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Tan Y, Li M, Zhou Z, Tan P, Yu H, Fan G, Hong L. PETA: evaluating the impact of protein transfer learning with sub-word tokenization on downstream applications. J Cheminform 2024; 16:92. [PMID: 39095917 PMCID: PMC11297785 DOI: 10.1186/s13321-024-00884-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/13/2024] [Indexed: 08/04/2024] Open
Abstract
Protein language models (PLMs) play a dominant role in protein representation learning. Most existing PLMs regard proteins as sequences of 20 natural amino acids. The problem with this representation method is that it simply divides the protein sequence into sequences of individual amino acids, ignoring the fact that certain residues often occur together. Therefore, it is inappropriate to view amino acids as isolated tokens. Instead, the PLMs should recognize the frequently occurring combinations of amino acids as a single token. In this study, we use the byte-pair-encoding algorithm and unigram to construct advanced residue vocabularies for protein sequence tokenization, and we have shown that PLMs pre-trained using these advanced vocabularies exhibit superior performance on downstream tasks when compared to those trained with simple vocabularies. Furthermore, we introduce PETA, a comprehensive benchmark for systematically evaluating PLMs. We find that vocabularies comprising 50 and 200 elements achieve optimal performance. Our code, model weights, and datasets are available at https://github.com/ginnm/ProteinPretraining . SCIENTIFIC CONTRIBUTION: This study introduces advanced protein sequence tokenization analysis, leveraging the byte-pair-encoding algorithm and unigram. By recognizing frequently occurring combinations of amino acids as single tokens, our proposed method enhances the performance of PLMs on downstream tasks. Additionally, we present PETA, a new comprehensive benchmark for the systematic evaluation of PLMs, demonstrating that vocabularies of 50 and 200 elements offer optimal performance.
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Affiliation(s)
- Yang Tan
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai National Center for Applied Mathematics (SJTU Center), & Institute of Natural Science, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200240, China
- Chongqing Artificial Intelligence Research Institute of Shanghai Jiao Tong University, Chongqing, 200240, China
| | - Mingchen Li
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai National Center for Applied Mathematics (SJTU Center), & Institute of Natural Science, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200240, China
- Chongqing Artificial Intelligence Research Institute of Shanghai Jiao Tong University, Chongqing, 200240, China
| | - Ziyi Zhou
- Shanghai National Center for Applied Mathematics (SJTU Center), & Institute of Natural Science, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Pan Tan
- Shanghai National Center for Applied Mathematics (SJTU Center), & Institute of Natural Science, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200240, China
| | - Huiqun Yu
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Guisheng Fan
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Liang Hong
- Shanghai National Center for Applied Mathematics (SJTU Center), & Institute of Natural Science, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200240, China.
- Chongqing Artificial Intelligence Research Institute of Shanghai Jiao Tong University, Chongqing, 200240, China.
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2
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Ueta M, Wada A, Wada C. The hibernation promoting factor of Betaproteobacteria Comamonas testosteroni cannot induce 100S ribosome formation but stabilizes 70S ribosomal particles. Genes Cells 2024; 29:613-634. [PMID: 38937957 DOI: 10.1111/gtc.13137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 06/29/2024]
Abstract
Bacteria use several means to survive under stress conditions such as nutrient depletion. One such response is the formation of hibernating 100S ribosomes, which are translationally inactive 70S dimers. In Gammaproteobacteria (Enterobacterales), 100S ribosome formation requires ribosome modulation factor (RMF) and short hibernation promoting factor (HPF), whereas it is mediated by only long HPF in the majority of bacteria. Here, we investigated the role of HPFs of Comamonas testosteroni, which belongs to the Betaproteobacteria with common ancestor to the Gammaproteobacteria. C. testosteroni has two genes of HPF homologs of differing length (CtHPF-125 and CtHPF-119). CtHPF-125 was induced in the stationary phase, whereas CtHPF-119 conserved in many other Betaproteobacteria was not expressed in the culture conditions used here. Unlike short HPF and RMF, and long HPF, CtHPF-125 could not form 100S ribosome. We first constructed the deletion mutant of Cthpf-125 gene. When the deletion mutant grows in the stationary phase, 70S particles were degraded faster than in the wild strain. CtHPF-125 contributes to stabilizing the 70S ribosome. CtHPF-125 and CtHPF-119 both inhibited protein synthesis by transcription-translation in vitro. Our findings suggest that CtHPF-125 binds to ribosome, and stabilizes 70S ribosomes, inhibits translation without forming 100S ribosomes and supports prolonging life.
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Affiliation(s)
- Masami Ueta
- Biological Information Research, Yoshida Biological Laboratory Inc., Yoshida Biological Laboratory, Kyoto, Japan
| | - Akira Wada
- Biological Information Research, Yoshida Biological Laboratory Inc., Yoshida Biological Laboratory, Kyoto, Japan
| | - Chieko Wada
- Biological Information Research, Yoshida Biological Laboratory Inc., Yoshida Biological Laboratory, Kyoto, Japan
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3
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Taguchi H, Niwa T. Reconstituted Cell-free Translation Systems for Exploring Protein Folding and Aggregation. J Mol Biol 2024; 436:168726. [PMID: 39074633 DOI: 10.1016/j.jmb.2024.168726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024]
Abstract
Protein folding is crucial for achieving functional three-dimensional structures. However, the process is often hampered by aggregate formation, necessitating the presence of chaperones and quality control systems within the cell to maintain protein homeostasis. Despite a long history of folding studies involving the denaturation and subsequent refolding of translation-completed purified proteins, numerous facets of cotranslational folding, wherein nascent polypeptides are synthesized by ribosomes and folded during translation, remain unexplored. Cell-free protein synthesis (CFPS) systems are invaluable tools for studying cotranslational folding, offering a platform not only for elucidating mechanisms but also for large-scale analyses to identify aggregation-prone proteins. This review provides an overview of the extensive use of CFPS in folding studies to date. In particular, we discuss a comprehensive aggregation formation assay of thousands of Escherichia coli proteins conducted under chaperone-free conditions using a reconstituted translation system, along with its derived studies.
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Affiliation(s)
- Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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4
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Sakuma C, Iwamoto T, Masuda K, Shimizu Y, Obata F, Kanuka H. Fibrinopeptide A-induced blood-feeding arrest in the yellow fever mosquito Aedes aegypti. Cell Rep 2024; 43:114354. [PMID: 38906147 DOI: 10.1016/j.celrep.2024.114354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 04/24/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024] Open
Abstract
Female mosquitoes engage in blood feeding from their hosts to facilitate egg maturation but cease feeding once a sufficient blood meal has been acquired. Abdominal distention has been proposed as a contributing factor; however, it has also been suggested that there are chemical controls. In this study, we focus on negative chemical regulators of blood feeding, particularly those present in the host blood. Serum derived from animal blood inhibits the feeding of ATP, a phagostimulant of blood feeding in Aedes aegypti. Fibrinopeptide A (FPA), a 16-amino acid peptide cleaved from fibrinogen during blood coagulation, serves as an inhibitory factor in the serum. Our findings suggest that blood-feeding arrest in female mosquitoes is triggered by the detection of FPA in the host blood, which increases as blood coagulation proceeds in the mosquito's midgut, highlighting the role of host-derived substances as negative regulators of mosquito behavior.
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Affiliation(s)
- Chisako Sakuma
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo 105-8461, Japan; Center for Medical Entomology, The Jikei University School of Medicine, Tokyo 105-8461, Japan; Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Hyogo 650-0047, Japan.
| | - Takeo Iwamoto
- Core Research Facilities for Basic Science, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Keiko Masuda
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Osaka 565-0874, Japan
| | - Fumiaki Obata
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Hyogo 650-0047, Japan; Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto 606-8561, Japan
| | - Hirotaka Kanuka
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo 105-8461, Japan; Center for Medical Entomology, The Jikei University School of Medicine, Tokyo 105-8461, Japan.
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5
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Schröder MP, Pfeiffer IPM, Mordhorst S. Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry. Beilstein J Org Chem 2024; 20:1652-1670. [PMID: 39076295 PMCID: PMC11285071 DOI: 10.3762/bjoc.20.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
This review article aims to highlight the role of methyltransferases within the context of ribosomally synthesised and post-translationally modified peptide (RiPP) natural products. Methyltransferases play a pivotal role in the biosynthesis of diverse natural products with unique chemical structures and bioactivities. They are highly chemo-, regio-, and stereoselective allowing methylation at various positions. The different possible acceptor regions in ribosomally synthesised peptides are described in this article. Furthermore, we will discuss the potential application of these methyltransferases as powerful biocatalytic tools in the synthesis of modified peptides and other bioactive compounds. By providing an overview of the various methylation options available, this review is intended to emphasise the biocatalytic potential of RiPP methyltransferases and their impact on the field of natural product chemistry.
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Affiliation(s)
- Maria-Paula Schröder
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Isabel P-M Pfeiffer
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Silja Mordhorst
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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6
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Enninful GN, Kuppusamy R, Tiburu EK, Kumar N, Willcox MDP. Non-canonical amino acid bioincorporation into antimicrobial peptides and its challenges. J Pept Sci 2024; 30:e3560. [PMID: 38262069 DOI: 10.1002/psc.3560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/01/2023] [Accepted: 11/14/2023] [Indexed: 01/25/2024]
Abstract
The rise of antimicrobial resistance and multi-drug resistant pathogens has necessitated explorations for novel antibiotic agents as the discovery of conventional antibiotics is becoming economically less viable and technically more challenging for biopharma. Antimicrobial peptides (AMPs) have emerged as a promising alternative because of their particular mode of action, broad spectrum and difficulty that microbes have in becoming resistant to them. The AMPs bacitracin, gramicidin, polymyxins and daptomycin are currently used clinically. However, their susceptibility to proteolytic degradation, toxicity profile, and complexities in large-scale manufacture have hindered their development. To improve their proteolytic stability, methods such as integrating non-canonical amino acids (ncAAs) into their peptide sequence have been adopted, which also improves their potency and spectrum of action. The benefits of ncAA incorporation have been made possible by solid-phase peptide synthesis. However, this method is not always suitable for commercial production of AMPs because of poor yield, scale-up difficulties, and its non-'green' nature. Bioincorporation of ncAA as a method of integration is an emerging field geared towards tackling the challenges of solid-phase synthesis as a green, cheaper, and scalable alternative for commercialisation of AMPs. This review focusses on the bioincorporation of ncAAs; some challenges associated with the methods are outlined, and notes are given on how to overcome these challenges. The review focusses particularly on addressing two key challenges: AMP cytotoxicity towards microbial cell factories and the uptake of ncAAs that are unfavourable to them. Overcoming these challenges will draw us closer to a greater yield and an environmentally friendly and sustainable approach to make AMPs more druggable.
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Affiliation(s)
| | - Rajesh Kuppusamy
- University of New South Wales, Kensington, New South Wales, Australia
| | | | - Naresh Kumar
- University of New South Wales, Kensington, New South Wales, Australia
| | - Mark D P Willcox
- University of New South Wales, Kensington, New South Wales, Australia
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7
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Li B, Ming D. GATSol, an enhanced predictor of protein solubility through the synergy of 3D structure graph and large language modeling. BMC Bioinformatics 2024; 25:204. [PMID: 38824535 DOI: 10.1186/s12859-024-05820-8] [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: 12/20/2023] [Accepted: 05/29/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Protein solubility is a critically important physicochemical property closely related to protein expression. For example, it is one of the main factors to be considered in the design and production of antibody drugs and a prerequisite for realizing various protein functions. Although several solubility prediction models have emerged in recent years, many of these models are limited to capturing information embedded in one-dimensional amino acid sequences, resulting in unsatisfactory predictive performance. RESULTS In this study, we introduce a novel Graph Attention network-based protein Solubility model, GATSol, which represents the 3D structure of proteins as a protein graph. In addition to the node features of amino acids extracted by the state-of-the-art protein large language model, GATSol utilizes amino acid distance maps generated using the latest AlphaFold technology. Rigorous testing on independent eSOL and the Saccharomyces cerevisiae test datasets has shown that GATSol outperforms most recently introduced models, especially with respect to the coefficient of determination R2, which reaches 0.517 and 0.424, respectively. It outperforms the current state-of-the-art GraphSol by 18.4% on the S. cerevisiae_test set. CONCLUSIONS GATSol captures 3D dimensional features of proteins by building protein graphs, which significantly improves the accuracy of protein solubility prediction. Recent advances in protein structure modeling allow our method to incorporate spatial structure features extracted from predicted structures into the model by relying only on the input of protein sequences, which simplifies the entire graph neural network prediction process, making it more user-friendly and efficient. As a result, GATSol may help prioritize highly soluble proteins, ultimately reducing the cost and effort of experimental work. The source code and data of the GATSol model are freely available at https://github.com/binbinbinv/GATSol .
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Affiliation(s)
- Bin Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing, 211816, Jiangsu, People's Republic of China
| | - Dengming Ming
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing, 211816, Jiangsu, People's Republic of China.
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8
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Tripp A, Braun M, Wieser F, Oberdorfer G, Lechner H. Click, Compute, Create: A Review of Web-based Tools for Enzyme Engineering. Chembiochem 2024:e202400092. [PMID: 38634409 DOI: 10.1002/cbic.202400092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Enzyme engineering, though pivotal across various biotechnological domains, is often plagued by its time-consuming and labor-intensive nature. This review aims to offer an overview of supportive in silico methodologies for this demanding endeavor. Starting from methods to predict protein structures, to classification of their activity and even the discovery of new enzymes we continue with describing tools used to increase thermostability and production yields of selected targets. Subsequently, we discuss computational methods to modulate both, the activity as well as selectivity of enzymes. Last, we present recent approaches based on cutting-edge machine learning methods to redesign enzymes. With exception of the last chapter, there is a strong focus on methods easily accessible via web-interfaces or simple Python-scripts, therefore readily useable for a diverse and broad community.
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Affiliation(s)
- Adrian Tripp
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Markus Braun
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Florian Wieser
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Gustav Oberdorfer
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
- BioTechMed, Graz, Austria
| | - Horst Lechner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
- BioTechMed, Graz, Austria
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9
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Hiroshima Y, Kido R, Kido JI, Bando M, Yoshida K, Murakami A, Shinohara Y. Synthesis of secretory leukocyte protease inhibitor using cell-free protein synthesis system. Odontology 2024:10.1007/s10266-024-00910-8. [PMID: 38502469 DOI: 10.1007/s10266-024-00910-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/07/2024] [Indexed: 03/21/2024]
Abstract
Secretory leukocyte protease inhibitor (SLPI) functions as a protease inhibitor that modulates excessive proteolysis in the body, exhibits broad-spectrum antimicrobial activity, regulates inflammatory responses, and plays an important role in the innate immunity. The purpose of the study was to artificially synthesize a SLPI, an antimicrobial peptide, and investigate its effect on antimicrobial activity against Porphyromonas gingivalis and interleukin-6 (IL-6) production. SLPI protein with a molecular weight of approximately 13 kDa was artificially synthesized using a cell-free protein synthesis (CFPS) system and investigated by western blotting and enzyme-linked immunosorbent assay (ELISA). Disulfide bond isomerase in the protein synthesis mixture increased the amount of SLPI synthesized. The synthesized SLPI (sSLPI) protein was purified and its antimicrobial activity was investigated based on the growth of Porphyromonas gingivalis and bacterial adhesion to oral epithelial cells. The effect of sSLPI on IL-6 production in human periodontal ligament fibroblasts (HPLFs) was examined by ELISA. Our results showed that sSLPI significantly inhibited the growth of Porphyromonas gingivalis and bacterial adhesion to oral epithelial cells and further inhibited IL-6 production by HPLFs. These results suggested that SLPI artificially synthesized using the CFPS system may play a role in the prevention of periodontal diseases through its antimicrobial and anti-inflammatory effects.
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Affiliation(s)
- Yuka Hiroshima
- Department of Oral Microbiology, Tokushima University Graduate School of Biomedical Sciences, 3-18-15, Kuramoto, Tokushima, 770-8504, Japan.
| | - Rie Kido
- Department of Periodontology and Endodontology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Jun-Ichi Kido
- Department of Periodontology and Endodontology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Mika Bando
- Department of Periodontology and Endodontology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Kaya Yoshida
- Department of Oral Healthcare Promotion, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Akikazu Murakami
- Department of Oral Microbiology, Tokushima University Graduate School of Biomedical Sciences, 3-18-15, Kuramoto, Tokushima, 770-8504, Japan
| | - Yasuo Shinohara
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
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10
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Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S, Suzuki H, Kambara F, Fukasawa G, Cooney A, Di Michele L, Elani Y, Matsuura T, Kawano R. Lipid vesicle-based molecular robots. LAB ON A CHIP 2024; 24:996-1029. [PMID: 38239102 PMCID: PMC10898420 DOI: 10.1039/d3lc00860f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.
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Affiliation(s)
- Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoji Iwabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Misa Yamaji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoko Fujita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Harune Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Fumika Kambara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Genki Fukasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Aileen Cooney
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
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11
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Sugii S, Hagino K, Mizuuchi R, Ichihashi N. Cell-free expression of RuBisCO for ATP production in the synthetic cells. Synth Biol (Oxf) 2023; 8:ysad016. [PMID: 38149045 PMCID: PMC10750972 DOI: 10.1093/synbio/ysad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/28/2023] [Accepted: 12/19/2023] [Indexed: 12/28/2023] Open
Abstract
Recent advances in bottom-up synthetic biology have made it possible to reconstitute cellular systems from non-living components, yielding artificial cells with potential applications in industry, medicine and basic research. Although a variety of cellular functions and components have been reconstituted in previous studies, sustained biological energy production remains a challenge. ATP synthesis via ribulose-1,5-diphosphate carboxylase/oxygenase (RuBisCO), a central enzyme in biological CO2 fixation, holds potential as an energy production system, but its feasibility in a cell-free expression system has not yet been tested. In this study, we test RuBisCO expression and its activity-mediated ATP synthesis in a reconstituted Escherichia coli-based cell-free translation system. We then construct a system in which ATP is synthesized by RuBisCO activity in giant vesicles and used as energy for translation reactions. These results represent an advance toward independent energy production in artificial cells. Graphical Abstract.
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Affiliation(s)
| | - Katsumi Hagino
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
| | - Ryo Mizuuchi
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Shinjuku, Tokyo 162-8480, Japan
- JST FOREST, Kawaguchi, Saitama 332-0012, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- College of Arts and Science, the University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Department of Medicine, the University of Tokyo, Bunkyo, Tokyo 113-8654, Japan
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12
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Wang T, Lu Y. Toward Minimal Transcription-Translation Machinery. ACS Synth Biol 2023; 12:3312-3327. [PMID: 37852206 DOI: 10.1021/acssynbio.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
With the advantages of simple genetic composition, low metabolic background, low energy waste, and high genetic stability, genome-reduced strains, as promising functional chassis, have become an intensive direction for constructing potent biosynthesis factories. Herein, an innovative Genome-Reduced strain-based Active Cell-free Easy-to-make-protein (GRACE) system is built as minimal transcription-translation machinery. In this study, two Escherichia coli genome-reduced strains, ΔW3110 and ΔMG1655, with genome reduction of 11.53% and 37.85%, are fused with the cell-free transcription-translation (CFTT) system. The GRACE systems perform better than the corresponding CFTT systems derived from their parental strains in representative valuable applications, such as the expression and solubilization of membrane proteins or protein polymers, biosensing of inorganic or organic molecules based on different principles, and unnatural amino acid embedding. Obviously, the GRACE system has provided a brand-new enabling platform for cell-free transcription-translation basic and applied studies and also would inspire the potential of genome-reduced strains for versatile applications.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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13
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Rolf J, Handke J, Burzinski F, Lütz S, Rosenthal K. Amino acid balancing for the prediction and evaluation of protein concentrations in cell-free protein synthesis systems. Biotechnol Prog 2023; 39:e3373. [PMID: 37408088 DOI: 10.1002/btpr.3373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/31/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Cell-free protein synthesis (CFPS) systems are an attractive method to complement the usual cell-based synthesis of proteins, especially for screening approaches. The literature describes a wide variety of CFPS systems, but their performance is difficult to compare since the reaction components are often used at different concentrations. Therefore, we have developed a calculation tool based on amino acid balancing to evaluate the performance of CFPS by determining the fractional yield as the ratio between theoretically achievable and experimentally achieved protein molar concentration. This tool was applied to a series of experiments from our lab and to various systems described in the literature to identify systems that synthesize proteins very efficiently and those that still have potential for higher yields. The well-established Escherichia coli system showed a high efficiency in the utilization of amino acids, but interestingly, less considered systems, such as those based on Vibrio natriegens or Leishmania tarentolae, also showed exceptional fractional yields of over 70% and 90%, respectively, implying very efficient conversions of amino acids. The methods and tools described here can quickly identify when a system has reached its maximum or has limitations. We believe that this approach will facilitate the evaluation and optimization of existing CFPS systems and provides the basis for the systematic development of new CFPS systems.
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Affiliation(s)
- Jascha Rolf
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
| | - Julian Handke
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
| | - Frank Burzinski
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
| | - Stephan Lütz
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
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14
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Hiroshima Y, Kido JI, Kido R, Yoshida K, Bando M, Kajimoto K, Yumoto H, Shinohara Y. β-defensin 2 synthesized by a cell-free protein synthesis system and encapsulated in liposomes inhibits adhesion of Porphyromonas gingivalis to oral epithelial cells. Odontology 2023; 111:830-838. [PMID: 36745267 DOI: 10.1007/s10266-023-00789-x] [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: 06/27/2022] [Accepted: 01/29/2023] [Indexed: 02/07/2023]
Abstract
β-defensin 2 (BD-2), an antimicrobial peptide (AMP), is expressed by oral epithelial cells and plays an important role in innate immunity of the oral cavity. Cell-free protein synthesis (CFPS) systems have been studied for the synthesis of various proteins, however, the synthesis of BD-2 by a CFPS system has not been extensively explored. Liposomes have been developed as tools for drug delivery. A delivery of liposome-encapsulated AMP to oral epithelium may be useful to prevent oral infectious diseases. In the present study, we investigated the antimicrobial activity of the BD-2 protein, artificially synthesized using a CFPS system and encapsulated in liposomes. BD-2 protein was artificially synthesized using template DNA and a reconstituted CFPS system and was identified by western blotting. Bilayer liposomes were prepared using 1,2-dioleoyl-sn-glycero-3-phospho-choline and 3-sn-phosphatidylcholine from egg yolk. The artificially synthesized BD-2 was encapsulated in liposomes, collected by ultrafiltration, and detected by western blotting. Human oral epithelial cells were cultured with the liposome-encapsulated BD-2 and the concentration of BD-2 in the cell lysate of the culture with the synthesized BD-2 was higher than that of the control cultures. The antimicrobial activity of the synthesized BD-2 was investigated by an adhesion assay of Porphyromonas gingivalis to oral epithelial cells. The artificially synthesized BD-2 and its liposome significantly inhibited adhesion of P. gingivalis to oral epithelial cells. These results suggest that artificially synthesized BD-2 and liposome-encapsulated BD-2 show antimicrobial activity and can potentially play a role in oral healthcare for periodontal diseases.
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Affiliation(s)
- Yuka Hiroshima
- Department of Oral Microbiology, Tokushima University, 3-18-15, Kuramoto, Tokushima, 770-8504, Japan.
| | - Jun-Ichi Kido
- Department of Periodontology and Endodontology, Tokushima University, Tokushima, Japan
| | - Rie Kido
- Department of Periodontology and Endodontology, Tokushima University, Tokushima, Japan
| | - Kaya Yoshida
- Department of Oral Healthcare Education, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Mika Bando
- Department of Periodontology and Endodontology, Tokushima University, Tokushima, Japan
| | - Kazuaki Kajimoto
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Hiromichi Yumoto
- Department of Periodontology and Endodontology, Tokushima University, Tokushima, Japan
| | - Yasuo Shinohara
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
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15
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Yokoyama T, Yamagata Y, Honna S, Mizuno S, Katagiri S, Oi R, Nogi T, Hizukuri Y, Akiyama Y. S2P intramembrane protease RseP degrades small membrane proteins and suppresses the cytotoxicity of intrinsic toxin HokB. mBio 2023; 14:e0108623. [PMID: 37409810 PMCID: PMC10470546 DOI: 10.1128/mbio.01086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/25/2023] [Indexed: 07/07/2023] Open
Abstract
The site2-protease (S2P) family of intramembrane proteases (IMPs) is conserved in all kingdoms of life and cleaves transmembrane proteins within the membrane to regulate and maintain various cellular activities. RseP, an Escherichia coli S2P peptidase, is involved in the regulation of gene expression through the regulated cleavage of the two target membrane proteins (RseA and FecR) and in membrane quality control through the proteolytic elimination of remnant signal peptides. RseP is expected to have additional substrates and to be involved in other cellular processes. Recent studies have shown that cells express small membrane proteins (SMPs; single-spanning membrane proteins of approximately 50-100 amino acid residues) with crucial cellular functions. However, little is known about their metabolism, which affects their functions. This study investigated the possible RseP-catalyzed cleavage of E. coli SMPs based on the apparent similarity of the sizes and structures of SMPs to those of remnant signal peptides. We screened SMPs cleaved by RseP in vivo and in vitro and identified 14 SMPs, including HokB, an endogenous toxin that induces persister formation, as potential substrates. We demonstrated that RseP suppresses the cytotoxicity and biological functions of HokB. The identification of several SMPs as novel potential substrates of RseP provides a clue to a comprehensive understanding of the cellular roles of RseP and other S2P peptidases and highlights a novel aspect of the regulation of SMPs. IMPORTANCE Membrane proteins play an important role in cell activity and survival. Thus, understanding their dynamics, including proteolytic degradation, is crucial. E. coli RseP, an S2P family intramembrane protease, cleaves membrane proteins to regulate gene expression in response to environmental changes and to maintain membrane quality. To identify novel substrates of RseP, we screened small membrane proteins (SMPs), a group of proteins that have recently been shown to have diverse cellular functions, and identified 14 potential substrates. We also showed that RseP suppresses the cytotoxicity of the intrinsic toxin, HokB, an SMP that has been reported to induce persister cell formation, by degrading it. These findings provide new insights into the cellular roles of S2P peptidases and the functional regulation of SMPs.
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Affiliation(s)
- Tatsuhiko Yokoyama
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yutaro Yamagata
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Saisei Honna
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Shinya Mizuno
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Shizuka Katagiri
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Rika Oi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Terukazu Nogi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Yohei Hizukuri
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yoshinori Akiyama
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
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16
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Bains J, Qureshi N, Ceylan B, Wacker A, Schwalbe H. Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function. Nucleic Acids Res 2023; 51:e82. [PMID: 37409574 PMCID: PMC10450168 DOI: 10.1093/nar/gkad574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/27/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Cell-free protein synthesis assays have become a valuable tool to understand transcriptional and translational processes. Here, we established a fluorescence-based coupled in vitro transcription-translation assay as a read-out system to simultaneously quantify mRNA and protein levels. We utilized the well-established quantification of the expression of shifted green fluorescent protein (sGFP) as a read-out of protein levels. In addition, we determined mRNA quantities using a fluorogenic Mango-(IV) RNA aptamer that becomes fluorescent upon binding to the fluorophore thiazole orange (TO). We utilized a Mango-(IV) RNA aptamer system comprising four subsequent Mango-(IV) RNA aptamer elements with improved sensitivity by building Mango arrays. The design of this reporter assay resulted in a sensitive read-out with a high signal-to-noise ratio, allowing us to monitor transcription and translation time courses in cell-free assays with continuous monitoring of fluorescence changes as well as snapshots of the reaction. Furthermore, we applied this dual read-out assay to investigate the function of thiamine-sensing riboswitches thiM and thiC from Escherichia coli and the adenine-sensing riboswitch ASW from Vibrio vulnificus and pbuE from Bacillus subtilis, which represent transcriptional and translational on- and off-riboswitches, respectively. This approach enabled a microplate-based application, a valuable addition to the toolbox for high-throughput screening of riboswitch function.
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Affiliation(s)
- Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
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17
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Godino E, Restrepo Sierra AM, Danelon C. Imaging Flow Cytometry for High-Throughput Phenotyping of Synthetic Cells. ACS Synth Biol 2023. [PMID: 37155828 PMCID: PMC10367129 DOI: 10.1021/acssynbio.3c00074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The reconstitution of basic cellular functions in micrometer-sized liposomes has led to a surge of interest in the construction of synthetic cells. Microscopy and flow cytometry are powerful tools for characterizing biological processes in liposomes with fluorescence readouts. However, applying each method separately leads to a compromise between information-rich imaging by microscopy and statistical population analysis by flow cytometry. To address this shortcoming, we here introduce imaging flow cytometry (IFC) for high-throughput, microscopy-based screening of gene-expressing liposomes in laminar flow. We developed a comprehensive pipeline and analysis toolset based on a commercial IFC instrument and software. About 60 thousands of liposome events were collected per run starting from one microliter of the stock liposome solution. Robust population statistics from individual liposome images was performed based on fluorescence and morphological parameters. This allowed us to quantify complex phenotypes covering a wide range of liposomal states that are relevant for building a synthetic cell. The general applicability, current workflow limitations, and future prospects of IFC in synthetic cell research are finally discussed.
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Affiliation(s)
- Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Ana Maria Restrepo Sierra
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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18
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Hagino K, Ichihashi N. In Vitro Transcription/Translation-Coupled DNA Replication through Partial Regeneration of 20 Aminoacyl-tRNA Synthetases. ACS Synth Biol 2023; 12:1252-1263. [PMID: 37053032 DOI: 10.1021/acssynbio.3c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
The in vitro reconstruction of life-like self-reproducing systems is a major challenge in in vitro synthetic biology. Self-reproduction requires regeneration of all molecules involved in DNA replication, transcription, and translation. This study demonstrated the continuous DNA replication and partial regeneration of major translation factors, 20 aminoacyl-tRNA synthetases (aaRS), in a reconstituted transcription/translation system (PURE system) for the first time. First, we replicated each DNA that encodes one of the 20 aaRSs through aaRS expression from the DNA by serial transfer experiments. Thereafter, we successively increased the number of aaRS genes and achieved simultaneous, continuous replication of DNA that encodes all 20 aaRSs, which comprised approximately half the number of protein factors in the PURE system, except for ribosomes, by employing dialyzed reaction and sequence optimization. This study provides a step-by-step methodology for continuous DNA replication with an increasing number of self-regenerative genes toward self-reproducing artificial systems.
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Affiliation(s)
- Katsumi Hagino
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
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19
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Kido JI, Hiroshima Y, Kido R, Yoshida K, Inagaki Y, Naruishi K, Kajimoto K, Kataoka M, Shinohara Y, Yumoto H. Lipocalin 2, synthesized using a cell-free protein synthesis system and encapsulated into liposomes, inhibits the adhesion of Porphyromonas gingivalis to human oral epithelial cells. J Periodontal Res 2023; 58:262-273. [PMID: 36579753 DOI: 10.1111/jre.13088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND OBJECTIVE Lipocalin 2 (LCN2), a glycoprotein expressed in epithelial cells and leukocytes, has an antibacterial effect and plays a role in innate immunity. The delivery of LCN2 encapsulated in liposomes to oral epithelium may be useful to prevent oral infectious diseases. This study aimed to investigate the inhibitory effect of LCN2, artificially synthesized using a cell-free protein synthesis (CFPS) system, on the adhesion of Porphyromonas gingivalis to oral epithelial cells in order to approach oral healthcare using LCN2. METHODS LCN 2 was synthesized using a CFPS system and assayed by Western blotting, mass spectrometry and enzyme-linked immunosorbent assay (ELISA). The bilayer liposomes were prepared by the spontaneous transfer method using 1,2-dioleoyl-sn-glycero-3 phosphocholine (DOPC), 3-sn-phosphatidylcholine from Egg Yolk (Egg-PC), and 1,2-dioleoyl-sn-glycero-3 phosphoethanolamine (DOPE). The cellular and medium fractions derived from the culture of oral epithelial cells with liposome-encapsulated LCN2 were assayed by Western blotting and ELISA. The effect of the synthesized LCN2 on adhesion of the labeled P. gingivalis to oral epithelial cells was investigated as an evaluation of its antibacterial activity. RESULTS The synthesized LCN2 protein was identified by Western blotting; its amino acid sequence was similar to that of recombinant LCN2 protein. The additions of DOPE and octa-arginine in the outer lipid-layer components of liposome significantly increased the delivery of liposomes to epithelial cells. When oral epithelial cells were cultured with the synthesized and liposome-encapsulated LCN2, LCN2 was identified in the cellular and medium fractions by Western blotting and its concentration in the cellular fraction from the culture with the synthesized LCN2 was significantly higher than that of a template DNA-free protein. The synthesized LCN2 and liposome-encapsulated LCN2 significantly inhibited the adhesion of P. gingivalis to oral epithelial cells compared with template DNA-free protein. CONCLUSION LCN2 was artificially synthesized by a CFPS system, encapsulated in liposomes, and delivered to oral epithelial cells, and demonstrated an antibacterial action against P. gingivalis. This approach may become a useful model for oral healthcare.
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Affiliation(s)
- Jun-Ichi Kido
- Department of Periodontology and Endodontology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Yuka Hiroshima
- Department of Oral Microbiology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Rie Kido
- Department of Periodontology and Endodontology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Kaya Yoshida
- Department of Oral Healthcare Education, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Yuji Inagaki
- Department of Periodontology and Endodontology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Koji Naruishi
- Department of Periodontology and Endodontology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Kazuaki Kajimoto
- Health and Medical Research Institute, National Institute of Advanced Industrial, Science and Technology, Tokushima, Japan
| | - Masatoshi Kataoka
- Health and Medical Research Institute, National Institute of Advanced Industrial, Science and Technology, Tokushima, Japan
| | - Yasuo Shinohara
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Hiromichi Yumoto
- Department of Periodontology and Endodontology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
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20
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Ishii S, Chino H, Ode KL, Kurikawa Y, Ueda HR, Matsuura A, Mizushima N, Itakura E. CCPG1 recognizes endoplasmic reticulum luminal proteins for selective ER-phagy. Mol Biol Cell 2023; 34:ar29. [PMID: 36735498 PMCID: PMC10092646 DOI: 10.1091/mbc.e22-09-0432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The endoplasmic reticulum (ER) is a major cell compartment where protein synthesis, folding, and posttranslational modifications occur with assistance from a wide variety of chaperones and enzymes. Quality control systems selectively eliminate abnormal proteins that accumulate inside the ER due to cellular stresses. ER-phagy, that is, selective autophagy of the ER, is a mechanism that maintains or reestablishes cellular and ER-specific homeostasis through removal of abnormal proteins. However, how ER luminal proteins are recognized by the ER-phagy machinery remains unclear. Here, we applied the aggregation-prone protein, six-repeated islet amyloid polypeptide (6xIAPP), as a model ER-phagy substrate and found that cell cycle progression 1 (CCPG1), which is an ER-phagy receptor, efficiently mediates its degradation via ER-phagy. We also identified prolyl 3-hydroxylase family member 4 (P3H4) as an endogenous cargo of CCPG1-dependent ER-phagy. The ER luminal region of CCPG1 contains several highly conserved regions that we refer to as cargo-interacting regions (CIRs); these interact directly with specific luminal cargos for ER-phagy. Notably, 6xIAPP and P3H4 interact directly with different CIRs. These findings indicate that CCPG1 is a bispecific ER-phagy receptor for ER luminal proteins and the autophagosomal membrane that contributes to the efficient removal of aberrant ER-resident proteins through ER-phagy.
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Affiliation(s)
- Shunsuke Ishii
- Department of Biology, Graduate School of Science and Engineering, Chiba University, Chiba 263-8522, Japan
| | - Haruka Chino
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Tokyo 113-0033, Japan
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshitaka Kurikawa
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Tokyo 113-0033, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-0871, Japan
| | - Akira Matsuura
- Department of Biology, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Tokyo 113-0033, Japan
| | - Eisuke Itakura
- Department of Biology, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
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21
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Godino E, Danelon C. Gene-Directed FtsZ Ring Assembly Generates Constricted Liposomes with Stable Membrane Necks. Adv Biol (Weinh) 2023; 7:e2200172. [PMID: 36593513 DOI: 10.1002/adbi.202200172] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/15/2022] [Indexed: 01/04/2023]
Abstract
Mimicking bacterial cell division in well-defined cell-free systems has the potential to elucidate the minimal set of proteins required for cytoskeletal formation, membrane constriction, and final abscission. Membrane-anchored FtsZ polymers are often regarded as a sufficient system to realize this chain of events. By using purified FtsZ and its membrane-binding protein FtsA or the gain-of-function mutant FtsA* expressed in PURE (Protein synthesis Using Reconstituted Elements) from a DNA template, it is shown in this study that cytoskeletal structures are formed, and yield constricted liposomes exhibiting various morphologies. However, the resulting buds remain attached to the parental liposome by a narrow membrane neck. No division events can be monitored even after long-time tracking by fluorescence microscopy, nor when the osmolarity of the external solution is increased. The results provide evidence that reconstituted FtsA-FtsZ proto-rings coating the membrane necks are too stable to enable abscission. The prospect of combining a DNA-encoded FtsZ system with assisting mechanisms to achieve synthetic cell division is discussed.
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Affiliation(s)
- Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands
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22
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Fromm SA, O'Connor KM, Purdy M, Bhatt PR, Loughran G, Atkins JF, Jomaa A, Mattei S. The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services. Nat Commun 2023; 14:1095. [PMID: 36841832 PMCID: PMC9968351 DOI: 10.1038/s41467-023-36742-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
Our understanding of protein synthesis has been conceptualised around the structure and function of the bacterial ribosome. This complex macromolecular machine is the target of important antimicrobial drugs, an integral line of defence against infectious diseases. Here, we describe how open access to cryo-electron microscopy facilities combined with bespoke user support enabled structural determination of the translating ribosome from Escherichia coli at 1.55 Å resolution. The obtained structures allow for direct determination of the rRNA sequence to identify ribosome polymorphism sites in the E. coli strain used in this study and enable interpretation of the ribosomal active and peripheral sites at unprecedented resolution. This includes scarcely populated chimeric hybrid states of the ribosome engaged in several tRNA translocation steps resolved at ~2 Å resolution. The current map not only improves our understanding of protein synthesis but also allows for more precise structure-based drug design of antibiotics to tackle rising bacterial resistance.
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Affiliation(s)
- Simon A Fromm
- EMBL Imaging Centre, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Kate M O'Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Michael Purdy
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland. .,MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Ahmad Jomaa
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA, USA. .,Centre for Cell and Membrane Physiology, University of Virginia, Charlottesville, VA, USA.
| | - Simone Mattei
- EMBL Imaging Centre, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany. .,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany.
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23
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Role of ribosome recycling factor in natural termination and translational coupling as a ribosome releasing factor. PLoS One 2023; 18:e0282091. [PMID: 36827443 PMCID: PMC9955659 DOI: 10.1371/journal.pone.0282091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/07/2023] [Indexed: 02/26/2023] Open
Abstract
The role of ribosome recycling factor (RRF) of E. coli was studied in vivo and in vitro. We used the translational coupling without the Shine-Dalgarno sequence of downstream ORF (d-ORF) as a model system of the RRF action in natural termination of protein synthesis. For the in vivo studies we used the translational coupling by the adjacent coat and lysis genes of RNA phage GA sharing the termination and initiation (UAAUG) and temperature sensitive RRF. The d-ORF translation was measured by the expression of the reporter lacZ gene connected to the 5'-terminal part of the lysis gene. The results showed that more ribosomes which finished upstream ORF (u-ORF) reading were used for downstream reading when RRF was inactivated. The in vitro translational coupling studies with 027mRNA having the junction sequence UAAUG with wild-type RRF were carried out with measuring amino acids incorporation. The results showed that ribosomes released by RRF read downstream from AUG of UAAUG. In the absence of RRF, ribosomes read downstream in frame with UAA. These in vivo and in vitro studies indicate that RRF releases ribosomes from mRNA at the termination codon of u-ORF. Furthermore, the non-dissociable ribosomes read downstream from AUG of UAAUG with RRF in vitro. This suggests that complete ribosomal splitting is not required for ribosome release by RRF in translational coupling. The data are consistent with the interpretation that RRF functions mostly as a ribosome releasing factor rather than ribosome splitting factor. Additionally, the in vivo studies showed that short (less than 5 codons) u-ORF inhibited d-ORF reading by ribosomes finishing u-ORF reading, suggesting that the termination process in short ORF is not similar to that in normal ORF. This means that all the preexisting studies on RRF with short mRNA may not represent what goes on in natural termination step.
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Wada A, Ueta M, Wada C. The Discovery of Ribosomal Protein bL31 from Escherichia coli: A Long Story Revisited. Int J Mol Sci 2023; 24:ijms24043445. [PMID: 36834855 PMCID: PMC9966373 DOI: 10.3390/ijms24043445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Ribosomal protein bL31 in Escherichia coli was initially detected as a short form (62 amino acids) using Kaltschmidt and Wittmann's two-dimensional polyacrylamide gel electrophoresis (2D PAGE), but the intact form (70 amino acids) was subsequently identified by means of Wada's improved radical-free and highly reducing (RFHR) 2D PAGE, which was consistent with the analysis of its encoding gene rpmE. Ribosomes routinely prepared from the K12 wild-type strain contained both forms of bL31. ΔompT cells, which lack protease 7, only contained intact bL31, suggesting that protease 7 cleaves intact bL31 and generates short bL31 during ribosome preparation from wild-type cells. Intact bL31 was required for subunit association, and its eight cleaved C-terminal amino acids contributed to this function. 70S ribosomes protected bL31 from cleavage by protease 7, but free 50S did not. In vitro translation was assayed using three systems. The translational activities of wild-type and ΔrpmE ribosomes were 20% and 40% lower than those of ΔompT ribosomes, which contained one copy of intact bL31. The deletion of bL31 reduces cell growth. A structural analysis predicted that bL31 spans the 30S and 50S subunits, consistent with its functions in 70S association and translation. It is important to re-analyze in vitro translation with ribosomes containing only intact bL31.
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Lee K, Willi JA, Cho N, Kim I, Jewett MC, Lee J. Cell-free Biosynthesis of Peptidomimetics. BIOTECHNOL BIOPROC E 2023; 28:1-17. [PMID: 36778039 PMCID: PMC9896473 DOI: 10.1007/s12257-022-0268-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/16/2022] [Accepted: 11/13/2022] [Indexed: 02/05/2023]
Abstract
A wide variety of peptidomimetics (peptide analogs) possessing innovative biological functions have been brought forth as therapeutic candidates through cell-free protein synthesis (CFPS) systems. A key feature of these peptidomimetic drugs is the use of non-canonical amino acid building blocks with diverse biochemical properties that expand functional diversity. Here, we summarize recent technologies leveraging CFPS platforms to expand the reach of peptidomimetics drugs. We also offer perspectives on engineering the translational machinery that may open new opportunities for expanding genetically encoded chemistry to transform drug discovery practice beyond traditional boundaries.
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Affiliation(s)
- Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
| | - Jessica A. Willi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
| | - Inseon Kim
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208 USA
| | - Joongoo Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
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26
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Song Y, Wang Y, Yan S, Nakamura K, Kikukawa T, Ayabe T, Aizawa T. Efficient recombinant production of mouse-derived cryptdin family peptides by a novel facilitation strategy for inclusion body formation. Microb Cell Fact 2023; 22:9. [PMID: 36635697 PMCID: PMC9838031 DOI: 10.1186/s12934-023-02016-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/01/2023] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND A number of antimicrobial peptides (AMPs) hold promise as new drugs owing to their potent bactericidal activity and because they are often refractory to the development of drug resistance. Cryptdins (Crps) are a family of antimicrobial peptides found in the small intestine of mice, comprising six isoforms containing three sets of disulfide bonds. Although Crp4 is actively being investigated, there have been few studies to date on the other Crp isoforms. A prerequisite for detailed characterization of the other Crp isoforms is establishment of efficient sample preparation methods. RESULTS To avoid degradation during recombinant expression of Crps in E. coli, co-expression of Crps with the aggregation-prone protein human α-lactalbumin (HLA) was used to promote the formation of stable inclusion bodies. Using this method, the production of Crp4 and Crp6 by the BL21 strain was effective, but the expression of other Crp isoforms was not as efficient. The results of a cell-free system study suggested that Crps were degraded, even though a substantial amounts of Crps were synthesized. Therefore, using the Origami™ B strain, we were able to significantly increase the expression efficiency of Crps by promoting the formation of erroneous intermolecular disulfide bonds between HLA and Crps, thereby promoting protein aggregation and inclusion body formation, which prevented degradation. The various Crp isoforms were successfully refolded in vitro and purified using reversed-phase HPLC. In addition, the yield was further improved by deformylation of formyl-Crps. We measured the antibacterial activity of Crps against both Gram-positive and Gram-negative bacteria. Each Crp isoform exhibited a completely different trend in antimicrobial activity, although conformational analysis by circular dichroism did not reveal any significant steric differences. CONCLUSION In this study, we established a novel and efficient method for the production of the cryptdin family of cysteine-containing antimicrobial peptides. Additionally, we found that there were notable differences in the antibacterial activities of the various Crp family members. The expression system established in this study is expected to provide new insights regarding the mechanisms underlying the different antibacterial activities of the Crp family of peptides.
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Affiliation(s)
- Yuchi Song
- grid.39158.360000 0001 2173 7691Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Yi Wang
- grid.39158.360000 0001 2173 7691Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Shaonan Yan
- grid.39158.360000 0001 2173 7691Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Kiminori Nakamura
- grid.39158.360000 0001 2173 7691Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Takashi Kikukawa
- grid.39158.360000 0001 2173 7691Laboratory of Biological Information Analysis Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Tokiyoshi Ayabe
- grid.39158.360000 0001 2173 7691Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Tomoyasu Aizawa
- grid.39158.360000 0001 2173 7691Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
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Yue K, Li Y, Cao M, Shen L, Gu J, Kai L. Bottom-Up Synthetic Biology Using Cell-Free Protein Synthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:1-20. [PMID: 37526707 DOI: 10.1007/10_2023_232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Technical advances in biotechnology have greatly accelerated the development of bottom-up synthetic biology. Unlike top-down approaches, bottom-up synthetic biology focuses on the construction of a minimal cell from scratch and the application of these principles to solve challenges. Cell-free protein synthesis (CFPS) systems provide minimal machinery for transcription and translation, from either a fractionated cell lysate or individual purified protein elements, thus speeding up the development of synthetic cell projects. In this review, we trace the history of the cell-free technique back to the first in vitro fermentation experiment using yeast cell lysate. Furthermore, we summarized progresses of individual cell mimicry modules, such as compartmentalization, gene expression regulation, energy regeneration and metabolism, growth and division, communication, and motility. Finally, current challenges and future perspectives on the field are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mengjiao Cao
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lulu Shen
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingsheng Gu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
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28
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Choi YN, Cho N, Lee K, Gwon DA, Lee JW, Lee J. Programmable Synthesis of Biobased Materials Using Cell-Free Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203433. [PMID: 36108274 DOI: 10.1002/adma.202203433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.
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Affiliation(s)
- Yun-Nam Choi
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joongoo Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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29
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Sánchez-Costa M, López-Gallego F. Solid-Phase Cell-Free Protein Synthesis and Its Applications in Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:21-46. [PMID: 37306703 DOI: 10.1007/10_2023_226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free systems for the in vitro production of proteins have revolutionized the synthetic biology field. In the last decade, this technology is gaining momentum in molecular biology, biotechnology, biomedicine and even education. Materials science has burst into the field of in vitro protein synthesis to empower the value of existing tools and expand its applications. In this sense, the combination of solid materials (normally functionalized with different biomacromolecules) together with cell-free components has made this technology more versatile and robust. In this chapter, we discuss the combination of solid materials with DNA and transcription-translation machinery to synthesize proteins within compartments, to immobilize and purify in situ the nascent protein, to transcribe and transduce DNAs immobilized on solid surfaces, and the combination of all or some of these strategies.
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Affiliation(s)
- Mercedes Sánchez-Costa
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain.
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30
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Mermans D, Nicolaus F, Baygin A, von Heijne G. Cotranslational folding of human growth hormone in vitro and in Escherichia coli. FEBS Lett 2022; 597:1355-1362. [PMID: 36520514 DOI: 10.1002/1873-3468.14562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/01/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Human growth hormone (hGH) is a four-helix bundle protein of considerable pharmacological interest. Recombinant hGH is produced in bacteria, yet little is known about its folding during expression in Escherichia coli. We have studied the cotranslational folding of hGH using force profile analysis (FPA), both during in vitro translation in the absence and presence of the chaperone trigger factor (TF), and when expressed in E. coli. We find that the main folding transition starts before hGH is completely released from the ribosome, and that it can interact with TF and possibly other chaperones.
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Affiliation(s)
- Daphne Mermans
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Felix Nicolaus
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Aysel Baygin
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Sweden.,Science for Life Laboratory Stockholm University, Solna, Sweden
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31
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Rational Strategy for Designing Peptidomimetic Small Molecules Based on Cyclic Peptides Targeting Protein-Protein Interaction between CTLA-4 and B7-1. Pharmaceuticals (Basel) 2022; 15:ph15121506. [PMID: 36558957 PMCID: PMC9784018 DOI: 10.3390/ph15121506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/07/2022] Open
Abstract
Currently, various pharmaceutical modalities are being developed rapidly. Targeting protein-protein interactions (PPIs) is an important objective in such development. Cyclic peptides, because they have good specificity and activity, have been attracting much attention as an alternative to antibody drugs. However, cyclic peptides involve some difficulties, such as oral availability and cell permeability. Therefore, while small-molecule drugs still present many benefits, the screening of functional small-molecule compounds targeting PPIs requires a great deal of time and effort, including structural analysis of targets and hits. In this study, we investigated a rational two-step strategy to design small-molecule compounds targeting PPIs. First, we obtained inhibitory cyclic peptides that bind to cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) by ribosomal display using PUREfrex® (PUREfrex®RD) to get structure-activity relation (SAR) information. Based on that information, we converted cyclic peptides to small molecules using PepMetics® scaffolds that can mimic the α-helix or β-turn of the peptide. Finally, we succeeded in generating small-molecule compounds with good IC50 (single-digit μM values) against CTLA-4. This strategy is expected to be a useful approach for small-molecule design targeting PPIs, even without having structural information such as that associated with X-ray crystal structures.
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32
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Chauhan G, Norred SE, Dabbs RM, Caveney PM, George JKV, Collier CP, Simpson ML, Abel SM. Crowding-Induced Spatial Organization of Gene Expression in Cell-Sized Vesicles. ACS Synth Biol 2022; 11:3733-3742. [PMID: 36260840 DOI: 10.1021/acssynbio.2c00336] [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] [Indexed: 01/27/2023]
Abstract
Cell-free protein synthesis is an important tool for studying gene expression and harnessing it for applications. In cells, gene expression is regulated in part by the spatial organization of transcription and translation. Unfortunately, current cell-free approaches are unable to control the organization of molecular components needed for gene expression, which limits the ability to probe and utilize its effects. Here, we show, using complementary computational and experimental approaches, that macromolecular crowding can be used to control the spatial organization and translational efficiency of gene expression in cell-sized vesicles. Computer simulations and imaging experiments reveal that, as crowding is increased, DNA plasmids become localized at the inner surface of vesicles. Ribosomes, in contrast, remain uniformly distributed, demonstrating that crowding can be used to differentially organize components of gene expression. We further carried out cell-free protein synthesis reactions in cell-sized vesicles and quantified mRNA and protein abundance. At sufficiently high levels of crowding, we observed localization of mRNA near vesicle surfaces, a decrease in translational efficiency and protein abundance, and anomalous scaling of protein abundance as a function of vesicle size. These results are consistent with high levels of crowding causing altered spatial organization and slower diffusion. Our work demonstrates a straightforward way to control the organization of gene expression in cell-sized vesicles and provides insight into the spatial regulation of gene expression in cells.
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Affiliation(s)
- Gaurav Chauhan
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee37996, United States
| | - S Elizabeth Norred
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Knoxville, Tennessee37996, United States
| | - Rosemary M Dabbs
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Knoxville, Tennessee37996, United States
| | - Patrick M Caveney
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Knoxville, Tennessee37996, United States
| | - John K Vincent George
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Knoxville, Tennessee37996, United States
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Michael L Simpson
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Knoxville, Tennessee37996, United States
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee37996, United States
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33
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Stano P. Commentary: Rapid and facile preparation of giant vesicles by the droplet transfer method for artificial cell construction. Front Bioeng Biotechnol 2022; 10:1037809. [PMID: 36312559 PMCID: PMC9614326 DOI: 10.3389/fbioe.2022.1037809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/26/2022] [Indexed: 11/15/2022] Open
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34
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Ramírez Rojas AA, Swidah R, Schindler D. Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges. Front Bioeng Biotechnol 2022; 10:982975. [PMID: 36185425 PMCID: PMC9523148 DOI: 10.3389/fbioe.2022.982975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
Microbial diversity is magnificent and essential to almost all life on Earth. Microbes are an essential part of every human, allowing us to utilize otherwise inaccessible resources. It is no surprise that humans started, initially unconsciously, domesticating microbes for food production: one may call this microbial domestication 1.0. Sourdough bread is just one of the miracles performed by microbial fermentation, allowing extraction of more nutrients from flour and at the same time creating a fluffy and delicious loaf. There are a broad range of products the production of which requires fermentation such as chocolate, cheese, coffee and vinegar. Eventually, with the rise of microscopy, humans became aware of microbial life. Today our knowledge and technological advances allow us to genetically engineer microbes - one may call this microbial domestication 2.0. Synthetic biology and microbial chassis adaptation allow us to tackle current and future food challenges. One of the most apparent challenges is the limited space on Earth available for agriculture and its major tolls on the environment through use of pesticides and the replacement of ecosystems with monocultures. Further challenges include transport and packaging, exacerbated by the 24/7 on-demand mentality of many customers. Synthetic biology already tackles multiple food challenges and will be able to tackle many future food challenges. In this perspective article, we highlight recent microbial synthetic biology research to address future food challenges. We further give a perspective on how synthetic biology tools may teach old microbes new tricks, and what standardized microbial domestication could look like.
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35
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Cui Y, Chen X, Wang Z, Lu Y. Cell-Free PURE System: Evolution and Achievements. BIODESIGN RESEARCH 2022; 2022:9847014. [PMID: 37850137 PMCID: PMC10521753 DOI: 10.34133/2022/9847014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/16/2022] [Indexed: 10/19/2023] Open
Abstract
The cell-free protein synthesis (CFPS) system, as a technical core of synthetic biology, can simulate the transcription and translation process in an in vitro open environment without a complete living cell. It has been widely used in basic and applied research fields because of its advanced engineering features in flexibility and controllability. Compared to a typical crude extract-based CFPS system, due to defined and customizable components and lacking protein-degrading enzymes, the protein synthesis using recombinant elements (PURE) system draws great attention. This review first discusses the elemental composition of the PURE system. Then, the design and preparation of functional proteins for the PURE system, especially the critical ribosome, were examined. Furthermore, we trace the evolving development of the PURE system in versatile areas, including prototyping, synthesis of unnatural proteins, peptides and complex proteins, and biosensors. Finally, as a state-of-the-art engineering strategy, this review analyzes the opportunities and challenges faced by the PURE system in future scientific research and diverse applications.
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Affiliation(s)
- Yi Cui
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- College of Life Sciences, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Xinjie Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ze Wang
- College of Life Sciences, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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36
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Imaizumi Y, Takanuki K, Miyake T, Takemoto M, Hirata K, Hirose M, Oi R, Kobayashi T, Miyoshi K, Aruga R, Yokoyama T, Katagiri S, Matsuura H, Iwasaki K, Kato T, Kaneko MK, Kato Y, Tajiri M, Akashi S, Nureki O, Hizukuri Y, Akiyama Y, Nogi T. Mechanistic insights into intramembrane proteolysis by E. coli site-2 protease homolog RseP. SCIENCE ADVANCES 2022; 8:eabp9011. [PMID: 36001659 PMCID: PMC9401612 DOI: 10.1126/sciadv.abp9011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/01/2022] [Indexed: 05/31/2023]
Abstract
Site-2 proteases are a conserved family of intramembrane proteases that cleave transmembrane substrates to regulate signal transduction and maintain proteostasis. Here, we elucidated crystal structures of inhibitor-bound forms of bacterial site-2 proteases including Escherichia coli RseP. Structure-based chemical modification and cross-linking experiments indicated that the RseP domains surrounding the active center undergo conformational changes to expose the substrate-binding site, suggesting that RseP has a gating mechanism to regulate substrate entry. Furthermore, mutational analysis suggests that a conserved electrostatic linkage between the transmembrane and peripheral membrane-associated domains mediates the conformational changes. In vivo cleavage assays also support that the substrate transmembrane helix is unwound by strand addition to the intramembrane β sheet of RseP and is clamped by a conserved asparagine residue at the active center for efficient cleavage. This mechanism underlying the substrate binding, i.e., unwinding and clamping, appears common across distinct families of intramembrane proteases that cleave transmembrane segments.
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Affiliation(s)
- Yuki Imaizumi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kazunori Takanuki
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takuya Miyake
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Mizuki Takemoto
- Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kunio Hirata
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mika Hirose
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Rika Oi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tatsuya Kobayashi
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kenichi Miyoshi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Rie Aruga
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tatsuhiko Yokoyama
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shizuka Katagiri
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hiroaki Matsuura
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kenji Iwasaki
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mika K. Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Sendai, Miyagi 980-8575, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Sendai, Miyagi 980-8575, Japan
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Sendai, Miyagi 980-8575, Japan
| | - Michiko Tajiri
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Osamu Nureki
- Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yohei Hizukuri
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshinori Akiyama
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Terukazu Nogi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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37
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Rolf J, Ngo ACR, Lütz S, Tischler D, Rosenthal K. Cell-Free Protein Synthesis for the Screening of Novel Azoreductases and Their Preferred Electron Donor. Chembiochem 2022; 23:e202200121. [PMID: 35593146 PMCID: PMC9401864 DOI: 10.1002/cbic.202200121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/19/2022] [Indexed: 11/26/2022]
Abstract
Azoreductases are potent biocatalysts for the cleavage of azo bonds. Various gene sequences coding for potential azoreductases are available in databases, but many of their gene products are still uncharacterized. To avoid the laborious heterologous expression in a host organism, we developed a screening approach involving cell-free protein synthesis (CFPS) combined with a colorimetric activity assay, which allows the parallel screening of putative azoreductases in a short time. First, we evaluated different CFPS systems and optimized the synthesis conditions of a model azoreductase. With the findings obtained, 10 azoreductases, half of them undescribed so far, were screened for their ability to degrade the azo dye methyl red. All novel enzymes catalyzed the degradation of methyl red and can therefore be referred to as azoreductases. In addition, all enzymes degraded the more complex and bulkier azo dye Brilliant Black and four of them also showed the ability to reduce p-benzoquinone. NADH was the preferred electron donor for the most enzymes, although the synthetic nicotinamide co-substrate analogue 1-benzyl-1,4-dihydronicotinamide (BNAH) was also accepted by all active azoreductases. This screening approach allows accelerated identification of potential biocatalysts for various applications.
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Affiliation(s)
- Jascha Rolf
- Department of Biochemical and Chemical EngineeringChair for Bioprocess EngineeringTU Dortmund UniversityEmil-Figge-Str. 6644227DortmundGermany
| | - Anna Christina Reyes Ngo
- Microbial BiotechnologyFaculty of Biology and BiotechnologyRuhr-Universität BochumUniversitätsstr. 15044780BochumGermany
| | - Stephan Lütz
- Department of Biochemical and Chemical EngineeringChair for Bioprocess EngineeringTU Dortmund UniversityEmil-Figge-Str. 6644227DortmundGermany
| | - Dirk Tischler
- Microbial BiotechnologyFaculty of Biology and BiotechnologyRuhr-Universität BochumUniversitätsstr. 15044780BochumGermany
| | - Katrin Rosenthal
- Department of Biochemical and Chemical EngineeringChair for Bioprocess EngineeringTU Dortmund UniversityEmil-Figge-Str. 6644227DortmundGermany
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38
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Godino E, Doerr A, Danelon C. Min waves without MinC can pattern FtsA-anchored FtsZ filaments on model membranes. Commun Biol 2022; 5:675. [PMID: 35798943 PMCID: PMC9262947 DOI: 10.1038/s42003-022-03640-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/28/2022] [Indexed: 11/14/2022] Open
Abstract
Although the essential proteins that drive bacterial cytokinesis have been identified, the precise mechanisms by which they dynamically interact to enable symmetrical division are largely unknown. In Escherichia coli, cell division begins with the formation of a proto-ring composed of FtsZ and its membrane-tethering proteins FtsA and ZipA. In the broadly proposed molecular scenario for ring positioning, Min waves composed of MinD and MinE distribute the FtsZ-polymerization inhibitor MinC away from mid-cell, where the Z-ring can form. Therefore, MinC is believed to be an essential element connecting the Min and FtsZ subsystems. Here, by combining cell-free protein synthesis with planar lipid membranes and microdroplets, we demonstrate that MinDE drive the formation of dynamic, antiphase patterns of FtsA-anchored FtsZ filaments even in the absence of MinC. These results suggest that Z-ring positioning may be achieved with a more minimal set of proteins than previously envisaged, providing a fresh perspective about synthetic cell division. Cell-free protein synthesis of bacterial cytokinesis factors reveals that MinDE surface waves regulate FtsA-anchored FtsZ filaments in time and space independently of MinC.
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Affiliation(s)
- Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Anne Doerr
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands.
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39
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Jew K, Smith PEJ, So B, Kasman J, Oza JP, Black MW. Characterizing and Improving pET Vectors for Cell-free Expression. Front Bioeng Biotechnol 2022; 10:895069. [PMID: 35814024 PMCID: PMC9259831 DOI: 10.3389/fbioe.2022.895069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/26/2022] [Indexed: 11/15/2022] Open
Abstract
Cell-free protein synthesis (CFPS) is an in vitro process that enables diverse applications in research, biomanufacturing, point-of-care diagnostics, therapeutics, and education using minimal laboratory equipment and reagents. One of the major limitations of CFPS implementation is its sensitivity to plasmid type. Specifically, plasmid templates based on commonly used vector backbones such as the pET series of bacterial expression vectors result in the inferior production of proteins. To overcome this limitation, we have evaluated the effect of expression cassette elements present in the pET30 vector on protein production across three different CFPS systems: NEBExpress, PURExpress, and CFAI-based E. coli extracts. Through the systematic elimination of genetic elements within the pET30 vector, we have identified elements that are responsible for the poor performance of pET30 vectors in the various CFPS systems. As a result, we demonstrate that through the removal of the lac operator (lacO) and N-terminal tags included in the vector backbone sequence, a pET vector can support high titers of protein expression when using extract-based CFPS systems. This work provides two key advances for the research community: 1) identification of vector sequence elements that affect robust production of proteins; 2) evaluation of expression across three unique CFPS systems including CFAI extracts, NEBexpress, and PURExpress. We anticipate that this work will improve access to CFPS by enabling researchers to choose the correct expression backbone within the context of their preferred expression system.
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Affiliation(s)
- Kara Jew
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Philip E. J. Smith
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Byungcheol So
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Jillian Kasman
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Javin P. Oza
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Michael W. Black
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, United States
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40
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McGaw C, Garrity AJ, Munoz GZ, Haswell JR, Sengupta S, Keston-Smith E, Hunnewell P, Ornstein A, Bose M, Wessells Q, Jakimo N, Yan P, Zhang H, Alfonse LE, Ziblat R, Carte JM, Lu WC, Cerchione D, Hilbert B, Sothiselvam S, Yan WX, Cheng DR, Scott DA, DiTommaso T, Chong S. Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing. Nat Commun 2022; 13:2833. [PMID: 35595757 PMCID: PMC9122993 DOI: 10.1038/s41467-022-30465-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/03/2022] [Indexed: 12/11/2022] Open
Abstract
The CRISPR-Cas type V-I is a family of Cas12i-containing programmable nuclease systems guided by a short crRNA without requirement for a tracrRNA. Here we present an engineered Type V-I CRISPR system (Cas12i), ABR-001, which utilizes a tracr-less guide RNA. The compact Cas12i effector is capable of self-processing pre-crRNA and cleaving dsDNA targets, which facilitates versatile delivery options and multiplexing, respectively. We apply an unbiased mutational scanning approach to enhance initially low editing activity of Cas12i2. The engineered variant, ABR-001, exhibits broad genome editing capability in human cell lines, primary T cells, and CD34+ hematopoietic stem and progenitor cells, with both robust efficiency and high specificity. In addition, ABR-001 achieves a high level of genome editing when delivered via AAV vector to HEK293T cells. This work establishes ABR-001 as a versatile, specific, and high-performance platform for ex vivo and in vivo gene therapy.
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Affiliation(s)
- Colin McGaw
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Anthony J Garrity
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Gabrielle Z Munoz
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Jeffrey R Haswell
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Sejuti Sengupta
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Elise Keston-Smith
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | | | - Alexa Ornstein
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Mishti Bose
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Quinton Wessells
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Noah Jakimo
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Paul Yan
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Huaibin Zhang
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Lauren E Alfonse
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Roy Ziblat
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Jason M Carte
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Wei-Cheng Lu
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Derek Cerchione
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Brendan Hilbert
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | | | - Winston X Yan
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - David R Cheng
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - David A Scott
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
| | - Tia DiTommaso
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA.
| | - Shaorong Chong
- Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500, Cambridge, MA, USA
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41
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Li J, Tang M, Qi H. Codon-Reduced Protein Synthesis With Manipulating tRNA Components in Cell-Free System. Front Bioeng Biotechnol 2022; 10:891808. [PMID: 35646841 PMCID: PMC9136035 DOI: 10.3389/fbioe.2022.891808] [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: 03/08/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Manipulating transfer RNAs (tRNAs) for emancipating sense codons to simplify genetic codons in a cell-free protein synthesis (CFPS) system can offer more flexibility and controllability. Here, we provide an overview of the tRNA complement protein synthesis system construction in the tRNA-depleted Protein synthesis Using purified Recombinant Elements (PURE) system or S30 extract. These designed polypeptide coding sequences reduce the genetic codon and contain only a single tRNA corresponding to a single amino acid in this presented system. Strategies for removing tRNAs from cell lysates and synthesizing tRNAs in vivo/vitro are summarized and discussed in detail. Furthermore, we point out the trend toward a minimized genetic codon for reducing codon redundancy by manipulating tRNAs in the different proteins. It is hoped that the tRNA complement protein synthesis system can facilitate the construction of minimal cells and expand the biomedical application scope of synthetic biology.
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Affiliation(s)
- Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Mengtong Tang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- *Correspondence: Hao Qi,
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42
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Thakur M, Breger JC, Susumu K, Oh E, Spangler JR, Medintz IL, Walper SA, Ellis GA. Self-assembled nanoparticle-enzyme aggregates enhance functional protein production in pure transcription-translation systems. PLoS One 2022; 17:e0265274. [PMID: 35298538 PMCID: PMC8929567 DOI: 10.1371/journal.pone.0265274] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/27/2022] [Indexed: 11/19/2022] Open
Abstract
Cell-free protein synthesis systems (CFPS) utilize cellular transcription and translation (TX-TL) machinery to synthesize proteins in vitro. These systems are useful for multiple applications including production of difficult proteins, as high-throughput tools for genetic circuit screening, and as systems for biosensor development. Though rapidly evolving, CFPS suffer from some disadvantages such as limited reaction rates due to longer diffusion times, significant cost per assay when using commercially sourced materials, and reduced reagent stability over prolonged periods. To address some of these challenges, we conducted a series of proof-of-concept experiments to demonstrate enhancement of CFPS productivity via nanoparticle assembly driven nanoaggregation of its constituent proteins. We combined a commercially available CFPS that utilizes purified polyhistidine-tagged (His-tag) TX-TL machinery with CdSe/CdS/ZnS core/shell/shell quantum dots (QDs) known to readily coordinate His-tagged proteins in an oriented fashion. We show that nanoparticle scaffolding of the CFPS cross-links the QDs into nanoaggregate structures while enhancing the production of functional recombinant super-folder green fluorescent protein and phosphotriesterase, an organophosphate hydrolase; the latter by up to 12-fold. This enhancement, which occurs by an undetermined mechanism, has the potential to improve CFPS in general and specifically CFPS-based biosensors (faster response time) while also enabling rapid detoxification/bioremediation through point-of-concern synthesis of similar catalytic enzymes. We further show that such nanoaggregates improve production in diluted CFPS reactions, which can help to save money and extend the amount of these costly reagents. The results are discussed in the context of what may contribute mechanistically to the enhancement and how this can be applied to other CFPS application scenarios.
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Affiliation(s)
- Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
- College of Science, George Mason University, Fairfax, Virginia, United States of America
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
- Jacobs Corporation, Dallas, Texas, United States of America
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Joseph R. Spangler
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
- * E-mail:
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43
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Tabuchi T, Yokobayashi Y. High-throughput screening of cell-free riboswitches by fluorescence-activated droplet sorting. Nucleic Acids Res 2022; 50:3535-3550. [PMID: 35253887 PMCID: PMC8989549 DOI: 10.1093/nar/gkac152] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 11/14/2022] Open
Abstract
Cell-free systems that display complex functions without using living cells are emerging as new platforms to test our understanding of biological systems as well as for practical applications such as biosensors and biomanufacturing. Those that use cell-free protein synthesis (CFPS) systems to enable genetically programmed protein synthesis have relied on genetic regulatory components found or engineered in living cells. However, biological constraints such as cell permeability, metabolic stability, and toxicity of signaling molecules prevent development of cell-free devices using living cells even if cell-free systems are not subject to such constraints. Efforts to engineer regulatory components directly in CFPS systems thus far have been based on low-throughput experimental approaches, limiting the availability of basic components to build cell-free systems with diverse functions. Here, we report a high-throughput screening method to engineer cell-free riboswitches that respond to small molecules. Droplet-sorting of riboswitch variants in a CFPS system rapidly identified cell-free riboswitches that respond to compounds that are not amenable to bacterial screening methods. Finally, we used a histamine riboswitch to demonstrate chemical communication between cell-sized droplets.
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Affiliation(s)
- Takeshi Tabuchi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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44
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Blackholly LR, Harris NJ, Findlay HE, Booth PJ. Cell-Free Expression to Probe Co-Translational Insertion of an Alpha Helical Membrane Protein. Front Mol Biosci 2022; 9:795212. [PMID: 35187078 PMCID: PMC8847741 DOI: 10.3389/fmolb.2022.795212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/11/2022] [Indexed: 01/23/2023] Open
Abstract
The majority of alpha helical membrane proteins fold co-translationally during their synthesis on the ribosome. In contrast, most mechanistic folding studies address refolding of full-length proteins from artificially induced denatured states that are far removed from the natural co-translational process. Cell-free translation of membrane proteins is emerging as a useful tool to address folding during translation by a ribosome. We summarise the benefits of this approach and show how it can be successfully extended to a membrane protein with a complex topology. The bacterial leucine transporter, LeuT can be synthesised and inserted into lipid membranes using a variety of in vitro transcription translation systems. Unlike major facilitator superfamily transporters, where changes in lipids can optimise the amount of correctly inserted protein, LeuT insertion yields are much less dependent on the lipid composition. The presence of a bacterial translocon either in native membrane extracts or in reconstituted membranes also has little influence on the yield of LeuT incorporated into the lipid membrane, except at high reconstitution concentrations. LeuT is considered a paradigm for neurotransmitter transporters and possesses a knotted structure that is characteristic of this transporter family. This work provides a method in which to probe the formation of a protein as the polypeptide chain is being synthesised on a ribosome and inserting into lipids. We show that in comparison with the simpler major facilitator transporter structures, LeuT inserts less efficiently into membranes when synthesised cell-free, suggesting that more of the protein aggregates, likely as a result of the challenging formation of the knotted topology in the membrane.
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Affiliation(s)
| | | | | | - Paula J. Booth
- Department of Chemistry, King’s College London, London, United Kingdom
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45
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Gonzales D, Yandrapalli N, Robinson T, Zechner C, Tang TYD. Cell-Free Gene Expression Dynamics in Synthetic Cell Populations. ACS Synth Biol 2022; 11:205-215. [PMID: 35057626 PMCID: PMC8787815 DOI: 10.1021/acssynbio.1c00376] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Indexed: 11/29/2022]
Abstract
The ability to build synthetic cellular populations from the bottom-up provides the groundwork to realize minimal living tissues comprising single cells which can communicate and bridge scales into multicellular systems. Engineered systems made of synthetic micron-sized compartments and integrated reaction networks coupled with mathematical modeling can facilitate the design and construction of complex and multiscale chemical systems from the bottom-up. Toward this goal, we generated populations of monodisperse liposomes encapsulating cell-free expression systems (CFESs) using double-emulsion microfluidics and quantified transcription and translation dynamics within individual synthetic cells of the population using a fluorescent Broccoli RNA aptamer and mCherry protein reporter. CFE dynamics in bulk reactions were used to test different coarse-grained resource-limited gene expression models using model selection to obtain transcription and translation rate parameters by likelihood-based parameter estimation. The selected model was then applied to quantify cell-free gene expression dynamics in populations of synthetic cells. In combination, our experimental and theoretical approaches provide a statistically robust analysis of CFE dynamics in bulk and monodisperse synthetic cell populations. We demonstrate that compartmentalization of CFESs leads to different transcription and translation rates compared to bulk CFE and show that this is due to the semipermeable lipid membrane that allows the exchange of materials between the synthetic cells and the external environment.
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Affiliation(s)
- David
T. Gonzales
- Max
Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center
for Systems Biology Dresden, 01307 Dresden, Germany
| | | | - Tom Robinson
- Max
Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Christoph Zechner
- Max
Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center
for Systems Biology Dresden, 01307 Dresden, Germany
- Physics
of Life, Cluster of Excellence, TU Dresden, 01603 Dresden, Germany
| | - T-Y. Dora Tang
- Max
Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center
for Systems Biology Dresden, 01307 Dresden, Germany
- Physics
of Life, Cluster of Excellence, TU Dresden, 01603 Dresden, Germany
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46
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Tamiya-Ishitsuka H, Tsuruga M, Noda N, Yokota A. Conserved Amino Acid Moieties of Candidatus Desulforudis audaxviator MazF Determine Ribonuclease Activity and Specificity. Front Microbiol 2021; 12:748619. [PMID: 34867867 PMCID: PMC8634880 DOI: 10.3389/fmicb.2021.748619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
The toxin-antitoxin (TA) system, inherent to various prokaryotes, plays a critical role in survival and adaptation to diverse environmental stresses. The toxin MazF, belonging to the type II TA system, functions as a sequence-specific ribonuclease that recognizes 3 to 7 bases. In recent studies, crystallographic analysis of MazFs from several species have suggested the presence of amino acid sites important for MazF substrate RNA binding and for its catalytic activity. Herein, we characterized MazF obtained from Candidatus Desulforudis audaxviator (MazF-Da) and identified the amino acid residues necessary for its catalytic function. MazF-Da, expressed using a cell-free protein synthesis system, is a six-base-recognition-specific ribonuclease that preferentially cleaves UACAAA sequences and weakly cleaves UACGAA and UACUAA sequences. We found that MazF-Da exhibited the highest activity at around 60°C. Analysis using mutants with a single mutation at an amino acid residue site that is well conserved across various MazF toxins showed that G18, E20, R25, and P26 were important for the ribonuclease activity of MazF-Da. The recognition sequence of the N36A mutant differed from that of the wild type. This mutant cleaved UACAAG sequences in addition to UACAAA sequences, but did not cleave UACGAA or UACUAA sequences, suggesting that Asn36 affects the loosening and narrowing of MazF-Da cleavage sequence recognition. Our study posits UACAAA as the recognition sequence of MazF-Da and provides insight into the amino acid sites that are key to its unique enzymatic properties.
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Affiliation(s)
- Hiroko Tamiya-Ishitsuka
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Masako Tsuruga
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Naohiro Noda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Akiko Yokota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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47
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Uyeda A, Reyes SG, Kanamori T, Matsuura T. Identification of conditions for efficient cell-sized liposome preparation using commercially available reconstituted in vitro transcription-translation system. J Biosci Bioeng 2021; 133:181-186. [PMID: 34789414 DOI: 10.1016/j.jbiosc.2021.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/14/2021] [Accepted: 10/24/2021] [Indexed: 12/29/2022]
Abstract
Attempts to create complex molecular systems that mimic parts of cellular systems using a bottom-up approach have become important in the field of biology. Among various molecular systems, in vitro protein synthesis inside lipid vesicles (liposomes), which we refer to as the artificial cell, has become an attractive system because it possesses two fundamental features of living cells: central dogma, and compartmentalization. Here, we investigated the effect of altering the amount or concentration of four constituents of the artificial cell consisting of a commercially available reconstituted in vitro transcription-translation (IVTT) system. As this IVTT system is available worldwide, the results will be useful to the scientific community when shared, unlike those from a lab-made IVTT system. We succeeded in revealing the effect and trend of altering each parameter and identified a suitable condition for preparing liposomes that are unilamellar and can synthesize proteins equally as well as the original IVTT system. Because the commercially available reconstituted IVTT system is an important standardization tool and the constituents can be adjusted as desired, our results will be useful for the bottom-up creation of more complex molecular systems.
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Affiliation(s)
- Atsuko Uyeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Sabrina Galiñanes Reyes
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-i7E Ookayama, Meguro-Ku, Tokyo 152-8550, Japan.
| | - Takashi Kanamori
- GeneFrontier Corporation, SHARP Kashiwa Building, 4F, 273-1 Kashiwa, Kashiwa-shi, Chiba 277-0005, Japan.
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-i7E Ookayama, Meguro-Ku, Tokyo 152-8550, Japan.
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48
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Islam MS, Gaston JP, Baker MAB. Fluorescence Approaches for Characterizing Ion Channels in Synthetic Bilayers. MEMBRANES 2021; 11:857. [PMID: 34832086 PMCID: PMC8619978 DOI: 10.3390/membranes11110857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022]
Abstract
Ion channels are membrane proteins that play important roles in a wide range of fundamental cellular processes. Studying membrane proteins at a molecular level becomes challenging in complex cellular environments. Instead, many studies focus on the isolation and reconstitution of the membrane proteins into model lipid membranes. Such simpler, in vitro, systems offer the advantage of control over the membrane and protein composition and the lipid environment. Rhodopsin and rhodopsin-like ion channels are widely studied due to their light-interacting properties and are a natural candidate for investigation with fluorescence methods. Here we review techniques for synthesizing liposomes and for reconstituting membrane proteins into lipid bilayers. We then summarize fluorescence assays which can be used to verify the functionality of reconstituted membrane proteins in synthetic liposomes.
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Affiliation(s)
- Md. Sirajul Islam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - James P. Gaston
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
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Tabuchi T, Yokobayashi Y. Cell-free riboswitches. RSC Chem Biol 2021; 2:1430-1440. [PMID: 34704047 PMCID: PMC8496063 DOI: 10.1039/d1cb00138h] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/26/2021] [Indexed: 12/16/2022] Open
Abstract
The emerging community of cell-free synthetic biology aspires to build complex biochemical and genetic systems with functions that mimic or even exceed those in living cells. To achieve such functions, cell-free systems must be able to sense and respond to the complex chemical signals within and outside the system. Cell-free riboswitches can detect chemical signals via RNA-ligand interaction and respond by regulating protein synthesis in cell-free protein synthesis systems. In this article, we review synthetic cell-free riboswitches that function in both prokaryotic and eukaryotic cell-free systems reported to date to provide a current perspective on the state of cell-free riboswitch technologies and their limitations.
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Affiliation(s)
- Takeshi Tabuchi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna Okinawa 904-0495 Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna Okinawa 904-0495 Japan
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50
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Alcinesio A, Krishna Kumar R, Bayley H. Functional Multivesicular Structures with Controlled Architecture from 3D‐Printed Droplet Networks. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Alessandro Alcinesio
- Department of Chemistry University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | | | - Hagan Bayley
- Department of Chemistry University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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