151
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Merz F, Boehringer D, Schaffitzel C, Preissler S, Hoffmann A, Maier T, Rutkowska A, Lozza J, Ban N, Bukau B, Deuerling E. Molecular mechanism and structure of Trigger Factor bound to the translating ribosome. EMBO J 2008; 27:1622-32. [PMID: 18497744 DOI: 10.1038/emboj.2008.89] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 04/10/2008] [Indexed: 11/09/2022] Open
Abstract
Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome-nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors.
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Affiliation(s)
- Frieder Merz
- Zentrum für Molekulare Biologie Heidelberg, DKFZ-ZMBH Alliance, Universität Heidelberg, Heidelberg, Germany
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152
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Lowry M, Fakayode SO, Geng ML, Baker GA, Wang L, McCarroll ME, Patonay G, Warner IM. Molecular Fluorescence, Phosphorescence, and Chemiluminescence Spectrometry. Anal Chem 2008; 80:4551-74. [DOI: 10.1021/ac800749v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Mark Lowry
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Sayo O. Fakayode
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Maxwell L. Geng
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Gary A. Baker
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Lin Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Matthew E. McCarroll
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Gabor Patonay
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Isiah M. Warner
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
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153
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Thermal unfolding of Escherichia coli trigger factor studied by ultra-sensitive differential scanning calorimetry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1728-34. [PMID: 18539163 DOI: 10.1016/j.bbapap.2008.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Revised: 04/22/2008] [Accepted: 05/08/2008] [Indexed: 11/22/2022]
Abstract
Temperature-induced unfolding of Escherichia coli trigger factor (TF) and its domain truncation mutants, NM and MC, were studied by ultra-sensitive differential scanning calorimetry (UC-DSC). Detailed thermodynamic analysis showed that thermal induced unfolding of TF and MC involves population of dimeric intermediates. In contrast, the thermal unfolding of the NM mutant involves population of only monomeric states. Covalent cross-linking experiments confirmed the presence of dimeric intermediates during thermal unfolding of TF and MC. These data not only suggest that the dimeric form of TF is extremely resistant to thermal unfolding, but also provide further evidence that the C-terminal domain of TF plays a vital role in forming and stabilizing the dimeric structure of the TF molecule. Since TF is the first molecular chaperone that nascent polypeptides encounter in eubacteria, the stable dimeric intermediates of TF populated during thermal denaturation might be important in responding to stress damage to the cell, such as heat shock.
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154
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155
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Kosmaoglou M, Schwarz N, Bett JS, Cheetham ME. Molecular chaperones and photoreceptor function. Prog Retin Eye Res 2008; 27:434-49. [PMID: 18490186 PMCID: PMC2568879 DOI: 10.1016/j.preteyeres.2008.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Molecular chaperones facilitate and regulate protein conformational
change within cells. This encompasses many fundamental cellular processes:
including the correct folding of nascent chains; protein transport and
translocation; signal transduction and protein quality control. Chaperones are,
therefore, important in several forms of human disease, including
neurodegeneration. Within the retina, the highly specialized photoreceptor cell
presents a fascinating paradigm to investigate the specialization of molecular
chaperone function and reveals unique chaperone requirements essential to
photoreceptor function. Mutations in several photoreceptor proteins lead to
protein misfolding mediated neurodegeneration. The best characterized of these
are mutations in the molecular light sensor, rhodopsin, which cause autosomal
dominant retinitis pigmentosa. Rhodopsin biogenesis is likely to require
chaperones, while rhodopsin misfolding involves molecular chaperones in quality
control and the cellular response to protein aggregation. Furthermore, the
specialization of components of the chaperone machinery to photoreceptor
specific roles has been revealed by the identification of mutations in molecular
chaperones that cause inherited retinal dysfunction and degeneration. These
chaperones are involved in several important cellular pathways and further
illuminate the essential and diverse roles of molecular
chaperones.
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Affiliation(s)
- Maria Kosmaoglou
- Division of Molecular and Cellular Neuroscience, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 V 9EL, UK
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156
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Han KY, Park JS, Seo HS, Ahn KY, Lee J. Multiple Stressor-Induced Proteome Responses of Escherichia coli BL21(DE3). J Proteome Res 2008; 7:1891-903. [DOI: 10.1021/pr700631c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kyung-Yeon Han
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-713, South Korea
| | - Jin-Seung Park
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-713, South Korea
| | - Hyuk-Seong Seo
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-713, South Korea
| | - Keum-Young Ahn
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-713, South Korea
| | - Jeewon Lee
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-713, South Korea
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157
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A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing. Nature 2008; 452:108-11. [PMID: 18288106 DOI: 10.1038/nature06683] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Accepted: 01/11/2008] [Indexed: 11/08/2022]
Abstract
Messenger-RNA-directed protein synthesis is accomplished by the ribosome. In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine (tRNA(fMet)). The amino-terminal formylated methionine of all bacterial nascent polypeptides blocks the reactive amino group to prevent unfavourable side-reactions and to enhance the efficiency of translation initiation. The first enzymatic factor that processes nascent chains is peptide deformylase (PDF); it removes this formyl group as polypeptides emerge from the ribosomal tunnel and before the newly synthesized proteins can adopt their native fold, which may bury the N terminus. Next, the N-terminal methionine is excised by methionine aminopeptidase. Bacterial PDFs are metalloproteases sharing a conserved N-terminal catalytic domain. All Gram-negative bacteria, including Escherichia coli, possess class-1 PDFs characterized by a carboxy-terminal alpha-helical extension. Studies focusing on PDF as a target for antibacterial drugs have not revealed the mechanism of its co-translational mode of action despite indications in early work that it co-purifies with ribosomes. Here we provide biochemical evidence that E. coli PDF interacts directly with the ribosome via its C-terminal extension. Crystallographic analysis of the complex between the ribosome-interacting helix of PDF and the ribosome at 3.7 A resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co-translational processing of emerging nascent chains. Furthermore, we have found that the interaction of PDF with the ribosome enhances cell viability. These results provide the structural basis for understanding the coupling between protein synthesis and enzymatic processing of nascent chains, and offer insights into the interplay of PDF with the ribosome-associated chaperone trigger factor.
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158
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Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schütz A, Heinemann U, Yokoyama S, Büssow K, Gunsalus KC. Protein production and purification. Nat Methods 2008; 5:135-46. [PMID: 18235434 PMCID: PMC3178102 DOI: 10.1038/nmeth.f.202] [Citation(s) in RCA: 614] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.
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159
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Transport proteins PotD and Crr of Escherichia coli, novel fusion partners for heterologous protein expression. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1536-43. [DOI: 10.1016/j.bbapap.2007.09.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2007] [Revised: 09/08/2007] [Accepted: 09/24/2007] [Indexed: 11/23/2022]
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160
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Rutkowska A, Mayer MP, Hoffmann A, Merz F, Zachmann-Brand B, Schaffitzel C, Ban N, Deuerling E, Bukau B. Dynamics of trigger factor interaction with translating ribosomes. J Biol Chem 2007; 283:4124-32. [PMID: 18045873 DOI: 10.1074/jbc.m708294200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In all organisms ribosome-associated chaperones assist early steps of protein folding. To elucidate the mechanism of their action, we determined the kinetics of individual steps of the ribosome binding/release cycle of bacterial trigger factor (TF), using fluorescently labeled chaperone and ribosome-nascent chain complexes. Both the association and dissociation rates of TF-ribosome complexes are modulated by nascent chains, whereby their length, sequence, and folding status are influencing parameters. However, the effect of the folding status is modest, indicating that TF can bind small globular domains and accommodate them within its substrate binding cavity. In general, the presence of a nascent chain causes an up to 9-fold increase in the rate of TF association, which provides a kinetic explanation for the observed ability of TF to efficiently compete with other cytosolic chaperones for binding to nascent chains. Furthermore, a subset of longer nascent polypeptides promotes the stabilization of TF-ribosome complexes, which increases the half-life of these complexes from 15 to 50 s. Nascent chains thus regulate their folding environment generated by ribosome-associated chaperones.
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Affiliation(s)
- Anna Rutkowska
- Zentrum für Molekulare Biologie Heidelberg, University of Heidelberg, Heidelberg 69120, Germany
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161
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Hsu STD, Fucini P, Cabrita LD, Launay H, Dobson CM, Christodoulou J. Structure and dynamics of a ribosome-bound nascent chain by NMR spectroscopy. Proc Natl Acad Sci U S A 2007; 104:16516-21. [PMID: 17940046 PMCID: PMC2034214 DOI: 10.1073/pnas.0704664104] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Indexed: 11/18/2022] Open
Abstract
Protein folding in living cells is inherently coupled to protein synthesis and chain elongation. There is considerable evidence that some nascent chains fold into their native structures in a cotranslational manner before release from the ribosome, but, despite its importance, a detailed description of such a process at the atomic level remains elusive. We show here at a residue-specific level that a nascent protein chain can reach its native tertiary structure on the ribosome. By generating translation-arrested ribosomes in which the newly synthesized polypeptide chain is selectively (13)C/(15)N-labeled, we observe, using ultrafast NMR techniques, a large number of resonances of a ribosome-bound nascent chain complex corresponding to a pair of C-terminally truncated immunoglobulin (Ig) domains. Analysis of these spectra reveals that the nascent chain adopts a structure in which a native-like N-terminal Ig domain is tethered to the ribosome by a largely unfolded and highly flexible C-terminal domain. Selective broadening of resonances for a group of residues that are colocalized in the structure demonstrates that there are specific but transient interactions between the ribosome and the N-terminal region of the folded Ig domain. These findings represent a step toward a detailed structural understanding of the cellular processes of cotranslational folding.
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Affiliation(s)
- Shang-Te Danny Hsu
- *Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Paola Fucini
- AG-Ribosome, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany; and
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universitaet Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Lisa D. Cabrita
- *Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Hélène Launay
- *Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Christopher M. Dobson
- *Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John Christodoulou
- *Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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162
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Greene D, Whitney S, Matsumura I. Artificially evolved Synechococcus PCC6301 Rubisco variants exhibit improvements in folding and catalytic efficiency. Biochem J 2007; 404:517-24. [PMID: 17391103 PMCID: PMC1896282 DOI: 10.1042/bj20070071] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The photosynthetic CO2-fixing enzyme, Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), is responsible for most of the world's biomass, but is a slow non-specific catalyst. We seek to identify and overcome the chemical and biological constraints that limit the evolutionary potential of Rubisco in Nature. Recently, the horizontal transfer of Calvin cycle genes (rbcL, rbcS and prkA) from cyanobacteria (Synechococcus PCC6301) to gamma-proteobacteria (Escherichia coli) was emulated in the laboratory. Three unique Rubisco variants containing single (M259T) and double (M259T/A8S, M259T/F342S) amino acid substitutions in the L (large) subunit were identified after three rounds of random mutagenesis and selection in E. coli. Here we show that the M259T mutation did not increase steady-state levels of rbcL mRNA or L protein. It instead improved the yield of properly folded L subunit in E. coli 4-9-fold by decreasing its natural propensity to misfold in vivo and/or by enhancing its interaction with the GroES-GroEL chaperonins. The addition of osmolites to the growth media enhanced productive folding of the M259T L subunit relative to the wild-type L subunit, while overexpression of the trigger factor and DnaK/DnaJ/GrpE chaperones impeded Rubisco assembly. The evolved enzymes showed improvement in their kinetic properties with the M259T variant showing a 12% increase in carboxylation turnover rate (k(c)cat), a 15% improvement in its K(M) for CO2 and no change in its K(M) for ribulose-1,5-bisphosphate or its CO2/O2 selectivity. The results of the present study show that the directed evolution of the Synechococcus Rubisco in E. coli can elicit improvements in folding and catalytic efficiency.
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Affiliation(s)
- Dina N. Greene
- *Department of Biochemistry, Center for Fundamental and Applied Molecular Evolution, Emory University School of Medicine, Rollins Research Center, Atlanta, GA 30322, U.S.A
| | - Spencer M. Whitney
- †Molecular Plant Physiology, Research School of Biological Sciences, The Australian National University, Canberra ACT 0200, Australia
| | - Ichiro Matsumura
- *Department of Biochemistry, Center for Fundamental and Applied Molecular Evolution, Emory University School of Medicine, Rollins Research Center, Atlanta, GA 30322, U.S.A
- To whom correspondence should be addressed (email )
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163
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Han KY, Song JA, Ahn KY, Park JS, Seo HS, Lee J. Enhanced solubility of heterologous proteins by fusion expression using stress-induced Escherichia coli protein, Tsf. FEMS Microbiol Lett 2007; 274:132-8. [PMID: 17608803 DOI: 10.1111/j.1574-6968.2007.00824.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Through two-dimensional electrophoresis, Escherichia coli proteome response to a protein denaturant, guanidine hydrochloride, was analyzed and elongation factor Ts (Tsf) detected as a stress-induced protein. Many host proteins aggregated, or their synthesis levels decreased significantly under conditions of protein denaturation as 34 out of 699 soluble proteins knocked out and 63 proteins decreased by over 2.5-fold. Interestingly, the expression level of Tsf increased 1.61-fold compared with a nonstress condition. Contrary to direct expression, various heterologous proteins were solubly expressed in E. coli when subjected to N-terminus fusions of Tsf. Owing most likely to an intrinsic high folding efficiency, Tsf seemed to play critical roles in sequestering interactive surfaces of heterologous proteins from nonspecific protein-protein interactions leading to formation of inclusion bodies. It has been also demonstrated that Tsf is effective in aiding the production of a biologically active bacterial cutinase, which could be of interest to biotechnology and commercial applications.
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Affiliation(s)
- Kyung-Yeon Han
- Department of Chemical and Biological Engineering, Korea University, Seoul, South Korea
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164
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Elad N, Farr GW, Clare DK, Orlova EV, Horwich AL, Saibil HR. Topologies of a substrate protein bound to the chaperonin GroEL. Mol Cell 2007; 26:415-26. [PMID: 17499047 PMCID: PMC1885994 DOI: 10.1016/j.molcel.2007.04.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 03/19/2007] [Accepted: 04/04/2007] [Indexed: 12/22/2022]
Abstract
The chaperonin GroEL assists polypeptide folding through sequential steps of binding nonnative protein in the central cavity of an open ring, via hydrophobic surfaces of its apical domains, followed by encapsulation in a hydrophilic cavity. To examine the binding state, we have classified a large data set of GroEL binary complexes with nonnative malate dehydrogenase (MDH), imaged by cryo-electron microscopy, to sort them into homogeneous subsets. The resulting electron density maps show MDH associated in several characteristic binding topologies either deep inside the cavity or at its inlet, contacting three to four consecutive GroEL apical domains. Consistent with visualization of bound polypeptide distributed over many parts of the central cavity, disulfide crosslinking could be carried out between a cysteine in a bound substrate protein and cysteines substituted anywhere inside GroEL. Finally, substrate binding induced adjustments in GroEL itself, observed mainly as clustering together of apical domains around sites of substrate binding.
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Affiliation(s)
- Nadav Elad
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
| | - George W. Farr
- Department of Genetics, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Daniel K. Clare
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
| | - Elena V. Orlova
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
| | - Arthur L. Horwich
- Department of Genetics, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Helen R. Saibil
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
- Corresponding author
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165
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Perham M, Wittung-Stafshede P. Folding and assembly of co-chaperonin heptamer probed by forster resonance energy transfer. Arch Biochem Biophys 2007; 464:306-13. [PMID: 17521602 DOI: 10.1016/j.abb.2007.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 04/17/2007] [Indexed: 10/23/2022]
Abstract
The ring-shaped heptameric co-chaperonin protein 10 (cpn10) is one of few oligomeric beta-sheet proteins that unfold and disassemble reversibly in vitro. Here, we labeled human mitochondrial cpn10 with donor and acceptor dyes to obtain FRET signals. Cpn10 mixed in a 1:1:5 ratio of donor:acceptor:unlabeled monomers form heptamers that are active in an in vitro functional assay. Monomer-monomer affinity, as well as thermal and chemical stability, of the labeled cpn10 is similar to the unlabeled protein, demonstrating that the labels do not perturb the system. Using changes in FRET, we then probed for the first time cpn10 heptamer-monomer assembly/disassembly kinetics. Heptamer dissociation is very slow (1/k(diss) approximately 3h; 20 degrees C, pH 7) corresponding to an activation energy of approximately 50kJ/mol. Ring-ring mixing experiments reveal that cpn10 heptamer dissociation is rate limiting; subsequent associations events are faster. Kinetic inertness explains how cpn10 cycles on and off cpn60 as an intact heptamer in vivo.
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Affiliation(s)
- Michael Perham
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77251, United States
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166
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Lakshmipathy SK, Tomic S, Kaiser CM, Chang HC, Genevaux P, Georgopoulos C, Barral JM, Johnson AE, Hartl FU, Etchells SA. Identification of nascent chain interaction sites on trigger factor. J Biol Chem 2007; 282:12186-93. [PMID: 17296610 DOI: 10.1074/jbc.m609871200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The role of ribosome-binding molecular chaperones in protein folding is not yet well understood. Trigger factor (TF) is the first chaperone to interact with nascent polypeptides as they emerge from the bacterial ribosome. It binds to the ribosome as a monomer but forms dimers in free solution. Based on recent crystal structures, TF has an elongated shape, with the peptidyl-prolyl-cis/trans-isomerase (PPIase) domain and the N-terminal ribosome binding domain positioned at opposite ends of the molecule and the C-terminal domain, which forms two arms, positioned in between. By using site specifically labeled TF proteins, we have demonstrated that all three domains of TF interact with nascent chains during translation. Interactions with the PPIase domain were length-dependent but independent of PPIase activity. Interestingly, with free TF, these same sites were found to be involved in forming the dimer interface, suggesting that dimerization partially occludes TF-nascent chain binding sites. Our data indicate the existence of two regions on TF along which nascent chains can interact, the NC-domains as the main site and the PPIase domain as an auxiliary site.
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Affiliation(s)
- Sathish K Lakshmipathy
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
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Schaffitzel C, Ban N. Generation of ribosome nascent chain complexes for structural and functional studies. J Struct Biol 2007; 158:463-71. [PMID: 17350284 DOI: 10.1016/j.jsb.2007.01.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 01/10/2007] [Accepted: 01/13/2007] [Indexed: 10/23/2022]
Abstract
Biochemical and structural studies of co-translational folding, targeting and translocation depend on an efficient methodology to prepare ribosome nascent chain complexes (RNCs). Here we present our approach for the generation of homogenous and stable RNCs involving in vitro translation and affinity purification. Fusing the SecM arrest sequence, which tightly interacts with the ribosomal tunnel, to the nascent polypeptide chain significantly enhanced the stability of the RNCs. We have been able to increase the yield of the affinity purification step by engineering a tag with higher affinity. The RNCs generated with this approach have been successfully used to obtain 3D cryo-electron microscopic reconstructions of complexes with the signal recognition particle and the translocon. The established procedure is highly efficient and if scaled up could yield milligram amounts of RNCs sufficient for crystallization experiments.
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Affiliation(s)
- Christiane Schaffitzel
- ETH Zürich, Institute for Molecular Biology and Biophysics, HPK Building, Schafmattstr. 20, 8093 Zürich, Switzerland.
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