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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] [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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2
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Yukhnovets O, Höfig H, Bustorff N, Katranidis A, Fitter J. Impact of Molecule Concentration, Diffusion Rates and Surface Passivation on Single-Molecule Fluorescence Studies in Solution. Biomolecules 2022; 12:biom12030468. [PMID: 35327660 PMCID: PMC8946791 DOI: 10.3390/biom12030468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
For single-molecule studies in solution, very small concentrations of dye-labelled molecules are employed in order to achieve single-molecule sensitivity. In typical studies with confocal microscopes, often concentrations in the pico-molar regime are required. For various applications that make use of single-molecule Förster resonance energy transfer (smFRET) or two-color coincidence detection (TCCD), the molecule concentration must be set explicitly to targeted values and furthermore needs to be stable over a period of several hours. As a consequence, specific demands must be imposed on the surface passivation of the cover slides during the measurements. The aim of having only one molecule in the detection volume at the time is not only affected by the absolute molecule concentration, but also by the rate of diffusion. Therefore, we discuss approaches to control and to measure absolute molecule concentrations. Furthermore, we introduce an approach to calculate the probability of chance coincidence events and demonstrate that measurements with challenging smFRET samples require a strict limit of maximal sample concentrations in order to produce meaningful results.
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Affiliation(s)
- Olessya Yukhnovets
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany;
- Correspondence: (O.Y.); (J.F.)
| | - Henning Höfig
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany;
| | - Nuno Bustorff
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3), Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich, 52425 Jülich, Germany; (N.B.); (A.K.)
| | - Alexandros Katranidis
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3), Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich, 52425 Jülich, Germany; (N.B.); (A.K.)
| | - Jörg Fitter
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany;
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3), Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich, 52425 Jülich, Germany; (N.B.); (A.K.)
- Correspondence: (O.Y.); (J.F.)
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3
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Wruck F, Tian P, Kudva R, Best RB, von Heijne G, Tans SJ, Katranidis A. The ribosome modulates folding inside the ribosomal exit tunnel. Commun Biol 2021; 4:523. [PMID: 33953328 PMCID: PMC8100117 DOI: 10.1038/s42003-021-02055-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/29/2021] [Indexed: 12/16/2022] Open
Abstract
Proteins commonly fold co-translationally at the ribosome, while the nascent chain emerges from the ribosomal exit tunnel. Protein domains that are sufficiently small can even fold while still located inside the tunnel. However, the effect of the tunnel on the folding dynamics of these domains is not well understood. Here, we combine optical tweezers with single-molecule FRET and molecular dynamics simulations to investigate folding of the small zinc-finger domain ADR1a inside and at the vestibule of the ribosomal tunnel. The tunnel is found to accelerate folding and stabilize the folded state, reminiscent of the effects of chaperonins. However, a simple mechanism involving stabilization by confinement does not explain the results. Instead, it appears that electrostatic interactions between the protein and ribosome contribute to the observed folding acceleration and stabilization of ADR1a.
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Affiliation(s)
- Florian Wruck
- AMOLF, Amsterdam, The Netherlands.,Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Pengfei Tian
- Protein Engineering, Novozymes A/S, Lyngby, Denmark
| | - Renuka Kudva
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Sander J Tans
- AMOLF, Amsterdam, The Netherlands. .,Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, The Netherlands. .,Kavli Institute of Nanoscience, Delft, The Netherlands.
| | - Alexandros Katranidis
- Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich (FZJ), Jülich, Germany.
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4
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Distinct pre-initiation steps in human mitochondrial translation. Nat Commun 2020; 11:2932. [PMID: 32522994 PMCID: PMC7287080 DOI: 10.1038/s41467-020-16503-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/07/2020] [Indexed: 11/08/2022] Open
Abstract
Translation initiation in human mitochondria relies upon specialized mitoribosomes and initiation factors, mtIF2 and mtIF3, which have diverged from their bacterial counterparts. Here we report two distinct mitochondrial pre-initiation assembly steps involving those factors. Single-particle cryo-EM revealed that in the first step, interactions between mitochondria-specific protein mS37 and mtIF3 keep the small mitoribosomal subunit in a conformation favorable for a subsequent accommodation of mtIF2 in the second step. Combination with fluorescence cross-correlation spectroscopy analyses suggests that mtIF3 promotes complex assembly without mRNA or initiator tRNA binding, where exclusion is achieved by the N-terminal and C-terminal domains of mtIF3. Finally, the association of large mitoribosomal subunit is required for initiator tRNA and leaderless mRNA recruitment to form a stable initiation complex. These data reveal fundamental aspects of mammalian protein synthesis that are specific to mitochondria. Translation within mitochondria relies upon specialized mitoribosomes and initiation factors. Here the authors use Cryo-EM and single molecule approaches to describe the early steps leading to translation initiation in human mitochondria, and the roles of mitochondria-specific ribosomal proteins and initiation factors mtIF2 and mtIF3.
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5
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Laohakunakorn N, Grasemann L, Lavickova B, Michielin G, Shahein A, Swank Z, Maerkl SJ. Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:213. [PMID: 32266240 PMCID: PMC7105575 DOI: 10.3389/fbioe.2020.00213] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude extract systems, as well as breakthroughs in enabling technologies, that have facilitated increased throughput, compartmentalization, and spatial control of cell-free protein synthesis reactions. Combined with a deeper understanding of the cell-free systems themselves, these advances improve our ability to address a range of scientific questions. By mastering control of the cell-free platform, we will be in a position to construct increasingly complex biomolecular systems, and approach natural biological complexity in a bottom-up manner.
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Affiliation(s)
- Nadanai Laohakunakorn
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Grasemann
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbora Lavickova
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michielin
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amir Shahein
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zoe Swank
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J. Maerkl
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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6
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Höfig H, Yukhnovets O, Remes C, Kempf N, Katranidis A, Kempe D, Fitter J. Brightness-gated two-color coincidence detection unravels two distinct mechanisms in bacterial protein translation initiation. Commun Biol 2019; 2:459. [PMID: 31840104 PMCID: PMC6897966 DOI: 10.1038/s42003-019-0709-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 11/22/2019] [Indexed: 01/19/2023] Open
Abstract
Life on the molecular scale is based on a complex interplay of biomolecules under which the ability of binding is crucial. Fluorescence based two-color coincidence detection (TCCD) is commonly used to characterize molecular binding, but suffers from an underestimation of coincident events. Here, we introduce a brightness-gated TCCD which overcomes this limitation and benchmark our approach with two custom-made calibration samples. Applied to a cell-free protein synthesis assay, brightness-gated TCCD unraveled a previously disregarded mode of translation initiation in bacteria.
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Affiliation(s)
- Henning Höfig
- I. Physikalisches Institut (IA), RWTH Aachen University, Aachen, Germany
- Institute of Complex Systems ICS-5, Forschungszentrum Jülich, Jülich, Germany
| | - Olessya Yukhnovets
- I. Physikalisches Institut (IA), RWTH Aachen University, Aachen, Germany
- Institute of Complex Systems ICS-5, Forschungszentrum Jülich, Jülich, Germany
| | - Cristina Remes
- Institute of Complex Systems ICS-5, Forschungszentrum Jülich, Jülich, Germany
- Present Address: Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - Noemie Kempf
- Institute of Complex Systems ICS-5, Forschungszentrum Jülich, Jülich, Germany
- Present Address: Laboratoire de Biologie Moléculaire Eucaryote LBME—Center for Integrative Biology CBI, University of Toulouse, Toulouse, France
| | | | - Daryan Kempe
- I. Physikalisches Institut (IA), RWTH Aachen University, Aachen, Germany
- Present Address: EMBL Australia, Single Molecule Science Node, School of Medical Sciences, University of New South Wales, Sydney, NSW Australia
| | - Jörg Fitter
- I. Physikalisches Institut (IA), RWTH Aachen University, Aachen, Germany
- Institute of Complex Systems ICS-5, Forschungszentrum Jülich, Jülich, Germany
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7
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Junker NO, Vaghefikia F, Albarghash A, Höfig H, Kempe D, Walter J, Otten J, Pohl M, Katranidis A, Wiegand S, Fitter J. Impact of Molecular Crowding on Translational Mobility and Conformational Properties of Biological Macromolecules. J Phys Chem B 2019; 123:4477-4486. [PMID: 31059260 DOI: 10.1021/acs.jpcb.9b01239] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Effects of molecular crowding on structural and dynamical properties of biological macromolecules do depend on the concentration of crowding agents but also on the molecular mass and the structural compactness of the crowder molecules. By employing fluorescence correlation spectroscopy (FCS), we investigated the translational mobility of several biological macromolecules ranging from 17 kDa to 2.7 MDa. Polyethylene glycol and Ficoll polymers of different molecular masses were used in buffer solutions to mimic a crowded environment. The reduction in translational mobility of the biological tracer molecules was analyzed as a function of crowder volume fractions and was generally more pronounced in PEG as compared to Ficoll solutions. For several crowding conditions, we observed a molecular sieving effect, in which the diffusion coefficient of larger tracer molecules is reduced to a larger extent than predicted by the Stokes-Einstein relation. By employing a FRET-based biosensor, we also showed that a multiprotein complex is significantly compacted in the presence of macromolecular crowders. Importantly, with respect to sensor in vivo applications, ligand concentration determining sensors would need a crowding specific calibration in order to deliver correct cytosolic ligand concentration.
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Affiliation(s)
- Niklas O Junker
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Farzaneh Vaghefikia
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Alyazan Albarghash
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Henning Höfig
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Daryan Kempe
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Julia Walter
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | | | | | | | - Simone Wiegand
- Physikalische Chemie , Universität zu Köln , 50923 Köln , Germany
| | - Jörg Fitter
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
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8
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Yue K, Zhu Y, Kai L. Cell-Free Protein Synthesis: Chassis toward the Minimal Cell. Cells 2019; 8:cells8040315. [PMID: 30959805 PMCID: PMC6523147 DOI: 10.3390/cells8040315] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 11/16/2022] Open
Abstract
The quest for a minimal cell not only sheds light on the fundamental principles of life but also brings great advances in related applied fields such as general biotechnology. Minimal cell projects came from the study of a plausible route to the origin of life. Later on, research extended and also referred to the construction of artificial cells, or even more broadly, as in vitro synthetic biology. The cell-free protein synthesis (CFPS) techniques harness the central cellular activity of transcription/translation in an open environment, providing the framework for multiple cellular processes assembling. Therefore, CFPS systems have become the first choice in the construction of the minimal cell. In this review, we focus on the recent advances in the quantitative analysis of CFPS and on its advantage for addressing the bottom-up assembly of a minimal cell and illustrate the importance of systemic chassis behavior, such as stochasticity under a compartmentalized micro-environment.
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Affiliation(s)
- Ke Yue
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, Xuzhou 221116, China.
| | - Yiyong Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Lei Kai
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, Xuzhou 221116, China.
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany.
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9
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Katranidis A, Fitter J. Single-Molecule Techniques and Cell-Free Protein Synthesis: A Perfect Marriage. Anal Chem 2019; 91:2570-2576. [PMID: 30648382 DOI: 10.1021/acs.analchem.8b03855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-molecule techniques are currently an essential tool to study conformational changes as well as the synthesis and folding of proteins. However, the preparation of suitable protein samples is often time-consuming and demanding. The rapid development of cell-free protein synthesis over the last few years opened new perspectives for fast and easy sample preparation, but this was not fully exploited until now. Here, we take a look at the advancements in sample preparation as well as in the development of technical approaches and analytical tools, which unavoidably lead to the combination of single-molecule techniques and cell-free protein synthesis. It is an ideal combination that can unlock the full potential of studying complex biological processes in the near future.
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Affiliation(s)
| | - Jörg Fitter
- Forschungszentrum Jülich , Institute of Complex Systems ICS-5, Jülich , Germany.,RWTH Aachen , I. Physikalisches Institut (IA) , Aachen , Germany
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10
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Höfig H, Otten J, Steffen V, Pohl M, Boersma AJ, Fitter J. Genetically Encoded Förster Resonance Energy Transfer-Based Biosensors Studied on the Single-Molecule Level. ACS Sens 2018; 3:1462-1470. [PMID: 29979038 DOI: 10.1021/acssensors.8b00143] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetically encoded Förster resonance energy transfer (FRET)-based biosensors for the quantification of ligand molecules change the magnitude of FRET between two fluorescent proteins upon binding a target metabolite. When highly sensitive sensors are being designed, extensive sensor optimization is essential. However, it is often difficult to verify the ideas of modifications made to a sensor during the sensor optimization process because of the limited information content of ensemble FRET measurements. In contrast, single-molecule detection provides detailed information and higher accuracy. Here, we investigated a set of glucose and crowding sensors on the single-molecule level. We report the first comprehensive single-molecule study of FRET-based biosensors with reasonable counting statistics and identify characteristics in the single-molecule FRET histograms that constitute fingerprints of sensor performance. Hence, our single-molecule approach extends the toolbox of methods aiming to understand and optimize the design of FRET-based biosensors.
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Affiliation(s)
- Henning Höfig
- I. Physikalisches Institut (IA), RWTH Aachen, 52074 Aachen, Germany
- ICS-5: Molecular Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Julia Otten
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Victoria Steffen
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Arnold J. Boersma
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700 AB Groningen, Netherlands
| | - Jörg Fitter
- I. Physikalisches Institut (IA), RWTH Aachen, 52074 Aachen, Germany
- ICS-5: Molecular Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
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11
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Failmezger J, Scholz S, Blombach B, Siemann-Herzberg M. Cell-Free Protein Synthesis From Fast-Growing Vibrio natriegens. Front Microbiol 2018; 9:1146. [PMID: 29910785 PMCID: PMC5992293 DOI: 10.3389/fmicb.2018.01146] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/14/2018] [Indexed: 12/02/2022] Open
Abstract
Vibrio natriegens constitutes one of the fastest-growing nonpathogenic bacteria and a potential novel workhorse for many biotechnological applications. Here, we report the development of a Vibrio-based cell-free protein synthesis system (CFPS). Specifically, up to 0.4 g L-1 eGFP could be successfully synthesized in small-scale batch reactions using cell-free extract obtained from fast-growing V. natriegens cultures. Versatile CFPS system characterization attained by combining the analyses of key metabolites for translation and ribosomes revealed limitations regarding rRNA stability and critical substrate consumption (e.g., amino acids). Alternatively, rRNA showed increased stability by inducing Mg2+homeostasis in the reaction. Although the enormous translation capacity of the CFPS system based on the available ribosome concentration could not yet be fully exploited, its potential was successfully demonstrated by activating an endogenous transcription unit with V. natriegensRNA polymerase (RNAP) for protein expression. This allowed the use of in vitro screening for promoter strength, a critical factor for efficient gene expression in vitro and in vivo. Three different promoters were tested and output signals corresponded well with the expected affinity for V. natriegens RNAP. This established CFPS toolbox may provide a foundation to establish V. natriegens as a valuable platform in biotechnology as well as synthetic biology.
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12
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Failmezger J, Rauter M, Nitschel R, Kraml M, Siemann-Herzberg M. Cell-free protein synthesis from non-growing, stressed Escherichia coli. Sci Rep 2017; 7:16524. [PMID: 29184159 PMCID: PMC5705671 DOI: 10.1038/s41598-017-16767-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/16/2017] [Indexed: 01/01/2023] Open
Abstract
Cell-free protein synthesis is a versatile protein production system. Performance of the protein synthesis depends on highly active cytoplasmic extracts. Extracts from E. coli are believed to work best; they are routinely obtained from exponential growing cells, aiming to capture the most active translation system. Here, we report an active cell-free protein synthesis system derived from cells harvested at non-growth, stressed conditions. We found a downshift of ribosomes and proteins. However, a characterization revealed that the stoichiometry of ribosomes and key translation factors was conserved, pointing to a fully intact translation system. This was emphasized by synthesis rates, which were comparable to those of systems obtained from fast-growing cells. Our approach is less laborious than traditional extract preparation methods and multiplies the yield of extract per cultivation. This simplified growth protocol has the potential to attract new entrants to cell-free protein synthesis and to broaden the pool of applications. In this respect, a translation system originating from heat stressed, non-growing E. coli enabled an extension of endogenous transcription units. This was demonstrated by the sigma factor depending activation of parallel transcription. Our cell-free expression platform adds to the existing versatility of cell-free translation systems and presents a tool for cell-free biology.
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Affiliation(s)
- Jurek Failmezger
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Michael Rauter
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Robert Nitschel
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Michael Kraml
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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