51
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Thomson NM, Pallen MJ. Restoration of wild-type motility to flagellin-knockout Escherichia coli by varying promoter, copy number and induction strength in plasmid-based expression of flagellin. CURRENT RESEARCH IN BIOTECHNOLOGY 2021; 2:45-52. [PMID: 33381753 PMCID: PMC7758877 DOI: 10.1016/j.crbiot.2020.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Flagellin is the major constituent of the flagellar filament and faithful restoration of wild-type motility to flagellin mutants may be beneficial for studies of flagellar biology and biotechnological exploitation of the flagellar system. However, gene complementation studies often fail to report whether true wild-type motility was restored by expressing flagellin from a plasmid. Therefore, we explored the restoration of motility by flagellin expressed from a variety of combinations of promoter, plasmid copy number and induction strength. Motility was only partially (~50%) restored using the tightly regulated rhamnose promoter due to weak flagellin gene expression, but wild-type motility was regained with the T5 promoter, which, although leaky, allowed titration of induction strength. The endogenous E. coli flagellin promoter also restored wild-type motility. However, flagellin gene transcription levels increased 3.1–27.9-fold when wild-type motility was restored, indicating disturbances in the flagellar regulatory mechanisms. Motility was little affected by plasmid copy number when dependent on inducible promoters. However, plasmid copy number was important when expression was controlled by the native E. coli flagellin promoter. Motility was poorly correlated with flagellin transcription levels, but strongly correlated with the amount of flagellin associated with the flagellar filament, suggesting that excess monomers are either not exported or not assembled into filaments. This study provides a useful reference for further studies of flagellar function and a simple blueprint for similar studies with other proteins. Restoration of motility to flagellin-knockout E. coli depends on choice of promoter. Plasmid copy number is important when using the natural flagellin promoter. For inducible promoters, induction strength is more important than copy number. Large increase in flagellin transcription but not flagella-associated protein. Plasmid-based expression interrupts flagellin expression control mechanisms.
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Affiliation(s)
- Nicholas M Thomson
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
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52
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Li J, Ye BC. Metabolic engineering of Pseudomonas putida KT2440 for high-yield production of protocatechuic acid. BIORESOURCE TECHNOLOGY 2021; 319:124239. [PMID: 33254462 DOI: 10.1016/j.biortech.2020.124239] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 06/12/2023]
Abstract
Protocatechuic acid (PCA) has been widely utilized in conventional pharmaceutical, cosmetic and functional food industries. Currently, chemical synthesis and solvent extraction are the main methods for commercial production, indicating several disadvantages. In this study, we developed a method for the biosynthesis of PCA in Pseudomonas putida KT2440 in high yield. First, we developed constitutive promoters with different expression intensities for fine-tuned gene expression. Second, we improved the biosynthesis of "natural" PCA in P. putida KT2440 via multilevel metabolic engineering strategies: overexpression of rate-limiting enzymes, removal of negative regulators, attenuation of pathway competition, and enhancement of precursor supply. Finally, by further bioprocess engineering efforts, the best-producing strain reached a titer of 12.5 g/L PCA from glucose at 72 h in a shake flask and 21.7 g/L in fed-batch fermentation without antibiotic pressure. This was the highest PCA titer from glucose using metabolically engineered microbial cell factories reported to date.
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Affiliation(s)
- Jin Li
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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53
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Kanoi BN, Nagaoka H, Morita M, Tsuboi T, Takashima E. Leveraging the wheat germ cell-free protein synthesis system to accelerate malaria vaccine development. Parasitol Int 2020; 80:102224. [PMID: 33137499 DOI: 10.1016/j.parint.2020.102224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/04/2020] [Accepted: 09/16/2020] [Indexed: 01/29/2023]
Abstract
Vaccines against infectious diseases have had great successes in the history of public health. Major breakthroughs have occurred in the development of vaccine-based interventions against viral and bacterial pathogens through the application of classical vaccine design strategies. In contrast the development of a malaria vaccine has been slow. Plasmodium falciparum malaria affects millions of people with nearly half of the world population at risk of infection. Decades of dedicated research has taught us that developing an effective vaccine will be time consuming, challenging, and expensive. Nevertheless, recent advancements such as the optimization of robust protein synthesis platforms, high-throughput immunoscreening approaches, reverse vaccinology, structural design of immunogens, lymphocyte repertoire sequencing, and the utilization of artificial intelligence, have renewed the prospects of an accelerated discovery of the key antigens in malaria. A deeper understanding of the major factors underlying the immunological and molecular mechanisms of malaria might provide a comprehensive approach to identifying novel and highly efficacious vaccines. In this review we discuss progress in novel antigen discoveries that leverage on the wheat germ cell-free protein synthesis system (WGCFS) to accelerate malaria vaccine development.
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Affiliation(s)
- Bernard N Kanoi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Masayuki Morita
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takafumi Tsuboi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan.
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54
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Lammens EM, Nikel PI, Lavigne R. Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nat Commun 2020; 11:5294. [PMID: 33082347 PMCID: PMC7576135 DOI: 10.1038/s41467-020-19124-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022] Open
Abstract
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host.
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Affiliation(s)
- Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium
| | - Pablo Ivan Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, DK, Denmark
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium.
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55
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Thompson MG, Incha MR, Pearson AN, Schmidt M, Sharpless WA, Eiben CB, Cruz-Morales P, Blake-Hedges JM, Liu Y, Adams CA, Haushalter RW, Krishna RN, Lichtner P, Blank LM, Mukhopadhyay A, Deutschbauer AM, Shih PM, Keasling JD. Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing. Appl Environ Microbiol 2020; 86:e01665-20. [PMID: 32826213 PMCID: PMC7580535 DOI: 10.1128/aem.01665-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
With its ability to catabolize a wide variety of carbon sources and a growing engineering toolkit, Pseudomonas putida KT2440 is emerging as an important chassis organism for metabolic engineering. Despite advances in our understanding of the organism, many gaps remain in our knowledge of the genetic basis of its metabolic capabilities. The gaps are particularly noticeable in our understanding of both fatty acid and alcohol catabolism, where many paralogs putatively coding for similar enzymes coexist, making biochemical assignment via sequence homology difficult. To rapidly assign function to the enzymes responsible for these metabolisms, we leveraged random barcode transposon sequencing (RB-Tn-Seq). Global fitness analyses of transposon libraries grown on 13 fatty acids and 10 alcohols produced strong phenotypes for hundreds of genes. Fitness data from mutant pools grown on fatty acids of varying chain lengths indicated specific enzyme substrate preferences and enabled us to hypothesize that DUF1302/DUF1329 family proteins potentially function as esterases. From the data, we also postulate catabolic routes for the two biogasoline molecules isoprenol and isopentanol, which are catabolized via leucine metabolism after initial oxidation and activation with coenzyme A (CoA). Because fatty acids and alcohols may serve as both feedstocks and final products of metabolic-engineering efforts, the fitness data presented here will help guide future genomic modifications toward higher titers, rates, and yields.IMPORTANCE To engineer novel metabolic pathways into P. putida, a comprehensive understanding of the genetic basis of its versatile metabolism is essential. Here, we provide functional evidence for the putative roles of hundreds of genes involved in the fatty acid and alcohol metabolism of the bacterium. These data provide a framework facilitating precise genetic changes to prevent product degradation and to channel the flux of specific pathway intermediates as desired.
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Affiliation(s)
- Mitchell G Thompson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant Biology, University of California, Davis, California, USA
| | - Matthew R Incha
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Allison N Pearson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Matthias Schmidt
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - William A Sharpless
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher B Eiben
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Joint Program in Bioengineering, University of California, Berkeley, California, USA
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Centro de Biotecnología FEMSA, Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, México
| | - Jacquelyn M Blake-Hedges
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Catharine A Adams
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Robert W Haushalter
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rohith N Krishna
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Patrick Lichtner
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Patrick M Shih
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant Biology, University of California, Davis, California, USA
- Environmental and Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Joint Program in Bioengineering, University of California, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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56
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Biggs BW, Bedore SR, Arvay E, Huang S, Subramanian H, McIntyre EA, Duscent-Maitland CV, Neidle EL, Tyo KEJ. Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1. Nucleic Acids Res 2020; 48:5169-5182. [PMID: 32246719 PMCID: PMC7229861 DOI: 10.1093/nar/gkaa167] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/20/2020] [Accepted: 03/04/2020] [Indexed: 01/10/2023] Open
Abstract
One primary objective of synthetic biology is to improve the sustainability of chemical manufacturing. Naturally occurring biological systems can utilize a variety of carbon sources, including waste streams that pose challenges to traditional chemical processing, such as lignin biomass, providing opportunity for remediation and valorization of these materials. Success, however, depends on identifying micro-organisms that are both metabolically versatile and engineerable. Identifying organisms with this combination of traits has been a historic hindrance. Here, we leverage the facile genetics of the metabolically versatile bacterium Acinetobacter baylyi ADP1 to create easy and rapid molecular cloning workflows, including a Cas9-based single-step marker-less and scar-less genomic integration method. In addition, we create a promoter library, ribosomal binding site (RBS) variants and test an unprecedented number of rationally integrated bacterial chromosomal protein expression sites and variants. At last, we demonstrate the utility of these tools by examining ADP1’s catabolic repression regulation, creating a strain with improved potential for lignin bioprocessing. Taken together, this work highlights ADP1 as an ideal host for a variety of sustainability and synthetic biology applications.
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Affiliation(s)
- Bradley W Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Biotechnology Training Program, Northwestern University, Evanston, IL 60208, USA
| | - Stacy R Bedore
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Erika Arvay
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Biotechnology Training Program, Northwestern University, Evanston, IL 60208, USA
| | - Shu Huang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Harshith Subramanian
- Master of Science in Biotechnology Program, Northwestern University, Evanston, IL 60208, USA
| | - Emily A McIntyre
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | | | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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57
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Weimer A, Kohlstedt M, Volke DC, Nikel PI, Wittmann C. Industrial biotechnology of Pseudomonas putida: advances and prospects. Appl Microbiol Biotechnol 2020; 104:7745-7766. [PMID: 32789744 PMCID: PMC7447670 DOI: 10.1007/s00253-020-10811-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 08/02/2020] [Indexed: 11/17/2022]
Abstract
Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications of P. putida as a cell factory. KEY POINTS: • Pseudomonas putida advances to a global industrial cell factory. • Novel tools enable system-wide understanding and streamlined genomic engineering. • Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
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Affiliation(s)
- Anna Weimer
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany.
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58
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Capeness MJ, Horsfall LE. Synthetic biology approaches towards the recycling of metals from the environment. Biochem Soc Trans 2020; 48:1367-1378. [PMID: 32627824 PMCID: PMC7458392 DOI: 10.1042/bst20190837] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/29/2020] [Accepted: 06/08/2020] [Indexed: 01/05/2023]
Abstract
Metals are a finite resource and their demand for use within existing and new technologies means metal scarcity is increasingly a global challenge. Conversely, there are areas containing such high levels of metal pollution that they are hazardous to life, and there is loss of material at every stage of the lifecycle of metals and their products. While traditional resource extraction methods are becoming less cost effective, due to a lowering quality of ore, industrial practices have begun turning to newer technologies to tap into metal resources currently locked up in contaminated land or lost in the extraction and manufacturing processes. One such technology uses biology for the remediation of metals, simultaneously extracting resources, decontaminating land, and reducing waste. Using biology for the identification and recovery of metals is considered a much 'greener' alternative to that of chemical methods, and this approach is about to undergo a renaissance thanks to synthetic biology. Synthetic biology couples molecular genetics with traditional engineering principles, incorporating a modular and standardised practice into the assembly of genetic parts. This has allowed the use of non-model organisms in place of the normal laboratory strains, as well as the adaption of environmentally sourced genetic material to standardised parts and practices. While synthetic biology is revolutionising the genetic capability of standard model organisms, there has been limited incursion into current practices for the biological recovery of metals from environmental sources. This mini-review will focus on some of the areas that have potential roles to play in these processes.
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Affiliation(s)
- Michael J. Capeness
- Centre for Systems and Synthetic Biology, and the Centre for Science at Extreme Conditions, School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, U.K
| | - Louise E. Horsfall
- Centre for Systems and Synthetic Biology, and the Centre for Science at Extreme Conditions, School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, U.K
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59
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Kim NM, Sinnott RW, Sandoval NR. Transcription factor-based biosensors and inducible systems in non-model bacteria: current progress and future directions. Curr Opin Biotechnol 2020; 64:39-46. [DOI: 10.1016/j.copbio.2019.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 10/25/2022]
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60
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Incha MR, Thompson MG, Blake-Hedges JM, Liu Y, Pearson AN, Schmidt M, Gin JW, Petzold CJ, Deutschbauer AM, Keasling JD. Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida. Metab Eng Commun 2020; 10:e00119. [PMID: 32280587 PMCID: PMC7136493 DOI: 10.1016/j.mec.2019.e00119] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas putida is a saprophytic bacterium with robust metabolisms and strong solvent tolerance making it an attractive host for metabolic engineering and bioremediation. Due to its diverse carbon metabolisms, its genome encodes an array of proteins and enzymes that can be readily applied to produce valuable products. In this work we sought to identify design principles and bottlenecks in the production of type III polyketide synthase (T3PKS)-derived compounds in P. putida. T3PKS products are widely used as nutraceuticals and medicines and often require aromatic starter units, such as coumaroyl-CoA, which is also an intermediate in the native coumarate catabolic pathway of P. putida. Using a randomly barcoded transposon mutant (RB-TnSeq) library, we assayed gene functions for a large portion of aromatic catabolism, confirmed known pathways, and proposed new annotations for two aromatic transporters. The 1,3,6,8-tetrahydroxynapthalene synthase of Streptomyces coelicolor (RppA), a microbial T3PKS, was then used to rapidly assay growth conditions for increased T3PKS product accumulation. The feruloyl/coumaroyl CoA synthetase (Fcs) of P. putida was used to supply coumaroyl-CoA for the curcuminoid synthase (CUS) of Oryza sativa, a plant T3PKS. We identified that accumulation of coumaroyl-CoA in this pathway results in extended growth lag times in P. putida. Deletion of the second step in coumarate catabolism, the enoyl-CoA hydratase-lyase (Ech), resulted in increased production of the type III polyketide bisdemethoxycurcumin.
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Affiliation(s)
- Matthew R. Incha
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jacquelyn M. Blake-Hedges
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Allison N. Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Matthias Schmidt
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer W. Gin
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J. Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam M. Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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61
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Thompson MG, Moore WM, Hummel NFC, Pearson AN, Barnum CR, Scheller HV, Shih PM. Agrobacterium tumefaciens: A Bacterium Primed for Synthetic Biology. BIODESIGN RESEARCH 2020; 2020:8189219. [PMID: 37849895 PMCID: PMC10530663 DOI: 10.34133/2020/8189219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 04/26/2020] [Indexed: 10/19/2023] Open
Abstract
Agrobacterium tumefaciens is an important tool in plant biotechnology due to its natural ability to transfer DNA into the genomes of host plants. Genetic manipulations of A. tumefaciens have yielded considerable advances in increasing transformational efficiency in a number of plant species and cultivars. Moreover, there is overwhelming evidence that modulating the expression of various mediators of A. tumefaciens virulence can lead to more successful plant transformation; thus, the application of synthetic biology to enable targeted engineering of the bacterium may enable new opportunities for advancing plant biotechnology. In this review, we highlight engineering targets in both A. tumefaciens and plant hosts that could be exploited more effectively through precision genetic control to generate high-quality transformation events in a wider range of host plants. We then further discuss the current state of A. tumefaciens and plant engineering with regard to plant transformation and describe how future work may incorporate a rigorous synthetic biology approach to tailor strains of A. tumefaciens used in plant transformation.
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Affiliation(s)
- Mitchell G. Thompson
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
| | - William M. Moore
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Niklas F. C. Hummel
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
| | - Allison N. Pearson
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Collin R. Barnum
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
| | - Henrik V. Scheller
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Patrick M. Shih
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
- Genome Center, University of California-Davis, Davis, CA, USA
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Pham NN, Chen CY, Li H, Nguyen MTT, Nguyen PKP, Tsai SL, Chou JY, Ramli TC, Hu YC. Engineering Stable Pseudomonas putida S12 by CRISPR for 2,5-Furandicarboxylic Acid (FDCA) Production. ACS Synth Biol 2020; 9:1138-1149. [PMID: 32298581 DOI: 10.1021/acssynbio.0c00006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
FDCA (2,5-furandicarboxylic acid) can be enzymatically converted from HMF (5-hydroxymethylfurfural). Pseudomonas putida S12 is promising for FDCA production, but generating stable P. putida S12 is difficult due to its polyploidy and lack of genome engineering tools. Here we showed that coupling CRISPR and λ-Red recombineering enabled one-step gene integration with high efficiency and frequency, and simultaneously replaced endogenous genes in all chromosomes. Using this approach, we generated two stable P. putida S12 strains expressing HMF/furfural oxidoreductase (HMFH) and HMF oxidase (HMFO), both being able to convert 50 mM HMF to ≈42-43 mM FDCA in 24 h. Cosupplementation of MnO2 and CaCO3 to the medium drastically improved the cell tolerance to HMF and enhanced FDCA production. Cointegrating HMFH and HMFT1 (HMF transporter) genes further improved FDCA production, enabling the cells to convert 250 mM HMF to 196 mM (30.6 g/L) FDCA in 24 h. This study implicates the potentials of CRISPR for generating stable P. putida S12 strains for FDCA production.
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Affiliation(s)
- Nam Ngoc Pham
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Cho-Yi Chen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hung Li
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Mai Thanh Thi Nguyen
- Faculty of Chemistry, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City 72711, Vietnam
| | - Phung Kim Phi Nguyen
- Faculty of Chemistry, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City 72711, Vietnam
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - June-Yen Chou
- Innovation and R&D Division, Chang Chun Group, Taipei 10483, Taiwan
| | - Theresia Cecylia Ramli
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
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Ramesh A, Ong T, Garcia JA, Adams J, Wheeldon I. Guide RNA Engineering Enables Dual Purpose CRISPR-Cpf1 for Simultaneous Gene Editing and Gene Regulation in Yarrowia lipolytica. ACS Synth Biol 2020; 9:967-971. [PMID: 32208677 DOI: 10.1021/acssynbio.9b00498] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Yarrowia lipolytica has fast become a biotechnologically significant yeast for its ability to accumulate lipids to high levels. While there exists a suite of synthetic biology tools for genetic engineering in this yeast, there is a need for multipurposed tools for rapid strain generation. Here, we describe a dual purpose CRISPR-Cpf1 system that is capable of simultaneous gene disruption and gene regulation. Truncating guide RNA spacer length to 16 nt inhibited nuclease activity but not binding to the target loci, enabling gene activation and repression with Cpf1-fused transcriptional regulators. Gene repression was demonstrated using a Cpf1-Mxi1 fusion achieving a 7-fold reduction in mRNA, while CRISPR-activation with Cpf1-VPR increased hrGFP expression by 10-fold. High efficiency disruptions were achieved with gRNAs 23-25 bp in length, and efficiency and repression levels were maintained with multiplexed expression of truncated and full-length gRNAs. The developed CRISPR-Cpf1 system should prove useful in metabolic engineering, genome wide screening, and functional genomics studies.
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Affiliation(s)
- Adithya Ramesh
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Thomas Ong
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Jaime A Garcia
- Department of Physics and Environmental Science, St. Mary's University, San Antonio, Texas 78228, United States
| | - Jessica Adams
- Molecular and Cell Biology Department, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
- Center for Industrial Biotechnology, Bourns College of Engineering, University of California Riverside, Riverside, California 92521, United States
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Apura P, Saramago M, Peregrina A, Viegas SC, Carvalho SM, Saraiva LM, Arraiano CM, Domingues S. Tailor-made sRNAs: a plasmid tool to control the expression of target mRNAs in Pseudomonas putida. Plasmid 2020; 109:102503. [PMID: 32209400 DOI: 10.1016/j.plasmid.2020.102503] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 11/25/2022]
Abstract
Pseudomonas putida is a highly attractive production system for industrial needs. However, for its improvement as a biocatalyst at the industrial level, modulation of its gene expression is urgently needed. We report the construction of a plasmid expressing a small RNA-based system with the potential to be used for different purposes. Due to the small RNAs modular composition, the design facilities and ability to tune gene expression, they constitute a powerful tool in genetic and metabolic engineering. In the tool presented here, customized sRNAs are expressed from a plasmid and specifically directed to any region of a chosen target. Expression of these customized sRNAs is shown to differentially modulate the level of endogenous and heterologous reporter genes. The antisense interaction of the sRNA with the mRNA produces different outcomes. Depending on the particularity of each sRNA-target mRNA pair, we demonstrate the duality of this system, which is able either to decrease or increase the expression of the same given gene. This system combines high specificity with the potential to be widely applied, due to its predicted ability to modulate the expression of virtually any given gene. This plasmid can be used to redesign P. putida metabolism, fulfilling an important industrial gap.
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Affiliation(s)
- Patrícia Apura
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Margarida Saramago
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alexandra Peregrina
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sandra C Viegas
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Sandra M Carvalho
- Molecular Mechanisms of Pathogen Resistance Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lígia M Saraiva
- Molecular Mechanisms of Pathogen Resistance Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Susana Domingues
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Ho J, Zhao M, Wojcik S, Taiaroa G, Butler M, Poulter R. The application of the CRISPR–Cas9 system in Pseudomonas syringae pv. actinidiae. J Med Microbiol 2020; 69:478-486. [DOI: 10.1099/jmm.0.001124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Introduction.Pseudomonas syringaepv. actinidiae (Psa) has emerged as a major bacterial pathogen of kiwifruit cultivation throughout the world.Aim.We aim to introduce a CRISPR–Cas9 system, a commonly used genome editing tool, into Psa. The protocols may also be useful in otherPseudomonasspecies.Methodology.Using standard molecular biology techniques, we modified plasmid pCas9, which carries the CRISPR–Cas9 sequences fromStreptococcus pyogenes,for use in Psa. The final plasmid, pJH1, was produced in a series of steps and is maintained with selection in bothEscherichia coliand Psa.Results.We have constructed plasmids carrying a CRISPR–Cas9 system based on that ofS. pyogenes, which can be maintained, under selection, in Psa. We have shown that the gene targeting capacity of the CRISPR–Cas9 system is active and that the Cas9 protein is able to cleave the targeted sites. The Cas9 was directed to several different sites in theP. syringaegenome. Using Cas9 we have generated Psa transformants that no longer carry the native plasmid present in Psa, and other transformants that lack the integrative, conjugative element, Pac_ICE1. Targeting of a specific gene, a chromosomal non-ribosomal peptide synthetase, led to gene knockouts with the transformants having deletions encompassing the target site.Conclusion.We have constructed shuttle plasmids carrying a CRISPR–Cas9 system that are maintained in bothE. coliandP. syringaepv. actinidiae. We have used this gene editing system to eliminate features of the accessory genome (plasmids or ICEs) from Psa and to target a single chromosomal gene.
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Affiliation(s)
- Joycelyn Ho
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Min Zhao
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Samuel Wojcik
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - George Taiaroa
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Margi Butler
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Russell Poulter
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Schäfer L, Karande R, Bühler B. Maximizing Biocatalytic Cyclohexane Hydroxylation by Modulating Cytochrome P450 Monooxygenase Expression in P. taiwanensis VLB120. Front Bioeng Biotechnol 2020; 8:140. [PMID: 32175317 PMCID: PMC7056670 DOI: 10.3389/fbioe.2020.00140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/11/2020] [Indexed: 01/31/2023] Open
Abstract
Cytochrome P450 monooxygenases (Cyps) effectively catalyze the regiospecific oxyfunctionalization of inert C-H bonds under mild conditions. Due to their cofactor dependency and instability in isolated form, oxygenases are preferably applied in living microbial cells with Pseudomonas strains constituting potent host organisms for Cyps. This study presents a holistic genetic engineering approach, considering gene dosage, transcriptional, and translational levels, to engineer an effective Cyp-based whole-cell biocatalyst, building on recombinant Pseudomonas taiwanensis VLB120 for cyclohexane hydroxylation. A lac-based regulation system turned out to be favorable in terms of orthogonality to the host regulatory network and enabled a remarkable specific whole-cell activity of 34 U gCDW -1. The evaluation of different ribosomal binding sites (RBSs) revealed that a moderate translation rate was favorable in terms of the specific activity. An increase in gene dosage did only slightly elevate the hydroxylation activity, but severely impaired growth and resulted in a large fraction of inactive Cyp. Finally, the introduction of a terminator reduced leakiness. The optimized strain P. taiwanensis VLB120 pSEVA_Cyp allowed for a hydroxylation activity of 55 U gCDW -1. Applying 5 mM cyclohexane, molar conversion and biomass-specific yields of 82.5% and 2.46 mmolcyclohexanol gbiomass -1 were achieved, respectively. The strain now serves as a platform to design in vivo cascades and bioprocesses for the production of polymer building blocks such as ε-caprolactone.
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Affiliation(s)
- Lisa Schäfer
- Department of Solar Materials, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Rohan Karande
- Department of Solar Materials, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany
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67
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Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis. Nat Chem Biol 2020; 16:113-121. [DOI: 10.1038/s41589-019-0452-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
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Wirth NT, Kozaeva E, Nikel PI. Accelerated genome engineering of Pseudomonas putida by I-SceI-mediated recombination and CRISPR-Cas9 counterselection. Microb Biotechnol 2020; 13:233-249. [PMID: 30861315 PMCID: PMC6922521 DOI: 10.1111/1751-7915.13396] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas species have become reliable platforms for bioproduction due to their capability to tolerate harsh conditions imposed by large-scale bioprocesses and their remarkable resistance to diverse physicochemical stresses. The last few years have brought forth a variety of synthetic biology tools for the genetic manipulation of pseudomonads, but most of them are either applicable only to obtain certain types of mutations, lack efficiency, or are not easily accessible to be used in different Pseudomonas species (e.g. natural isolates). In this work, we describe a versatile, robust and user-friendly procedure that facilitates virtually any kind of genomic manipulation in Pseudomonas species in 3-5 days. The protocol presented here is based on DNA recombination forced by double-stranded DNA cuts (through the activity of the I-SceI homing meganuclease from yeast) followed by highly efficient counterselection of mutants (aided by a synthetic CRISPR-Cas9 device). The individual parts of the genome engineering toolbox, tailored for knocking genes in and out, have been standardized to enable portability and easy exchange of functional gene modules as needed. The applicability of the procedure is illustrated both by eliminating selected genomic regions in the platform strain P. putida KT2440 (including difficult-to-delete genes) and by integrating different reporter genes (comprising novel variants of fluorescent proteins) into a defined landing site in the target chromosome.
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Affiliation(s)
- Nicolas T. Wirth
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
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69
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Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
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70
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Li X, Zheng Y. Biotransformation of lignin: Mechanisms, applications and future work. Biotechnol Prog 2019; 36:e2922. [PMID: 31587530 DOI: 10.1002/btpr.2922] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 01/04/2023]
Abstract
As one of the most abundant polymers in biosphere, lignin has attracted extensive attention as a kind of promising feedstock for biofuel and bio-based products. However, the utilization of lignin presents various challenges in that its complex composition and structure and high resistance to degradation. Lignin conversion through biological platform harnesses the catalytic power of microorganisms to decompose complex lignin molecules and obtain value-added products through biosynthesis. Given the heterogeneity of lignin, various microbial metabolic pathways are involved in lignin bioconversion processes, which has been characterized in extensive research work. With different types of lignin substrates (e.g., model compounds, technical lignin, and lignocellulosic biomass), several bacterial and fungal species have been proved to own lignin-degrading abilities and accumulate microbial products (e.g., lipid and polyhydroxyalkanoates), while the lignin conversion efficiencies are still relatively low. Genetic and metabolic strategies have been developed to enhance lignin biodegradation by reprogramming microbial metabolism, and diverse products, such as vanillin and dicarboxylic acids were also produced from lignin. This article aims at presenting a comprehensive review on lignin bioconversion including lignin degradation mechanisms, metabolic pathways, and applications for the production of value-added bioproducts. Advanced techniques on genetic and metabolic engineering are also covered in the recent development of biological platforms for lignin utilization. To conclude this article, the existing challenges for efficient lignin bioprocessing are analyzed and possible directions for future work are proposed.
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Affiliation(s)
- Xiang Li
- Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas
| | - Yi Zheng
- Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas
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71
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Pseudomonas putida in the quest of programmable chemistry. Curr Opin Biotechnol 2019; 59:111-121. [DOI: 10.1016/j.copbio.2019.03.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/15/2019] [Accepted: 03/12/2019] [Indexed: 11/19/2022]
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72
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Kampers LFC, Volkers RJM, Martins dos Santos VAP. Pseudomonas putida KT2440 is HV1 certified, not GRAS. Microb Biotechnol 2019; 12:845-848. [PMID: 31199068 PMCID: PMC6680625 DOI: 10.1111/1751-7915.13443] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 01/13/2023] Open
Abstract
Pseudomonas putida is rapidly becoming a workhorse for industrial production due to its metabolic versatility, genetic accessibility and stress-resistance properties. The P. putida strain KT2440 is often described as Generally Regarded as Safe, or GRAS, indicating the strain is safe to use as food additive. This description is incorrect. P. putida KT2440 is classified by the FDA as HV1 certified, indicating it is safe to use in a P1 or ML1 environment.
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Affiliation(s)
- Linde F. C. Kampers
- Laboratory of Systems and Synthetic BiologyWageningen University and Research CentreStippeneng 46708WageningenThe Netherlands
| | - Rita J. M. Volkers
- Laboratory of Systems and Synthetic BiologyWageningen University and Research CentreStippeneng 46708WageningenThe Netherlands
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic BiologyWageningen University and Research CentreStippeneng 46708WageningenThe Netherlands
- Lifeglimmer GmbHMarkelstr. 3812163BerlinGermany
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73
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Nora LC, Westmann CA, Guazzaroni ME, Siddaiah C, Gupta VK, Silva-Rocha R. Recent advances in plasmid-based tools for establishing novel microbial chassis. Biotechnol Adv 2019; 37:107433. [PMID: 31437573 DOI: 10.1016/j.biotechadv.2019.107433] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 12/28/2022]
Abstract
A key challenge for domesticating alternative cultivable microorganisms with biotechnological potential lies in the development of innovative technologies. Within this framework, a myriad of genetic tools has flourished, allowing the design and manipulation of complex synthetic circuits and genomes to become the general rule in many laboratories rather than the exception. More recently, with the development of novel technologies such as DNA automated synthesis/sequencing and powerful computational tools, molecular biology has entered the synthetic biology era. In the beginning, most of these technologies were established in traditional microbial models (known as chassis in the synthetic biology framework) such as Escherichia coli and Saccharomyces cerevisiae, enabling fast advances in the field and the validation of fundamental proofs of concept. However, it soon became clear that these organisms, although extremely useful for prototyping many genetic tools, were not ideal for a wide range of biotechnological tasks due to intrinsic limitations in their molecular/physiological properties. Over the last decade, researchers have been facing the great challenge of shifting from these model systems to non-conventional chassis with endogenous capacities for dealing with specific tasks. The key to address these issues includes the generation of narrow and broad host plasmid-based molecular tools and the development of novel methods for engineering genomes through homologous recombination systems, CRISPR/Cas9 and other alternative methods. Here, we address the most recent advances in plasmid-based tools for the construction of novel cell factories, including a guide for helping with "build-your-own" microbial host.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | | | - Vijai Kumar Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil.
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Cook TB, Pfleger BF. Leveraging synthetic biology for producing bioactive polyketides and non-ribosomal peptides in bacterial heterologous hosts. MEDCHEMCOMM 2019; 10:668-681. [PMID: 31191858 PMCID: PMC6540960 DOI: 10.1039/c9md00055k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/06/2019] [Indexed: 12/14/2022]
Abstract
Bacteria have historically been a rich source of natural products (e.g. polyketides and non-ribosomal peptides) that possess medically-relevant activities. Despite extensive discovery programs in both industry and academia, a plethora of biosynthetic pathways remain uncharacterized and the corresponding molecular products untested for potential bioactivities. This knowledge gap comes in part from the fact that many putative natural product producers have not been cultured in conventional laboratory settings in which the corresponding products are produced at detectable levels. Next-generation sequencing technologies are further increasing the knowledge gap by obtaining metagenomic sequence information from complex communities where production of the desired compound cannot be isolated in the laboratory. For these reasons, many groups are turning to synthetic biology to produce putative natural products in heterologous hosts. This strategy depends on the ability to heterologously express putative biosynthetic gene clusters and produce relevant quantities of the corresponding products. Actinobacteria remain the most abundant source of natural products and the most promising heterologous hosts for natural product discovery and production. However, researchers are discovering more natural products from other groups of bacteria, such as myxobacteria and cyanobacteria. Therefore, phylogenetically similar heterologous hosts have become promising candidates for synthesizing these novel molecules. The downside of working with these microbes is the lack of well-characterized genetic tools for optimizing expression of gene clusters and product titers. This review examines heterologous expression of natural product gene clusters in terms of the motivations for this research, the traits desired in an ideal host, tools available to the field, and a survey of recent progress.
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Affiliation(s)
- Taylor B Cook
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Dr. Room 3629 , Madison , WI 53706 , USA .
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Dr. Room 3629 , Madison , WI 53706 , USA .
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75
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Lin GM, Warden-Rothman R, Voigt CA. Retrosynthetic design of metabolic pathways to chemicals not found in nature. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.04.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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76
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Volke DC, Turlin J, Mol V, Nikel PI. Physical decoupling of XylS/Pm regulatory elements and conditional proteolysis enable precise control of gene expression in Pseudomonas putida. Microb Biotechnol 2019; 13:222-232. [PMID: 30864281 PMCID: PMC6922516 DOI: 10.1111/1751-7915.13383] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 01/28/2023] Open
Abstract
Most of the gene expression systems available for Gram‐negative bacteria are afflicted by relatively high levels of basal (i.e. leaky) expression of the target gene(s). This occurrence affects the system dynamics, ultimately reducing the output and productivity of engineered pathways and synthetic circuits. In order to circumvent this problem, we have designed a novel expression system based on the well‐known XylS/Pm transcriptional regulator/promoter pair from the soil bacterium Pseudomonas putida mt‐2, in which the key functional elements are physically decoupled. By integrating the xylS gene into the chromosome of the platform strain KT2440, while placing the Pm promoter into a set of standard plasmid vectors, the inducibility of the system (i.e. the output difference between the induced and uninduced state) improved up to 170‐fold. We further combined this modular system with an extra layer of post‐translational control by means of conditional proteolysis. In this setup, the target gene is tagged with a synthetic motif dictating protein degradation. When the system features were characterized using the monomeric superfolder GFP as a model protein, the basal levels of fluorescence were brought down to zero (i.e. below the limit of detection). In all, these novel expression systems constitute an alternative tool to altogether suppress leaky gene expression, and they can be easily adapted to other vector formats and plugged‐in into different Gram‐negative bacterial species at the user's will.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Justine Turlin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Viviënne Mol
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
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Yin J, Zheng W, Gao Y, Jiang C, Shi H, Diao X, Li S, Chen H, Wang H, Li R, Li A, Xia L, Yin Y, Stewart AF, Zhang Y, Fu J. Single-Stranded DNA-Binding Protein and Exogenous RecBCD Inhibitors Enhance Phage-Derived Homologous Recombination in Pseudomonas. iScience 2019; 14:1-14. [PMID: 30921732 PMCID: PMC6438905 DOI: 10.1016/j.isci.2019.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/28/2018] [Accepted: 03/07/2019] [Indexed: 12/25/2022] Open
Abstract
The limited efficiency of the available tools for genetic manipulation of Pseudomonas limits fundamental research and utilization of this genus. We explored the properties of a lambda Red-like operon (BAS) from Pseudomonas aeruginosa phage Ab31 and a Rac bacteriophage RecET-like operon (RecTEPsy) from Pseudomonas syringae pv. syringae B728a. Compared with RecTEPsy, the BAS operon was functional at a higher temperature indicating potential to be a generic system for Pseudomonas. Owing to the lack of RecBCD inhibitor in the BAS operon, we added Redγ or Pluγ and found increased recombineering efficiencies in P. aeruginosa and Pseudomonas fluorescens but not in Pseudomonas putida and P. syringae. Overexpression of single-stranded DNA-binding protein enhanced recombineering in several contexts including RecET recombination in E. coli. The utility of these systems was demonstrated by engineering P. aeruginosa genomes to create an attenuated rhamnolipid producer. Our work enhances the potential for functional genomics in Pseudomonas. The BAS operon is a generic recombineering system for Pseudomonas species Single-stranded DNA-binding proteins (SSBs) can stimulate homologous recombination The heterologous gam genes can inhibit RecBCD function in Pseudomonas
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Affiliation(s)
- Jia Yin
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China; Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China
| | - Wentao Zheng
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Yunsheng Gao
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Chanjuan Jiang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Hongbo Shi
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Xiaotong Diao
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Shanshan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Hanna Chen
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China
| | - Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Ruijuan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Liqiu Xia
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China
| | - Yulong Yin
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China; Chinese Academy of Science, Institute of Subtropical Agriculture, Research Center for Healthy Breeding of Livestock and Poultry, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, 410125 Changsha, China
| | - A Francis Stewart
- Biotechnology Research Center, Center for Molecular and Cellular Bioengineering, Dresden University of Technology, BioInnovationsZentrum, Tatzberg 47-51, 01307 Dresden, Germany.
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China.
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China.
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78
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Kim SK, Yoon PK, Kim SJ, Woo SG, Rha E, Lee H, Yeom SJ, Kim H, Lee DH, Lee SG. CRISPR interference-mediated gene regulation in Pseudomonas putida KT2440. Microb Biotechnol 2019; 13:210-221. [PMID: 30793496 PMCID: PMC6922533 DOI: 10.1111/1751-7915.13382] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 01/08/2023] Open
Abstract
Targeted gene regulation is indispensable for reprogramming a cellular network to modulate a microbial phenotype. Here, we adopted the type II CRISPR interference (CRISPRi) system for simple and efficient regulation of target genes in Pseudomonas putida KT2440. A single CRISPRi plasmid was generated to express a nuclease-deficient Cas9 gene and a designed single guide RNA, under control of l-rhamnose-inducible Prha BAD and the constitutive Biobrick J23119 promoter respectively. Two target genes were selected to probe the CRISPRi-mediated gene regulation: exogenous green fluorescent protein on the multicopy plasmid and endogenous glpR on the P. putida KT2440 chromosome, encoding GlpR, a transcriptional regulator that represses expression of the glpFKRD gene cluster for glycerol utilization. The CRISPRi system successfully repressed the two target genes, as evidenced by a reduction in the fluorescence intensity and the lag phase of P. putida KT2440 cell growth on glycerol. Furthermore, CRISPRi-mediated repression of glpR improved both the cell growth and glycerol utilization, resulting in the enhanced production of mevalonate in an engineered P. putida KT2440 harbouring heterologous genes for the mevalonate pathway. CRISPRi is expected to become a robust tool to reprogram P. putida KT2440 for the development of microbial cell factories producing industrially valuable products.
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Affiliation(s)
- Seong Keun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Paul K Yoon
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Soo-Jung Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Seung-Gyun Woo
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Eugene Rha
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Hyewon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Soo-Jin Yeom
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
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79
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Choi KR, Lee SY. Protocols for RecET-based markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida. Microb Biotechnol 2019; 13:199-209. [PMID: 30761747 PMCID: PMC6922525 DOI: 10.1111/1751-7915.13374] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/19/2019] [Accepted: 01/19/2019] [Indexed: 11/27/2022] Open
Abstract
Pseudomonas putida has emerged as a promising host for the production of chemicals and materials thanks to its metabolic versatility and cellular robustness. In particular, P. putida KT2440 has been officially classified as a generally recognized as safe (GRAS) strain, which makes it suitable for the production of compounds that humans directly consume, including secondary metabolites of high importance. Although various tools and strategies have been developed to facilitate metabolic engineering of P. putida, modification of large genes/clusters essential for heterologous expression of natural products with large biosynthetic gene clusters (BGCs) has not been straightforward. Recently, we reported a RecET-based markerless recombineering system for engineering P. putida and demonstrated deletion of multiple regions as large as 101.7 kb throughout the chromosome by single rounds of recombineering. In addition, development of a donor plasmid system allowed successful markerless integration of heterologous BGCs to P. putida chromosome using the recombineering system with examples of - but not limited to - integrating multiple heterologous BGCs as large as 7.4 kb to the chromosome of P. putida KT2440. In response to the increasing interest in our markerless recombineering system, here we provide detailed protocols for markerless gene knockout and integration for the genome engineering of P. putida and related species of high industrial importance.
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Affiliation(s)
- Kyeong Rok Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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80
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Combination of ssDNA recombineering and CRISPR-Cas9 for Pseudomonas putida KT2440 genome editing. Appl Microbiol Biotechnol 2019; 103:2783-2795. [DOI: 10.1007/s00253-019-09654-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/11/2018] [Accepted: 01/17/2019] [Indexed: 12/17/2022]
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81
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Millacura FA, Janssen PJ, Monsieurs P, Janssen A, Provoost A, Van Houdt R, Rojas LA. Unintentional Genomic Changes Endow Cupriavidus metallidurans with an Augmented Heavy-Metal Resistance. Genes (Basel) 2018; 9:E551. [PMID: 30428624 PMCID: PMC6266692 DOI: 10.3390/genes9110551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 12/04/2022] Open
Abstract
For the past three decades, Cupriavidus metallidurans has been one of the major model organisms for bacterial tolerance to heavy metals. Its type strain CH34 contains at least 24 gene clusters distributed over four replicons, allowing for intricate and multilayered metal responses. To gain organic mercury resistance in CH34, broad-spectrum mer genes were introduced in a previous work via conjugation of the IncP-1β plasmid pTP6. However, we recently noted that this CH34-derived strain, MSR33, unexpectedly showed an increased resistance to other metals (i.e., Co2+, Ni2+, and Cd2+). To thoroughly investigate this phenomenon, we resequenced the entire genome of MSR33 and compared its DNA sequence and basal gene expression profile to those of its parental strain CH34. Genome comparison identified 11 insertions or deletions (INDELs) and nine single nucleotide polymorphisms (SNPs), whereas transcriptomic analysis displayed 107 differentially expressed genes. Sequence data implicated the transposition of IS1088 in higher Co2+ and Ni2+ resistances and altered gene expression, although the precise mechanisms of the augmented Cd2+ resistance in MSR33 remains elusive. Our work indicates that conjugation procedures involving large complex genomes and extensive mobilomes may pose a considerable risk toward the introduction of unwanted, undocumented genetic changes. Special efforts are needed for the applied use and further development of small nonconjugative broad-host plasmid vectors, ideally involving CRISPR-related and advanced biosynthetic technologies.
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Affiliation(s)
- Felipe A Millacura
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JQ, UK.
| | - Paul J Janssen
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Pieter Monsieurs
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Ann Janssen
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Ann Provoost
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Rob Van Houdt
- Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium.
| | - Luis A Rojas
- Chemistry Department, Faculty of Sciences, Universidad Católica del Norte, UCN, Antofagasta 1240000, Chile.
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82
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Nikel PI, de Lorenzo V. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng 2018; 50:142-155. [DOI: 10.1016/j.ymben.2018.05.005] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/12/2022]
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83
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Freed E, Fenster J, Smolinski SL, Walker J, Henard CA, Gill R, Eckert CA. Building a genome engineering toolbox in nonmodel prokaryotic microbes. Biotechnol Bioeng 2018; 115:2120-2138. [PMID: 29750332 DOI: 10.1002/bit.26727] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/02/2018] [Accepted: 03/10/2018] [Indexed: 12/26/2022]
Abstract
The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop "design rules" for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.
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Affiliation(s)
- Emily Freed
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Jacob Fenster
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | | | - Julie Walker
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Calvin A Henard
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO
| | - Ryan Gill
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | - Carrie A Eckert
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
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84
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Markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida. Metab Eng 2018; 47:463-474. [PMID: 29751103 DOI: 10.1016/j.ymben.2018.05.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/05/2018] [Accepted: 05/06/2018] [Indexed: 11/22/2022]
Abstract
Pseudomonas putida has gained much interest among metabolic engineers as a workhorse for producing valuable natural products. While a few gene knockout tools for P. putida have been reported, integration of heterologous genes into the chromosome of P. putida, an essential strategy to develop stable industrial strains producing heterologous bioproducts, requires development of a more efficient method. Current methods rely on time-consuming homologous recombination techniques and transposon-mediated random insertions. Here we report a RecET recombineering system for markerless integration of heterologous genes into the P. putida chromosome. The efficiency and capacity of the recombineering system were first demonstrated by knocking out various genetic loci on the P. putida chromosome with knockout lengths widely spanning 0.6-101.7 kb. The RecET recombineering system developed here allowed successful integration of biosynthetic gene clusters for four proof-of-concept bioproducts, including protein, polyketide, isoprenoid, and amino acid derivative, into the target genetic locus of P. putida chromosome. The markerless recombineering system was completed by combining Cre/lox system and developing efficient plasmid curing systems, generating final strains free of antibiotic markers and plasmids. This markerless recombineering system for efficient gene knockout and integration will expedite metabolic engineering of P. putida, a bacterial host strain of increasing academic and industrial interest.
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85
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Qin Q, Ling C, Zhao Y, Yang T, Yin J, Guo Y, Chen GQ. CRISPR/Cas9 editing genome of extremophile Halomonas spp. Metab Eng 2018; 47:219-229. [PMID: 29609045 DOI: 10.1016/j.ymben.2018.03.018] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/29/2018] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Extremophiles are suitable chassis for developing the next generation industrial biotechnology (NGIB) due to their resistance to microbial contamination. However, engineering extremophiles are not an easy task. Halomonas, an industrially interesting halophile able to grow under unsterile and continuous conditions in large-scale processes, can only be engineered using suicide plasmid-mediated two-step homologous recombination which is very laborious and time-consuming (up to half a year). A convenient approach for the engineering of halophiles that can possibly be extended to other extremophiles is therefore urgently required. To meet this requirement, a rapid, efficient and scarless method via CRISPR/Cas9 system was developed in this study for genome editing in Halomonas. The method achieved the highest efficiency of 100%. When eight different mutants were constructed via this special CRISPR/Cas9 method to study the combinatorial influences of four different genes on the glucose catabolism in H. bluephagenesis TD01, it took only three weeks to complete the deletion and insertion of up to 4.5 kb DNA. H. bluephagenesis was designed to produce a microbial copolymer P(3HB-co-3HV) consisting of 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV). The CRISPR/Cas9 was employed to delete the prpC gene in H. bluephagenesis TD01. Shake flask studies showed that the 3HV fraction in the copolymers increased approximately 16-folds, demonstrating enhanced effectiveness of the ΔprpC mutant to synthesize PHBV. This genome engineering strategy significantly speeds up the studies on Halomonas engineering, opening up a wide area for developing NGIB.
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Affiliation(s)
- Qin Qin
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chen Ling
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yiqing Zhao
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tian Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jin Yin
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yingying Guo
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Guo Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; MOE Key Lab of Bioinformatics, Center for Nano and Micro Mechanics, Tsinghua University, Beijing 100084, China; MOE Key Lab of Industrial Biocatalysis, Tsinghua University, Beijing 100084, China.
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