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Kong Y, Du Q, Li J, Xing H. Engineering bacterial surface interactions using DNA as a programmable material. Chem Commun (Camb) 2022; 58:3086-3100. [PMID: 35077527 DOI: 10.1039/d1cc06138k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The diverse surface interactions and functions of a bacterium play an important role in cell signaling, host infection, and colony formation. To understand and synthetically control the biological functions of individual cells as well as the whole community, there is growing attention on the development of chemical and biological tools that can integrate artificial functional motifs onto the bacterial surface to replace the native interactions, enabling a variety of applications in biosynthesis, environmental protection, and human health. Among all these functional motifs, DNA emerges as a powerful tool that can precisely control bacterial interactions at the bio-interface due to its programmability and biorecognition properties. Compared with conventional chemical and genetic approaches, the sequence-specific Watson-Crick interaction enables almost unlimited programmability in DNA nanostructures, realizing one base-pair spatial control and bio-responsive properties. This highlight aims to provide an overview on this emerging research topic of DNA-engineered bacterial interactions from the aspect of synthetic chemists. We start with the introduction of native bacterial surface ligands and established synthetic approaches to install artificial ligands, including direct modification, metabolic engineering, and genetic engineering. A brief overview of DNA nanotechnology, reported DNA-bacteria conjugation chemistries, and several examples of DNA-engineered bacteria are included in this highlight. The future perspectives and challenges in this field are also discussed, including the development of dynamic bacterial surface chemistry, assembly of programmable multicellular community, and realization of bacteria-based theranostic agents and synthetic microbiota as long-term goals.
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Affiliation(s)
- Yuhan Kong
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Qi Du
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Juan Li
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
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2
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Smith TJ, Sondermann H, O’Toole GA. Co-opting the Lap System of Pseudomonas fluorescens To Reversibly Customize Bacterial Cell Surfaces. ACS Synth Biol 2018; 7:2612-2617. [PMID: 30278125 DOI: 10.1021/acssynbio.8b00278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Initial attachment to a surface is a key and highly regulated step in biofilm formation. In this study, we present a platform for reversibly functionalizing bacterial cell surfaces with an emphasis on designing biofilms. We engineered the Lap system of Pseudomonas fluorescens Pf0-1, which is normally used to regulate initial cell surface attachment, to display various protein cargo at the bacterial cell surface and control extracellular release of the cargo in response to changing levels of the second messenger c-di-GMP. To accomplish this goal, we fused the protein cargo between the N-terminal retention module and C-terminal secretion signal of LapA and controlled surface localization of the cargo with natural signals known to stimulate or deplete c-di-GMP levels in P. fluorescens Pf0-1. We show this system can tolerate large cargo in excess of 500 amino acids, direct P. fluorescens Pf0-1 to surfaces it does not typically colonize, and program this microbe to sequester the toxic medal cadmium.
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Affiliation(s)
- T. Jarrod Smith
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Room 202 Remsen
Building, Hanover, New Hampshire 03755, United States
| | - Holger Sondermann
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Room 202 Remsen
Building, Hanover, New Hampshire 03755, United States
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Scott FY, Heyde KC, Rice MK, Ruder WC. Engineering a living biomaterial via bacterial surface capture of environmental molecules. Synth Biol (Oxf) 2018; 3:ysy017. [PMID: 32995524 PMCID: PMC7445765 DOI: 10.1093/synbio/ysy017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 11/13/2022] Open
Abstract
Synthetic biology holds significant potential in biomaterials science as synthetically engineered cells can produce new biomaterials, or alternately, can function as living components of new biomaterials. Here, we describe the creation of a new biomaterial that incorporates living bacterial constituents that interact with their environment using engineered surface display. We first developed a gene construct that enabled simultaneous expression of cytosolic mCherry and a surface-displayed, catalytically active enzyme capable of covalently bonding with benzylguanine (BG) groups. We then created a functional living material within a microfluidic channel using these genetically engineered cells. The material forms when engineered cells covalently bond to ambient BG-modified molecules upon induction. Given the wide range of materials amenable to functionalization with BG-groups, our system provides a proof-of-concept for the sequestration and assembly of BG-functionalized molecules on a fluid-swept, living biomaterial surface.
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Affiliation(s)
- Felicia Y Scott
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Keith C Heyde
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - MaryJoe K Rice
- Department of Mechanical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Warren C Ruder
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.,Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
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Chen F, Wegner SV. Implementation of Blue Light Switchable Bacterial Adhesion for Design of Biofilms. Bio Protoc 2018; 8:e2893. [PMID: 34286002 DOI: 10.21769/bioprotoc.2893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/27/2018] [Accepted: 06/05/2018] [Indexed: 11/02/2022] Open
Abstract
Control of bacterial adhesions to a substrate with high precision in space and time is important to form a well-defined biofilm. Here, we present a method to engineer bacteria such that they adhere specifically to substrates under blue light through the photoswitchable proteins nMag and pMag. This provides exquisite spatiotemporal remote control over these interactions. The engineered bacteria express pMag protein on the surface so that they can adhere to substrates with nMag protein immobilization under blue light, and reversibly detach in the dark. This process can be repeatedly turned on and off. In addition, the bacterial adhesion property can be adjusted by expressing different pMag proteins on the bacterial surface and altering light intensity. This protocol provides light switchable, reversible and tunable control of bacteria adhesion with high spatial and temporal resolution, which enables us to pattern bacteria on substrates with great flexibility.
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Affiliation(s)
- Fei Chen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Seraphine V Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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5
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Heyde KC, Ruder WC. Programming Biomaterial Interactions Using Engineered Living Cells. Methods Mol Biol 2018; 1772:249-265. [PMID: 29754233 DOI: 10.1007/978-1-4939-7795-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
We have developed a biomaterials interface that allows the properties of a functionalized surface to be controlled by a population of genetically engineered bacteria. This interface was engineered by linking a genetically modified E. coli strain with a chemically functionalized surface. Critically, the E. coli was engineered to upregulate the production of biotin when induced by a small signaling molecule. This biotin would then interact with the functionalized surface to modulate the surface's binding dynamics. In this chapter, we detail three protocols: one protocol for developing a population of biotin-producing genetically engineered cells, and two protocols for creating different types of functionalized surfaces. These methods will enable scientists to readily explore strategies for controlling surface-based material assembly and modification using a linked culture of engineered cells.
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Affiliation(s)
- Keith C Heyde
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Warren C Ruder
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA.
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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Chen F, Wegner SV. Blue Light Switchable Bacterial Adhesion as a Key Step toward the Design of Biofilms. ACS Synth Biol 2017; 6:2170-2174. [PMID: 28803472 DOI: 10.1021/acssynbio.7b00197] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The control of where and when bacteria adhere to a substrate is a key step toward controlling the formation and organization in biofilms. This study shows how we engineer bacteria to adhere specifically to substrates with high spatial and temporal control under blue light, but not in the dark, by using photoswitchable interaction between nMag and pMag proteins. For this, we express pMag proteins on the surface of E. coli so that the bacteria can adhere to substrates with immobilized nMag protein under blue light. These adhesions are reversible in the dark and can be repeatedly turned on and off. Further, the number of bacteria that can adhere to the substrate as well as the attachment and detachment dynamics are adjustable by using different point mutants of pMag and altering light intensity. Overall, the blue light switchable bacteria adhesions offer reversible, tunable and bioorthogonal control with exceptional spatial and temporal resolution. This enables us to pattern bacteria on substrates with great flexibility.
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Affiliation(s)
- Fei Chen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Seraphine V. Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Samodelov SL, Zurbriggen MD. Quantitatively Understanding Plant Signaling: Novel Theoretical-Experimental Approaches. TRENDS IN PLANT SCIENCE 2017; 22:685-704. [PMID: 28668509 DOI: 10.1016/j.tplants.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
With the need to respond to and integrate a multitude of external and internal stimuli, plant signaling is highly complex, exhibiting signaling component redundancy and high interconnectedness between individual pathways. We review here novel theoretical-experimental approaches in manipulating plant signaling towards the goal of a comprehensive understanding and targeted quantitative control of plant processes. We highlight approaches taken in the field of synthetic biology used in other systems and discuss their applicability in plants. Finally, we introduce existing tools for the quantitative analysis and monitoring of plant signaling and the integration of experimentally obtained quantitative data into mathematical models. Incorporating principles of synthetic biology into plant sciences more widely will lead this field forward in both fundamental and applied research.
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Affiliation(s)
- Sophia L Samodelov
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany.
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9
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Heyde KC, Scott FY, Paek SH, Zhang R, Ruder WC. Using Synthetic Biology to Engineer Living Cells That Interface with Programmable Materials. J Vis Exp 2017. [PMID: 28362372 DOI: 10.3791/55300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We have developed an abiotic-biotic interface that allows engineered cells to control the material properties of a functionalized surface. This system is made by creating two modules: a synthetically engineered strain of E. coli cells and a functionalized material interface. Within this paper, we detail a protocol for genetically engineering selected behaviors within a strain of E. coli using molecular cloning strategies. Once developed, this strain produces elevated levels of biotin when exposed to a chemical inducer. Additionally, we detail protocols for creating two different functionalized surfaces, each of which is able to respond to cell-synthesized biotin. Taken together, we present a methodology for creating a linked, abiotic-biotic system that allows engineered cells to control material composition and assembly on nonliving substrates.
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Affiliation(s)
- Keith C Heyde
- Department of Mechanical Engineering, Carnegie Mellon University; Engineering Science and Mechanics Program, Virginia Polytechnic Institute and State University
| | - Felicia Y Scott
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University
| | - Sung-Ho Paek
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University
| | - Ruihua Zhang
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University
| | - Warren C Ruder
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University; Department of Bioengineering, University of Pittsburgh;
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