1
|
Pastore AJ, Montoya A, Kamat M, Basso KB, Italia JS, Chatterjee A, Drosou M, Pantazis DA, Angerhofer A. Selective incorporation of 5-hydroxytryptophan blocks long range electron transfer in oxalate decarboxylase. Protein Sci 2023; 32:e4537. [PMID: 36482787 PMCID: PMC9801070 DOI: 10.1002/pro.4537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Oxalate decarboxylase from Bacillus subtilis is a binuclear Mn-dependent acid stress response enzyme that converts the mono-anion of oxalic acid into formate and carbon dioxide in a redox neutral unimolecular disproportionation reaction. A π-stacked tryptophan dimer, W96 and W274, at the interface between two monomer subunits facilitates long-range electron transfer between the two Mn ions and plays an important role in the catalytic mechanism. Substitution of W96 with the unnatural amino acid 5-hydroxytryptophan leads to a persistent EPR signal which can be traced back to the neutral radical of 5-hydroxytryptophan with its hydroxyl proton removed. 5-Hydroxytryptophan acts as a hole sink preventing the formation of Mn(III) at the N-terminal active site and strongly suppresses enzymatic activity. The lower boundary of the standard reduction potential for the active site Mn(II)/Mn(III) couple can therefore be estimated as 740 mV against the normal hydrogen electrode at pH 4, the pH of maximum catalytic efficiency. Our results support the catalytic importance of long-range electron transfer in oxalate decarboxylase while at the same time highlighting the utility of unnatural amino acid incorporation and specifically the use of 5-hydroxytryptophan as an energetic sink for hole hopping to probe electron transfer in redox proteins.
Collapse
Affiliation(s)
| | - Alvaro Montoya
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - Manasi Kamat
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - Kari B. Basso
- Department of ChemistryUniversity of FloridaGainesvilleFloridaUSA
| | - James S. Italia
- Department of ChemistryBoston CollegeChestnut HillMassachusettsUSA
| | | | - Maria Drosou
- Max‐Planck‐Institut für KohlenforschungMülheim an der RuhrGermany
| | | | | |
Collapse
|
2
|
Maleckis A, Abdelkader EH, Herath ID, Otting G. Synthesis of fluorinated leucines, valines and alanines for use in protein NMR. Org Biomol Chem 2022; 20:2424-2432. [PMID: 35262139 DOI: 10.1039/d2ob00145d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Efficient syntheses of fluorinated leucines, valines and alanines are described. The synthetic routes provide expedient access to various 13C/15N/D isotopologues requiring solely readily available and inexpensive isotope containing reagents such as NaBD4, carbon-13C dioxide and sodium azide-1-15N. The lightly fluorinated leucines and valines were found to be good substrates for cell-free protein expression and even 3-fluoroalanine, which is highly toxic to bacteria in vivo, could be incorporated into proteins this way. 19F-NMR spectra of the protein GB1 produced with these amino acids showed large chemical shift dispersions. Particularly high incorporation yields and clean 19F-NMR spectra were obtained for GB1 produced with valine residues, which had been synthesized with a single fluorine substituting a hydrogen stereospecifically in one of the methyl groups.
Collapse
Affiliation(s)
- Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006, Riga, Latvia.
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Iresha D Herath
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| |
Collapse
|
3
|
Bhadra S, Nguyen V, Torres JA, Kar S, Fadanka S, Gandini C, Akligoh H, Paik I, Maranhao AC, Molloy J, Ellington AD. Producing molecular biology reagents without purification. PLoS One 2021; 16:e0252507. [PMID: 34061896 PMCID: PMC8168896 DOI: 10.1371/journal.pone.0252507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022] Open
Abstract
We recently developed 'cellular' reagents-lyophilized bacteria overexpressing proteins of interest-that can replace commercial pure enzymes in typical diagnostic and molecular biology reactions. To make cellular reagent technology widely accessible and amenable to local production with minimal instrumentation, we now report a significantly simplified method for preparing cellular reagents that requires only a common bacterial incubator to grow and subsequently dry enzyme-expressing bacteria at 37°C with the aid of inexpensive chemical desiccants. We demonstrate application of such dried cellular reagents in common molecular and synthetic biology processes, such as PCR, qPCR, reverse transcription, isothermal amplification, and Golden Gate DNA assembly, in building easy-to-use testing kits, and in rapid reagent production for meeting extraordinary diagnostic demands such as those being faced in the ongoing SARS-CoV-2 pandemic. Furthermore, we demonstrate feasibility of local production by successfully implementing this minimized procedure and preparing cellular reagents in several countries, including the United Kingdom, Cameroon, and Ghana. Our results demonstrate possibilities for readily scalable local and distributed reagent production, and further instantiate the opportunities available via synthetic biology in general.
Collapse
Affiliation(s)
- Sanchita Bhadra
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Vylan Nguyen
- Freshman Research Initiative, DIY Diagnostics Stream, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jose-Angel Torres
- Freshman Research Initiative, DIY Diagnostics Stream, The University of Texas at Austin, Austin, Texas, United States of America
| | - Shaunak Kar
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | | | - Chiara Gandini
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | | | - Inyup Paik
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Andre C. Maranhao
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Andrew D. Ellington
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| |
Collapse
|
4
|
Full incorporation of the noncanonical amino acid hydroxylysine as a surrogate for lysine in green fluorescent protein. Bioorg Med Chem 2021; 41:116207. [PMID: 34000506 DOI: 10.1016/j.bmc.2021.116207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/28/2022]
Abstract
The canonical set of amino acids leads to an exceptionally wide range of protein functionality, nevertheless, this set still exhibits limitations. The incorporation of noncanonical amino acids into proteins can enlarge its functional scope. Although proofreading will counteract the charging of tRNAs with other amino acids than the canonical ones, the translation machinery may still accept noncanonical amino acids as surrogates and incorporate them at the canonically prescribed locations within the protein sequence. Here, we use a cell-free expression system to demonstrate the full replacement of l-lysine by l-hydroxylysine at all lysine sites of recombinantly produced GFP. In vivo, as a main component of collagen, post-translational l-hydroxylysine generation enables the formation of cross-links. Our work represents a first step towards in vitro production of (modified) collagens, more generally of proteins that can easily be crosslinked.
Collapse
|
5
|
Gimenez D, Phelan A, Murphy CD, Cobb SL. 19F NMR as a tool in chemical biology. Beilstein J Org Chem 2021; 17:293-318. [PMID: 33564338 PMCID: PMC7849273 DOI: 10.3762/bjoc.17.28] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132-140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein-protein interactions, protein-ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.
Collapse
Affiliation(s)
- Diana Gimenez
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
| | - Aoife Phelan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cormac D Murphy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven L Cobb
- Department of Chemistry, Durham University, South Road, Durham, DH13LE, UK
| |
Collapse
|
6
|
Cole SD, Miklos AE, Chiao AC, Sun ZZ, Lux MW. Methodologies for preparation of prokaryotic extracts for cell-free expression systems. Synth Syst Biotechnol 2020; 5:252-267. [PMID: 32775710 PMCID: PMC7398980 DOI: 10.1016/j.synbio.2020.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
Cell-free systems that mimic essential cell functions, such as gene expression, have dramatically expanded in recent years, both in terms of applications and widespread adoption. Here we provide a review of cell-extract methods, with a specific focus on prokaryotic systems. Firstly, we describe the diversity of Escherichia coli genetic strains available and their corresponding utility. We then trace the history of cell-extract methodology over the past 20 years, showing key improvements that lower the entry level for new researchers. Next, we survey the rise of new prokaryotic cell-free systems, with associated methods, and the opportunities provided. Finally, we use this historical perspective to comment on the role of methodology improvements and highlight where further improvements may be possible.
Collapse
Affiliation(s)
- Stephanie D. Cole
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Aleksandr E. Miklos
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Abel C. Chiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synvitrobio Inc., San Francisco, CA, USA
| | - Zachary Z. Sun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synvitrobio Inc., San Francisco, CA, USA
| | - Matthew W. Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| |
Collapse
|
7
|
Cui Z, Johnston WA, Alexandrov K. Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides. Front Bioeng Biotechnol 2020; 8:1031. [PMID: 33117774 PMCID: PMC7550873 DOI: 10.3389/fbioe.2020.01031] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs in vivo requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used Escherichia coli-based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for in situ acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use in vivo but are equally applicable to the in vitro systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in E. coli strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.
Collapse
Affiliation(s)
- Zhenling Cui
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Wayne A Johnston
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kirill Alexandrov
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| |
Collapse
|
8
|
Wu Y, Wang Z, Qiao X, Li J, Shu X, Qi H. Emerging Methods for Efficient and Extensive Incorporation of Non-canonical Amino Acids Using Cell-Free Systems. Front Bioeng Biotechnol 2020; 8:863. [PMID: 32793583 PMCID: PMC7387428 DOI: 10.3389/fbioe.2020.00863] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022] Open
Abstract
Cell-free protein synthesis (CFPS) has emerged as a novel protein expression platform. Especially the incorporation of non-canonical amino acids (ncAAs) has led to the development of numerous flexible methods for efficient and extensive expression of artificial proteins. Approaches were developed to eliminate the endogenous competition for ncAAs and engineer translation factors, which significantly enhanced the incorporation efficiency. Furthermore, in vitro aminoacylation methods can be conveniently combined with cell-free systems, extensively expanding the available ncAAs with novel and unique moieties. In this review, we summarize the recent progresses on the efficient and extensive incorporation of ncAAs by different strategies based on the elimination of competition by endogenous factors, translation factors engineering and extensive incorporation of novel ncAAs coupled with in vitro aminoacylation methods in CFPS. We also aim to offer new ideas to researchers working on ncAA incorporation techniques in CFPS and applications in various emerging fields.
Collapse
Affiliation(s)
- Yang Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Xin Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Xiangrong Shu
- Department of Pharmacy, Tianjin Huanhu Hospital, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| |
Collapse
|
9
|
Wang PH, Fujishima K, Berhanu S, Kuruma Y, Jia TZ, Khusnutdinova AN, Yakunin AF, McGlynn SE. A Bifunctional Polyphosphate Kinase Driving the Regeneration of Nucleoside Triphosphate and Reconstituted Cell-Free Protein Synthesis. ACS Synth Biol 2020; 9:36-42. [PMID: 31829622 DOI: 10.1021/acssynbio.9b00456] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reconstituted cell-free protein synthesis systems (e.g., the PURE system) allow the expression of toxic proteins, hetero-oligomeric protein subunits, and proteins with noncanonical amino acids with high levels of homogeneity. In these systems, an artificial ATP/GTP regeneration system is required to drive protein synthesis, which is accomplished using three kinases and phosphocreatine. Here, we demonstrate the replacement of these three kinases with one bifunctional Cytophaga hutchinsonii polyphosphate kinase that phosphorylates nucleosides in an exchange reaction from polyphosphate. The optimized single-kinase system produced a final sfGFP concentration (∼530 μg/mL) beyond that of the three-kinase system (∼400 μg/mL), with a 5-fold faster mRNA translation rate in the first 90 min. The single-kinase system is also compatible with the expression of heat-sensitive firefly luciferase at 37 °C. Potentially, the single-kinase nucleoside triphosphate regeneration approach developed herein could expand future applications of cell-free protein synthesis systems and could be used to drive other biochemical processes in synthetic biology which require both ATP and GTP.
Collapse
Affiliation(s)
- Po-Hsiang Wang
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, 108-8345, Japan
| | - Samuel Berhanu
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Yutetsu Kuruma
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- JST, PRESTO, Saitama, 102-0076, Japan
| | - Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Blue Marble Space Institute of Science, Seattle, Washington 98154, United States
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario ON M5S, Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario ON M5S, Canada
- Centre for Environmental Biotechnology, Bangor University, Bangor, Wales LL57 2DG, United Kingdom
| | - Shawn E. McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Blue Marble Space Institute of Science, Seattle, Washington 98154, United States
| |
Collapse
|
10
|
Finkler M, Kurt Ö, Grimm F, Hartz P, Ott A. A bead-based method for the removal of the amino acid lysine from cell-free transcription-translation systems. J Biotechnol 2020; 324S:100024. [PMID: 34154732 DOI: 10.1016/j.btecx.2020.100024] [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: 01/06/2020] [Revised: 06/22/2020] [Accepted: 07/19/2020] [Indexed: 12/26/2022]
Abstract
Cell-free transcription-translation systems are a versatile tool to study gene expression, enzymatic reactions and biochemical regulation mechanisms. Because cell-free transcription-translation systems are often derived from cell lysates, many different substances, among them amino acids, are present. However, experiments concerning the incorporation of non-canonical amino acids into proteins require a system with negligible amounts of canonical analogs. Here we propose a two-step method for the removal of residual free lysine in an all Escherichia coli-based cell-free expression system. The first step consists of the expression of a high-lysine dummy protein. The second step consists of direct removal via binding between lysine and DNA. The presented method is an efficient, fast and simple way to remove residual lysine without altering the system ability to perform gene expression.
Collapse
Affiliation(s)
- Marc Finkler
- Universität des Saarlandes, Biologische Experimentalphysik, Naturwissenschaftlich-Technische Fakultät, B2 1, Campus, 66123, Saarbrücken, Germany.
| | - Ömer Kurt
- Universität des Saarlandes, Biologische Experimentalphysik, Naturwissenschaftlich-Technische Fakultät, B2 1, Campus, 66123, Saarbrücken, Germany.
| | - Florent Grimm
- Universität des Saarlandes, Biologische Experimentalphysik, Naturwissenschaftlich-Technische Fakultät, B2 1, Campus, 66123, Saarbrücken, Germany.
| | - Philip Hartz
- Universität des Saarlandes, Institut für Biochemie, Naturwissenschaftlich-Technische Fakultät, B2 2,Campus, 66123, Saarbrücken, Germany.
| | - Albrecht Ott
- Universität des Saarlandes, Biologische Experimentalphysik, Naturwissenschaftlich-Technische Fakultät, B2 1, Campus, 66123, Saarbrücken, Germany.
| |
Collapse
|
11
|
Sharma A, Gupta G, Ahmad T, Mansoor S, Kaur B. Enzyme Engineering: Current Trends and Future Perspectives. FOOD REVIEWS INTERNATIONAL 2019. [DOI: 10.1080/87559129.2019.1695835] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anshula Sharma
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Gaganjot Gupta
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Tawseef Ahmad
- Department of Biotechnology, Punjabi University, Patiala, India
| | | | - Baljinder Kaur
- Department of Biotechnology, Punjabi University, Patiala, India
| |
Collapse
|
12
|
Gao W, Cho E, Liu Y, Lu Y. Advances and Challenges in Cell-Free Incorporation of Unnatural Amino Acids Into Proteins. Front Pharmacol 2019; 10:611. [PMID: 31191324 PMCID: PMC6549004 DOI: 10.3389/fphar.2019.00611] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/15/2019] [Indexed: 12/17/2022] Open
Abstract
Incorporation of unnatural amino acids (UNAAs) into proteins currently is an active biological research area for various fundamental and applied science. In this context, cell-free synthetic biology (CFSB) has been developed and recognized as a robust testing and biomanufacturing platform for highly efficient UNAA incorporation. It enables the orchestration of unnatural biological machinery toward an exclusive user-defined objective of unnatural protein synthesis. This review aims to overview the principles of cell-free unnatural protein synthesis (CFUPS) systems, their advantages, different UNAA incorporation approaches, and recent achievements. These have catalyzed cutting-edge research and diverse emerging applications. Especially, present challenges and future trends are focused and discussed. With the development of CFSB and the fusion with other advanced next-generation technologies, CFUPS systems would explicitly deliver their values for biopharmaceutical applications.
Collapse
Affiliation(s)
- Wei Gao
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- College of Life Science, Shenyang Normal University, Shenyang, China
| | - Eunhee Cho
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yingying Liu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- College of Life Science, Shenyang Normal University, Shenyang, China
| | - Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| |
Collapse
|
13
|
Chernoff N, Hill DJ, Diggs DL, Faison BD, Francis BM, Lang JR, Larue MM, Le TT, Loftin KA, Lugo JN, Schmid JE, Winnik WM. A critical review of the postulated role of the non-essential amino acid, β-N-methylamino-L-alanine, in neurodegenerative disease in humans. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2017; 20:1-47. [PMID: 28598725 PMCID: PMC6503681 DOI: 10.1080/10937404.2017.1297592] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The compound BMAA (β-N-methylamino-L-alanine) has been postulated to play a significant role in four serious neurological human diseases: Amyotrophic Lateral Sclerosis/Parkinsonism Dementia Complex (ALS/PDC) found on Guam, and ALS, Parkinsonism, and dementia that occur globally. ALS/PDC with symptoms of all three diseases first came to the attention of the scientific community during and after World War II. It was initially associated with cycad flour used for food because BMAA is a product of symbiotic cycad root-dwelling cyanobacteria. Human consumption of flying foxes that fed on cycad seeds was later suggested as a source of BMAA on Guam and a cause of ALS/PDC. Subsequently, the hypothesis was expanded to include a causative role for BMAA in other neurodegenerative diseases including Alzheimer's disease (AD) through exposures attributed to proximity to freshwaters and/or consumption of seafood due to its purported production by most species of cyanobacteria. The hypothesis that BMAA is the critical factor in the genesis of these neurodegenerative diseases received considerable attention in the medical, scientific, and public arenas. This review examines the history of ALS/PDC and the BMAA-human disease hypotheses; similarities and differences between ALS/PDC and the other diseases with similar symptomologies; the relationship of ALS/PDC to other similar diseases, studies of BMAA-mediated effects in lab animals, inconsistencies and data gaps in the hypothesis; and other compounds and agents that were suggested as the cause of ALS/PDC on Guam. The review concludes that the hypothesis of a causal BMAA neurodegenerative disease relationship is not supported by existing data.
Collapse
Affiliation(s)
- N. Chernoff
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC, USA
| | - D. J. Hill
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC, USA
| | - D. L. Diggs
- Oak Ridge Institute for Science and Education Internship/Research Participation Program at the U.S. Environmental Protection Agency, NHEERL, Research Triangle Park, NC, USA
| | - B. D. Faison
- U.S. Environmental Protection Agency, Office of Water, Office of Science and Technology, Washington, DC, USA
| | - B. M. Francis
- Department of Entomology, University of Illinois, Champaign-Urbana, IL, USA
| | - J. R Lang
- Oak Ridge Institute for Science and Education Internship/Research Participation Program at the U.S. Environmental Protection Agency, NHEERL, Research Triangle Park, NC, USA
| | - M. M. Larue
- Oak Ridge Institute for Science and Education Internship/Research Participation Program at the U.S. Environmental Protection Agency, NHEERL, Research Triangle Park, NC, USA
| | - T.-T. Le
- Oak Ridge Institute for Science and Education Internship/Research Participation Program at the U.S. Environmental Protection Agency, NHEERL, Research Triangle Park, NC, USA
| | | | - J. N. Lugo
- Department of Psychology and Neuroscience, Baylor University, Waco, TX, USA
| | - J. E. Schmid
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC, USA
| | - W. M. Winnik
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC, USA
| |
Collapse
|
14
|
|
15
|
Worst EG, Exner MP, De Simone A, Schenkelberger M, Noireaux V, Budisa N, Ott A. Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System. J Vis Exp 2016. [PMID: 27500416 PMCID: PMC5091720 DOI: 10.3791/54273] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The canonical set of amino acids leads to an exceptionally wide range of protein functionality. Nevertheless, the set of residues still imposes limitations on potential protein applications. The incorporation of noncanonical amino acids can enlarge this scope. There are two complementary approaches for the incorporation of noncanonical amino acids. For site-specific incorporation, in addition to the endogenous canonical translational machineries, an orthogonal aminoacyl-tRNA-synthetase-tRNA pair must be provided that does not interact with the canonical ones. Consequently, a codon that is not assigned to a canonical amino acid, usually a stop codon, is also required. This genetic code expansion enables the incorporation of a noncanonical amino acid at a single, given site within the protein. The here presented work describes residue-specific incorporation where the genetic code is reassigned within the endogenous translational system. The translation machinery accepts the noncanonical amino acid as a surrogate to incorporate it at canonically prescribed locations, i.e., all occurrences of a canonical amino acid in the protein are replaced by the noncanonical one. The incorporation of noncanonical amino acids can change the protein structure, causing considerably modified physical and chemical properties. Noncanonical amino acid analogs often act as cell growth inhibitors for expression hosts since they modify endogenous proteins, limiting in vivo protein production. In vivo incorporation of toxic noncanonical amino acids into proteins remains particularly challenging. Here, a cell-free approach for a complete replacement of L-arginine by the noncanonical amino acid L-canavanine is presented. It circumvents the inherent difficulties of in vivo expression. Additionally, a protocol to prepare target proteins for mass spectral analysis is included. It is shown that L-lysine can be replaced by L-hydroxy-lysine, albeit with lower efficiency. In principle, any noncanonical amino acid analog can be incorporated using the presented method as long as the endogenous in vitro translation system recognizes it.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Albrecht Ott
- Department of Experimental Physics, Saarland University;
| |
Collapse
|
16
|
Harada R, Furumoto S, Yoshikawa T, Ishikawa Y, Shibuya K, Okamura N, Ishiwata K, Iwata R, Yanai K. Synthesis and Characterization of ¹⁸F-Interleukin-8 Using a Cell-Free Translation System and 4-¹⁸F-Fluoro-L-Proline. J Nucl Med 2016; 57:634-9. [PMID: 26742712 DOI: 10.2967/jnumed.115.162602] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/01/2015] [Indexed: 11/16/2022] Open
Abstract
UNLABELLED Macromolecules such as proteins are attracting increasing interest for molecular imaging. We previously proposed a novel strategy for preparing macromolecules labeled with a PET radionuclide, (11)C, using a cell-free translation system with (11)C-methionine. However, macromolecules tend to exhibit slower kinetics, thus requiring a longer scanning time. Here, we expand our strategy using (18)F, which has a longer half-life, with the cell-free translation system with 4-(18)F-fluoro-L-proline ((18)F-FPro). We evaluated (18)F-interleukin-8 ((18)F-IL-8) produced by this method in vitro and in vivo to provide a proof of concept of our strategy. METHODS We tested some fluorinated amino acids to be incorporated into a protein. Trans-(18)F-FPro was radiolabeled from the corresponding precursor. (18)F-IL-8 was produced using the cell-free translation system with trans-(18)F-FPro instead of natural L-proline with incubation at 37°C for 120 min. An in vitro binding assay of (18)F-IL-8 was performed using IL-8 receptor-expressing cells. After intravenous administration of (18)F-IL-8, in vivo PET imaging of IL-8 receptor-expressing xenograft-bearing mice was performed using a small-animal PET system. RESULTS FPro was identified as an amino acid incorporated into the protein. (18)F-IL-8 was successfully prepared using the cell-free translation system and trans-(18)F-FPro with the radiochemical yield of 1.5% (decay-corrected) based on trans-(18)F-FPro. In vitro binding assays of (18)F-IL-8 demonstrated its binding to IL-8 receptor. In vivo PET imaging demonstrated that (18)F-IL-8 clearly accumulated in IL-8 receptor-expressing xenografts in mice, unlike trans-(18)F-FPro. CONCLUSION (18)F-IL-8 produced by this method binds to IL-8 receptors in vitro, and (18)F-IL-8 PET clearly visualizes its target receptor-expressing xenograft in vivo. Therefore, this technique might be useful for labeling macromolecules and performing preclinical evaluations of proteins of interest in vitro and in vivo.
Collapse
Affiliation(s)
- Ryuichi Harada
- Division of Neuro-imaging, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Shozo Furumoto
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, Sendai, Japan
| | - Takeo Yoshikawa
- Department of Pharmacology, Tohoku University School of Medicine, Sendai, Japan; and
| | - Yoichi Ishikawa
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, Sendai, Japan
| | - Katsuhiko Shibuya
- Department of Pharmacology, Tohoku University School of Medicine, Sendai, Japan; and
| | - Nobuyuki Okamura
- Division of Neuro-imaging, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan Department of Pharmacology, Tohoku University School of Medicine, Sendai, Japan; and
| | - Kiichi Ishiwata
- Research Team for Neuroimaging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Ren Iwata
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, Sendai, Japan
| | - Kazuhiko Yanai
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, Sendai, Japan Department of Pharmacology, Tohoku University School of Medicine, Sendai, Japan; and
| |
Collapse
|
17
|
Robust production of recombinant phosphoproteins using cell-free protein synthesis. Nat Commun 2015; 6:8168. [PMID: 26350765 PMCID: PMC4566161 DOI: 10.1038/ncomms9168] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/25/2015] [Indexed: 01/18/2023] Open
Abstract
Understanding the functional and structural consequences of site-specific protein phosphorylation has remained limited by our inability to produce phosphoproteins at high yields. Here we address this limitation by developing a cell-free protein synthesis (CFPS) platform that employs crude extracts from a genomically recoded strain of Escherichia coli for site-specific, co-translational incorporation of phosphoserine into proteins. We apply this system to the robust production of up to milligram quantities of human MEK1 kinase. Then, we recapitulate a physiological signalling cascade in vitro to evaluate the contributions of site-specific phosphorylation of mono- and doubly phosphorylated forms on MEK1 activity. We discover that only one phosphorylation event is necessary and sufficient for MEK1 activity. Our work sets the stage for using CFPS as a rapid high-throughput technology platform for direct expression of programmable phosphoproteins containing multiple phosphorylated residues. This work will facilitate study of phosphorylation-dependent structure–function relationships, kinase signalling networks and kinase inhibitor drugs. The inability to produce recombinant phosphoproteins has hindered research into their structure and function. Here the authors develop a cell-free protein synthesis platform to site-specifically incorporate phosphoserine into proteins at high yields, and recapitulate a MEK1 kinase signalling cascade.
Collapse
|
18
|
Worst EG, Exner MP, De Simone A, Schenkelberger M, Noireaux V, Budisa N, Ott A. Cell-free expression with the toxic amino acid canavanine. Bioorg Med Chem Lett 2015; 25:3658-60. [DOI: 10.1016/j.bmcl.2015.06.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/12/2015] [Accepted: 06/13/2015] [Indexed: 01/29/2023]
|
19
|
Quast RB, Mrusek D, Hoffmeister C, Sonnabend A, Kubick S. Cotranslational incorporation of non-standard amino acids using cell-free protein synthesis. FEBS Lett 2015; 589:1703-12. [PMID: 25937125 DOI: 10.1016/j.febslet.2015.04.041] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 11/30/2022]
Abstract
Over the last years protein engineering using non-standard amino acids has gained increasing attention. As a result, improved methods are now available, enabling the efficient and directed cotranslational incorporation of various non-standard amino acids to equip proteins with desired characteristics. In this context, the utilization of cell-free protein synthesis is particularly useful due to the direct accessibility of the translational machinery and synthesized proteins without having to maintain a vital cellular host. We review prominent methods for the incorporation of non-standard amino acids into proteins using cell-free protein synthesis. Furthermore, a list of non-standard amino acids that have been successfully incorporated into proteins in cell-free systems together with selected applications is provided.
Collapse
Affiliation(s)
- Robert B Quast
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Devid Mrusek
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany.
| |
Collapse
|
20
|
Kwon YC, Jewett MC. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci Rep 2015; 5:8663. [PMID: 25727242 PMCID: PMC4345344 DOI: 10.1038/srep08663] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/15/2015] [Indexed: 12/24/2022] Open
Abstract
Crude extract based cell-free protein synthesis (CFPS) has emerged as a powerful technology platform for high-throughput protein production and genetic part characterization. Unfortunately, robust preparation of highly active extracts generally requires specialized and costly equipment and can be labor and time intensive. Moreover, cell lysis procedures can be hard to standardize, leading to different extract performance across laboratories. These challenges limit new entrants to the field and new applications, such as comprehensive genome engineering programs to improve extract performance. To address these challenges, we developed a generalizable and easily accessible high-throughput crude extract preparation method for CFPS based on sonication. To validate our approach, we investigated two Escherichia coli strains: BL21 Star™ (DE3) and a K12 MG1655 variant, achieving similar productivity (defined as CFPS yield in g/L) by varying only a few parameters. In addition, we observed identical productivity of cell extracts generated from culture volumes spanning three orders of magnitude (10 mL culture tubes to 10 L fermentation). We anticipate that our rapid and robust extract preparation method will speed-up screening of genomically engineered strains for CFPS applications, make possible highly active extracts from non-model organisms, and promote a more general use of CFPS in synthetic biology and biotechnology.
Collapse
Affiliation(s)
- Yong-Chan Kwon
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA [3] Robert H. Lurie Comprehensive Cancer Center, Medicine Northwestern University, Chicago, IL 60611, USA [4] Institute of Bionanotechnology in Medicine Northwestern University, Chicago, IL 60611, USA
| |
Collapse
|
21
|
Hong SH, Kwon YC, Jewett MC. Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis. Front Chem 2014; 2:34. [PMID: 24959531 PMCID: PMC4050362 DOI: 10.3389/fchem.2014.00034] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 05/19/2014] [Indexed: 12/20/2022] Open
Abstract
Incorporating non-standard amino acids (NSAAs) into proteins enables new chemical properties, new structures, and new functions. In recent years, improvements in cell-free protein synthesis (CFPS) systems have opened the way to accurate and efficient incorporation of NSAAs into proteins. The driving force behind this development has been three-fold. First, a technical renaissance has enabled high-yielding (>1 g/L) and long-lasting (>10 h in batch operation) CFPS in systems derived from Escherichia coli. Second, the efficiency of orthogonal translation systems (OTSs) has improved. Third, the open nature of the CFPS platform has brought about an unprecedented level of control and freedom of design. Here, we review recent developments in CFPS platforms designed to precisely incorporate NSAAs. In the coming years, we anticipate that CFPS systems will impact efforts to elucidate structure/function relationships of proteins and to make biomaterials and sequence-defined biopolymers for medical and industrial applications.
Collapse
Affiliation(s)
- Seok Hoon Hong
- Chemical and Biological Engineering, Northwestern University Evanston, IL, USA ; Chemistry of Life Processes Institute, Northwestern University Evanston, IL, USA
| | - Yong-Chan Kwon
- Chemical and Biological Engineering, Northwestern University Evanston, IL, USA ; Chemistry of Life Processes Institute, Northwestern University Evanston, IL, USA
| | - Michael C Jewett
- Chemical and Biological Engineering, Northwestern University Evanston, IL, USA ; Chemistry of Life Processes Institute, Northwestern University Evanston, IL, USA ; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Chicago, IL, USA ; Institute of Bionanotechnology in Medicine, Northwestern University Chicago, IL, USA
| |
Collapse
|