1
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Thornton EL, Paterson SM, Stam MJ, Wood CW, Laohakunakorn N, Regan L. Applications of cell free protein synthesis in protein design. Protein Sci 2024; 33:e5148. [PMID: 39180484 PMCID: PMC11344276 DOI: 10.1002/pro.5148] [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: 05/30/2024] [Revised: 07/26/2024] [Accepted: 08/02/2024] [Indexed: 08/26/2024]
Abstract
In protein design, the ultimate test of success is that the designs function as desired. Here, we discuss the utility of cell free protein synthesis (CFPS) as a rapid, convenient and versatile method to screen for activity. We champion the use of CFPS in screening potential designs. Compared to in vivo protein screening, a wider range of different activities can be evaluated using CFPS, and the scale on which it can easily be used-screening tens to hundreds of designed proteins-is ideally suited to current needs. Protein design using physics-based strategies tended to have a relatively low success rate, compared with current machine-learning based methods. Screening steps (such as yeast display) were often used to identify proteins that displayed the desired activity from many designs that were highly ranked computationally. We also describe how CFPS is well-suited to identify the reasons designs fail, which may include problems with transcription, translation, and solubility, in addition to not achieving the desired structure and function.
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Affiliation(s)
- Ella Lucille Thornton
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Sarah Maria Paterson
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Michael J. Stam
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Christopher W. Wood
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Nadanai Laohakunakorn
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Lynne Regan
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological SciencesUniversity of EdinburghEdinburghUK
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2
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Alsup TA, Li Z, McCadden CA, Jagels A, Łomowska-Keehner DP, Marshall EM, Dong LB, Loesgen S, Rudolf JD. Early-stage biosynthesis of phenalinolactone diterpenoids involves sequential prenylation, epoxidation, and cyclization. RSC Chem Biol 2024:d4cb00138a. [PMID: 39144403 PMCID: PMC11317874 DOI: 10.1039/d4cb00138a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 08/02/2024] [Indexed: 08/16/2024] Open
Abstract
The chemical logic associated with assembly of many bacterial terpenoids remains poorly understood. We focused our efforts on the early-stage biosynthesis of the phenalinolactone diterpenoids, demonstrating that the anti/anti/syn-perhydrophenanthrene core is constructed by sequential prenylation, epoxidation, and cyclization. The functions and timing of PlaT1-PlaT3 were assigned by comprehensive heterologous reconstitution. We illustrated that the UbiA prenyltransferase PlaT3 acts on geranylgeranyl diphosphate (GGPP) in the first step of phenalinolactone biosynthesis, prior to epoxidation by the flavin-dependent monooxygenase PlaT1 and cyclization by the type II terpene cyclase PlaT2. Finally, we isolated eight new-to-nature terpenoids, expanding the scope of the bacterial terpenome. The biosynthetic strategy employed in the assembly of the phenalinolactone core, with cyclization occurring after prenylation, is rare in bacteria and resembles fungal meroterpenoid biosynthesis. The findings presented here set the stage for future discovery, engineering, and enzymology efforts in bacterial meroterpenoids.
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Affiliation(s)
- Tyler A Alsup
- Department of Chemistry, University of Florida Gainesville Florida USA
| | - Zining Li
- Department of Chemistry, University of Florida Gainesville Florida USA
| | | | - Annika Jagels
- Department of Chemistry, University of Florida Gainesville Florida USA
- Whitney Laboratory for Marine Bioscience, University of Florida St. Augustine FL USA
| | | | - Erin M Marshall
- Department of Chemistry, University of Florida Gainesville Florida USA
- Whitney Laboratory for Marine Bioscience, University of Florida St. Augustine FL USA
| | - Liao-Bin Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University Nanjing 211198 Jiangsu China
| | - Sandra Loesgen
- Department of Chemistry, University of Florida Gainesville Florida USA
- Whitney Laboratory for Marine Bioscience, University of Florida St. Augustine FL USA
| | - Jeffrey D Rudolf
- Department of Chemistry, University of Florida Gainesville Florida USA
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3
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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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4
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Li Z, Xu B, Alsup TA, Wei X, Ning W, Icenhour DG, Ehrenberger MA, Ghiviriga I, Giang BD, Rudolf JD. Cryptic Isomerization in Diterpene Biosynthesis and the Restoration of an Evolutionarily Defunct P450. J Am Chem Soc 2023; 145:22361-22365. [PMID: 37813821 PMCID: PMC11209839 DOI: 10.1021/jacs.3c09446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Biosynthetic modifications of the 6/10-bicyclic hydrocarbon skeletons of the eunicellane family of diterpenoids are unknown. We explored the biosynthesis of a bacterial trans-eunicellane natural product, albireticulone A (3), and identified a novel isomerase that catalyzes cryptic isomerization in the biosynthetic pathway. We also assigned functions of two cytochromes P450 that oxidize the eunicellane skeleton, one of which was a naturally evolved non-functional P450 that, when genetically repaired, catalyzes allylic oxidation. Finally, we described the chemical susceptibility of the trans-eunicellane skeleton to undergo Cope rearrangement to yield inseparable atropisomers.
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Affiliation(s)
- Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, United States
| | | | - Tyler A. Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, United States
| | - Xiuting Wei
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, United States
| | - Wenbo Ning
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, United States
| | - Daniel G. Icenhour
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, United States
| | - Michelle A. Ehrenberger
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, United States
| | - Ion Ghiviriga
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, United States
| | - Bao-Doan Giang
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, United States
| | - Jeffrey D. Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, United States
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5
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Fábrega MJ, Knödlseder N, Nevot G, Sanvicente M, Toloza L, Santos-Moreno J, Güell M. Establishing a Cell-Free Transcription-Translation Platform for Cutibacterium acnes to Prototype Engineered Metabolic and Synthetic Biology. ACS Biomater Sci Eng 2023; 9:5101-5110. [PMID: 34971313 PMCID: PMC10498419 DOI: 10.1021/acsbiomaterials.1c00894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In the past few years, new bacterial-cell-free transcription-translation systems have emerged as potent and quick platforms for protein production as well as for prototyping of DNA regulatory elements, genetic circuits, and metabolic pathways. The Gram-positive commensal Cutibacterium acnes is one of the most abundant bacteria present in the human skin microbiome. However, it has recently been reported that some C. acnes phylotypes can be associated with common inflammatory skin conditions, such as acne vulgaris, whereas others seem to play a protective role, acting as possible "skin probiotics". This fact has made C. acnes become a bacterial model of interest for the cosmetic industry. In the present study we report for the first time the development and optimization of a C. acnes-based cell-free system (CFS) that is able to produce 85 μg/mL firefly luciferase. We highlight the importance of harvesting the bacterial pellet in mid log phase and maintaining CFS reactions at 30 °C and physiological pH to obtain the optimal yield. Additionally, a C. acnes promoter library was engineered to compare coupled in vitro TX-TL activities, and a temperature biosensor was tested, demonstrating the wide range of applications of this toolkit in the synthetic biology field.
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Affiliation(s)
- María-José Fábrega
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Nastassia Knödlseder
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Guillermo Nevot
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Marta Sanvicente
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Lorena Toloza
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Javier Santos-Moreno
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Marc Güell
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
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6
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Cruz-Bautista R, Ruíz-Villafán B, Romero-Rodríguez A, Rodríguez-Sanoja R, Sánchez S. Trends in the two-component system's role in the synthesis of antibiotics by Streptomyces. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12623-z. [PMID: 37341754 DOI: 10.1007/s00253-023-12623-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
Despite the advances in understanding the regulatory networks for secondary metabolite production in Streptomyces, the participation of the two-component systems (TCS) in this process still requires better characterization. These sensing systems and their responses to environmental stimuli have been described by evaluating mutant strains with techniques that allow in-depth regulatory responses. However, defining the stimulus that triggers their activation is still a task. The transmembrane nature of the sensor kinases and the high content of GC in the streptomycetes represent significant challenges in their study. In some examples, adding elements to the assay medium has determined the respective ligand. However, a complete TCS description and characterization requires specific amounts of the involved proteins that are most difficult to obtain. The availability of enough sensor histidine kinase concentrations could facilitate the identification of the ligand-protein interaction, and besides would allow the establishment of its phosphorylation mechanisms and determine their tridimensional structure. Similarly, the advances in the development of bioinformatics tools and novel experimental techniques also promise to accelerate the TCSs description and provide knowledge on their participation in the regulation processes of secondary metabolite formation. This review aims to summarize the recent advances in the study of TCSs involved in antibiotic biosynthesis and to discuss alternatives to continue their characterization. KEY POINTS: • TCSs are the environmental signal transducers more abundant in nature. • The Streptomyces have some of the highest number of TCSs found in bacteria. • The study of signal transduction between SHKs and RRs domains is a big challenge.
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Affiliation(s)
- Rodrigo Cruz-Bautista
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
| | - Beatriz Ruíz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
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7
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Sakai A, Jonker AJ, Nelissen FHT, Kalb EM, van Sluijs B, Heus HA, Adamala KP, Glass JI, Huck WTS. Cell-Free Expression System Derived from a Near-Minimal Synthetic Bacterium. ACS Synth Biol 2023; 12:1616-1623. [PMID: 37278603 PMCID: PMC10278164 DOI: 10.1021/acssynbio.3c00114] [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: 02/22/2023] [Indexed: 06/07/2023]
Abstract
Cell-free expression (CFE) systems are fundamental to reconstituting metabolic pathways in vitro toward the construction of a synthetic cell. Although an Escherichia coli-based CFE system is well-established, simpler model organisms are necessary to understand the principles behind life-like behavior. Here, we report the successful creation of a CFE system derived from JCVI-syn3A (Syn3A), the minimal synthetic bacterium. Previously, high ribonuclease activity in Syn3A lysates impeded the establishment of functional CFE systems. Now, we describe how an unusual cell lysis method (nitrogen decompression) yielded Syn3A lysates with reduced ribonuclease activity that supported in vitro expression. To improve the protein yields in the Syn3A CFE system, we optimized the Syn3A CFE reaction mixture using an active machine learning tool. The optimized reaction mixture improved the CFE 3.2-fold compared to the preoptimized condition. This is the first report of a functional CFE system derived from a minimal synthetic bacterium, enabling further advances in bottom-up synthetic biology.
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Affiliation(s)
- Andrei Sakai
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Aafke J. Jonker
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Frank H. T. Nelissen
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Evan M. Kalb
- Department
of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Bob van Sluijs
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Hans A. Heus
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John I. Glass
- Synthetic
Biology & Bioenergy, J. Craig Venter
Institute, La Jolla, California 92037, United States
| | - Wilhelm T. S. Huck
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
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8
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Dinglasan JLN, Sword TT, Barker JW, Doktycz MJ, Bailey CB. Investigating and Optimizing the Lysate-Based Expression of Nonribosomal Peptide Synthetases Using a Reporter System. ACS Synth Biol 2023; 12:1447-1460. [PMID: 37039644 PMCID: PMC11236431 DOI: 10.1021/acssynbio.2c00658] [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] [Indexed: 04/12/2023]
Abstract
Lysate-based cell-free expression (CFE) systems are accessible platforms for expressing proteins that are difficult to synthesize in vivo, such as nonribosomal peptide synthetases (NRPSs). NRPSs are large (>100 kDa), modular enzyme complexes that synthesize bioactive peptide natural products. This synthetic process is analogous to transcription/translation (TX/TL) in lysates, resulting in potential resource competition between NRPS expression and NRPS activity in cell-free environments. Moreover, CFE conditions depend on the size and structure of the protein. Here, a reporter system for rapidly investigating and optimizing reaction environments for NRPS CFE is described. This strategy is demonstrated in E. coli lysate reactions using blue pigment synthetase A (BpsA), a model NRPS, carrying a C-terminal tetracysteine (TC) tag which forms a fluorescent complex with the biarsenical dye, FlAsH. A colorimetric assay was adapted for lysate reactions to detect the blue pigment product, indigoidine, of cell-free expressed BpsA-TC, confirming that the tagged enzyme is catalytically active. An optimized protocol for end point TC/FlAsH complex measurements in reactions enables quick comparisons of full-length BpsA-TC expressed under different reaction conditions, defining unique requirements for NRPS expression that are related to the protein's catalytic activity and size. Importantly, these protein-dependent CFE conditions enable higher indigoidine titer and improve the expression of other monomodular NRPSs. Notably, these conditions differ from those used for the expression of superfolder GFP (sfGFP), a common reporter for optimizing lysate-based CFE systems, indicating the necessity for tailored reporters to optimize expression for specific enzyme classes. The reporter system is anticipated to advance lysate-based CFE systems for complex enzyme synthesis, enabling natural product discovery.
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Affiliation(s)
- Jaime Lorenzo N Dinglasan
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - J William Barker
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
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9
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Zhang S, Chen Y, Zhu J, Lu Q, Cryle MJ, Zhang Y, Yan F. Structural diversity, biosynthesis, and biological functions of lipopeptides from Streptomyces. Nat Prod Rep 2023; 40:557-594. [PMID: 36484454 DOI: 10.1039/d2np00044j] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2022Streptomyces are ubiquitous in terrestrial and marine environments, where they display a fascinating metabolic diversity. As a result, these bacteria are a prolific source of active natural products. One important class of these natural products is the nonribosomal lipopeptides, which have diverse biological activities and play important roles in the lifestyle of Streptomyces. The importance of this class is highlighted by the use of related antibiotics in the clinic, such as daptomycin (tradename Cubicin). By virtue of recent advances spanning chemistry and biology, significant progress has been made in biosynthetic studies on the lipopeptide antibiotics produced by Streptomyces. This review will serve as a comprehensive guide for researchers working in this multidisciplinary field, providing a summary of recent progress regarding the investigation of lipopeptides from Streptomyces. In particular, we highlight the structures, properties, biosynthetic mechanisms, chemical and chemoenzymatic synthesis, and biological functions of lipopeptides. In addition, the application of genome mining techniques to Streptomyces that have led to the discovery of many novel lipopeptides is discussed, further demonstrating the potential of lipopeptides from Streptomyces for future development in modern medicine.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunliang Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 1000050, China.
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qiujie Lu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800 Australia
- EMBL Australia, Monash University, Clayton, Victoria, 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, 3800 Australia
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Fu Yan
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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10
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Rasor BJ, Karim AS, Alper HS, Jewett MC. Cell Extracts from Bacteria and Yeast Retain Metabolic Activity after Extended Storage and Repeated Thawing. ACS Synth Biol 2023; 12:904-908. [PMID: 36848582 DOI: 10.1021/acssynbio.2c00685] [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: 03/01/2023]
Abstract
Cell-free synthetic biology enables rapid prototyping of biological parts and synthesis of proteins or metabolites in the absence of cell growth constraints. Cell-free systems are frequently made from crude cell extracts, where composition and activity can vary significantly based on source strain, preparation and processing, reagents, and other considerations. This variability can cause extracts to be treated as black boxes for which empirical observations guide practical laboratory practices, including a hesitance to use dated or previously thawed extracts. To better understand the robustness of cell extracts over time, we assessed the activity of cell-free metabolism during storage. As a model, we studied conversion of glucose to 2,3-butanediol. We found that cell extracts from Escherichia coli and Saccharomyces cerevisiae subjected to an 18-month storage period and repeated freeze-thaw cycles retain consistent metabolic activity. This work gives users of cell-free systems a better understanding of the impacts of storage on extract behavior.
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11
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Moore SJ, Lai HE, Li J, Freemont PS. Streptomyces cell-free systems for natural product discovery and engineering. Nat Prod Rep 2023; 40:228-236. [PMID: 36341536 PMCID: PMC9945932 DOI: 10.1039/d2np00057a] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Indexed: 11/09/2022]
Abstract
Streptomyces bacteria are a major microbial source of natural products, which are encoded within so-called biosynthetic gene clusters (BGCs). This highlight discusses the emergence of native Streptomyces cell-free systems as a new tool to accelerate the study of the fundamental chemistry and biology of natural product biosynthesis from these bacteria. Cell-free systems provide a prototyping platform to study plug-and-play reactions in microscale reactions. So far, Streptomyces cell-free systems have been used to rapidly characterise gene expression regulation, access secondary metabolite biosynthetic enzymes, and catalyse cell-free transcription, translation, and biosynthesis of example natural products. With further progress, we anticipate the development of more complex systems to complement existing experimental tools for the discovery and engineering of natural product biosynthesis from Streptomyces and related high G + C (%) bacteria.
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Affiliation(s)
- Simon J Moore
- School of Biosciences, University of Kent, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, UK.
| | - Hung-En Lai
- School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, China
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12
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Nagappa LK, Sato W, Alam F, Chengan K, Smales CM, Von Der Haar T, Polizzi KM, Adamala KP, Moore SJ. A ubiquitous amino acid source for prokaryotic and eukaryotic cell-free transcription-translation systems. Front Bioeng Biotechnol 2022; 10:992708. [PMID: 36185432 PMCID: PMC9524191 DOI: 10.3389/fbioe.2022.992708] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022] Open
Abstract
Cell-free gene expression (CFE) systems are an attractive tool for engineering within synthetic biology and for industrial production of high-value recombinant proteins. CFE reactions require a cell extract, energy system, amino acids, and DNA, to catalyse mRNA transcription and protein synthesis. To provide an amino acid source, CFE systems typically use a commercial standard, which is often proprietary. Herein we show that a range of common microbiology rich media (i.e., tryptone, peptone, yeast extract and casamino acids) unexpectedly provide an effective and low-cost amino acid source. We show that this approach is generalisable, by comparing batch variability and protein production in the following range of CFE systems: Escherichia coli (Rosetta™ 2 (DE3), BL21(DE3)), Streptomyces venezuelae and Pichia pastoris. In all CFE systems, we show equivalent or increased protein synthesis capacity upon replacement of the commercial amino acid source. In conclusion, we suggest rich microbiology media provides a new amino acid source for CFE systems with potential broad use in synthetic biology and industrial biotechnology applications.
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Affiliation(s)
| | - Wakana Sato
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States
| | - Farzana Alam
- Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | | | | | | | - Karen M Polizzi
- Centre for Synthetic Biology, Imperial College London, London, United Kingdom
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States
| | - Simon J Moore
- School of Biosciences, University of Kent, Canterbury, United Kingdom
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13
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Del Carratore F, Hanko EK, Breitling R, Takano E. Biotechnological application of Streptomyces for the production of clinical drugs and other bioactive molecules. Curr Opin Biotechnol 2022; 77:102762. [PMID: 35908316 DOI: 10.1016/j.copbio.2022.102762] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/30/2022]
Abstract
Streptomyces is one of the most relevant genera in biotechnology, and its rich secondary metabolism is responsible for the biosynthesis of a plethora of bioactive compounds, including several clinically relevant drugs. The use of Streptomyces species for the manufacture of natural products has been established for more than half a century; however, the tremendous advances observed in recent years in genetic engineering and molecular biology have revolutionised the optimisation of Streptomyces as cell factories and drastically expanded the biotechnological potential of these bacteria. Here, we illustrate the most exciting advances reported in the past few years, with a particular focus on the approaches significantly improving the biotechnological capacity of Streptomyces to produce clinical drugs and other valuable secondary metabolites.
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Affiliation(s)
- Francesco Del Carratore
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Erik Kr Hanko
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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14
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Yang C, Yang M, Zhao W, Ding Y, Wang Y, Li J. Establishing a Klebsiella pneumoniae-Based Cell-Free Protein Synthesis System. Molecules 2022; 27:molecules27154684. [PMID: 35897861 PMCID: PMC9330377 DOI: 10.3390/molecules27154684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/25/2022] [Accepted: 07/18/2022] [Indexed: 02/01/2023] Open
Abstract
Cell-free protein synthesis (CFPS) systems are emerging as powerful platforms for in vitro protein production, which leads to the development of new CFPS systems for different applications. To expand the current CFPS toolkit, here we develop a novel CFPS system derived from a chassis microorganism Klebsiella pneumoniae, an important industrial host for heterologous protein expression and the production of many useful chemicals. First, we engineered the K. pneumoniae strain by deleting a capsule formation-associated wzy gene. This capsule-deficient strain enabled easy collection of the cell biomass for preparing cell extracts. Then, we optimized the procedure of cell extract preparation and the reaction conditions for CFPS. Finally, the optimized CFPS system was able to synthesize a reporter protein (superfolder green fluorescent protein, sfGFP) with a maximum yield of 253 ± 15.79 μg/mL. Looking forward, our K. pneumoniae-based CFPS system will not only expand the toolkit for protein synthesis, but also provide a new platform for constructing in vitro metabolic pathways for the synthesis of high-value chemicals.
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Affiliation(s)
- Chen Yang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China;
| | - Miaomiao Yang
- Clinical Pathology Center, The Fourth Affiliated Hospital of Anhui Medical University, Hefei 230012, China;
- Department of Biological Physics, University of Science and Technology of China, Hefei 230026, China
| | - Wanhua Zhao
- College of Life Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (W.Z.); (Y.D.)
| | - Yue Ding
- College of Life Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (W.Z.); (Y.D.)
| | - Yu Wang
- College of Life Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (W.Z.); (Y.D.)
- Correspondence: (Y.W.); (J.L.)
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China;
- Correspondence: (Y.W.); (J.L.)
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15
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Ji X, Liu WQ, Li J. Recent advances in applying cell-free systems for high-value and complex natural product biosynthesis. Curr Opin Microbiol 2022; 67:102142. [DOI: 10.1016/j.mib.2022.102142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 11/03/2022]
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16
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Guzman-Chavez F, Arce A, Adhikari A, Vadhin S, Pedroza-Garcia JA, Gandini C, Ajioka JW, Molloy J, Sanchez-Nieto S, Varner JD, Federici F, Haseloff J. Constructing Cell-Free Expression Systems for Low-Cost Access. ACS Synth Biol 2022; 11:1114-1128. [PMID: 35259873 PMCID: PMC9098194 DOI: 10.1021/acssynbio.1c00342] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Indexed: 11/29/2022]
Abstract
Cell-free systems for gene expression have gained attention as platforms for the facile study of genetic circuits and as highly effective tools for teaching. Despite recent progress, the technology remains inaccessible for many in low- and middle-income countries due to the expensive reagents required for its manufacturing, as well as specialized equipment required for distribution and storage. To address these challenges, we deconstructed processes required for cell-free mixture preparation and developed a set of alternative low-cost strategies for easy production and sharing of extracts. First, we explored the stability of cell-free reactions dried through a low-cost device based on silica beads, as an alternative to commercial automated freeze dryers. Second, we report the positive effect of lactose as an additive for increasing protein synthesis in maltodextrin-based cell-free reactions using either circular or linear DNA templates. The modifications were used to produce active amounts of two high-value reagents: the isothermal polymerase Bst and the restriction enzyme BsaI. Third, we demonstrated the endogenous regeneration of nucleoside triphosphates and synthesis of pyruvate in cell-free systems (CFSs) based on phosphoenol pyruvate (PEP) and maltodextrin (MDX). We exploited this novel finding to demonstrate the use of a cell-free mixture completely free of any exogenous nucleotide triphosphates (NTPs) to generate high yields of sfGFP expression. Together, these modifications can produce desiccated extracts that are 203-424-fold cheaper than commercial versions. These improvements will facilitate wider use of CFS for research and education purposes.
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Affiliation(s)
| | - Anibal Arce
- ANID
− Millennium Institute for Integrative Biology (iBio), FONDAP
Center for Genome Regulation, Institute for Biological and Medical
Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8330005, Chile
| | - Abhinav Adhikari
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Sandra Vadhin
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jose Antonio Pedroza-Garcia
- Department
of Biochemistry, Faculty of Chemistry, National
Autonomous University of Mexico (UNAM), 04510 Mexico City, Mexico
| | - Chiara Gandini
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0FD Cambridge, U.K.
| | - Jim W. Ajioka
- Department
of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP Cambridge, U.K.
| | - Jenny Molloy
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0FD Cambridge, U.K.
| | - Sobeida Sanchez-Nieto
- Department
of Biochemistry, Faculty of Chemistry, National
Autonomous University of Mexico (UNAM), 04510 Mexico City, Mexico
| | - Jeffrey D. Varner
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Fernan Federici
- ANID
− Millennium Institute for Integrative Biology (iBio), FONDAP
Center for Genome Regulation, Institute for Biological and Medical
Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8330005, Chile
| | - Jim Haseloff
- Department
of Plant Sciences, University of Cambridge, CB2 3EA Cambridge, U.K.
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17
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Xu H, Yang C, Tian X, Chen Y, Liu WQ, Li J. Regulatory Part Engineering for High-Yield Protein Synthesis in an All- Streptomyces-Based Cell-Free Expression System. ACS Synth Biol 2022; 11:570-578. [PMID: 35129330 DOI: 10.1021/acssynbio.1c00587] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Streptomyces-based cell-free expression systems have been developed to meet the demand for synthetic biology applications. However, protein yields from the previous Streptomyces systems are relatively low, and there is a serious limitation of available genetic tools such as plasmids for gene (co)expression. Here, we sought to expand the plasmid toolkit with a focus on the enhancement of protein production. By screening native promoters and ribosome binding sites, we were able to construct a panel of plasmids with different abilities for protein synthesis, which covered a nearly 3-fold range of protein yields. Using the most efficient plasmid, the protein yield reached up to a maximum value of 515.7 ± 25.3 μg/mL. With the plasmid toolkit, we anticipate that our Streptomyces cell-free system will offer great opportunities for cell-free synthetic biology applications such as in vitro biosynthesis of valuable natural products when cell-based systems remain difficult or not amenable.
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Affiliation(s)
- Huiling Xu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chen Yang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xintong Tian
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yilin Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
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18
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Hwang S, Lee Y, Kim JH, Kim G, Kim H, Kim W, Cho S, Palsson BO, Cho BK. Streptomyces as Microbial Chassis for Heterologous Protein Expression. Front Bioeng Biotechnol 2022; 9:804295. [PMID: 34993191 PMCID: PMC8724576 DOI: 10.3389/fbioe.2021.804295] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/30/2021] [Indexed: 12/29/2022] Open
Abstract
Heterologous production of recombinant proteins is gaining increasing interest in biotechnology with respect to productivity, scalability, and wide applicability. The members of genus Streptomyces have been proposed as remarkable hosts for heterologous production due to their versatile nature of expressing various secondary metabolite biosynthetic gene clusters and secretory enzymes. However, there are several issues that limit their use, including low yield, difficulty in genetic manipulation, and their complex cellular features. In this review, we summarize rational engineering approaches to optimizing the heterologous production of secondary metabolites and recombinant proteins in Streptomyces species in terms of genetic tool development and chassis construction. Further perspectives on the development of optimal Streptomyces chassis by the design-build-test-learn cycle in systems are suggested, which may increase the availability of secondary metabolites and recombinant proteins.
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Affiliation(s)
- Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Gahyeon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Hyeseong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Innovative Biomaterials Research Center, KAIST Institutes, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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19
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Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters. iScience 2021; 24:103410. [PMID: 34877485 PMCID: PMC8627960 DOI: 10.1016/j.isci.2021.103410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/05/2021] [Accepted: 11/04/2021] [Indexed: 11/20/2022] Open
Abstract
Streptomyces species have attracted considerable interest as a reservoir of medically important secondary metabolites, which are even diverse and different between strains. Here, we reassess ten Streptomyces venezuelae strains by presenting the highly resolved classification, using 16S rRNA sequencing, MALDI-TOF MS protein profiling, and whole-genome sequencing. The results revealed that seven of the ten strains were misclassified as S. venezuelae species. Secondary metabolite biosynthetic gene cluster (smBGC) mining and targeted LC-MS/MS based metabolite screening of S. venezuelae and misclassified strains identified in total 59 secondary metabolites production. In addition, a comparison of pyrrolamide-type antibiotic BGCs of four misclassified strains, followed by functional genomics, revealed that athv28 is critical in the synthesis of the anthelvencin precursor, 5-amino-3,4-dihydro-2H-pyrrole-2-carboxylate (ADPC). Our findings illustrate the importance of the accurate classification and better utilization of misclassified Streptomyces strains to discover smBGCs and their secondary metabolite products.
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20
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Toh M, Chengan K, Hanson T, Freemont PS, Moore SJ. A High-Yield Streptomyces Transcription-Translation Toolkit for Synthetic Biology and Natural Product Applications. J Vis Exp 2021:10.3791/63012. [PMID: 34570109 PMCID: PMC7614929 DOI: 10.3791/63012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Streptomyces spp. are a major source of clinical antibiotics and industrial chemicals. Streptomyces venezuelae ATCC 10712 is a fast-growing strain and a natural producer of chloramphenicol, jadomycin, and pikromycin, which makes it an attractive candidate as a next-generation synthetic biology chassis. Therefore, genetic tools that accelerate the development of S. venezuelae ATCC 10712, as well as other Streptomyces spp. models, are highly desirable for natural product engineering and discovery. To this end, a dedicated S. venezuelae ATCC 10712 cell-free system is provided in this protocol to enable high-yield heterologous expression of high G+C (%) genes. This protocol is suitable for small-scale (10-100 μL) batch reactions in either 96-well or 384-well plate format, while reactions are potentially scalable. The cell-free system is robust and can achieve high yields (~5-10 μM) for a range of recombinant proteins in a minimal setup. This work also incorporates a broad plasmid toolset for real-time measurement of mRNA and protein synthesis, as well as in-gel fluorescence staining of tagged proteins. This protocol can also be integrated with high-throughput gene expression characterization workflows or the study of enzyme pathways from high G+C (%) genes present in Actinomycetes genomes.
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Affiliation(s)
- Ming Toh
- Centre for Synthetic Biology and Innovation, South Kensington Campus; Department of Medicine, South Kensington Campus; Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London; Sir Alexander Fleming Building, South Kensington Campus
| | | | - Tanith Hanson
- School of Biosciences, Division of Natural Sciences, University of Kent
| | - Paul S Freemont
- Centre for Synthetic Biology and Innovation, South Kensington Campus; Department of Medicine, South Kensington Campus; Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London; Sir Alexander Fleming Building, South Kensington Campus; UK Dementia Research Institute Care Research and Technology Centre, Imperial College London; Hammersmith Campus; UK Innovation and Knowledge Centre for Synthetic Biology (SynbiCITE) and the London Biofoundry, Imperial College Translation & Innovation Hub;
| | - Simon J Moore
- School of Biosciences, Division of Natural Sciences, University of Kent;
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21
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Undabarrena A, Pereira CF, Kruasuwan W, Parra J, Sélem-Mojica N, Vind K, Schniete JK. Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001084. [PMID: 34515628 PMCID: PMC8549240 DOI: 10.1099/mic.0.001084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022]
Abstract
Last year ActinoBase, a Wiki-style initiative supported by the UK Microbiology Society, published a review highlighting the research of particular interest to the actinomycete community. Here, we present the second ActinoBase review showcasing selected reports published in 2020 and early 2021, integrating perspectives in the actinomycete field. Actinomycetes are well-known for their unsurpassed ability to produce specialised metabolites, of which many are used as therapeutic agents with antibacterial, antifungal, or immunosuppressive activities. Much research is carried out to understand the purpose of these metabolites in the environment, either within communities or in host interactions. Moreover, many efforts have been placed in developing computational tools to handle big data, simplify experimental design, and find new biosynthetic gene cluster prioritisation strategies. Alongside, synthetic biology has provided advances in tools to elucidate the biosynthesis of these metabolites. Additionally, there are still mysteries to be uncovered in understanding the fundamentals of filamentous actinomycetes' developmental cycle and regulation of their metabolism. This review focuses on research using integrative methodologies and approaches to understand the bigger picture of actinomycete biology, covering four research areas: i) technology and methodology; ii) specialised metabolites; iii) development and regulation; and iv) ecology and host interactions.
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Affiliation(s)
- Agustina Undabarrena
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile
| | - Camila F Pereira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Worarat Kruasuwan
- Microbial Cell Factory Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jonathan Parra
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Nelly Sélem-Mojica
- Centro de Ciencias Matemáticas, Antigua Carretera a Pátzcuaro # 8701, Col. Ex Hacienda San José de la Huerta, Morelia C.P. 58089, Michoacán, México
| | - Kristiina Vind
- NAICONS Srl, Viale Ortles 22/4, 20139 Milan (MI), Italy
- Host-Microbe Interactomics Group, Wageningen University, De Elst 1 6708 WD, Wageningen, Netherlands
| | - Jana K. Schniete
- Biology, Edge Hill University, St Helens Road, Ormskirk, L39 4QP, UK
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22
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An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts. Nat Commun 2021; 12:5139. [PMID: 34446711 PMCID: PMC8390474 DOI: 10.1038/s41467-021-25233-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Cell-free systems using crude cell extracts present appealing opportunities for designing biosynthetic pathways and enabling sustainable chemical synthesis. However, the lack of tools to effectively manipulate the underlying host metabolism in vitro limits the potential of these systems. Here, we create an integrated framework to address this gap that leverages cell extracts from host strains genetically rewired by multiplexed CRISPR-dCas9 modulation and other metabolic engineering techniques. As a model, we explore conversion of glucose to 2,3-butanediol in extracts from flux-enhanced Saccharomyces cerevisiae strains. We show that cellular flux rewiring in several strains of S. cerevisiae combined with systematic optimization of the cell-free reaction environment significantly increases 2,3-butanediol titers and volumetric productivities, reaching productivities greater than 0.9 g/L-h. We then show the generalizability of the framework by improving cell-free itaconic acid and glycerol biosynthesis. Our coupled in vivo/in vitro metabolic engineering approach opens opportunities for synthetic biology prototyping efforts and cell-free biomanufacturing.
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23
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Yang C, Liu Y, Liu WQ, Wu C, Li J. Designing Modular Cell-free Systems for Tunable Biotransformation of l-phenylalanine to Aromatic Compounds. Front Bioeng Biotechnol 2021; 9:730663. [PMID: 34395411 PMCID: PMC8355704 DOI: 10.3389/fbioe.2021.730663] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
Cell-free systems have been used to synthesize chemicals by reconstitution of in vitro expressed enzymes. However, coexpression of multiple enzymes to reconstitute long enzymatic pathways is often problematic due to resource limitation/competition (e.g., energy) in the one-pot cell-free reactions. To address this limitation, here we aim to design a modular, cell-free platform to construct long biosynthetic pathways for tunable synthesis of value-added aromatic compounds, using (S)-1-phenyl-1,2-ethanediol ((S)-PED) and 2-phenylethanol (2-PE) as models. Initially, all enzymes involved in the biosynthetic pathways were individually expressed by an E. coli-based cell-free protein synthesis (CFPS) system and their catalytic activities were confirmed. Then, three sets of enzymes were coexpressed in three cell-free modules and each with the ability to complete a partial pathway. Finally, the full biosynthetic pathways were reconstituted by mixing two related modules to synthesize (S)-PED and 2-PE, respectively. After optimization, the final conversion rates for (S)-PED and 2-PE reached 100 and 82.5%, respectively, based on the starting substrate of l-phenylalanine. We anticipate that the modular cell-free approach will make a possible efficient and high-yielding biosynthesis of value-added chemicals.
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Affiliation(s)
- Chen Yang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China.,Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yushi Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Changzhu Wu
- Danish Institute for Advanced Study (DIAS) and Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
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24
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Qian Y, Kong W, Lu T. Precise and reliable control of gene expression in Agrobacterium tumefaciens. Biotechnol Bioeng 2021; 118:3962-3972. [PMID: 34180537 DOI: 10.1002/bit.27872] [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: 04/15/2021] [Revised: 06/07/2021] [Accepted: 06/17/2021] [Indexed: 11/07/2022]
Abstract
Agrobacterium tumefaciens is a soil-borne bacterium that is known for its DNA delivery ability and widely exploited for plant transformation. Despite continued interest in improving the utility of the organism, the lack of well-characterized engineering tools limits the realization of its full potential. Here, we present a synthetic biology toolkit that enables precise and effective control of gene expression in A. tumefaciens. We constructed and characterized six inducible expression systems. Then, we optimized the one regulated by cumic acid through amplifier introduction and promoter engineering and evaluated its 15 cognate promoters. To establish fine-tunability, we constructed a series of spacers and a promoter library to systematically modulate both translational and transcriptional rates. We finally demonstrated the application of the tools by co-expressing genes with altered expression levels using a single signal. This study provides precise expression tools for A. tumefaciens, facilitating rational engineering of the bacterium for advanced plant biotechnological applications.
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Affiliation(s)
- Yuanchao Qian
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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25
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The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes. Essays Biochem 2021; 65:261-275. [PMID: 33956071 DOI: 10.1042/ebc20200132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/08/2023]
Abstract
Streptomycetes are producers of a wide range of specialized metabolites of great medicinal and industrial importance, such as antibiotics, antifungals, or pesticides. Having been the drivers of the golden age of antibiotics in the 1950s and 1960s, technological advancements over the last two decades have revealed that very little of their biosynthetic potential has been exploited so far. Given the great need for new antibiotics due to the emerging antimicrobial resistance crisis, as well as the urgent need for sustainable biobased production of complex molecules, there is a great renewed interest in exploring and engineering the biosynthetic potential of streptomycetes. Here, we describe the Design-Build-Test-Learn (DBTL) cycle for metabolic engineering experiments in streptomycetes and how it can be used for the discovery and production of novel specialized metabolites.
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