, Berlin, D-10099, Germany
| | - Josef Deutscher
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, F-78350, France.,Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique, UMR8261, Paris, F-75005, France
| | - Anke Licht
- Institut für Biologie/Physiologie der Mikroorganismen, Humboldt-Universität zu Berlin, Berlin, D-10099, Germany
| | - Erwin Schneider
- Institut für Biologie/Physiologie der Mikroorganismen, Humboldt-Universität zu Berlin, Berlin, D-10099, Germany
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8
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Wuttge S, Licht A, Timachi MH, Bordignon E, Schneider E. Mode of Interaction of the Signal-Transducing Protein EIIA(Glc) with the Maltose ABC Transporter in the Process of Inducer Exclusion. Biochemistry 2016; 55:5442-52. [PMID: 27571040 DOI: 10.1021/acs.biochem.6b00721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Enzyme IIA(Glc) (EIIA(Glc)) of the phosphoenolpyruvate phosphotransferase system for the uptake of glucose in Escherichia coli and Salmonella inhibits the maltose ATP-binding cassette transporter (MalE-FGK2) by interaction with the nucleotide-binding and -hydrolyzing subunit MalK, a process termed inducer exclusion. We have investigated binding of EIIA(Glc) to the MalK dimer by cysteine cross-linking in proteoliposomes. The results prove that the binding site I of EIIA(Glc) is contacting the N-terminal subdomain of MalK while the binding site II is relatively close to the C-terminal (regulatory) subdomain, in agreement with a crystal structure [ Chen , S. , Oldham , M. L. , Davidson , A. L. , and Chen , J. ( 2013 ) Nature 499 , 364 - 368 ]. Moreover, EIIA(Glc) was found to bind to the MalK dimer regardless of its conformational state. Deletion of the amphipathic N-terminal peptide of EIIA(Glc), which is required for inhibition, reduced formation of cross-linked products. Using a spin-labeled transporter variant and EPR spectroscopy, we demonstrate that EIIA(Glc) arrests the transport cycle by inhibiting the ATP-dependent closure of the MalK dimer.
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Affiliation(s)
- Steven Wuttge
- Institut für Biologie, AG Bakterienphysiologie, Humboldt-Universität zu Berlin , Unter den Linden 6, 10099 Berlin, Germany
| | - Anke Licht
- Institut für Biologie, AG Bakterienphysiologie, Humboldt-Universität zu Berlin , Unter den Linden 6, 10099 Berlin, Germany
| | - M Hadi Timachi
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Enrica Bordignon
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Erwin Schneider
- Institut für Biologie, AG Bakterienphysiologie, Humboldt-Universität zu Berlin , Unter den Linden 6, 10099 Berlin, Germany
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9
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Moe LL, Maekawa S, Kawamura-Konishi Y. The pro-enzyme C-terminal processing domain of Pholiota nameko tyrosinase is responsible for folding of the N-terminal catalytic domain. Appl Microbiol Biotechnol 2015; 99:5499-510. [PMID: 25904132 DOI: 10.1007/s00253-015-6597-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/12/2014] [Accepted: 11/13/2014] [Indexed: 10/23/2022]
Abstract
Pholiota nameko (Pholiota microspore) tyrosinase is expressed as a latent 67-kDa pro-tyrosinase, comprising a 42-kDa N-terminal catalytic domain with a binuclear copper centre and a 25-kDa C-terminal domain and is activated by proteolytic digestion of the C-terminal domain. To investigate the role of the C-terminal processing domain of pro-tyrosinase, we constructed a recombinant tyrosinase lacking the C-terminal domain and four recombinant pro-tyrosinase mutants (F515G, H539N, L540G and Y543G) carrying substituted amino acid residues on the C-terminal domain. The recombinant tyrosinase lacking the C-terminal domain had no catalytic activity; whereas the mutant L540G was copper depleted, the other mutants had copper contents similar to that of the wild-type pro-tyrosinase. Proteolytic digestion activated the mutants H539N and Y543G following release of the C-terminal domain, and the resulting tyrosinases had higher K m values for t-butyl catechol than the wild-type pro-tyrosinase. The mutants F515G and L540G were degraded by proteolytic digestion and yielded smaller proteins with no activity. These data suggest that the C-terminal processing domain of P. nameko pro-tyrosinase is essential for correct folding of the N-terminal catalytic domain and acts as an intramolecular chaperone during assembly of the active-site conformation.
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Affiliation(s)
- Lai Lai Moe
- Department of Food Science, Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
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10
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Smollett K, Blombach F, Werner F. Transcription in Archaea: preparation of Methanocaldococcus jannaschii transcription machinery. Methods Mol Biol 2015; 1276:291-303. [PMID: 25665571 DOI: 10.1007/978-1-4939-2392-2_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Archaeal RNA polymerase and general transcription factors are more closely related to those of eukaryotes than of bacteria. As such the study of transcription of archaea is important both in terms of examination of the evolution of the transcriptional machinery and as a simplified tool for eukaryotic transcription. In particular, the hyperthermophilic Methanocaldococcus jannaschii provides us with a fully recombinant RNA polymerase system allowing for much more detailed in vitro examination of the roles of different components during the transcription cycle than otherwise possible. The individual subunits of M. jannaschii enzyme are easily expressed and purified from heterologous expression systems. Forming functional RNA polymerase involves simply combining the different subunits under denaturing conditions and slowly removing the denaturant.
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Affiliation(s)
- Katherine Smollett
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London, WC1E 6BT, UK,
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11
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Wyre C, Overton TW. Use of a stress-minimisation paradigm in high cell density fed-batch Escherichia coli fermentations to optimise recombinant protein production. J Ind Microbiol Biotechnol 2014; 41:1391-404. [PMID: 25056840 DOI: 10.1007/s10295-014-1489-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 07/08/2014] [Indexed: 11/25/2022]
Abstract
Production of recombinant proteins is an industrially important technique in the biopharmaceutical sector. Many recombinant proteins are problematic to generate in a soluble form in bacteria as they readily form insoluble inclusion bodies. Recombinant protein solubility can be enhanced by minimising stress imposed on bacteria through decreasing growth temperature and the rate of recombinant protein production. In this study, we determined whether these stress-minimisation techniques can be successfully applied to industrially relevant high cell density Escherichia coli fermentations generating a recombinant protein prone to forming inclusion bodies, CheY-GFP. Flow cytometry was used as a routine technique to rapidly determine bacterial productivity and physiology at the single cell level, enabling determination of culture heterogeneity. We show that stress minimisation can be applied to high cell density fermentations (up to a dry cell weight of >70 g L(-1)) using semi-defined media and glucose or glycerol as carbon sources, and using early or late induction of recombinant protein production, to produce high yields (up to 6 g L(-1)) of aggregation-prone recombinant protein in a soluble form. These results clearly demonstrate that stress minimisation is a viable option for the optimisation of high cell density industrial fermentations for the production of high yields of difficult-to-produce recombinant proteins, and present a workflow for the application of stress-minimisation techniques in a variety of fermentation protocols.
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Affiliation(s)
- Chris Wyre
- Bioengineering, School of Chemical Engineering, and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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12
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Peikon ID, Gizatullina DI, Zador AM. In vivo generation of DNA sequence diversity for cellular barcoding. Nucleic Acids Res 2014; 42:e127. [PMID: 25013177 PMCID: PMC4176322 DOI: 10.1093/nar/gku604] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/08/2014] [Accepted: 06/23/2014] [Indexed: 11/14/2022] Open
Abstract
Heterogeneity is a ubiquitous feature of biological systems. A complete understanding of such systems requires a method for uniquely identifying and tracking individual components and their interactions with each other. We have developed a novel method of uniquely tagging individual cells in vivo with a genetic 'barcode' that can be recovered by DNA sequencing. Our method is a two-component system comprised of a genetic barcode cassette whose fragments are shuffled by Rci, a site-specific DNA invertase. The system is highly scalable, with the potential to generate theoretical diversities in the billions. We demonstrate the feasibility of this technique in Escherichia coli. Currently, this method could be employed to track the dynamics of populations of microbes through various bottlenecks. Advances of this method should prove useful in tracking interactions of cells within a network, and/or heterogeneity within complex biological samples.
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Affiliation(s)
- Ian D Peikon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Anthony M Zador
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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13
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Akbari V, Mir Mohammad Sadeghi H, Jafrian-Dehkordi A, Abedi D, Chou CP. Functional expression of a single-chain antibody fragment against human epidermal growth factor receptor 2 (HER2) in Escherichia coli. ACTA ACUST UNITED AC 2014; 41:947-56. [DOI: 10.1007/s10295-014-1437-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 03/10/2014] [Indexed: 11/30/2022]
Abstract
Abstract
The human epidermal growth factor receptor (HER) family plays an important role in cell growth and signaling and alteration of its function has been demonstrated in many different kinds of cancer. Receptor dimerization is necessary for the HER signal transduction pathway and tyrosine kinase activity. Recently, several monoclonal antibodies have been developed to directly interfere with ligand–HER receptor binding and receptor dimerization. A single chain variable fragment (ScFv) is a valuable alternative to an intact antibody. This report describes the production and purification of an ScFv specific for domain II of the HER2 receptor in Escherichia coli BL21 (DE3) cytoplasm. The majority of expressed of anti-her2his-ScFv protein was produced as inclusion bodies. A Ni-NTA affinity column was used to purify the anti-her2his-ScFv protein. The molecular weight of anti-her2his-ScFv protein was estimated to be approximately 27 kDa, as confirmed by SDS-PAGE and Western blotting assay. The anti-her2his-ScFv showed near 95 % purity and reached a yield of approximately 29 mg/l in flask fermentation. The purified anti-her2his-ScFv showed its biological activity by binding to HER2 receptor on the surface of BT-474 cells. This ScFv may be a potential pharmaceutical candidate for targeting tumour cells overexpressing HER2 receptor.
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Affiliation(s)
- Vajihe Akbari
- grid.411036.1 000000011498685X Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy Isfahan University of Medical Sciences Hezar Jarib Avenue Isfahan Iran
| | - Hamid Mir Mohammad Sadeghi
- grid.411036.1 000000011498685X Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy Isfahan University of Medical Sciences Hezar Jarib Avenue Isfahan Iran
| | - Abbas Jafrian-Dehkordi
- grid.411036.1 000000011498685X Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy Isfahan University of Medical Sciences Hezar Jarib Avenue Isfahan Iran
| | - Daryoush Abedi
- grid.411036.1 000000011498685X Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Research Center, Faculty of Pharmacy Isfahan University of Medical Sciences Hezar Jarib Avenue Isfahan Iran
| | - C Perry Chou
- grid.46078.3d 0000000086441405 Department of Chemical Engineering University of Waterloo 200 University Avenue N2L 3G1 Waterloo ON Canada
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14
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Bacterial Expression, Refolding, Functional Characterization, and Mass Spectrometric Identification of Full-Length Human PPAR-γ. Biosci Biotechnol Biochem 2014; 74:1173-80. [DOI: 10.1271/bbb.90864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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15
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Kojima H, Moll J, Kahnt J, Fukui M, Shima S. A reversed genetic approach reveals the coenzyme specificity and other catalytic properties of three enzymes putatively involved in anaerobic oxidation of methane with sulfate. Environ Microbiol 2014; 16:3431-42. [DOI: 10.1111/1462-2920.12475] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 03/09/2014] [Accepted: 03/24/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Hisaya Kojima
- The Institute of Low Temperature Science; Hokkaido University; Sapporo Japan
| | - Johanna Moll
- Department of Biochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Jörg Kahnt
- Department of Biochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Manabu Fukui
- The Institute of Low Temperature Science; Hokkaido University; Sapporo Japan
| | - Seigo Shima
- The Institute of Low Temperature Science; Hokkaido University; Sapporo Japan
- Department of Biochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
- PRESTO; Japan Science and Technology Agency (JST); Saitama Japan
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16
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Identification and characterization of re-citrate synthase in Syntrophus aciditrophicus. J Bacteriol 2013; 195:1689-96. [PMID: 23378508 DOI: 10.1128/jb.02185-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Glutamate is usually synthesized from acetyl coenzyme A (acetyl-CoA) via citrate, isocitrate, and 2-oxoglutarate. Genome analysis revealed that in Syntrophus aciditrophicus, the gene for Si-citrate synthase is lacking. An alternative pathway starting from the catabolic intermediate glutaconyl-CoA via 2-hydroxyglutarate could be excluded by genomic analysis. On the other hand, a putative gene (SYN_02536; NCBI gene accession no. CP000252.1) annotated as coding for isopropylmalate/citramalate/homocitrate synthase has been shown to share 49% deduced amino acid sequence identity with the gene encoding Re-citrate synthase of Clostridium kluyveri. We cloned and overexpressed this gene in Escherichia coli together with the genes encoding the chaperone GroEL. The recombinant homotetrameric enzyme with a C-terminal Strep-tag (4 × 72,892 Da) was separated from GroEL on a Strep-Tactin column by incubation with ATP, K(+), and Mg(2+). The pure Re-citrate synthase used only acetyl-CoA and oxaloacetate as the substrates. As isolated, the enzyme contained stoichiometric amounts of Ca(2+) (0.9 Ca/73 kDa) but achieved higher specific activities in the presence of Mn(2+) (1.2 U/mg) or Co(2+) (2.0 U/mg). To determine the stereospecificity of the enzyme, [(14)C]citrate was enzymatically synthesized from oxaloacetate and [1-(14)C]acetyl-CoA; the subsequent cleavage by Si-citrate lyase yielded unlabeled acetate and labeled oxaloacetate, demonstrating that the enzyme is a Re-citrate synthase. The production of Re-citrate synthase by S. aciditrophicus grown axenically on crotonate was revealed by synthesis of [(14)C]citrate in a cell extract followed by stereochemical analysis. This result was supported by detection of transcripts of the Re-citrate synthase gene in axenic as well as in syntrophic cultures using quantitative reverse transcriptase PCR (qRT-PCR).
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Cloning, Expression, Purification, and Characterization of an Organophosphate-Degrading Enzyme in Escherichia Coli. ACTA ACUST UNITED AC 2012. [DOI: 10.4028/www.scientific.net/amr.610-613.203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
OpdA is one of organic phosphorus degradation enzyme gene from Agrobacterium radiobacter that may be the most promising targets for the digestion of digestion. In this study, we describe for the cloning and expression in Escherichia coli (E. coli) of plasmid pET28b-opdA, followed by purification by NTA-Ni2+ agarose affinity chromatography. Protein expression and purification were evaluated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE).The Results showed that the optimal value of inoculum OD600 before induction, inducing time, final IPTG concentration and inducing temperature respectively were 0.5,5h,1 mmol/L,37°C. We obtained the concentration of renatured protein was 18.312mg / L. The Km was 4.26μmol/L at 37 °C, and the maximum reaction velocity (Vmax) was 3.2669μmol/L • min.
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18
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Wuttge S, Bommer M, Jäger F, Martins BM, Jacob S, Licht A, Scheffel F, Dobbek H, Schneider E. Determinants of substrate specificity and biochemical properties of the sn-glycerol-3-phosphate ATP binding cassette transporter (UgpB-AEC2 ) of Escherichia coli. Mol Microbiol 2012; 86:908-20. [PMID: 23013274 DOI: 10.1111/mmi.12025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2012] [Indexed: 12/20/2022]
Abstract
Under phosphate starvation conditions, Escherichia coli can utilize sn-glycerol-3-phosphate (G3P) and G3P diesters as phosphate source when transported by an ATP binding cassette importer composed of the periplasmic binding protein, UgpB, the transmembrane subunits, UgpA and UgpE, and a homodimer of the nucleotide binding subunit, UgpC. The current knowledge on the Ugp transporter is solely based on genetic evidence and transport assays using intact cells. Thus, we set out to characterize its properties at the level of purified protein components. UgpB was demonstrated to bind G3P and glycerophosphocholine with dissociation constants of 0.68 ± 0.02 μM and 5.1 ± 0.3 μM, respectively, while glycerol-2-phosphate (G2P) is not a substrate. The crystal structure of UgpB in complex with G3P was solved at 1.8 Å resolution and revealed the interaction with two tryptophan residues as key to the preferential binding of linear G3P in contrast to the branched G2P. Mutational analysis validated the crucial role of Trp-169 for G3P binding. The purified UgpAEC2 complex displayed UgpB/G3P-stimulated ATPase activity in proteoliposomes that was neither inhibited by phosphate nor by the signal transducing protein PhoU or the phosphodiesterase UgpQ. Furthermore, a hybrid transporter composed of MalFG-UgpC could be functionally reconstituted while a UgpAE-MalK complex was unstable.
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Affiliation(s)
- Steven Wuttge
- Division of Microbial Physiology, Humboldt-Universität zu Berlin, Unter den Linden 6, D-10099, Berlin, Germany
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19
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Abstract
Recombinant production has become an invaluable tool for supplying research and therapy with proteins of interest. The target proteins are not in every case soluble and/or correctly folded. That is why different production parameters such as host, cultivation conditions and co-expression of chaperones and foldases are applied in order to yield functional recombinant protein. There has been a constant increase and success in the use of folding promoting agents in recombinant protein production. Recent cases are reviewed and discussed in this chapter. Any impact of such strategies cannot be predicted and has to be analyzed and optimized for the corresponding target protein. The in vivo effects of the agents are at least partially comparable to their in vitro mode of action and have been studied by means of modern systems approaches and even in combination with folding/activity screening assays. Resulting data can be used directly for experimental planning or can be fed into knowledge-based modelling. An overview of such technologies is included in the chapter in order to facilitate a decision about the potential in vivo use of folding promoting agents.
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Affiliation(s)
- Beatrix Fahnert
- Cardiff School of Biosciences, Cardiff University, Wales, UK.
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20
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Ruiz J, Haneburger I, Jung K. Identification of ArgP and Lrp as transcriptional regulators of lysP, the gene encoding the specific lysine permease of Escherichia coli. J Bacteriol 2011; 193:2536-48. [PMID: 21441513 PMCID: PMC3133163 DOI: 10.1128/jb.00815-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 03/14/2011] [Indexed: 11/20/2022] Open
Abstract
Expression of lysP, which encodes the lysine-specific transporter LysP in Escherichia coli, is regulated by the concentration of exogenous available lysine. In this study, the LysR-type transcriptional regulator ArgP was identified as the activator of lysP expression. At lysine concentrations higher than 25 μM, lysP expression was shut off and phenocopied an argP deletion mutant. Purified ArgP-His(6) bound to the lysP promoter/control region at a sequence containing a conserved T-N(11)-A motif. Its affinity increased in the presence of lysine but not in the presence of the other known coeffector, arginine. In vivo data suggest that lysine-loaded ArgP and arginine-loaded ArgP compete at the lysP promoter. We propose that lysine-loaded ArgP prevents lysP transcription at the promoter clearance step, as described for the lysine-dependent regulation of argO (R. S. Laishram and J. Gowrishankar, Genes Dev. 21:1258-1272, 2007). The global regulator Lrp also bound to the lysP promoter/control region. An lrp mutant exhibited reduced lysP expression in the absence of external lysine. These results indicate that ArgP is a major regulator of lysP expression but that Lrp modulates lysP transcription under lysine-limiting conditions.
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Affiliation(s)
| | - Ina Haneburger
- Ludwig-Maximilians-Universität München, Munich Center for integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Grosshaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Ludwig-Maximilians-Universität München, Munich Center for integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Grosshaderner Strasse 2-4, 82152 Martinsried, Germany
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21
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DiScipio RG, Khaldoyanidi SK, Schraufstatter IU. Expression of soluble proteins in Escherichia coli by linkage with the acidic propiece of eosinophil major basic protein. Protein Expr Purif 2011; 79:72-80. [PMID: 21550406 DOI: 10.1016/j.pep.2011.04.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Revised: 04/23/2011] [Accepted: 04/26/2011] [Indexed: 01/10/2023]
Abstract
An expression method has been developed to produce soluble cationic polypeptides in Escherichia coli while avoiding inclusion body deposition. For this technique the recombinant product is linked through a thrombin or factor Xa susceptible bond to the amino-terminal domain of the precursor of eosinophil major basic protein (MBP). This N-terminal domain is strongly acidic and is apparently able to shield eosinophils from the potentially injurious activities of MBP. It was reasoned that constructs of this acidic domain with small heterologous cationic proteins expressed in E. coli could result in soluble expression while preventing trafficking and packaging into insoluble inclusion bodies. This has been demonstrated using four examples: complement C5a, CCL18, fibroblast growth factor-β, and leukemia inhibitory factor, whose isoelectric points range from 8.93 to 9.59. Further general applicability of this technique has been shown by using two different expression systems, one which encodes an amino-terminal oligo-histidine leash, and another that codes for an amino-terminal glutathione-S-transferase. Thus the utility of coupling MAP to cationic polypeptides for the purpose of soluble heterologous protein expression in E. coli has been demonstrated.
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Affiliation(s)
- Richard G DiScipio
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121, United States.
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22
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Abstract
[Fe]-hydrogenase is one of the three types of hydrogenases. This enzyme is found in many hydrogenotrophic methanogenic archaea and catalyzes the reversible hydride transfer from H(2) to methenyl-H(4)MPT(+) in methanogenesis from H(2) and CO(2). The enzyme harbors a unique iron-guanylyl pyridinol (FeGP) cofactor as a prosthetic group. Here, we describe the purification of [Fe]-hydrogenase from Methanothermobacter marburgensis, the isolation of the FeGP cofactor from the native holoenzyme, and the reconstitution of [Fe]-hydrogenase from the isolated FeGP cofactor and the heterologously produced apoenzyme.
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Affiliation(s)
- Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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23
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Kawamura-Konishi Y, Maekawa S, Tsuji M, Goto H. C-terminal processing of tyrosinase is responsible for activation of Pholiota microspora proenzyme. Appl Microbiol Biotechnol 2010; 90:227-34. [DOI: 10.1007/s00253-010-3039-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Revised: 11/26/2010] [Accepted: 11/26/2010] [Indexed: 10/18/2022]
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24
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Feng W, Mei S, Wenjie Y, Luyuan H. High-level soluble expression of recombinant human manganese superoxide dismutase in Escherichia coli, and its effects on proliferation of the leukemia cell. Protein Expr Purif 2010; 77:46-52. [PMID: 21172440 DOI: 10.1016/j.pep.2010.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 12/14/2010] [Accepted: 12/14/2010] [Indexed: 11/25/2022]
Abstract
Manganese superoxide dismutase (Mn-SOD) is one of the major enzymes responsible for the defense against oxidative damage due to reactive oxygen species (ROS) in the mitochondria. The present study aimed to produce and evaluate the genetically engineered manganese superoxide dismutase protein. A recombinant plasmid containing DNA segment coding Mn-SOD protein was transformed into Escherichia coli (E. coli) Rosetta-gami strain, for expression. After induction with IPTG, an expected molecular mass of 25 kDa was detected by SDS-PAGE. After Ni-NTA affinity chromatography purification, the purity rate came up to 95%. UV spectroscopy data for our preparations indicated that a peak at 275 nm existed in the spectrum. SOD activity assay showed that the activity of the rhMn-SOD was 1890.9 U/mg. The ORAC level of rhMn-SOD was 151492.2 uM Trolox equiv/mg. Furthermore, in vitro bioactivity assay indicated that the rhMn-SOD protein can inhibit the proliferation of the leukemia K562 cells.
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Affiliation(s)
- Wang Feng
- College of Pharmacy, Jinan University, Guangzhou 510632, China.
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25
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Effects of polynitrogen compounds on the activity of recombinant human HIF-1α prolyl hydroxylase 3 in E. coli. J Inorg Biochem 2010; 105:391-9. [PMID: 21421125 DOI: 10.1016/j.jinorgbio.2010.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2010] [Revised: 12/04/2010] [Accepted: 12/06/2010] [Indexed: 11/22/2022]
Abstract
Hypoxia inducible factor 1α (HIF-1α) becomes an important regulation factor within the histiocyte when it is under the hypoxia condition. Recently, prolyl hydroxylases (PHDs) have been identified to inactivation HIF-lα by hydroxylation. In this study, polynitrogen compounds were screened as HIF-1α PHD3 inhibitors. The coding region of human PHD3 DNA was optimized by using synonymous codons according to the code bias of Escherichia coli. Soluble and active human PHD3 was expressed in the E. coli with a Trx fusion tag under a lower induction temperature of 25°C. Mass spectrometry analysis of the resultant peptide product indicated a mass increase of 16 daltons, consistent with hydroxylation of the proline residue in the HIF-1α (556-574) peptide substrate. Polynitrogen compounds (1-4) inhibited the enzymatic hydroxylation of HIF-1α peptide in a concentration-dependent manner, and the apparent IC(50) values were 29.5, 16.0, 12.8 and 60.4 μM respectively. Double reciprocal (1/V versus 1/[HIF-1α peptide]) plots showed that these compounds are noncompetitive inhibitors of the hydroxylation by recombinant human PHD3 with K(i) values of 67.0, 25.3, 67.3, and 82.1 μM respectively. On the other hand, the metal complexes of these polynitrogen compounds (1-4) cannot inhibit the catalytical activity of PHD3. We hypothesized that the inhibitory mechanism of PHD3 activity by polynitrogen compounds is due to their binding to iron to form stable coordination complexes. Our results in this study indicated that polynitrogen compounds (1-4) could be potential inhibitors of PHD3 to regulate the transcriptional activity of HIF-1α.
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26
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Tandang-Silvas MR, Carrazco-Peña L, Barba de la Rosa AP, Osuna-Castro JA, Utsumi S, Mikami B, Maruyama N. Expression, purification and preliminary crystallization of amaranth 11S proglobulin seed storage protein from Amaranthus hypochondriacus L. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:919-22. [PMID: 20693668 PMCID: PMC2917291 DOI: 10.1107/s1744309110021032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 06/02/2010] [Indexed: 11/11/2022]
Abstract
11S globulin is one of the major seed storage proteins in amaranth. Recombinant protein was produced as up to approximately 80% of the total bacterial protein using Escherichia coli Rosetta-gami (DE3) containing pET21d with amaranth 11S globulin cDNA. The best expression condition was at 302 K for 20 h using LB medium containing 0.5 M NaCl. The recombinant protein was easily separated from most of the Escherichia coli proteins by precipitation with 0-40% ammonium sulfate solution. It formed aggregates at low temperature and at low salt concentrations. This behaviour may imply that it has a more hydrophobic nature than other 11S seed globulins. The crystals diffracted to 6 A resolution and belonged to space group P6(3), with unit-cell parameters a=b=97.6, c=74.8 A, gamma=120.0 degrees. One subunit of a trimer was estimated to be present in the asymmetric unit, assuming a Vsol of 41%. To obtain the complete structure solution, experiments to improve crystallization and flash-cooling conditions are in progress.
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Affiliation(s)
- Mary Rose Tandang-Silvas
- Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Laura Carrazco-Peña
- Facultad de Ciencias Químicas, Universidad de Colima, Carretera Colima-Coquimatalán Km 9 Coquimatalán, Col, México, CP28400
- Molecular Biology Division, Institute for Scientific and Technological Research at San Luis Potosi, Camino a la Presa San Jose No. 2055, Lomas 4a Seccion, 78216 San Luis Potosi, SLP, México
| | - Ana Paulina Barba de la Rosa
- Molecular Biology Division, Institute for Scientific and Technological Research at San Luis Potosi, Camino a la Presa San Jose No. 2055, Lomas 4a Seccion, 78216 San Luis Potosi, SLP, México
| | - Juan Alberto Osuna-Castro
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad de Colima, Autopista Colima-Manzanillo Km 40, Tecomán, COL, México, CP 28100
| | - Shigeru Utsumi
- Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan.
| | - Nobuyuki Maruyama
- Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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27
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Expression and purification of an anti-clenbuterol single chain Fv antibody in Escherichia coli. Protein Expr Purif 2010; 72:26-31. [DOI: 10.1016/j.pep.2010.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 02/23/2010] [Accepted: 03/01/2010] [Indexed: 11/23/2022]
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28
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Cartier G, Lorieux F, Allemand F, Dreyfus M, Bizebard T. Cold adaptation in DEAD-box proteins. Biochemistry 2010; 49:2636-46. [PMID: 20166751 DOI: 10.1021/bi902082d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spontaneous rearrangements of RNA structures are usually characterized by large activation energies and thus become very slow at low temperatures, yet RNA structure must remain dynamic even in cold-adapted (psychrophilic) organisms. DEAD-box proteins constitute a ubiquitous family of RNA-dependent ATPases that can often unwind short RNA duplexes in vitro (helicase activity), hence the belief that one of their major (though not exclusive) roles in vivo is to assist in RNA rearrangements. Here, we compare two Escherichia coli DEAD-box proteins and their orthologs from the psychrophilic bacteria Pseudoalteromonas haloplanktis and Colwellia psychrerythraea from the point of view of enzymatic properties. One of these proteins (SrmB) is involved in ribosome assembly, whereas the other (RhlE) presumably participates in both mRNA degradation and ribosome assembly; in vitro, RhlE is far more active as a helicase than SrmB. The activation energy associated with the ATPase activity of the psychrophilic SrmB is lower than for its mesophilic counterpart, making it more active at low temperatures. In contrast, in the case of psychrophilic RhlE, it is the RNA unwinding activity, not the ATPase activity, that has a reduced activation energy and is therefore cold-adapted. We argue that these different modes of cold adaptation reflect the likely function of these proteins in vivo: RNA helicase for RhlE and ATP-dependent RNA binding for SrmB. The cold adaptation of helicases like RhlE presumably facilitates RNA metabolism in psychrophilic bacteria.
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Affiliation(s)
- Gwendoline Cartier
- CNRS UPR9073, University Paris VII, Institut de Biologie Physico-chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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29
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Butty FD, Aucoin M, Morrison L, Ho N, Shaw G, Creuzenet C. Elucidating the Formation of 6-Deoxyheptose: Biochemical Characterization of the GDP-d-glycero-d-manno-heptose C6 Dehydratase, DmhA, and Its Associated C4 Reductase, DmhB. Biochemistry 2009; 48:7764-75. [DOI: 10.1021/bi901065t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frank D. Butty
- Department of Microbiology and Immunology, Infectious Diseases Research Group
| | - Monique Aucoin
- Department of Microbiology and Immunology, Infectious Diseases Research Group
| | - Leslie Morrison
- Department of Microbiology and Immunology, Infectious Diseases Research Group
| | - Nathan Ho
- Department of Microbiology and Immunology, Infectious Diseases Research Group
| | | | - Carole Creuzenet
- Department of Microbiology and Immunology, Infectious Diseases Research Group
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30
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Koder RL, Anderson JLR, Solomon LA, Reddy KS, Moser CC, Dutton PL. Design and engineering of an O(2) transport protein. Nature 2009; 458:305-9. [PMID: 19295603 PMCID: PMC3539743 DOI: 10.1038/nature07841] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 01/27/2009] [Indexed: 11/09/2022]
Abstract
The principles of natural protein engineering are obscured by overlapping functions and complexity accumulated through natural selection and evolution. Completely artificial proteins offer a clean slate on which to define and test these protein engineering principles, while recreating and extending natural functions. Here we introduce this method with the design of an oxygen transport protein, akin to human neuroglobin. Beginning with a simple and unnatural helix-forming sequence with just three different amino acids, we assembled a four-helix bundle, positioned histidines to bis-histidine ligate haems, and exploited helical rotation and glutamate burial on haem binding to introduce distal histidine strain and facilitate O(2) binding. For stable oxygen binding without haem oxidation, water is excluded by simple packing of the protein interior and loops that reduce helical-interface mobility. O(2) affinities and exchange timescales match natural globins with distal histidines, with the remarkable exception that O(2) binds tighter than CO.
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Affiliation(s)
- Ronald L Koder
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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31
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Kurosawa N, Hirata T, Suzuki H. Characterization of putative tryptophan monooxygenase from Ralstonia solanasearum. J Biochem 2009; 146:23-32. [DOI: 10.1093/jb/mvp040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Effects of selenium on the structure and function of recombinant human S-adenosyl-L-methionine dependent arsenic (+3 oxidation state) methyltransferase in E. coli. J Biol Inorg Chem 2009; 14:485-96. [PMID: 19159958 DOI: 10.1007/s00775-008-0464-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2008] [Accepted: 12/26/2008] [Indexed: 10/21/2022]
Abstract
The effects of Se(IV) on the structure and function of recombinant human arsenic (+3 oxidation state) methyltransferase (AS3MT) purified from the cytoplasm of Escherichia coli were studied. The coding region of human AS3MT complementary DNA was amplified from total RNA extracted from HepG2 cell by reverse transcription PCR. Soluble and active human AS3MT was expressed in the E. coli with a Trx fusion tag under a lower induction temperature of 25 degrees C. Spectra (UV-vis, circular dichroism, and fluorescence) were first used to probe the interaction of Se(IV) and recombinant human AS3MT and the structure-function relationship of the enzyme. The recombinant human AS3MT had a secondary structure of 29.0% alpha-helix, 23.9% beta-pleated sheet, 17.9% beta-turn, and 29.2% random coil. When Se(IV) was added, the content of the alpha-helix did not change, but that of the beta-pleated sheet increased remarkably in the conformation of recombinant human AS3MT. Se(IV) inhibited the enzymatic methylation of inorganic As(III) in a concentration-dependent manner. The IC(50) value for Se(IV) was 2.38 muM. Double-reciprocal (1/V vs. 1/[inorganic As(III)]) plots showed Se(IV) to be a noncompetitive inhibitor of the methylation of inorganic As(III) by recombinant human AS3MT with a K (i) value of 2.61 muM. We hypothesized that Se(IV) interacts with the sulfhydryl group of cysteine(s) in the structural residues rather than the cysteines of the active site (Cys156 and Cys206). When Se(IV) was combined with cysteine(s) in the structural residues, the conformation of recombinant human AS3MT changed and the enzymatic activity decreased. Considering the quenching of tryptophan fluorescence, Cys72 and/or Cys226 are deduced to be primary targets for Se(IV).
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Abstract
The advent of high-throughput protein production and the vast amount of data it is capable of generating has created both new opportunities and problems. Automation and miniaturization allow experimentation to be performed more efficiently, justifying the cost involved in establishing a high-throughput platform. These changes have also magnified the need for effective statistical methods to identify trends and relationships in the data. The application of quantitative management tools to this process provides the means of ensuring maximum efficiency and productivity.
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34
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Co-Expression of Recombinant Nucleoside Phosphorylase from Escherichia coli and its Application. Appl Biochem Biotechnol 2008; 159:168-77. [DOI: 10.1007/s12010-008-8429-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 10/31/2008] [Indexed: 10/21/2022]
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35
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Reddy VA, Venu K, Rao DECS, Rao KV, Reddy VD. Chimeric gene construct coding for bi-functional enzyme endowed with endoglucanase and phytase activities. Arch Microbiol 2008; 191:171-5. [DOI: 10.1007/s00203-008-0437-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 09/29/2008] [Accepted: 10/08/2008] [Indexed: 10/21/2022]
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Vogt S, Lyon EJ, Shima S, Thauer RK. The exchange activities of [Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases. J Biol Inorg Chem 2008; 13:97-106. [PMID: 17924153 PMCID: PMC2757585 DOI: 10.1007/s00775-007-0302-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 09/08/2007] [Indexed: 12/27/2022]
Abstract
[Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) catalyzes the reversible reduction of methenyltetrahydromethanopterin (methenyl-H4MPT+) with H2 to methylene-H4MPT, a reaction involved in methanogenesis from H2 and CO2 in many methanogenic archaea. The enzyme harbors an iron-containing cofactor, in which a low-spin iron is complexed by a pyridone, two CO and a cysteine sulfur. [Fe] hydrogenase is thus similar to [NiFe] and [FeFe] hydrogenases, in which a low-spin iron carbonyl complex, albeit in a dinuclear metal center, is also involved in H2 activation. Like the [NiFe] and [FeFe] hydrogenases, [Fe] hydrogenase catalyzes an active exchange of H2 with protons of water; however, this activity is dependent on the presence of the hydride-accepting methenyl-H4MPT+. In its absence the exchange activity is only 0.01% of that in its presence. The residual activity has been attributed to the presence of traces of methenyl-H4MPT+ in the enzyme preparations, but it could also reflect a weak binding of H2 to the iron in the absence of methenyl-H4MPT+. To test this we reinvestigated the exchange activity with [Fe] hydrogenase reconstituted from apoprotein heterologously produced in Escherichia coli and highly purified iron-containing cofactor and found that in the absence of added methenyl-H4MPT+ the exchange activity was below the detection limit of the tritium method employed (0.1 nmol min(-1) mg(-1)). The finding reiterates that for H2 activation by [Fe] hydrogenase the presence of the hydride-accepting methenyl-H4MPT+ is essentially required. This differentiates [Fe] hydrogenase from [FeFe] and [NiFe] hydrogenases, which actively catalyze H2/H2O exchange in the absence of exogenous electron acceptors.
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Affiliation(s)
- Sonja Vogt
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany
| | - Erica J. Lyon
- Bellarmine University, 2001 Newburg Rd, Louisville, KY 40205 USA
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany
| | - Rudolf K. Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany
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Bair CL, Black LW. A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs. J Mol Biol 2006; 366:768-78. [PMID: 17188297 PMCID: PMC1855630 DOI: 10.1016/j.jmb.2006.11.051] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2006] [Revised: 11/01/2006] [Accepted: 11/14/2006] [Indexed: 11/25/2022]
Abstract
The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs. The protein products GmrS (36 kDa) and GmrD (27 kDa) were purified and found to be inactive separately, but together degraded several different glc-HMC modified DNAs (T4, T2 and T6). The GMR enzyme is able to degrade both alpha-glucosy-HMC T4 DNA and beta-glucosyl-HMC T4 DNA, whereas no activity was observed against non-modified DNAs including unmodified T4 cytosine (C) DNA or non-glucosylated T4 HMC DNA. Enzyme activity requires NTP, favors UTP, is stimulated by calcium, and initially produces 4 kb DNA fragments that are further degraded to low molecular mass products. The enzyme is inhibited by the T4 phage internal protein I* (IPI*) to which it was found to bind. Overall activities of the purified GmrSD enzyme are in good agreement with the properties of the cloned gmr genes in vivo and suggest a restriction enzyme specific for sugar modified HMC DNAs. IPI* thus represents a third generation bacteriophage defense against restriction nucleases of the Gmr type.
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Affiliation(s)
- Catherine L Bair
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201-1503, USA
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38
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Lechtken A, Zündorf I, Dingermann T, Firla B, Steinhilber D. Overexpression, refolding, and purification of polyhistidine-tagged human retinoic acid related orphan receptor RORα4. Protein Expr Purif 2006; 49:114-20. [PMID: 16682227 DOI: 10.1016/j.pep.2006.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2006] [Revised: 03/24/2006] [Accepted: 03/25/2006] [Indexed: 11/29/2022]
Abstract
RORalpha4 is a nuclear receptor activating the transcription of genes that are important for a variety of physiological processes like muscle differentiation, lipid and bone metabolism, cerebellar development, and inflammation. Furthermore, it plays an essential role in maintaining circadian rhythmicity of the core clock in the suprachiasmatic nuclei (SCN). Here, we describe the successful overexpression and purification of human full-length RORalpha4 in Escherichia coli using a T7 expression system. The expressed protein formed inclusion bodies which were solubilized in the presence of 6M guanidinium-HCl and renatured by gradual removal of guanidinium-HCl and addition of l-arginine. The refolded protein was purified by nickel affinity chromatography due to an N-terminal polyhistidine tag which can be cleaved with thrombin subsequently. This method permitted us to obtain up to 20mg of pure and native RORalpha4 protein per liter of E. coli culture. The DNA binding activity of the refolded protein was demonstrated by electrophoretic mobility shift assay (EMSA) using an oligonucleotide comprising the ROR-response element (RORE) motif (A/G)GGTCA. In addition, we developed a new monoclonal antibody to human RORalpha in mice with high sensitivity and specificity.
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Affiliation(s)
- Adriane Lechtken
- Institute of Pharmaceutical Chemistry/ZAFES, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
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Korbas M, Vogt S, Meyer-Klaucke W, Bill E, Lyon EJ, Thauer RK, Shima S. The iron-sulfur cluster-free hydrogenase (Hmd) is a metalloenzyme with a novel iron binding motif. J Biol Chem 2006; 281:30804-13. [PMID: 16887798 DOI: 10.1074/jbc.m605306200] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The iron-sulfur cluster-free hydrogenase (Hmd) from methanogenic archaea harbors an iron-containing cofactor of yet unknown structure. X-ray absorption spectroscopy of the active, as isolated enzyme from Methanothermobacter marburgensis (mHmd) and of the active, reconstituted enzyme from Methanocaldococcus jannaschii (jHmd) revealed the presence of mononuclear iron with two CO, one sulfur and one or two N/O in coordination distance. In jHmd, the single sulfur ligand is most probably provided by Cys176, as deduced from a comparison of the activity and of the x-ray absorption and Mössbauer spectra of the enzyme mutated in any of the three conserved cysteines. In the isolated Hmd cofactor, two CO, one sulfur, and two nitrogen/oxygen atoms coordinate the iron, the sulfur ligand being most probably provided by mercaptoethanol, which is absolutely required for the extraction of the iron-containing cofactor from the holoenzyme and for the stabilization of the extracted cofactor. In active mHmd holoenzyme, the number of iron ligands increased by one when one of the Hmd inhibitors (CO or KCN) were present, indicating that in active Hmd, the iron contains an open coordination site, which is proposed to be the site of H2 interaction.
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Affiliation(s)
- Malgorzata Korbas
- European Molecular Biology Laboratory (EMBL), Outstation Hamburg at Deutsches Electronen Synchroton (DESY), Notkestrasse 85, D-22603 Hamburg, Germany
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40
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Pilak O, Mamat B, Vogt S, Hagemeier CH, Thauer RK, Shima S, Vonrhein C, Warkentin E, Ermler U. The crystal structure of the apoenzyme of the iron-sulphur cluster-free hydrogenase. J Mol Biol 2006; 358:798-809. [PMID: 16540118 DOI: 10.1016/j.jmb.2006.02.035] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 02/09/2006] [Accepted: 02/12/2006] [Indexed: 10/25/2022]
Abstract
The iron-sulphur cluster-free hydrogenase (Hmd, EC 1.12.98.2) from methanogenic archaea is a novel type of hydrogenase that tightly binds an iron-containing cofactor. The iron is coordinated by two CO molecules, one sulphur and a pyridone derivative, which is linked via a phosphodiester bond to a guanosine base. We report here on the crystal structure of the Hmd apoenzyme from Methanocaldococcus jannaschii at 1.75 A and from Methanopyrus kandleri at 2.4 A resolution. Homodimeric Hmd reveals a unique architecture composed of one central and two identical peripheral globular units. The central unit is composed of the intertwined C-terminal segments of both subunits, forming a novel intersubunit fold. The two peripheral units consist of the N-terminal domain of each subunit. The Rossmann fold-like structure of the N-terminal domain contains a mononucleotide-binding site, which could harbour the GMP moiety of the cofactor. Another binding site for the iron-containing cofactor is most probably Cys176, which is located at the bottom of a deep intersubunit cleft and which has been shown to be essential for enzyme activity. Adjacent to the iron of the cofactor modelled as a ligand to Cys176, an extended U-shaped extra electron density, interpreted as a polyethyleneglycol fragment, suggests a binding site for the substrate methenyltetrahydromethanopterin.
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Affiliation(s)
- Oliver Pilak
- Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Marburg, Karl-von-Frisch Strasse D-35043 Marburg, Germany
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41
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Bu S, Tsang PWK, Fu RZ. GroEL-GroES solubilizes abundantly expressed xylulokinase in Escherichia coli. J Appl Microbiol 2005; 98:210-5. [PMID: 15610434 DOI: 10.1111/j.1365-2672.2004.02446.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS The aims of the present work were to solubilize the abundantly expressed recombinant xylulokinase in Escherichia coli and to develop a reliable xylulokinase assay. METHODS AND RESULTS Three mutants of xylulokinase of Bacillus megaterium that were expressed at high level but formed insoluble protein in E. coli BL21(DE3)pLysS were selected for solubility study. The solubility of xylulokinase increased eight to 77-fold after introduction of molecular chaperones GroEL-GroES into the host. CONCLUSION This investigation reports that GroEL-GroES minimizes the formation of insoluble protein in three highly expressed recombinant xylulokinases and an improved xylulokinase assay. SIGNIFICANCE AND IMPACT OF THE STUDY Commercial production of bioethanol is critically dependent on the development of an efficient and low-cost process of enzymatic conversion of xylan, a major component in lignocellulose biomass, to xylulose-5-phosphate, which can then be channelled into pentose phosphate pathway and metabolized to ethanol. The improved intracellular xylulokinase activity is expected to facilitate the xylose degradation.
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Affiliation(s)
- S Bu
- Department of Biochemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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42
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Minimizing inclusion body formation during recombinant protein production in Escherichia coli at bench and pilot plant scale. Enzyme Microb Technol 2004. [DOI: 10.1016/j.enzmictec.2003.10.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Dalmia BK, Schütte K, Nikolov ZL. Domain E ofBacillus maceranscyclodextrin glucanotransferase: An independent starch-binding domain. Biotechnol Bioeng 2004; 47:575-84. [DOI: 10.1002/bit.260470510] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Lubitz SP, Weiner JH. The Escherichia coli ynfEFGHI operon encodes polypeptides which are paralogues of dimethyl sulfoxide reductase (DmsABC). Arch Biochem Biophys 2003; 418:205-16. [PMID: 14522592 DOI: 10.1016/j.abb.2003.08.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ynfEFGHI operon is a paralogue of the Escherichia coli dmsABC operon. ynfE and ynfF are paralogues of dmsA. ynfG and ynfH are paralogues of dmsB and dmsC, respectively. YnfI (dmsD) has no dms paralogue. YnfE/F and YnfG could be detected by immunoblotting with anti-DmsAB antibodies when expressed under the control of a tac or dms promoter. Cells harbouring ynfFGH on a multicopy plasmid supported anaerobic growth with dimethyl sulfoxide (DMSO) as respiratory oxidant in a dmsABC deletion, suggesting that YnfFGH forms a heterotimeric enzyme complex similar to DmsABC. Exchange of DmsC by YnfH (DmsAB-YnfH) resulted in membrane localization, anaerobic growth on DMSO, and binding of 2-n-heptyl 4-hydroxyquinoline-N-oxide, indicating that YnfH was a competent anchor. YnfG can also replace DmsB as the electron transfer subunit and assembled [Fe-S] clusters as judged by electron paramagnetic resonance spectroscopy. YnfE and/or YnfF could not form a functional complex with DmsBC and expression of YnfE prevented the accumulation of YnfFGH.
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Affiliation(s)
- Shannon P Lubitz
- CIHR Membrane Protein Research Group, Department of Biochemistry, University of Alberta, Alta., T6G 2H7, Edmonton, Canada
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45
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Creuzenet C, Urbanic RV, Lam JS. Structure-function studies of two novel UDP-GlcNAc C6 dehydratases/C4 reductases. Variation from the SYK dogma. J Biol Chem 2002; 277:26769-78. [PMID: 12004063 DOI: 10.1074/jbc.m202882200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two subfamilies of UDP-GlcNAc C6 dehydratases were recently identified. FlaA1, a short soluble protein that exhibits a typical SYK catalytic triad, characterizes one of these subfamilies, and WbpM, a large membrane protein that harbors an altered SMK triad that was not predicted to sustain activity, represents the other subfamily. This study focuses on investigating the structure and function of these C6 dehydratases and the role of the altered triad as well as additional amino acid residues involved in catalysis. The significant activity retained by the FlaA1 Y141M triad mutant and the low activity of the WbpM M438Y mutant indicated that the methionine residue was involved in catalysis. A Glu(589) residue, which is conserved only within the large homologues, was shown to be essential for activity in WbpM. Introduction of this residue in FlaA1 enhanced the activity of the corresponding V266E mutant. Hence, this glutamate residue might be responsible for the retention of catalytic efficiency in the large homologues despite alteration of their catalytic triad. Mutations of residues specific for the short homologues (Asp(70), Asp(149)-Lys(150), Cys(103)) abolished the activity of FlaA1. Among them, C103M prevented dimerization but did not significantly affect the secondary structure. The fact that we could identify subfamily-specific residues that are essential for catalysis suggested an independent evolution for each subfamily of C6 dehydratases. Finally, the loss of activity of the FlaA1 G20A mutant provided evidence that a cofactor is involved in catalysis, and kinetic study of the FlaA1 H86A mutant revealed that this conserved histidine is involved in substrate binding. None of the mutations investigated altered the substrate, product, and function specificity of these enzymes.
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Affiliation(s)
- Carole Creuzenet
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
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46
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Abstract
Bacterial inclusion bodies (IBs) are refractile aggregates of protease-resistant misfolded protein that often occur in recombinant bacteria upon gratuitous overexpression of cloned genes. In biotechnology, the formation of IBs represents a main obstacle for protein production since even favouring high protein yields, the in vitro recovery of functional protein from insoluble deposits depends on technically diverse and often complex re-folding procedures. On the other hand, IBs represent an exciting model to approach the in vivo analysis of protein folding and to explore aggregation dynamics. Recent findings on the molecular organisation of embodied polypeptides and on the kinetics of inclusion body formation have revealed an unexpected dynamism of these protein aggregates, from which polypeptides are steadily released in living cells to be further refolded or degraded. The close connection between in vivo protein folding, aggregation, solubilisation and proteolytic digestion offers an integrated view of the bacterial protein quality control system of which IBs might be an important component especially in recombinant bacteria.
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Affiliation(s)
- M M Carrió
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
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47
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Coffman JD, Zhu J, Roach JM, Bavari S, Ulrich RG, Giardina SL. Production and purification of a recombinant Staphylococcal enterotoxin B vaccine candidate expressed in Escherichia coli. Protein Expr Purif 2002; 24:302-12. [PMID: 11858726 DOI: 10.1006/prep.2001.1556] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An attenuated, recombinant form of Staphylococcus enterotoxin B (rSEB) was overexpressed in Escherichia coli under transcriptional control of the T7 promoter. The 28-kDa rSEB was partially purified from soluble, intracellular protein by tangential flow filtration and differential ammonium sulfate precipitation. The intermediate product was then further purified using low-pressure liquid chromatography including hydrophobic interaction, cation exchange, and size-exclusion matrices. The final vialed product was >95% pure as determined by Coomassie blue-stained sodium dodecyl sulfate-polyacrylamide gel electrophoresis, high-pressure size-exclusion chromatography, and capillary zonal electrophoresis. The endotoxin level was <0.6 EU/mg. Final estimated yield of purified rSEB was 147 mg/L of starting culture. Purified rSEB was stable, elicited an immune response in mice, and protected mice against a lethal challenge with the native toxin.
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Affiliation(s)
- J Daniel Coffman
- Biopharmaceutical Development Program, SAIC Frederick, National Cancer Institute at Frederick, Maryland 21702-1201, USA
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48
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Affiliation(s)
- G Rotondo
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, USA
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49
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Esipov RS, Gurevich AI, Chuvikovsky DV, Chupova LA, Muravyova TI, Miroshnikov AI. Overexpression of Escherichia coli genes encoding nucleoside phosphorylases in the pET/Bl21(DE3) system yields active recombinant enzymes. Protein Expr Purif 2002; 24:56-60. [PMID: 11812223 DOI: 10.1006/prep.2001.1524] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Escherichia coli genes encoding purine nucleoside phosphorylase, uridine phosphorylase, and thymidine phosphorylase were cloned into pET plasmids to generate highly effective E. coli BL21(DE3) strains producing each of these enzymes. Optimum conditions for biosynthesis of each enzyme as a soluble protein with intact biological activity were found. The crude preparations are approximately 80% pure and can be used immediately for enzymatic transglycosylation. The enzyme preparations were purified to homogeneity by two steps including fractional precipitation with ammonium sulfate and subsequent chromatography on Sephadex G-100 and DEAE-Sephacel.
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Affiliation(s)
- Roman S Esipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia.
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50
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Leffers G, Rao VB. Biochemical characterization of an ATPase activity associated with the large packaging subunit gp17 from bacteriophage T4. J Biol Chem 2000; 275:37127-36. [PMID: 10967092 DOI: 10.1074/jbc.m003357200] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Double-stranded DNA-packaging in icosahedral bacteriophages is believed to be driven by a packaging "machine" constituted by the portal protein and the two packaging/terminase proteins assembled at the unique portal vertex of the empty prohead shell. Although ATP hydrolysis is evidently the principal driving force, which component of the packaging machinery functions as the translocating ATPase has not been elucidated. Evidence suggests that the large packaging subunit is a strong candidate for the translocating ATPase. We have constructed new phage T4 terminase recombinants under the control of phage T7 promoter and overexpressed the packaging/terminase proteins gp16 and gp17 in various configurations. The hexahistidine-tagged-packaging proteins were purified to near homogeneity by Ni(2+)-agarose chromatography and were shown to be highly active for packaging DNA in vitro. The large packaging subunit gp17 but not the small subunit gp16 exhibited an ATPase activity. Although gp16 lacked ATPase activity, it enhanced the gp17-associated ATPase activity by >50-fold. The gp16 enhancement was specific and was due to an increased catalytic rate for ATP hydrolysis. A phosphorylated gp17 was demonstrated under conditions of low catalytic rates but not under high catalytic rates in the presence of gp16. The data are consistent with the hypothesis that a weak ATPase is transformed into a translocating ATPase of high catalytic capacity after assembly of the packaging machine.
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Affiliation(s)
- G Leffers
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA
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