951
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Chang HC, Kaiser CM, Hartl FU, Barral JM. De novo Folding of GFP Fusion Proteins: High Efficiency in Eukaryotes but Not in Bacteria. J Mol Biol 2005; 353:397-409. [PMID: 16171814 DOI: 10.1016/j.jmb.2005.08.052] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 08/18/2005] [Accepted: 08/19/2005] [Indexed: 10/25/2022]
Abstract
Eukaryotic genomes encode a considerably higher fraction of multi-domain proteins than their prokaryotic counterparts. It has been postulated that efficient co-translational and sequential domain folding has facilitated the explosive evolution of multi-domain proteins in eukaryotes by the recombination of pre-existent domains. Here, we tested whether eukaryotes and bacteria differ generally in the folding efficiency of multi-domain proteins generated by domain recombination. To this end, we compared the folding behavior of a series of recombinant proteins comprised of green fluorescent protein (GFP) fused to four different robustly folding proteins through six different linkers upon expression in Escherichia coli and the yeast Saccharomyces cerevisiae. We found that, unlike yeast, bacteria are remarkably inefficient at folding these fusion proteins, even at comparable levels of expression. In vitro and in vivo folding experiments demonstrate that the GFP domain imposes significant constraints on de novo folding of its fusion partners in bacteria, consistent with a largely post-translational folding mechanism. This behavior may result from an interference of GFP with adjacent domains during folding due to the particular topology of the beta-barrel GFP structure. By following the accumulation of enzymatic activity, we found that the rate of appearance of correctly folded fusion protein per ribosome is indeed considerably higher in yeast than in bacteria.
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Affiliation(s)
- Hung-Chun Chang
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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952
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Chow IT, Baneyx F. Coordinated synthesis of the two ClpB isoforms improves the ability of Escherichia coli to survive thermal stress. FEBS Lett 2005; 579:4235-41. [PMID: 16038902 DOI: 10.1016/j.febslet.2005.06.054] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Revised: 06/09/2005] [Accepted: 06/29/2005] [Indexed: 10/25/2022]
Abstract
Eubacteria synthesize a full-length (ClpB95) and a N-terminally truncated (ClpB80) version of the ClpB disaggregase owing to the presence of a translation initiation site within the clpB transcript. Why these two isoforms have been evolutionary conserved is poorly understood. Here, we constructed a series of E. coli strains and plasmids allowing production of the ClpB95/ClpB80 pair, ClpB95 alone, or ClpB80 alone from near physiological concentrations to a 6-10-fold excess over normal cellular levels. We found that although overexpressed ClpB95 or ClpB80 can independently restore basal thermotolerance to DeltaclpB cells, strains expressing ClpB80 from the clpB chromosomal locus do not exhibit increased resistance to thermal killing at 50 degrees C relative to clpB null cells. Furthermore, synthesis of physiological levels of ClpB95 is less effective than coordinated expression of ClpB95/ClpB80 in protecting E. coli from thermal killing. These results provide an explanation for the conservation of the two ClpB isoforms in eubacteria and are consistent with the fact that wild type E. coli maintains the ClpB80 to ClpB95 ratio at a nearly constant value of 0.4-0.5 under a variety of stress conditions.
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Affiliation(s)
- I-Ting Chow
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, WA 98195, USA
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953
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Maynard J, Adams EJ, Krogsgaard M, Petersson K, Liu CW, Garcia KC. High-level bacterial secretion of single-chain alphabeta T-cell receptors. J Immunol Methods 2005; 306:51-67. [PMID: 16198365 DOI: 10.1016/j.jim.2005.07.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Revised: 07/14/2005] [Accepted: 07/25/2005] [Indexed: 10/25/2022]
Abstract
While numerous antibody-antigen systems have been structurally characterized, studies of structurally analogous T-cell receptor MHC systems have lagged behind largely due to the lack of a general TCR expression system. Efforts to develop bacterial systems have resulted in low yields (< 0.5 mg/l) of active material which is prone to proteolysis and aggregation. Here we report a strategy to secrete folded, soluble single chain T-cell receptors (scTCR) in the Escherichia coli periplasm using three representative alphabeta TCRs (172.10, 1934.4/c19 and 2B4). Shake flask yields between 0.5 and 30 mg/l active, purified material were attained for all TCRs studied and found to depend on the introduction of solubility-increasing amino acid substitutions, skp chaperone co-expression and C-terminal fusion to a human kappa constant domain in the context of a tightly regulated expression vector. This system will greatly enable crystallographic, thermodynamic and other biophysical analyses of TCRs which require large quantities of homogeneous material.
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Affiliation(s)
- Jennifer Maynard
- Department of Microbiology and Immunology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94304, USA.
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954
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García-Fruitós E, González-Montalbán N, Morell M, Vera A, Ferraz RM, Arís A, Ventura S, Villaverde A. Aggregation as bacterial inclusion bodies does not imply inactivation of enzymes and fluorescent proteins. Microb Cell Fact 2005; 4:27. [PMID: 16156893 PMCID: PMC1224866 DOI: 10.1186/1475-2859-4-27] [Citation(s) in RCA: 229] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Accepted: 09/12/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many enzymes of industrial interest are not in the market since they are bio-produced as bacterial inclusion bodies, believed to be biologically inert aggregates of insoluble protein. RESULTS By using two structurally and functionally different model enzymes and two fluorescent proteins we show that physiological aggregation in bacteria might only result in a moderate loss of biological activity and that inclusion bodies can be used in reaction mixtures for efficient catalysis. CONCLUSION This observation offers promising possibilities for the exploration of inclusion bodies as catalysts for industrial purposes, without any previous protein-refolding step.
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Affiliation(s)
- Elena García-Fruitós
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Nuria González-Montalbán
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Montse Morell
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Andrea Vera
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Rosa María Ferraz
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Anna Arís
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Bioloquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
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955
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Stemp MJ, Guha S, Hartl FU, Barral JM. Efficient production of native actin upon translation in a bacterial lysate supplemented with the eukaryotic chaperonin TRiC. Biol Chem 2005; 386:753-7. [PMID: 16201870 DOI: 10.1515/bc.2005.088] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Recombinant expression of actin in bacteria results in non-native species that aggregate into inclusion bodies. Actin is a folding substrate of TRiC, the chaperonin of the eukaryotic cytosol. By employing bacterial in vitro translation lysates supplemented with purified chaperones, we have found that TRiC is the only eukaryotic chaperone necessary for correct folding of newly translated actin. The actin thus produced binds deoxyribonuclease I and polymerizes into filaments, hallmarks of its native state. In contrast to its rapid folding in the eukaryotic cytosol, actin translated in TRiC-supplemented bacterial lysate folds with slower kinetics, resembling the kinetics upon refolding from denaturant. Lysate supplementation with the bacterial chaperonin GroEL/ES or the DnaK/DnaJ/GrpE chaperones leads to prevention of actin aggregation, yet fails to support its correct folding. This combination of in vitro bacterial translation and TRiC-assisted folding allows a detailed analysis of the mechanisms necessary for efficient actin folding in vivo. In addition, it provides a robust alternative for the production of substantial amounts of eukaryotic proteins that otherwise misfold or lead to cellular toxicity upon expression in heterologous hosts.
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Affiliation(s)
- Markus J Stemp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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956
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Centeno NB, Planas-Iglesias J, Oliva B. Comparative modelling of protein structure and its impact on microbial cell factories. Microb Cell Fact 2005; 4:20. [PMID: 15989691 PMCID: PMC1183243 DOI: 10.1186/1475-2859-4-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 06/30/2005] [Indexed: 11/22/2022] Open
Abstract
Comparative modeling is becoming an increasingly helpful technique in microbial cell factories as the knowledge of the three-dimensional structure of a protein would be an invaluable aid to solve problems on protein production. For this reason, an introduction to comparative modeling is presented, with special emphasis on the basic concepts, opportunities and challenges of protein structure prediction. This review is intended to serve as a guide for the biologist who has no special expertise and who is not involved in the determination of protein structure. Selected applications of comparative modeling in microbial cell factories are outlined, and the role of microbial cell factories in the structural genomics initiative is discussed.
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Affiliation(s)
- Nuria B Centeno
- Structural Bioinformatics Laboratory, Research Group on Biomedical Informatics (GRIB), IMIM/UPF. c/ Dr. Aiguader 80. 08003 Barcelona, Spain
| | - Joan Planas-Iglesias
- Structural Bioinformatics Laboratory, Research Group on Biomedical Informatics (GRIB), IMIM/UPF. c/ Dr. Aiguader 80. 08003 Barcelona, Spain
| | - Baldomero Oliva
- Structural Bioinformatics Laboratory, Research Group on Biomedical Informatics (GRIB), IMIM/UPF. c/ Dr. Aiguader 80. 08003 Barcelona, Spain
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957
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Abstract
The biotechnology of recombinant protein production is now entering its most advanced stage, and the growth of industrial protein pharmaceuticals provides solid proof of this evolution. However, the systematic conversion of genetic information into a biologically active protein is constantly confronted by the fundamental problem of protein folding in cells, and many recombinant proteins are not produced in their native state. Instead, they aggregate into a biologically inactive state. Although this aggregation reaction has some practical advantages, in vitro renaturation of recombinant proteins, after solubilization of cellular aggregates, is still an empiric and random process. Thus, it is better to control cellular expression conditions to minimize this problem inside the cells. The most attractive approach is certainly the development of high throughput genetic screens to monitor efficient protein folding.
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Affiliation(s)
- Jean-Michel Betton
- Unité de repliement et modélisation des protéines, Institut Pasteur, Paris, France.
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958
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Rukhman V, Anati R, Melamed-Frank M, Adir N. The MntC crystal structure suggests that import of Mn2+ in cyanobacteria is redox controlled. J Mol Biol 2005; 348:961-9. [PMID: 15843026 DOI: 10.1016/j.jmb.2005.03.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 02/23/2005] [Accepted: 03/02/2005] [Indexed: 11/21/2022]
Abstract
The MntC protein is the periplasmic solute-binding protein component of the high-affinity manganese ATP-binding cassette-type transport system in the cyanobacterium Synechocytis PCC sp. 6803. We have determined the structure of recombinant MntC at 2.9 A resolution by X-ray crystallography using a combination of multi-wavelength anomalous diffraction and molecular replacement. The presence of Mn2+ in the metal ion-binding site was ascertained by use of anomalous difference electron density maps using diffraction data collected at the Mn absorption edge. The MntC protein is similar to previously determined metal ion-binding, solute-binding proteins with two globular domains connected by an extended alpha-helix. However, the metal ion-binding site is asymmetric, with two of the four ligating residues (Glu220 and Asp295) situated closer to the ion than the two histidine residues (His89 and His154). A unique characteristic of the MntC is the existence of a disulfide bond between Cys219 and Cys268. Analysis of amino acid sequences of homologous proteins shows that conservation of the cysteine residues forming the disulfide bond occurs only in cyanobacterial manganese solute-binding proteins. One of the monomers in the MntC asymmetric unit trimer is disordered significantly in the globular domain containing the disulfide bond. The electron density on the manganese ion and on the disulfide bond in this monomer indicates that reduction of this bond changes the relative position of the lower domain and of the Glu220 ligand, potentially lowering the affinity towards Mn2+. This is confirmed by reduction of the disulfide bond in vitro, showing the release of bound Mn2+. We propose that the reduction or oxidation state of the disulfide bond can alter the binding affinity of the protein towards Mn2+ and thus determine whether these ions will be transported into the cytoplasm, or be available for photosystem II biogenesis in the periplasm.
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Affiliation(s)
- Valeria Rukhman
- Department of Chemistry and Institute of Catalysis, Science and Technology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
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959
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Abstract
By immunostaining and transmission electron microscopy, chaperones DnaK and GroEL have been identified at the solvent-exposed surface of bacterial inclusion bodies and entrapped within these aggregates, respectively. Functional implications of this distinct localization are discussed in the context of Escherichia coli protein quality control.
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Affiliation(s)
- M Mar Carrió
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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960
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Zhang A, Cantor EJ, Barshevsky T, Chong S. Productive interaction of chaperones with substrate protein domains allows correct folding of the downstream GFP domain. Gene 2005; 350:25-31. [PMID: 15780997 DOI: 10.1016/j.gene.2005.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Revised: 01/20/2005] [Accepted: 01/24/2005] [Indexed: 11/28/2022]
Abstract
Green fluorescent protein (GFP) has been used to report protein folding by correlating solubility with fluorescence. In a GFP fusion protein, an upstream aggregation-prone domain can disrupt de novo folding of the GFP domain in Escherichia coli, resulting in a loss of fluorescence. Previously, we showed that prevention of misfolding of the upstream aggregation-prone domain by a coupled folding and binding interaction during protein synthesis restored both GFP fluorescence and solubility. Since molecular chaperones often fold nascent polypeptides through a bind-and-release interaction, the question remains whether the chaperone interaction with the upstream aggregation-prone domain enhances GFP fluorescence. Here, we demonstrate that a significant increase in GFP fluorescence occurred only when appropriate chaperones that recognized the aggregation-prone protein and helped its folding were co-expressed. A possible correlation between GFP fluorescence and the productive folding by chaperones is proposed. This study may provide a general strategy for identifying chaperones specific for difficult-to-fold proteins.
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Affiliation(s)
- Aihua Zhang
- New England Biolabs, Inc., 32 Tozer Road, Beverly, MA 01915, USA
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