1
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Laurent JM, Jain A, Kan A, Steinacher M, Enrriquez Casimiro N, Stavrakis S, deMello AJ, Studart AR. Directed evolution of material-producing microorganisms. Proc Natl Acad Sci U S A 2024; 121:e2403585121. [PMID: 39042685 PMCID: PMC11295069 DOI: 10.1073/pnas.2403585121] [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: 02/21/2024] [Accepted: 06/20/2024] [Indexed: 07/25/2024] Open
Abstract
Nature is home to a variety of microorganisms that create materials under environmentally friendly conditions. While this offers an attractive approach for sustainable manufacturing, the production of materials by native microorganisms is usually slow and synthetic biology tools to engineer faster microorganisms are only available when prior knowledge of genotype-phenotype links is available. Here, we utilize a high-throughput directed evolution platform to enhance the fitness of whole microorganisms under selection pressure and identify genetic pathways to enhance the material production capabilities of native species. Using Komagataeibacter sucrofermentans as a model cellulose-producing microorganism, we show that our droplet-based microfluidic platform enables the directed evolution of these bacteria toward a small number of cellulose overproducers from an initial pool of 40,000 random mutants. Sequencing of the evolved strains reveals an unexpected link between the cellulose-forming ability of the bacteria and a gene encoding a protease complex responsible for protein turnover in the cell. The ability to enhance the fitness of microorganisms toward a specific phenotype and to unravel genotype-phenotype links makes this high-throughput directed evolution platform a promising tool for the development of new strains for the sustainable manufacturing of materials.
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Affiliation(s)
- Julie M. Laurent
- Department of Materials, Complex Materials, ETH Zürich, Zürich8093, Switzerland
| | - Ankit Jain
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich8093, Switzerland
| | - Anton Kan
- Department of Materials, Complex Materials, ETH Zürich, Zürich8093, Switzerland
| | - Mathias Steinacher
- Department of Materials, Complex Materials, ETH Zürich, Zürich8093, Switzerland
| | | | - Stavros Stavrakis
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich8093, Switzerland
| | - Andrew J. deMello
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich8093, Switzerland
| | - André R. Studart
- Department of Materials, Complex Materials, ETH Zürich, Zürich8093, Switzerland
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2
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Wang H, Tao J, Wu Z, Weiland K, Wang Z, Masania K, Wang B. Fabrication of Living Entangled Network Composites Enabled by Mycelium. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309370. [PMID: 38477443 PMCID: PMC11200020 DOI: 10.1002/advs.202309370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/19/2024] [Indexed: 03/14/2024]
Abstract
Organic polymer-based composite materials with favorable mechanical performance and functionalities are keystones to various modern industries; however, the environmental pollution stemming from their processing poses a great challenge. In this study, by finding an autonomous phase separating ability of fungal mycelium, a new material fabrication approach is introduced that leverages such biological metabolism-driven, mycelial growth-induced phase separation to bypass high-energy cost and labor-intensive synthetic methods. The resulting self-regenerative composites, featuring an entangled network structure of mycelium and assembled organic polymers, exhibit remarkable self-healing properties, being capable of reversing complete separation and restoring ≈90% of the original strength. These composites further show exceptional mechanical strength, with a high specific strength of 8.15 MPa g.cm-3, and low water absorption properties (≈33% after 15 days of immersion). This approach spearheads the development of state-of-the-art living composites, which directly utilize bioactive materials to "self-grow" into materials endowed with exceptional mechanical and functional properties.
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Affiliation(s)
- Hao Wang
- Department of Mechanical EngineeringCity University of Hong KongKowloonHong Kong
- Shaping Matter LabFaculty of Aerospace EngineeringDelft University of TechnologyDelft2629 HSNetherlands
| | - Jie Tao
- School of Materials Science and TechnologyNanjing University of Aeronautics and AstronauticsNanjingJiangsu211106China
| | - Zhangyu Wu
- School of Materials Science and EngineeringSoutheast UniversityNanjing211189China
| | - Kathrin Weiland
- Shaping Matter LabFaculty of Aerospace EngineeringDelft University of TechnologyDelft2629 HSNetherlands
| | - Zuankai Wang
- Department of Mechanical EngineeringThe Hong Kong Polytechnic UniversityHung HomKowloonHong Kong
| | - Kunal Masania
- Shaping Matter LabFaculty of Aerospace EngineeringDelft University of TechnologyDelft2629 HSNetherlands
| | - Bin Wang
- Department of Mechanical EngineeringCity University of Hong KongKowloonHong Kong
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3
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Jones EM, Marken JP, Silver PA. Synthetic microbiology in sustainability applications. Nat Rev Microbiol 2024; 22:345-359. [PMID: 38253793 DOI: 10.1038/s41579-023-01007-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.
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Affiliation(s)
- Ethan M Jones
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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4
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Graham AJ, Partipilo G, Dundas CM, Miniel Mahfoud IE, Halwachs KN, Holwerda AJ, Simmons TR, FitzSimons TM, Coleman SM, Rinehart R, Chiu D, Tyndall AE, Sajbel KC, Rosales AM, Keitz BK. Transcriptional regulation of living materials via extracellular electron transfer. Nat Chem Biol 2024:10.1038/s41589-024-01628-y. [PMID: 38783133 DOI: 10.1038/s41589-024-01628-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Engineered living materials combine the advantages of biological and synthetic systems by leveraging genetic and metabolic programming to control material-wide properties. Here, we demonstrate that extracellular electron transfer (EET), a microbial respiration process, can serve as a tunable bridge between live cell metabolism and synthetic material properties. In this system, EET flux from Shewanella oneidensis to a copper catalyst controls hydrogel cross-linking via two distinct chemistries to form living synthetic polymer networks. We first demonstrate that synthetic biology-inspired design rules derived from fluorescence parameterization can be applied toward EET-based regulation of polymer network mechanics. We then program transcriptional Boolean logic gates to govern EET gene expression, which enables design of computational polymer networks that mechanically respond to combinations of molecular inputs. Finally, we control fibroblast morphology using EET as a bridge for programmed material properties. Our results demonstrate how rational genetic circuit design can emulate physiological behavior in engineered living materials.
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Affiliation(s)
- Austin J Graham
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Christopher M Dundas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Ismar E Miniel Mahfoud
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA
| | - Kathleen N Halwachs
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Alexis J Holwerda
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA
| | - Trevor R Simmons
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Thomas M FitzSimons
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Sarah M Coleman
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Rebecca Rinehart
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Darian Chiu
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Avery E Tyndall
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, USA
| | - Kenneth C Sajbel
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA.
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5
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Altin-Yavuzarslan G, Sadaba N, Brooks SM, Alper HS, Nelson A. Engineered Living Material Bioreactors with Tunable Mechanical Properties using Vat Photopolymerization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306564. [PMID: 38105580 DOI: 10.1002/smll.202306564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/29/2023] [Indexed: 12/19/2023]
Abstract
3D-printed engineered living materials (ELM) are promising bioproduction platforms for agriculture, biotechnology, sustainable energy, and green technology applications. However, the design of these platforms faces several challenges, such as the processability of these materials into complex form factors and control over their mechanical properties. Herein, ELM are presented as 3D-printed bioreactors with arbitrary shape geometries and tunable mechanical properties (moduli and toughness). Poly(ethylene glycol) diacrylate (PEGDA) is used as the precursor to create polymer networks that encapsulate the microorganisms during the vat photopolymerization process. A major limitation of PEGDA networks is their propensity to swell and fracture when submerged in water. The authors overcame this issue by adding glycerol to the resin formulation to 3D print mechanically tough ELM hydrogels. While polymer concentration affects the modulus and reduces bioproduction, ELM bioreactors still maintain their metabolic activity regardless of polymer concentration. These ELM bioreactors have the potential to be used in different applications for sustainable architecture, food production, and biomedical devices that require different mechanical properties from soft to stiff.
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Affiliation(s)
- Gokce Altin-Yavuzarslan
- Molecular Engineering and Sciences Institute, University of Washington, Box 351700, Seattle, WA, 98195, USA
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195, USA
| | - Naroa Sadaba
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195, USA
| | - Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Hal S Alper
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Alshakim Nelson
- Molecular Engineering and Sciences Institute, University of Washington, Box 351700, Seattle, WA, 98195, USA
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195, USA
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6
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Lee MS, Lee JA, Biondo JR, Lux JE, Raig RM, Berger PN, Bernhards CB, Kuhn DL, Gupta MK, Lux MW. Cell-Free Protein Expression in Polymer Materials. ACS Synth Biol 2024; 13:1152-1164. [PMID: 38467017 PMCID: PMC11036507 DOI: 10.1021/acssynbio.3c00628] [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: 10/12/2023] [Revised: 01/26/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024]
Abstract
While synthetic biology has advanced complex capabilities such as sensing and molecular synthesis in aqueous solutions, important applications may also be pursued for biological systems in solid materials. Harsh processing conditions used to produce many synthetic materials such as plastics make the incorporation of biological functionality challenging. One technology that shows promise in circumventing these issues is cell-free protein synthesis (CFPS), where core cellular functionality is reconstituted outside the cell. CFPS enables genetic functions to be implemented without the complications of membrane transport or concerns over the cellular viability or release of genetically modified organisms. Here, we demonstrate that dried CFPS reactions have remarkable tolerance to heat and organic solvent exposure during the casting processes for polymer materials. We demonstrate the utility of this observation by creating plastics that have spatially patterned genetic functionality, produce antimicrobials in situ, and perform sensing reactions. The resulting materials unlock the potential to deliver DNA-programmable biofunctionality in a ubiquitous class of synthetic materials.
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Affiliation(s)
- Marilyn S. Lee
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Jennifer A. Lee
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
- Defense
Threat Reduction Agency, 2800 Bush River Road, Gunpowder, Maryland 21010, United States
| | - John R. Biondo
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
- Excet
Inc., 6225 Brandon Avenue,
Suite 360, Springfield, Virginia 22150, United States
| | - Jeffrey E. Lux
- US
Air Force Research Laboratory, 2179 12th Street, B652/R122, Wright-Patterson Air Force Base, Ohio 45433, United States
- UES
Inc., 4401 Dayton-Xenia
Road, Dayton, Ohio 45432, United States
| | - Rebecca M. Raig
- US
Air Force Research Laboratory, 2179 12th Street, B652/R122, Wright-Patterson Air Force Base, Ohio 45433, United States
- UES
Inc., 4401 Dayton-Xenia
Road, Dayton, Ohio 45432, United States
| | - Pierce N. Berger
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Casey B. Bernhards
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Danielle L. Kuhn
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Maneesh K. Gupta
- US
Air Force Research Laboratory, 2179 12th Street, B652/R122, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Matthew W. Lux
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
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7
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Herdman M, Isbilir B, von Kügelgen A, Schulze U, Wainman A, Bharat TAM. Cell cycle dependent coordination of surface layer biogenesis in Caulobacter crescentus. Nat Commun 2024; 15:3355. [PMID: 38637514 PMCID: PMC11026435 DOI: 10.1038/s41467-024-47529-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Surface layers (S-layers) are proteinaceous, two-dimensional paracrystalline arrays that constitute a major component of the cell envelope in many prokaryotic species. In this study, we investigated S-layer biogenesis in the bacterial model organism Caulobacter crescentus. Fluorescence microscopy revealed localised incorporation of new S-layer at the poles and mid-cell, consistent with regions of cell growth in the cell cycle. Light microscopy and electron cryotomography investigations of drug-treated bacteria revealed that localised S-layer insertion is retained when cell division is inhibited, but is disrupted upon dysregulation of MreB or lipopolysaccharide. We further uncovered that S-layer biogenesis follows new peptidoglycan synthesis and localises to regions of high cell wall turnover. Finally, correlated cryo-light microscopy and electron cryotomographic analysis of regions of S-layer insertion showed the presence of discontinuities in the hexagonal S-layer lattice, contrasting with other S-layers completed by defined symmetric defects. Our findings present insights into how C. crescentus cells form an ordered S-layer on their surface in coordination with the biogenesis of other cell envelope components.
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Affiliation(s)
- Matthew Herdman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Buse Isbilir
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Ulrike Schulze
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Alan Wainman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
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8
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Zhu R, Zhang J, Wang L, Zhang Y, Zhao Y, Han Y, Sun J, Zhang X, Dou Y, Yao H, Yan W, Luo X, Dai J, Dai Z. Engineering functional materials through bacteria-assisted living grafting. Cell Syst 2024; 15:264-274.e9. [PMID: 38460522 DOI: 10.1016/j.cels.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 09/15/2023] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
Functionalizing materials with biomacromolecules such as enzymes has broad applications in biotechnology and biomedicine. Here, we introduce a grafting method mediated by living cells to functionalize materials. We use polymeric scaffolds to trap engineered bacteria and micron-sized particles with chemical groups serving as active sites for grafting. The bacteria synthesize the desired protein for grafting and autonomously lyse to release it. The released functional moieties are locally grafted onto the active sites, generating the materials engineered by living grafting (MELGs). MELGs are resilient to perturbations because of both the bonding and the regeneration of functional domains synthesized by living cells. The programmability of the bacteria enables us to fabricate MELGs that can respond to external input, decompose a pollutant, reconstitute synthetic pathways for natural product synthesis, and purify mismatched DNA. Our work establishes a bacteria-assisted grafting strategy to functionalize materials with a broad range of biological activities in an integrated, flexible, and modular manner. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Runtao Zhu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiao Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lin Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunfeng Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yang Zhao
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ying Han
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jing Sun
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xi Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ying Dou
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Huaxiong Yao
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei Yan
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaozhou Luo
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Junbiao Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhuojun Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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9
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Xie Q, On Lee S, Vissamsetti N, Guo S, Johnson ME, Fried SD. Secretion-Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface. Angew Chem Int Ed Engl 2023; 62:e202305178. [PMID: 37469298 DOI: 10.1002/anie.202305178] [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: 04/12/2023] [Revised: 06/28/2023] [Accepted: 07/18/2023] [Indexed: 07/21/2023]
Abstract
Protein-based biomaterials have played a key role in tissue engineering, and additional exciting applications as self-healing materials and sustainable polymers are emerging. Over the past few decades, recombinant expression and production of various fibrous proteins from microbes have been demonstrated; however, the resulting proteins typically must then be purified and processed by humans to form usable fibers and materials. Here, we show that the Gram-positive bacterium Bacillus subtilis can be programmed to secrete silk through its translocon via an orthogonal signal peptide/peptidase pair. Surprisingly, we discover that this translocation mechanism drives the silk proteins to assemble into fibers spontaneously on the cell surface, in a process we call secretion-catalyzed assembly (SCA). Secreted silk fibers form self-healing hydrogels with minimal processing. Alternatively, the fibers retained on the membrane provide a facile route to create engineered living materials from Bacillus cells. This work provides a blueprint to achieve autonomous assembly of protein biomaterials in useful morphologies directly from microbial factories.
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Affiliation(s)
- Qi Xie
- Department of Chemistry, Johns Hopkins University, 21218, Baltimore, MD, USA
| | - Sea On Lee
- Department of Chemistry, Johns Hopkins University, 21218, Baltimore, MD, USA
| | - Nitya Vissamsetti
- Department of Chemistry, Johns Hopkins University, 21218, Baltimore, MD, USA
| | - Sikao Guo
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 21218, Baltimore, MD, USA
| | - Margaret E Johnson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 21218, Baltimore, MD, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, 21218, Baltimore, MD, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 21218, Baltimore, MD, USA
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10
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Lin AJ, Sihorwala AZ, Belardi B. Engineering Tissue-Scale Properties with Synthetic Cells: Forging One from Many. ACS Synth Biol 2023; 12:1889-1907. [PMID: 37417657 PMCID: PMC11017731 DOI: 10.1021/acssynbio.3c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
In metazoans, living cells achieve capabilities beyond individual cell functionality by assembling into multicellular tissue structures. These higher-order structures represent dynamic, heterogeneous, and responsive systems that have evolved to regenerate and coordinate their actions over large distances. Recent advances in constructing micrometer-sized vesicles, or synthetic cells, now point to a future where construction of synthetic tissue can be pursued, a boon to pressing material needs in biomedical implants, drug delivery systems, adhesives, filters, and storage devices, among others. To fully realize the potential of synthetic tissue, inspiration has been and will continue to be drawn from new molecular findings on its natural counterpart. In this review, we describe advances in introducing tissue-scale features into synthetic cell assemblies. Beyond mere complexation, synthetic cells have been fashioned with a variety of natural and engineered molecular components that serve as initial steps toward morphological control and patterning, intercellular communication, replication, and responsiveness in synthetic tissue. Particular attention has been paid to the dynamics, spatial constraints, and mechanical strengths of interactions that drive the synthesis of this next-generation material, describing how multiple synthetic cells can act as one.
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Affiliation(s)
- Alexander J Lin
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ahmed Z Sihorwala
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian Belardi
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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11
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An B, Wang Y, Huang Y, Wang X, Liu Y, Xun D, Church GM, Dai Z, Yi X, Tang TC, Zhong C. Engineered Living Materials For Sustainability. Chem Rev 2023; 123:2349-2419. [PMID: 36512650 DOI: 10.1021/acs.chemrev.2c00512] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.
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Affiliation(s)
- Bolin An
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yanyi Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuanyuan Huang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xinyu Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuzhu Liu
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dongmin Xun
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - George M Church
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Zhuojun Dai
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiao Yi
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tzu-Chieh Tang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Chao Zhong
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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12
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Synchronized Swarmers and Sticky Stalks: Caulobacter crescentus as a Model for Bacterial Cell Biology. J Bacteriol 2023; 205:e0038422. [PMID: 36715542 PMCID: PMC9945503 DOI: 10.1128/jb.00384-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
First isolated and classified in the 1960s, Caulobacter crescentus has been instrumental in the study of bacterial cell biology and differentiation. C. crescentus is a Gram-negative alphaproteobacterium that exhibits a dimorphic life cycle composed of two distinct cell types: a motile swarmer cell and a nonmotile, division-competent stalked cell. Progression through the cell cycle is accentuated by tightly controlled biogenesis of appendages, morphological transitions, and distinct localization of developmental regulators. These features as well as the ability to synchronize populations of cells and follow their progression make C. crescentus an ideal model for answering questions relevant to how development and differentiation are achieved at the single-cell level. This review will explore the discovery and development of C. crescentus as a model organism before diving into several key features and discoveries that have made it such a powerful organism to study. Finally, we will summarize a few of the ongoing areas of research that are leveraging knowledge gained over the last century with C. crescentus to highlight its continuing role at the forefront of cell and developmental biology.
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13
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Mehta HH, Song X, Shamoo Y. Intracellular Experimental Evolution of Francisella tularensis Subsp. holarctica Live Vaccine Strain (LVS) to Antimicrobial Resistance. ACS Infect Dis 2023; 9:308-321. [PMID: 36662533 PMCID: PMC9996545 DOI: 10.1021/acsinfecdis.2c00483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In vitro experimental evolution has complemented clinical studies as an excellent tool to identify genetic changes responsible for the de novo evolution of antimicrobial resistance. However, the in vivo context for adaptation contributes to the success of particular evolutionary trajectories, especially in intracellular niches where the adaptive landscape of virulence and resistance are strongly coupled. In this work, we designed an ex vivo evolution approach to identify evolutionary trajectories responsible for antibiotic resistance in the Live Vaccine Strain (LVS) of Francisella tularensis subsp. holarctica while being passaged to increasing ciprofloxacin (CIP) and doxycycline (DOX) concentrations within macrophages. Overall, adaptation within macrophages advanced much slower when compared to previous in vitro evolution studies reflecting a limiting capacity for the expansion of adaptive mutations within the macrophage. Longitudinal genomic analysis identified resistance conferring gyrase mutations outside the Quinolone Resistance Determining Region. Strikingly, FupA/B mutations that are uniquely associated with in vitro CIP resistance in Francisella were not observed ex vivo, reflecting the coupling of intracellular survival and resistance during intracellular adaptation. To our knowledge, this is the first experimental study demonstrating the ability to conduct experimental evolution to antimicrobial resistance within macrophages. The results provide evidence of differences in mutational profiles of populations adapted to the same antibiotic in different environments/cellular compartments and underscore the significance of host mediated stress during resistance evolution.
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Affiliation(s)
- Heer H Mehta
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Xinhao Song
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
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14
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Binelli MR, Kan A, Rozas LEA, Pisaturo G, Prakash N, Studart AR. Complex Living Materials Made by Light-Based Printing of Genetically Programmed Bacteria. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207483. [PMID: 36444840 DOI: 10.1002/adma.202207483] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/23/2022] [Indexed: 06/16/2023]
Abstract
Living materials with embedded microorganisms can genetically encode attractive sensing, self-repairing, and responsive functionalities for applications in medicine, robotics, and infrastructure. While the synthetic toolbox for genetically engineering bacteria continues to expand, technologies to shape bacteria-laden living materials into complex 3D geometries are still rather limited. Here, it is shown that bacteria-laden hydrogels can be shaped into living materials with unusual architectures and functionalities using readily available light-based printing techniques. Bioluminescent and melanin-producing bacteria are used to create complex materials with autonomous chemical-sensing capabilities by harnessing the metabolic activity of wild-type and engineered microorganisms. The shaping freedom offered by printing technologies and the rich biochemical diversity available in bacteria provides ample design space for the creation and exploration of complex living materials with programmable functionalities for a broad range of applications.
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Affiliation(s)
- Marco R Binelli
- Complex Materials, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, Zürich, 8093, Switzerland
| | - Anton Kan
- Complex Materials, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, Zürich, 8093, Switzerland
| | - Luis E A Rozas
- Complex Materials, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, Zürich, 8093, Switzerland
| | - Giovanni Pisaturo
- Complex Materials, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, Zürich, 8093, Switzerland
| | - Namita Prakash
- Complex Materials, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, Zürich, 8093, Switzerland
| | - André R Studart
- Complex Materials, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, Zürich, 8093, Switzerland
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15
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Engineering Mechanical Strong Biomaterials Inspired by Structural Building Blocks in Nature. Chem Res Chin Univ 2023. [DOI: 10.1007/s40242-023-2357-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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