1
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Guo L, Xi B, Lu L. Strategies to enhance production of metabolites in microbial co-culture systems. BIORESOURCE TECHNOLOGY 2024; 406:131049. [PMID: 38942211 DOI: 10.1016/j.biortech.2024.131049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/06/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Increasing evidence shows that microbial synthesis plays an important role in producing high value-added products. However, microbial monoculture generally hampers metabolites production and limits scalability due to the increased metabolic burden on the host strain. In contrast, co-culture is a more flexible approach to improve the environmental adaptability and reduce the overall metabolic burden. The well-defined co-culturing microbial consortia can tap their metabolic potential to obtain yet-to-be discovered and pre-existing metabolites. This review focuses on the use of a co-culture strategy and its underlying mechanisms to enhance the production of products. Notably, the significance of comprehending the microbial interactions, diverse communication modes, genetic information, and modular co-culture involved in co-culture systems were highlighted. Furthermore, it addresses the current challenges and outlines potential future directions for microbial co-culture. This review provides better understanding the diversity and complexity of the interesting interaction and communication to advance the development of co-culture techniques.
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Affiliation(s)
- Lichun Guo
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Bingwen Xi
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China
| | - Liushen Lu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China.
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2
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Radde N, Mortensen GA, Bhat D, Shah S, Clements JJ, Leonard SP, McGuffie MJ, Mishler DM, Barrick JE. Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology. Nat Commun 2024; 15:6242. [PMID: 39048554 PMCID: PMC11269670 DOI: 10.1038/s41467-024-50639-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
Engineered DNA will slow the growth of a host cell if it redirects limiting resources or otherwise interferes with homeostasis. Escape mutants that alleviate this burden can rapidly evolve and take over cell populations, making genetic engineering less reliable and predictable. Synthetic biologists often use genetic parts encoded on plasmids, but their burden is rarely characterized. We measured how 301 BioBrick plasmids affected Escherichia coli growth and found that 59 (19.6%) were burdensome, primarily because they depleted the limited gene expression resources of host cells. Overall, no BioBricks reduced the growth rate of E. coli by >45%, which agreed with a population genetic model that predicts such plasmids should be unclonable. We made this model available online for education ( https://barricklab.org/burden-model ) and added our burden measurements to the iGEM Registry. Our results establish a fundamental limit on what DNA constructs and genetic modifications can be successfully engineered into cells.
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Affiliation(s)
- Noor Radde
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Genevieve A Mortensen
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Diya Bhat
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Shireen Shah
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Joseph J Clements
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Sean P Leonard
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Matthew J McGuffie
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Dennis M Mishler
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
- The Freshman Research Initiative, College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
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3
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Fedorec AJH, Treloar NJ, Wen KY, Dekker L, Ong QH, Jurkeviciute G, Lyu E, Rutter JW, Zhang KJY, Rosa L, Zaikin A, Barnes CP. Emergent digital bio-computation through spatial diffusion and engineered bacteria. Nat Commun 2024; 15:4896. [PMID: 38851790 PMCID: PMC11162413 DOI: 10.1038/s41467-024-49264-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Biological computing is a promising field with potential applications in biosafety, environmental monitoring, and personalized medicine. Here we present work on the design of bacterial computers using spatial patterning to process information in the form of diffusible morphogen-like signals. We demonstrate, mathematically and experimentally, that single, modular, colonies can perform simple digital logic, and that complex functions can be built by combining multiple colonies, removing the need for further genetic engineering. We extend our experimental system to incorporate sender colonies as morphogen sources, demonstrating how one might integrate different biochemical inputs. Our approach will open up ways to perform biological computation, with applications in bioengineering, biomaterials and biosensing. Ultimately, these computational bacterial communities will help us explore information processing in natural biological systems.
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Affiliation(s)
- Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
| | - Neythen J Treloar
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Ke Yan Wen
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Linda Dekker
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Qing Hsuan Ong
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Gabija Jurkeviciute
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Enbo Lyu
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Jack W Rutter
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Kathleen J Y Zhang
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Luca Rosa
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Alexey Zaikin
- Department of Mathematics, University College London, London, WC1E 6BT, UK
- Institute for Women's Health, University College London, London, WC1E 6BT, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
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4
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Shomar H, Bokinsky G. Harnessing iron‑sulfur enzymes for synthetic biology. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119718. [PMID: 38574823 DOI: 10.1016/j.bbamcr.2024.119718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Reactions catalysed by iron-sulfur (Fe-S) enzymes appear in a variety of biosynthetic pathways that produce valuable natural products. Harnessing these biosynthetic pathways by expression in microbial cell factories grown on an industrial scale would yield enormous economic and environmental benefits. However, Fe-S enzymes often become bottlenecks that limits the productivity of engineered pathways. As a consequence, achieving the production metrics required for industrial application remains a distant goal for Fe-S enzyme-dependent pathways. Here, we identify and review three core challenges in harnessing Fe-S enzyme activity, which all stem from the properties of Fe-S clusters: 1) limited Fe-S cluster supply within the host cell, 2) Fe-S cluster instability, and 3) lack of specialized reducing cofactor proteins often required for Fe-S enzyme activity, such as enzyme-specific flavodoxins and ferredoxins. We highlight successful methods developed for a variety of Fe-S enzymes and electron carriers for overcoming these difficulties. We use heterologous nitrogenase expression as a grand case study demonstrating how each of these challenges can be addressed. We predict that recent breakthroughs in protein structure prediction and design will prove well-suited to addressing each of these challenges. A reliable toolkit for harnessing Fe-S enzymes in engineered metabolic pathways will accelerate the development of industry-ready Fe-S enzyme-dependent biosynthesis pathways.
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Affiliation(s)
- Helena Shomar
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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5
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McGuffie MJ, Barrick JE. Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences. PLoS One 2024; 19:e0304164. [PMID: 38805426 PMCID: PMC11132462 DOI: 10.1371/journal.pone.0304164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and to reprogram cells by combining these parts in new ways. Historically, many genetic parts on plasmids were copied and reused without routinely checking their DNA sequences. With the widespread use of high-throughput DNA sequencing technologies, we now know that plasmids often contain variants of common genetic parts that differ slightly from their canonical sequences. Because the exact provenance of a genetic part on a particular plasmid is usually unknown, it is difficult to determine whether these differences arose due to mutations during plasmid construction and propagation or due to intentional editing by researchers. In either case, it is important to understand how the sequence changes alter the properties of the genetic part. We analyzed the sequences of over 50,000 engineered plasmids using depositor metadata and a metric inspired by the natural language processing field. We detected 217 uncatalogued genetic part variants that were especially widespread or were likely the result of convergent evolution or engineering. Several of these uncatalogued variants are known mutants of plasmid origins of replication or antibiotic resistance genes that are missing from current annotation databases. However, most are uncharacterized, and 3/5 of the plasmids we analyzed contained at least one of the uncatalogued variants. Our results include a list of genetic parts to prioritize for refining engineered plasmid annotation pipelines, highlight widespread variants of parts that warrant further investigation to see whether they have altered characteristics, and suggest cases where unintentional evolution of plasmid parts may be affecting the reliability and reproducibility of science.
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Affiliation(s)
- Matthew J. McGuffie
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
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6
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Vazquez-Uribe R, Hedin KA, Licht TR, Nieuwdorp M, Sommer MOA. Advanced microbiome therapeutics as a novel modality for oral delivery of peptides to manage metabolic diseases. Trends Endocrinol Metab 2024:S1043-2760(24)00115-2. [PMID: 38782649 DOI: 10.1016/j.tem.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The rising prevalence of metabolic diseases calls for innovative treatments. Peptide-based drugs have transformed the management of conditions such as obesity and type 2 diabetes. Yet, challenges persist in oral delivery of these peptides. This review explores the potential of 'advanced microbiome therapeutics' (AMTs), which involve engineered microbes for delivery of peptides in situ, thereby enhancing their bioavailability. Preclinical work on AMTs has shown promise in treating animal models of metabolic diseases, including obesity, type 2 diabetes, and metabolic dysfunction-associated steatotic liver disease. Outstanding challenges toward realizing the potential of AMTs involve improving peptide expression, ensuring predictable colonization control, enhancing stability, and managing safety and biocontainment concerns. Still, AMTs have potential for revolutionizing the treatment of metabolic diseases, potentially offering dynamic and personalized novel therapeutic approaches.
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Affiliation(s)
- Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Karl Alex Hedin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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7
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Duperray M, Delvenne M, François JM, Delvigne F, Capp JP. Genomic and metabolic instability during long-term fermentation of an industrial Saccharomyces cerevisiae strain engineered for C5 sugar utilization. Front Bioeng Biotechnol 2024; 12:1357671. [PMID: 38595997 PMCID: PMC11002265 DOI: 10.3389/fbioe.2024.1357671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/07/2024] [Indexed: 04/11/2024] Open
Abstract
The genetic stability and metabolic robustness of production strains is one of the key criteria for the production of bio-based products by microbial fermentation on an industrial scale. These criteria were here explored in an industrial ethanol-producer strain of Saccharomyces cerevisiae able to co-ferment D-xylose and L-arabinose with glucose through the chromosomal integration of several copies of pivotal genes for the use of these pentose (C5) sugars. Using batch sequential cultures in a controlled bioreactor that mimics long-term fermentation in an industrial setting, this strain was found to exhibit significant fluctuations in D-xylose and L-arabinose consumption as early as the 50th generation and beyond. These fluctuations seem not related to the few low-consumption C5 sugar clones that appeared throughout the sequential batch cultures at a frequency lower than 1.5% and that were due to the reduction in the number of copies of transgenes coding for C5 sugar assimilation enzymes. Also, subpopulations enriched with low or high RAD52 expression, whose expression level was reported to be proportional to homologous recombination rate did not exhibit defect in C5-sugar assimilation, arguing that other mechanisms may be responsible for copy number variation of transgenes. Overall, this work highlighted the existence of genetic and metabolic instabilities in an industrial yeast which, although modest in our conditions, could be more deleterious in harsher industrial conditions, leading to reduced production performance.
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Affiliation(s)
- Maëlle Duperray
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
| | - Mathéo Delvenne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Jean Marie François
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
- Toulouse White Biotechnology, INSA, INRAE, CNRS, Toulouse, France
| | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
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8
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Arbel-Groissman M, Menuhin-Gruman I, Naki D, Bergman S, Tuller T. Fighting the battle against evolution: designing genetically modified organisms for evolutionary stability. Trends Biotechnol 2023; 41:1518-1531. [PMID: 37442714 DOI: 10.1016/j.tibtech.2023.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Synthetic biology has made significant progress in many areas, but a major challenge that has received limited attention is the evolutionary stability of synthetic constructs made of heterologous genes. The expression of these constructs in microorganisms, that is, production of proteins that are not necessary for the organism, is a metabolic burden, leading to a decrease in relative fitness and make the synthetic constructs unstable over time. This is a significant concern for the synthetic biology community, particularly when it comes to bringing this technology out of the laboratory. In this review, we discuss the issue of evolutionary stability in synthetic biology and review the available tools to address this challenge.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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9
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Cordell WT, Avolio G, Takors R, Pfleger BF. Milligrams to kilograms: making microbes work at scale. Trends Biotechnol 2023; 41:1442-1457. [PMID: 37271589 DOI: 10.1016/j.tibtech.2023.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023]
Abstract
If biomanufacturing can become a sustainable route for producing chemicals, it will provide a critical step in reducing greenhouse gas emissions to fight climate change. However, efforts to industrialize microbial synthesis of chemicals have met with varied success, due, in part, to challenges in translating laboratory successes to industrial scale. With a particular focus on Escherichia coli, this review examines the lessons learned when studying microbial physiology and metabolism under conditions that simulate large-scale bioreactors and methods to minimize cellular waste through reduction of maintenance energy, optimizing the stress response and minimizing culture heterogeneity. With general strategies to overcome these challenges, biomanufacturing process scale-up could be de-risked and the time and cost of bringing promising syntheses to market could be reduced.
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Affiliation(s)
- William T Cordell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gennaro Avolio
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Center Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.
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10
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Tavares LF, Ribeiro NV, Zocca VFB, Corrêa GG, Amorim LAS, Lins MRCR, Pedrolli DB. Preventing Production Escape Using an Engineered Glucose-Inducible Genetic Circuit. ACS Synth Biol 2023; 12:3124-3130. [PMID: 37772403 DOI: 10.1021/acssynbio.3c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
A proper balance of metabolic pathways is crucial for engineering microbial strains that can efficiently produce biochemicals on an industrial scale while maintaining cell fitness. High production loads can negatively impact cell fitness and hinder industrial-scale production. To address this, fine-tuning gene expression using engineered promoters and genetic circuits can promote control over multiple targets in pathways and reduce the burden. We took advantage of the robust carbon catabolite repression system of Bacillus subtilis to engineer a glucose-inducible genetic circuit that supports growth and production. The circuit is resilient, enabling a quick switch in the production status when exposed to the correct carbon source. By performing serial cultivations for 61 generations under repressive conditions, we preserved the production capacity of the cells, which could be fully accessed by switching to glucose in the next cultivation step. Switching to glucose after 61 generations resulted in 34-fold activation and generated 70% higher production in comparison to standard cultivation in glucose. Conversely, serial cultivation under permanent induction resulted in 62% production loss after 67 generations alongside an increase in the culture growth rate. As a pathway-independent circuit activated by the preferred carbon source, our engineered glucose-inducible genetic circuit is broadly useful and imposes no additional cost to traditional production processes.
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Affiliation(s)
- Leonardo F Tavares
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Araraquara, 14800-903, Brazil
| | - Nathan V Ribeiro
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Araraquara, 14800-903, Brazil
| | - Vitória F B Zocca
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Araraquara, 14800-903, Brazil
| | - Graciely G Corrêa
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Araraquara, 14800-903, Brazil
| | - Laura A S Amorim
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Araraquara, 14800-903, Brazil
| | - Milca R C R Lins
- Federal University of ABC (UFABC), Center for Natural and Human Sciences, Campus Santo André, 09210-580, Brazil
| | - Danielle B Pedrolli
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Araraquara, 14800-903, Brazil
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11
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Bragdon MDJ, Patel N, Chuang J, Levien E, Bashor CJ, Khalil AS. Cooperative assembly confers regulatory specificity and long-term genetic circuit stability. Cell 2023; 186:3810-3825.e18. [PMID: 37552983 PMCID: PMC10528910 DOI: 10.1016/j.cell.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/17/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023]
Abstract
A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc-finger-based TFs. We show that circuits "wired" using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.
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Affiliation(s)
- Meghan D J Bragdon
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA
| | - Nikit Patel
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James Chuang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ethan Levien
- Department of Mathematics, Dartmouth College, Hanover, NH 03755, USA
| | - Caleb J Bashor
- Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77030, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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12
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Liu L, Li J, Gai Y, Tian Z, Wang Y, Wang T, Liu P, Yuan Q, Ma H, Lee SY, Zhang D. Protein engineering and iterative multimodule optimization for vitamin B 6 production in Escherichia coli. Nat Commun 2023; 14:5304. [PMID: 37652926 PMCID: PMC10471632 DOI: 10.1038/s41467-023-40928-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Vitamin B6 is an essential nutrient with extensive applications in the medicine, food, animal feed, and cosmetics industries. Pyridoxine (PN), the most common commercial form of vitamin B6, is currently chemically synthesized using expensive and toxic chemicals. However, the low catalytic efficiencies of natural enzymes and the tight regulation of the metabolic pathway have hindered PN production by the microbial fermentation process. Here, we report an engineered Escherichia coli strain for PN production. Parallel pathway engineering is performed to decouple PN production and cell growth. Further, protein engineering is rationally designed including the inefficient enzymes PdxA, PdxJ, and the initial enzymes Epd and Dxs. By the iterative multimodule optimization strategy, the final strain produces 1.4 g/L of PN with productivity of 29.16 mg/L/h by fed-batch fermentation. The strategies reported here will be useful for developing microbial strains for the production of vitamins and other bioproducts having inherently low metabolic fluxes.
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Affiliation(s)
- Linxia Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jinlong Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanming Gai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhizhong Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yanyan Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tenghe Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qianqian Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 four program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- University of Chinese Academy of Sciences, Beijing, China.
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13
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Hoang MD, Polte I, Frantzmann L, von den Eichen N, Heins AL, Weuster-Botz D. Impact of mixing insufficiencies on L-phenylalanine production with an Escherichia coli reporter strain in a novel two-compartment bioreactor. Microb Cell Fact 2023; 22:153. [PMID: 37574555 PMCID: PMC10424407 DOI: 10.1186/s12934-023-02165-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023] Open
Abstract
BACKGROUND The omnipresence of population heterogeneity in industrial bioprocesses originates from prevailing dynamic bioprocess conditions, which promote differences in the expression of cellular characteristics. Despite the awareness, the concrete consequences of this phenomenon remain poorly understood. RESULTS Therefore, for the first time, a L-phenylalanine overproducing Escherichia coli quadruple reporter strain was established for monitoring of general stress response, growth behavior, oxygen limitation and product formation of single cells based on mTagBFP2, mEmerald, CyOFP1, and mCardinal2 expression measured by flow cytometry. This strain was applied for the fed-batch production of L-phenylalanine from glycerol and ammonia in a stirred-tank bioreactor at homogeneous conditions compared to the same process in a novel two-compartment bioreactor. This two-compartment bioreactor consists of a stirred-tank bioreactor with an initial volume of 0.9 L (homogeneous zone) with a coiled flow inverter with a fixed working volume of 0.45 L as a bypass (limitation zone) operated at a mean hydraulic residence time of 102 s. The product formation was similar in both bioreactor setups with maximum L-phenylalanine concentrations of 21.1 ± 0.6 g L-1 demonstrating the consistency of this study's microbial L-phenylalanine production. However, cell growth was vulnerable to repetitive exposure to the dynamically changing conditions in the two-compartment bioreactor with maximum biomass yields reduced by 21%. The functionality of reporter molecules was approved in the stirred-tank bioreactor cultivation, in which expressed fluorescence levels of all four markers were in accordance with respective process state variables. Additional evaluation of the distributions on single-cell level revealed the presence of population heterogeneity in both bioprocesses. Especially for the marker of the general stress response and the product formation, the corresponding histograms were characterized by bimodal shapes and broad distributions. These phenomena were pronounced particularly at the beginning and the end of the fed-batch process. CONCLUSIONS The here shown findings confirm multiple reporter strains to be a noninvasive tool for monitoring cellular characteristics and identifying potential subpopulations in bioprocesses. In combination with experiments in scale-down setups, these can be utilized for a better physiological understanding of bioprocesses and support future scale-up procedures.
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Affiliation(s)
- Manh Dat Hoang
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
| | - Ingmar Polte
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
| | - Lukas Frantzmann
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
| | - Nikolas von den Eichen
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
| | - Anna-Lena Heins
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany.
| | - Dirk Weuster-Botz
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
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14
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Zhi R, Cheng N, Li G, Deng Y. Biosensor-based high-throughput screening enabled efficient adipic acid production. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12669-z. [PMID: 37421473 DOI: 10.1007/s00253-023-12669-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/10/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
Adipic acid is an industrially important chemical, but the current approach to synthesize it can be of serious pollution to the environment. Rencently, bio-based production of adipic acid has significantly advanced with the development of metabolic engineering and synthetic biology. However, genetic heterogeneity-caused decrease of product titer has largely limited the industrialization of chemicals like adipic acid. Therefore, in the attempt to overcome this challenge, we constitutively expressed the reverse adipate degradation pathway, designed and optimized an adipic acid biosensor, and established a high-throughput screening platform to screen for high-performance strains based on the optimized biosensor. Using this platform, we successfully screened a strain with an adipic acid titer of 188.08 mg·L-1. Coupling the screening platform with fermentation optimization, the titer of adipic acid reached 531.88 mg·L-1 under shake flask fermentation, which achieved an 18.78-fold improvement comparing to the initial strain. Scale-up fermentation in a 5-L fermenter utilizing the screened high-performance strain was eventually conducted, in which the adipic acid titer reached 3.62 g·L-1. Overall, strategies developed in this study proved to be a potentially efficient method in reducing the genetic heterogeneity and was expected to provide guidance in helping to build a more efficient industrial screening process. KEY POINTS: • Developed a fine-tuned adipic acid biosensor. • Established a high-throughput screening platform to screen high-performance strains. • The titer of adipic acid reached 3.62 g·L-1 in a 5-L fermenter.
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Affiliation(s)
- Rui Zhi
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, Jiangsu, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Nan Cheng
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, Jiangsu, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Guohui Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Yu Deng
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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15
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Heieck K, Brück T. Localization of Insertion Sequences in Plasmids for L-Cysteine Production in E. coli. Genes (Basel) 2023; 14:1317. [PMID: 37510222 PMCID: PMC10379815 DOI: 10.3390/genes14071317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Insertion sequence elements (ISE) are often found to be responsible for the collapse of production in synthetically engineered Escherichia coli. By the transposition of ISE into the open reading frame of the synthetic pathway, E. coli cells gain selection advantage over cells expressing the metabolic burdensome production genes. Here, we present the exact entry sites of insertion sequence (IS) families 3 and 5 within plasmids for l-cysteine production in evolved E. coli populations. Furthermore, we identified an uncommon occurrence of an 8-bp direct repeat of IS5 which is atypical for this particular family, potentially indicating a new IS5 target site.
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Affiliation(s)
- Kevin Heieck
- School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Thomas Brück
- School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
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16
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Ingram D, Stan GB. Modelling genetic stability in engineered cell populations. Nat Commun 2023; 14:3471. [PMID: 37308512 DOI: 10.1038/s41467-023-38850-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/19/2023] [Indexed: 06/14/2023] Open
Abstract
Predicting the evolution of engineered cell populations is a highly sought-after goal in biotechnology. While models of evolutionary dynamics are far from new, their application to synthetic systems is scarce where the vast combination of genetic parts and regulatory elements creates a unique challenge. To address this gap, we here-in present a framework that allows one to connect the DNA design of varied genetic devices with mutation spread in a growing cell population. Users can specify the functional parts of their system and the degree of mutation heterogeneity to explore, after which our model generates host-aware transition dynamics between different mutation phenotypes over time. We show how our framework can be used to generate insightful hypotheses across broad applications, from how a device's components can be tweaked to optimise long-term protein yield and genetic shelf life, to generating new design paradigms for gene regulatory networks that improve their functionality.
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Affiliation(s)
- Duncan Ingram
- Centre of Excellence in Synthetic Biology and Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Guy-Bart Stan
- Centre of Excellence in Synthetic Biology and Department of Bioengineering, Imperial College London, London, United Kingdom.
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17
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Chen S, Fu J, Yu B, Wang L. Development of a Conjugation-Based Genome Editing System in an Undomesticated Bacillus subtilis Strain for Poly-γ-glutamic Acid Production with Diverse Molecular Masses. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7734-7743. [PMID: 37186794 DOI: 10.1021/acs.jafc.3c01505] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Poly-γ-glutamic acid (γ-PGA) is a biodegradable polymer produced by microorganisms. Biosynthesizing γ-PGA with diverse molecular masses (Mw) is an urgent industrial technical problem to be solved. Bacillus subtilis KH2, a high-Mw γ-PGA producer, is an ideal candidate for de novo production of γ-PGA with diverse Mw values. However, the inability to transfer DNA to this strain has limited its industrial use. In this study, a conjugation-based genetic operating system was developed in strain KH2. This system enabled us to modify the promoter of γ-PGA hydrolase PgdS in strain KH2 chromosome to de novo biosynthesize γ-PGA with diverse Mws. The conjugation efficiency was improved to 1.23 × 10-4 by establishing a plasmid replicon sharing strategy. A further increase to 3.15 × 10-3 was achieved after knocking out two restriction endonucleases. To demonstrate the potential of our newly established system, the pgdS promoter was replaced by different phase-dependent promoters. A series of strains producing γ-PGA with specific Mws of 411.73, 1356.80, 2233.30, and 2411.87 kDa, respectively, were obtained. The maximum yield of γ-PGA was 23.28 g/L. Therefore, we have successfully constructed ideal candidate strains for efficient γ-PGA production with a specific Mw value, which provides an important research basis for sustainable production of desirable γ-PGA.
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Affiliation(s)
- Shengbao Chen
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaming Fu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Limin Wang
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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18
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McGuffie MJ, Barrick JE. Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536277. [PMID: 37090600 PMCID: PMC10120640 DOI: 10.1101/2023.04.10.536277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and to reprogram cells by combining these parts in new ways. Historically, many genetic parts on plasmids were copied and reused without routinely checking their DNA sequences. With the widespread use of high-throughput DNA sequencing technologies, we now know that plasmids often contain variants of common genetic parts that differ slightly from their canonical sequences. Because the exact provenance of a genetic part on a particular plasmid is usually unknown, it is difficult to determine whether these differences arose due to mutations during plasmid construction and propagation or due to intentional editing by researchers. In either case, it is important to understand how the sequence changes alter the properties of the genetic part. We analyzed the sequences of over 50,000 engineered plasmids using depositor metadata and a metric inspired by the natural language processing field. We detected 217 uncatalogued genetic part variants that were especially widespread or were likely the result of convergent evolution or engineering. Several of these uncatalogued variants are known mutants of plasmid origins of replication or antibiotic resistance genes that are missing from current annotation databases. However, most are uncharacterized, and 3/5 of the plasmids we analyzed contained at least one of the uncatalogued variants. Our results include a list of genetic parts to prioritize for refining engineered plasmid annotation pipelines, highlight widespread variants of parts that warrant further investigation to see whether they have altered characteristics, and suggest cases where unintentional evolution of plasmid parts may be affecting the reliability and reproducibility of science.
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Affiliation(s)
- Matthew J. McGuffie
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States
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19
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Assessing and reducing phenotypic instability in cyanobacteria. Curr Opin Biotechnol 2023; 80:102899. [PMID: 36724584 DOI: 10.1016/j.copbio.2023.102899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/23/2022] [Accepted: 01/06/2023] [Indexed: 01/31/2023]
Abstract
Cyanobacteria have promising potential as sustainable cell factories. However, one challenge that is still largely unreported in scaling-up cyanobacteria bioproduction is phenotypic instability, where the emergence and selection of nonproducing cells leading to loss in production has longer evolutionary timescales to take place in industrial-scale bioreactors. Quantifying phenotypic instability early on in strain development allows researchers to make informed decisions on whether to proceed with scalable designs, or if present, devise countermeasures to reduce instability. One particularly effective strategy to mitigate instability is the use of genome-scale metabolic models to design growth-coupled production strains. In silico studies have predicted that creating certain cofactor imbalances or removing recycling reactions in cyanobacteria can be exploited to stably produce a wide variety of metabolites.
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20
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Li Q, Sun M, Lv L, Zuo Y, Zhang S, Zhang Y, Yang S. Improving the Editing Efficiency of CRISPR-Cas9 by Reducing the Generation of Escapers Based on the Surviving Mechanism. ACS Synth Biol 2023; 12:672-680. [PMID: 36867054 DOI: 10.1021/acssynbio.2c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Due to the high specificity in targeting DNA and highly convenient programmability, CRISPR-Cas-based antimicrobials applied for eliminating specific strains such as antibiotic-resistant bacteria in the microbiome were gradually developed. However, the generation of escapers makes the elimination efficiency far lower than the acceptable rate (10-8) recommended by the National Institutes of Health. Here, a systematic study was carried out providing insight into the escaping mechanisms in Escherichia coli, and strategies for reducing the escapers were devised accordingly. We first showed an escape rate of 10-5-10-3 in E. coli MG1655 under the editing of pEcCas/pEcgRNA established previously. Detailed analysis of the escapers obtained at ligA site in E. coli MG1655 uncovered that the disruption of cas9 was the main cause of the generation of survivors, notably the frequent insertion of IS5. Hence, the sgRNA was next designed to target the "perpetrator" IS5, and subsequently the killing efficiency was improved 4-fold. Additionally, the escape rate in IS-free E. coli MDS42 was also tested at the ligA site, ∼10-fold decrease compared with MG1655, but the disruption of cas9 was still observed in all survivors manifested in the form of frameshifts or point mutations. Thus, we optimized the tool itself by increasing the copy number of cas9 to retain some cas9 that still has the correct DNA sequence. Fortunately, the escape rates dropped below 10-8 at 9 of the 16 tested genes. Furthermore, the λ-Red recombination system was added to generate the pEcCas-2.0, and a 100% gene deletion efficiency was achieved at genes cadA, maeB, and gntT in MG1655, whereas those genes were edited with low efficiency previously. Last, the application of pEcCas-2.0 was then expanded to the E. coli B strain BL21(DE3) and W strain ATCC9637. This study reveals the mechanism of E. coli surviving Cas9-mediated death, and a highly efficient editing tool is established based on the mechanism, which will accelerate the further application of CRISPR-Cas.
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Affiliation(s)
- Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Mingjun Sun
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Lu Lv
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Yong Zuo
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Suyi Zhang
- Luzhou Laojiao Co., Ltd, Luzhou 646000, Sichuan China
| | - Ying Zhang
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
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21
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Lennox-Hvenekilde D, Bali AP, Gronenberg LS, Acevedo-Rocha C, Sommer MOA, Genee HJ. Metabolic engineering of Escherichia coli for high-level production of free lipoic acid. Metab Eng 2023; 76:39-49. [PMID: 36639019 DOI: 10.1016/j.ymben.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023]
Abstract
L-Lipoic acid (LA) is an important antioxidant with various industrial applications as a nutraceutical and therapeutic. Currently, LA is produced by chemical synthesis. Cell factory development is complex as LA and its direct precursors only occur naturally in protein-bound forms. Here we report a rationally engineered LA cell factory and demonstrate de novo free LA production from glucose for the first time in E. coli. The pathway represents a significant challenge as the three key enzymes, native Octanoyltransferase (LipB) and Lipoyl Synthase (LipA), and heterologous Lipoamidase (LpA), are all toxic to overexpress in E. coli. To overcome the toxicity of LipB, functional metagenomic selection was used to identify a highly active and non-toxic LipB and LipA from S. liquefaciens. Using high throughput screening, we balanced translation initiation rates and dual, orthogonal induction systems for the toxic genes, LipA and LpA. The optimized strain yielded 2.5 mg free LA per gram of glucose in minimal media, expressing carefully balanced LipB and LipA, Enterococcus faecalis LpA, and a truncated, native, Dihydrolipoyllysine-residue acetyltransferase (AceF) lipoylation domain. When the optimized cell factory strain was cultivated in a fed-batch fermentation, a titer of 87 mg/L free LA in the supernatant was reached after 48 h. This titer is ∼3000-fold higher than previously reported free LA titer and ∼8-fold higher than the previous best total, protein-bound LA titer. The strategies presented here could be helpful in designing, constructing and balancing biosynthetic pathways that harbor toxic enzymes with protein-bound intermediates or products.
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Affiliation(s)
- David Lennox-Hvenekilde
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark; Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark
| | - Anne P Bali
- Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark
| | | | | | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Hans J Genee
- Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark.
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22
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Mu X, Zhang F. Diverse mechanisms of bioproduction heterogeneity in fermentation and their control strategies. J Ind Microbiol Biotechnol 2023; 50:kuad033. [PMID: 37791393 PMCID: PMC10583207 DOI: 10.1093/jimb/kuad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023]
Abstract
Microbial bioproduction often faces challenges related to populational heterogeneity, where cells exhibit varying biosynthesis capabilities. Bioproduction heterogeneity can stem from genetic and non-genetic factors, resulting in decreased titer, yield, stability, and reproducibility. Consequently, understanding and controlling bioproduction heterogeneity are crucial for enhancing the economic competitiveness of large-scale biomanufacturing. In this review, we provide a comprehensive overview of current understandings of the various mechanisms underlying bioproduction heterogeneity. Additionally, we examine common strategies for controlling bioproduction heterogeneity based on these mechanisms. By implementing more robust measures to mitigate heterogeneity, we anticipate substantial enhancements in the scalability and stability of bioproduction processes. ONE-SENTENCE SUMMARY This review summarizes current understandings of different mechanisms of bioproduction heterogeneity and common control strategies based on these mechanisms.
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Affiliation(s)
- Xinyue Mu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
- Institute of Materials Science & Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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23
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Heieck K, Arnold ND, Brück TB. Metabolic stress constrains microbial L-cysteine production in Escherichia coli by accelerating transposition through mobile genetic elements. Microb Cell Fact 2023; 22:10. [PMID: 36642733 PMCID: PMC9841684 DOI: 10.1186/s12934-023-02021-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/09/2023] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND L-cysteine is an essential chemical building block in the pharmaceutical-, cosmetic-, food and agricultural sector. Conventionally, L-cysteine production relies on the conversion of keratinous biomass mediated by hydrochloric acid. Today, fermentative production based on recombinant E. coli, where L-cysteine production is streamlined and facilitated by synthetic plasmid constructs, is an alternative process at industrial scale. However, metabolic stress and the resulting production escape mechanisms in evolving populations are severely limiting factors during industrial biomanufacturing. We emulate high generation numbers typically reached in industrial fermentation processes with Escherichia coli harbouring L-cysteine production plasmid constructs. So far no genotypic and phenotypic alterations in early and late L-cysteine producing E. coli populations have been studied. RESULTS In a comparative experimental design, the E. coli K12 production strain W3110 and the reduced genome strain MDS42, almost free of insertion sequences, were used as hosts. Data indicates that W3110 populations acquire growth fitness at the expense of L-cysteine productivity within 60 generations, while production in MDS42 populations remains stable. For the first time, the negative impact of predominantly insertion sequence family 3 and 5 transposases on L-cysteine production is reported, by combining differential transcriptome analysis with NGS based deep plasmid sequencing. Furthermore, metabolic clustering of differentially expressed genes supports the hypothesis, that metabolic stress induces rapid propagation of plasmid rearrangements, leading to reduced L-cysteine yields in evolving populations over industrial fermentation time scales. CONCLUSION The results of this study implicate how selective deletion of insertion sequence families could be a new route for improving industrial L-cysteine or even general amino acid production using recombinant E. coli hosts. Instead of using minimal genome strains, a selective deletion of certain IS families could offer the benefits of adaptive laboratory evolution (ALE) while maintaining enhanced L-cysteine production stability.
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Affiliation(s)
- Kevin Heieck
- grid.6936.a0000000123222966Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Nathanael David Arnold
- grid.6936.a0000000123222966Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Thomas Bartholomäus Brück
- grid.6936.a0000000123222966Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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24
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Humphreys JR, Debebe BJ, Diggle SP, Winzer K. Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity. Front Microbiol 2023; 13:1075609. [PMID: 36704551 PMCID: PMC9871927 DOI: 10.3389/fmicb.2022.1075609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
Solventogenic clostridia represent a diverse group of anaerobic, spore-forming bacteria capable of producing acetone, butanol and ethanol through their unique biphasic metabolism. An intrinsic problem with these organisms however is their tendency to degenerate when repeatedly subcultured or when grown continuously. This phenomenon sees cells lose their ability to produce solvents and spores, posing a significant problem for industrial applications. To investigate the mechanistic and evolutionary basis of degeneration we combined comparative genomics, ultra-deep sequencing, and concepts of sociomicrobiology using Clostridium beijerinckii NCIMB 8052 as our model organism. These approaches revealed spo0A, the master regulator gene involved in spore and solvent formation, to be key to the degeneration process in this strain. Comparative genomics of 71 degenerate variants revealed four distinct hotspot regions that contained considerably more mutations than the rest of the genome. These included spo0A as well as genes suspected to regulate its expression and activity. Ultra-deep sequencing of populations during the subculturing process showed transient increases in mutations we believe linked to the spo0A network, however, these were ultimately dominated by mutations in the master regulator itself. Through frequency-dependent fitness assays, we found that spo0A mutants gained a fitness advantage, relative to the wild type, presumably allowing for propagation throughout the culture. Combined, our data provides new insights into the phenomenon of clostridial strain degeneration and the C. beijerinckii NCIMB 8052 solvent and spore regulation network.
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Affiliation(s)
- Jonathan R. Humphreys
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, United Kingdom
| | - Bisrat J. Debebe
- DeepSeq, Centre for Genetics and Genomics, The University of Nottingham, Nottingham, United Kingdom
| | - Stephen P. Diggle
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, United Kingdom,*Correspondence: Klaus Winzer, ✉
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25
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Minireview: Engineering evolution to reconfigure phenotypic traits in microbes for biotechnological applications. Comput Struct Biotechnol J 2022; 21:563-573. [PMID: 36659921 PMCID: PMC9816911 DOI: 10.1016/j.csbj.2022.12.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022] Open
Abstract
Adaptive laboratory evolution (ALE) has long been used as the tool of choice for microbial engineering applications, ranging from the production of commodity chemicals to the innovation of complex phenotypes. With the advent of systems and synthetic biology, the ALE experimental design has become increasingly sophisticated. For instance, implementation of in silico metabolic model reconstruction and advanced synthetic biology tools have facilitated the effective coupling of desired traits to adaptive phenotypes. Furthermore, various multi-omic tools now enable in-depth analysis of cellular states, providing a comprehensive understanding of the biology of even the most genomically perturbed systems. Emerging machine learning approaches would assist in streamlining the interpretation of massive and multiplexed datasets and promoting our understanding of complexity in biology. This review covers some of the representative case studies among the 700 independent ALE studies reported to date, outlining key ideas, principles, and important mechanisms underlying ALE designs in bioproduction and synthetic cell engineering, with evidence from literatures to aid comprehension.
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Fenster JA, Werner AZ, Tay JW, Gillen M, Schirokauer L, Hill NC, Watson A, Ramirez KJ, Johnson CW, Beckham GT, Cameron JC, Eckert CA. Dynamic and single cell characterization of a CRISPR-interference toolset in Pseudomonas putida KT2440 for β-ketoadipate production from p-coumarate. Metab Eng Commun 2022; 15:e00204. [PMID: 36093381 PMCID: PMC9460563 DOI: 10.1016/j.mec.2022.e00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/22/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Pseudomonas putida KT2440 is a well-studied bacterium for the conversion of lignin-derived aromatic compounds to bioproducts. The development of advanced genetic tools in P. putida has reduced the turnaround time for hypothesis testing and enabled the construction of strains capable of producing various products of interest. Here, we evaluate an inducible CRISPR-interference (CRISPRi) toolset on fluorescent, essential, and metabolic targets. Nuclease-deficient Cas9 (dCas9) expressed with the arabinose (8K)-inducible promoter was shown to be tightly regulated across various media conditions and when targeting essential genes. In addition to bulk growth data, single cell time lapse microscopy was conducted, which revealed intrinsic heterogeneity in knockdown rate within an isoclonal population. The dynamics of knockdown were studied across genomic targets in exponentially-growing cells, revealing a universal 1.75 ± 0.38 h quiescent phase after induction where 1.5 ± 0.35 doublings occur before a phenotypic response is observed. To demonstrate application of this CRISPRi toolset, β-ketoadipate, a monomer for performance-advantaged nylon, was produced at a 4.39 ± 0.5 g/L and yield of 0.76 ± 0.10 mol/mol from p-coumarate, a hydroxycinnamic acid that can be derived from grasses. These cultivation metrics were achieved by using the higher strength IPTG (1K)-inducible promoter to knockdown the pcaIJ operon in the βKA pathway during early exponential phase. This allowed the majority of the carbon to be shunted into the desired product while eliminating the need for a supplemental carbon and energy source to support growth and maintenance. Developed an inducible dCas9-based CRISPR interference toolset in Pseudomonas putida KT2440. Characterized single-cell dynamics of fluorescent and essential gene knockdown. Applied the toolset for glucose-free production of β-ketoadipate from p-coumarate. Produced β-ketoadipate at titer of 4.39 ± 0.5 g/L and 0.76 ± 0.10 mol/mol yield.
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Affiliation(s)
- Jacob A. Fenster
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Allison Z. Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Jian Wei Tay
- BioFrontiers Institute, 3415 Colorado Avenue, Boulder, CO, 80309, USA
| | - Matthew Gillen
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Leo Schirokauer
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Nicholas C. Hill
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Audrey Watson
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- BioFrontiers Institute, 3415 Colorado Avenue, Boulder, CO, 80309, USA
| | - Kelsey J. Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Christopher W. Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Jeffrey C. Cameron
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Corresponding author. Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO 80309, USA.
| | - Carrie A. Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Corresponding author. PO Box 2008, MS6060 Oak Ridge, TN 37831-6060.
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Kasari M, Kasari V, Kärmas M, Jõers A. Decoupling Growth and Production by Removing the Origin of Replication from a Bacterial Chromosome. ACS Synth Biol 2022; 11:2610-2622. [PMID: 35798328 DOI: 10.1021/acssynbio.1c00618] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Efficient production of biochemicals and proteins in cell factories frequently benefits from a two-stage bioprocess in which growth and production phases are decoupled. Here, we describe a novel growth switch based on the permanent removal of the origin of replication (oriC) from the Escherichia coli chromosome. Without oriC, cells cannot initiate a new round of replication, and they stop growing while their metabolism remains active. Our system relies on a serine recombinase from bacteriophage phiC31 whose expression is controlled by the temperature-sensitive cI857 repressor from phage lambda. The reporter protein expression in switched cells continues after cessation of growth, leading to protein levels up to 5 times higher compared to nonswitching cells. Switching induces a unique physiological state that is different from both normal exponential and stationary phases. The switched cells remain in this state even when not growing, retain their protein synthesis capacity, and do not induce proteins associated with the stationary phase. Our switcher technology is potentially useful for a range of products and applicable in many bacterial species for decoupling growth and production.
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Affiliation(s)
- Marje Kasari
- Institute of Technology, University of Tartu, Nooruse 1, 50104 Tartu, Estonia
| | - Villu Kasari
- Institute of Technology, University of Tartu, Nooruse 1, 50104 Tartu, Estonia
| | - Mirjam Kärmas
- Institute of Technology, University of Tartu, Nooruse 1, 50104 Tartu, Estonia
| | - Arvi Jõers
- Institute of Technology, University of Tartu, Nooruse 1, 50104 Tartu, Estonia
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Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight. Nat Commun 2022; 13:3363. [PMID: 35690608 PMCID: PMC9188569 DOI: 10.1038/s41467-022-31033-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/31/2022] [Indexed: 12/19/2022] Open
Abstract
Small-scale, low-cost bioreactors provide exquisite control of environmental parameters of microbial cultures over long durations. Their use is gaining popularity in quantitative systems and synthetic biology. However, existing setups are limited in their measurement capabilities. Here, we present ReacSight, a strategy to enhance bioreactor arrays for automated measurements and reactive experiment control. ReacSight leverages low-cost pipetting robots for sample collection, handling and loading, and provides a flexible instrument control architecture. We showcase ReacSight capabilities on three applications in yeast. First, we demonstrate real-time optogenetic control of gene expression. Second, we explore the impact of nutrient scarcity on fitness and cellular stress using competition assays. Third, we perform dynamic control of the composition of a two-strain consortium. We combine custom or chi.bio reactors with automated cytometry. To further illustrate ReacSight's genericity, we use it to enhance plate-readers with pipetting capabilities and perform repeated antibiotic treatments on a bacterial clinical isolate.
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Wang H, Wang L, Zhong B, Dai Z. Protein Splicing of Inteins: A Powerful Tool in Synthetic Biology. Front Bioeng Biotechnol 2022; 10:810180. [PMID: 35265596 PMCID: PMC8899391 DOI: 10.3389/fbioe.2022.810180] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/25/2022] [Indexed: 12/21/2022] Open
Abstract
Inteins are protein segments that are capable of enabling the ligation of flanking extein into a new protein, a process known as protein splicing. Since its discovery, inteins have become powerful biotechnological tools for applications such as protein engineering. In the last 10 years, the development in synthetic biology has further endowed inteins with enhanced functions and diverse utilizations. Here we review these efforts and discuss the future directions.
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Affiliation(s)
- Hao Wang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lin Wang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Baihua Zhong
- Materials Interfaces Center, Institute of Advanced Materials Science and Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhuojun Dai
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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Ye Z, Huang Y, Shi B, Xiang Z, Tian Z, Huang M, Wu L, Deng Z, Shen K, Liu T. Coupling cell growth and biochemical pathway induction in Saccharomyces cerevisiae for production of (+)-valencene and its chemical conversion to (+)-nootkatone. Metab Eng 2022; 72:107-115. [DOI: 10.1016/j.ymben.2022.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/05/2022] [Accepted: 03/10/2022] [Indexed: 11/29/2022]
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Harnessing plasmid replication mechanism to enable dynamic control of gene copy in bacteria. Metab Eng 2022; 70:67-78. [PMID: 35033655 PMCID: PMC8844098 DOI: 10.1016/j.ymben.2022.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/17/2021] [Accepted: 01/09/2022] [Indexed: 01/03/2023]
Abstract
Dynamic regulation has been proved efficient in controlling gene expression at transcriptional, translational, and post-translational level. However, the dynamic regulation at gene replication level has been rarely explored so far. In this study, we established dynamic regulation at gene copy level through engineering controllable plasmid replication to dynamically control the gene expression. Prototypic genetic circuits with different control logic were applied to enable diversified dynamic behaviors of gene copy. To explore the applicability of this strategy, the dynamic gene copy control was employed in regulating the biosynthesis of p-coumaric acid, which resulted in an up to 78% increase in p-coumaric acid titer to 1.69 g/L in shake flasks. These results indicated the great potential of applying dynamic gene copy control for engineering biosynthesis of valuable compounds in metabolic engineering.
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Hussain MH, Mohsin MZ, Zaman WQ, Yu J, Zhao X, Wei Y, Zhuang Y, Mohsin A, Guo M. Multiscale engineering of microbial cell factories: A step forward towards sustainable natural products industry. Synth Syst Biotechnol 2022; 7:586-601. [PMID: 35155840 PMCID: PMC8816652 DOI: 10.1016/j.synbio.2021.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/08/2021] [Accepted: 12/30/2021] [Indexed: 01/09/2023] Open
Abstract
Microbial cell factories (bacteria and fungi) are the leading producers of beneficial natural products such as lycopene, carotene, herbal medicine, and biodiesel etc. These microorganisms are considered efficient due to their effective bioprocessing strategy (monoculture- and consortial-based approach) under distinct processing conditions. Meanwhile, the advancement in genetic and process optimization techniques leads to enhanced biosynthesis of natural products that are known functional ingredients with numerous applications in the food, cosmetic and medical industries. Natural consortia and monoculture thrive in nature in a small proportion, such as wastewater, food products, and soils. In similitude to natural consortia, it is possible to engineer artificial microbial consortia and program their behaviours via synthetic biology tools. Therefore, this review summarizes the optimization of genetic and physicochemical parameters of the microbial system for improved production of natural products. Also, this review presents a brief history of natural consortium and describes the functional properties of monocultures. This review focuses on synthetic biology tools that enable new approaches to design synthetic consortia; and highlights the syntropic interactions that determine the performance and stability of synthetic consortia. In particular, the effect of processing conditions and advanced genetic techniques to improve the productibility of both monoculture and consortial based systems have been greatly emphasized. In this context, possible strategies are also discussed to give an insight into microbial engineering for improved production of natural products in the future. In summary, it is concluded that the coupling of genomic modifications with optimum physicochemical factors would be promising for producing a robust microbial cell factory that shall contribute to the increased production of natural products.
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Affiliation(s)
- Muhammad Hammad Hussain
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Muhammad Zubair Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Waqas Qamar Zaman
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Junxiong Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Xueli Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yanlong Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, PR China.
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. P.O. box 329#, East China University of Science and Technology, 130 Meilong Rd., Shanghai, 200237, PR China.
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Liang Y, Ma A, Zhuang G. Construction of Environmental Synthetic Microbial Consortia: Based on Engineering and Ecological Principles. Front Microbiol 2022; 13:829717. [PMID: 35283862 PMCID: PMC8905317 DOI: 10.3389/fmicb.2022.829717] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 01/30/2023] Open
Abstract
In synthetic biology, engineering principles are applied to system design. The development of synthetic microbial consortia represents the intersection of synthetic biology and microbiology. Synthetic community systems are constructed by co-cultivating two or more microorganisms under certain environmental conditions, with broad applications in many fields including ecological restoration and ecological theory. Synthetic microbial consortia tend to have high biological processing efficiencies, because the division of labor reduces the metabolic burden of individual members. In this review, we focus on the environmental applications of synthetic microbial consortia. Although there are many strategies for the construction of synthetic microbial consortia, we mainly introduce the most widely used construction principles based on cross-feeding. Additionally, we propose methods for constructing synthetic microbial consortia based on traits and spatial structure from the perspective of ecology to provide a basis for future work.
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Affiliation(s)
- Yu Liang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Anzhou Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guoqiang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
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Robustness: linking strain design to viable bioprocesses. Trends Biotechnol 2022; 40:918-931. [PMID: 35120750 DOI: 10.1016/j.tibtech.2022.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 12/18/2022]
Abstract
Microbial cell factories are becoming increasingly popular for the sustainable production of various chemicals. Metabolic engineering has led to the design of advanced cell factories; however, their long-term yield, titer, and productivity falter when scaled up and subjected to industrial conditions. This limitation arises from a lack of robustness - the ability to maintain a constant phenotype despite the perturbations of such processes. This review describes predictable and stochastic industrial perturbations as well as state-of-the-art technologies to counter process variability. Moreover, we distinguish robustness from tolerance and discuss the potential of single-cell studies for improving system robustness. Finally, we highlight ways of achieving consistent and comparable quantification of robustness that can guide the selection of strains for industrial bioprocesses.
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Moore JC, Ramos I, Van Dien S. OUP accepted manuscript. J Ind Microbiol Biotechnol 2022; 49:6520437. [PMID: 35108392 PMCID: PMC9118995 DOI: 10.1093/jimb/kuab088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022]
Abstract
Optimization of metabolism to maximize production of bio-based chemicals must consistently balance cellular resources for biocatalyst growth and desired compound synthesis. This mini-review discusses synthetic biology strategies for dynamically controlling expression of genes to enable dual-phase fermentations in which growth and production are separated into dedicated phases. Emphasis is placed on practical examples which can be reliably scaled to commercial production with the current state of technology. Recent case studies are presented, and recommendations are provided for environmental signals and genetic control circuits.
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Affiliation(s)
| | - Itzel Ramos
- BP Biosciences Center, San Diego, CA 92121, USA
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Li C, Jiang T, Li M, Zou Y, Yan Y. Fine-tuning gene expression for improved biosynthesis of natural products: From transcriptional to post-translational regulation. Biotechnol Adv 2022; 54:107853. [PMID: 34637919 PMCID: PMC8724446 DOI: 10.1016/j.biotechadv.2021.107853] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 02/08/2023]
Abstract
Microbial production of natural compounds has attracted extensive attention due to their high value in pharmaceutical, cosmetic, and food industries. Constructing efficient microbial cell factories for biosynthesis of natural products requires the fine-tuning of gene expressions to minimize the accumulation of toxic metabolites, reduce the competition between cell growth and product generation, as well as achieve the balance of redox or co-factors. In this review, we focus on recent advances in fine-tuning gene expression at the DNA, RNA, and protein levels to improve the microbial biosynthesis of natural products. Commonly used regulatory toolsets in each level are discussed, and perspectives for future direction in this area are provided.
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Affiliation(s)
- Chenyi Li
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Tian Jiang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Michelle Li
- North Oconee High School, Bogart, GA 30622, USA
| | - Yusong Zou
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
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Brkljacic J, Wittler B, Lindsey BE, Ganeshan VD, Sovic MG, Niehaus J, Ajibola W, Bachle SM, Fehér T, Somers DE. Frequency, composition and mobility of Escherichia coli-derived transposable elements in holdings of plasmid repositories. Microb Biotechnol 2021; 15:455-468. [PMID: 34875147 PMCID: PMC8867978 DOI: 10.1111/1751-7915.13962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022] Open
Abstract
By providing the scientific community with uniform and standardized resources of consistent quality, plasmid repositories play an important role in enabling scientific reproducibility. Plasmids containing insertion sequence elements (IS elements) represent a challenge from this perspective, as they can change the plasmid structure and function. In this study, we conducted a systematic analysis of a subset of plasmid stocks distributed by plasmid repositories (The Arabidopsis Biological Resource Center and Addgene) which carry unintended integrations of bacterial mobile genetic elements. The integration of insertion sequences was most often found in, but not limited to, pBR322‐derived vectors, and did not affect the function of the specific plasmids. In certain cases, the entire stock was affected, but the majority of the stocks tested contained a mixture of the wild‐type and the mutated plasmids, suggesting that the acquisition of IS elements likely occurred after the plasmids were acquired by the repositories. However, comparison of the sequencing results of the original samples revealed that some plasmids already carried insertion mutations at the time of donation. While an extensive BLAST analysis of 47 877 plasmids sequenced from the Addgene repository uncovered IS elements in only 1.12%, suggesting that IS contamination is not widespread, further tests showed that plasmid integration of IS elements can propagate in conventional Escherichia coli hosts over a few tens of generations. Use of IS‐free E. coli hosts prevented the emergence of IS insertions as well as that of small indels, suggesting that the use of IS‐free hosts by donors and repositories could help limit unexpected and unwanted IS integrations into plasmids.
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Affiliation(s)
| | | | | | | | - Michael G Sovic
- Center For Applied Plant Sciences, The Ohio State University, Columbus, OH, USA
| | | | - Walliyulahi Ajibola
- Systems and Synthetic Biology Unit, Institute of Biochemistry, Biological Research Centre of the Eötvös Lóránd Research Network, Szeged, Hungary.,Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | | | - Tamás Fehér
- Systems and Synthetic Biology Unit, Institute of Biochemistry, Biological Research Centre of the Eötvös Lóránd Research Network, Szeged, Hungary
| | - David E Somers
- Arabidopsis Biological Resource Center, Columbus, OH, USA.,Center For Applied Plant Sciences, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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Schnabel T, Sattely E. Improved Stability of Engineered Ammonia Production in the Plant-Symbiont Azospirillum brasilense. ACS Synth Biol 2021; 10:2982-2996. [PMID: 34591447 PMCID: PMC8604774 DOI: 10.1021/acssynbio.1c00287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioavailable nitrogen is the limiting nutrient for most agricultural food production. Associative diazotrophs can colonize crop roots and fix their own bioavailable nitrogen from the atmosphere. Wild-type (WT) associative diazotrophs, however, do not release fixed nitrogen in culture and are not known to directly transfer fixed nitrogen resources to plants. Efforts to engineer diazotrophs for plant nitrogen provision as an alternative to chemical fertilization have yielded several strains that transiently release ammonia. However, these strains suffer from selection pressure for nonproducers, which rapidly deplete ammonia accumulating in culture, likely limiting their potential for plant growth promotion (PGP). Here we report engineered Azospirillum brasilense strains with significantly extend ammonia production lifetimes of up to 32 days in culture. Our approach relies on multicopy genetic redundancy of a unidirectional adenylyltransferase (uAT) as a posttranslational mechanism to induce ammonia release via glutamine synthetase deactivation. Testing our multicopy stable strains with the model monocot Setaria viridis in hydroponic monoassociation reveals improvement in plant growth promotion compared to single copy strains. In contrast, inoculation of Zea mays in nitrogen-poor, nonsterile soil does not lead to increased PGP relative to WT, suggesting strain health, resource competition, or colonization capacity in soil may also be limiting factors. In this context, we show that while engineered strains fix more nitrogen per cell compared to WT strains, the expression strength of multiple uAT copies needs to be carefully balanced to maximize ammonia production rates and avoid excessive fitness defects caused by excessive glutamine synthetase shutdown.
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Affiliation(s)
- Tim Schnabel
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Elizabeth Sattely
- Department of Chemical Engineering, Stanford University and HHMI, Stanford, California 94305, United States
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Ropers D, Couté Y, Faure L, Ferré S, Labourdette D, Shabani A, Trouilh L, Vasseur P, Corre G, Ferro M, Teste MA, Geiselmann J, de Jong H. Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application. ACS Synth Biol 2021; 10:2910-2926. [PMID: 34739215 DOI: 10.1021/acssynbio.1c00115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the scalability of a previously developed growth switch based on external control of RNA polymerase expression. Our results indicate that, in liter-scale bioreactors operating in fed-batch mode, growth-arrested Escherichia coli cells are able to convert glucose to glycerol at an increased yield. A multiomics quantification of the physiology of the cells shows that, apart from acetate production, few metabolic side effects occur. However, a number of specific responses to growth slow-down and growth arrest are launched at the transcriptional level. These notably include the downregulation of genes involved in growth-associated processes, such as amino acid and nucleotide metabolism and translation. Interestingly, the transcriptional responses are buffered at the proteome level, probably due to the strong decrease of the total mRNA concentration after the diminution of transcriptional activity and the absence of growth dilution of proteins. Growth arrest thus reduces the opportunities for dynamically adjusting the proteome composition, which poses constraints on the design of biotechnological production processes but may also avoid the initiation of deleterious stress responses.
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Affiliation(s)
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | | | - Sabrina Ferré
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Delphine Labourdette
- GeT-Biopuces, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Arieta Shabani
- Université Grenoble Alpes, Inria, 38000 Grenoble, France
| | - Lidwine Trouilh
- GeT-Biopuces, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | | | | | - Myriam Ferro
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Marie-Ange Teste
- GeT-Biopuces, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Johannes Geiselmann
- Université Grenoble Alpes, Inria, 38000 Grenoble, France
- Université Grenoble Alpes, CNRS, LIPhy, 38000 Grenoble, France
| | - Hidde de Jong
- Université Grenoble Alpes, Inria, 38000 Grenoble, France
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40
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Lee SW, Rugbjerg P, Sommer MOA. Exploring Selective Pressure Trade-Offs for Synthetic Addiction to Extend Metabolite Productive Lifetimes in Yeast. ACS Synth Biol 2021; 10:2842-2849. [PMID: 34699715 DOI: 10.1021/acssynbio.1c00240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Engineered microbes often suffer from reduced fitness resulting from metabolic burden and various stresses. The productive lifetime of a bioreactor with engineered microbes is therefore susceptible to the rise of nonproductive mutants with better fitness. Synthetic addiction is emerging as a concept to artificially couple the growth rate of the microbe to production to tackle this problem. However, only a few successful cases of synthetic addiction systems have been reported to date. To understand the limitations and design constraints in long-term cultivations, we designed and studied conditional synthetic addiction circuits in Saccharomyces cerevisiae. This allowed us to probe a range of selective pressure strengths and identify the optimal balance between circuit stability and production-to-growth coupling. In the optimal balance, the productive lifetime was greatly extended compared with suboptimal circuit tuning. With a too-high or -low pressure, we found that production declines mainly through homologous recombination. These principles of trade-off in the design of synthetic addition systems should lead to the better control of bioprocess performance.
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Affiliation(s)
- Sang-Woo Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Peter Rugbjerg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Enduro Genetics ApS, 2200 Copenhagen, Denmark
| | - Morten Otto Alexander Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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41
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Le HTQ, Nguyen AD, Park YR, Lee EY. Sustainable biosynthesis of chemicals from methane and glycerol via reconstruction of multi-carbon utilizing pathway in obligate methanotrophic bacteria. Microb Biotechnol 2021; 14:2552-2565. [PMID: 33830652 PMCID: PMC8601198 DOI: 10.1111/1751-7915.13809] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 01/26/2023] Open
Abstract
Obligate methanotrophic bacteria can utilize methane, an inexpensive carbon feedstock, as a sole energy and carbon substrate, thus are considered as the only nature-provided biocatalyst for sustainable biomanufacturing of fuels and chemicals from methane. To address the limitation of native C1 metabolism of obligate type I methanotrophs, we proposed a novel platform strain that can utilize methane and multi-carbon substrates, such as glycerol, simultaneously to boost growth rates and chemical production in Methylotuvimicrobium alcaliphilum 20Z. To demonstrate the uses of this concept, we reconstructed a 2,3-butanediol biosynthetic pathway and achieved a fourfold higher titer of 2,3-butanediol production by co-utilizing methane and glycerol compared with that of methanotrophic growth. In addition, we reported the creation of a methanotrophic biocatalyst for one-step bioconversion of methane to methanol in which glycerol was used for cell growth, and methane was mainly used for methanol production. After the deletion of genes encoding methanol dehydrogenase (MDH), 11.6 mM methanol was obtained after 72 h using living cells in the absence of any chemical inhibitors of MDH and exogenous NADH source. A further improvement of this bioconversion was attained by using resting cells with a significantly increased titre of 76 mM methanol after 3.5 h with the supply of 40 mM formate. The work presented here provides a novel framework for a variety of approaches in methane-based biomanufacturing.
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Affiliation(s)
- Hoa Thi Quynh Le
- Department of Chemical Engineering (Integrated Engineering)Kyung Hee University17104Yongin‐siGyeonggi‐doSouth Korea
| | - Anh Duc Nguyen
- Department of Chemical Engineering (Integrated Engineering)Kyung Hee University17104Yongin‐siGyeonggi‐doSouth Korea
| | - Ye Rim Park
- Department of Chemical Engineering (Integrated Engineering)Kyung Hee University17104Yongin‐siGyeonggi‐doSouth Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (Integrated Engineering)Kyung Hee University17104Yongin‐siGyeonggi‐doSouth Korea
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42
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Decrulle AL, Frénoy A, Meiller-Legrand TA, Bernheim A, Lotton C, Gutierrez A, Lindner AB. Engineering gene overlaps to sustain genetic constructs in vivo. PLoS Comput Biol 2021; 17:e1009475. [PMID: 34624014 PMCID: PMC8528312 DOI: 10.1371/journal.pcbi.1009475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 10/20/2021] [Accepted: 09/23/2021] [Indexed: 11/20/2022] Open
Abstract
Evolution is often an obstacle to the engineering of stable biological systems due to the selection of mutations inactivating costly gene circuits. Gene overlaps induce important constraints on sequences and their evolution. We show that these constraints can be harnessed to increase the stability of costly genes by purging loss-of-function mutations. We combine computational and synthetic biology approaches to rationally design an overlapping reading frame expressing an essential gene within an existing gene to protect. Our algorithm succeeded in creating overlapping reading frames in 80% of E. coli genes. Experimentally, scoring mutations in both genes of such overlapping construct, we found that a significant fraction of mutations impacting the gene to protect have a deleterious effect on the essential gene. Such an overlap thus protects a costly gene from removal by natural selection by associating the benefit of this removal with a larger or even lethal cost. In our synthetic constructs, the overlap converts many of the possible mutants into evolutionary dead-ends, reducing the evolutionary potential of the system and thus increasing its stability over time. Genomes are translated by triplets of nucleotides on two different strands, allowing for six different reading frames. This permits the existence of gene overlaps, often observed in microbial genomes, where two different proteins are encoded on the same piece of DNA, but in different reading frames. Gene overlaps are classically considered an obstacle for both evolution and genetic engineering, as mutations in overlapping regions likely have pleitrotropic effects on several genes. In 2013, we identified specific evolutionary scenarios where the decrease in evolutionary potential caused by gene overlaps could instead be advantageous and selected for. In this work, we demonstrate the use of gene overlaps in another context where reducing evolutionary potential can be useful: preventing evolution from inactivating synthetic circuits. We show that gene overlaps can be engineered to increase the evolutionary stability of genes that are costly to their hosts, by entangling these costly genes with essential genes.
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Affiliation(s)
| | - Antoine Frénoy
- Université de Paris, INSERM U1001, Paris, France
- Université Grenoble Alpes, CNRS UMR5525, Grenoble, France
- * E-mail: (AF); (ABL)
| | | | | | | | | | - Ariel B. Lindner
- Université de Paris, INSERM U1001, Paris, France
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France
- * E-mail: (AF); (ABL)
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43
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Cao Y, Tian R, Lv X, Li J, Liu L, Du G, Chen J, Liu Y. Inducible Population Quality Control of Engineered Bacillus subtilis for Improved N-Acetylneuraminic Acid Biosynthesis. ACS Synth Biol 2021; 10:2197-2209. [PMID: 34404207 DOI: 10.1021/acssynbio.1c00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Biosynthesis by microorganisms using renewable feedstocks is an important approach for realizing sustainable chemical manufacturing. However, cell-to-cell variation in biosynthesis capability during fermentation restricts the robustness and efficiency of bioproduction, hampering the industrialization of biosynthesis. Herein, we developed an inducible population quality control system (iPopQC) for dynamically modulating the producing and nonproducing subpopulations of engineered Bacillus subtilis, which was constructed via inducible promoter- and metabolite-responsive biosensor-based genetic circuit for regulating essential genes. Moreover, iPopQC achieved a 1.97-fold increase in N-acetylneuraminic acid (NeuAc) titer by enriching producing cell subpopulation during cultivation, representing 52% higher than that of previous PopQC. Strains with double-output iPopQC cocoupling the expression of double essential genes with NeuAc production improved production robustness further, retaining NeuAc production throughout 96 h of fermentation, upon which the strains cocoupling one essential gene expression with NeuAc production abolished the production ability.
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Affiliation(s)
- Yanting Cao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Rongzhen Tian
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
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44
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A Guideline to Set Up Cascaded Continuous Cultivation with E. coli Bl21 (DE3). METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2436:223-240. [PMID: 34519978 DOI: 10.1007/7651_2021_424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Continuous processing allows to maximize space-time yields and is implemented in many industrial branches. However, in manufacturing of value added compounds produced with microbial hosts, continuous processing is not state-of-the-art yet. This is because fluctuating productivity causes unwanted process deviations. Cascaded continuous bioprocessing, unlike conventional continuous process modes, was found to result in stable productivity. This manuscript serves as a guideline how to set up a cascaded continuous cultivation with Escherichia coli BL21 DE(3).
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45
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Deatherage DE, Barrick JE. High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing. Cell Syst 2021; 12:1187-1200.e4. [PMID: 34536379 DOI: 10.1016/j.cels.2021.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/14/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
Understanding how cells are likely to evolve can guide medical interventions and bioengineering efforts that must contend with unwanted mutations. The adaptome of a cell-the neighborhood of genetic changes that are most likely to drive adaptation in a given environment-can be mapped by tracking rare beneficial variants during the early stages of clonal evolution. We used multiplex adaptome capture sequencing (mAdCap-seq), a procedure that combines unique molecular identifiers and hybridization-based enrichment, to characterize mutations in eight Escherichia coli genes known to be under selection in a laboratory environment. We tracked 301 mutations at frequencies as low as 0.01% and inferred the fitness effects of 240 of these mutations. There were distinct molecular signatures of selection on protein structure and function for the three genes with the most beneficial mutations. Our results demonstrate how mAdCap-seq can be used to deeply profile a targeted portion of a cell's adaptome.
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Affiliation(s)
- Daniel E Deatherage
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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46
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Bowen CH, Sargent CJ, Wang A, Zhu Y, Chang X, Li J, Mu X, Galazka JM, Jun YS, Keten S, Zhang F. Microbial production of megadalton titin yields fibers with advantageous mechanical properties. Nat Commun 2021; 12:5182. [PMID: 34462443 PMCID: PMC8405620 DOI: 10.1038/s41467-021-25360-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
Manmade high-performance polymers are typically non-biodegradable and derived from petroleum feedstock through energy intensive processes involving toxic solvents and byproducts. While engineered microbes have been used for renewable production of many small molecules, direct microbial synthesis of high-performance polymeric materials remains a major challenge. Here we engineer microbial production of megadalton muscle titin polymers yielding high-performance fibers that not only recapture highly desirable properties of natural titin (i.e., high damping capacity and mechanical recovery) but also exhibit high strength, toughness, and damping energy - outperforming many synthetic and natural polymers. Structural analyses and molecular modeling suggest these properties derive from unique inter-chain crystallization of folded immunoglobulin-like domains that resists inter-chain slippage while permitting intra-chain unfolding. These fibers have potential applications in areas from biomedicine to textiles, and the developed approach, coupled with the structure-function insights, promises to accelerate further innovation in microbial production of high-performance materials.
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Affiliation(s)
- Christopher H Bowen
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Cameron J Sargent
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Ao Wang
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, USA
| | - Yaguang Zhu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Xinyuan Chang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Jingyao Li
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Xinyue Mu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Young-Shin Jun
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
- Institute of Materials Science & Engineering, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, USA.
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47
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Abstract
In the age of antibiotic resistance and precise microbiome engineering, CRISPR-Cas antimicrobials promise to have a substantial impact on the way we treat diseases in the future. However, the efficacy of these antimicrobials and their mechanisms of resistance remain to be elucidated. We systematically investigated how a target E. coli strain can escape killing by episomally-encoded CRISPR-Cas9 antimicrobials. Using Cas9 from Streptococcus pyogenes (SpCas9) we studied the killing efficiency and resistance mutation rate towards CRISPR-Cas9 antimicrobials and elucidated the underlying genetic alterations. We find that killing efficiency is not correlated with the number of cutting sites or the type of target. While the number of targets did not significantly affect efficiency of killing, it did reduce the emergence of chromosomal mutations conferring resistance. The most frequent target of resistance mutations was the plasmid-encoded SpCas9 that was inactivated by bacterial genome rearrangements involving translocation of mobile genetic elements such as insertion elements. This resistance mechanism can be overcome by re-introduction of an intact copy of SpCas9. The work presented here provides a guide to design strategies that reduce resistance and improve the activity of CRISPR-Cas antimicrobials.
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48
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Abstract
Few classes of natural products rival the structural audacity of oligosaccharides. Their complexity, however, has stood as an immense roadblock to translational research, as access to homogeneous material from nature is challenging. Thus, while carbohydrates are critical to the myriad functional and structural aspects of the biological sciences, their behavior is largely descriptive. This challenge presents an attractive opportunity for synthetic chemistry, particularly in the area of human milk science. First, there is an inordinate need for synthesizing homogeneous human milk oligosaccharides (HMOs). Superimposed on this goal is the mission of conducting syntheses at scale to enable animal studies. Herein, we present a personalized rumination of our involvement, and that of our colleagues, which has led to the synthesis and characterization of HMOs and mechanistic probes. Along the way, we highlight chemical, chemoenzymatic, and synthetic biology based approaches. We close with a discussion on emergent challenges and opportunities for synthesis, broadly defined, in human milk science.
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Affiliation(s)
- Lianyan L Xu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Steven D Townsend
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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49
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Son HI, Weiss A, You L. Design patterns for engineering genetic stability. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 19. [PMID: 34308010 DOI: 10.1016/j.cobme.2021.100297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The past 20 years have witnessed enormous progress in synthetic biology in the development of engineered cells for diverse applications, including biomanufacturing, materials fabrication, and potential therapeutics and diagnostics. However, it still remains a major challenge to maintain long-term performance of synthetic gene circuits, due to the emergence of mutants that lose circuit function. Here, we highlight major vulnerabilities of synthetic gene circuits resulting in circuit failure and mutant escape. We also discuss engineering strategies to enhance long-term circuit stability and performance. These approaches can be divided into two strategies: the suppression of the emergence of mutants and the suppression of their relative fitness if mutants do emerge. We anticipate that mechanistic understanding of the modes of circuit failure will facilitate future efforts to design evolutionarily robust synthetic biology-inspired applications.
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Affiliation(s)
- Hye-In Son
- Department of Biomedical Engineering, Duke University
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University
| | - Lingchong You
- Department of Biomedical Engineering, Duke University.,Center for Genomic and Computational Biology, Duke University.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine
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50
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Cascaded processing enables continuous upstream processing with E. coli BL21(DE3). Sci Rep 2021; 11:11477. [PMID: 34075099 PMCID: PMC8169658 DOI: 10.1038/s41598-021-90899-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
In many industrial sectors continuous processing is already the golden standard to maximize productivity. However, when working with living cells, subpopulation formation causes instabilities in long-term cultivations. In cascaded continuous cultivation, biomass formation and recombinant protein expression can be spatially separated. This cultivation mode was found to facilitate stable protein expression using microbial hosts, however mechanistic knowledge of this cultivation strategy is scarce. In this contribution we present a method workflow to reduce workload and accelerate the establishment of stable continuous processes with E. coli BL21(DE3) exclusively based on bioengineering methods.
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