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Ding N, Yuan Z, Ma Z, Wu Y, Yin L. AI-Assisted Rational Design and Activity Prediction of Biological Elements for Optimizing Transcription-Factor-Based Biosensors. Molecules 2024; 29:3512. [PMID: 39124917 PMCID: PMC11313831 DOI: 10.3390/molecules29153512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
The rational design, activity prediction, and adaptive application of biological elements (bio-elements) are crucial research fields in synthetic biology. Currently, a major challenge in the field is efficiently designing desired bio-elements and accurately predicting their activity using vast datasets. The advancement of artificial intelligence (AI) technology has enabled machine learning and deep learning algorithms to excel in uncovering patterns in bio-element data and predicting their performance. This review explores the application of AI algorithms in the rational design of bio-elements, activity prediction, and the regulation of transcription-factor-based biosensor response performance using AI-designed elements. We discuss the advantages, adaptability, and biological challenges addressed by the AI algorithms in various applications, highlighting their powerful potential in analyzing biological data. Furthermore, we propose innovative solutions to the challenges faced by AI algorithms in the field and suggest future research directions. By consolidating current research and demonstrating the practical applications and future potential of AI in synthetic biology, this review provides valuable insights for advancing both academic research and practical applications in biotechnology.
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Affiliation(s)
- Nana Ding
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China;
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Zenan Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China;
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China;
| | - Yefei Wu
- Zhejiang Qianjiang Biochemical Co., Ltd., Haining 314400, China;
| | - Lianghong Yin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China;
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
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2
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Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [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: 04/12/2024]
Abstract
In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
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3
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Joshi SHN, Jenkins C, Ulaeto D, Gorochowski TE. Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0037. [PMID: 38919711 PMCID: PMC11197468 DOI: 10.34133/bdr.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024] Open
Abstract
Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.
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Affiliation(s)
| | - Christopher Jenkins
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - David Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - Thomas E. Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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4
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Durmusoglu D, Haller DJ, Al'Abri IS, Day K, Sands C, Clark A, San-Miguel A, Vazquez-Uribe R, Sommer MOA, Crook NC. Programming Probiotics: Diet-Responsive Gene Expression and Colonization Control in Engineered S. boulardii. ACS Synth Biol 2024; 13:1851-1865. [PMID: 38787439 DOI: 10.1021/acssynbio.4c00145] [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: 05/25/2024]
Abstract
Saccharomyces boulardii (Sb) is an emerging probiotic chassis for delivering biomolecules to the mammalian gut, offering unique advantages as the only eukaryotic probiotic. However, precise control over gene expression and gut residence time in Sb have remained challenging. To address this, we developed five ligand-responsive gene expression systems and repaired galactose metabolism in Sb, enabling inducible gene expression in this strain. Engineering these systems allowed us to construct AND logic gates, control the surface display of proteins, and turn on protein production in the mouse gut in response to dietary sugar. Additionally, repairing galactose metabolism expanded Sb's habitat within the intestines and resulted in galactose-responsive control over gut residence time. This work opens new avenues for precise dosing of therapeutics by Sb via control over its in vivo gene expression levels and localization within the gastrointestinal tract.
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Affiliation(s)
- Deniz Durmusoglu
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Daniel J Haller
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Ibrahim S Al'Abri
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Katie Day
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Carmen Sands
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Andrew Clark
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Adriana San-Miguel
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Nathan C Crook
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
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5
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Ali MZ, Guharajan S, Parisutham V, Brewster RC. Regulatory properties of transcription factors with diverse mechanistic function. PLoS Comput Biol 2024; 20:e1012194. [PMID: 38857275 PMCID: PMC11192337 DOI: 10.1371/journal.pcbi.1012194] [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: 01/18/2024] [Revised: 06/21/2024] [Accepted: 05/24/2024] [Indexed: 06/12/2024] Open
Abstract
Transcription factors (TFs) regulate the process of transcription through the modulation of different kinetic steps. Although models can often describe the observed transcriptional output of a measured gene, predicting a TFs role on a given promoter requires an understanding of how the TF alters each step of the transcription process. In this work, we use a simple model of transcription to assess the role of promoter identity, and the degree to which TFs alter binding of RNAP (stabilization) and initiation of transcription (acceleration) on three primary characteristics: the range of steady-state regulation, cell-to-cell variability in expression, and the dynamic response time of a regulated gene. We find that steady state regulation and the response time of a gene behave uniquely for TFs that regulate incoherently, i.e that speed up one step but slow the other. We also find that incoherent TFs have dynamic implications, with one type of incoherent mode configuring the promoter to respond more slowly at intermediate TF concentrations. We also demonstrate that the noise of gene expression for these TFs is sensitive to promoter strength, with a distinct non-monotonic profile that is apparent under stronger promoters. Taken together, our work uncovers the coupling between promoters and TF regulatory modes with implications for understanding natural promoters and engineering synthetic gene circuits with desired expression properties.
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Affiliation(s)
- Md Zulfikar Ali
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Geology, Physics and Environmental Science, University of Southern Indiana, Evansville, Indiana, United States of America
| | - Sunil Guharajan
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Vinuselvi Parisutham
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robert C. Brewster
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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6
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Ji CH, Je HW, Kim H, Kang HS. Promoter engineering of natural product biosynthetic gene clusters in actinomycetes: concepts and applications. Nat Prod Rep 2024; 41:672-699. [PMID: 38259139 DOI: 10.1039/d3np00049d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Covering 2011 to 2022Low titers of natural products in laboratory culture or fermentation conditions have been one of the challenging issues in natural products research. Many natural product biosynthetic gene clusters (BGCs) are also transcriptionally silent in laboratory culture conditions, making it challenging to characterize the structures and activities of their metabolites. Promoter engineering offers a potential solution to this problem by providing tools for transcriptional activation or optimization of biosynthetic genes. In this review, we summarize the 10 years of progress in promoter engineering approaches in natural products research focusing on the most metabolically talented group of bacteria actinomycetes.
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Affiliation(s)
- Chang-Hun Ji
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hyun-Woo Je
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hiyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
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7
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Cautereels C, Smets J, Bircham P, De Ruysscher D, Zimmermann A, De Rijk P, Steensels J, Gorkovskiy A, Masschelein J, Verstrepen KJ. Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast. Nat Commun 2024; 15:1112. [PMID: 38326309 PMCID: PMC10850122 DOI: 10.1038/s41467-024-44997-7] [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: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Microbes are increasingly employed as cell factories to produce biomolecules. This often involves the expression of complex heterologous biosynthesis pathways in host strains. Achieving maximal product yields and avoiding build-up of (toxic) intermediates requires balanced expression of every pathway gene. However, despite progress in metabolic modeling, the optimization of gene expression still heavily relies on trial-and-error. Here, we report an approach for in vivo, multiplexed Gene Expression Modification by LoxPsym-Cre Recombination (GEMbLeR). GEMbLeR exploits orthogonal LoxPsym sites to independently shuffle promoter and terminator modules at distinct genomic loci. This approach facilitates creation of large strain libraries, in which expression of every pathway gene ranges over 120-fold and each strain harbors a unique expression profile. When applied to the biosynthetic pathway of astaxanthin, an industrially relevant antioxidant, a single round of GEMbLeR improved pathway flux and doubled production titers. Together, this shows that GEMbLeR allows rapid and efficient gene expression optimization in heterologous biosynthetic pathways, offering possibilities for enhancing the performance of microbial cell factories.
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Affiliation(s)
- Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Jolien Smets
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Peter Bircham
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Dries De Ruysscher
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, box 2438, Leuven, 3001, Belgium
- Laboratory for Biomolecular Discovery & Engineering, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
| | - Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, 2610, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Joleen Masschelein
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, box 2438, Leuven, 3001, Belgium
- Laboratory for Biomolecular Discovery & Engineering, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium.
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8
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Zeng M, Sarker B, Howitz N, Shah I, Andrews LB. Synthetic Homoserine Lactone Sensors for Gram-Positive Bacillus subtilis Using LuxR-Type Regulators. ACS Synth Biol 2024; 13:282-299. [PMID: 38079538 PMCID: PMC10805106 DOI: 10.1021/acssynbio.3c00504] [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: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 01/23/2024]
Abstract
A universal biochemical signal for bacterial cell-cell communication could facilitate programming dynamic responses in diverse bacterial consortia. However, the classical quorum sensing paradigm is that Gram-negative and Gram-positive bacteria generally communicate via homoserine lactones (HSLs) or oligopeptide molecular signals, respectively, to elicit population responses. Here, we create synthetic HSL sensors for Gram-positive Bacillus subtilis 168 using allosteric LuxR-type regulators (RpaR, LuxR, RhlR, and CinR) and synthetic promoters. Promoters were combinatorially designed from different sequence elements (-35, -16, -10, and transcriptional start regions). We quantified the effects of these combinatorial promoters on sensor activity and determined how regulator expression affects its activation, achieving up to 293-fold activation. Using the statistical design of experiments, we identified significant effects of promoter regions and pairwise interactions on sensor activity, which helped to understand the sequence-function relationships for synthetic promoter design. We present the first known set of functional HSL sensors (≥20-fold dynamic range) in B. subtilis for four different HSL chemical signals: p-coumaroyl-HSL, 3-oxohexanoyl-HSL, n-butyryl-HSL, and n-(3-hydroxytetradecanoyl)-HSL. This set of synthetic HSL sensors for a Gram-positive bacterium can pave the way for designable interspecies communication within microbial consortia.
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Affiliation(s)
- Min Zeng
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Nathaniel Howitz
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Ishita Shah
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B. Andrews
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Molecular
and Cellular Biology Graduate Program, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
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9
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Ma Y, Ye JW, Lin Y, Yi X, Wang X, Wang H, Huang R, Wu F, Wu Q, Liu X, Chen GQ. Flux optimization using multiple promoters in Halomonas bluephagenesis as a model chassis of the next generation industrial biotechnology. Metab Eng 2024; 81:249-261. [PMID: 38159902 DOI: 10.1016/j.ymben.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/16/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
Predictability and robustness are challenges for bioproduction because of the unstable intracellular synthetic activities. With the deeper understanding of the gene expression process, fine-tuning has become a meaningful tool for biosynthesis optimization. This study characterized several gene expression elements and constructed a multiple inducible system that responds to ten different small chemical inducers in halophile bacterium Halomonas bluephagenesis. Genome insertion of regulators was conducted for the purpose of gene cluster stabilization and regulatory plasmid simplification. Additionally, dynamic ranges of the multiple inducible systems were tuned by promoter sequence mutations to achieve diverse scopes for high-resolution gene expression control. The multiple inducible system was successfully employed to precisely control chromoprotein expression, lycopene and poly-3-hydroxybutyrate (PHB) biosynthesis, resulting in colorful bacterial pictures, optimized cell growth, lycopene and PHB accumulation. This study demonstrates a desirable approach for fine-tuning of rational and efficient gene expressions, displaying the significance for metabolic pathway optimization.
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Affiliation(s)
- Yueyuan Ma
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yina Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xueqing Yi
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ruiyan Huang
- Garrison Forest School, Owings Mills, MD, 21117, USA
| | - Fuqing Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Beijing, 101309, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; MOE Key Laboratory for Industrial Biocatalysts, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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10
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Liu H, Zhang L, Wang W, Hu H, Ouyang X, Xu P, Tang H. An Intelligent Synthetic Bacterium for Chronological Toxicant Detection, Biodegradation, and Its Subsequent Suicide. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304318. [PMID: 37705081 PMCID: PMC10625131 DOI: 10.1002/advs.202304318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Indexed: 09/15/2023]
Abstract
Modules, toolboxes, and synthetic biology systems may be designed to address environmental bioremediation. However, weak and decentralized functional modules require complex control. To address this issue, an integrated system for toxicant detection and biodegradation, and subsequent suicide in chronological order without exogenous inducers is constructed. Salicylic acid, a typical pollutant in industrial wastewater, is selected as an example to demonstrate this design. Biosensors are optimized by regulating the expression of receptors and reporters to get 2-fold sensitivity and 6-fold maximum output. Several stationary phase promoters are compared, and promoter Pfic is chosen to express the degradation enzyme. Two concepts for suicide circuits are developed, with the toxin/antitoxin circuit showing potent lethality. The three modules are coupled in a stepwise manner. Detection and biodegradation, and suicide are sequentially completed with partial attenuation compared to pre-integration, except for biodegradation, being improved by the replacements of ribosome binding site. Finally, a long-term stability test reveals that the engineered strain maintained its function for ten generations. The study provides a novel concept for integrating and controlling functional modules that can accelerate the transition of synthetic biology from conceptual to practical applications.
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Affiliation(s)
- Huan Liu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Lige Zhang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Weiwei Wang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Haiyang Hu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Xingyu Ouyang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Ping Xu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Hongzhi Tang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
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11
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Mao Y, Huang C, Zhou X, Han R, Deng Y, Zhou S. Genetically Encoded Biosensor Engineering for Application in Directed Evolution. J Microbiol Biotechnol 2023; 33:1257-1267. [PMID: 37449325 PMCID: PMC10619561 DOI: 10.4014/jmb.2304.04031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023]
Abstract
Although rational genetic engineering is nowadays the favored method for microbial strain improvement, building up mutant libraries based on directed evolution for improvement is still in many cases the better option. In this regard, the demand for precise and efficient screening methods for mutants with high performance has stimulated the development of biosensor-based high-throughput screening strategies. Genetically encoded biosensors provide powerful tools to couple the desired phenotype to a detectable signal, such as fluorescence and growth rate. Herein, we review recent advances in engineering several classes of biosensors and their applications in directed evolution. Furthermore, we compare and discuss the screening advantages and limitations of two-component biosensors, transcription-factor-based biosensors, and RNA-based biosensors. Engineering these biosensors has focused mainly on modifying the expression level or structure of the biosensor components to optimize the dynamic range, specificity, and detection range. Finally, the applications of biosensors in the evolution of proteins, metabolic pathways, and genome-scale metabolic networks are described. This review provides potential guidance in the design of biosensors and their applications in improving the bioproduction of microbial cell factories through directed evolution.
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Affiliation(s)
- Yin Mao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Chao Huang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Xuan Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yu Deng
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Shenghu Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
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12
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Velazquez Sanchez AK, Klopprogge B, Zimmermann KH, Ignatova Z. Tailored Synthetic sRNAs Dynamically Tune Multilayer Genetic Circuits. ACS Synth Biol 2023; 12:2524-2535. [PMID: 37595156 DOI: 10.1021/acssynbio.2c00614] [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: 08/20/2023]
Abstract
Predictable and controllable tuning of genetic circuits to regulate gene expression, including modulation of existing circuits or constructs without the need for redesign or rebuilding, is a persistent challenge in synthetic biology. Here, we propose rationally designed new small RNAs (sRNAs) that dynamically modulate gene expression of genetic circuits with a broad range (high, medium, and low) of repression. We designed multiple multilayer genetic circuits in which the variable effector element is a transcription factor (TF) controlling downstream the production of a reporter protein. The sRNAs target TFs instead of a reporter gene, and harnessing the intrinsic RNA-interference pathway in E. coli allowed for a wide range of expression modulation of the reporter protein, including the most difficult to achieve dynamic switch to an OFF state. The synthetic sRNAs are expressed independently of the circuit(s), thus allowing for repression without modifying the circuit itself. Our work provides a frame for achieving independent modulation of gene expression and dynamic and modular control of the multilayer genetic circuits by only including an independent control circuit expressing synthetic sRNAs, without altering the structure of existing genetic circuits.
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Affiliation(s)
- Ana K Velazquez Sanchez
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Bjarne Klopprogge
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Karl-Heinz Zimmermann
- Algebraic Engineering, Institute of Embedded Systems, Hamburg University of Technology, 21073 Hamburg, Germany
| | - Zoya Ignatova
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
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13
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Koirala P, Doody C, Blackwell H, Chandler JR. Regulation of an antibiotic resistance efflux pump by quorum sensing and a TetR-family repressor in Chromobacterium subtsugae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.02.556004. [PMID: 37693375 PMCID: PMC10491235 DOI: 10.1101/2023.09.02.556004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The soil bacterium Chromobacterium substugae uses a single LuxI-R-type quorum-sensing system, CviI-R, to regulate genes in a cell density-dependent manner. CviI synthesizes the signal N-hexanoyl-homoserine lactone (C6-HSL) and CviR is a C6-HSL-responsive cytoplasmic transcription regulator. C6-HSL-bound CviR activates dozens of genes, for example the cdeAB-oprM cluster coding for an efflux pump conferring antibiotic resistance. The cdeAB-oprM genes are also regulated by an antibiotic-responsive transcription factor, CdeR, which represses expression of these genes. We are interested in understanding how C. subtsugae integrates different environmental cues to regulate antibiotic resistance. In this study, we sought to delineate the mechanism of regulation of the cdeAB-oprM genes by CviR and CdeR. In recombinant E. coli, the cdeA promoter is activated by CviR and repressed by CdeR. We identify non-overlapping sequence elements in the cdeA promoter that are required for CviR activation and CdeR repression, respectively. We also examined the role of CdeR in modulating cdeA activation by C6-HSL in C. subtsugae. We show that CviR and CdeR can independently modulate transcription from the cdeA promoter in C. subtsugae, consistent with the conclusion that CviR and CdeR regulate the cdeAB-oprM genes by interacting directly with different binding sites in the cdeA promoter. These results contribute to a molecular understanding of how the cdeAB-oprM genes are regulated and provide new insight into how C. subtsugae integrates different environmental cues to regulate antibiotic resistance.
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Affiliation(s)
- Pratik Koirala
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA
| | - Cassie Doody
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Helen Blackwell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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14
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Nasr MA, Martin VJJ, Kwan DH. Divergent directed evolution of a TetR-type repressor towards aromatic molecules. Nucleic Acids Res 2023; 51:7675-7690. [PMID: 37377432 PMCID: PMC10415137 DOI: 10.1093/nar/gkad503] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/18/2023] [Accepted: 06/25/2023] [Indexed: 06/29/2023] Open
Abstract
Reprogramming cellular behaviour is one of the hallmarks of synthetic biology. To this end, prokaryotic allosteric transcription factors (aTF) have been repurposed as versatile tools for processing small molecule signals into cellular responses. Expanding the toolbox of aTFs that recognize new inducer molecules is of considerable interest in many applications. Here, we first establish a resorcinol responsive aTF-based biosensor in Escherichia coli using the TetR-family repressor RolR from Corynebacterium glutamicum. We then perform an iterative walk along the fitness landscape of RolR to identify new inducer specificities, namely catechol, methyl catechol, caffeic acid, protocatechuate, L-DOPA, and the tumour biomarker homovanillic acid. Finally, we demonstrate the versatility of these engineered aTFs by transplanting them into the model eukaryote Saccharomyces cerevisiae. This work provides a framework for efficient aTF engineering to expand ligand specificity towards novel molecules on laboratory timescales, which, more broadly, is invaluable across a wide range of applications such as protein and metabolic engineering, as well as point-of-care diagnostics.
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Affiliation(s)
- Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
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15
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Alba Burbano D, Cardiff RAL, Tickman BI, Kiattisewee C, Maranas CJ, Zalatan JG, Carothers JM. Engineering activatable promoters for scalable and multi-input CRISPRa/i circuits. Proc Natl Acad Sci U S A 2023; 120:e2220358120. [PMID: 37463216 PMCID: PMC10374173 DOI: 10.1073/pnas.2220358120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
Dynamic, multi-input gene regulatory networks (GRNs) are ubiquitous in nature. Multilayer CRISPR-based genetic circuits hold great promise for building GRNs akin to those found in naturally occurring biological systems. We develop an approach for creating high-performing activatable promoters that can be assembled into deep, wide, and multi-input CRISPR-activation and -interference (CRISPRa/i) GRNs. By integrating sequence-based design and in vivo screening, we engineer activatable promoters that achieve up to 1,000-fold dynamic range in an Escherichia coli-based cell-free system. These components enable CRISPRa GRNs that are six layers deep and four branches wide. We show the generalizability of the promoter engineering workflow by improving the dynamic range of the light-dependent EL222 optogenetic system from 6-fold to 34-fold. Additionally, high dynamic range promoters enable CRISPRa systems mediated by small molecules and protein-protein interactions. We apply these tools to build input-responsive CRISPRa/i GRNs, including feedback loops, logic gates, multilayer cascades, and dynamic pulse modulators. Our work provides a generalizable approach for the design of high dynamic range activatable promoters and enables classes of gene regulatory functions in cell-free systems.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, WA98195
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
| | - Ryan A. L. Cardiff
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Benjamin I. Tickman
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Cholpisit Kiattisewee
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Cassandra J. Maranas
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Jesse G. Zalatan
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
- Department of Chemistry, University of Washington, Seattle, WA98195
| | - James M. Carothers
- Department of Chemical Engineering, University of Washington, Seattle, WA98195
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
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16
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Huttanus HM, Triola EKH, Velasquez-Guzman JC, Shin SM, Granja-Travez RS, Singh A, Dale T, Jha RK. Targeted mutagenesis and high-throughput screening of diversified gene and promoter libraries for isolating gain-of-function mutations. Front Bioeng Biotechnol 2023; 11:1202388. [PMID: 37545889 PMCID: PMC10400447 DOI: 10.3389/fbioe.2023.1202388] [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: 04/08/2023] [Accepted: 06/25/2023] [Indexed: 08/08/2023] Open
Abstract
Targeted mutagenesis of a promoter or gene is essential for attaining new functions in microbial and protein engineering efforts. In the burgeoning field of synthetic biology, heterologous genes are expressed in new host organisms. Similarly, natural or designed proteins are mutagenized at targeted positions and screened for gain-of-function mutations. Here, we describe methods to attain complete randomization or controlled mutations in promoters or genes. Combinatorial libraries of one hundred thousands to tens of millions of variants can be created using commercially synthesized oligonucleotides, simply by performing two rounds of polymerase chain reactions. With a suitably engineered reporter in a whole cell, these libraries can be screened rapidly by performing fluorescence-activated cell sorting (FACS). Within a few rounds of positive and negative sorting based on the response from the reporter, the library can rapidly converge to a few optimal or extremely rare variants with desired phenotypes. Library construction, transformation and sequence verification takes 6-9 days and requires only basic molecular biology lab experience. Screening the library by FACS takes 3-5 days and requires training for the specific cytometer used. Further steps after sorting, including colony picking, sequencing, verification, and characterization of individual clones may take longer, depending on number of clones and required experiments.
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Affiliation(s)
- Herbert M. Huttanus
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- Agile BioFoundry, Emeryville, CA, United States
| | - Ellin-Kristina H. Triola
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- Agile BioFoundry, Emeryville, CA, United States
| | - Jeanette C. Velasquez-Guzman
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- Agile BioFoundry, Emeryville, CA, United States
| | - Sang-Min Shin
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- BOTTLE Consortium, Golden, CO, United States
| | - Rommel S. Granja-Travez
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- BOTTLE Consortium, Golden, CO, United States
| | - Anmoldeep Singh
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Taraka Dale
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- Agile BioFoundry, Emeryville, CA, United States
- BOTTLE Consortium, Golden, CO, United States
| | - Ramesh K. Jha
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- Agile BioFoundry, Emeryville, CA, United States
- BOTTLE Consortium, Golden, CO, United States
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17
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Gyorgy A, Menezes A, Arcak M. A blueprint for a synthetic genetic feedback optimizer. Nat Commun 2023; 14:2554. [PMID: 37137895 PMCID: PMC10156725 DOI: 10.1038/s41467-023-37903-0] [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: 08/18/2022] [Accepted: 04/05/2023] [Indexed: 05/05/2023] Open
Abstract
Biomolecular control enables leveraging cells as biomanufacturing factories. Despite recent advancements, we currently lack genetically encoded modules that can be deployed to dynamically fine-tune and optimize cellular performance. Here, we address this shortcoming by presenting the blueprint of a genetic feedback module to optimize a broadly defined performance metric by adjusting the production and decay rate of a (set of) regulator species. We demonstrate that the optimizer can be implemented by combining available synthetic biology parts and components, and that it can be readily integrated with existing pathways and genetically encoded biosensors to ensure its successful deployment in a variety of settings. We further illustrate that the optimizer successfully locates and tracks the optimum in diverse contexts when relying on mass action kinetics-based dynamics and parameter values typical in Escherichia coli.
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Affiliation(s)
- Andras Gyorgy
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Amor Menezes
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL, USA
| | - Murat Arcak
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
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18
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Zhou GJ, Zhang F. Applications and Tuning Strategies for Transcription Factor-Based Metabolite Biosensors. BIOSENSORS 2023; 13:428. [PMID: 37185503 PMCID: PMC10136082 DOI: 10.3390/bios13040428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 05/17/2023]
Abstract
Transcription factor (TF)-based biosensors are widely used for the detection of metabolites and the regulation of cellular pathways in response to metabolites. Several challenges hinder the direct application of TF-based sensors to new hosts or metabolic pathways, which often requires extensive tuning to achieve the optimal performance. These tuning strategies can involve transcriptional or translational control depending on the parameter of interest. In this review, we highlight recent strategies for engineering TF-based biosensors to obtain the desired performance and discuss additional design considerations that may influence a biosensor's performance. We also examine applications of these sensors and suggest important areas for further work to continue the advancement of small-molecule biosensors.
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Affiliation(s)
- Gloria J. Zhou
- 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 Biology & 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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19
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Qin C, Xiang Y, Liu J, Zhang R, Liu Z, Li T, Sun Z, Ouyang X, Zong Y, Zhang HM, Ouyang Q, Qian L, Lou C. Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system. Nat Commun 2023; 14:1500. [PMID: 36932109 PMCID: PMC10023750 DOI: 10.1038/s41467-023-37244-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/09/2023] [Indexed: 03/19/2023] Open
Abstract
Context-dependency of mammalian transcriptional elements has hindered the quantitative investigation of multigene expression stoichiometry and its biological functions. Here, we describe a host- and local DNA context-independent transcription system to gradually fine-tune single and multiple gene expression with predictable stoichiometries. The mammalian transcription system is composed of a library of modular and programmable promoters from bacteriophage and its cognate RNA polymerase (RNAP) fused to a capping enzyme. The relative expression of single genes is quantitatively determined by the relative binding affinity of the RNAP to the promoters, while multigene expression stoichiometry is predicted by a simple biochemical model with resource competition. We use these programmable and modular promoters to predictably tune the expression of three components of an influenza A virus-like particle (VLP). Optimized stoichiometry leads to a 2-fold yield of intact VLP complexes. The host-independent orthogonal transcription system provides a platform for dose-dependent control of multiple protein expression which may be applied for advanced vaccine engineering, cell-fate programming and other therapeutic applications.
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Affiliation(s)
- Chenrui Qin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Yanhui Xiang
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Jie Liu
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Ruilin Zhang
- Yuanpei College, Peking University, 100871, Beijing, China
| | - Ziming Liu
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Tingting Li
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Zhi Sun
- College of Life Science, University of Chinese Academy of Science, 100149, Beijing, China
| | - Xiaoyi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | | | | | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Long Qian
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.
| | - Chunbo Lou
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
- College of Life Science, University of Chinese Academy of Science, 100149, Beijing, China.
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20
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Zhu Y, Gao H, Zhang J, Zhao J, Qi Q, Wang Q. De novo design of the global transcriptional factor Cra-regulated promoters enables highly sensitive glycolysis flux biosensor for dynamic metabolic control. Microb Biotechnol 2023; 16:605-617. [PMID: 36541030 PMCID: PMC9948231 DOI: 10.1111/1751-7915.14166] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Glycolytic flux is a fundamental index in microbial cell factories. A glycolytic flux biosensor that can monitor glucose metabolism efficiency is a promising strategy in rewiring metabolic flux to balance growth and biosynthesis. A key design feature of the glycolytic flux biosensors is the interaction between the global transcriptional factor Cra and its regulated promoters. However, overexpression and mutation of Cra has unpredictable effects on global metabolism in Escherichia coli. Therefore, new orthogonal biosensor design strategies should be developed to circumvent metabolic issues. In this report, the promoters in glycolytic flux biosensor were replaced with synthetic promoters of varying strengths or phage-derived promoters, and the Cra DNA-binding sites were deployed into promoters at different positions and distances to yield biosensors. The de nova biosensors that depended on Cra could sense Fructose-1,6-diphosphate (FBP) with broad dynamic ranges and low basal leakage. Then the negative-response biosensors were applied to fine-tune the target ATP synthesis gene, leading to the desired increase in pyruvate production (the highest 9.66 g/L) and cell growth. Moreover, the membrane synthesis gene plsC was also dynamically activated by the positive-response biosensor, leading to effective accumulation of lycopene in the cell membrane and a 50-fold increase in lycopene titre (100.3 mg/L) when compared with the control strain, demonstrating the effective and broader usages of our biosensors.
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Affiliation(s)
- Yuan Zhu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaxiao Gao
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian Zhang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jingyu Zhao
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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21
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Tellechea-Luzardo J, Stiebritz MT, Carbonell P. Transcription factor-based biosensors for screening and dynamic regulation. Front Bioeng Biotechnol 2023; 11:1118702. [PMID: 36814719 PMCID: PMC9939652 DOI: 10.3389/fbioe.2023.1118702] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Advances in synthetic biology and genetic engineering are bringing into the spotlight a wide range of bio-based applications that demand better sensing and control of biological behaviours. Transcription factor (TF)-based biosensors are promising tools that can be used to detect several types of chemical compounds and elicit a response according to the desired application. However, the wider use of this type of device is still hindered by several challenges, which can be addressed by increasing the current metabolite-activated transcription factor knowledge base, developing better methods to identify new transcription factors, and improving the overall workflow for the design of novel biosensor circuits. These improvements are particularly important in the bioproduction field, where researchers need better biosensor-based approaches for screening production-strains and precise dynamic regulation strategies. In this work, we summarize what is currently known about transcription factor-based biosensors, discuss recent experimental and computational approaches targeted at their modification and improvement, and suggest possible future research directions based on two applications: bioproduction screening and dynamic regulation of genetic circuits.
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Affiliation(s)
- Jonathan Tellechea-Luzardo
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Martin T. Stiebritz
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Pablo Carbonell
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain,Institute for Integrative Systems Biology I2SysBio, Universitat de València-CSIC, Paterna, Spain,*Correspondence: Pablo Carbonell,
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22
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Carrillo Rincón AF, Farny NG. Unlocking the strength of inducible promoters in Gram-negative bacteria. Microb Biotechnol 2023; 16:961-976. [PMID: 36738130 PMCID: PMC10128130 DOI: 10.1111/1751-7915.14219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 02/05/2023] Open
Abstract
Inducible bacterial promoters are ubiquitous biotechnology tools that have a consistent architecture including two key elements: the operator region recognized by the transcriptional regulatory proteins, and the -10 and -35 consensus sequences required to recruit the sigma (σ) 70 subunits of RNA polymerase to initiate transcription. Despite their widespread use, leaky transcription in the OFF state remains a challenge. We have updated the architecture of the lac and tet promoters to improve their strength, control and portability by the adaptation of the consensus -10 and -35 sequence boxes strongly targeted by σ70 , incorporation of a strong ribosome binding site recognized broadly by Gram-negative bacteria, and independent control of the transcriptional regulators by constitutive promoters. To test the promoters, we use the far-red fluorescent protein mCardinal, which significantly improves the signal-to-background ratio of promoter measurements over widely utilized green fluorescent proteins. We validate the improvement in OFF state control and inducibility by demonstrating production of the toxic and aggregate-prone cocaine esterase enzyme CocE. We further demonstrate portability of the promoters to additional Gram-negative species Pseudomonas putida and Vibrio natriegens. Our results represent a significant improvement over existing protein expression systems that will enable advances in protein production for various biotechnology applications.
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Affiliation(s)
| | - Natalie G Farny
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
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23
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Kutraite I, Malys N. Development and Application of Whole-Cell Biosensors for the Detection of Gallic Acid. ACS Synth Biol 2023; 12:533-543. [PMID: 36724292 PMCID: PMC9942251 DOI: 10.1021/acssynbio.2c00537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Gallic acid is a prevalent secondary plant metabolite distinguished as one of the most effective free-radical scavengers among phenolic acids. This compound is also known for its cytotoxic, anti-inflammatory, and antimicrobial activities. Bulk quantities of gallic acid are conventionally produced by acid hydrolysis of tannins, a costly and environmentally hazardous process. With the aim to develop more sustainable approaches, microbial bioproduction strategies have been attempted recently. To advance synthetic biology and metabolic engineering of microorganisms for gallic acid production, we characterize here a transcription factor-based inducible system PpGalR/PPP_RS13150 that responds to the extracellular gallic acid in a dose-dependent manner in Pseudomonas putida KT2440. Surprisingly, this compound does not mediate induction when PpGalR/PPP_RS13150 is used in non-native host background. We show that the activation of the inducible system requires gallate dioxygenase activity encoded by galA gene. The 4-oxalomesaconic acid, an intermediate of gallic acid-metabolism, is identified as the effector molecule that interacts with the transcription factor GalR mediating activation of gene expression. Introduction of galA gene along galR enables development of biosensors suitable for detection and monitoring of gallic acid extracellularly using non-native hosts such as E. coli and C. necator. Moreover, the P. putida-based biosensor's applicability is demonstrated by detecting and measuring gallic acid in extracts of Camellia sinensis leaves. This study reports the strategy, which can be applied for developing gallic acid biosensors using bacterial species outside Pseudomonas genus.
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Affiliation(s)
- Ingrida Kutraite
- Bioprocess
Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų Street 19, LT-50254Kaunas, Lithuania
| | - Naglis Malys
- Bioprocess
Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų Street 19, LT-50254Kaunas, Lithuania,Department
of Organic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų Street 19, LT-50254Kaunas, Lithuania,
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24
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Zhao N, Wang J, Jia A, Lin Y, Zheng S. Development of a Transcriptional Factor PuuR-Based Putrescine-Specific Biosensor in Corynebacterium glutamicum. Bioengineering (Basel) 2023; 10:bioengineering10020157. [PMID: 36829651 PMCID: PMC9951944 DOI: 10.3390/bioengineering10020157] [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: 12/10/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Corynebacterium glutamicum is regarded as an industrially important microbial cell factory and is widely used to produce various value-added chemicals. Because of the importance of C. glutamicum applications, current research is increasingly focusing on developing C. glutamicum synthetic biology platforms. Because of its ability to condense with adipic acid to synthesize the industrial plastic nylon-46, putrescine is an important platform compound of industrial interest. Developing a high-throughput putrescine biosensor can aid in accelerating the design-build-test cycle of cell factories (production strains) to achieve high putrescine-generating strain production in C. glutamicum. This study developed a putrescine-specific biosensor (pSenPuuR) in C. glutamicum using Escherichia coli-derived transcriptional factor PuuR. The response characteristics of the biosensor to putrescine were further improved by optimizing the genetic components of pSenPuuR, such as the response promoter, reporter protein, and promoter for controlling PuuR expression. According to the findings of the study, pSenPuuR has the potential to be used to assess putrescine production in C. glutamicum and is suitable for high-throughput genetic variant screening.
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Affiliation(s)
- Nannan Zhao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Animal Husbandry and Fisheries Research Center of Guangdong Haid Group Co., Ltd., Guangzhou 511400, China
| | - Jian Wang
- Animal Husbandry and Fisheries Research Center of Guangdong Haid Group Co., Ltd., Guangzhou 511400, China
| | - Aiqing Jia
- Animal Husbandry and Fisheries Research Center of Guangdong Haid Group Co., Ltd., Guangzhou 511400, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Correspondence: ; Tel.: +86-13822153344
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25
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Joshi SHN, Yong C, Gyorgy A. Inducible plasmid copy number control for synthetic biology in commonly used E. coli strains. Nat Commun 2022; 13:6691. [PMID: 36335103 PMCID: PMC9637173 DOI: 10.1038/s41467-022-34390-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The ability to externally control gene expression has been paradigm shifting for all areas of biological research, especially for synthetic biology. Such control typically occurs at the transcriptional and translational level, while technologies enabling control at the DNA copy level are limited by either (i) relying on a handful of plasmids with fixed and arbitrary copy numbers; or (ii) require multiple plasmids for replication control; or (iii) are restricted to specialized strains. To overcome these limitations, we present TULIP (TUnable Ligand Inducible Plasmid): a self-contained plasmid with inducible copy number control, designed for portability across various Escherichia coli strains commonly used for cloning, protein expression, and metabolic engineering. Using TULIP, we demonstrate through multiple application examples that flexible plasmid copy number control accelerates the design and optimization of gene circuits, enables efficient probing of metabolic burden, and facilitates the prototyping and recycling of modules in different genetic contexts.
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Affiliation(s)
- Shivang Hina-Nilesh Joshi
- grid.440573.10000 0004 1755 5934Division of Engineering, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Chentao Yong
- grid.440573.10000 0004 1755 5934Division of Engineering, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates ,grid.137628.90000 0004 1936 8753Department of Chemical and Biomolecular Engineering, New York University, New York, NY USA
| | - Andras Gyorgy
- grid.440573.10000 0004 1755 5934Division of Engineering, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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26
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“Structure”-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation. Mol Cell 2022; 82:3970-3984. [DOI: 10.1016/j.molcel.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/19/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
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27
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Development of a Glycerol-Inducible Expression System for High-Yield Heterologous Protein Production in Bacillus subtilis. Microbiol Spectr 2022; 10:e0132222. [PMID: 36036634 PMCID: PMC9604022 DOI: 10.1128/spectrum.01322-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The development of efficient, low-cost, and robust expression systems is important for the mass production of proteins and natural products in large amounts using cell factories. Glycerol is an ideal carbon source for large-scale fermentation due to its low cost and favorable maintenance of the fermentation process. Here, we used the antiterminator protein GlpP and its target promoter PglpD to construct a highly efficient glycerol-inducible expression system (GIES) in Bacillus subtilis. This system was able to express heterologous genes in an autoinducible manner based on the sequential utilization of glucose and glycerol under the regulation of carbon catabolite repression. In such a system, the concentration of glycerol regulated the strength of gene expression, and the concentration of glucose affected both the timing of induction and the strength of gene expression. By enhancing GlpP, the GIES was further strengthened for high-level intracellular expression of aspartase and secretory expression of nattokinase. High yields of nattokinase in a 5-L fermenter through batch and fed-batch fermentation demonstrated the potential to apply the GIES for large-scale enzyme production. Through the evolution of the -10 box of PglpD, mutants with gradient activities were obtained. In addition, hybrid glycerol-inducible promoters were successfully constructed by combining the constitutive promoters and the 5' untranslated region of PglpD. Collectively, this study developed a GIES to obtain high-value products from inexpensive glycerol. More importantly, the great potential of the pair of inherent terminator and antiterminator protein as a portable biological tool for various purposes in synthetic biology is proposed. IMPORTANCE In this study, a GIES was constructed in B. subtilis by employing the antiterminator protein GlpP and the GlpP-regulated promoter PglpD. Based on the sequential utilization of glucose and glycerol by B. subtilis, the GIES was able to express genes in an autoinducible manner. The amounts and ratio of glucose and glycerol can regulate the gene induction timing and expression strength. The GIES was further applied for high yields of nattokinase, and its robustness in production scale-up was confirmed in a 5-L fermenter. The high-level expression of heterologous proteins demonstrated the huge application potential of the GIES. Furthermore, mutants of PglpD with gradient activities and hybrid glycerol-inducible promoters were obtained through the evolution of the -10 box of PglpD and the combination of the constitutive promoters and the 5' untranslated region of PglpD, respectively. These results demonstrated the use of the antiterminator protein as a regulator for various purposes in synthetic biology.
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28
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Zou ZP, Yang Y, Wang J, Zhou Y, Ye BC. Coupling split-lux cassette with a toggle switch in bacteria for ultrasensitive blood markers detection in feces and urine. Biosens Bioelectron 2022; 214:114520. [DOI: 10.1016/j.bios.2022.114520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 11/29/2022]
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29
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Lebovich M, Andrews LB. Surveying the Genetic Design Space for Transcription Factor-Based Metabolite Biosensors: Synthetic Gamma-Aminobutyric Acid and Propionate Biosensors in E. coli Nissle 1917. Front Bioeng Biotechnol 2022; 10:938056. [PMID: 36091463 PMCID: PMC9452892 DOI: 10.3389/fbioe.2022.938056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/22/2022] [Indexed: 11/25/2022] Open
Abstract
Engineered probiotic bacteria have been proposed as a next-generation strategy for noninvasively detecting biomarkers in the gastrointestinal tract and interrogating the gut-brain axis. A major challenge impeding the implementation of this strategy has been the difficulty to engineer the necessary whole-cell biosensors. Creation of transcription factor-based biosensors in a clinically-relevant strain often requires significant tuning of the genetic parts and gene expression to achieve the dynamic range and sensitivity required. Here, we propose an approach to efficiently engineer transcription-factor based metabolite biosensors that uses a design prototyping construct to quickly assay the gene expression design space and identify an optimal genetic design. We demonstrate this approach using the probiotic bacterium Escherichia coli Nissle 1917 (EcN) and two neuroactive gut metabolites: the neurotransmitter gamma-aminobutyric acid (GABA) and the short-chain fatty acid propionate. The EcN propionate sensor, utilizing the PrpR transcriptional activator from E. coli, has a large 59-fold dynamic range and >500-fold increased sensitivity that matches biologically-relevant concentrations. Our EcN GABA biosensor uses the GabR transcriptional repressor from Bacillus subtilis and a synthetic GabR-regulated promoter created in this study. This work reports the first known synthetic microbial whole-cell biosensor for GABA, which has an observed 138-fold activation in EcN at biologically-relevant concentrations. Using this rapid design prototyping approach, we engineer highly functional biosensors for specified in vivo metabolite concentrations that achieve a large dynamic range and high output promoter activity upon activation. This strategy may be broadly useful for accelerating the engineering of metabolite biosensors for living diagnostics and therapeutics.
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Affiliation(s)
- Matthew Lebovich
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA, United States
| | - Lauren B. Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Graduate, Program University of Massachusetts Amherst, Amherst, MA, United States
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30
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Wang HD, Xu JZ, Zhang WG. Metabolic engineering of Escherichia coli for efficient production of L-arginine. Appl Microbiol Biotechnol 2022; 106:5603-5613. [PMID: 35931894 DOI: 10.1007/s00253-022-12109-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/15/2022] [Accepted: 07/27/2022] [Indexed: 11/02/2022]
Abstract
As an important semi-essential amino acid, L-arginine (L-Arg) has important application prospects in medicine and health care. However, it remains a challenge to efficiently produce L-Arg by Escherichia coli (E. coli). In the present study, we obtained an E. coli A1 with L-Arg accumulation ability, and carried out a series of metabolic engineering on it, and finally obtained an E. coli strain A7 with high L-Arg production ability. First, genome analysis of strain A1 was performed to explore the related genes affecting L-Arg accumulation. We found that gene speC and gene speF played an important role in the accumulation of L-Arg. Second, we used two strategies to solve the feedback inhibition of the L-Arg pathway in E. coli. One was the combination of a mutation of the gene argA and the deletion of the gene argR, and the other was the combination of a heterologous insertion of the gene argJ and the deletion of the gene argR. The combination of exogenous argJ gene insertion and argR gene deletion achieved higher titer accumulation with less impact on strain growth. Finally, we inserted the gene cluster argCJBDF of Corynebacterium glutamicum (C. glutamicum) to enhance the metabolic flux of the L-Arg pathway in E. coli. The final strain obtained 70.1 g/L L-Arg in a 5-L bioreactor, with a yield of 0.326 g/g glucose and a productivity of 1.17 g/(L· h). This was the highest level of L-Arg production by E. coli ever reported. Collectively, our findings provided valuable insights into the possibility of the industrial production of L-Arg by E. coli. KEY POINTS: • Genetic background of E. coli A1 genome analysis. • Heterologous argJ substitution of argA mutation promoted excessive accumulation of L-Arg in E. coli A1. • The overexpression of L-Arg synthesis gene cluster argCJBDF of Corynebacterium glutamicum (C. glutamate) promoted the accumulation of L-Arg, and 70.1 g/L L-Arg was finally obtained in fed-batch fermentation.
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Affiliation(s)
- Hai-De Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1,800# Lihu Road, 214122, WuXi, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1,800# Lihu Road, 214122, WuXi, People's Republic of China.
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1,800# Lihu Road, 214122, WuXi, People's Republic of China.
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31
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Andon JS, Lee B, Wang T. Enzyme directed evolution using genetically encodable biosensors. Org Biomol Chem 2022; 20:5891-5906. [PMID: 35437559 DOI: 10.1039/d2ob00443g] [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] [Indexed: 11/21/2022]
Abstract
Directed evolution has been remarkably successful in identifying enzyme variants with new or improved properties, such as altered substrate scope or novel reactivity. Genetically encodable biosensors (GEBs), which convert the concentration of a small molecule ligand into an easily detectable output signal, have seen increasing application to enzyme directed evolution in the last decade. GEBs enable the use of high-throughput methods to assess enzyme activity of very large libraries, which can accelerate the search for variants with desirable activity. Here, we review different classes of GEBs and their properties in the context of enzyme evolution, how GEBs have been integrated into directed evolution workflows, and recent examples of enzyme evolution efforts utilizing GEBs. Finally, we discuss the advantages, challenges, and opportunities for using GEBs in the directed evolution of enzymes.
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Affiliation(s)
- James S Andon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - ByungUk Lee
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Tina Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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32
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Hartline CJ, Zhang F. The Growth Dependent Design Constraints of Transcription-Factor-Based Metabolite Biosensors. ACS Synth Biol 2022; 11:2247-2258. [PMID: 35700119 PMCID: PMC9994378 DOI: 10.1021/acssynbio.2c00143] [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: 11/30/2022]
Abstract
Metabolite biosensors based on metabolite-responsive transcription factors are key synthetic biology components for sensing and precisely controlling cellular metabolism. Biosensors are often designed under laboratory conditions but are deployed in applications where cellular growth rate differs drastically from its initial characterization. Here we asked how growth rate impacts the minimum and maximum biosensor outputs and the dynamic range, which are key metrics of biosensor performance. Using LacI, TetR, and FadR-based biosensors in Escherichia coli as models, we find that the dynamic range of different biosensors have different growth rate dependencies. We developed a kinetic model to explore how tuning biosensor parameters impact the dynamic range growth rate dependence. Our modeling and experimental results revealed that the effects to dynamic range and its growth rate dependence are often coupled, and the metabolite transport mechanisms shape the dynamic range-growth rate response. This work provides a systematic understanding of biosensor performance under different growth rates, which will be useful for predicting biosensor behavior in broad synthetic biology and metabolic engineering applications.
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Affiliation(s)
- Christopher J Hartline
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States.,Division of Biology & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missouri 63130, United States.,Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
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33
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Liu X, Inda ME, Lai Y, Lu TK, Zhao X. Engineered Living Hydrogels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2201326. [PMID: 35243704 PMCID: PMC9250645 DOI: 10.1002/adma.202201326] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/01/2022] [Indexed: 05/31/2023]
Abstract
Living biological systems, ranging from single cells to whole organisms, can sense, process information, and actuate in response to changing environmental conditions. Inspired by living biological systems, engineered living cells and nonliving matrices are brought together, which gives rise to the technology of engineered living materials. By designing the functionalities of living cells and the structures of nonliving matrices, engineered living materials can be created to detect variability in the surrounding environment and to adjust their functions accordingly, thereby enabling applications in health monitoring, disease treatment, and environmental remediation. Hydrogels, a class of soft, wet, and biocompatible materials, have been widely used as matrices for engineered living cells, leading to the nascent field of engineered living hydrogels. Here, the interactions between hydrogel matrices and engineered living cells are described, focusing on how hydrogels influence cell behaviors and how cells affect hydrogel properties. The interactions between engineered living hydrogels and their environments, and how these interactions enable versatile applications, are also discussed. Finally, current challenges facing the field of engineered living hydrogels for their applications in clinical and environmental settings are highlighted.
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Affiliation(s)
- Xinyue Liu
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Maria Eugenia Inda
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yong Lai
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Timothy K Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Xuanhe Zhao
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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34
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Parisutham V, Chhabra S, Ali MZ, Brewster RC. Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli. Mol Syst Biol 2022; 18:e10843. [PMID: 35694815 PMCID: PMC9189660 DOI: 10.15252/msb.202110843] [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: 11/30/2021] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/12/2022] Open
Abstract
Predicting the quantitative regulatory function of transcription factors (TFs) based on factors such as binding sequence, binding location, and promoter type is not possible. The interconnected nature of gene networks and the difficulty in tuning individual TF concentrations make the isolated study of TF function challenging. Here, we present a library of Escherichia coli strains designed to allow for precise control of the concentration of individual TFs enabling the study of the role of TF concentration on physiology and regulation. We demonstrate the usefulness of this resource by measuring the regulatory function of the zinc‐responsive TF, ZntR, and the paralogous TF pair, GalR/GalS. For ZntR, we find that zinc alters ZntR regulatory function in a way that enables activation of the regulated gene to be robust with respect to ZntR concentration. For GalR and GalS, we are able to demonstrate that these paralogous TFs have fundamentally distinct regulatory roles beyond differences in binding affinity.
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Affiliation(s)
- Vinuselvi Parisutham
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Shivani Chhabra
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Md Zulfikar Ali
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Robert C Brewster
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
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35
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Chen SY, Zhang Y, Li R, Wang B, Ye BC. De Novo Design of the ArsR Regulated P ars Promoter Enables a Highly Sensitive Whole-Cell Biosensor for Arsenic Contamination. Anal Chem 2022; 94:7210-7218. [PMID: 35537205 PMCID: PMC9134189 DOI: 10.1021/acs.analchem.2c00055] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Whole-cell biosensors for arsenic contamination are typically designed based on natural bacterial sensing systems, which are often limited by their poor performance for precisely tuning the genetic response to environmental stimuli. Promoter design remains one of the most important approaches to address such issues. Here, we use the arsenic-responsive ArsR-Pars regulation system from Escherichia coli MG1655 as the sensing element and coupled gfp or lacZ as the reporter gene to construct the genetic circuit for characterizing the refactored promoters. We first analyzed the ArsR binding site and a library of RNA polymerase binding sites to mine potential promoter sequences. A set of tightly regulated Pars promoters by ArsR was designed by placing the ArsR binding sites into the promoter's core region, and a novel promoter with maximal repression efficiency and optimal fold change was obtained. The fluorescence sensor PlacV-ParsOC2 constructed with the optimized ParsOC2 promoter showed a fold change of up to 63.80-fold (with green fluorescence visible to the naked eye) at 9.38 ppb arsenic, and the limit of detection was as low as 0.24 ppb. Further, the optimized colorimetric sensor PlacV-ParsOC2-lacZ with a linear response between 0 and 5 ppb was used to perform colorimetric reactions in 24-well plates combined with a smartphone application for the quantification of the arsenic level in groundwater. This study offers a new approach to improve the performance of bacterial sensing promoters and will facilitate the on-site application of arsenic whole-cell biosensors.
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Affiliation(s)
- Sheng-Yan Chen
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China
| | - Yan Zhang
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China
| | - Renjie Li
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China
| | - Baojun Wang
- College
of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific
and Technological Innovation Center, Zhejiang
University, Hangzhou 311200, China,Research
Center of Biological Computation, Zhejiang
Laboratory, Hangzhou 311100, China,Centre
for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom,
| | - Bang-Ce Ye
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China,Institute
of Engineering Biology and Health, Collaborative Innovation Center
of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical
Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China,Lab of Biosystem
and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China,. Tel/Fax: 0086-21-64252094
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36
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Lawrence JM, Yin Y, Bombelli P, Scarampi A, Storch M, Wey LT, Climent-Catala A, Baldwin GS, O’Hare D, Howe CJ, Zhang JZ, Ouldridge TE, Ledesma-Amaro R. Synthetic biology and bioelectrochemical tools for electrogenetic system engineering. SCIENCE ADVANCES 2022; 8:eabm5091. [PMID: 35507663 PMCID: PMC9067924 DOI: 10.1126/sciadv.abm5091] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Synthetic biology research and its industrial applications rely on deterministic spatiotemporal control of gene expression. Recently, electrochemical control of gene expression has been demonstrated in electrogenetic systems (redox-responsive promoters used alongside redox inducers and electrodes), allowing for the direct integration of electronics with biological processes. However, the use of electrogenetic systems is limited by poor activity, tunability, and standardization. In this work, we developed a strong, unidirectional, redox-responsive promoter before deriving a mutant promoter library with a spectrum of strengths. We constructed genetic circuits with these parts and demonstrated their activation by multiple classes of redox molecules. Last, we demonstrated electrochemical activation of gene expression under aerobic conditions using a novel, modular bioelectrochemical device. These genetic and electrochemical tools facilitate the design and improve the performance of electrogenetic systems. Furthermore, the genetic design strategies used can be applied to other redox-responsive promoters to further expand the available tools for electrogenetics.
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Affiliation(s)
- Joshua M. Lawrence
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Yutong Yin
- Department of Bioengineering, Imperial College London, London, UK
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Bioengineering, Imperial College London, London, UK
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | - Alberto Scarampi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Marko Storch
- London DNA Foundry, Imperial College Translation and Innovation Hub, London, UK
| | - Laura T. Wey
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - Geoff S. Baldwin
- Department of Life Sciences, Imperial College London, London, UK
| | - Danny O’Hare
- Department of Bioengineering, Imperial College London, London, UK
| | | | - Jenny Z. Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College London, London, UK
- Corresponding author.
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Ma Y, Zheng X, Lin Y, Zhang L, Yuan Y, Wang H, Winterburn J, Wu F, Wu Q, Ye JW, Chen GQ. Engineering an oleic acid-induced system for Halomonas, E. coli and Pseudomonas. Metab Eng 2022; 72:325-336. [PMID: 35513297 DOI: 10.1016/j.ymben.2022.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/11/2022] [Accepted: 04/20/2022] [Indexed: 11/17/2022]
Abstract
Ligand-induced system plays an important role for microbial engineering due to its tunable gene expression control over timings and levels. An oleic acid (OA)-induced system was recently constructed based on protein FadR, a transcriptional regulator involved in fatty acids metabolism, for metabolic control in Escherichia coli. In this study, we constructed a synthetic FadR-based OA-induced systems in Halomonas bluephagenesis by hybridizing the porin promoter core region and FadR-binding operator (fadO). The dynamic control range was optimized over 150-fold, and expression leakage was significantly reduced by tuning FadR expression and positioning fadO, forming a series of OA-induced systems with various expression strengths, respectively. Additionally, ligand orthogonality and cross-species portability were also studied and showed highly linear correlation among Halomonas spp., Escherichia coli and Pseudomonas spp. Finally, OA-induced systems with medium- and small-dynamic control ranges were employed to dynamically control the expression levels of morphology associated gene minCD, and monomer precursor 4-hydroxybutyrate-CoA (4HB-CoA) synthesis pathway for polyhydroxyalkanoates (PHA), respectively, in the presence of oleic acid as an inducer. As a result, over 10 g/L of poly-3-hydroxybutyrate (PHB) accumulated by elongated cell sizes, and 6 g/L of P(3HB-co-9.57 mol% 4HB) were obtained by controlling the dose and induction time of oleic acid only. This study provides a systematic approach for ligand-induced system engineering, and demonstrates an alternative genetic tool for dynamic control of industrial biotechnology.
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Affiliation(s)
- Yueyuan Ma
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiangrui Zheng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Department of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Yina Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lizhan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yiping Yuan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - James Winterburn
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Fuqing Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; MOE Key Laboratory for Industrial Biocatalysts, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
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38
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Yan Q, Han L, Liu X, You C, Zhou S, Zhou Z. Development of an auto-inducible expression system by nitrogen sources switching based on the nitrogen catabolite repression regulation. Microb Cell Fact 2022; 21:73. [PMID: 35484589 PMCID: PMC9047365 DOI: 10.1186/s12934-022-01794-5] [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: 02/24/2022] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The construction of protein expression systems is mainly focused on carbon catabolite repression and quorum-sensing systems. However, each of these regulatory modes has an inherent flaw, which is difficult to overcome. Organisms also prioritize using different nitrogen sources, which is called nitrogen catabolite repression. To date, few gene regulatory systems based on nitrogen catabolite repression have been reported. RESULTS In this study, we constructed a nitrogen switching auto-inducible expression system (NSAES) based on nitrogen catabolite regulation and nitrogen utilization in Aspergillus nidulans. The PniaD promoter that is highly induced by nitrate and inhibition by ammonia was used as the promoter. Glucuronidase was the reporter protein. Glucuronidase expression occurred after ammonium was consumed in an ammonium and nitrate compounding medium, achieving stage auto-switching for cell growth and gene expression. This system maintained a balance between cell growth and protein production to maximize stress products. Expressions of glycosylated and secretory proteins were successfully achieved using this auto-inducible system. CONCLUSIONS We described an efficient auto-inducible protein expression system based on nitrogen catabolite regulation. The system could be useful for protein production in the laboratory and industrial applications. Simultaneously, NSAES provides a new auto-inducible expression regulation mode for other filamentous fungi.
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Affiliation(s)
- Qin Yan
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xinyue Liu
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Cuiping You
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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39
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Zhou S, Alper HS, Zhou J, Deng Y. Intracellular biosensor-based dynamic regulation to manipulate gene expression at the spatiotemporal level. Crit Rev Biotechnol 2022; 43:646-663. [PMID: 35450502 DOI: 10.1080/07388551.2022.2040415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The use of intracellular, biosensor-based dynamic regulation strategies to regulate and improve the production of useful compounds have progressed significantly over previous decades. By employing such an approach, it is possible to simultaneously realize high productivity and optimum growth states. However, industrial fermentation conditions contain a mixture of high- and low-performance non-genetic variants, as well as young and aged cells at all growth phases. Such significant individual variations would hinder the precise controlling of metabolic flux at the single-cell level to achieve high productivity at the macroscopic population level. Intracellular biosensors, as the regulatory centers of metabolic networks, can real-time sense intra- and extracellular conditions and, thus, could be synthetically adapted to balance the biomass formation and overproduction of compounds by individual cells. Herein, we highlight advances in the designing and engineering approaches to intracellular biosensors. Then, the spatiotemporal properties of biosensors associated with the distribution of inducers are compared. Also discussed is the use of such biosensors to dynamically control the cellular metabolic flux. Such biosensors could achieve single-cell regulation or collective regulation goals, depending on whether or not the inducer distribution is only intracellular.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.,McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
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40
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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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41
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Miller CA, Ho JML, Bennett MR. Strategies for Improving Small-Molecule Biosensors in Bacteria. BIOSENSORS 2022; 12:bios12020064. [PMID: 35200325 PMCID: PMC8869690 DOI: 10.3390/bios12020064] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 05/03/2023]
Abstract
In recent years, small-molecule biosensors have become increasingly important in synthetic biology and biochemistry, with numerous new applications continuing to be developed throughout the field. For many biosensors, however, their utility is hindered by poor functionality. Here, we review the known types of mechanisms of biosensors within bacterial cells, and the types of approaches for optimizing different biosensor functional parameters. Discussed approaches for improving biosensor functionality include methods of directly engineering biosensor genes, considerations for choosing genetic reporters, approaches for tuning gene expression, and strategies for incorporating additional genetic modules.
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Affiliation(s)
- Corwin A. Miller
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
| | - Joanne M. L. Ho
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
| | - Matthew R. Bennett
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
- Department of Bioengineering, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA
- Correspondence:
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42
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Chitboonthavisuk C, Luo CH, Huss P, Fernholz M, Raman S. Engineering a Dynamic Controllable Infectivity Switch in Bacteriophage T7. ACS Synth Biol 2022; 11:286-296. [PMID: 34985866 PMCID: PMC9059553 DOI: 10.1021/acssynbio.1c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Transcriptional repressors play an important role in regulating phage life cycle. Here, we examine how synthetic transcription repressors can be used in bacteriophage T7 to create a dynamic, controllable infectivity switch. We engineered T7 phage by replacing a large region of the early phage genome with different combinations of ligand-responsive promoters and ribosome binding sites (RBS) designed to control the phage RNA polymerase, gp1. Phages with engineered infectivity switch are fully viable at levels comparable to wildtype T7, when not repressed, indicating the phage can be engineered without loss of fitness. The most effective switch used a TetR-responsive promoter and an attenuated RBS, resulting in a 2-fold increase in latent period and a 10-fold decrease in phage titer when repressed. Phage activity can be further tuned using different inducer concentrations. Our study provides a proof of concept for how a simple synthetic circuit introduced into the phage genome enables user control over phage infectivity.
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Affiliation(s)
- Chutikarn Chitboonthavisuk
- Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Dept. of Bacteriology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Chun Huai Luo
- Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Dept. of Bacteriology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Phil Huss
- Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Dept. of Bacteriology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Mikayla Fernholz
- Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Srivatsan Raman
- Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Dept. of Bacteriology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Dept. of Chemical & Biological Eng., Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
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43
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d’Oelsnitz S, Nguyen V, Alper HS, Ellington AD. Evolving a Generalist Biosensor for Bicyclic Monoterpenes. ACS Synth Biol 2022; 11:265-272. [PMID: 34985281 DOI: 10.1021/acssynbio.1c00402] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Prokaryotic transcription factors can be repurposed as analytical and synthetic tools for precise chemical measurement and regulation. Monoterpenes encompass a broad chemical family that are commercially valuable as flavors, cosmetics, and fragrances, but have proven difficult to measure, especially in cells. Herein, we develop genetically encoded, generalist monoterpene biosensors by using directed evolution to expand the effector specificity of the camphor-responsive TetR-family regulator CamR from Pseudomonas putida. Using a novel negative selection coupled with a high-throughput positive screen (Seamless Enrichment of Ligand-Inducible Sensors, SELIS), we evolve CamR biosensors that can recognize four distinct monoterpenes: borneol, fenchol, eucalyptol, and camphene. Different evolutionary trajectories surprisingly yielded common mutations, emphasizing the utility of CamR as a platform for creating generalist biosensors. Systematic promoter optimization driving the reporter increased the system's signal-to-noise ratio to 150-fold. These sensors can serve as a starting point for the high-throughput screening and dynamic regulation of bicyclic monoterpene production strains.
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Affiliation(s)
- Simon d’Oelsnitz
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Vylan Nguyen
- Freshman Research Initiative, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
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44
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Jiao C, Beisel CL. Reprogramming TracrRNAs for Multiplexed RNA Detection. Methods Mol Biol 2022; 2518:217-235. [PMID: 35666448 DOI: 10.1007/978-1-0716-2421-0_13] [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: 06/15/2023]
Abstract
CRISPR-based detection and recording technologies are gaining increasing attention in disease surveillance and prevention. In this chapter, we describe how our recent discovery of noncanonical crRNAs inspired the engineering of reprogrammed tracrRNAs and led to a powerful platform for multiplexed RNA detection. We provide detailed protocols regarding how to design reprogrammed tracrRNA and carry out assays in vitro and in vivo.
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Affiliation(s)
- Chunlei Jiao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany.
- Medical Faculty, University of Würzburg, Würzburg, Germany.
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45
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Picard HR, Schwingen KS, Green LM, Shis DL, Egan SM, Bennett MR, Swint-Kruse L. Allosteric regulation within the highly interconnected structural scaffold of AraC/XylS homologs tolerates a wide range of amino acid changes. Proteins 2022; 90:186-199. [PMID: 34369028 PMCID: PMC8671227 DOI: 10.1002/prot.26206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 01/03/2023]
Abstract
To create bacterial transcription "circuits" for biotechnology, one approach is to recombine natural transcription factors, promoters, and operators. Additional novel functions can be engineered from existing transcription factors such as the E. coli AraC transcriptional activator, for which binding to DNA is modulated by binding L-arabinose. Here, we engineered chimeric AraC/XylS transcription activators that recognized ara DNA binding sites and responded to varied effector ligands. The first step, identifying domain boundaries in the natural homologs, was challenging because (i) no full-length, dimeric structures were available and (ii) extremely low sequence identities (≤10%) among homologs precluded traditional assemblies of sequence alignments. Thus, to identify domains, we built and aligned structural models of the natural proteins. The designed chimeric activators were assessed for function, which was then further improved by random mutagenesis. Several mutational variants were identified for an XylS•AraC chimera that responded to benzoate; two enhanced activation to near that of wild-type AraC. For an RhaR•AraC chimera, a variant with five additional substitutions enabled transcriptional activation in response to rhamnose. These five changes were dispersed across the protein structure, and combinatorial experiments testing subsets of substitutions showed significant non-additivity. Combined, the structure modeling and epistasis suggest that the common AraC/XylS structural scaffold is highly interconnected, with complex intra-protein and inter-domain communication pathways enabling allosteric regulation. At the same time, the observed epistasis and the low sequence identities of the natural homologs suggest that the structural scaffold and function of transcriptional regulation are nevertheless highly accommodating of amino acid changes.
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Affiliation(s)
- Hunter R. Picard
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - Kristen S. Schwingen
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - Lisa M. Green
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - David L. Shis
- Department of Biosciences and Department of Bioengineering, Rice University, Houston, TX 77005
| | - Susan M. Egan
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045
| | - Matthew R. Bennett
- Department of Biosciences and Department of Bioengineering, Rice University, Houston, TX 77005
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160,To whom correspondence should be addressed: ; 913-588-0399
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46
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Hai-De W, Shuai L, Bing-Bing W, Jie L, Jian-Zhong X, Wei-Guo Z. Metabolic engineering of Escherichia coli for efficient production of l-arginine. ADVANCES IN APPLIED MICROBIOLOGY 2022; 122:127-150. [PMID: 37085192 DOI: 10.1016/bs.aambs.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As a semi-essential amino acid, l-arginine (l-Arg) plays an important role in food, health care, and medical treatment. At present, the main method of producing l-Arg is the use of microbial fermentation. Therefore, the selection and breeding of high-efficiency microbial strains is the top priority. To continuously improve the l-Arg production performance of the strains, a series of metabolic engineering strategies have been tried to transform the strains. The production of l-Arg by metabolically engineered Corynebacterium glutamicum (C. glutamicum) reached a relatively high level. Escherichia coli (E. coli), as a strain with great potential for l-Arg production, also has a large number of research strategies aimed at screening effective E. coli for producing l-Arg. E. coli also has a number of advantages over C. glutamicum in producing l-Arg. Therefore, it is of great significance to screen out excellent and stable E. coli to produce l-Arg. Here, based on recent research results, we review the metabolic pathways of l-Arg production in E. coli, the research progress of l-Arg production in E. coli, and various regulatory strategies implemented in E. coli.
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47
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Zúñiga A, Camacho M, Chang HJ, Fristot E, Mayonove P, Hani EH, Bonnet J. Engineered l-Lactate Responding Promoter System Operating in Glucose-Rich and Anoxic Environments. ACS Synth Biol 2021; 10:3527-3536. [PMID: 34851606 PMCID: PMC8689689 DOI: 10.1021/acssynbio.1c00456] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Indexed: 12/19/2022]
Abstract
Bacteria equipped with genetically encoded lactate biosensors are promising tools for biopharmaceutical production, diagnostics, and cellular therapies. However, many applications involve glucose-rich and anoxic environments, in which current whole-cell lactate biosensors show low performance. Here we engineer an optimized, synthetic lactate biosensor system by repurposing the natural LldPRD promoter regulated by the LldR transcriptional regulator. We removed glucose catabolite and anoxic repression by designing a hybrid promoter, containing LldR operators and tuned both regulator and reporter gene expressions to optimize biosensor signal-to-noise ratio. The resulting lactate biosensor, termed ALPaGA (A Lactate Promoter Operating in Glucose and Anoxia), can operate in glucose-rich, aerobic and anoxic conditions. We show that ALPaGA works reliably in the probiotic chassisEscherichia coliNissle 1917 and can detect endogenous l-lactate produced by 3D tumor spheroids with an improved dynamic range. In the future, the ALPaGA system could be used to monitor bioproduction processes and improve the specificity of engineered bacterial cancer therapies by restricting their activity to the lactate-rich microenvironment of solid tumors.
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Affiliation(s)
- Ana Zúñiga
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - Miguel Camacho
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - Hung-Ju Chang
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - Elsa Fristot
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - Pauline Mayonove
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - El-Habib Hani
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - Jerome Bonnet
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
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48
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [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: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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49
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Zhao N, Song J, Zhang H, Lin Y, Han S, Huang Y, Zheng S. Development of a Transcription Factor-Based Diamine Biosensor in Corynebacterium glutamicum. ACS Synth Biol 2021; 10:3074-3083. [PMID: 34662101 DOI: 10.1021/acssynbio.1c00363] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diamines serve as major platform chemicals that can be employed to a variety of industrial scenarios, particularly as monomers for polymer synthesis. High-throughput sensors for diamine biosynthesis can greatly improve the biological production of diamines. Here, we identified and characterized a transcription factor-driven biosensor for putrescine and cadaverine in Corynebacterium glutamicum. The transcriptional TetR-family regulatory protein CgmR (CGL2612) is used for the specific detection of diamine compounds. This study also improved the dynamic range and the sensitivity to putrescine by systematically optimizing genetic components of pSenPut. By a single cell-based screening strategy for a library of CgmR with random mutations, this study obtained the most sensitive variant CgmRI152T, which possessed an experimentally determined limit of detection (LoD) of ≤0.2 mM, a K of 11.4 mM, and a utility of 720. Using this highly sensitive putrescine biosensor pSenPutI152T, we demonstrated that CgmRI152T can be used as a sensor to detect putrescine produced biologically in a C. glutamicum system. This high sensitivity and the range of CgmR will be an influential tool for rewiring metabolic circuits and facilitating the directed evolution of recombinant strains toward the biological synthesis of diamine compounds.
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Affiliation(s)
- Nannan Zhao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jie Song
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Hao Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuanyuan Huang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, P. R. China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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Chae YK, Kim H. Development of an Autoinducible Plasmid for Recombinant Protein Production. Protein Pept Lett 2021; 28:1398-1407. [PMID: 34749604 DOI: 10.2174/0929866528666211105113750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/09/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The production of recombinant proteins in E. coli involves such factors as host strains, expression vectors, culture media, and induction methods. The typical procedure to produce heterologous proteins consists of the following: (1) insertion of the target gene into a suitable vector to construct an overexpression plasmid, (2) transformation of a strain specialized for protein production with the constructed plasmid DNA, (3) growth of the host in a suitable medium and induction of the protein production at a right moment, and (4) further growth to get the maximum yield. There are hurdles involved in each of these steps, and researchers have developed many materials or methods, which often require special recipes or procedures. OBJECTIVE To eliminate the special requirements for the recombinant protein production by using readily available materials. Also to save time and effort in the routine protein production work. METHOD We started with a vector capable of producing a target protein fused to the C-terminus of the maltose binding protein (MBP). The mCherry (red fluorescent protein) gene was fused to MBP. It acted as a reporter in the initial screening procedure. The original lethal gene (barnase) was replaced with sacB. We chose 3 stationary phase promoters, and made hybrids of them by mixing halves from each one. The T5 promoter was replaced with these stationary phase promoters or their hybrids. The best plasmid was selected by the color intensity of the cell pellet. MBP and GST genes were inserted in place of sacB, and their production yields were compared with the original plasmid in the conventional way of expression. RESULTS We constructed an expression plasmid with an autoinducible promoter working in a host that was not specially designed for protein production and in a TB medium which did not contain any secret ingredient, nor was difficult to prepare unlike Studier's defined medium. This plasmid also contains a color indicator which turns red when protein production is successful. We tested our system with the maltose binding protein (MBP) and the glutathione S-transferase (GST), and showed that both proteins were produced to a level comparable to what the commercial medium and/or the specialized strain yielded. CONCLUSION We developed a plasmid equipped with an autoinducible promoter, a hybrid of the two promoters which were activated at the stationary phase. This plasmid does not need a special E. coli strain nor a sophisticated nor an expensive medium. It produces an intense red (or pink) color, which can be used as an indicator of a successful production of the target protein and as a predictive measure of the amount of the produced target protein. We speculate that this plasmid will have its greatest advantage when growing cells at low temperatures which would inevitably take a long time. .
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Affiliation(s)
- Young Kee Chae
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul. Korea
| | - Hakbeom Kim
- Department of Chemistry, Sejong University, 209 Neungdong-Ro, Gwangjin-Gu, Seoul. Korea
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