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André Y, Richard E, Leroux M, Jeacomine I, Bayma E, Armand S, Priem B. Production of unsulfated chondroitin and associated chondro-oligosaccharides in recombinant Escherichia coli. Carbohydr Res 2024; 544:109243. [PMID: 39182394 DOI: 10.1016/j.carres.2024.109243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/02/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024]
Abstract
We designed metabolically engineered non-pathogenic strains of Escherichia coli to produce unsulfated chondroitin with and without chondroitin lyase to produce the chondroitin polymer or its related oligosaccharides. Chondroitin was synthesized using chondroitin synthase KfoC and chondroitin was degraded using Pl35, a chondroitin lyase from Pedobacter heparinus. Pl35 behaved as a true endo-enzyme generating a large panel of oligosaccharides ranging from trimers to 18-mers instead of the di- and tetramers obtained with most chondroitin lyases. Two series of oligosaccharides were characterized, sharing an unsaturated uronic acid (4-deoxy-α-L-threo-hex-4-enepyranosyluronic acid, △UA) residue at their non-reducing end. The major "even-numbered" series was characterized by a terminal reducing N-acetylgalactosaminyl residue. The minor "odd-numbered" series oligosaccharides carried a terminal reducing glucuronic acid residue instead. Cultures were conducted in fed-batch conditions, and led to the production of up to 10 g L-1 chondroitin or chondroitin oligosaccharides. All products were purified and fully characterized using NMR and mass spectrometry analyses. This is the first report of the microbial production of large chondro-oligosaccharides.
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Affiliation(s)
- Yanna André
- Centre de Recherche sur Les Macromolécules Végétales, Groupe Chimie et Biotechnologie des Oligosaccharides, 601 rue de La Chimie, BP 53X, 38041, Grenoble, Cedex 09, France
| | - Emeline Richard
- Centre de Recherche sur Les Macromolécules Végétales, Groupe Chimie et Biotechnologie des Oligosaccharides, 601 rue de La Chimie, BP 53X, 38041, Grenoble, Cedex 09, France
| | - Mélanie Leroux
- Centre de Recherche sur Les Macromolécules Végétales, Groupe Chimie et Biotechnologie des Oligosaccharides, 601 rue de La Chimie, BP 53X, 38041, Grenoble, Cedex 09, France; HTL Biotechnology, 7 rue Alfred Kastler, 35133, Javené, France
| | - Isabelle Jeacomine
- Centre de Recherche sur Les Macromolécules Végétales, Groupe Chimie et Biotechnologie des Oligosaccharides, 601 rue de La Chimie, BP 53X, 38041, Grenoble, Cedex 09, France
| | - Eric Bayma
- Centre de Recherche sur Les Macromolécules Végétales, Groupe Chimie et Biotechnologie des Oligosaccharides, 601 rue de La Chimie, BP 53X, 38041, Grenoble, Cedex 09, France
| | - Sylvie Armand
- Centre de Recherche sur Les Macromolécules Végétales, Groupe Chimie et Biotechnologie des Oligosaccharides, 601 rue de La Chimie, BP 53X, 38041, Grenoble, Cedex 09, France
| | - Bernard Priem
- Centre de Recherche sur Les Macromolécules Végétales, Groupe Chimie et Biotechnologie des Oligosaccharides, 601 rue de La Chimie, BP 53X, 38041, Grenoble, Cedex 09, France.
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Mecha MF, Hutchinson RB, Lee JH, Cavagnero S. Protein folding in vitro and in the cell: From a solitary journey to a team effort. Biophys Chem 2022; 287:106821. [PMID: 35667131 PMCID: PMC9636488 DOI: 10.1016/j.bpc.2022.106821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 12/22/2022]
Abstract
Correct protein folding is essential for the health and function of living organisms. Yet, it is not well understood how unfolded proteins reach their native state and avoid aggregation, especially within the cellular milieu. Some proteins, especially small, single-domain and apparent two-state folders, successfully attain their native state upon dilution from denaturant. Yet, many more proteins undergo misfolding and aggregation during this process, in a concentration-dependent fashion. Once formed, native and aggregated states are often kinetically trapped relative to each other. Hence, the early stages of protein life are absolutely critical for proper kinetic channeling to the folded state and for long-term solubility and function. This review summarizes current knowledge on protein folding/aggregation mechanisms in buffered solution and within the bacterial cell, highlighting early stages. Remarkably, teamwork between nascent chain, ribosome, trigger factor and Hsp70 molecular chaperones enables all proteins to overcome aggregation propensities and reach a long-lived bioactive state.
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Affiliation(s)
- Miranda F Mecha
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States of America
| | - Rachel B Hutchinson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States of America
| | - Jung Ho Lee
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States of America
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States of America.
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3
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Hutchinson RB, Chen X, Zhou N, Cavagnero S. Fluorescence Anisotropy Decays and Microscale-Volume Viscometry Reveal the Compaction of Ribosome-Bound Nascent Proteins. J Phys Chem B 2021; 125:6543-6558. [PMID: 34110829 PMCID: PMC8741338 DOI: 10.1021/acs.jpcb.1c04473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This work introduces a technology that combines fluorescence anisotropy decay with microscale-volume viscometry to investigate the compaction and dynamics of ribosome-bound nascent proteins. Protein folding in the cell, especially when nascent chains emerge from the ribosomal tunnel, is poorly understood. Previous investigations based on fluorescence anisotropy decay determined that a portion of the ribosome-bound nascent protein apomyoglobin (apoMb) forms a compact structure. This work, however, could not assess the size of the compact region. The combination of fluorescence anisotropy with microscale-volume viscometry, presented here, enables identifying the size of compact nascent-chain subdomains using a single fluorophore label. Our results demonstrate that the compact region of nascent apoMb contains 57-83 amino acids and lacks residues corresponding to the two native C-terminal helices. These amino acids are necessary for fully burying the nonpolar residues in the native structure, yet they are not available for folding before ribosome release. Therefore, apoMb requires a significant degree of post-translational folding for the generation of its native structure. In summary, the combination of fluorescence anisotropy decay and microscale-volume viscometry is a powerful approach to determine the size of independently tumbling compact regions of biomolecules. This technology is of general applicability to compact macromolecules linked to larger frameworks.
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Affiliation(s)
| | - Xi Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ningkun Zhou
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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4
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Jiang C, Wynne M, Huber D. How Quality Control Systems AID Sec-Dependent Protein Translocation. Front Mol Biosci 2021; 8:669376. [PMID: 33928127 PMCID: PMC8076867 DOI: 10.3389/fmolb.2021.669376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The evolutionarily conserved Sec machinery is responsible for transporting proteins across the cytoplasmic membrane. Protein substrates of the Sec machinery must be in an unfolded conformation in order to be translocated across (or inserted into) the cytoplasmic membrane. In bacteria, the requirement for unfolded proteins is strict: substrate proteins that fold (or misfold) prematurely in the cytoplasm prior to translocation become irreversibly trapped in the cytoplasm. Partially folded Sec substrate proteins and stalled ribosomes containing nascent Sec substrates can also inhibit translocation by blocking (i.e., “jamming”) the membrane-embedded Sec machinery. To avoid these issues, bacteria have evolved a complex network of quality control systems to ensure that Sec substrate proteins do not fold in the cytoplasm. This quality control network can be broken into three branches, for which we have defined the acronym “AID”: (i) avoidance of cytoplasmic intermediates through cotranslationally channeling newly synthesized Sec substrates to the Sec machinery; (ii) inhibition of folding Sec substrate proteins that transiently reside in the cytoplasm by molecular chaperones and the requirement for posttranslational modifications; (iii) destruction of products that could potentially inhibit translocation. In addition, several stress response pathways help to restore protein-folding homeostasis when environmental conditions that inhibit translocation overcome the AID quality control systems.
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Affiliation(s)
- Chen Jiang
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Max Wynne
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Damon Huber
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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5
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Jia M, Wu B, Yang Z, Chen C, Zhao M, Hou X, Niu X, Jin C, Hu Y. Conformational Dynamics of the Periplasmic Chaperone SurA. Biochemistry 2020; 59:3235-3246. [PMID: 32786408 DOI: 10.1021/acs.biochem.0c00507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The periplasmic protein SurA is the primary chaperone involved in the biogenesis of bacterial outer membrane proteins and is a potential antibacterial drug target. The three-dimensional structure of SurA can be divided into three parts, a core module formed by the N- and C-terminal regions and two peptidyl-prolyl isomerase (PPIase) domains, P1 and P2. Despite the determination of the structures of several SurA-peptide complexes, the functional mechanism of this chaperone remains elusive and the roles of the two PPIase domains are yet unclear. Herein, we characterize the conformational dynamics of SurA by using solution nuclear magnetic resonance and single-molecule fluorescence resonance energy transfer methods. We demonstrate a "closed-to-open" structural transition of the P1 domain that is correlated with both chaperone activity and peptide binding and show that the flexible P2 domain can also occupy conformations that closely contact the NC core module. Our results offer a structural basis for the counteracting roles of the two PPIase domains in regulating the SurA chaperone activity.
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Affiliation(s)
- Moye Jia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bo Wu
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.,MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.,MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xianhui Hou
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Yunfei Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Hu X, Fan G, Liao H, Fu Z, Ma C, Ni H, Li X. Optimized soluble expression of a novel endoglucanase from Burkholderia pyrrocinia in Escherichia coli. 3 Biotech 2020; 10:387. [PMID: 32832337 DOI: 10.1007/s13205-020-02327-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022] Open
Abstract
Burkholderia pyrrocinia B1213, a novel microbe isolated from a Baijiu-producing environment, displayed strong cellulolytic activity on agar plates with glucan as the carbon source and had an activity of 674.5 U/mL after culturing with barley. Genome annotation of B. pyrrocinia identificated a single endoglucanase (EG)-encoding gene, designated as BpEG01790. The endoglucanase BpEG01790 shows 98.28% sequence similarity with an endo-β-1,4-glucanase (EC 3.2.1.4) from Burkholderia stabilis belonging to glycoside hydrolase family 8 (GH8). The gene BpEG01790 has an open reading frame of 1218 bp encoding a 406 amino acid (AA) residue protein (43.0 kDa) with a 40-AA signal peptide. BpEG01790 was successfully cloned into pET28a( +) with and without the signal peptide; however, attempts to overexpress this protein in Escherichia coli BL21(DE3) cells using this expression system failed. BpEG01790 was also cloned into the pCold TF vector. Active BpEG01790 was successfully overexpressed with or without the signal peptide using the pCold TF vector expression system and E. coli BL21 (DE3) cells. Overexpression of recombinant BpEG01790 without the signal peptide was higher compared with the construct that included the signal peptide. Optimization of culture conditions improved the enzyme activity by 12.5-fold. This is the first report describing the heterologous soluble overexpression of an EG belonging to GH8 from B. pyrrocinia using TF as a molecular chaperone.
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Affiliation(s)
- Xiaoqing Hu
- College of Food and Biological Engineering, Jimei University, Yindou Road, Jimei District, Xiamen, 361021 Fujian China
| | - Guangsen Fan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), No 11 Fucheng Street, Haidian District, Beijing, 100048 China
| | - Hui Liao
- College of Food and Biological Engineering, Jimei University, Yindou Road, Jimei District, Xiamen, 361021 Fujian China
| | - Zhilei Fu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
| | - Chao Ma
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Yindou Road, Jimei District, Xiamen, 361021 Fujian China
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), No 11 Fucheng Street, Haidian District, Beijing, 100048 China
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7
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Pellowe G, Findlay HE, Lee K, Gemeinhardt TM, Blackholly LR, Reading E, Booth PJ. Capturing Membrane Protein Ribosome Nascent Chain Complexes in a Native-like Environment for Co-translational Studies. Biochemistry 2020; 59:2764-2775. [PMID: 32627541 PMCID: PMC7551657 DOI: 10.1021/acs.biochem.0c00423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/02/2020] [Indexed: 01/02/2023]
Abstract
Co-translational folding studies of membrane proteins lag behind cytosolic protein investigations largely due to the technical difficulty in maintaining membrane lipid environments for correct protein folding. Stalled ribosome-bound nascent chain complexes (RNCs) can give snapshots of a nascent protein chain as it emerges from the ribosome during biosynthesis. Here, we demonstrate how SecM-facilitated nascent chain stalling and native nanodisc technologies can be exploited to capture in vivo-generated membrane protein RNCs within their native lipid compositions. We reveal that a polytopic membrane protein can be successfully stalled at various stages during its synthesis and the resulting RNC extracted within either detergent micelles or diisobutylene-maleic acid co-polymer native nanodiscs. Our approaches offer tractable solutions for the structural and biophysical interrogation of nascent membrane proteins of specified lengths, as the elongating nascent chain emerges from the ribosome and inserts into its native lipid milieu.
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Affiliation(s)
- Grant
A. Pellowe
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Heather E. Findlay
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Karen Lee
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Tim M. Gemeinhardt
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Laura R. Blackholly
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Eamonn Reading
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Paula J. Booth
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
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Simpson LJ, Tzima E, Reader JS. Mechanical Forces and Their Effect on the Ribosome and Protein Translation Machinery. Cells 2020; 9:cells9030650. [PMID: 32156009 PMCID: PMC7140433 DOI: 10.3390/cells9030650] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/12/2022] Open
Abstract
Mechanical forces acting on biological systems, at both the macroscopic and microscopic levels, play an important part in shaping cellular phenotypes. There is a growing realization that biomolecules that respond to force directly applied to them, or via mechano-sensitive signalling pathways, can produce profound changes to not only transcriptional pathways, but also in protein translation. Forces naturally occurring at the molecular level can impact the rate at which the bacterial ribosome translates messenger RNA (mRNA) transcripts and influence processes such as co-translational folding of a nascent protein as it exits the ribosome. In eukaryotes, force can also be transduced at the cellular level by the cytoskeleton, the cell’s internal filamentous network. The cytoskeleton closely associates with components of the translational machinery such as ribosomes and elongation factors and, as such, is a crucial determinant of localized protein translation. In this review we will give (1) a brief overview of protein translation in bacteria and eukaryotes and then discuss (2) how mechanical forces are directly involved with ribosomes during active protein synthesis and (3) how eukaryotic ribosomes and other protein translation machinery intimately associates with the mechanosensitive cytoskeleton network.
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9
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Co-translational assembly of mammalian nuclear multisubunit complexes. Nat Commun 2019; 10:1740. [PMID: 30988355 PMCID: PMC6465333 DOI: 10.1038/s41467-019-09749-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/29/2019] [Indexed: 01/07/2023] Open
Abstract
Cells dedicate significant energy to build proteins often organized in multiprotein assemblies with tightly regulated stoichiometries. As genes encoding subunits assembling in a multisubunit complex are dispersed in the genome of eukaryotes, it is unclear how these protein complexes assemble. Here, we show that mammalian nuclear transcription complexes (TFIID, TREX-2 and SAGA) composed of a large number of subunits, but lacking precise architectural details are built co-translationally. We demonstrate that dimerization domains and their positions in the interacting subunits determine the co-translational assembly pathway (simultaneous or sequential). The lack of co-translational interaction can lead to degradation of the partner protein. Thus, protein synthesis and complex assembly are linked in building mammalian multisubunit complexes, suggesting that co-translational assembly is a general principle in mammalian cells to avoid non-specific interactions and protein aggregation. These findings will also advance structural biology by defining endogenous co-translational building blocks in the architecture of multisubunit complexes. Genes encoding protein complex subunits are often dispersed in the genome of eukaryotes, raising the question how these protein complexes assemble. Here, the authors provide evidence that mammalian nuclear transcription complexes are formed co-translationally to ensure specific and functional interactions.
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10
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Fan D, Cao S, Zhou Q, Zhang Y, Yue L, Han C, Yang B, Wang Y, Ma Z, Zhu L, Liu C. Exploring the roles of substrate-binding surface of the chaperone site in the chaperone activity of trigger factor. FASEB J 2018; 32:fj201701576. [PMID: 29906241 DOI: 10.1096/fj.201701576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Trigger factor (TF) is a key component of the prokaryotic chaperone network, which is involved in many basic cellular processes, such as protein folding, protein trafficking, and ribosome assembly. The major chaperone site of TF has a cradle-like structure in which protein substrate may fold without interference from other proteins. Here, we investigated in vivo and in vitro the roles of hydrophobic and charged patches on the edge and interior of cradle during TF-assisted protein folding. Our results showed that most of the surface of the cradle was involved in TF-assisted protein folding, which was larger than found in early studies. Although the inner surface of cradle was mostly hydrophobic, both hydrophobic and electrostatic patches were indispensable for TF to facilitate correct protein folding. However, hydrophobic patches were more important for the antiaggregation activity of TF. Furthermore, it was found that the patches on the surface of cradle were involved in TF-assisted protein folding in a spatial and temporal order. These results suggest that the folding-favorable interface between the cradle and substrate was dynamic during TF-assisted protein folding, which enabled TF to be involved in the folding of substrate in an aggressive manner rather than acting as a classic holdase.-Fan, D., Cao, S., Zhou, Q., Zhang, Y., Yue, L., Han, C., Yang, B., Wang, Y., Ma, Z., Zhu, L., Liu, C. Exploring the roles of substrate-binding surface of chaperone site in the chaperone activity of trigger factor.
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Affiliation(s)
- Dongjie Fan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shunan Cao
- Key Laboratory for Polar Science, State Ocean Administration, Polar Research Institute of China, Shanghai, China
| | - Qiming Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
- ChosenMed Technology Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, China
| | - You Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Lei Yue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Chang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Bo Yang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Yu Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhuo Ma
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Lingxiang Zhu
- National Research Institute for Family Planning (NRIFP), Beijing, China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
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11
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Abstract
Proteins fold under mechanical forces in a number of biological processes, ranging from muscle contraction to co-translational folding. As force hinders the folding transition, chaperones must play a role in this scenario, although their influence on protein folding under force has not been directly monitored yet. Here, we introduce single-molecule magnetic tweezers to study the folding dynamics of protein L in presence of the prototypical molecular chaperone trigger factor over the range of physiological forces (4–10 pN). Our results show that trigger factor increases prominently the probability of folding against force and accelerates the refolding kinetics. Moreover, we find that trigger factor catalyzes the folding reaction in a force-dependent manner; as the force increases, higher concentrations of trigger factor are needed to rescue folding. We propose that chaperones such as trigger factor can work as foldases under force, a mechanism which could be of relevance for several physiological processes. Proteins fold under mechanical force during co-translational folding at the ribosome. Here, the authors use single molecule magnetic tweezers to study the influence of chaperones on protein folding and show that the ribosomal chaperone trigger factor acts as a mechanical foldase by promoting protein folding under force.
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12
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Sorokina I, Mushegian A. Rotational restriction of nascent peptides as an essential element of co-translational protein folding: possible molecular players and structural consequences. Biol Direct 2017; 12:14. [PMID: 28569180 PMCID: PMC5452302 DOI: 10.1186/s13062-017-0186-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/23/2017] [Indexed: 12/13/2022] Open
Abstract
Background A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in protein folding in vivo. Recently, we hypothesized that energy-dependent twisting of the protein backbone is an unappreciated essential factor guiding the protein folding process in vivo. Torque force may be applied by the ribosome co-translationally, and when accompanied by simultaneous restriction of the rotational mobility of the distal part of the growing chain, the resulting tension in the protein backbone would facilitate the formation of local secondary structure and direct the folding process. Results Our model of the early stages of protein folding in vivo postulates that the free motion of both terminal regions of the protein during its synthesis and maturation is restricted. The long-known but unexplained phenomenon of statistical overrepresentation of protein termini on the surfaces of the protein structures may be an indication of the backbone twist-based folding mechanism; sustained maintenance of a twist requires that both ends of the protein chain are anchored in space, and if the ends are released only after the majority of folding is complete, they are much more likely to remain on the surface of the molecule. We identified the molecular components that are likely to play a role in the twisting of the nascent protein chain and in the anchoring of its N-terminus. The twist may be induced at the C-terminus of the nascent polypeptide by the peptidyltransferase center of the ribosome. Several ribosome-associated proteins, including the trigger factor in bacteria and the nascent polypeptide-associated complex in archaea and eukaryotes, may restrict the rotational mobility of the N-proximal regions of the peptides. Conclusions Many experimental observations are consistent with the hypothesis of co-translational twisting of the protein backbone. Several molecular players in this hypothetical mechanism of protein folding can be suggested. In addition, the new view of protein folding in vivo opens the possibility of novel potential drug targets to combat human protein folding diseases. Reviewers This article was reviewed by Lakshminarayan Iyer and István Simon. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0186-1) contains supplementary material, which is available to authorized users.
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13
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Koubek J, Chang YC, Yang SYC, Huang JJT. Trigger Factor-Induced Nascent Chain Dynamics Changes Suggest Two Different Chaperone-Nascent Chain Interactions during Translation. J Mol Biol 2017; 429:1733-1745. [PMID: 28385637 DOI: 10.1016/j.jmb.2017.03.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/30/2017] [Accepted: 03/30/2017] [Indexed: 11/25/2022]
Abstract
Protein biogenesis is poorly understood due to the ribosome that perturbs measurement attempted on the ribosome-bound nascent chain (RNC). Investigating nascent chain dynamics may provide invaluable insight into the co-translational processes such as structure formation or interaction with a chaperone [e.g., the bacterial trigger factor (TF)]. In this study, we aim to establish a platform for studying nascent chain dynamics by exploring the local environment near the fluorescent dye on site-specifically labeled RNCs with time-resolved fluorescence anisotropy. To prepare a quantitative model of fluorescence depolarization, we utilized intrinsically disordered protein bound to ribosome, which helped us couple the sub-nanosecond depolarization with the motion of the nascent chain backbone. This was consistent with zinc-finger-domain-containing RNCs, where the extent of sub-nanosecond motion decreased upon the addition of zinc when the fluorophore was in close proximity of the domain. After the characterization of disordered nascent chain dynamics, we investigated the synthesis of a model cytosolic protein, Entner-Doudoroff aldolase, labeled at different sites during various stages of translation. Depending on the stage of translation, the addition of the TF to the nascent chain led to two different responses in the nascent chain dynamics serendipitously, suggesting steric hindrance between the nascent chain and the chaperone as a mechanism for TF dissociation from the ribosome during translation. Overall, our study demonstrates the possible use of site-specific labeling and time-resolved anisotropy to gain insight on chaperone binding event at various stages of translation and hints on TF co-translational mechanism.
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Affiliation(s)
- Jiří Koubek
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, 11529, R.O.C
| | - Yi-Che Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, 11529, R.O.C
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14
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Abstract
Accurate protein folding is essential for proper cellular and organismal function. In the cell, protein folding is carefully regulated; changes in folding homeostasis (proteostasis) can disrupt many cellular processes and have been implicated in various neurodegenerative diseases and other pathologies. For many proteins, the initial folding process begins during translation while the protein is still tethered to the ribosome; however, most biophysical studies of a protein's energy landscape are carried out in isolation under idealized, dilute conditions and may not accurately report on the energy landscape in vivo. Thus, the energy landscape of ribosome nascent chains and the effect of the tethered ribosome on nascent chain folding remain unclear. Here we have developed a general assay for quantitatively measuring the folding stability of ribosome nascent chains, and find that the ribosome exerts a destabilizing effect on the polypeptide chain. This destabilization decreases as a function of the distance away from the peptidyl transferase center. Thus, the ribosome may add an additional layer of robustness to the protein-folding process by avoiding the formation of stable partially folded states before the protein has completely emerged from the ribosome.
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Chan CS, Turner RJ. Biogenesis of Escherichia coli DMSO Reductase: A Network of Participants for Protein Folding and Complex Enzyme Maturation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:215-34. [PMID: 26621470 DOI: 10.1007/978-3-319-23603-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Protein folding and structure have been of interest since the dawn of protein chemistry. Following translation from the ribosome, a protein must go through various steps to become a functional member of the cellular society. Every protein has a unique function in the cell and is classified on this basis. Proteins that are involved in cellular respiration are the bioenergetic workhorses of the cell. Bacteria are resilient organisms that can survive in diverse environments by fine tuning these workhorses. One class of proteins that allow survival under anoxic conditions are anaerobic respiratory oxidoreductases, which utilize many different compounds other than oxygen as its final electron acceptor. Dimethyl sulfoxide (DMSO) is one such compound. Respiration using DMSO as a final electron acceptor is performed by DMSO reductase, converting it to dimethyl sulfide in the process. Microbial respiration using DMSO is reviewed in detail by McCrindle et al. (Adv Microb Physiol 50:147-198, 2005). In this chapter, we discuss the biogenesis of DMSO reductase as an example of the participant network for complex iron-sulfur molybdoenzyme maturation pathways.
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Affiliation(s)
- Catherine S Chan
- Department of Biological Sciences, University of Calgary, BI156 Biological Sciences Bldg, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, BI156 Biological Sciences Bldg, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.
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16
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Bjerga GEK, Williamson AK. Cold shock induction of recombinant Arctic environmental genes. BMC Biotechnol 2015; 15:78. [PMID: 26286037 PMCID: PMC4544801 DOI: 10.1186/s12896-015-0185-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/24/2015] [Indexed: 11/16/2022] Open
Abstract
Background Heterologous expression of psychrophilic enzymes in E. coli is particularly challenging due to their intrinsic instability. The low stability is regarded as a consequence of adaptation that allow them to function at low temperatures. Recombinant production presents a significant barrier to their exploitation for commercial applications in industry. Methods As part of an enzyme discovery project we have investigated the utility of a cold-shock inducible promoter for low-temperature expression of five diverse genes derived from the metagenomes of marine Arctic sediments. After evaluation of their production, we further optimized for soluble production by building a vector suite from which the environmental genes could be expressed as fusions with solubility tags. Results We found that the low-temperature optimized system produced high expression levels for all putatively cold-active proteins, as well as reducing host toxicity for several candidates. As a proof of concept, activity assays with one of the candidates, a putative chitinase, showed that functional protein was obtained using the low-temperature optimized vector suite. Conclusions We conclude that a cold-shock inducible system is advantageous for the heterologous expression of psychrophilic proteins, and may also be useful for expression of toxic mesophilic and thermophilic proteins where properties of the proteins are deleterious to the host cell growth. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0185-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gro Elin Kjæreng Bjerga
- Norstruct, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway. .,Centre for Applied Biotechnology, Uni Research AS, Thormøhlensgt. 55, N-5008, Bergen, Norway.
| | - Adele Kim Williamson
- Norstruct, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway.
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17
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Rathore YS, Dhoke RR, Badmalia M, Sagar A, Ashish. SAXS data based global shape analysis of trigger factor (TF) proteins from E. coli, V. cholerae, and P. frigidicola: resolving the debate on the nature of monomeric and dimeric forms. J Phys Chem B 2015; 119:6101-12. [PMID: 25950744 DOI: 10.1021/acs.jpcb.5b00759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dimerization of bacterial chaperone trigger factor (TF) is an inherent protein concentration based property which available biophysical characterization and crystal structures have kept debatable. We acquired small-angle X-ray scattering (SAXS) intensity data from different TF homologues from Escherichia coli (ECTF), Vibrio cholerae (VCTF), and Psychrobacter frigidicola (PFTF) while varying each protein concentration. We found that ECTF and VCTF adopt a compact dimeric shape at higher concentrations which did not resemble the "back-to-back" conformation reported earlier for ECTF from crystallography (PDB ID: 1W26 ). In contrast, PFTF remained monomeric throughout the concentration range 2-90 μM displaying a multimodal open extended conformation. OLIGOMER analysis showed that both the ECTF and VCTF remained completely monomeric at lower concentrations (2-11 μM), while, at higher concentrations (60-90 μM), they adopted a dimeric form. Interestingly, the equilibrium existed in the medium concentration range (>11 and <60 μM), which correlates with the physiological concentration (40-50 μM) of TF in cell cytoplasm. Additionally, circular dichroism data revealed that solution structures of ECTF and VCTF contain predominantly α-helical content, while PFTF contains 310-helical content.
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Affiliation(s)
| | - Reema R Dhoke
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Amin Sagar
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ashish
- CSIR-Institute of Microbial Technology, Chandigarh, India
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18
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Schmidpeter PAM, Schmid FX. Prolyl isomerization and its catalysis in protein folding and protein function. J Mol Biol 2015; 427:1609-31. [PMID: 25676311 DOI: 10.1016/j.jmb.2015.01.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/30/2015] [Indexed: 12/20/2022]
Abstract
Prolyl isomerizations are intrinsically slow processes. They determine the rates of many protein folding reactions and control regulatory events in folded proteins. Prolyl isomerases are able to catalyze these isomerizations, and thus, they have the potential to assist protein folding and to modulate protein function. Here, we provide examples for how prolyl isomerizations limit protein folding and are accelerated by prolyl isomerases and how native-state prolyl isomerizations regulate protein functions. The roles of prolines in protein folding and protein function are closely interrelated because both of them depend on the coupling between cis/trans isomerization and conformational changes that can involve extended regions of a protein.
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Affiliation(s)
- Philipp A M Schmidpeter
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Franz X Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany.
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19
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Bhandari V, Houry WA. Substrate Interaction Networks of the Escherichia coli Chaperones: Trigger Factor, DnaK and GroEL. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:271-94. [PMID: 26621473 DOI: 10.1007/978-3-319-23603-2_15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In the dense cellular environment, protein misfolding and inter-molecular protein aggregation compete with protein folding. Chaperones associate with proteins to prevent misfolding and to assist in folding to the native state. In Escherichia coli, the chaperones trigger factor, DnaK/DnaJ/GrpE, and GroEL/ES are the major chaperones responsible for insuring proper de novo protein folding. With multitudes of proteins produced by the bacterium, the chaperones have to be selective for their substrates. Yet, chaperone selectivity cannot be too specific. Recent biochemical and high-throughput studies have provided important insights highlighting the strategies used by chaperones in maintaining proteostasis in the cell. Here, we discuss the substrate networks and cooperation among these protein folding chaperones.
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Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 5308, Toronto, ON, M5S 1A8, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 5308, Toronto, ON, M5S 1A8, Canada.
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20
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Saini P, Wani SI, Kumar R, Chhabra R, Chimni SS, Sareen D. Trigger factor assisted folding of the recombinant epoxide hydrolases identified from C. pelagibacter and S. nassauensis. Protein Expr Purif 2014; 104:71-84. [PMID: 25229949 DOI: 10.1016/j.pep.2014.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/04/2014] [Accepted: 09/05/2014] [Indexed: 11/17/2022]
Abstract
Epoxide hydrolases (EHs), are enantioselective enzymes as they catalyze the kinetic resolution of racemic epoxides into the corresponding enantiopure vicinal diols, which are useful precursors in the synthesis of chiral pharmaceutical compounds. Here, we have identified and cloned two putative epoxide hydrolase genes (cpeh and sneh) from marine bacteria, Candidatus pelagibacter ubique and terrestrial bacteria, Stackebrandtia nassauensis, respectively and overexpressed them in pET28a vector in Escherichia coli BL21(DE3). The CPEH protein (42kDa) was found to be overexpressed as inactive inclusion bodies while SNEH protein (40kDa) was found to form soluble aggregates. In this study, the recombinant CPEH was successfully transformed from insoluble aggregates to the soluble and functionally active form, using pCold TF vector, though with low EH activity. To prevent the soluble aggregate formation of SNEH, it was co-expressed with GroEL/ES chaperone and was also fused with trigger factor (TF) chaperone at its N-terminus. The TF chaperone-assisted correct folding of SNEH led to a purified active EH with a specific activity of 3.85μmol/min/mg. The pure enzyme was further used to biocatalyze the hydrolysis of 10mM benzyl glycidyl ether (BGE) and α-methyl styrene oxide (MSO) with an enantiomeric excess of the product (eep) of 86% and 73% in 30 and 15min, respectively. In conclusion, this is the first report about the heterologous expression of epoxide hydrolases using TF as a molecular chaperone in pCold TF expression vector, resulting in remarkable increase in the solubility and activity of the otherwise improperly folded recombinant epoxide hydrolases.
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Affiliation(s)
- Priya Saini
- Department of Biochemistry, Panjab University, Sector 14, Chandigarh 160 014, India.
| | - Shadil Ibrahim Wani
- Department of Biochemistry, Panjab University, Sector 14, Chandigarh 160 014, India.
| | - Ranjai Kumar
- Department of Biochemistry, Panjab University, Sector 14, Chandigarh 160 014, India.
| | - Ravneet Chhabra
- Department of Biochemistry, Panjab University, Sector 14, Chandigarh 160 014, India.
| | | | - Dipti Sareen
- Department of Biochemistry, Panjab University, Sector 14, Chandigarh 160 014, India.
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Saio T, Guan X, Rossi P, Economou A, Kalodimos CG. Structural basis for protein antiaggregation activity of the trigger factor chaperone. Science 2014; 344:1250494. [PMID: 24812405 DOI: 10.1126/science.1250494] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular chaperones prevent aggregation and misfolding of proteins, but scarcity of structural data has impeded an understanding of the recognition and antiaggregation mechanisms. We report the solution structure, dynamics, and energetics of three trigger factor (TF) chaperone molecules in complex with alkaline phosphatase (PhoA) captured in the unfolded state. Our data show that TF uses multiple sites to bind to several regions of the PhoA substrate protein primarily through hydrophobic contacts. Nuclear magnetic resonance (NMR) relaxation experiments show that TF interacts with PhoA in a highly dynamic fashion, but as the number and length of the PhoA regions engaged by TF increase, a more stable complex gradually emerges. Multivalent binding keeps the substrate protein in an extended, unfolded conformation. The results show how molecular chaperones recognize unfolded polypeptides and, by acting as unfoldases and holdases, prevent the aggregation and premature (mis)folding of unfolded proteins.
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Affiliation(s)
- Tomohide Saio
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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22
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Gloge F, Becker AH, Kramer G, Bukau B. Co-translational mechanisms of protein maturation. Curr Opin Struct Biol 2013; 24:24-33. [PMID: 24721450 DOI: 10.1016/j.sbi.2013.11.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 11/05/2013] [Accepted: 11/21/2013] [Indexed: 10/25/2022]
Abstract
Protein biogenesis integrates multiple finely regulated mechanisms, ensuring nascent polypeptide chains are correctly enzymatically processed, targeted to membranes and folded to native structure. Recent studies show that the cellular translation machinery serves as hub that coordinates the maturation events in space and time at various levels. The ribosome itself serves as docking site for a multitude of nascent chain-interacting factors. The movement of ribosomes along open reading frames is non-uniformous and includes pausing sites, which facilitates nascent chain folding and perhaps factor engagement. Here we summarize current knowledge and discuss emerging concepts underlying the critical interplay between translation and protein maturation in E. coli.
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Affiliation(s)
- Felix Gloge
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Annemarie H Becker
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Günter Kramer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.
| | - Bernd Bukau
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.
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Castanié-Cornet MP, Bruel N, Genevaux P. Chaperone networking facilitates protein targeting to the bacterial cytoplasmic membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1442-56. [PMID: 24269840 DOI: 10.1016/j.bbamcr.2013.11.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/10/2013] [Accepted: 11/13/2013] [Indexed: 12/22/2022]
Abstract
Nascent polypeptides emerging from the ribosome are assisted by a pool of molecular chaperones and targeting factors, which enable them to efficiently partition as cytosolic, integral membrane or exported proteins. Extensive genetic and biochemical analyses have significantly expanded our knowledge of chaperone tasking throughout this process. In bacteria, it is known that the folding of newly-synthesized cytosolic proteins is mainly orchestrated by three highly conserved molecular chaperones, namely Trigger Factor (TF), DnaK (HSP70) and GroEL (HSP60). Yet, it has been reported that these major chaperones are strongly involved in protein translocation pathways as well. This review describes such essential molecular chaperone functions, with emphasis on both the biogenesis of inner membrane proteins and the post-translational targeting of presecretory proteins to the Sec and the twin-arginine translocation (Tat) pathways. Critical interplay between TF, DnaK, GroEL and other molecular chaperones and targeting factors, including SecB, SecA, the signal recognition particle (SRP) and the redox enzyme maturation proteins (REMPs) is also discussed. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Marie-Pierre Castanié-Cornet
- Laboratoire de Microbiologie et Génétique Moléculaire (LMGM), Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, Toulouse, France
| | - Nicolas Bruel
- Laboratoire de Microbiologie et Génétique Moléculaire (LMGM), Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaire (LMGM), Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, Toulouse, France.
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24
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Waudby CA, Launay H, Cabrita LD, Christodoulou J. Protein folding on the ribosome studied using NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 74:57-75. [PMID: 24083462 PMCID: PMC3991860 DOI: 10.1016/j.pnmrs.2013.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 05/11/2023]
Abstract
NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity.
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25
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Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding. Nat Struct Mol Biol 2013; 20:843-50. [DOI: 10.1038/nsmb.2615] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/15/2013] [Indexed: 12/23/2022]
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Singhal K, Vreede J, Mashaghi A, Tans SJ, Bolhuis PG. Hydrophobic collapse of trigger factor monomer in solution. PLoS One 2013; 8:e59683. [PMID: 23565160 PMCID: PMC3615003 DOI: 10.1371/journal.pone.0059683] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 02/16/2013] [Indexed: 11/30/2022] Open
Abstract
Trigger factor (TF) is a chaperone, found in bacterial cells and chloroplasts, that interacts with nascent polypeptide chains to suppress aggregation. While its crystal structure has been resolved, the solution structure and dynamics are largely unknown. We performed multiple molecular dynamics simulations on Trigger factor in solution, and show that its tertiary domains display collective motions hinged about inter-domain linkers with minimal or no loss in secondary structure. Moreover, we find that isolated TF typically adopts a collapsed state, with the formation of domain pairs. This collapse of TF in solution is induced by hydrophobic interactions and stabilised by hydrophilic contacts. To determine the nature of the domain interactions, we analysed the hydrophobicity of the domain surfaces by using the hydrophobic probe method of Acharya et al.[1], [2], as the standard hydrophobicity scales predictions are limited due to the complex environment. We find that the formation of domain pairs changes the hydrophobic map of TF, making the N-terminal and arm2 domain pair more hydrophilic and the head and arm1 domain pair more hydrophobic. These insights into the dynamics and interactions of the TF domains are important to eventually understand chaperone-substrate interactions and chaperone function.
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Affiliation(s)
- Kushagra Singhal
- van ‘t Hoff Institute of Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jocelyne Vreede
- van ‘t Hoff Institute of Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Alireza Mashaghi
- Department of Systems Biophysics, FOM Institute AMOLF, Amsterdam, The Netherlands
| | - Sander J. Tans
- Department of Systems Biophysics, FOM Institute AMOLF, Amsterdam, The Netherlands
| | - Peter G. Bolhuis
- van ‘t Hoff Institute of Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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Stepanenko OV, Stepanenko OV, Kuznetsova IM, Verkhusha VV, Turoverov KK. Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:221-78. [PMID: 23351712 DOI: 10.1016/b978-0-12-407699-0.00004-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review focuses on the current view of the interaction between the β-barrel scaffold of fluorescent proteins and their unique chromophore located in the internal helix. The chromophore originates from the polypeptide chain and its properties are influenced by the surrounding protein matrix of the β-barrel. On the other hand, it appears that a chromophore tightens the β-barrel scaffold and plays a crucial role in its stability. Furthermore, the presence of a mature chromophore causes hysteresis of protein unfolding and refolding. We survey studies measuring protein unfolding and refolding using traditional methods as well as new approaches, such as mechanical unfolding and reassembly of truncated fluorescent proteins. We also analyze models of fluorescent protein unfolding and refolding obtained through different approaches, and compare the results of protein folding in vitro to co-translational folding of a newly synthesized polypeptide chain.
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Affiliation(s)
- Olesya V Stepanenko
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
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28
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Abstract
In this issue of Molecular Cell, Hoffmann et al. (2012) demonstrate that the ribosome-associated bacterial chaperone Trigger Factor assists in the maturation of ribosome-attached nascent chains by acting as both a holdase and an unfoldase.
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Affiliation(s)
- Daniel N Hebert
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA.
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29
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Basters A, Ketscher L, Deuerling E, Arkona C, Rademann J, Knobeloch KP, Fritz G. High yield expression of catalytically active USP18 (UBP43) using a Trigger Factor fusion system. BMC Biotechnol 2012; 12:56. [PMID: 22916876 PMCID: PMC3478164 DOI: 10.1186/1472-6750-12-56] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 07/18/2012] [Indexed: 12/18/2022] Open
Abstract
Background Covalent linkage of the ubiquitin-like protein ISG15 interferes with viral infection and USP18 is the major protease which specifically removes ISG15 from target proteins. Thus, boosting ISG15 modification by protease inhibition of USP18 might represent a new strategy to interfere with viral replication. However, so far no heterologous expression system was available to yield sufficient amounts of catalytically active protein for high-throughput based inhibitor screens. Results High-level heterologous expression of USP18 was achieved by applying a chaperone-based fusion system in E. coli. Pure protein was obtained in a single-step on IMAC via a His6-tag. The USP18 fusion protein exhibited enzymatic activity towards cell derived ISG15 conjugated substrates and efficiently hydrolyzed ISG15-AMC. Specificity towards ISG15 was shown by covalent adduct formation with ISG15 vinyl sulfone but not with ubiquitin vinyl sulfone. Conclusion The results presented here show that a chaperone fusion system can provide high yields of proteins that are difficult to express. The USP18 protein obtained here is suited to setup high-throughput small molecule inhibitor screens and forms the basis for detailed biochemical and structural characterization.
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Affiliation(s)
- Anja Basters
- Department of Neuropathology, University of Freiburg, Freiburg, Germany
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Hoffmann A, Becker AH, Zachmann-Brand B, Deuerling E, Bukau B, Kramer G. Concerted action of the ribosome and the associated chaperone trigger factor confines nascent polypeptide folding. Mol Cell 2012; 48:63-74. [PMID: 22921937 DOI: 10.1016/j.molcel.2012.07.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 04/17/2012] [Accepted: 07/16/2012] [Indexed: 01/13/2023]
Abstract
How nascent polypeptides emerging from ribosomes fold into functional structures is poorly understood. Here, we monitor disulfide bond formation, protease resistance, and enzymatic activity in nascent polypeptides to show that in close proximity to the ribosome, conformational space and kinetics of folding are restricted. Folding constraints decrease incrementally with distance from the ribosome surface. Upon ribosome binding, the chaperone Trigger Factor counters folding also of longer nascent chains, to extents varying between different chain segments. Trigger Factor even binds and unfolds pre-existing folded structures, the unfolding activity being limited by the thermodynamic stability of nascent chains. Folding retardation and unfolding activities are not shared by the DnaK chaperone assisting later folding steps. These ribosome- and Trigger Factor-specific activities together constitute an efficient mechanism to prevent or even revert premature folding, effectively limiting misfolded intermediates during protein synthesis.
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Affiliation(s)
- Anja Hoffmann
- Center for Molecular Biology of the University of Heidelberg, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
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31
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O'Brien EP, Christodoulou J, Vendruscolo M, Dobson CM. Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions. J Am Chem Soc 2012; 134:10920-32. [PMID: 22680285 DOI: 10.1021/ja302305u] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The E. coli chaperone trigger factor (TF) interacts directly with nascent polypeptide chains as they emerge from the ribosome exit tunnel. Small protein domains can fold under the cradle created by TF, but the co-translational folding of larger proteins is slowed down by its presence. Because of the great experimental challenges in achieving high spatial and time resolution, it is not yet known whether or not TF alters the folding properties of small proteins and if the reduced rate of folding of larger proteins is the result of kinetic or thermodynamic effects. We show, by molecular simulations employing a coarse-grained model of a series of ribosome nascent-chain complexes, that TF does not alter significantly the co-translational folding process of a small protein G domain but delays that of a large β-galactosidase domain as a result of kinetic trapping of its unfolded ensemble. We demonstrate that this trapping occurs through a combination of three distinct mechanisms: a decrease in the rate of structural rearrangements within the nascent chain, an increase in the effective exit tunnel length due to folding outside the cradle, and entanglement of the nascent chain with TF. We present evidence that this TF-induced trapping represents a trade-off between promoting co-translational folding and sterically shielding the nascent chain from aberrant cytosolic interactions that could lead to its aggregation or degradation.
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32
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Global analysis of chaperone effects using a reconstituted cell-free translation system. Proc Natl Acad Sci U S A 2012; 109:8937-42. [PMID: 22615364 DOI: 10.1073/pnas.1201380109] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein folding is often hampered by protein aggregation, which can be prevented by a variety of chaperones in the cell. A dataset that evaluates which chaperones are effective for aggregation-prone proteins would provide an invaluable resource not only for understanding the roles of chaperones, but also for broader applications in protein science and engineering. Therefore, we comprehensively evaluated the effects of the major Escherichia coli chaperones, trigger factor, DnaK/DnaJ/GrpE, and GroEL/GroES, on ∼800 aggregation-prone cytosolic E. coli proteins, using a reconstituted chaperone-free translation system. Statistical analyses revealed the robustness and the intriguing properties of chaperones. The DnaK and GroEL systems drastically increased the solubilities of hundreds of proteins with weak biases, whereas trigger factor had only a marginal effect on solubility. The combined addition of the chaperones was effective for a subset of proteins that were not rescued by any single chaperone system, supporting the synergistic effect of these chaperones. The resource, which is accessible via a public database, can be used to investigate the properties of proteins of interest in terms of their solubilities and chaperone effects.
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33
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Preissler S, Deuerling E. Ribosome-associated chaperones as key players in proteostasis. Trends Biochem Sci 2012; 37:274-83. [PMID: 22503700 DOI: 10.1016/j.tibs.2012.03.002] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 02/17/2012] [Accepted: 03/06/2012] [Indexed: 01/14/2023]
Abstract
De novo protein folding is delicate and error-prone and requires the guidance of molecular chaperones. Besides cytosolic and organelle-specific chaperones, cells have evolved ribosome-associated chaperones that support early folding events and prevent misfolding and aggregation. This class of chaperones includes the bacterial trigger factor (TF), the archaeal and eukaryotic nascent polypeptide-associated complex (NAC) and specialized eukaryotic heat shock protein (Hsp) 70/40 chaperones. This review focuses on the cellular activities of ribosome-associated chaperones and highlights new findings indicating additional functions beyond de novo folding. These activities include the assembly of oligomeric complexes, such as ribosomes, modulation of translation and targeting of proteins.
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Affiliation(s)
- Steffen Preissler
- Molecular Microbiology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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34
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Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman JS, Bukau B. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 2012; 147:1295-308. [PMID: 22153074 PMCID: PMC3277850 DOI: 10.1016/j.cell.2011.10.044] [Citation(s) in RCA: 332] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 08/10/2011] [Accepted: 10/18/2011] [Indexed: 11/29/2022]
Abstract
As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting, and folding factors. Here, we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone trigger factor (TF) reveal that, though TF can interact with many polypeptides, β-barrel outer-membrane proteins are the most prominent substrates. Loss of TF leads to broad outer-membrane defects and premature, cotranslational protein translocation. Whereas in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting, and folding factors.
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Affiliation(s)
- Eugene Oh
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
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35
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Nannenga BL, Baneyx F. Folding engineering strategies for efficient membrane protein production in E. coli. Methods Mol Biol 2012; 899:187-202. [PMID: 22735954 DOI: 10.1007/978-1-61779-921-1_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Membrane proteins are notoriously difficult to produce at the high levels required for structural and biochemical characterization. Among the various expression systems used to date, the enteric bacterium Escherichia coli remains one of the best characterized and most versatile. However, membrane protein overexpression in E. coli is often accompanied by toxicity and low yields of functional product. Here, we briefly review the involvement of signal recognition particle, trigger factor, and YidC in α-helical membrane protein biogenesis and describe a set of strains, vectors, and chaperone co-expression plasmids that can lead to significant gains in the production of recombinant membrane proteins in E. coli. Methods to quantify membrane proteins by sodium dodecyl sulfate polyacrylamide gel electrophoresis are also provided.
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Affiliation(s)
- Brent L Nannenga
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
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36
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Kelkar DA, Khushoo A, Yang Z, Skach WR. Kinetic analysis of ribosome-bound fluorescent proteins reveals an early, stable, cotranslational folding intermediate. J Biol Chem 2011; 287:2568-78. [PMID: 22128180 DOI: 10.1074/jbc.m111.318766] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Protein folding in cells reflects a delicate interplay between biophysical properties of the nascent polypeptide, the vectorial nature and rate of translation, molecular crowding, and cellular biosynthetic machinery. To better understand how this complex environment affects de novo folding pathways as they occur in the cell, we expressed β-barrel fluorescent proteins derived from GFP and RFP in an in vitro system that allows direct analysis of cotranslational folding intermediates. Quantitative analysis of ribosome-bound eCFP and mCherry fusion proteins revealed that productive folding exhibits a sharp threshold as the length of polypeptide from the C terminus to the ribosome peptidyltransferase center is increased. Fluorescence spectroscopy, urea denaturation, and limited protease digestion confirmed that sequestration of only 10-15 C-terminal residues within the ribosome exit tunnel effectively prevents stable barrel formation, whereas folding occurs unimpeded when the C terminus is extended beyond the ribosome exit site. Nascent FPs with 10 of the 11 β-strands outside the ribosome exit tunnel acquire a non-native conformation that is remarkably stable in diverse environments. Upon ribosome release, these structural intermediates fold efficiently with kinetics that are unaffected by the cytosolic crowding or cellular chaperones. Our results indicate that during synthesis, fluorescent protein folding is initiated cotranslationally via rapid formation of a highly stable, on-pathway structural intermediate and that the rate-limiting step of folding involves autonomous incorporation of the 11th β-strand into the mature barrel structure.
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Affiliation(s)
- Devaki A Kelkar
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239, USA
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37
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Knoops K, Schoehn G, Schaffitzel C. Cryo-electron microscopy of ribosomal complexes in cotranslational folding, targeting, and translocation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:429-41. [PMID: 22095783 DOI: 10.1002/wrna.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) became a well-established method to study the structure and function of large macromolecular assemblies in a close to physiological environment. Cryo-EM reconstructions of ribosomal complexes trapped at different stages during translation, cotranslational targeting, and translocation provide new insights on a molecular level into these processes, which are vital for the correct localization and folding of all proteins in the cell. The EM structures in combination with biochemical experiments and available high-resolution crystal or nuclear magnetic resonance (NMR) structures of individual factors and of the ribosome allow for interpretation in quasi-atomic detail of the molecular mechanism of ribosomal complexes, their conformational changes and dynamic interactions with factors like the signal recognition particle, SRP receptor, the translocon, and the chaperone trigger factor. The snapshots obtained by single-particle EM reconstructions enable us to follow the path of a nascent protein from the peptidyl-transferase center, through the ribosomal tunnel, to and across the translocon in the membrane. With new developments in image processing techniques it is possible to sort a biological homogenous sample into different conformational states and to reach subnanometer resolution such that folding of the nascent chain into secondary structure elements can be directly visualized. With improved cryo-electron tomography and correlative light microscopy and EM, it will be possible to visualize ribosomal complexes in their cellular context.
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Affiliation(s)
- Kèvin Knoops
- European Molecular Biology Laboratory-EMBL, Grenoble Outstation, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble Cedex 9, France
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38
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Mogk A, Huber D, Bukau B. Integrating protein homeostasis strategies in prokaryotes. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a004366. [PMID: 21441580 DOI: 10.1101/cshperspect.a004366] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacterial cells are frequently exposed to dramatic fluctuations in their environment, which cause perturbation in protein homeostasis and lead to protein misfolding. Bacteria have therefore evolved powerful quality control networks consisting of chaperones and proteases that cooperate to monitor the folding states of proteins and to remove misfolded conformers through either refolding or degradation. The levels of the quality control components are adjusted to the folding state of the cellular proteome through the induction of compartment specific stress responses. In addition, the activities of several quality control components are directly controlled by these stresses, allowing for fast activation. Severe stress can, however, overcome the protective function of the proteostasis network leading to the formation of protein aggregates, which are sequestered at the cell poles. Protein aggregates are either solubilized by AAA+ chaperones or eliminated through cell division, allowing for the generation of damage-free daughter cells.
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Affiliation(s)
- Axel Mogk
- Zentrum für Molekulare Biologie Heidelberg, DKFZ-ZMBH Alliance, Universität Heidelberg, Heidelberg, Germany
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39
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Abstract
Over five decades of research have yielded a large body of information on how purified proteins attain their native state when refolded in the test tube, starting from a chemically or thermally denatured state. Nevertheless, we still know little about how proteins fold and unfold in their natural biological habitat: the living cell. Indeed, a variety of cellular components, including molecular chaperones, the ribosome, and crowding of the intracellular medium, modulate folding mechanisms in physiologically relevant environments. This review focuses on the current state of knowledge in protein folding in the cell with emphasis on the early stage of a protein's life, as the nascent polypeptide traverses and emerges from the ribosomal tunnel. Given the vectorial nature of ribosome-assisted translation, the transient degree of chain elongation becomes a relevant variable expected to affect nascent protein foldability, aggregation propensity and extent of interaction with chaperones and the ribosome.
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Affiliation(s)
- Daria V Fedyukina
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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40
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Weinreis SA, Ellis JP, Cavagnero S. Dynamic fluorescence depolarization: a powerful tool to explore protein folding on the ribosome. Methods 2010; 52:57-73. [PMID: 20685617 PMCID: PMC2934862 DOI: 10.1016/j.ymeth.2010.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/28/2010] [Accepted: 06/01/2010] [Indexed: 11/25/2022] Open
Abstract
Protein folding is a fundamental biological process of great significance for cell function and life-related processes. Surprisingly, very little is presently known about how proteins fold in vivo. The influence of the cellular environment is of paramount importance, as molecular chaperones, the ribosome, and the crowded medium affect both folding pathways and potentially even equilibrium structures. Studying protein folding in physiologically relevant environments, however, poses a number of technical challenges due to slow tumbling rates, low concentrations and potentially non-homogenous populations. Early work in this area relied on biological assays based on antibody recognition, proteolysis, and activity studies. More recently, it has been possible to directly observe the structure and dynamics of nascent polypeptides at high resolution by spectroscopic and microscopic techniques. The fluorescence depolarization decay of nascent polypeptides labeled with a small extrinsic fluorophore is a particularly powerful tool to gain insights into the dynamics of newly synthesized proteins. The fluorophore label senses both its own local mobility and the motions of the macromolecule to which it is attached. Fluorescence anisotropy decays can be measured both in the time and frequency domains. The latter mode of data collection is extremely convenient to capture the nanosecond motions in ribosome-bound nascent proteins, indicative of the development of independent structure and folding on the ribosome. In this review, we discuss the theory of fluorescence depolarization and its exciting applications to the study of the dynamics of nascent proteins in the cellular environment.
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Affiliation(s)
- Sarah A. Weinreis
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
| | | | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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41
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Puertas JM, Nannenga BL, Dornfeld KT, Betton JM, Baneyx F. Enhancing the secretory yields of leech carboxypeptidase inhibitor in Escherichia coli: influence of trigger factor and signal recognition particle. Protein Expr Purif 2010; 74:122-8. [PMID: 20600941 DOI: 10.1016/j.pep.2010.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 06/07/2010] [Accepted: 06/17/2010] [Indexed: 11/29/2022]
Abstract
The signal recognition particle (SRP) dependent secretion pathway is as an attractive alternative to Sec-dependent export for the production of disulfide-bonded and/or fast-folding recombinant proteins in the Escherichia coli periplasm. SRP, which shares a ribosomal attachment site with the molecular chaperone trigger factor (TF), recognizes highly hydrophobic signal sequence as they emerge from the ribosome and delivers ribosome nascent chain complexes to FtsY for subsequent cotranslational translocation of target proteins across the SecYEG pore. However, like in the case of Sec-dependent export, secretory yields can be limited by the accumulation of precursor proteins in the cytoplasm. Using leech carboxypeptidase inhibitor (LCI) fused to the SRP-dependent DsbA signal sequence as a model system, we show that a null mutation in the gene encoding TF (Deltatig) or SRP co-expression reduce pre-LCI accumulation by half, and that quantitative export can be achieved by combining the two strategies. Interestingly, enhanced precursor processing did not alter periplasmic LCI levels but increased the amount of protein excreted in the growth medium. All mature LCI was nearly fully active and an 80% increase in productivity was achieved in Deltatig cells alone due to their faster growth. Our results show that competition between SRP and TF can interfere with efficient export of recombinant proteins targeted to the SRP pathway and establish TF-deficient strains and SRP co-expression as a simple solution to improve yields.
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Affiliation(s)
- Juan-Miguel Puertas
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-1750, USA
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42
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Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy. Proc Natl Acad Sci U S A 2010; 107:9111-6. [PMID: 20439768 DOI: 10.1073/pnas.0914300107] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The folding of proteins in living cells may start during their synthesis when the polypeptides emerge gradually at the ribosomal exit tunnel. However, our current understanding of cotranslational folding processes at the atomic level is limited. We employed NMR spectroscopy to monitor the conformation of the SH3 domain from alpha-spectrin at sequential stages of elongation via in vivo ribosome-arrested (15)N,(13)C-labeled nascent polypeptides. These nascent chains exposed either the entire SH3 domain or C-terminally truncated segments thereof, thus providing snapshots of the translation process. We show that nascent SH3 polypeptides remain unstructured during elongation but fold into a compact, native-like beta-sheet assembly when the entire sequence information is available. Moreover, the ribosome neither imposes major conformational constraints nor significantly interacts with exposed unfolded nascent SH3 domain moieties. Our data provide evidence for a domainwise folding of the SH3 domain on ribosomes without significant population of folding intermediates. The domain follows a thermodynamically favorable pathway in which sequential folding units are stabilized, thus avoiding kinetic traps during the process of cotranslational folding.
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43
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Kirstein J, Hoffmann A, Lilie H, Schmidt R, Rübsamen-Waigmann H, Brötz-Oesterhelt H, Mogk A, Turgay K. The antibiotic ADEP reprogrammes ClpP, switching it from a regulated to an uncontrolled protease. EMBO Mol Med 2010; 1:37-49. [PMID: 20049702 PMCID: PMC3378108 DOI: 10.1002/emmm.200900002] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel class of antibiotic acyldepsipeptides (designated ADEPs) exerts its unique antibacterial activity by targeting the peptidase caseinolytic protease P (ClpP). ClpP forms proteolytic complexes with heat shock proteins (Hsp100) that select and process substrate proteins for ClpP-mediated degradation. Here, we analyse the molecular mechanism of ADEP action and demonstrate that ADEPs abrogate ClpP interaction with cooperating Hsp100 adenosine triphosphatases (ATPases). Consequently, ADEP treated bacteria are affected in ClpP-dependent general and regulatory proteolysis. At the same time, ADEPs also activate ClpP by converting it from a tightly regulated peptidase, which can only degrade short peptides, into a proteolytic machinery that recognizes and degrades unfolded polypeptides. In vivo nascent polypeptide chains represent the putative primary target of ADEP-activated ClpP, providing a rationale for the antibacterial activity of the ADEPs. Thus, ADEPs cause a complete functional reprogramming of the Clp–protease complex.
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Affiliation(s)
- Janine Kirstein
- Institut für Biologie-Mikrobiologie, FU Berlin, Berlin, Germany
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44
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Li H, Chang L, Howell JM, Turner RJ. DmsD, a Tat system specific chaperone, interacts with other general chaperones and proteins involved in the molybdenum cofactor biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1301-9. [PMID: 20153451 DOI: 10.1016/j.bbapap.2010.01.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 12/23/2009] [Accepted: 01/28/2010] [Indexed: 10/19/2022]
Abstract
Many bacterial oxidoreductases depend on the Tat translocase for correct cell localization. Substrates for the Tat translocase possess twin-arginine leaders. System specific chaperones or redox enzyme maturation proteins (REMPs) are a group of proteins implicated in oxidoreductase maturation. DmsD is a REMP discovered in Escherichia coli, which interacts with the twin-arginine leader sequence of DmsA, the catalytic subunit of DMSO reductase. In this study, we identified several potential interacting partners of DmsD by using several in vitro protein-protein interaction screening approaches, including affinity chromatography, co-precipitation, and cross-linking. Candidate hits from these in vitro findings were analyzed by in vivo methods of bacterial two-hybrid (BACTH) and bimolecular fluorescence complementation (BiFC). From these data, DmsD was confirmed to interact with the general molecular chaperones DnaK, DnaJ, GrpE, GroEL, Tig and Ef-Tu. In addition, DmsD was also found to interact with proteins involved in the molybdenum cofactor biosynthesis pathway. Our data suggests that DmsD may play a role as a "node" in escorting its substrate through a cascade of chaperone assisted protein-folding maturation events.
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Affiliation(s)
- Haiming Li
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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45
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Hoffmann A, Bukau B, Kramer G. Structure and function of the molecular chaperone Trigger Factor. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:650-61. [PMID: 20132842 DOI: 10.1016/j.bbamcr.2010.01.017] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 01/22/2010] [Indexed: 01/16/2023]
Abstract
Newly synthesized proteins often require the assistance of molecular chaperones to efficiently fold into functional three-dimensional structures. At first, ribosome-associated chaperones guide the initial folding steps and protect growing polypeptide chains from misfolding and aggregation. After that folding into the native structure may occur spontaneously or require support by additional chaperones which do not bind to the ribosome such as DnaK and GroEL. Here we review the current knowledge on the best-characterized ribosome-associated chaperone at present, the Escherichia coli Trigger Factor. We describe recent progress on structural and dynamic aspects of Trigger Factor's interactions with the ribosome and substrates and discuss how these interactions affect co-translational protein folding. In addition, we discuss the newly proposed ribosome-independent function of Trigger Factor as assembly factor of multi-subunit protein complexes. Finally, we cover the functional cooperation between Trigger Factor, DnaK and GroEL in folding of cytosolic proteins and the interplay between Trigger Factor and other ribosome-associated factors acting in enzymatic processing and translocation of nascent polypeptide chains.
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Affiliation(s)
- Anja Hoffmann
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
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46
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Lambert C, Chang CY, Capeness MJ, Sockett RE. The first bite--profiling the predatosome in the bacterial pathogen Bdellovibrio. PLoS One 2010; 5:e8599. [PMID: 20062540 PMCID: PMC2797640 DOI: 10.1371/journal.pone.0008599] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 11/09/2009] [Indexed: 11/18/2022] Open
Abstract
Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes. We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs to monitor changes in Bdellovibrio gene expression at a timepoint of early-stage prey infection and prey killing in comparison to control cultures of predator and prey alone and also in comparison to Bdellovibrio growing axenically (in a prey-or host independent “HI” manner) on artificial media containing peptone and tryptone. From this we have highlighted genes of the early predatosome with predicted roles in prey killing and digestion and have gained insights into possible regulatory mechanisms as Bdellovibrio enter and establish within the prey bdelloplast. Approximately seven percent of all Bdellovibrio genes were significantly up-regulated at 30 minutes of infection- but not in HI growth- implicating the role of these genes in prey digestion. Five percent were down-regulated significantly, implicating their role in free-swimming, attack-phase physiology. This study gives the first post- genomic insight into the predatory process and reveals some of the important genes that Bdellovibrio expresses inside the prey bacterium during the initial attack.
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Affiliation(s)
- Carey Lambert
- Institute of Genetics, School of Biology, Nottingham University, Queen's Medical Centre, Nottingham, United Kingdom
| | - Chien-Yi Chang
- Institute of Genetics, School of Biology, Nottingham University, Queen's Medical Centre, Nottingham, United Kingdom
| | - Michael J. Capeness
- Institute of Genetics, School of Biology, Nottingham University, Queen's Medical Centre, Nottingham, United Kingdom
| | - R. Elizabeth Sockett
- Institute of Genetics, School of Biology, Nottingham University, Queen's Medical Centre, Nottingham, United Kingdom
- * E-mail:
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47
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Ellis JP, Culviner PH, Cavagnero S. Confined dynamics of a ribosome-bound nascent globin: Cone angle analysis of fluorescence depolarization decays in the presence of two local motions. Protein Sci 2009; 18:2003-15. [PMID: 19569194 DOI: 10.1002/pro.196] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We still know very little about how proteins achieve their native three-dimensional structure in vitro and in the cell. Folding studies as proteins emerge from the mega Dalton-sized ribosome pose special challenges due to the large size and complicated nature of the ribosome-nascent chain complex. This work introduces a combination of three-component analysis of fluorescence depolarization decays (including the presence of two local motions) and in-cone analysis of diffusive local dynamics to investigate the spatial constraints experienced by a protein emerging from the ribosomal tunnel. We focus on E. coli ribosomes and an all-alpha-helical nascent globin in the presence and absence of the cotranslationally active chaperones DnaK and trigger factor. The data provide insights on the dynamic nature and structural plasticity of ribosome-nascent chain complexes. We find that the sub-ns motions of the N-terminal fluorophore, reporting on the globin dynamics in the vicinity of the N terminus, are highly constrained both inside and outside the ribosomal tunnel, resulting in high-order parameters (>0.85) and small cone semiangles (<30 degrees ). The shorter globin chains buried inside the tunnel are less spatially constrained than those of a reference sequence from a natively unfolded protein, suggesting either that the two nascent chain sequences have a different secondary structure and therefore sample different regions of the tunnel or that the tunnel undergoes local structural adjustments to accommodate the globin sequence. Longer globins emerging out of the ribosomal tunnel are also found to have highly spatially constrained slow (ns) motions. There are no observable spectroscopic changes in the absence of bound chaperones.
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Affiliation(s)
- Jamie P Ellis
- Department of Chemistry, University of Wisconsin-Madison, 53706, USA
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Clark PL, Ugrinov KG. Measuring cotranslational folding of nascent polypeptide chains on ribosomes. Methods Enzymol 2009; 466:567-90. [PMID: 21609877 DOI: 10.1016/s0076-6879(09)66024-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein folding has been studied extensively in vitro, but much less is known about how folding proceeds in vivo. A particular distinction of folding in vivo is that folding begins while the nascent polypeptide chain is still undergoing synthesis by the ribosome. Studies of cotranslational protein folding are inherently much more complex than classical in vitro protein folding studies, and historically there have been few methods available to produce the quantities of pure material required for biophysical studies of the nascent chain, or assays to specifically interrogate its conformation. However, the past few years have produced dramatic methodological advances, which now place cotranslational folding studies within reach of more biochemists, enabling a detailed comparison of the earliest stages of protein folding on the ribosome to the wealth of information available for the refolding of full-length polypeptide chains in vitro.
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Affiliation(s)
- Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone. Cell 2009; 138:923-34. [PMID: 19737520 DOI: 10.1016/j.cell.2009.07.044] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 03/28/2009] [Accepted: 07/31/2009] [Indexed: 11/22/2022]
Abstract
Trigger factor (TF) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. Thereby, we obtained an atomic-level picture of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding, and suggests a role for TF in the biogenesis of protein complexes.
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