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Shimada A, Baba J, Nagao S, Shinzawa-Itoh K, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S. Crystallographic cyanide-probing for cytochrome c oxidase reveals structural bases suggesting that a putative proton transfer H-pathway pumps protons. J Biol Chem 2023; 299:105277. [PMID: 37742916 PMCID: PMC10598403 DOI: 10.1016/j.jbc.2023.105277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023] Open
Abstract
Cytochrome c oxidase (CcO) reduces O2 in the O2-reduction site by sequential four-electron donations through the low-potential metal sites (CuA and Fea). Redox-coupled X-ray crystal structural changes have been identified at five distinct sites including Asp51, Arg438, Glu198, the hydroxyfarnesyl ethyl group of heme a, and Ser382, respectively. These sites interact with the putative proton-pumping H-pathway. However, the metal sites responsible for each structural change have not been identified, since these changes were detected as structural differences between the fully reduced and fully oxidized CcOs. Thus, the roles of these structural changes in the CcO function are yet to be revealed. X-ray crystal structures of cyanide-bound CcOs under various oxidation states showed that the O2-reduction site controlled only the Ser382-including site, while the low-potential metal sites induced the other changes. This finding indicates that these low-potential site-inducible structural changes are triggered by sequential electron-extraction from the low-potential sites by the O2-reduction site and that each structural change is insensitive to the oxidation and ligand-binding states of the O2-reduction site. Because the proton/electron coupling efficiency is constant (1:1), regardless of the reaction progress in the O2-reduction site, the structural changes induced by the low-potential sites are assignable to those critically involved in the proton pumping, suggesting that the H-pathway, facilitating these low-potential site-inducible structural changes, pumps protons. Furthermore, a cyanide-bound CcO structure suggests that a hypoxia-inducible activator, Higd1a, activates the O2-reduction site without influencing the electron transfer mechanism through the low-potential sites, kinetically confirming that the low-potential sites facilitate proton pump.
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Affiliation(s)
- Atsuhiro Shimada
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Jumpei Baba
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Shuhei Nagao
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Kyoko Shinzawa-Itoh
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan; Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Akoh, Hyogo, Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kazumasa Muramoto
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Akoh, Hyogo, Japan.
| | - Tomitake Tsukihara
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan; Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
| | - Shinya Yoshikawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan; Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Akoh, Hyogo, Japan.
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Walter RM, Zemella A, Schramm M, Kiebist J, Kubick S. Vesicle-based cell-free synthesis of short and long unspecific peroxygenases. Front Bioeng Biotechnol 2022; 10:964396. [PMID: 36394036 PMCID: PMC9663805 DOI: 10.3389/fbioe.2022.964396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
Unspecific peroxygenases (UPOs, EC 1.11.2.1) are fungal enzymes that catalyze the oxyfunctionalization of non-activated hydrocarbons, making them valuable biocatalysts. Despite the increasing interest in UPOs that has led to the identification of thousands of putative UPO genes, only a few of these have been successfully expressed and characterized. There is currently no universal expression system in place to explore their full potential. Cell-free protein synthesis has proven to be a sophisticated technique for the synthesis of difficult-to-express proteins. In this work, we aimed to establish an insect-based cell-free protein synthesis (CFPS) platform to produce UPOs. CFPS relies on translationally active cell lysates rather than living cells. The system parameters can thus be directly manipulated without having to account for cell viability, thereby making it highly adaptable. The insect-based lysate contains translocationally active, ER-derived vesicles, called microsomes. These microsomes have been shown to allow efficient translocation of proteins into their lumen, promoting post-translational modifications such as disulfide bridge formation and N-glycosylations. In this study the ability of a redox optimized, vesicle-based, eukaryotic CFPS system to synthesize functional UPOs was explored. The influence of different reaction parameters as well as the influence of translocation on enzyme activity was evaluated for a short UPO from Marasmius rotula and a long UPO from Agrocybe aegerita. The capability of the CFPS system described here was demonstrated by the successful synthesis of a novel UPO from Podospora anserina, thus qualifying CFPS as a promising tool for the identification and evaluation of novel UPOs and variants thereof.
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Affiliation(s)
- Ruben Magnus Walter
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Marina Schramm
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Jan Kiebist
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry – Biochemistry, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus – Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
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Cell-Free Protein Synthesis with Fungal Lysates for the Rapid Production of Unspecific Peroxygenases. Antioxidants (Basel) 2022; 11:antiox11020284. [PMID: 35204167 PMCID: PMC8868270 DOI: 10.3390/antiox11020284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Unspecific peroxygenases (UPOs, EC 1.11.2.1) are fungal biocatalysts that have attracted considerable interest for application in chemical syntheses due to their ability to selectively incorporate peroxide-oxygen into non-activated hydrocarbons. However, the number of available and characterized UPOs is limited, as it is difficult to produce these enzymes in homologous or hetero-logous expression systems. In the present study, we introduce a third approach for the expression of UPOs: cell-free protein synthesis using lysates from filamentous fungi. Biomass of Neurospora crassa and Aspergillus niger, respectively, was lysed by French press and tested for translational activity with a luciferase reporter enzyme. The upo1 gene from Cyclocybe (Agrocybe) aegerita (encoding the main peroxygenase, AaeUPO) was cell-free expressed with both lysates, reaching activities of up to 105 U L−1 within 24 h (measured with veratryl alcohol as substrate). The cell-free expressed enzyme (cfAaeUPO) was successfully tested in a substrate screening that included prototypical UPO substrates, as well as several pharmaceuticals. The determined activities and catalytic performance were comparable to that of the wild-type enzyme (wtAaeUPO). The results presented here suggest that cell-free expression could become a valuable tool to gain easier access to the immense pool of putative UPO genes and to expand the spectrum of these sought-after biocatalysts.
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Batista AC, Soudier P, Kushwaha M, Faulon J. Optimising protein synthesis in cell‐free systems, a review. ENGINEERING BIOLOGY 2021; 5:10-19. [PMID: 36968650 PMCID: PMC9996726 DOI: 10.1049/enb2.12004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/25/2022] Open
Abstract
Over the last decades, cell-free systems have been extensively used for in vitro protein expression. A vast range of protocols and cellular sources varying from prokaryotes and eukaryotes are now available for cell-free technology. However, exploiting the maximum capacity of cell free systems is not achieved by using traditional protocols. Here, what are the strategies and choices one can apply to optimise cell-free protein synthesis have been reviewed. These strategies provide robust and informative improvements regarding transcription, translation and protein folding which can later be used for the establishment of individual best cell-free reactions per lysate batch.
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Affiliation(s)
- Angelo C. Batista
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Paul Soudier
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Manish Kushwaha
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Jean‐Loup Faulon
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
- SYNBIOCHEM Center School of Chemistry Manchester Institute of Biotechnology The University of Manchester Manchester UK
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Affiliation(s)
- Shinya Yoshikawa
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
| | - Atsuhiro Shimada
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
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Whittaker JW. Cell-free protein synthesis: the state of the art. Biotechnol Lett 2013; 35:143-52. [PMID: 23086573 PMCID: PMC3553302 DOI: 10.1007/s10529-012-1075-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/10/2012] [Indexed: 10/27/2022]
Abstract
Cell-free protein synthesis harnesses the synthetic power of biology, programming the ribosomal translational machinery of the cell to create macromolecular products. Like PCR, which uses cellular replication machinery to create a DNA amplifier, cell-free protein synthesis is emerging as a transformative technology with broad applications in protein engineering, biopharmaceutical development, and post-genomic research. By breaking free from the constraints of cell-based systems, it takes the next step towards synthetic biology. Recent advances in reconstituted cell-free protein synthesis (Protein synthesis Using Recombinant Elements expression systems) are creating new opportunities to tailor the reactions for specialized applications including in vitro protein evolution, printing protein microarrays, isotopic labeling, and incorporating nonnatural amino acids.
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Affiliation(s)
- James W Whittaker
- Division of Environmental and Biomolecular Systems, Institute for Environmental Health, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006-8921, USA.
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Jaehme M, Michel H. Evaluation of cell-free protein synthesis for the crystallization of membrane proteins--a case study on a member of the glutamate transporter family from Staphylothermus marinus. FEBS J 2013; 280:1112-25. [PMID: 23279902 DOI: 10.1111/febs.12105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 12/07/2012] [Accepted: 12/18/2012] [Indexed: 12/25/2022]
Abstract
Cell-free in vitro synthesis of proteins using coupled transcription/translation is considered to be a powerful alternative to the use of traditional cell-based expression systems. Recently, promising developments have been reported applying cell-free production to membrane proteins for structural biology and in particular for NMR spectroscopy. However, the general applicability of this system to produce large amounts of stable, functional and homogeneous membrane proteins as required for X-ray crystallography remains to be determined. Here, we present a systematic study comparing structural and functional properties of membrane proteins produced using Escherichia coli derived in vitro and in vivo expression systems. The function of the target membrane protein, a previously uncharacterized bacterial glutamate transporter homolog from Staphylothermus marinus, was analyzed using ligand binding and transport assays. In addition, the protein structure was investigated with respect to its overall fold and oligomeric state in different detergents. We found that the protein synthesized in vitro is highly stable and monodisperse. However, in contrast to the protein produced using an in vivo system, it was not able to assemble into the native trimeric state nor to bind substrate. We thus conclude that cell-free expression systems can compromise folding and function of such complex secondary active transporters. The expression product has to be carefully characterized prior to biophysical investigations like crystallography of membrane proteins.
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Affiliation(s)
- Michael Jaehme
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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Luo Z, Zhang S. Designer nanomaterials using chiral self-assembling peptide systems and their emerging benefit for society. Chem Soc Rev 2012; 41:4736-54. [DOI: 10.1039/c2cs15360b] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Matthies D, Haberstock S, Joos F, Dötsch V, Vonck J, Bernhard F, Meier T. Cell-Free Expression and Assembly of ATP Synthase. J Mol Biol 2011; 413:593-603. [DOI: 10.1016/j.jmb.2011.08.055] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 08/11/2011] [Accepted: 08/30/2011] [Indexed: 11/16/2022]
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He M. In vitro protein expression: an emerging alternative to cell-based approaches. N Biotechnol 2010; 28:209-10. [PMID: 20804874 DOI: 10.1016/j.nbt.2010.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 08/23/2010] [Indexed: 11/17/2022]
Abstract
Protein expression remains a bottleneck in the production of proteins. Owing to several advantages, cell-free translation is emerging as an alternative to cell-based methods for the generation of proteins. Recent advances have led to many novel applications of cell-free systems in biotechnology, proteomics and fundamental biological research. This special issue of New Biotechnology describes recent advances in cell-free protein expression systems and their applications.
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Affiliation(s)
- Mingyue He
- Protein Expression Facility, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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