1
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Lassak J, Sieber A, Hellwig M. Exceptionally versatile take II: post-translational modifications of lysine and their impact on bacterial physiology. Biol Chem 2022; 403:819-858. [PMID: 35172419 DOI: 10.1515/hsz-2021-0382] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 01/16/2023]
Abstract
Among the 22 proteinogenic amino acids, lysine sticks out due to its unparalleled chemical diversity of post-translational modifications. This results in a wide range of possibilities to influence protein function and hence modulate cellular physiology. Concomitantly, lysine derivatives form a metabolic reservoir that can confer selective advantages to those organisms that can utilize it. In this review, we provide examples of selected lysine modifications and describe their role in bacterial physiology.
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Affiliation(s)
- Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Alina Sieber
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Michael Hellwig
- Technische Universität Braunschweig - Institute of Food Chemistry, Schleinitzstraße 20, D-38106 Braunschweig, Germany
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2
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Genetic-code-expanded cell-based therapy for treating diabetes in mice. Nat Chem Biol 2022; 18:47-55. [PMID: 34782743 DOI: 10.1038/s41589-021-00899-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 09/13/2021] [Indexed: 12/13/2022]
Abstract
Inducer-triggered therapeutic protein expression from designer cells is a promising strategy for disease treatment. However, as most inducer systems harness transcriptional machineries, protein expression timeframes are unsuitable for many therapeutic applications. Here, we engineered a genetic code expansion-based therapeutic system, termed noncanonical amino acids (ncAAs)-triggered therapeutic switch (NATS), to achieve fast therapeutic protein expression in response to cognate ncAAs at the translational level. The NATS system showed response within 2 hours of triggering, whereas no signal was detected in a transcription-machinery-based system. Moreover, NATS system is compatible with transcriptional switches for multi-regulatory-layer control. Diabetic mice with microencapsulated cell implants harboring the NATS system could alleviate hyperglycemia within 90 min on oral delivery of ncAA. We also prepared ncAA-containing 'cookies' and achieved long-term glycemic control in diabetic mice implanted with NATS cells. Our proof-of-concept study demonstrates the use of NATS system for the design of next-generation cell-based therapies to achieve fast orally induced protein expression.
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3
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Graf von Armansperg B, Koller F, Gericke N, Hellwig M, Jagtap PKA, Heermann R, Hennig J, Henle T, Lassak J. Transcriptional regulation of the N ε -fructoselysine metabolism in Escherichia coli by global and substrate-specific cues. Mol Microbiol 2020; 115:175-190. [PMID: 32979851 DOI: 10.1111/mmi.14608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022]
Abstract
Thermally processed food is an important part of the human diet. Heat-treatment, however, promotes the formation of so-called Amadori rearrangement products, such as fructoselysine. The gut microbiota including Escherichia coli can utilize these compounds as a nutrient source. While the degradation route for fructoselysine is well described, regulation of the corresponding pathway genes frlABCD remained poorly understood. Here, we used bioinformatics combined with molecular and biochemical analyses and show that fructoselysine metabolism in E. coli is tightly controlled at the transcriptional level. The global regulator CRP (CAP) as well as the alternative sigma factor σ32 (RpoH) contribute to promoter activation at high cAMP-levels and inside warm-blooded hosts, respectively. In addition, we identified and characterized a transcriptional regulator FrlR, encoded adjacent to frlABCD, as fructoselysine-6-phosphate specific repressor. Our study provides profound evidence that the interplay of global and substrate-specific regulation is a perfect adaptation strategy to efficiently utilize unusual substrates within the human gut environment.
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Affiliation(s)
| | - Franziska Koller
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Gericke
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Hellwig
- Chair of Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | | | - Ralf Heermann
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thomas Henle
- Chair of Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
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4
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Titrating bacterial growth and chemical biosynthesis for efficient N-acetylglucosamine and N-acetylneuraminic acid bioproduction. Nat Commun 2020; 11:5078. [PMID: 33033266 PMCID: PMC7544899 DOI: 10.1038/s41467-020-18960-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/21/2020] [Indexed: 12/27/2022] Open
Abstract
Metabolic engineering facilitates chemical biosynthesis by rewiring cellular resources to produce target compounds. However, an imbalance between cell growth and bioproduction often reduces production efficiency. Genetic code expansion (GCE)-based orthogonal translation systems incorporating non-canonical amino acids (ncAAs) into proteins by reassigning non-canonical codons to ncAAs qualify for balancing cellular metabolism. Here, GCE-based cell growth and biosynthesis balance engineering (GCE-CGBBE) is developed, which is based on titrating expression of cell growth and metabolic flux determinant genes by constructing ncAA-dependent expression patterns. We demonstrate GCE-CGBBE in genome-recoded Escherichia coli Δ321AM by precisely balancing glycolysis and N-acetylglucosamine production, resulting in a 4.54-fold increase in titer. GCE-CGBBE is further expanded to non-genome-recoded Bacillus subtilis to balance growth and N-acetylneuraminic acid bioproduction by titrating essential gene expression, yielding a 2.34-fold increase in titer. Moreover, the development of ncAA-dependent essential gene expression regulation shows efficient biocontainment of engineered B. subtilis to avoid unintended proliferation in nature. An imbalance between cell growth and bioproduction of engineered microbes often reduces production efficiency. Here, the authors report genetic code expansion-based cell growth and biosynthesis balance engineering to achieve high levels production of N-acetylglucosamine in E. coli and N-acetylneuraminic acid in B. subtilis.
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5
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Pfab M, Kielkowski P, Krafczyk R, Volkwein W, Sieber SA, Lassak J, Jung K. Synthetic post-translational modifications of elongation factor P using the ligase EpmA. FEBS J 2020; 288:663-677. [PMID: 32337775 DOI: 10.1111/febs.15346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/24/2020] [Accepted: 04/23/2020] [Indexed: 12/20/2022]
Abstract
Canonically, tRNA synthetases charge tRNA. However, the lysyl-tRNA synthetase paralog EpmA catalyzes the attachment of (R)-β-lysine to the ε-amino group of lysine 34 of the translation elongation factor P (EF-P) in Escherichia coli. This modification is essential for EF-P-mediated translational rescue of ribosomes stalled at consecutive prolines. In this study, we determined the kinetics of EpmA and its variant EpmA_A298G to catalyze the post-translational modification of K34 in EF-P with eight noncanonical substrates. In addition, acetylated EF-P was generated using an amber suppression system. The impact of these synthetically modified EF-P variants on in vitro translation of a polyproline-containing NanoLuc luciferase reporter was analyzed. Our results show that natural (R)-β-lysylation was more effective in rescuing stalled ribosomes than any other synthetic modification tested. Thus, our work not only provides new biochemical insights into the function of EF-P, but also opens a new route to post-translationally modify proteins using EpmA.
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Affiliation(s)
- Miriam Pfab
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Pavel Kielkowski
- Organic Chemistry II, Technical University of Munich, Garching, Germany
| | - Ralph Krafczyk
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Wolfram Volkwein
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Stephan A Sieber
- Organic Chemistry II, Technical University of Munich, Garching, Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
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6
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Kato Y. Extremely Low Leakage Expression Systems Using Dual Transcriptional-Translational Control for Toxic Protein Production. Int J Mol Sci 2020; 21:ijms21030705. [PMID: 31973139 PMCID: PMC7037476 DOI: 10.3390/ijms21030705] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/25/2019] [Accepted: 01/19/2020] [Indexed: 02/01/2023] Open
Abstract
Expression systems for highly toxic protein genes must be conditional and suppress leakage expression to almost zero because even faint leakage expression may kill host cells, inhibit host growth, and cause loss of plasmids containing the toxic protein genes. The most widely used conditional expression systems are controlled only at the transcriptional level, and complete suppression of leakage expression is challenging. Recent progress on translational control has enabled construction of dual transcriptional-translational control systems in which leakage expression is strongly suppressed. This review summarizes the principles, features, and practical examples of dual transcriptional-translational control systems in bacteria, and provides future perspectives on these systems.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
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7
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Lassak J, Koller F, Krafczyk R, Volkwein W. Exceptionally versatile – arginine in bacterial post-translational protein modifications. Biol Chem 2019; 400:1397-1427. [DOI: 10.1515/hsz-2019-0182] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/01/2019] [Indexed: 12/24/2022]
Abstract
Abstract
Post-translational modifications (PTM) are the evolutionary solution to challenge and extend the boundaries of genetically predetermined proteomic diversity. As PTMs are highly dynamic, they also hold an enormous regulatory potential. It is therefore not surprising that out of the 20 proteinogenic amino acids, 15 can be post-translationally modified. Even the relatively inert guanidino group of arginine is subject to a multitude of mostly enzyme mediated chemical changes. The resulting alterations can have a major influence on protein function. In this review, we will discuss how bacteria control their cellular processes and develop pathogenicity based on post-translational protein-arginine modifications.
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Affiliation(s)
- Jürgen Lassak
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Franziska Koller
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Ralph Krafczyk
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Wolfram Volkwein
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
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8
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Volkwein W, Krafczyk R, Jagtap PKA, Parr M, Mankina E, Macošek J, Guo Z, Fürst MJLJ, Pfab M, Frishman D, Hennig J, Jung K, Lassak J. Switching the Post-translational Modification of Translation Elongation Factor EF-P. Front Microbiol 2019; 10:1148. [PMID: 31178848 PMCID: PMC6544042 DOI: 10.3389/fmicb.2019.01148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/06/2019] [Indexed: 12/31/2022] Open
Abstract
Tripeptides with two consecutive prolines are the shortest and most frequent sequences causing ribosome stalling. The bacterial translation elongation factor P (EF-P) relieves this arrest, allowing protein biosynthesis to continue. A seven amino acids long loop between beta-strands β3/β4 is crucial for EF-P function and modified at its tip by lysylation of lysine or rhamnosylation of arginine. Phylogenetic analyses unveiled an invariant proline in the -2 position of the modification site in EF-Ps that utilize lysine modifications such as Escherichia coli. Bacteria with the arginine modification like Pseudomonas putida on the contrary have selected against it. Focusing on the EF-Ps from these two model organisms we demonstrate the importance of the β3/β4 loop composition for functionalization by chemically distinct modifications. Ultimately, we show that only two amino acid changes in E. coli EF-P are needed for switching the modification strategy from lysylation to rhamnosylation.
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Affiliation(s)
- Wolfram Volkwein
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ralph Krafczyk
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Marina Parr
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany.,St. Petersburg State Polytechnic University, Saint Petersburg, Russia
| | - Elena Mankina
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Jakub Macošek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Heidelberg, Germany
| | - Zhenghuan Guo
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian Josef Ludwig Johannes Fürst
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany.,Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
| | - Miriam Pfab
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany.,St. Petersburg State Polytechnic University, Saint Petersburg, Russia
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kirsten Jung
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jürgen Lassak
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
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9
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Crnković A, Vargas-Rodriguez O, Söll D. Plasticity and Constraints of tRNA Aminoacylation Define Directed Evolution of Aminoacyl-tRNA Synthetases. Int J Mol Sci 2019; 20:ijms20092294. [PMID: 31075874 PMCID: PMC6540133 DOI: 10.3390/ijms20092294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 04/29/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023] Open
Abstract
Genetic incorporation of noncanonical amino acids (ncAAs) has become a powerful tool to enhance existing functions or introduce new ones into proteins through expanded chemistry. This technology relies on the process of nonsense suppression, which is made possible by directing aminoacyl-tRNA synthetases (aaRSs) to attach an ncAA onto a cognate suppressor tRNA. However, different mechanisms govern aaRS specificity toward its natural amino acid (AA) substrate and hinder the engineering of aaRSs for applications beyond the incorporation of a single l-α-AA. Directed evolution of aaRSs therefore faces two interlinked challenges: the removal of the affinity for cognate AA and improvement of ncAA acylation. Here we review aspects of AA recognition that directly influence the feasibility and success of aaRS engineering toward d- and β-AAs incorporation into proteins in vivo. Emerging directed evolution methods are described and evaluated on the basis of aaRS active site plasticity and its inherent constraints.
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Affiliation(s)
- Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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10
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Kato Y. Translational Control using an Expanded Genetic Code. Int J Mol Sci 2019; 20:ijms20040887. [PMID: 30781713 PMCID: PMC6412442 DOI: 10.3390/ijms20040887] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 11/16/2022] Open
Abstract
A bio-orthogonal and unnatural substance, such as an unnatural amino acid (Uaa), is an ideal regulator to control target gene expression in a synthetic gene circuit. Genetic code expansion technology has achieved Uaa incorporation into ribosomal synthesized proteins in vivo at specific sites designated by UAG stop codons. This site-specific Uaa incorporation can be used as a controller of target gene expression at the translational level by conditional read-through of internal UAG stop codons. Recent advances in optimization of site-specific Uaa incorporation for translational regulation have enabled more precise control over a wide range of novel important applications, such as Uaa-auxotrophy-based biological containment, live-attenuated vaccine, and high-yield zero-leakage expression systems, in which Uaa translational control is exclusively used as an essential genetic element. This review summarizes the history and recent advance of the translational control by conditional stop codon read-through, especially focusing on the methods using the site-specific Uaa incorporation.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan.
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11
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Britton ZT, London TB, Carrell J, Dosanjh B, Wilkinson T, Bowen MA, Wu H, Dall’Acqua WF, Marelli M, Mazor Y. Tag-on-Demand: exploiting amber codon suppression technology for the enrichment of high-expressing membrane protein cell lines. Protein Eng Des Sel 2019; 31:389-398. [DOI: 10.1093/protein/gzy032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/16/2018] [Accepted: 12/18/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Zachary T Britton
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD, USA
| | - Timothy B London
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, UK
- Current affiliation: TC BioPharm Limited, Glasgow, UK
| | - Jeffrey Carrell
- Respiratory, Inflammation and Autoimmune, MedImmune, Gaithersburg, MD, USA
| | - Bhupinder Dosanjh
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, UK
| | - Trevor Wilkinson
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, UK
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD, USA
| | - Herren Wu
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD, USA
| | | | - Marcello Marelli
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD, USA
| | - Yariv Mazor
- Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD, USA
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12
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Shi T, Burton S, Wang Y, Xu S, Zhang W, Yu L. Metabolomic analysis of honey bee, Apis mellifera L. response to thiacloprid. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2018; 152:17-23. [PMID: 30497706 DOI: 10.1016/j.pestbp.2018.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/21/2018] [Accepted: 08/08/2018] [Indexed: 06/09/2023]
Abstract
The cyano-substituted neonicotinoid insecticide, thiacloprid, is nowadays widely used in agriculture for controlling insect pests. However, it also simultaneously has adverse effects on the health of important pollinators, such as honey bees. Previous studies have reported that sublethal doses of neonicotinoids impaired immunocompetence, learning and memory performance, and homing behaviour in honey bees. In the present study, using LC-MS-based combined with GC-MS-based metabolomic approaches, we profiled the metabolic changes that occur in the head of honey bee after subchronic exposure to 2 mg/L thiacloprid over 3 days. The estimated total dose of thiacloprid fed to each bee was 0.12 μg. The results showed that there were 115 metabolites significantly affected in thiacloprid-treated bees compared to control. The metabolites with high level of abundance enriched to wide range pathways associated with oxidative stress and detoxification suggest that the honey bees have activated their detoxification system to resistant toxicity of thiacloprid. While, the reduction of serotonin suggest thiacloprid may hinder the brain activity implicated in learning and behaviour development. Our study expand the understanding of the molecular basis of the complex interactions between neonicotinoids and honey bees.
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Affiliation(s)
- Tengfei Shi
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Sawyer Burton
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Yufei Wang
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Shengyun Xu
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Wenxin Zhang
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Linsheng Yu
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; School of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.
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13
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Kato Y. Tight Translational Control Using Site-Specific Unnatural Amino Acid Incorporation with Positive Feedback Gene Circuits. ACS Synth Biol 2018; 7:1956-1963. [PMID: 29979867 DOI: 10.1021/acssynbio.8b00204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tight regulatory system for gene expression, which is ideally controlled by unnatural and bio-orthogonal substances, is a keystone for successful construction of synthetic gene circuits. Here, we present a widely applicable approach to construct tight protein translational switches using site-specific unnatural amino acid (Uaa) incorporation systems. As a key mechanism to obtain excellent tightness, we installed gene circuits for positive feedback derepression. This mechanism dramatically suppressed leakage translation in the absence of the Uaa. In a translational switch with the feedback circuit in Escherichia coli, a 1.4 × 103 ON/OFF ratio was achieved which was 3 × 102-fold greater than that of the parent system and was comparable to that of the well-known tight expression system using the araBAD promoter and the araC regulator. This method offers an avenue for generation of novel tight genetic switches from over a hundred site-specific unnatural amino acid incorporation systems which have already been established. These tight translational switches will facilitate the development of fine gene control systems in synthetic biology, especially for Uaa-auxotrophy-based biological containments and live attenuated vaccines.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
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14
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Bartholomae M, Baumann T, Nickling JH, Peterhoff D, Wagner R, Budisa N, Kuipers OP. Expanding the Genetic Code of Lactococcus lactis and Escherichia coli to Incorporate Non-canonical Amino Acids for Production of Modified Lantibiotics. Front Microbiol 2018; 9:657. [PMID: 29681891 PMCID: PMC5897534 DOI: 10.3389/fmicb.2018.00657] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
The incorporation of non-canonical amino acids (ncAAs) into ribosomally synthesized and post-translationally modified peptides, e.g., nisin from the Gram-positive bacterium Lactococcus lactis, bears great potential to expand the chemical space of various antimicrobials. The ncAA Nε-Boc-L-lysine (BocK) was chosen for incorporation into nisin using the archaeal pyrrolysyl-tRNA synthetase–tRNAPyl pair to establish orthogonal translation in L. lactis for read-through of in-frame amber stop codons. In parallel, recombinant nisin production and orthogonal translation were combined in Escherichia coli cells. Both organisms synthesized bioactive nisin(BocK) variants. Screening of a nisin amber codon library revealed suitable sites for ncAA incorporation and two variants displayed high antimicrobial activity. Orthogonal translation in E. coli and L. lactis presents a promising tool to create new-to-nature nisin derivatives.
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Affiliation(s)
- Maike Bartholomae
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Tobias Baumann
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin (Berlin Institute of Technology), Berlin, Germany
| | - Jessica H Nickling
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin (Berlin Institute of Technology), Berlin, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, Universität Regensburg, Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, Universität Regensburg, Regensburg, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Department of Chemistry, Technische Universität Berlin (Berlin Institute of Technology), Berlin, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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