1
|
Xu W, Liu Z, Wang J, Jin K, Yue L, Yu L, Niu L, Dou Q, Liu J, Zhang Y, Zhu X, Wu Y. Extending visual range of bacteria with upconversion nanoparticles and constructing NIR-responsive bio-microrobots. J Colloid Interface Sci 2025; 682:608-618. [PMID: 39642547 DOI: 10.1016/j.jcis.2024.11.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 11/16/2024] [Accepted: 11/27/2024] [Indexed: 12/09/2024]
Abstract
The motility of bacteria is crucial for navigating competitive environments and is closely linked to physiological activities essential for their survival, such as biofilm development. Precise regulation of bacterial motility enhances our understanding of these complex processes. While optogenetic tools have been used to control and investigate bacterial motility, the excitation light in most existing systems are limited to the visible light spectrum. Here, we introduce a new type of bio-microrobot comprising genetically engineered E. coli cells and orthogonally emissive upconversion nanoparticles that can respond to both 980 nm and 808 nm NIR light. This system allows toggling of bacterial states between tumbling and swimming via simply alternating the NIR light between different wavelengths. It is believed that the use of NIR light with deeper tissue penetration suggests potential applications for these bio-microrobots in areas like targeted drug delivery.
Collapse
Affiliation(s)
- Wei Xu
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Zhen Liu
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Jing Wang
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Kai Jin
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Lulu Yue
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Lin Yu
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China; School of Medicine, Shanghai University, Shanghai, China
| | - Luqi Niu
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Qingqing Dou
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Jinliang Liu
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Yuzhe Zhang
- School of Environmental Science and Engineering, Changzhou University, Changzhou, China
| | - Xiaohui Zhu
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China.
| | - Yihan Wu
- Department of Environmental and Chemical Engineering, Shanghai University, Shanghai, China.
| |
Collapse
|
2
|
Kaufman D, Chen CY, Tsao CY, Zhao Z, Lavon A, Payne GF, Bentley WE, Ben-Yoav H. Redox-mediated Biomolecular information transfer in single electrogenetic biological cells. Biosens Bioelectron 2024; 262:116546. [PMID: 38968774 DOI: 10.1016/j.bios.2024.116546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
Electronic communication in natural systems makes use, inter alia, of molecular transmission, where electron transfer occurs within networks of redox reactions, which play a vital role in many physiological systems. In view of the limited understanding of redox signaling, we developed an approach and an electrochemical-optical lab-on-a-chip to observe cellular responses in localized redox environments. The developed fluidic micro-system uses electrogenetic bacteria in which a cellular response is activated to electrically and chemically induced stimulations. Specifically, controlled environments for the cells are created by using microelectrodes to generate spatiotemporal redox gradients. The in-situ cellular responses at both single-cell and population levels are monitored by optical microscopy. The elicited electrogenetic fluorescence intensities after 210 min in response to electrochemical and chemical activation were 1.3 × 108±0.30 × 108 arbitrary units (A.U.) and 1.2 × 108±0.30 × 108 A.U. per cell population, respectively, and 1.05 ± 0.01 A.U. and 1.05 ± 0.01 A.U. per-cell, respectively. We demonstrated that redox molecules' mass transfer between the electrode and cells - and not the applied electrical field - activated the electrogenetic cells. Specifically, we found an oriented amplified electrogenetic response on the charged electrodes' downstream side, which was determined by the location of the stimulating electrodes and the flow profile. We then focused on the cellular responses and observed distinct subpopulations that were attributed to electrochemical rather than chemical stimulation, with the distance between the cells and the stimulating electrode being the main determinant. These observations provide a comprehensive understanding of the mechanisms by which diffusible redox mediators serve as electron shuttles, imposing context and activating electrogenetic responses.
Collapse
Affiliation(s)
- Daniel Kaufman
- Nanobioelectronics Laboratory (NBEL), Department of Biomedical Engineering and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Chen-Yu Chen
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, United States
| | - Chen-Yu Tsao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, United States
| | - Zhiling Zhao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, United States
| | - Avia Lavon
- Nanobioelectronics Laboratory (NBEL), Department of Biomedical Engineering and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, United States
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, 20742, United States
| | - Hadar Ben-Yoav
- Nanobioelectronics Laboratory (NBEL), Department of Biomedical Engineering and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
| |
Collapse
|
3
|
Zhao Y, Kurzthaler C, Zhou N, Schwarz-Linek J, Devailly C, Arlt J, Huang JD, Poon WCK, Franosch T, Martinez VA, Tailleur J. Quantitative characterization of run-and-tumble statistics in bulk bacterial suspensions. Phys Rev E 2024; 109:014612. [PMID: 38366485 DOI: 10.1103/physreve.109.014612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 12/04/2023] [Indexed: 02/18/2024]
Abstract
We introduce a numerical method to extract the parameters of run-and-tumble dynamics from experimental measurements of the intermediate scattering function. We show that proceeding in Laplace space is unpractical and employ instead renewal processes to work directly in real time. We first validate our approach against data produced using agent-based simulations. This allows us to identify the length and time scales required for an accurate measurement of the motility parameters, including tumbling frequency and swim speed. We compare different models for the run-and-tumble dynamics by accounting for speed variability at the single-cell and population level, respectively. Finally, we apply our approach to experimental data on wild-type Escherichia coli obtained using differential dynamic microscopy.
Collapse
Affiliation(s)
- Yongfeng Zhao
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong, People's Republic of China
- Université de Paris, MSC, UMR 7057 CNRS, 75205 Paris, France
| | - Christina Kurzthaler
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Nan Zhou
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Jana Schwarz-Linek
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Clemence Devailly
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Jochen Arlt
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wilson C K Poon
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Thomas Franosch
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Vincent A Martinez
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Julien Tailleur
- Université de Paris, MSC, UMR 7057 CNRS, 75205 Paris, France
| |
Collapse
|
4
|
Wang XG, Zou ZP, Du Y, Ye BC, Zhou Y. Construction of an Engineered Escherichia coli with Efficient Chemotactic and Metabolizing Ability toward Tetrathionate. ACS Synth Biol 2023; 12:3414-3423. [PMID: 37939253 DOI: 10.1021/acssynbio.3c00445] [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: 11/10/2023]
Abstract
The emergence of genetically engineered bacteria has provided a new means for the diagnosis and treatment of diseases. However, in vivo applications of these engineered bacteria are hindered by their inefficient accumulation in areas of inflammation. In this study, we constructed an engineered Escherichia coli (E. coli) for directional migration toward tetrathionate (a biomarker of gut inflammation), which is regulated by the TtrSR two-component system (TCS) from Shewanella baltica OS195 (S. baltica). Specifically, we removed endogenous cheZ to control the motility of E. coli. Moreover, we introduced the reductase gene cluster (ttrBCA) from Salmonella enterica serotype typhimurium (S. typhimurium), a major pathogen causing gut inflammation, into E. coli to metabolize tetrathionate. The resulting strain was tested for its motility along the gradients of tetrathionate; the engineered strain exhibits tropism to tetrathionate compared with the original strain. Furthermore, the engineered E. coli could only restore its smooth swimming ability when tetrathionate existed. With these modifications enabling tetrathionate-mediated chemotactic and metabolizing activity, this strategy with therapeutic elements will provide a great potential opportunity for target treatment of various diseases by swapping the corresponding genetic circuits.
Collapse
Affiliation(s)
- Xin-Ge Wang
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Zhen-Ping Zou
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Yue Du
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Ying Zhou
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| |
Collapse
|
5
|
Deletion of the cheZ gene results in the loss of swimming ability and the decrease of adhesion ability to Caco-2 cells in Escherichia coli Nissle 1917. Folia Microbiol (Praha) 2022; 68:395-402. [DOI: 10.1007/s12223-022-01019-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
|
6
|
Huang Y, Lin X, Yu S, Chen R, Chen W. Intestinal Engineered Probiotics as Living Therapeutics: Chassis Selection, Colonization Enhancement, Gene Circuit Design, and Biocontainment. ACS Synth Biol 2022; 11:3134-3153. [PMID: 36094344 DOI: 10.1021/acssynbio.2c00314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Intestinal probiotics are often used for the in situ treatment of diseases, such as metabolic disorders, tumors, and chronic inflammatory infections. Recently, there has been an increased emphasis on intelligent, customized treatments with a focus on long-term efficacy; however, traditional probiotic therapy has not kept up with this trend. The use of synthetic biology to construct gut-engineered probiotics as live therapeutics is a promising avenue in the treatment of specific diseases, such as phenylketonuria and inflammatory bowel disease. These studies generally involve a series of fundamental design issues: choosing an engineered chassis, improving the colonization ability of engineered probiotics, designing functional gene circuits, and ensuring the safety of engineered probiotics. In this review, we summarize the relevant past research, the progress of current research, and discuss the key issues that restrict the widespread application of intestinal engineered probiotic living therapeutics.
Collapse
Affiliation(s)
- Yan Huang
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiaojun Lin
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Siyang Yu
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Ruiyue Chen
- Team SZU-China at iGEM 2021, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Weizhao Chen
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.,Shenzhen Key Laboratory for Microbial Gene Engineering, Shenzhen University, Shenzhen 518060, China
| |
Collapse
|
7
|
Stephens K, Zakaria FR, VanArsdale E, Payne GF, Bentley WE. Electronic signals are electrogenetically relayed to control cell growth and co-culture composition. Metab Eng Commun 2021; 13:e00176. [PMID: 34194997 PMCID: PMC8233222 DOI: 10.1016/j.mec.2021.e00176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 01/17/2023] Open
Abstract
There is much to be gained by enabling electronic interrogation and control of biological function. While the benefits of bioelectronics that rely on potential-driven ionic flows are well known (electrocardiograms, defibrillators, neural prostheses, etc) there are relatively few advances targeting nonionic molecular networks, including genetic circuits. Redox activities combine connectivity to electronics with the potential for specific genetic control in cells. Here, electrode-generated hydrogen peroxide is used to actuate an electrogenetic "relay" cell population, which interprets the redox cue and synthesizes a bacterial signaling molecule (quorum sensing autoinducer AI-1) that, in turn, signals increased growth rate in a second population. The dramatically increased growth rate of the second population is enabled by expression of a phosphotransferase system protein, HPr, which is important for glucose transport. The potential to electronically modulate cell growth via direct genetic control will enable new opportunities in the treatment of disease and manufacture of biological therapeutics and other molecules.
Collapse
Affiliation(s)
- Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - Fauziah Rahma Zakaria
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| |
Collapse
|
8
|
Schneier M, Razdan S, Miller AM, Briceno ME, Barua S. Current technologies to endotoxin detection and removal for biopharmaceutical purification. Biotechnol Bioeng 2020; 117:2588-2609. [PMID: 32333387 DOI: 10.1002/bit.27362] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/21/2022]
Abstract
Endotoxins are the major contributors to the pyrogenic response caused by contaminated pharmaceutical products, formulation ingredients, and medical devices. Recombinant biopharmaceutical products are manufactured using living organisms, including Gram-negative bacteria. Upon the death of a Gram-negative bacterium, endotoxins (also known as lipopolysaccharides) in the outer cell membrane are released into the lysate where they can interact with and form bonds with biomolecules, including target therapeutic compounds. Endotoxin contamination of biologic products may also occur through water, raw materials such as excipients, media, additives, sera, equipment, containers closure systems, and expression systems used in manufacturing. The manufacturing process is, therefore, in critical need of methods to reduce and remove endotoxins by monitoring raw materials and in-process intermediates at critical steps, in addition to final drug product release testing. This review paper highlights a discussion on three major topics about endotoxin detection techniques, upstream processes for the production of therapeutic molecules, and downstream processes to eliminate endotoxins during product purification. Finally, we have evaluated the effectiveness of endotoxin removal processes from a perspective of high purity and low cost.
Collapse
Affiliation(s)
- Mason Schneier
- Department of Chemical and Biochemical Engineering, Missouri University of Science and Technology, Rolla, Missouri
| | - Sidharth Razdan
- Department of Chemical and Biochemical Engineering, Missouri University of Science and Technology, Rolla, Missouri
| | - Allison M Miller
- Department of Chemical and Biochemical Engineering, Missouri University of Science and Technology, Rolla, Missouri
| | - Maria E Briceno
- Department of Chemical and Biochemical Engineering, Missouri University of Science and Technology, Rolla, Missouri
| | - Sutapa Barua
- Department of Chemical and Biochemical Engineering, Missouri University of Science and Technology, Rolla, Missouri
| |
Collapse
|
9
|
Bhokisham N, VanArsdale E, Stephens KT, Hauk P, Payne GF, Bentley WE. A redox-based electrogenetic CRISPR system to connect with and control biological information networks. Nat Commun 2020; 11:2427. [PMID: 32415193 PMCID: PMC7228920 DOI: 10.1038/s41467-020-16249-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 04/15/2020] [Indexed: 01/04/2023] Open
Abstract
Electronic information can be transmitted to cells directly from microelectronics via electrode-activated redox mediators. These transmissions are decoded by redox-responsive promoters which enable user-specified control over biological function. Here, we build on this redox communication modality by establishing an electronic eCRISPR conduit of information exchange. This system acts as a biological signal processor, amplifying signal reception and filtering biological noise. We electronically amplify bacterial quorum sensing (QS) signaling by activating LasI, the autoinducer-1 synthase. Similarly, we filter out unintended noise by inhibiting the native SoxRS-mediated oxidative stress response regulon. We then construct an eCRISPR based redox conduit in both E. coli and Salmonella enterica. Finally, we display eCRISPR based information processing that allows transmission of spatiotemporal redox commands which are then decoded by gelatin-encapsulated E. coli. We anticipate that redox communication channels will enable biohybrid microelectronic devices that could transform our abilities to electronically interpret and control biological function.
Collapse
Affiliation(s)
- Narendranath Bhokisham
- Biological Sciences Graduate Program-College of Computer, Mathematical and Natural Sciences, University of Maryland, 4066 Campus Drive, College Park, MD, 20742, USA.,Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD, 20742, USA
| | - Eric VanArsdale
- Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD, 20742, USA.,Fischell Department of Bioengineering, A. James Clark Hall, University of Maryland, 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
| | - Kristina T Stephens
- Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD, 20742, USA.,Fischell Department of Bioengineering, A. James Clark Hall, University of Maryland, 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
| | - Pricila Hauk
- Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, 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.,Fischell Department of Bioengineering, A. James Clark Hall, University of Maryland, 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
- Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD, 20742, USA. .,Fischell Department of Bioengineering, A. James Clark Hall, University of Maryland, 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.
| |
Collapse
|
10
|
VanArsdale E, Hörnström D, Sjöberg G, Järbur I, Pitzer J, Payne GF, van Maris AJA, Bentley WE. A Coculture Based Tyrosine-Tyrosinase Electrochemical Gene Circuit for Connecting Cellular Communication with Electronic Networks. ACS Synth Biol 2020; 9:1117-1128. [PMID: 32208720 DOI: 10.1021/acssynbio.9b00469] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is a growing interest in mediating information transfer between biology and electronics. By the addition of redox mediators to various samples and cells, one can both electronically obtain a redox "portrait" of a biological system and, conversely, program gene expression. Here, we have created a cell-based synthetic biology-electrochemical axis in which engineered cells process molecular cues, producing an output that can be directly recorded via electronics-but without the need for added redox mediators. The process is robust; two key components must act together to provide a valid signal. The system builds on the tyrosinase-mediated conversion of tyrosine to L-DOPA and L-DOPAquinone, which are both redox active. "Catalytic" transducer cells provide for signal-mediated surface expression of tyrosinase. Additionally, "reagent" transducer cells synthesize and export tyrosine, a substrate for tyrosinase. In cocultures, this system enables real-time electrochemical transduction of cell activating molecular cues. To demonstrate, we eavesdrop on quorum sensing signaling molecules that are secreted by Pseudomonas aeruginosa, N-(3-oxododecanoyl)-l-homoserine lactone and pyocyanin.
Collapse
Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
| | - David Hörnström
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - Gustav Sjöberg
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - Ida Järbur
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
| | - Gregory F. Payne
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
| | - Antonius J. A. van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
| |
Collapse
|
11
|
Kim E, Li J, Kang M, Kelly DL, Chen S, Napolitano A, Panzella L, Shi X, Yan K, Wu S, Shen J, Bentley WE, Payne GF. Redox Is a Global Biodevice Information Processing Modality. PROCEEDINGS OF THE IEEE. INSTITUTE OF ELECTRICAL AND ELECTRONICS ENGINEERS 2019; 107:1402-1424. [PMID: 32095023 PMCID: PMC7036710 DOI: 10.1109/jproc.2019.2908582] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Biology is well-known for its ability to communicate through (i) molecularly-specific signaling modalities and (ii) a globally-acting electrical modality associated with ion flow across biological membranes. Emerging research suggests that biology uses a third type of communication modality associated with a flow of electrons through reduction/oxidation (redox) reactions. This redox signaling modality appears to act globally and has features of both molecular and electrical modalities: since free electrons do not exist in aqueous solution, the electrons must flow through molecular intermediates that can be switched between two states - with electrons (reduced) or without electrons (oxidized). Importantly, this global redox modality is easily accessible through its electrical features using convenient electrochemical instrumentation. In this review, we explain this redox modality, describe our electrochemical measurements, and provide four examples demonstrating that redox enables communication between biology and electronics. The first two examples illustrate how redox probing can acquire biologically relevant information. The last two examples illustrate how redox inputs can transduce biologically-relevant transitions for patterning and the induction of a synbio transceiver for two-hop molecular communication. In summary, we believe redox provides a unique ability to bridge bio-device communication because simple electrochemical methods enable global access to biologically meaningful information. Further, we envision that redox may facilitate the application of information theory to the biological sciences.
Collapse
Affiliation(s)
- Eunkyoung Kim
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
| | - Jinyang Li
- Institute for Bioscience & Biotechnology Research, Fischell Department of Bioengineering University of Maryland, College Park, MD 20742, USA
| | - Mijeong Kang
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
| | - Deanna L Kelly
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD 21228, USA
| | - Shuo Chen
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD 21228, USA
| | - Alessandra Napolitano
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, I-80126 Naples, Italy
| | - Lucia Panzella
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, I-80126 Naples, Italy
| | - Xiaowen Shi
- School of Resource and Environmental Science, Hubei Biomass-Resource Chemistry, Environmental Biotechnology Key Laboratory, Wuhan University, Wuhan 430079, China
| | - Kun Yan
- School of Resource and Environmental Science, Hubei Biomass-Resource Chemistry, Environmental Biotechnology Key Laboratory, Wuhan University, Wuhan 430079, China
| | - Si Wu
- School of Resource and Environmental Science, Hubei Biomass-Resource Chemistry, Environmental Biotechnology Key Laboratory, Wuhan University, Wuhan 430079, China
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - William E Bentley
- Institute for Bioscience & Biotechnology Research, Fischell Department of Bioengineering University of Maryland, College Park, MD 20742, USA
| | - Gregory F Payne
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
12
|
Virgile C, Hauk P, Wu HC, Bentley WE. Plasmid-encoded protein attenuates Escherichia coli swimming velocity and cell growth, not reprogrammed regulatory functions. Biotechnol Prog 2019; 35:e2778. [PMID: 30666816 PMCID: PMC10711804 DOI: 10.1002/btpr.2778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/28/2018] [Accepted: 01/10/2019] [Indexed: 12/17/2023]
Abstract
In addition to engineering new pathways for synthesis, synthetic biologists rewire cells to carry out "programmable" functions, an example being the creation of wound-healing probiotics. Engineering regulatory circuits and synthetic machinery, however, can be deleterious to cell function, particularly if the "metabolic burden" is significant. Here, a synthetic regulatory circuit previously constructed to direct Escherichia coli to swim toward hydrogen peroxide, a signal of wound generation, was shown to work even with coexpression of antibiotic resistance genes and genes associated with lactose utilization. We found, however, that cotransformation with a second vector constitutively expressing GFP (as a marker) and additionally conferring resistance to kanamycin and tetracycline resulted in slower velocity (Δ~6 μm/s) and dramatically reduced growth rate (Δ > 50%). The additional vector did not, however, alter the run-and-tumble ratio or directional characteristics of H2 O2 -dependent motility. The main impact of this additional burden was limited to slowing cell velocity and growth, suggesting that reprogrammed cell motility by minimally altering native regulatory circuits can be maintained even when extraneous burden is placed on the host cell. © 2019 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2778, 2019.
Collapse
Affiliation(s)
- Chelsea Virgile
- Institute for Bioscience and Biotechnology Research, College Park, MD 20742
- Fischell Department of Bioengineering, Room 3122, Jeong H. Kim Engineering Building (Bldg. #225), University of Maryland, College Park, MD 20742
| | - Pricila Hauk
- Institute for Bioscience and Biotechnology Research, College Park, MD 20742
- Fischell Department of Bioengineering, Room 3122, Jeong H. Kim Engineering Building (Bldg. #225), University of Maryland, College Park, MD 20742
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei City, Taiwan
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research, College Park, MD 20742
- Fischell Department of Bioengineering, Room 3122, Jeong H. Kim Engineering Building (Bldg. #225), University of Maryland, College Park, MD 20742
| |
Collapse
|
13
|
McKay R, Ghodasra M, Schardt J, Quan D, Pottash AE, Shang W, Jay SM, Payne GF, Chang MW, March JC, Bentley WE. A platform of genetically engineered bacteria as vehicles for localized delivery of therapeutics: Toward applications for Crohn's disease. Bioeng Transl Med 2018; 3:209-221. [PMID: 30377661 PMCID: PMC6195910 DOI: 10.1002/btm2.10113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/22/2018] [Accepted: 08/22/2018] [Indexed: 12/14/2022] Open
Abstract
For therapies targeting diseases of the gastrointestinal tract, we and others envision probiotic bacteria that synthesize and excrete biotherapeutics at disease sites. Toward this goal, we have engineered commensal E. coli that selectively synthesize and secrete a model biotherapeutic in the presence of nitric oxide (NO), an intestinal biomarker for Crohn's disease (CD). This is accomplished by co‐expressing the pore forming protein TolAIII with the biologic, granulocyte macrophage‐colony stimulating factor (GM‐CSF). We have additionally engineered these bacteria to accumulate at sites of elevated NO by engineering their motility circuits and controlling pseudotaxis. Importantly, because we have focused on in vitro test beds, motility and biotherapeutics production are spatiotemporally characterized. Together, the targeted recognition, synthesis, and biomolecule delivery comprises a “smart” probiotics platform that may have utility in the treatment of CD. Further, this platform could be modified to accommodate other pursuits by swapping the promoter and therapeutic gene to reflect other disease biomarkers and treatments, respectively.
Collapse
Affiliation(s)
- Ryan McKay
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Monil Ghodasra
- Fischell Dept. of Bioengineering University of Maryland College Park MD
| | - John Schardt
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health Bethesda MD
| | - David Quan
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Alex Eli Pottash
- Fischell Dept. of Bioengineering University of Maryland College Park MD
| | - Wu Shang
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Steven M Jay
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health Bethesda MD.,Marlene and Stewart Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine Baltimore MD.,Program in Molecular and Cellular Biology University of Maryland College Park MD
| | - Gregory F Payne
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Matthew Wook Chang
- Dept. of Biochemistry, Yong Loo Lin School of Medicine National University of Singapore Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation, Life Sciences Institute National University of Singapore Singapore
| | - John C March
- Dept. of Biological and Environmental Engineering Cornell University Ithaca NY
| | - William E Bentley
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| |
Collapse
|
14
|
Hwang IY, Lee HL, Huang JG, Lim YY, Yew WS, Lee YS, Chang MW. Engineering microbes for targeted strikes against human pathogens. Cell Mol Life Sci 2018; 75:2719-2733. [PMID: 29736607 PMCID: PMC11105496 DOI: 10.1007/s00018-018-2827-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/06/2018] [Accepted: 04/23/2018] [Indexed: 12/24/2022]
Abstract
Lack of pathogen specificity in antimicrobial therapy causes non-discriminant microbial cell killing that disrupts the microflora present. As a result, potentially helpful microbial cells are killed along with the pathogen, altering the biodiversity and dynamic interactions within the population. Moreover, the unwarranted exposure of antibiotics to microbes increases the likelihood of developing resistance and perpetuates the emergence of multidrug resistance. Synthetic biology offers an alternative solution where specificity can be conferred to reduce the non-specific, non-targeted activity of currently available antibiotics, and instead provides targeted therapy against specific pathogens and minimising collateral damage to the host's inherent microbiota. With a greater understanding of the microbiome and the available genetic engineering tools for microbial cells, it is possible to devise antimicrobial strategies for novel antimicrobial therapy that are able to precisely and selectively remove infectious pathogens. Herein, we review the strategies developed by unlocking some of the natural mechanisms used by the microbes and how these may be utilised in targeted antimicrobial therapy, with the promise of reducing the current global bane of multidrug antimicrobial resistance.
Collapse
Affiliation(s)
- In Young Hwang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Hui Ling Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - James Guoxian Huang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Yvonne Yijuan Lim
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
| |
Collapse
|
15
|
Virgile C, Hauk P, Wu HC, Shang W, Tsao CY, Payne GF, Bentley WE. Engineering bacterial motility towards hydrogen-peroxide. PLoS One 2018; 13:e0196999. [PMID: 29750783 PMCID: PMC5947916 DOI: 10.1371/journal.pone.0196999] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/24/2018] [Indexed: 11/19/2022] Open
Abstract
Synthetic biologists construct innovative genetic/biological systems to treat environmental, energy, and health problems. Many systems employ rewired cells for non-native product synthesis, while a few have employed the rewired cells as 'smart' devices with programmable function. Building on the latter, we developed a genetic construct to control and direct bacterial motility towards hydrogen peroxide, one of the body's immune response signaling molecules. A motivation for this work is the creation of cells that can target and autonomously treat disease, the latter signaled by hydrogen peroxide release. Bacteria naturally move towards a variety of molecular cues (e.g., nutrients) in the process of chemotaxis. In this work, we engineered bacteria to recognize and move towards hydrogen peroxide, a non-native chemoattractant and potential toxin. Our system exploits oxyRS, the native oxidative stress regulon of E. coli. We first demonstrated H2O2-mediated upregulation motility regulator, CheZ. Using transwell assays, we showed a two-fold increase in net motility towards H2O2. Then, using a 2D cell tracking system, we quantified bacterial motility descriptors including velocity, % running (of tumble/run motions), and a dynamic net directionality towards the molecular cue. In CheZ mutants, we found that increased H2O2 concentration (0-200 μM) and induction time resulted in increased running speeds, ultimately reaching the native E. coli wild-type speed of ~22 μm/s with a ~45-65% ratio of running to tumbling. Finally, using a microfluidic device with stable H2O2 gradients, we characterized responses and the potential for "programmed" directionality towards H2O2 in quiescent fluids. Overall, the synthetic biology framework and tracking analysis in this work will provide a framework for investigating controlled motility of E. coli and other 'smart' probiotics for signal-directed treatment.
Collapse
Affiliation(s)
- Chelsea Virgile
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Pricila Hauk
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Wu Shang
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Chen-Yu Tsao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| |
Collapse
|
16
|
Padmanabhan S, Misteli T, DeVoe DL. Controlled droplet discretization and manipulation using membrane displacement traps. LAB ON A CHIP 2017; 17:3717-3724. [PMID: 28990023 PMCID: PMC7900922 DOI: 10.1039/c7lc00910k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
An innovative platform enabling complex discretization and manipulation of aqueous droplets is described. The system uses simple membrane displacement trap elements to perform multiple functions including droplet discretization, release, metering, capture, and merging. Multi-layer PDMS devices with membrane displacement trap arrays are used to discretize sample into nanoliter scale droplet volumes, and reliably manipulate individual droplets within the arrays. Performance is characterized for varying capillary number flows, membrane actuation pressures, trap and membrane geometries, and trapped droplet volumes, with operational domains established for each platform function. The novel approach to sample digitization and droplet manipulation is demonstrated through discretization of a dilute bacteria sample, metering of individual traps to generate droplets containing single bacteria, and merging of the resulting droplets to pair the selected bacteria within a single droplet.
Collapse
Affiliation(s)
- S Padmanabhan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, USA
| | | | | |
Collapse
|