1
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Zakaria FR, Chen CY, Li J, Wang S, Payne GF, Bentley WE. Redox active plant phenolic, acetosyringone, for electrogenetic signaling. Sci Rep 2024; 14:9666. [PMID: 38671069 PMCID: PMC11053109 DOI: 10.1038/s41598-024-60191-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Redox is a unique, programmable modality capable of bridging communication between biology and electronics. Previous studies have shown that the E. coli redox-responsive OxyRS regulon can be re-wired to accept electrochemically generated hydrogen peroxide (H2O2) as an inducer of gene expression. Here we report that the redox-active phenolic plant signaling molecule acetosyringone (AS) can also induce gene expression from the OxyRS regulon. AS must be oxidized, however, as the reduced state present under normal conditions cannot induce gene expression. Thus, AS serves as a "pro-signaling molecule" that can be activated by its oxidation-in our case by application of oxidizing potential to an electrode. We show that the OxyRS regulon is not induced electrochemically if the imposed electrode potential is in the mid-physiological range. Electronically sliding the applied potential to either oxidative or reductive extremes induces this regulon but through different mechanisms: reduction of O2 to form H2O2 or oxidation of AS. Fundamentally, this work reinforces the emerging concept that redox signaling depends more on molecular activities than molecular structure. From an applications perspective, the creation of an electronically programmed "pro-signal" dramatically expands the toolbox for electronic control of biological responses in microbes, including in complex environments, cell-based materials, and biomanufacturing.
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Affiliation(s)
- Fauziah Rahma Zakaria
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA
| | - Chen-Yu Chen
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA
| | - Jinyang Li
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA.
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, USA.
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2
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Zeng M, Sarker B, Rondthaler SN, Vu V, Andrews LB. Identifying LasR Quorum Sensors with Improved Signal Specificity by Mapping the Sequence-Function Landscape. ACS Synth Biol 2024; 13:568-589. [PMID: 38206199 DOI: 10.1021/acssynbio.3c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Programmable intercellular signaling using components of naturally occurring quorum sensing can allow for coordinated functions to be engineered in microbial consortia. LuxR-type transcriptional regulators are widely used for this purpose and are activated by homoserine lactone (HSL) signals. However, they often suffer from imperfect molecular discrimination of structurally similar HSLs, causing misregulation within engineered consortia containing multiple HSL signals. Here, we studied one such example, the regulator LasR from Pseudomonas aeruginosa. We elucidated its sequence-function relationship for ligand specificity using targeted protein engineering and multiplexed high-throughput biosensor screening. A pooled combinatorial saturation mutagenesis library (9,486 LasR DNA sequences) was created by mutating six residues in LasR's β5 sheet with single, double, or triple amino acid substitutions. Sort-seq assays were performed in parallel using cognate and noncognate HSLs to quantify each corresponding sensor's response to each HSL signal, which identified hundreds of highly specific variants. Sensor variants identified were individually assayed and exhibited up to 60.6-fold (p = 0.0013) improved relative activation by the cognate signal compared to the wildtype. Interestingly, we uncovered prevalent mutational epistasis and previously unidentified residues contributing to signal specificity. The resulting sensors with negligible signal crosstalk could be broadly applied to engineer bacteria consortia.
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Affiliation(s)
- Min Zeng
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen N Rondthaler
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Vanessa Vu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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3
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Zeng M, Sarker B, Howitz N, Shah I, Andrews LB. Synthetic Homoserine Lactone Sensors for Gram-Positive Bacillus subtilis Using LuxR-Type Regulators. ACS Synth Biol 2024; 13:282-299. [PMID: 38079538 PMCID: PMC10805106 DOI: 10.1021/acssynbio.3c00504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 01/23/2024]
Abstract
A universal biochemical signal for bacterial cell-cell communication could facilitate programming dynamic responses in diverse bacterial consortia. However, the classical quorum sensing paradigm is that Gram-negative and Gram-positive bacteria generally communicate via homoserine lactones (HSLs) or oligopeptide molecular signals, respectively, to elicit population responses. Here, we create synthetic HSL sensors for Gram-positive Bacillus subtilis 168 using allosteric LuxR-type regulators (RpaR, LuxR, RhlR, and CinR) and synthetic promoters. Promoters were combinatorially designed from different sequence elements (-35, -16, -10, and transcriptional start regions). We quantified the effects of these combinatorial promoters on sensor activity and determined how regulator expression affects its activation, achieving up to 293-fold activation. Using the statistical design of experiments, we identified significant effects of promoter regions and pairwise interactions on sensor activity, which helped to understand the sequence-function relationships for synthetic promoter design. We present the first known set of functional HSL sensors (≥20-fold dynamic range) in B. subtilis for four different HSL chemical signals: p-coumaroyl-HSL, 3-oxohexanoyl-HSL, n-butyryl-HSL, and n-(3-hydroxytetradecanoyl)-HSL. This set of synthetic HSL sensors for a Gram-positive bacterium can pave the way for designable interspecies communication within microbial consortia.
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Affiliation(s)
- Min Zeng
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Nathaniel Howitz
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Ishita Shah
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B. Andrews
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Molecular
and Cellular Biology Graduate Program, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
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4
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Wang S, Chen CY, Rzasa JR, Tsao CY, Li J, VanArsdale E, Kim E, Zakaria FR, Payne GF, Bentley WE. Redox-enabled electronic interrogation and feedback control of hierarchical and networked biological systems. Nat Commun 2023; 14:8514. [PMID: 38129428 PMCID: PMC10739708 DOI: 10.1038/s41467-023-44223-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Microelectronic devices can directly communicate with biology, as electronic information can be transmitted via redox reactions within biological systems. By engineering biology's native redox networks, we enable electronic interrogation and control of biological systems at several hierarchical levels: proteins, cells, and cell consortia. First, electro-biofabrication facilitates on-device biological component assembly. Then, electrode-actuated redox data transmission and redox-linked synthetic biology allows programming of enzyme activity and closed-loop electrogenetic control of cellular function. Specifically, horseradish peroxidase is assembled onto interdigitated electrodes where electrode-generated hydrogen peroxide controls its activity. E. coli's stress response regulon, oxyRS, is rewired to enable algorithm-based feedback control of gene expression, including an eCRISPR module that switches cell-cell quorum sensing communication from one autoinducer to another-creating an electronically controlled 'bilingual' cell. Then, these disparate redox-guided devices are wirelessly connected, enabling real-time communication and user-based control. We suggest these methodologies will help us to better understand and develop sophisticated control for biology.
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Affiliation(s)
- Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Fischell Institute of Biomedical Devices, University of Maryland, College Park, MD, USA
- Institute of Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA
| | - Chen-Yu Chen
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Fischell Institute of Biomedical Devices, University of Maryland, College Park, MD, USA
- Institute of Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA
| | - John R Rzasa
- Fischell Institute of Biomedical Devices, University of Maryland, College Park, MD, USA
| | - Chen-Yu Tsao
- Fischell Institute of Biomedical Devices, University of Maryland, College Park, MD, USA
- Institute of Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA
| | - Jinyang Li
- Fischell Institute of Biomedical Devices, University of Maryland, College Park, MD, USA
- Institute of Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Fischell Institute of Biomedical Devices, University of Maryland, College Park, MD, USA
- Institute of Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA
- National Research Council Postdoctoral Research Associate, United States Naval Research Laboratory, Washington, DC, USA
| | - Eunkyoung Kim
- Fischell Institute of Biomedical Devices, University of Maryland, College Park, MD, USA
- Institute of Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA
| | - Fauziah Rahma Zakaria
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- Fischell Institute of Biomedical Devices, University of Maryland, College Park, MD, USA
- Institute of Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA
| | - Gregory F Payne
- Fischell Institute of Biomedical Devices, University of Maryland, College Park, MD, USA
- Institute of Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA.
- Fischell Institute of Biomedical Devices, University of Maryland, College Park, MD, USA.
- Institute of Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA.
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5
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Atkinson JT, Chavez MS, Niman CM, El-Naggar MY. Living electronics: A catalogue of engineered living electronic components. Microb Biotechnol 2023; 16:507-533. [PMID: 36519191 PMCID: PMC9948233 DOI: 10.1111/1751-7915.14171] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/26/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.
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Affiliation(s)
- Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.,Department of Chemistry, University of Southern California, Los Angeles, California, USA
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6
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Wu S, Wu S, Zhang X, Feng T, Wu L. Chitosan-Based Hydrogels for Bioelectronic Sensing: Recent Advances and Applications in Biomedicine and Food Safety. BIOSENSORS 2023; 13:93. [PMID: 36671928 PMCID: PMC9856120 DOI: 10.3390/bios13010093] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/13/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Due to the lack of efficient bioelectronic interfaces, the communication between biology and electronics has become a great challenge, especially in constructing bioelectronic sensing. As natural polysaccharide biomaterials, chitosan-based hydrogels exhibit the advantages of flexibility, biocompatibility, mechanical tunability, and stimuli sensitivity, and could serve as an excellent interface for bioelectronic sensors. Based on the fabrication approaches, interaction mechanisms, and bioelectronic communication modalities, this review divided chitosan-based hydrogels into four types, including electrode-based hydrogels, conductive materials conjugated hydrogels, ionically conductive hydrogels, and redox-based hydrogels. To introduce the enhanced performance of bioelectronic sensors, as a complementary alternative, the incorporation of nanoparticles and redox species in chitosan-based hydrogels was discussed. In addition, the multifunctional properties of chitosan-based composite hydrogels enable their applications in biomedicine (e.g., smart skin patches, wood healing, disease diagnosis) and food safety (e.g., electrochemical sensing, smart sensing, artificial bioelectronic tongue, fluorescence sensors, surface-enhanced Raman scattering). We believe that this review will shed light on the future development of chitosan-based biosensing hydrogels for micro-implantable devices and human-machine interactions, as well as potential applications in medicine, food, agriculture, and other fields.
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Affiliation(s)
- Si Wu
- College of Resources and Environmental Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
- Hubei Key Laboratory for Efficient Utilization and Agglomeration of Metallurgic Mineral Resources, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Shijing Wu
- College of Resources and Environmental Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Xinyue Zhang
- College of Resources and Environmental Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Tao Feng
- College of Resources and Environmental Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
- Hubei Key Laboratory for Efficient Utilization and Agglomeration of Metallurgic Mineral Resources, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Long Wu
- School of Food Science and Engineering, Key Laboratory of Tropical and Vegetables Quality and Safety for State Market Regulation, Hainan University, Haikou 570228, China
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7
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Engineering Ag43 Signal Peptides with Bacterial Display and Selection. Methods Protoc 2022; 6:mps6010001. [PMID: 36648950 PMCID: PMC9844295 DOI: 10.3390/mps6010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
Protein display, secretion, and export in prokaryotes are essential for utilizing microbial systems as engineered living materials, medicines, biocatalysts, and protein factories. To select for improved signal peptides for Escherichia coli protein display, we utilized error-prone polymerase chain reaction (epPCR) coupled with single-cell sorting and microplate titer to generate, select, and detect improved Ag43 signal peptides. Through just three rounds of mutagenesis and selection using green fluorescence from the 56 kDa sfGFP-beta-lactamase, we isolated clones that modestly increased surface display from 1.4- to 3-fold as detected by the microplate plate-reader and native SDS-PAGE assays. To establish that the functional protein was displayed extracellularly, we trypsinized the bacterial cells to release the surface displayed proteins for analysis. This workflow demonstrated a fast and high-throughput method leveraging epPCR and single-cell sorting to augment bacterial surface display rapidly that could be applied to other bacterial proteins.
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8
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Atkinson JT, Su L, Zhang X, Bennett GN, Silberg JJ, Ajo-Franklin CM. Real-time bioelectronic sensing of environmental contaminants. Nature 2022; 611:548-553. [DOI: 10.1038/s41586-022-05356-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/15/2022] [Indexed: 11/07/2022]
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9
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Aliya M, Zare EN, Faridnouri H, Ghomi M, Makvandi P. Sulfonated Starch- Graft-Polyaniline@Graphene Electrically Conductive Nanocomposite: Application for Tyrosinase Immobilization. BIOSENSORS 2022; 12:bios12110939. [PMID: 36354447 PMCID: PMC9688083 DOI: 10.3390/bios12110939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 05/31/2023]
Abstract
The interaction of tyrosinase with sulfonated starch-graft-polyaniline@graphene (SSt-g-PANI@G) nanocomposite was investigated by electrochemical methods. The activity of the immobilized tyrosinase (Tyase) was proved by the electrochemical detection of three substrates (L-dopa, caffeic acid, and catechol). The SSt-g-PANI@G nanocomposite was characterized by Fourier-transform infrared spectra (FT-IR), X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), energy-dispersive X-ray analysis (EDX), and thermogravimetric analysis (TGA). To immobilize tyrosinase on the surface of the nanocomposite, a simple drop-casting technique was used. The presence of sulfuric acid and hydroxyl groups in SSt, amine groups in PANI, and high surface-to-volume ratio and electrical conductivity of graphene in the prepared nanocomposite led to good enzyme immobilization on the electrode surface. The modified electrode showed a suitable catalytic effect on the electrochemical redox agent, compared with the bare electrode. The peak current responses for three substrates were studied with a calibration curve derived using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). In addition, the fabricated SSt-g-PANI@G/Tyase/GCE showed a more suitable response to catechol, L-dopa, and caffeic acid substrates, respectively.
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Affiliation(s)
- Marzieh Aliya
- School of Chemistry, Damghan University, Damghan 36716-41167, Iran
| | | | | | - Matineh Ghomi
- School of Chemistry, Damghan University, Damghan 36716-41167, Iran
| | - Pooyan Makvandi
- Centre for Materials Interface, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera, 56025 Pisa, Italy
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10
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VanArsdale E, Pitzer J, Wang S, Stephens K, Chen CY, Payne GF, Bentley WE. Enhanced electrochemical measurement of β-galactosidase activity in whole cells by coexpression of lactose permease, LacY. Biotechniques 2022; 73:233-237. [DOI: 10.2144/btn-2022-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Whole-cell biosensing links the sensing and computing capabilities of microbes to the generation of a detectable reporter. Whole cells enable dynamic biological computation (filtered noise, amplified signals, logic gating etc.). Enzymatic reporters enable in situ signal amplification. Electrochemical measurements are easily quantified and work in turbid environments. In this work we show how the coexpression of the lactose permease, LacY, dramatically improves electrochemical sensing of β-galactosidase (LacZ) expressed as a reporter in whole cells. The permease facilitates transport of the LacZ substrate, 4-aminophenyl β-d-galactopyranoside, which is converted to redox active p-aminophenol, which, in turn, is detected via cyclic voltammetry or chronocoulometry. We show a greater than fourfold improvement enabled by lacY coexpression in cells engineered to respond to bacterial signal molecules, pyocyanin and quorum-sensing autoinducer-2.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Chen-yu Chen
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Gregory F Payne
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
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11
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VanArsdale E, Pitzer J, Wang S, Stephens K, Chen CY, Payne GF, Bentley WE. Electrogenetic Signal Transmission and Propagation in Coculture to Guide Production of a Small Molecule, Tyrosine. ACS Synth Biol 2022; 11:877-887. [PMID: 35113532 DOI: 10.1021/acssynbio.1c00522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There are many strategies to actuate and control genetic circuits, including providing stimuli like exogenous chemical inducers, light, magnetic fields, and even applied voltage, that are orthogonal to metabolic activity. Their use enables actuation of gene expression for the production of small molecules and proteins in many contexts. Additionally, there are a growing number of reports wherein cocultures, consortia, or even complex microbiomes are employed for the production of biologics, taking advantage of an expanded array of biological function. Combining stimuli-responsive engineered cell populations enhances design space but increases complexity. In this work, we co-opt nature's redox networks and electrogenetically route control signals into a consortium of microbial cells engineered to produce a model small molecule, tyrosine. In particular, we show how electronically programmed short-lived signals (i.e., hydrogen peroxide) can be transformed by one population and propagated into sustained longer-distance signals that, in turn, guide tyrosine production in a second population building on bacterial quorum sensing that coordinates their collective behavior. Two design methodologies are demonstrated. First, we use electrogenetics to transform redox signals into the quorum sensing autoinducer, AI-1, that, in turn, induces a tyrosine biosynthesis pathway transformed into a second population. Second, we use the electrogenetically stimulated AI-1 to actuate expression of ptsH, boosting the growth rate of tyrosine-producing cells, augmenting both their number and metabolic activity. In both cases, we show how signal propagation within the coculture helps to ensure tyrosine production. We suggest that this work lays a foundation for employing electrochemical stimuli and engineered cocultures for production of molecular products in biomanufacturing environments.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Chen-yu Chen
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
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12
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Bird LJ, Kundu BB, Tschirhart T, Corts AD, Su L, Gralnick JA, Ajo-Franklin CM, Glaven SM. Engineering Wired Life: Synthetic Biology for Electroactive Bacteria. ACS Synth Biol 2021; 10:2808-2823. [PMID: 34637280 DOI: 10.1021/acssynbio.1c00335] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Electroactive bacteria produce or consume electrical current by moving electrons to and from extracellular acceptors and donors. This specialized process, known as extracellular electron transfer, relies on pathways composed of redox active proteins and biomolecules and has enabled technologies ranging from harvesting energy on the sea floor, to chemical sensing, to carbon capture. Harnessing and controlling extracellular electron transfer pathways using bioengineering and synthetic biology promises to heighten the limits of established technologies and open doors to new possibilities. In this review, we provide an overview of recent advancements in genetic tools for manipulating native electroactive bacteria to control extracellular electron transfer. After reviewing electron transfer pathways in natively electroactive organisms, we examine lessons learned from the introduction of extracellular electron transfer pathways into Escherichia coli. We conclude by presenting challenges to future efforts and give examples of opportunities to bioengineer microbes for electrochemical applications.
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Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Biki B. Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Tanya Tschirhart
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Anna D. Corts
- Joyn Bio, Boston, Massachusetts 02210, United States
| | - Lin Su
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210018, People’s Republic of China
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | | | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
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13
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Yim SS, McBee RM, Song AM, Huang Y, Sheth RU, Wang HH. Robust direct digital-to-biological data storage in living cells. Nat Chem Biol 2021; 17:246-253. [PMID: 33432236 PMCID: PMC7904632 DOI: 10.1038/s41589-020-00711-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 02/06/2023]
Abstract
DNA has been the predominant information storage medium for biology and holds great promise as a next-generation high-density data medium in the digital era. Currently, the vast majority of DNA-based data storage approaches rely on in vitro DNA synthesis. As such, there are limited methods to encode digital data into the chromosomes of living cells in a single step. Here, we describe a new electrogenetic framework for direct storage of digital data in living cells. Using an engineered redox-responsive CRISPR adaptation system, we encoded binary data in 3-bit units into CRISPR arrays of bacterial cells by electrical stimulation. We demonstrate multiplex data encoding into barcoded cell populations to yield meaningful information storage and capacity up to 72 bits, which can be maintained over many generations in natural open environments. This work establishes a direct digital-to-biological data storage framework and advances our capacity for information exchange between silicon- and carbon-based entities.
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Affiliation(s)
- Sung Sun Yim
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Ross M McBee
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alan M Song
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Yiming Huang
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Ravi U Sheth
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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14
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Isogawa K, Asano M, Hayazaki M, Koga K, Watanabe M, Suzuki K, Kobayashi T, Kawaguchi K, Ishizuka A, Kato S, Ito H, Hamamoto A, Koyama H, Furuta K, Takemori H. Thioxothiazolidin derivative, 4-OST, inhibits melanogenesis by enhancing the specific recruitment of tyrosinase-containing vesicles to lysosome. J Cell Biochem 2021; 122:667-678. [PMID: 33480093 DOI: 10.1002/jcb.29895] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 12/15/2022]
Abstract
Tyrosinase catalyzes the rate-limiting step in melanin synthesis. Melanin is synthesized from l-tyrosin in the melanosomes, where tyrosinase and other melanogenic factors are recruited via the vesicle transport system. Genetic and biochemical approaches have revealed a correlation between impairments in the vesicle transport system and albinism. However, the specificity of the individual transport systems for the corresponding melanogenic factors has not been well elucidated yet. Here, we report that the thioxothiazolidin derivative, 4-OST (4-[(5E)-5-[(4-fluorophenyl)methylidene]-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]-4-azatricyclo [5.2.1.02 ,6]dec-8-ene-3,5-dione: CAS RN. 477766-87-3) strongly inhibited melanogenesis in mouse melanoma B16F10 cells. 4-OST reduces tyrosinase protein levels without affecting its messenger RNA levels or enzymatic activity. Although a reduction in tyrosinase protein level was observed in the presence of a protein synthesis inhibitor, the reduction may be coupled with protein synthesis. Similarly, GIF-2202 (a derivative of 4-OST) lowers tyrosinase protein levels without affecting the levels of another melanogenic enzyme, tyrosinase-related protein 1 (TYRP1) level. The reduction in tyrosinase protein level is associated with an increase in the levels of the lysosomal proteinase cathepsin S. Chloroquine, a lysosome inhibitor, restored the tyrosinase protein level downregulated by GIF-2202, although no effects of other inhibitors (against proteasome, autophagy, or exocytosis) were observed. In addition, GIF-2202 segregated the immunofluorescence signals of tyrosinase from those of TYRP1. Chloroquine treatment resulted in co-localization of tyrosinase and cathepsin S signals near the perinuclear region, suggesting that 4-OST and GIF-2202 may alter the destination of the tyrosinase vesicle from the melanosome to the lysosome. 4-OST and GIF-2202 can be new tools for studying the tyrosinase-specific vesicle transport system.
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Affiliation(s)
- Kenta Isogawa
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Masataka Asano
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Masumi Hayazaki
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Kenichi Koga
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Miyu Watanabe
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Keiichi Suzuki
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Takahiro Kobayashi
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Kyoka Kawaguchi
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Akane Ishizuka
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Shinya Kato
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Hironari Ito
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Akie Hamamoto
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Hiroko Koyama
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Kyoji Furuta
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
| | - Hiroshi Takemori
- Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
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15
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Ramiah Rajasekaran P, Chapin AA, Quan DN, Herberholz J, Bentley WE, Ghodssi R. 3D-Printed electrochemical sensor-integrated transwell systems. MICROSYSTEMS & NANOENGINEERING 2020; 6:100. [PMID: 34567709 PMCID: PMC8433167 DOI: 10.1038/s41378-020-00208-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/03/2020] [Accepted: 08/16/2020] [Indexed: 05/05/2023]
Abstract
This work presents a 3D-printed, modular, electrochemical sensor-integrated transwell system for monitoring cellular and molecular events in situ without sample extraction or microfluidics-assisted downstream omics. Simple additive manufacturing techniques such as 3D printing, shadow masking, and molding are used to fabricate this modular system, which is autoclavable, biocompatible, and designed to operate following standard operating protocols (SOPs) of cellular biology. Integral to the platform is a flexible porous membrane, which is used as a cell culture substrate similarly to a commercial transwell insert. Multimodal electrochemical sensors fabricated on the membrane allow direct access to cells and their products. A pair of gold electrodes on the top side of the membrane measures impedance over the course of cell attachment and growth, characterized by an exponential decrease (~160% at 10 Hz) due to an increase in the double layer capacitance from secreted extracellular matrix (ECM) proteins. Cyclic voltammetry (CV) sensor electrodes, fabricated on the bottom side of the membrane, enable sensing of molecular release at the site of cell culture without the need for downstream fluidics. Real-time detection of ferrocene dimethanol injection across the membrane showed a three order-of-magnitude higher signal at the membrane than in the bulk media after reaching equilibrium. This modular sensor-integrated transwell system allows unprecedented direct, real-time, and noninvasive access to physical and biochemical information, which cannot be obtained in a conventional transwell system.
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Affiliation(s)
| | - Ashley Augustiny Chapin
- Institute for Systems Research, University of Maryland, College Park, MD USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD USA
| | - David N. Quan
- Fischell Department of Bioengineering, University of Maryland, College Park, MD USA
| | - Jens Herberholz
- Department of Psychology and Neuroscience and Cognitive Science Program, University of Maryland, College Park, MD USA
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD USA
| | - Reza Ghodssi
- Institute for Systems Research, University of Maryland, College Park, MD USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD USA
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD USA
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16
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VanArsdale E, Pitzer J, Payne GF, Bentley WE. Redox Electrochemistry to Interrogate and Control Biomolecular Communication. iScience 2020; 23:101545. [PMID: 33083771 PMCID: PMC7516135 DOI: 10.1016/j.isci.2020.101545] [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] [Indexed: 12/11/2022] Open
Abstract
Cells often communicate by the secretion, transport, and perception of molecules. Information conveyed by molecules is encoded, transmitted, and decoded by cells within the context of the prevailing microenvironments. Conversely, in electronics, transmission reliability and message validation are predictable, robust, and less context dependent. In turn, many transformative advances have resulted by the formal consideration of information transfer. One way to explore this potential for biological systems is to create bio-device interfaces that facilitate bidirectional information transfer between biology and electronics. Redox reactions enable this linkage because reduction and oxidation mediate communication within biology and can be coupled with electronics. By manipulating redox reactions, one is able to combine the programmable features of electronics with the ability to interrogate and modulate biological function. In this review, we examine methods to electrochemically interrogate the various components of molecular communication using redox chemistry and to electronically control cell communication using redox electrogenetics.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall 8278 Paint Branch Drive, College Park, MD 20742, USA.,Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD 20742, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, Room 5102, A. James Clark Hall, College Park, MD 20742, USA
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall 8278 Paint Branch Drive, College Park, MD 20742, USA
| | - Gregory F Payne
- Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD 20742, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, Room 5102, A. James Clark Hall, College Park, MD 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall 8278 Paint Branch Drive, College Park, MD 20742, USA.,Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD 20742, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, Room 5102, A. James Clark Hall, College Park, MD 20742, USA
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