201
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Mageeney CM, Mohammed HT, Dies M, Anbari S, Cudkevich N, Chen Y, Buceta J, Ware VC. Mycobacterium Phage Butters-Encoded Proteins Contribute to Host Defense against Viral Attack. mSystems 2020; 5:e00534-20. [PMID: 33024050 PMCID: PMC7542560 DOI: 10.1128/msystems.00534-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/15/2020] [Indexed: 01/21/2023] Open
Abstract
A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems.IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance.
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Affiliation(s)
- Catherine M Mageeney
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Hamidu T Mohammed
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Marta Dies
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Samira Anbari
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Netta Cudkevich
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Yanyan Chen
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Javier Buceta
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Vassie C Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
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202
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Galizi R, Duncan JN, Rostain W, Quinn CM, Storch M, Kushwaha M, Jaramillo A. Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics. CRISPR J 2020; 3:398-408. [PMID: 33095053 DOI: 10.1089/crispr.2020.0029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CRISPR guide RNAs (gRNAs) can be programmed with relative ease to allow the genetic editing of nearly any DNA or RNA sequence. Here, we propose novel molecular architectures to achieve RNA-dependent modulation of CRISPR activity in response to specific RNA molecules. We designed and tested, in both living Escherichia coli cells and cell-free assays for rapid prototyping, cis-repressed RNA-interacting guide RNA (igRNA) that switch to their active state only upon interaction with small RNA fragments or long RNA transcripts, including pathogen-derived mRNAs of medical relevance such as the human immunodeficiency virus infectivity factor. The proposed CRISPR-igRNAs are fully customizable and easily adaptable to the majority if not all the available CRISPR-Cas variants to modulate a variety of genetic functions in response to specific cellular conditions, providing orthogonal activation and increased specificity. We thereby foresee a large scope of application for therapeutic, diagnostic, and biotech applications in both prokaryotic and eukaryotic systems.
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Affiliation(s)
- Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, United Kingdom
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - John N Duncan
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - William Rostain
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Charlotte M Quinn
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Marko Storch
- Department of Life Sciences, Imperial College London, London, United Kingdom
- London Biofoundry, Imperial College London, London, United Kingdom
| | - Manish Kushwaha
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Université Paris-Saclay, INRAE, AgroParisTech, MIcalis Institute, Paris, France
| | - Alfonso Jaramillo
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
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203
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Chekli Y, Peron-Cane C, Dell'Arciprete D, Allemand JF, Li C, Ghigo JM, Gautier A, Lebreton A, Desprat N, Beloin C. Visualizing the dynamics of exported bacterial proteins with the chemogenetic fluorescent reporter FAST. Sci Rep 2020; 10:15791. [PMID: 32978420 PMCID: PMC7519654 DOI: 10.1038/s41598-020-72498-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023] Open
Abstract
Bacterial proteins exported to the cell surface play key cellular functions. However, despite the interest to study the localisation of surface proteins such as adhesins, transporters or hydrolases, monitoring their dynamics in live imaging remains challenging, due to the limited availability of fluorescent probes remaining functional after secretion. In this work, we used the Escherichia coli intimin and the Listeria monocytogenes InlB invasin as surface exposed scaffolds fused with the recently developed chemogenetic fluorescent reporter protein FAST. Using both membrane permeant (HBR-3,5DM) and non-permeant (HBRAA-3E) fluorogens that fluoresce upon binding to FAST, we demonstrated that fully functional FAST can be exposed at the cell surface and used to specifically tag the external side of the bacterial envelop in both diderm and monoderm bacteria. Our work opens new avenues to study the organization and dynamics of the bacterial cell surface proteins.
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Affiliation(s)
- Yankel Chekli
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Caroline Peron-Cane
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Dario Dell'Arciprete
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
| | - Jean-François Allemand
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Chenge Li
- École Normale Supérieure, Université PSL, CNRS, Laboratoire Des Biomolécules (LBM), Sorbonne Université, 75005, Paris, France
| | - Jean-Marc Ghigo
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
| | - Arnaud Gautier
- École Normale Supérieure, Université PSL, CNRS, Laboratoire Des Biomolécules (LBM), Sorbonne Université, 75005, Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
- Institut Universitaire de France, Paris, France
| | - Alice Lebreton
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- INRAE, IBENS, 75005, Paris, France
| | - Nicolas Desprat
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France.
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.
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204
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Ireland WT, Beeler SM, Flores-Bautista E, McCarty NS, Röschinger T, Belliveau NM, Sweredoski MJ, Moradian A, Kinney JB, Phillips R. Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. eLife 2020; 9:e55308. [PMID: 32955440 PMCID: PMC7567609 DOI: 10.7554/elife.55308] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 09/18/2020] [Indexed: 01/28/2023] Open
Abstract
Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium Escherichia coli, for ≈65% of promoters we remain ignorant of their regulation. Until we crack this regulatory Rosetta Stone, efforts to read and write genomes will remain haphazard. We introduce a new method, Reg-Seq, that links massively parallel reporter assays with mass spectrometry to produce a base pair resolution dissection of more than a E. coli promoters in 12 growth conditions. We demonstrate that the method recapitulates known regulatory information. Then, we examine regulatory architectures for more than 80 promoters which previously had no known regulatory information. In many cases, we also identify which transcription factors mediate their regulation. This method clears a path for highly multiplexed investigations of the regulatory genome of model organisms, with the potential of moving to an array of microbes of ecological and medical relevance.
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Affiliation(s)
- William T Ireland
- Department of Physics, California Institute of TechnologyPasadenaUnited States
| | - Suzannah M Beeler
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Emanuel Flores-Bautista
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Nicholas S McCarty
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Tom Röschinger
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Nathan M Belliveau
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of TechnologyPasadenaUnited States
| | - Annie Moradian
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of TechnologyPasadenaUnited States
| | - Justin B Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Rob Phillips
- Department of Physics, California Institute of TechnologyPasadenaUnited States
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
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205
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Ultra-high throughput screening for novel protease specificities. Methods Enzymol 2020. [PMID: 32943144 DOI: 10.1016/bs.mie.2020.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The screening of large libraries of enzyme variants remains an essential tool in evolving biocatalysts toward improved properties for applications in medicine, chemistry, and a broad variety of other fields. Over the last decades, the technology for conducting systematic screens of arrayed members of a library of enzyme variants has made great strides in terms of increasing throughput and reducing assay volume. Here, we describe in detail an alternative to arrayed analysis, which is a screen based on density shifts in result of changed enzyme function, which allows highly parallelized screening. Specifically, we link changes in protease substrate specificity in vivo to the production of an alternative reporter protein, catalase. Depending on the catalase expression level, microcolonies of library bacteria with active protease variants contained in polymeric droplets generate an oxygen bubble, which causes a density shift in the droplet and enables it to float.
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206
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Dundas CM, Walker DJ, Keitz BK. Tuning Extracellular Electron Transfer by Shewanella oneidensis Using Transcriptional Logic Gates. ACS Synth Biol 2020; 9:2301-2315. [PMID: 32786362 DOI: 10.1021/acssynbio.9b00517] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extracellular electron transfer (EET) pathways, such as those in the bacterium Shewanella oneidensis, interface cellular metabolism with a variety of redox-driven applications. However, designer control over EET flux in S. oneidensis has proven challenging because a functional understanding of its EET pathway proteins and their effect on engineering parametrizations (e.g., response curves, dynamic range) is generally lacking. To address this, we systematically altered transcription and translation of single genes encoding parts of the primary EET pathway of S. oneidensis, CymA/MtrCAB, and examined how expression differences affected model-fitted parameters for Fe(III) reduction kinetics. Using a suite of plasmid-based inducible circuits maintained by appropriate S. oneidensis knockout strains, we pinpointed construct/strain pairings that expressed cymA, mtrA, and mtrC with maximal dynamic range of Fe(III) reduction rate. These optimized EET gene constructs were employed to create Buffer and NOT gate architectures that predictably turn on and turn off EET flux, respectively, in response to isopropyl β-D-1-thiogalactopyranoside (IPTG). Furthermore, we found that response functions generated by these logic gates (i.e., EET activity vs inducer concentration) were comparable to those generated by conventional synthetic biology circuits, where fluorescent reporters are the output. Our results provide insight on programming EET activity with transcriptional logic gates and suggest that previously developed transcriptional circuitry can be adapted to predictably control EET flux.
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Affiliation(s)
- Christopher M. Dundas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - David J.F. Walker
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Benjamin K. Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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207
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Rostain W, Shen S, Cordero T, Rodrigo G, Jaramillo A. Engineering a Circular Riboregulator in Escherichia coli. BIODESIGN RESEARCH 2020; 2020:1916789. [PMID: 37849901 PMCID: PMC10521646 DOI: 10.34133/2020/1916789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/17/2020] [Indexed: 10/19/2023] Open
Abstract
RNAs of different shapes and sizes, natural or synthetic, can regulate gene expression in prokaryotes and eukaryotes. Circular RNAs have recently appeared to be more widespread than previously thought, but their role in prokaryotes remains elusive. Here, by inserting a riboregulatory sequence within a group I permuted intron-exon ribozyme, we created a small noncoding RNA that self-splices to produce a circular riboregulator in Escherichia coli. We showed that the resulting riboregulator can trans-activate gene expression by interacting with a cis-repressed messenger RNA. We characterized the system with a fluorescent reporter and with an antibiotic resistance marker, and we modeled this novel posttranscriptional mechanism. This first reported example of a circular RNA regulating gene expression in E. coli adds to an increasing repertoire of RNA synthetic biology parts, and it highlights that topological molecules can play a role in the case of prokaryotic regulation.
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Affiliation(s)
- William Rostain
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
- Institute of Systems and Synthetic Biology, CNRS-Université d’Évry Val-d’Essonne, 91000 Évry, France
| | - Shensi Shen
- Institute of Systems and Synthetic Biology, CNRS-Université d’Évry Val-d’Essonne, 91000 Évry, France
| | - Teresa Cordero
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Guillermo Rodrigo
- Institute of Systems and Synthetic Biology, CNRS-Université d’Évry Val-d’Essonne, 91000 Évry, France
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, 46022 Valencia, Spain
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de València, 46980 Paterna, Spain
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
- Institute of Systems and Synthetic Biology, CNRS-Université d’Évry Val-d’Essonne, 91000 Évry, France
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de València, 46980 Paterna, Spain
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208
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CydDC functions as a cytoplasmic cystine reductase to sensitize Escherichia coli to oxidative stress and aminoglycosides. Proc Natl Acad Sci U S A 2020; 117:23565-23570. [PMID: 32900959 DOI: 10.1073/pnas.2007817117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
l-cysteine is the source of all bacterial sulfurous biomolecules. However, the cytoplasmic level of l-cysteine must be tightly regulated due to its propensity to reduce iron and drive damaging Fenton chemistry. It has been proposed that in Escherichia coli the component of cytochrome bd-I terminal oxidase, the CydDC complex, shuttles excessive l-cysteine from the cytoplasm to the periplasm, thereby maintaining redox homeostasis. Here, we provide evidence for an alternative function of CydDC by demonstrating that the cydD phenotype, unlike that of the bona fide l-cysteine exporter eamA, parallels that of the l-cystine importer tcyP. Chromosomal induction of eamA, but not of cydDC, from a strong pLtetO-1 promoter (Ptet) leads to the increased level of extracellular l-cysteine, whereas induction of cydDC or tcyP causes the accumulation of cytoplasmic l-cysteine. Congruently, inactivation of cydD renders cells resistant to hydrogen peroxide and to aminoglycoside antibiotics. In contrast, induction of cydDC sensitizes cells to oxidative stress and aminoglycosides, which can be suppressed by eamA overexpression. Furthermore, inactivation of the ferric uptake regulator (fur) in Ptet-cydDC or Ptet-tcyP cells results in dramatic loss of survival, whereas catalase (katG) overexpression suppresses the hypersensitivity of both strains to H2O2 These results establish CydDC as a reducer of cytoplasmic cystine, as opposed to an l-cysteine exporter, and further elucidate a link between oxidative stress, antibiotic resistance, and sulfur metabolism.
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209
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Abstract
Exposure of bacteria to sublethal concentrations of antibiotics can lead to bacterial adaptation and survival at higher doses of inhibitors, which in turn can lead to the emergence of antibiotic resistance. The presence of sublethal concentrations of antibiotics targeting translation results in an increase in the amount of ribosomes per cell but nonetheless a decrease in the cells’ growth rate. In this work, we have found that inhibition of ribosome activity can result in a decrease in the amount of free RNA polymerase available for transcription, thus limiting the protein expression rate via a different pathway than what was expected. This result can be explained by our observation that long genes, such as those coding for RNA polymerase subunits, have a higher probability of premature translation termination in the presence of ribosome inhibitors, while expression of short ribosomal genes is affected less, consistent with their increased concentration. In bacterial cells, inhibition of ribosomes by sublethal concentrations of antibiotics leads to a decrease in the growth rate despite an increase in ribosome content. The limitation of ribosomal activity results in an increase in the level of expression from ribosomal promoters; this can deplete the pool of RNA polymerase (RNAP) that is available for the expression of nonribosomal genes. However, the magnitude of this effect remains to be quantified. Here, we use the change in the activity of constitutive promoters with different affinities for RNAP to quantify the change in the concentration of free RNAP. The data are consistent with a significant decrease in the amount of RNAP available for transcription of both ribosomal and nonribosomal genes. Results obtained with different reporter genes reveal an mRNA length dependence on the amount of full-length translated protein, consistent with the decrease in ribosome processivity affecting more strongly the translation of longer genes. The genes coding for the β and β' subunits of RNAP are among the longest genes in the Escherichia coli genome, while the genes coding for ribosomal proteins are among the shortest genes. This can explain the observed decrease in transcription capacity that favors the expression of genes whose promoters have a high affinity for RNAP, such as ribosomal promoters. IMPORTANCE Exposure of bacteria to sublethal concentrations of antibiotics can lead to bacterial adaptation and survival at higher doses of inhibitors, which in turn can lead to the emergence of antibiotic resistance. The presence of sublethal concentrations of antibiotics targeting translation results in an increase in the amount of ribosomes per cell but nonetheless a decrease in the cells’ growth rate. In this work, we have found that inhibition of ribosome activity can result in a decrease in the amount of free RNA polymerase available for transcription, thus limiting the protein expression rate via a different pathway than what was expected. This result can be explained by our observation that long genes, such as those coding for RNA polymerase subunits, have a higher probability of premature translation termination in the presence of ribosome inhibitors, while expression of short ribosomal genes is affected less, consistent with their increased concentration.
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210
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García-García JD, Joshi J, Patterson JA, Trujillo-Rodriguez L, Reisch CR, Javanpour AA, Liu CC, Hanson AD. Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study. Life (Basel) 2020; 10:E179. [PMID: 32899502 PMCID: PMC7555113 DOI: 10.3390/life10090179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022] Open
Abstract
Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today's agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized more quickly than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics. Continuous directed evolution is a more efficient and scalable version that accomplishes the mutagenesis and selection steps simultaneously in vivo via error-prone replication of the target gene and coupling of the host cell's growth rate to the target gene's function. However, published continuous systems require custom plasmid assembly, and convenient multipurpose platforms are not available. We discuss two systems suitable for continuous directed evolution of enzymes, OrthoRep in Saccharomyces cerevisiae and EvolvR in Escherichia coli, and our pilot efforts to adapt each system for high-throughput plant enzyme engineering. To test our modified systems, we used the thiamin synthesis enzyme THI4, previously identified as a prime candidate for improvement. Our adapted OrthoRep system shows promise for efficient plant enzyme engineering.
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Affiliation(s)
| | - Jaya Joshi
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
| | - Jenelle A. Patterson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
| | - Lidimarie Trujillo-Rodriguez
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA; (L.T.-R.); (C.R.R.)
| | - Christopher R. Reisch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA; (L.T.-R.); (C.R.R.)
| | - Alex A. Javanpour
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA; (A.A.J.); (C.C.L.)
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA; (A.A.J.); (C.C.L.)
- Department of Chemistry, University of California, Irvine, CA 92617, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
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211
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Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity. Proc Natl Acad Sci U S A 2020; 117:22167-22172. [PMID: 32839318 DOI: 10.1073/pnas.2013543117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate protein synthesis is a tightly controlled biological process with multiple quality control steps safeguarded by aminoacyl-transfer RNA (tRNA) synthetases and the ribosome. Reduced translational accuracy leads to various physiological changes in both prokaryotes and eukaryotes. Termination of translation is signaled by stop codons and catalyzed by release factors. Occasionally, stop codons can be suppressed by near-cognate aminoacyl-tRNAs, resulting in protein variants with extended C termini. We have recently shown that stop-codon readthrough is heterogeneous among single bacterial cells. However, little is known about how environmental factors affect the level and heterogeneity of stop-codon readthrough. In this study, we have combined dual-fluorescence reporters, mass spectrometry, mathematical modeling, and single-cell approaches to demonstrate that a metabolic stress caused by excess carbon substantially increases both the level and heterogeneity of stop-codon readthrough. Excess carbon leads to accumulation of acid metabolites, which lower the pH and the activity of release factors to promote readthrough. Furthermore, our time-lapse microscopy experiments show that single cells with high readthrough levels are more adapted to severe acid stress conditions and are more sensitive to an aminoglycoside antibiotic. Our work thus reveals a metabolic stress that promotes translational heterogeneity and phenotypic diversity.
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212
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Kavčič B, Tkačik G, Bollenbach T. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nat Commun 2020; 11:4013. [PMID: 32782250 PMCID: PMC7421507 DOI: 10.1038/s41467-020-17734-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/14/2020] [Indexed: 02/03/2023] Open
Abstract
Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by "translation bottlenecks": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of "continuous epistasis" in bacterial physiology.
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Affiliation(s)
- Bor Kavčič
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Gašper Tkačik
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Tobias Bollenbach
- Institute for Biological Physics, University of Cologne, Zülpicher Str. 77, D-50937, Cologne, Germany.
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213
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Escherichia coli with a Tunable Point Mutation Rate for Evolution Experiments. G3-GENES GENOMES GENETICS 2020; 10:2671-2681. [PMID: 32503807 PMCID: PMC7407472 DOI: 10.1534/g3.120.401124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The mutation rate and mutations' effects on fitness are crucial to evolution. Mutation rates are under selection due to linkage between mutation rate modifiers and mutations' effects on fitness. The linkage between a higher mutation rate and more beneficial mutations selects for higher mutation rates, while the linkage between a higher mutation rate and more deleterious mutations selects for lower mutation rates. The net direction of selection on mutations rates depends on the fitness landscape, and a great deal of work has elucidated the fitness landscapes of mutations. However, tests of the effect of varying a mutation rate on evolution in a single organism in a single environment have been difficult. This has been studied using strains of antimutators and mutators, but these strains may differ in additional ways and typically do not allow for continuous variation of the mutation rate. To help investigate the effects of the mutation rate on evolution, we have genetically engineered a strain of Escherichia coli with a point mutation rate that can be smoothly varied over two orders of magnitude. We did this by engineering a strain with inducible control of the mismatch repair proteins MutH and MutL. We used this strain in an approximately 350 generation evolution experiment with controlled variation of the mutation rate. We confirmed the construct and the mutation rate were stable over this time. Sequencing evolved strains revealed a higher number of single nucleotide polymorphisms at higher mutations rates, likely due to either the beneficial effects of these mutations or their linkage to beneficial mutations.
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214
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Baumschlager A, Rullan M, Khammash M. Exploiting natural chemical photosensitivity of anhydrotetracycline and tetracycline for dynamic and setpoint chemo-optogenetic control. Nat Commun 2020; 11:3834. [PMID: 32737309 PMCID: PMC7395757 DOI: 10.1038/s41467-020-17677-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 07/02/2020] [Indexed: 01/02/2023] Open
Abstract
The transcriptional inducer anhydrotetracycline (aTc) and the bacteriostatic antibiotic tetracycline (Tc) are commonly used in all fields of biology for control of transcription or translation. A drawback of these and other small molecule inducers is the difficulty of their removal from cell cultures, limiting their application for dynamic control. Here, we describe a simple method to overcome this limitation, and show that the natural photosensitivity of aTc/Tc can be exploited to turn them into highly predictable optogenetic transcriptional- and growth-regulators. This new optogenetic class uniquely features both dynamic and setpoint control which act via population-memory adjustable through opto-chemical modulation. We demonstrate this method by applying it for dynamic gene expression control and for enhancing the performance of an existing optogenetic system. We then expand the utility of the aTc system by constructing a new chemical bandpass filter that increases its aTc response range. The simplicity of our method enables scientists and biotechnologists to use their existing systems employing aTc/Tc for dynamic optogenetic experiments without genetic modification.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Marc Rullan
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
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215
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Zhang K, Zhang Z, Kang J, Chen J, Liu J, Gao N, Fan L, Zheng P, Wang Y, Sun J. CRISPR/Cas13d-Mediated Microbial RNA Knockdown. Front Bioeng Biotechnol 2020; 8:856. [PMID: 32850723 PMCID: PMC7406568 DOI: 10.3389/fbioe.2020.00856] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-guided and RNA-targeting type IV-D CRISPR/Cas systems (CRISPR/Cas13d) have recently been identified and employed for efficient and specific RNA knockdown in mammalian and plant cells. Cas13d possesses dual RNase activities and is capable of processing CRISPR arrays and cleaving target RNAs in a protospacer flanking sequence (PFS)-independent manner. These properties make this system a promising tool for multiplex gene expression regulation in microbes. Herein, we aimed to establish a CRISPR/Cas13d-mediated RNA knockdown platform for bacterial chassis. CasRx, Cas13d from Ruminococcus flavefaciens XPD3002, was selected due to its high activity. However, CasRx was found to be highly toxic to both Escherichia coli and Corynebacterium glutamicum, especially when it cooperated with its guide and target RNAs. After employing a low copy number vector, a tightly controlled promoter, and a weakened ribosome binding site, we successfully constructed an inducible expression system for CasRx and applied it for repressing the expression of a green fluorescent protein (GFP) in E. coli. Despite our efforts to optimize inducer usage, guide RNA (gRNA) architecture and combination, and target gene expression level, the highest gene repression efficiency was 30–50% at the protein level and ∼70% at the mRNA level. The moderate RNA knockdown is possibly caused by the collateral cleavage activity toward bystander RNAs, which acts as a mechanism of type IV-D immunity and perturbs microbial metabolism. Further studies on cellular response to CRISPR/Cas13d and improvement in RNA knockdown efficiency are required prior to practical application of this system in microbes.
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Affiliation(s)
- Kun Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhihui Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jianan Kang
- College of Life Engineering, Shenyang Institute of Technology, Fushun, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ning Gao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liwen Fan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
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216
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Jahanshahi S, Li Y. An Effective Method for Quantifying RNA Expression of IbsC-SibC, a Type I Toxin-Antitoxin System in Escherichia coli. Chembiochem 2020; 21:3120-3130. [PMID: 32516493 DOI: 10.1002/cbic.202000280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/04/2020] [Indexed: 01/28/2023]
Abstract
Toxin and antitoxin (TA) systems are small genetic modules consisting of a toxin protein and an RNA or protein antitoxin. It is difficult to study their functions in a large part due to the lack of effective methods to study toxin RNAs, which usually exist at exceptionally low levels. Herein, we describe a sensitive reverse transcription quantitative PCR (RT-qPCR) method that is able to quantitate such RNA species. The method was directed at detection of the toxin mRNA of the ibsC-sibC TA pair, and its high specificity was validated by sequencing. The approach was used to determine relative expression of the IbsC and SibC RNAs at different cell-growth phases; this revealed an expression pattern that cannot be explained by the prevailing notion of growth stasis by the toxin and rescue by the antitoxin. The usefulness of the method was further showcased by the determination of average cellular copy numbers of the IbsC-SibC RNAs in wild-type E. coli cells and RNA abundance in E. coli cells engineered with extra copies of the ibsC-sibC genes. With a robust method to quantitate cellular small RNAs at very low concentrations, we are now equipped to study the expression of TA systems under different conditions to gain useful insights about their functions.
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Affiliation(s)
- Shahrzad Jahanshahi
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
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217
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Durante-Rodríguez G, Calles B, De Lorenzo V, Nikel PI. A SsrA/NIa-based Strategy for Post-Translational Regulation of Protein Levels in Gram-negative Bacteria. Bio Protoc 2020; 10:e3688. [PMID: 33659358 PMCID: PMC7842543 DOI: 10.21769/bioprotoc.3688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/27/2020] [Accepted: 05/11/2020] [Indexed: 11/02/2022] Open
Abstract
Strategies to control the levels of key enzymes of bacterial metabolism are commonly based on the manipulation of gene of interest within the target pathway. The development of new protocols towards the manipulation of biochemical processes is still a major challenge in the field of metabolic engineering. On this background, the FENIX (functional engineering of SsrA/NIa-based flux control) system allows for the post-translational regulation of protein levels, providing both independent control of the steady-state protein amounts and inducible accumulation of target proteins. This strategy enables an extra layer of control over metabolic fluxes in bacterial cell factories (see Graphical abstract below). The protocol detailed here describes the steps needed to design FENIX-tagged proteins and to adapt the system to virtually any pathway for fine-tuning of metabolic fluxes. Graphical abstract.
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Affiliation(s)
- Gonzalo Durante-Rodríguez
- Environmental Microbiology Group, Centro de Investigaciones Biológicas (CIB-CSIC), 28040 Madrid, Spain
| | - Belén Calles
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Víctor De Lorenzo
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Pablo I. Nikel
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
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218
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Long M, Xu M, Qiao Z, Ma Z, Osire T, Yang T, Zhang X, Shao M, Rao Z. Directed Evolution of Ornithine Cyclodeaminase Using an EvolvR-Based Growth-Coupling Strategy for Efficient Biosynthesis of l-Proline. ACS Synth Biol 2020; 9:1855-1863. [PMID: 32551572 DOI: 10.1021/acssynbio.0c00198] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
l-Proline takes a significant role in the pharmaceutical and chemical industries as well as graziery. Typical biosynthesis of l-proline is from l-glutamate, involving three enzyme reactions as well as a spontaneous cyclization. Alternatively, l-proline can be also synthesized in l-ornithine and/or l-arginine producing strains by an ornithine aminotransferase (OCD). In this study, a strategy of directed evolution combining rare codon selection and pEvolvR was developed to screen OCD with high catalytic efficiency, improving l-proline production from l-arginine chassis cells. The mutations were generated by CRISPR-assisted DNA polymerases and were screened by growth-coupled rare codon selection system. OCDK205G/M86K/T162A from Pseudomonas putida was identified with 2.85-fold increase in catalytic efficiency for the synthesis of l-proline. Furthermore, we designed and optimized RBS for the BaargI and Ppocd coupling cascade using RedLibs, as well as sRNA inhibition of argF to moderate l-proline biosynthesis in l-arginine overproducing Corynebacterium crenatum. The strain PS6 with best performance reached 15.3 g/L l-proline in the shake flask and showed a titer of 38.4 g/L in a 5 L fermenter with relatively low concentration of residual l-ornithine and/or l-arginine.
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Affiliation(s)
- Mengfei Long
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhina Qiao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhenfeng Ma
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Tolbert Osire
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Minglong Shao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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219
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Stargardt P, Feuchtenhofer L, Cserjan-Puschmann M, Striedner G, Mairhofer J. Bacteriophage Inspired Growth-Decoupled Recombinant Protein Production in Escherichia coli. ACS Synth Biol 2020; 9:1336-1348. [PMID: 32324989 DOI: 10.1021/acssynbio.0c00028] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Modulating resource allocation in bacteria to redirect metabolic building blocks to the formation of recombinant proteins rather than biomass formation remains a grand challenge in biotechnology. Here, we present a novel approach for improved recombinant protein production (RPP) using Escherichia coli (E. coli) by decoupling recombinant protein synthesis from cell growth. We show that cell division and host mRNA transcription can be successfully inhibited by coexpression of a bacteriophage-derived E. coli RNA polymerase (RNAP) inhibitor peptide and that genes overtranscribed by the orthogonal T7 RNAP can finally account to >55% of cell dry mass (CDM). This RNAP inhibitor peptide binds the E. coli RNAP and therefore prevents σ-factor 70 mediated formation of transcriptional qualified open promoter complexes. Thereby, the transcription of σ-factor 70 driven host genes is inhibited, and metabolic resources can be exclusively utilized for synthesis of the protein of interest (POI). Here, we mimic the late phase of bacteriophage infection by coexpressing a phage-derived xenogeneic regulator that reprograms the host cell and thereby are able to significantly improve RPP under industrial relevant fed-batch process conditions at bioreactor scale. We have evaluated production of several different recombinant proteins at different scales (from microscale to 20 L fed-batch scale) and have been able to improve total and soluble proteins yields up to 3.4-fold in comparison to the reference expression system E. coli BL21(DE3). This novel approach for growth-decoupled RPP has profound implications for biotechnology and bioengineering and helps to establish more cost-effective and generic manufacturing processes for biologics and biomaterials.
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Affiliation(s)
| | | | - Monika Cserjan-Puschmann
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
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220
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Qiu C, Zhai H, Hou J. Biosensors design in yeast and applications in metabolic engineering. FEMS Yeast Res 2020; 19:5645237. [PMID: 31778177 DOI: 10.1093/femsyr/foz082] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022] Open
Abstract
Engineering microbial cell factories is a potential approach of sustainable production of chemicals, fuels and pharmaceuticals. However, testing the production of molecules in high throughput is still a time-consuming and laborious process since product synthesis usually does not confer a clear phenotype. Therefore, it is necessary to develop new techniques for fast high-producer screening. Genetically encoded biosensors are considered to be promising devices for high-throughput analysis owing to their ability to sense metabolites and couple detection to an actuator, thereby facilitating the rapid detection of small molecules at single-cell level. Here, we review recent advances in the design and engineering of biosensors in Saccharomyces cerevisiae, and their applications in metabolic engineering. Three types of biosensor are introduced in this review: transcription factor based, RNA-based and enzyme-coupled biosensors. The studies to improve the features of biosensors are also described. Moreover, we summarized their metabolic engineering applications in dynamic regulation and high producer selection. Current challenges in biosensor design and future perspectives on sensor applications are also discussed.
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Affiliation(s)
- Chenxi Qiu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China
| | - Haotian Zhai
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China
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221
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Foster AD, Chung C, Hann MM, Simpson GL, Tavassoli A. Development of a fluorescent three‐hybrid system for the identification of protein‐protein associators. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | | | - Ali Tavassoli
- School of Chemistry University of Southampton Southampton UK
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222
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Brödel AK, Rodrigues R, Jaramillo A, Isalan M. Accelerated evolution of a minimal 63-amino acid dual transcription factor. SCIENCE ADVANCES 2020; 6:eaba2728. [PMID: 32577520 PMCID: PMC7286687 DOI: 10.1126/sciadv.aba2728] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/14/2020] [Indexed: 05/13/2023]
Abstract
Transcription factors control gene expression in all life. This raises the question of what is the smallest protein that can support such activity. In nature, Cro from bacteriophage λ is one of the smallest known repressors (66 amino acids), and activators are typically much larger (e.g., λ cI, 237 amino acids). Previous efforts to engineer a minimal activator from λ Cro resulted in no activity in vivo in cells. In this study, we show that directed evolution results in a new Cro activator-repressor that functions as efficiently as λ cI in vivo. To achieve this, we develop phagemid-assisted continuous evolution (PACEmid). We find that a peptide as small as 63 amino acids functions efficiently as an activator and/or repressor. To our knowledge, this is the smallest protein activator that enables polymerase recruitment, highlighting the capacity of transcription factors to evolve from very short peptide sequences.
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Affiliation(s)
- Andreas K. Brödel
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Rui Rodrigues
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- CNRS-UMR8030, Laboratoire iSSB and Université Paris-Saclay and Université d’Évry and CEA, DRF, IG, Genoscope, Évry 91000, France
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, 46980 Paterna, Spain
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
- Corresponding author.
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223
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Kemble H, Eisenhauer C, Couce A, Chapron A, Magnan M, Gautier G, Le Nagard H, Nghe P, Tenaillon O. Flux, toxicity, and expression costs generate complex genetic interactions in a metabolic pathway. SCIENCE ADVANCES 2020; 6:eabb2236. [PMID: 32537514 PMCID: PMC7269641 DOI: 10.1126/sciadv.abb2236] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 03/31/2020] [Indexed: 05/31/2023]
Abstract
Our ability to predict the impact of mutations on traits relevant for disease and evolution remains severely limited by the dependence of their effects on the genetic background and environment. Even when molecular interactions between genes are known, it is unclear how these translate to organism-level interactions between alleles. We therefore characterized the interplay of genetic and environmental dependencies in determining fitness by quantifying ~4000 fitness interactions between expression variants of two metabolic genes, starting from various environmentally modulated expression levels. We detect a remarkable variety of interactions dependent on initial expression levels and demonstrate that they can be quantitatively explained by a mechanistic model accounting for catabolic flux, metabolite toxicity, and expression costs. Complex fitness interactions between mutations can therefore be predicted simply from their simultaneous impact on a few connected molecular phenotypes.
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Affiliation(s)
- Harry Kemble
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
- Laboratory of Biochemistry (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL University, CNRS, 75005 Paris, France
| | | | - Alejandro Couce
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Audrey Chapron
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Mélanie Magnan
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Gregory Gautier
- Centre de Recherche sur l'Inflammation, INSERM, UMRS 1149, 75018 Paris, France
- Laboratoire d’Excellence INFLAMEX, Université de Paris, Sorbonne Paris Cité, 75018 Paris, France
| | - Hervé Le Nagard
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Philippe Nghe
- Laboratory of Biochemistry (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL University, CNRS, 75005 Paris, France
| | - Olivier Tenaillon
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
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224
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Crook N, Ferreiro A, Condiotte Z, Dantas G. Transcript Barcoding Illuminates the Expression Level of Synthetic Constructs in E. coli Nissle Residing in the Mammalian Gut. ACS Synth Biol 2020; 9:1010-1021. [PMID: 32324995 PMCID: PMC7293544 DOI: 10.1021/acssynbio.0c00040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The development of robust engineered probiotic therapies demands accurate knowledge of genetic construct expression in the gut. However, the monetary and ethical costs of testing engineered strains in vertebrate hosts are incompatible with current high-throughput design-build-test cycles. To enable parallel measurement of multiple construct designs, we placed unique DNA barcodes in engineered transcripts and measured barcode abundances via sequencing. In standard curve experiments, the barcode sequences exhibited consistent relationships between input and measured abundances, which allowed us to use transcript barcoding to measure expression levels of 30 GFP-expressing strains of E. coli Nissle in parallel. Applying this technology in culture and in the mouse gut, we found that GFP expression in the gut could often be predicted from expression levels in culture, but several strains exhibited gut-specific expression. This work establishes the experimental design parameters and advantages of transcript barcoding to measure the performance of many engineered probiotic designs in mammalian hosts.
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Affiliation(s)
- Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Aura Ferreiro
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Zevin Condiotte
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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225
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Gawin A, Ertesvåg H, Hansen SAH, Malmo J, Brautaset T. Translational regulation of periplasmic folding assistants and proteases as a valuable strategy to improve production of translocated recombinant proteins in Escherichia coli. BMC Biotechnol 2020; 20:24. [PMID: 32393331 PMCID: PMC7216727 DOI: 10.1186/s12896-020-00615-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/24/2020] [Indexed: 01/02/2023] Open
Abstract
Background Advantages of translocation of recombinant proteins to the periplasm in Escherichia coli include simplified downstream processing, and improved folding and in vivo activity of the target protein. There are, however, problems encountered in the periplasmic production that can be associated with the incorrect formation of disulfide bonds, incomplete cleavage of the signal peptide, and proteolytic degradation. A common strategy used to overcome these difficulties involves manipulating the cellular levels of proteases and periplasmic folding assistants like chaperones, signal peptide peptidases or thiol-disulfide oxidoreductases. To date, this has been achieved by plasmid-based over-expression or knockouts of the relevant genes. Results We changed the translation efficiencies of five native E. coli proteins, DsbA, DsbB, Skp, SppA, and DegP, by modifying the strength of their ribosome binding sites (RBS). The genomic RBS sequences were replaced with synthetic ones that provided a predicted translation initiation rate. Single- and double-gene mutant strains were created and tested for production of two pharmaceutically relevant proteins, PelB-scFv173–2-5-AP and OmpA-GM-CSF. Almost all the single-gene mutant strains showed improved periplasmic production of at least one of the recombinant proteins. No further positive effects were observed when the mutations were combined. Conclusions Our findings confirm that our strain engineering approach involving translational regulation of endogenous proteins, in addition to plasmid-based methods, can be used to manipulate the cellular levels of periplasmic folding assistants and proteases to improve the yields of translocated recombinant proteins. The positive effects of SppA overexpression should be further investigated in E. coli.
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Affiliation(s)
- Agnieszka Gawin
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, N-7491, Trondheim, Norway
| | - Helga Ertesvåg
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, N-7491, Trondheim, Norway
| | - Sine Alise Hartvigsen Hansen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, N-7491, Trondheim, Norway
| | - Jostein Malmo
- Vectron Biosolutions AS, Abels gt 5, N-7030, Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, N-7491, Trondheim, Norway.
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Addressing the role of centromere sites in activation of ParB proteins for partition complex assembly. PLoS One 2020; 15:e0226472. [PMID: 32379828 PMCID: PMC7205306 DOI: 10.1371/journal.pone.0226472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/15/2020] [Indexed: 11/19/2022] Open
Abstract
The ParB-parS partition complexes that bacterial replicons use to ensure their faithful inheritance also find employment in visualization of DNA loci, as less intrusive alternatives to fluorescent repressor-operator systems. The ability of ParB molecules to interact via their N-terminal domains and to bind to non-specific DNA enables expansion of the initial complex to a size both functional in partition and, via fusion to fluorescent peptides, visible by light microscopy. We have investigated whether it is possible to dispense with the need to insert parS in the genomic locus of interest, by determining whether ParB fused to proteins that bind specifically to natural DNA sequences can still assemble visible complexes. In yeast cells, coproduction of fusions of ParB to a fluorescent peptide and to a TALE protein targeting an endogenous sequence did not yield visible foci; nor did any of several variants of these components. In E.coli, coproduction of fusions of SopB (F plasmid ParB) to fluorescent peptide, and to dCas9 together with specific guide RNAs, likewise yielded no foci. The result of coproducing analogous fusions of SopB proteins with distinct binding specificities was also negative. Our observations imply that in order to assemble higher order partition complexes, ParB proteins need specific activation through binding to their cognate parS sites.
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227
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Laxhuber KS, Morrison MJ, Chure G, Belliveau NM, Strandkvist C, Naughton KL, Phillips R. Theoretical investigation of a genetic switch for metabolic adaptation. PLoS One 2020; 15:e0226453. [PMID: 32379825 PMCID: PMC7205307 DOI: 10.1371/journal.pone.0226453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/01/2020] [Indexed: 12/02/2022] Open
Abstract
Membrane transporters carry key metabolites across the cell membrane and, from a resource standpoint, are hypothesized to be produced when necessary. The expression of membrane transporters in metabolic pathways is often upregulated by the transporter substrate. In E. coli, such systems include for example the lacY, araFGH, and xylFGH genes, which encode for lactose, arabinose, and xylose transporters, respectively. As a case study of a minimal system, we build a generalizable physical model of the xapABR genetic circuit, which features a regulatory feedback loop via membrane transport (positive feedback) and enzymatic degradation (negative feedback) of an inducer. Dynamical systems analysis and stochastic simulations show that the membrane transport makes the model system bistable in certain parameter regimes. Thus, it serves as a genetic “on-off” switch, enabling the cell to only produce a set of metabolic enzymes when the corresponding metabolite is present in large amounts. We find that the negative feedback from the degradation enzyme does not significantly disturb the positive feedback from the membrane transporter. We investigate hysteresis in the switching and discuss the role of cooperativity and multiple binding sites in the model circuit. Fundamentally, this work explores how a stable genetic switch for a set of enzymes is obtained from transcriptional auto-activation of a membrane transporter through its substrate.
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Affiliation(s)
- Kathrin S Laxhuber
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Muir J Morrison
- Department of Physics, California Institute of Technology, Pasadena, CA, United States of America
| | - Griffin Chure
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Nathan M Belliveau
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States of America
| | - Charlotte Strandkvist
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
| | - Kyle L Naughton
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, United States of America
| | - Rob Phillips
- Department of Physics, California Institute of Technology, Pasadena, CA, United States of America
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
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228
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Fang Y, Wang J, Ma W, Yang J, Zhang H, Zhao L, Chen S, Zhang S, Hu X, Li Y, Wang X. Rebalancing microbial carbon distribution for L-threonine maximization using a thermal switch system. Metab Eng 2020; 61:33-46. [PMID: 32371091 DOI: 10.1016/j.ymben.2020.01.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/16/2020] [Accepted: 01/29/2020] [Indexed: 12/14/2022]
Abstract
In metabolic engineering, unbalanced microbial carbon distribution has long blocked the further improvement in yield and productivity of high-volume natural metabolites. Current studies mostly focus on regulating desired biosynthetic pathways, whereas few strategies are available to maximize L-threonine efficiently. Here, we present a strategy to guarantee the supply of reduced cofactors and actualize L-threonine maximization by regulating cellular carbon distribution in central metabolic pathways. A thermal switch system was designed and applied to divide the whole fermentation process into two stages: growth and production. This system could rebalance carbon substrates between pyruvate and oxaloacetate by controlling the heterogenous expression of pyruvate carboxylase and oxaloacetate decarboxylation that responds to temperature. The system was tested in an L-threonine producer Escherichia coli TWF001, and the resulting strain TWF106/pFT24rp overproduced L-threonine from glucose with 111.78% molar yield. The thermal switch system was then employed to switch off the L-alanine synthesis pathway, resulting in the highest L-threonine yield of 124.03%, which exceeds the best reported yield (87.88%) and the maximum available theoretical value of L-threonine production (122.47%). This inducer-free genetic circuit design can be also developed for other biosynthetic pathways to increase product conversion rates and shorten production cycles.
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Affiliation(s)
- Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jun Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Hailing Zhang
- Department of Biological Engineering, College of Life Science, Yantai University, Shandong, 264005, China
| | - Lei Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Shanshan Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Shuyan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ye Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
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229
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Bartoli V, Meaker GA, di Bernardo M, Gorochowski TE. Tunable genetic devices through simultaneous control of transcription and translation. Nat Commun 2020; 11:2095. [PMID: 32350250 PMCID: PMC7190835 DOI: 10.1038/s41467-020-15653-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 03/20/2020] [Indexed: 02/07/2023] Open
Abstract
Synthetic genetic circuits allow us to modify the behavior of living cells. However, changes in environmental conditions and unforeseen interactions with the host cell can cause deviations from a desired function, resulting in the need for time-consuming reassembly to fix these issues. Here, we use a regulatory motif that controls transcription and translation to create genetic devices whose response functions can be dynamically tuned. This allows us, after construction, to shift the on and off states of a sensor by 4.5- and 28-fold, respectively, and modify genetic NOT and NOR logic gates to allow their transitions between states to be varied over a >6-fold range. In all cases, tuning leads to trade-offs in the fold-change and the ability to distinguish cellular states. This work lays the foundation for adaptive genetic circuits that can be tuned after their physical assembly to maintain functionality across diverse environments and design contexts.
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Affiliation(s)
- Vittorio Bartoli
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, UK
- Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol, UK
| | - Grace A Meaker
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, UK
| | - Mario di Bernardo
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, UK
- Department of Engineering Mathematics, University of Bristol, Woodland Road, Bristol, UK
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Via Claudio 21, Napoli, Italy
| | - Thomas E Gorochowski
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, UK.
- School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol, UK.
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230
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Gengenbacher M, Zimmerman MD, Sarathy JP, Kaya F, Wang H, Mina M, Carter C, Hossen MA, Su H, Trujillo C, Ehrt S, Schnappinger D, Dartois V. Tissue Distribution of Doxycycline in Animal Models of Tuberculosis. Antimicrob Agents Chemother 2020; 64:e02479-19. [PMID: 32041718 PMCID: PMC7179585 DOI: 10.1128/aac.02479-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/06/2020] [Indexed: 01/31/2023] Open
Abstract
Doxycycline, an FDA-approved tetracycline, is used in tuberculosis in vivo models for the temporal control of mycobacterial gene expression. In these models, animals are infected with recombinant Mycobacterium tuberculosis carrying genes of interest under transcriptional control of the doxycycline-responsive TetR-tetO unit. To minimize fluctuations of plasma levels, doxycycline is usually administered in the diet. However, tissue penetration studies to identify the minimum doxycycline content in food achieving complete repression of TetR-controlled genes in tuberculosis (TB)-infected organs and lesions have not been conducted. Here, we first determined the tetracycline concentrations required to achieve silencing of M. tuberculosis target genes in vitro Next, we measured doxycycline concentrations in plasma, major organs, and lung lesions in TB-infected mice and rabbits and compared these values to silencing concentrations measured in vitro We found that 2,000 ppm doxycycline supplemented in mouse and rabbit feed is sufficient to reach target concentrations in TB lesions. In rabbit chow, the calcium content had to be reduced 5-fold to minimize chelation of doxycycline and deliver adequate oral bioavailability. Clearance kinetics from major organs and lung lesions revealed that doxycycline levels fall below concentrations that repress tet promoters within 7 to 14 days after doxycycline is removed from the diet. In summary, we have shown that 2,000 ppm doxycycline supplemented in standard mouse diet and in low-calcium rabbit diet delivers concentrations adequate to achieve full repression of tet promoters in infected tissues of mice and rabbits.
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Affiliation(s)
- Martin Gengenbacher
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Jansy P Sarathy
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Firat Kaya
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Han Wang
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Marizel Mina
- New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Claire Carter
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Md Amir Hossen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Hongwei Su
- Weill Cornell Medical College, New York, New York, USA
| | | | - Sabine Ehrt
- Weill Cornell Medical College, New York, New York, USA
| | | | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
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231
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Liow LT, Go MK, Chang MW, Yew WS. Toolkit Development for Cyanogenic and Gold Biorecovery Chassis Chromobacterium violaceum. ACS Synth Biol 2020; 9:953-961. [PMID: 32160465 DOI: 10.1021/acssynbio.0c00064] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Chromobacterium violaceum has been of interest recently due to its cyanogenic ability and its potential role in environmental sustainability via the biorecovery of gold from electronic waste. However, as with many nonmodel bacteria, there are limited genetic tools to implement the use of this Gram-negative chassis in synthetic biology. We propose a system that involves assaying spontaneous antibiotic resistances and using broad host range vectors to develop episomal vectors for nonmodel Gram-negative bacteria. These developed vectors can subsequently be used to characterize inducible promoters for gene expressions and implementing CRISPRi to inhibit endogenous gene expression for further studies. Here, we developed the first episomal genetic toolkit for C. violaceum consisting of two origins of replication, three antibiotic resistance genes, and four inducible promoter systems. We examined the occurrences of spontaneous resistances of the bacterium to the chosen selection markers to prevent incidences of false positives. We also tested broad host range vectors from four different incompatibility groups and characterized four inducible promoter systems, which potentially can be applied in other Gram-negative nonmodel bacteria. CRISPRi was also implemented to inhibit violacein pigment production in C. violaceum. This systematic toolkit will aid future genetic circuitry building in this chassis and other nonmodel bacteria for synthetic biology and biotechnological applications.
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Affiliation(s)
- Lu Ting Liow
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation, Centre for Life Sciences, 28 Medical Drive, 117456, Singapore
| | - Maybelle Kho Go
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation, Centre for Life Sciences, 28 Medical Drive, 117456, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation, Centre for Life Sciences, 28 Medical Drive, 117456, Singapore
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation, Centre for Life Sciences, 28 Medical Drive, 117456, Singapore
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232
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Bittihn P, Didovyk A, Tsimring LS, Hasty J. Genetically engineered control of phenotypic structure in microbial colonies. Nat Microbiol 2020; 5:697-705. [PMID: 32284568 DOI: 10.1038/s41564-020-0686-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
Rapid advances in cellular engineering1,2 have positioned synthetic biology to address therapeutic3,4 and industrial5 problems, but a substantial obstacle is the myriad of unanticipated cellular responses in heterogeneous real-world environments such as the gut6,7, solid tumours8,9, bioreactors10 or soil11. Complex interactions between the environment and cells often arise through non-uniform nutrient availability, which generates bidirectional coupling as cells both adjust to and modify their local environment through phenotypic differentiation12,13. Although synthetic spatial gene expression patterns14-17 have been explored under homogeneous conditions, the mutual interaction of gene circuits, growth phenotype and the environment remains a challenge. Here, we design gene circuits that sense and control phenotypic structure in microcolonies containing both growing and dormant bacteria. We implement structure modulation by coupling different downstream modules to a tunable sensor that leverages Escherichia coli's stress response and is activated on growth arrest. One is an actuator module that slows growth and thereby alters nutrient gradients. Environmental feedback in this circuit generates robust cycling between growth and dormancy in the interior of the colony, as predicted by a spatiotemporal computational model. We also use the sensor to drive an inducible gating module for selective gene expression in non-dividing cells, which allows us to radically alter population structure by eliminating the dormant phenotype with a 'stress-gated lysis circuit'. Our results establish a strategy to leverage and control microbial colony structure for synthetic biology applications in complex environments.
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Affiliation(s)
- Philip Bittihn
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA.,The San Diego Center for Systems Biology, La Jolla, CA, USA.,Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Andriy Didovyk
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA.,Vertex Pharmaceuticals, San Diego, CA, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA. .,The San Diego Center for Systems Biology, La Jolla, CA, USA.
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA. .,The San Diego Center for Systems Biology, La Jolla, CA, USA. .,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. .,Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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233
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Jia X, Ma Y, Bu R, Zhao T, Wu K. Directed evolution of a transcription factor PbrR to improve lead selectivity and reduce zinc interference through dual selection. AMB Express 2020; 10:67. [PMID: 32277291 PMCID: PMC7148400 DOI: 10.1186/s13568-020-01004-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 04/04/2020] [Indexed: 11/25/2022] Open
Abstract
Directed evolution has been proven as a powerful tool for developing proteins and strains with novel or enhanced features. In this study, a dual selection system was designed to tune the binding specificity of a transcription factor to a particular ligand with the ampicillin resistance gene amp (ON selection) as the positive selection marker and the levansucrase gene sacB (OFF selection) as the negative selection marker. It was applied to the lead responsive transcription factor PbrR in a whole-cell lead biosensor previously constructed in our lab (Jia et al. in Fems Microbiol Lett 365:fny157, 2018). After multiple rounds of ON–OFF selection, two mutants with higher specificity for lead were selected. Structural analysis revealed that the mutation C134 located on the metal-binding loop at the C-terminal of PbrR is likely associated with the enhanced binding to both lead and cadmium. The double mutations D64A and L68S close to the metal-binding residue C79 may lead to the reduced binding specificity toward zinc ions. This dual selection system can be applied to engineer the specificity of other transcription factors and provide fine-tuned tools to synthetic biology.
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234
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Montagud-Martínez R, Ventura J, Ballesteros-Garrido R, Rosado A, Rodrigo G. Probing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular changes and time. J Biol Eng 2020; 14:12. [PMID: 32226483 PMCID: PMC7098154 DOI: 10.1186/s13036-020-00234-5] [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: 11/07/2019] [Accepted: 03/10/2020] [Indexed: 11/16/2022] Open
Abstract
Synthetic biology aims at engineering gene regulatory circuits to end with cells (re)programmed on purpose to implement novel functions or discover natural behaviors. However, one overlooked question is whether the resulting circuits perform as intended in variety of environments or with time. Here, we considered a recently engineered genetic system that allows programming the cell to work as a minimal computer (arithmetic logic unit) in order to analyze its operability regime. This system involves transcriptional and post-transcriptional regulations. In particular, we studied the analog behavior of the system, the effect of physicochemical changes in the environment, the impact on cell growth rate of the heterologous expression, and the ability to maintain the arithmetic functioning over time. Conclusively, our results suggest 1) that there are wide input concentration ranges that the system can correctly process, the resulting outputs being predictable with a simple mathematical model, 2) that the engineered circuitry is quite sensitive to temperature effects, 3) that the expression of heterologous small RNAs is costly for the cell, not only of heterologous proteins, and 4) that a proper genetic reorganization of the system to reduce the amount of heterologous DNA in the cell can improve its evolutionary stability.
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Affiliation(s)
- Roser Montagud-Martínez
- 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain
| | - Jordi Ventura
- 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain
| | - Rafael Ballesteros-Garrido
- 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain.,2Present address: Department of Organic Chemistry, University of Valencia, 46100 Burjassot, Valencia Spain
| | - Arantxa Rosado
- 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain
| | - Guillermo Rodrigo
- 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain
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235
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Kimura Y, Kawai-Noma S, Saito K, Umeno D. Directed Evolution of the Stringency of the LuxR Vibrio fischeri Quorum Sensor without OFF-State Selection. ACS Synth Biol 2020; 9:567-575. [PMID: 31999435 DOI: 10.1021/acssynbio.9b00444] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Stringency (low leak) is one of the most important specifications required for genetic circuits and induction systems, but it is challenging to evolve without sacrificing the maximum output level. This problem also comes from the absence of truly tunable negative selection methods. This paper reports that stringently switching variants can sometimes emerge with surprising frequency upon mutations. We randomly mutated the previously generated leaky variants of LuxR, the quorum-sensing transcription activator from Vibrio fischeri, to restore the stringency. We found as much as 10-20% of the entire population exhibited significantly improved signal-to-noise ratios compared with their parents. This indicated that these mutants arose by the loss of folding capability by accumulating destabilizing mutations, not by introducing rare adaptive mutations, thereby becoming AHL-dependent folders. Only four rounds of mutagenesis and ON-state selection resulted in the domination of the entire population by the improved variants with low leak, without direct selection pressure for stringency. With this surprising frequency, conversion into the "ligand-addicted folders" should be one of the prevailing modes of evolving stringency both in the laboratory and in nature, and the workflow described here provides a rapid and versatile method of improving the signal-to-noise ratio of various genetic switches.
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Affiliation(s)
- Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
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236
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Berepiki A, Kent R, Machado LFM, Dixon N. Development of High-Performance Whole Cell Biosensors Aided by Statistical Modeling. ACS Synth Biol 2020; 9:576-589. [PMID: 32023410 PMCID: PMC7146887 DOI: 10.1021/acssynbio.9b00448] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Whole cell biosensors are genetic systems that link the presence of a chemical, or other stimulus, to a user-defined gene expression output for applications in sensing and control. However, the gene expression level of biosensor regulatory components required for optimal performance is nonintuitive, and classical iterative approaches do not efficiently explore multidimensional experimental space. To overcome these challenges, we used a design of experiments (DoE) methodology to efficiently map gene expression levels and provide biosensors with enhanced performance. This methodology was applied to two biosensors that respond to catabolic breakdown products of lignin biomass, protocatechuic acid and ferulic acid. Utilizing DoE we systematically modified biosensor dose-response behavior by increasing the maximum signal output (up to 30-fold increase), improving dynamic range (>500-fold), expanding the sensing range (∼4-orders of magnitude), increasing sensitivity (by >1500-fold), and modulated the slope of the curve to afford biosensors designs with both digital and analogue dose-response behavior. This DoE method shows promise for the optimization of regulatory systems and metabolic pathways constructed from novel, poorly characterized parts.
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Affiliation(s)
- Adokiye Berepiki
- †Manchester
Institute of Biotechnology (MIB), ‡SYNBIOCHEM, Department of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
| | - Ross Kent
- †Manchester
Institute of Biotechnology (MIB), ‡SYNBIOCHEM, Department of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
| | - Leopoldo F. M. Machado
- †Manchester
Institute of Biotechnology (MIB), ‡SYNBIOCHEM, Department of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
| | - Neil Dixon
- †Manchester
Institute of Biotechnology (MIB), ‡SYNBIOCHEM, Department of Chemistry, University of Manchester, Manchester M1 7DN, U.K.,E-mail:
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237
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Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation. PLoS Biol 2020; 18:e3000661. [PMID: 32196484 PMCID: PMC7112236 DOI: 10.1371/journal.pbio.3000661] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/01/2020] [Accepted: 02/24/2020] [Indexed: 01/07/2023] Open
Abstract
Some of the densest microbial ecosystems in nature thrive within the intestines of humans and other animals. To protect mucosal tissues and maintain immune tolerance, animal hosts actively sequester bacteria within the intestinal lumen. In response, numerous bacterial pathogens and pathobionts have evolved strategies to subvert spatial restrictions, thereby undermining immune homeostasis. However, in many cases, it is unclear how escaping host spatial control benefits gut bacteria and how changes in intestinal biogeography are connected to inflammation. A better understanding of these processes could uncover new targets for treating microbiome-mediated inflammatory diseases. To this end, we investigated the spatial organization and dynamics of bacterial populations within the intestine using larval zebrafish and live imaging. We discovered that a proinflammatory Vibrio symbiont native to zebrafish governs its own spatial organization using swimming motility and chemotaxis. Surprisingly, we found that Vibrio’s motile behavior does not enhance its growth rate but rather promotes its persistence by enabling it to counter intestinal flow. In contrast, Vibrio mutants lacking motility traits surrender to host spatial control, becoming aggregated and entrapped within the lumen. Consequently, nonmotile and nonchemotactic mutants are susceptible to intestinal expulsion and experience large fluctuations in absolute abundance. Further, we found that motile Vibrio cells induce expression of the proinflammatory cytokine tumor necrosis factor alpha (TNFα) in gut-associated macrophages and the liver. Using inducible genetic switches, we demonstrate that swimming motility can be manipulated in situ to modulate the spatial organization, persistence, and inflammatory activity of gut bacterial populations. Together, our findings suggest that host spatial control over resident microbiota plays a broader role in regulating the abundance and persistence of gut bacteria than simply protecting mucosal tissues. Moreover, we show that intestinal flow and bacterial motility are potential targets for therapeutically managing bacterial spatial organization and inflammatory activity within the gut. The use of live imaging and bacteria engineered to carry inducible genetic switches reveals how a gut symbiont uses swimming motility to escape the host's spatial control and persist within the physically dynamic confines of the intestine.
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238
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Snoek T, Chaberski EK, Ambri F, Kol S, Bjørn SP, Pang B, Barajas JF, Welner DH, Jensen MK, Keasling JD. Evolution-guided engineering of small-molecule biosensors. Nucleic Acids Res 2020; 48:e3. [PMID: 31777933 PMCID: PMC6943132 DOI: 10.1093/nar/gkz954] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/06/2019] [Accepted: 10/24/2019] [Indexed: 11/14/2022] Open
Abstract
Allosteric transcription factors (aTFs) have proven widely applicable for biotechnology and synthetic biology as ligand-specific biosensors enabling real-time monitoring, selection and regulation of cellular metabolism. However, both the biosensor specificity and the correlation between ligand concentration and biosensor output signal, also known as the transfer function, often needs to be optimized before meeting application needs. Here, we present a versatile and high-throughput method to evolve prokaryotic aTF specificity and transfer functions in a eukaryote chassis, namely baker's yeast Saccharomyces cerevisiae. From a single round of mutagenesis of the effector-binding domain (EBD) coupled with various toggled selection regimes, we robustly select aTF variants of the cis,cis-muconic acid-inducible transcription factor BenM evolved for change in ligand specificity, increased dynamic output range, shifts in operational range, and a complete inversion-of-function from activation to repression. Importantly, by targeting only the EBD, the evolved biosensors display DNA-binding affinities similar to BenM, and are functional when ported back into a prokaryotic chassis. The developed platform technology thus leverages aTF evolvability for the development of new host-agnostic biosensors with user-defined small-molecule specificities and transfer functions.
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Affiliation(s)
- Tim Snoek
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Evan K Chaberski
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Francesca Ambri
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sara P Bjørn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bo Pang
- Joint BioEnergy Institute, Emeryville, CA, USA
| | | | - Ditte H Welner
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.,Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, USA.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
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239
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Schramm T, Lempp M, Beuter D, Sierra SG, Glatter T, Link H. High-throughput enrichment of temperature-sensitive argininosuccinate synthetase for two-stage citrulline production in E. coli. Metab Eng 2020; 60:14-24. [PMID: 32179161 PMCID: PMC7225747 DOI: 10.1016/j.ymben.2020.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/03/2020] [Accepted: 03/08/2020] [Indexed: 12/20/2022]
Abstract
Controlling metabolism of engineered microbes is important to modulate cell growth and production during a bioprocess. For example, external parameters such as light, chemical inducers, or temperature can act on metabolism of production strains by changing the abundance or activity of enzymes. Here, we created temperature-sensitive variants of an essential enzyme in arginine biosynthesis of Escherichia coli (argininosuccinate synthetase, ArgG) and used them to dynamically control citrulline overproduction and growth of E. coli. We show a method for high-throughput enrichment of temperature-sensitive ArgG variants with a fluorescent TIMER protein and flow cytometry. With 90 of the thus derived ArgG variants, we complemented an ArgG deletion strain showing that 90% of the strains exhibit temperature-sensitive growth and 69% of the strains are auxotrophic for arginine at 42 °C and prototrophic at 30 °C. The best temperature-sensitive ArgG variant enabled precise and tunable control of cell growth by temperature changes. Expressing this variant in a feedback-dysregulated E. coli strain allowed us to realize a two-stage bioprocess: a 33 °C growth-phase for biomass accumulation and a 39 °C stationary-phase for citrulline production. With this two-stage strategy, we produced 3 g/L citrulline during 45 h cultivation in a 1-L bioreactor. These results show that temperature-sensitive enzymes can be created en masse and that they may function as metabolic valves in engineered bacteria. Method to enrich temperature-sensitive enzymes en masse. Temperature-sensitive enzymes function as metabolic valve. Temperature controlled two-stage production of citrulline.
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Affiliation(s)
- Thorben Schramm
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Martin Lempp
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Dominik Beuter
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Silvia González Sierra
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany.
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240
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Gene amplification as a form of population-level gene expression regulation. Nat Ecol Evol 2020; 4:612-625. [DOI: 10.1038/s41559-020-1132-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/29/2020] [Indexed: 11/08/2022]
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241
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Jiang W, Oikonomou P, Tavazoie S. Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity. Cell 2020; 180:1002-1017.e31. [PMID: 32109417 PMCID: PMC7169367 DOI: 10.1016/j.cell.2020.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/04/2019] [Accepted: 02/04/2020] [Indexed: 12/19/2022]
Abstract
Genome-wide CRISPR screens enable systematic interrogation of gene function. However, guide RNA libraries are costly to synthesize, and their limited diversity compromises the sensitivity of CRISPR screens. Using the Streptococcus pyogenes CRISPR-Cas adaptation machinery, we developed CRISPR adaptation-mediated library manufacturing (CALM), which turns bacterial cells into "factories" for generating hundreds of thousands of crRNAs covering 95% of all targetable genomic sites. With an average gene targeted by more than 100 distinct crRNAs, these highly comprehensive CRISPRi libraries produced varying degrees of transcriptional repression critical for uncovering novel antibiotic resistance determinants. Furthermore, by iterating CRISPR adaptation, we rapidly generated dual-crRNA libraries representing more than 100,000 dual-gene perturbations. The polarized nature of spacer adaptation revealed the historical contingency in the stepwise acquisition of genetic perturbations leading to increasing antibiotic resistance. CALM circumvents the expense, labor, and time required for synthesis and cloning of gRNAs, allowing generation of CRISPRi libraries in wild-type bacteria refractory to routine genetic manipulation.
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Affiliation(s)
- Wenyan Jiang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Panos Oikonomou
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Saeed Tavazoie
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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242
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Porse A, Jahn LJ, Ellabaan MMH, Sommer MOA. Dominant resistance and negative epistasis can limit the co-selection of de novo resistance mutations and antibiotic resistance genes. Nat Commun 2020; 11:1199. [PMID: 32139686 PMCID: PMC7057998 DOI: 10.1038/s41467-020-15080-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 02/12/2020] [Indexed: 01/24/2023] Open
Abstract
To tackle the global antibiotic resistance crisis, antibiotic resistance acquired either vertically by chromosomal mutations or horizontally through antibiotic resistance genes (ARGs) have been studied. Yet, little is known about the interactions between the two, which may impact the evolution of antibiotic resistance. Here, we develop a multiplexed barcoded approach to assess the fitness of 144 mutant-ARG combinations in Escherichia coli subjected to eight different antibiotics at 11 different concentrations. While most interactions are neutral, we identify significant interactions for 12% of the mutant-ARG combinations. The ability of most ARGs to confer high-level resistance at a low fitness cost shields the selective dynamics of mutants at low drug concentrations. Therefore, high-fitness mutants are often selected regardless of their resistance level. Finally, we identify strong negative epistasis between two unrelated resistance mechanisms: the tetA tetracycline resistance gene and loss-of-function nuo mutations involved in aminoglycoside tolerance. Our study highlights important constraints that may allow better prediction and control of antibiotic resistance evolution.
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Affiliation(s)
- Andreas Porse
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Leonie J Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Mostafa M H Ellabaan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark.
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243
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Hanko EKR, Paiva AC, Jonczyk M, Abbott M, Minton NP, Malys N. A genome-wide approach for identification and characterisation of metabolite-inducible systems. Nat Commun 2020; 11:1213. [PMID: 32139676 PMCID: PMC7057948 DOI: 10.1038/s41467-020-14941-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/07/2020] [Indexed: 12/21/2022] Open
Abstract
Inducible gene expression systems are vital tools for the advancement of synthetic biology. Their application as genetically encoded biosensors has the potential to contribute to diagnostics and to revolutionise the field of microbial cell factory development. Currently, the number of compounds of biological interest by far exceeds the number of available biosensors. Here, we address this limitation by developing a generic genome-wide approach to identify transcription factor-based inducible gene expression systems. We construct and validate 15 functional biosensors, provide a characterisation workflow to facilitate forward engineering efforts, exemplify their broad-host-range applicability, and demonstrate their utility in enzyme screening. Previously uncharacterised interactions between sensors and compounds of biological relevance are identified by employing the largest reported library of metabolite-responsive biosensors in an automated high-throughput screen. With the rapidly growing genomic data these innovative capabilities offer a platform to vastly increase the number of biologically detectable molecules. Inducible gene expression tools have important applications as genetically encoded biosensors. Here the authors conduct a genome-wide approach to identify and utilise functional sensors.
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Affiliation(s)
- Erik K R Hanko
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Ana C Paiva
- Centre for Biomolecular Sciences, School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Magdalena Jonczyk
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Matthew Abbott
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Naglis Malys
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK.
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244
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Wang H, Liu X, Wu C, Zhang M, Ke Z, Jiang W, Zhou Y, Qiu J, Hong Q. An angular dioxygenase gene cluster responsible for the initial phenazine-1-carboxylic acid degradation step in Rhodococcus sp. WH99 can protect sensitive organisms from toxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135726. [PMID: 31837849 DOI: 10.1016/j.scitotenv.2019.135726] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
A bacterial strain, Rhodococcus sp. WH99, capable of degrading phenazine-1-carboxylic acid (PCA) was isolated and characterized. Genome comparison revealed that a 21499-bp DNA fragment containing a putative angular dioxygenase gene cluster consisting of the dioxygenase-, ferredoxin reductase- and ferredoxin-encoding genes (pzcA1A2, pzcC and pzcD) is missed in the PCA degradation-deficient mutant WH99M. The pzcA1A2CD genes were expressed in Escherichia coli respectively and hydroxylation of PCA to 1,2-dihydroxyphenazine occurred in vitro only when all components were present. However, in vivo analyses showed that pzcA1A2 and pzcD were indispensable for PCA degradation, while PzcC can be partially replaced by other ferredoxin reductases. Hydroxylation of PCA not only initiates degradation of PCA in strain WH99 but also provides protection to sensitive organisms that would otherwise be inhibited by PCA toxicity. This study illustrates a new initial PCA degradation step in Gram-positive bacteria and enhances our understanding of the genes responsible for PCA hydroxylation, thus enabling targeted studies on protection by PCA degradation in diverse environments.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Xiaoan Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Chenglong Wu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Wankui Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Yidong Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China.
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245
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Li JW, Zhang XY, Wu H, Bai YP. Transcription Factor Engineering for High-Throughput Strain Evolution and Organic Acid Bioproduction: A Review. Front Bioeng Biotechnol 2020; 8:98. [PMID: 32140463 PMCID: PMC7042172 DOI: 10.3389/fbioe.2020.00098] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/03/2020] [Indexed: 01/15/2023] Open
Abstract
Metabolic regulation of gene expression for the microbial production of fine chemicals, such as organic acids, is an important research topic in post-genomic metabolic engineering. In particular, the ability of transcription factors (TFs) to respond precisely in time and space to various small molecules, signals and stimuli from the internal and external environment is essential for metabolic pathway engineering and strain development. As a key component, TFs are used to construct many biosensors in vivo using synthetic biology methods, which can be used to monitor the concentration of intracellular metabolites in organic acid production that would otherwise remain “invisible” within the intracellular environment. TF-based biosensors also provide a high-throughput screening method for rapid strain evolution. Furthermore, TFs are important global regulators that control the expression levels of key enzymes in organic acid biosynthesis pathways, therefore determining the outcome of metabolic networks. Here we review recent advances in TF identification, engineering, and applications for metabolic engineering, with an emphasis on metabolite monitoring and high-throughput strain evolution for the organic acid bioproduction.
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Affiliation(s)
- Jia-Wei Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiao-Yan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yun-Peng Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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246
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Mukhopadhyay S, Sarkar K, Srivastava R, Pal A, Bagh S. Processing two environmental chemical signals with a synthetic genetic IMPLY gate, a 2‐input‐2‐output integrated logic circuit, and a process pipeline to optimize its systems chemistry in
Escherichia coli. Biotechnol Bioeng 2020; 117:1502-1512. [DOI: 10.1002/bit.27286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Sayak Mukhopadhyay
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear PhysicsHomi Bhabha National Institute (HBNI)Kolkata India
| | - Kathakali Sarkar
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear PhysicsHomi Bhabha National Institute (HBNI)Kolkata India
| | - Rajkamal Srivastava
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear PhysicsHomi Bhabha National Institute (HBNI)Kolkata India
| | - Arijit Pal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear PhysicsHomi Bhabha National Institute (HBNI)Kolkata India
| | - Sangram Bagh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear PhysicsHomi Bhabha National Institute (HBNI)Kolkata India
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247
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Velagapudi P, Ghoubrial R, Shah R, Ghali H, Haas M, Patel KS, Riddell A, Blanar CA, Smith RP. A potential tradeoff between feeding rate and aversive learning determines intoxication in a Caenorhabditis elegans host-pathogen system. Microbes Infect 2020; 22:340-348. [PMID: 32014589 DOI: 10.1016/j.micinf.2020.01.002] [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: 06/03/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 11/29/2022]
Abstract
Despite being the first line of defense against infection, little is known about how host-pathogen interactions determine avoidance. Caenorhabditis elegans can become infected by chemoattractant-producing bacteria through ingestion. The worms can learn to associate these chemoattractants with harm through aversive learning. As a result, the worms will avoid the pathogen. Evolutionary constraints have likely shaped the attraction, intoxication and learning dynamics between bacteria and C. elegans, but these have not been explored. Using bacteria engineered to express an acylhomoserine lactone chemoattractant and a nematicidal protein, we explored how manipulating the amount of attractant produced by the bacteria affects learning and intoxication in mixed stage populations of C. elegans. We found that increasing the production rate of the chemoattractant increased the feeding rate in C. elegans, but decreased the time required for C. elegans to learn to avoid the chemoattractant. Learning generally coincided with a decreased feeding rate. We also observed that the percentage of intoxicated worms was maximized at intermediate production rates of the attractant. We propose that interactions between attractant driven feeding rate and aversive learning are likely responsible for this trend. Our results increase our understanding of behavioral avoidance in C. elegans and have implications in understanding host-pathogen dynamics that shape avoidance.
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Affiliation(s)
- Pallavi Velagapudi
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Rachel Ghoubrial
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Ratnavi Shah
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Helana Ghali
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Meghan Haas
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Krunal S Patel
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Ashleigh Riddell
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Christopher A Blanar
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Robert P Smith
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA.
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248
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Farzadfard F, Gharaei N, Higashikuni Y, Jung G, Cao J, Lu TK. Single-Nucleotide-Resolution Computing and Memory in Living Cells. Mol Cell 2020; 75:769-780.e4. [PMID: 31442423 DOI: 10.1016/j.molcel.2019.07.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/07/2019] [Accepted: 07/08/2019] [Indexed: 12/22/2022]
Abstract
The ability to process and store information in living cells is essential for developing next-generation therapeutics and studying biology in situ. However, existing strategies have limited recording capacity and are challenging to scale. To overcome these limitations, we developed DOMINO, a robust and scalable platform for encoding logic and memory in bacterial and eukaryotic cells. Using an efficient single-nucleotide-resolution Read-Write head for DNA manipulation, DOMINO converts the living cells' DNA into an addressable, readable, and writable medium for computation and storage. DOMINO operators enable analog and digital molecular recording for long-term monitoring of signaling dynamics and cellular events. Furthermore, multiple operators can be layered and interconnected to encode order-independent, sequential, and temporal logic, allowing recording and control over the combination, order, and timing of molecular events in cells. We envision that DOMINO will lay the foundation for building robust and sophisticated computation-and-memory gene circuits for numerous biotechnological and biomedical applications.
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Affiliation(s)
- Fahim Farzadfard
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA; MIT Microbiology Graduate Program, 77 Massachusetts Avenue, Cambridge MA 02139, USA.
| | - Nava Gharaei
- MCO Graduate Program, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yasutomi Higashikuni
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA
| | - Giyoung Jung
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Jicong Cao
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA
| | - Timothy K Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA; MIT Microbiology Graduate Program, 77 Massachusetts Avenue, Cambridge MA 02139, USA.
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249
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Liu X, Silverman AD, Alam KK, Iverson E, Lucks JB, Jewett MC, Raman S. Design of a Transcriptional Biosensor for the Portable, On-Demand Detection of Cyanuric Acid. ACS Synth Biol 2020; 9:84-94. [PMID: 31825601 PMCID: PMC7372534 DOI: 10.1021/acssynbio.9b00348] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rapid molecular biosensing is an emerging application area for synthetic biology. Here, we engineer a portable biosensor for cyanuric acid (CYA), an analyte of interest for human and environmental health, using a LysR-type transcription regulator (LTTR) from Pseudomonas within the context of Escherichia coli gene expression machinery. To overcome cross-host portability challenges of LTTRs, we rationally engineered hybrid Pseudomonas-E. coli promoters by integrating DNA elements required for transcriptional activity and ligand-dependent regulation from both hosts, which enabled E. coli to function as a whole-cell biosensor for CYA. To alleviate challenges of whole-cell biosensing, we adapted these promoter designs to function within a freeze-dried E. coli cell-free system to sense CYA. This portable, on-demand system robustly detects CYA within an hour from laboratory and real-world samples and works with both fluorescent and colorimetric reporters. This work elucidates general principles to facilitate the engineering of a wider array of LTTR-based environmental sensors.
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Affiliation(s)
- Xiangyang Liu
- Biophysics Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Adam D. Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Khalid K. Alam
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Erik Iverson
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
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Tellier M, Chalmers R. Compensating for over-production inhibition of the Hsmar1 transposon in Escherichia coli using a series of constitutive promoters. Mob DNA 2020; 11:5. [PMID: 31938044 PMCID: PMC6954556 DOI: 10.1186/s13100-020-0200-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/01/2020] [Indexed: 01/03/2023] Open
Abstract
Background Transposable elements (TEs) are a diverse group of self-mobilizing DNA elements. Transposition has been exploited as a powerful tool for molecular biology and genomics. However, transposition is sometimes limited because of auto-regulatory mechanisms that presumably allow them to cohabit within their hosts without causing excessive genomic damage. The papillation assay provides a powerful visual screen for hyperactive transposases. Transposition is revealed by the activation of a promoter-less lacZ gene when the transposon integrates into a non-essential gene on the host chromosome. Transposition events are detected as small blue speckles, or papillae, on the white background of the main Escherichia coli colony. Results We analysed the parameters of the papillation assay including the strength of the transposase transcriptional and translational signals. To overcome certain limitations of inducible promoters, we constructed a set of vectors based on constitutive promoters of different strengths to widen the range of transposase expression. We characterized and validated our expression vectors with Hsmar1, a member of the mariner transposon family. The highest rate of transposition was observed with the weakest promoters. We then took advantage of our approach to investigate how the level of transposition responds to selected point mutations and the effect of joining the transposase monomers into a single-chain dimer. Conclusions We generated a set of vectors to provide a wide range of transposase expression which will be useful for screening libraries of transposase mutants. The use of weak promoters should allow screening for truly hyperactive transposases rather than those that are simply resistant to auto-regulatory mechanisms, such as overproduction inhibition (OPI). We also found that mutations in the Hsmar1 dimer interface provide resistance to OPI in bacteria, which could be valuable for improving bacterial transposon mutagenesis techniques.
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Affiliation(s)
- Michael Tellier
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH UK.,2Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE UK
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH UK
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