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Liu W, Sun W, Liang C, Chen T, Zhuang W, Liu D, Chen Y, Ying H. Escherichia coli Surface Display: Advances and Applications in Biocatalysis. ACS Synth Biol 2025; 14:648-661. [PMID: 40047247 DOI: 10.1021/acssynbio.4c00793] [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: 03/22/2025]
Abstract
Escherichia coli surface display technology, which facilitates the stable display of target peptides and proteins on the bacterial surface through fusion with anchor proteins, has become a potent and versatile tool in biotechnology and biomedicine. The E. coli surface display strategy presents a unique alternative to classic intracellular and extracellular expression systems, facilitating the anchorage of target peptides and proteins on the cell surface for functional execution. This distinctive attribute also introduces a novel paradigm in the realm of biocatalysis, harnessing cells with surface-displayed enzymes to catalyze the conversion of substrates. This strategy effectively eliminates the requirement for enzyme purification, overcomes the limitations related to substrate transmembrane transport, improves enzyme activity and stability, and greatly reduces the cost of downstream product purification, thus making it widely used in biocatalysis. Here, we review recent advances in various surface display systems and surface display technology for biocatalytic applications. Additionally, we discuss the current limitations of this technology and several promising alternative display methods.
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Affiliation(s)
- Wei Liu
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Wenjun Sun
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - CaiCe Liang
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Tianpeng Chen
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Wei Zhuang
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Dong Liu
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Yong Chen
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Hanjie Ying
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- Soochow University, Suzhou, Jiangsu 215123, P.R. China
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2
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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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3
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Raj V, Raorane CJ, Shastri D, Kim SC, Lee S. Engineering a self-healing grafted chitosan-sodium alginate based hydrogel with potential keratinocyte cell migration property and inhibitory effect against fluconazole resistance Candida albicans biofilm. Int J Biol Macromol 2024; 261:129774. [PMID: 38286383 DOI: 10.1016/j.ijbiomac.2024.129774] [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: 11/02/2023] [Revised: 01/08/2024] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
Biofilms developed by microorganisms cause an extremely severe clinical problem that leads to drug failure. Bioactive polymeric hydrogels display potential for controlling the formation of microorganism-based biofilms, but their rapid biodegradability in these biofilm sites is still a major challenge. To overcome this, chitosan (CS), a natural functional biomaterial, has been used because of its effective penetrability in the cell wall of microorganisms; however, its fast biodegradability has restricted its further use. Hence, in this study, to improve the stability of CS and increase its penetration retention inside a biofilm, grafted CS was prepared and then crosslinked with sodium alginate (SA) to synthesize CS-poly(MA-co-AA)SA hydrogel via a free radical grafting method, therefore enhancing its antibiofilm efficiency against biofilms. The prepared hydrogel demonstrated excellent effectiveness against (≥90 % inhibition) biofilms of Candida albicans. Additionally, in vitro and in vivo safety assays established that the prepared hydrogel can be used in a biofilm microenvironment and might reduce drug resistance burden owing to its long-term antibiofilm effect and improved CS stability at the biofilm site. Furthermore, in vitro wound healing outcomes of hydrogel indicated its potential application for chronic wound treatment. This research opens a new advanced strategy for biofilm-associated infection treatment, including wound treatment.
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Affiliation(s)
- Vinit Raj
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, Republic of Korea
| | | | - Divya Shastri
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, Republic of Korea; College of Pharmacy, Keimyung University, 1095 Dalgubeol-daero, Dalseo-Gu, Daegu, 42601, Republic of Korea
| | - Seong Cheol Kim
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea.
| | - Sangkil Lee
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, Republic of Korea.
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4
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Gilmour KA, Aljannat M, Markwell C, James P, Scott J, Jiang Y, Torun H, Dade-Robertson M, Zhang M. Biofilm inspired fabrication of functional bacterial cellulose through ex-situ and in-situ approaches. Carbohydr Polym 2023; 304:120482. [PMID: 36641190 DOI: 10.1016/j.carbpol.2022.120482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/11/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Bacterial cellulose (BC) has been explored for use in a range of applications including tissue engineering and textiles. BC can be produced from waste streams, but sustainable approaches are needed for functionalisation. To this end, BslA, a B. subtilis biofilm protein was produced recombinantly with and without a cellulose binding module (CBM) and the cell free extract was used to treat BC either ex-situ, through drip coating or in-situ, by incorporating during fermentation. The results showed that ex-situ modified BC increased the hydrophobicity and water contact angle reached 120°. In-situ experiments led to a BC film morphological change and mechanical testing demonstrated that addition of BslA with CBM resulted in a stronger, more elastic material. This study presents a nature inspired approach to functionalise BC using a biofilm hydrophobin, and we demonstrate that recombinant proteins could be effective and sustainable molecules for functionalisation of BC materials.
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Affiliation(s)
- Katie A Gilmour
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University at Newcastle, NE1 8ST, UK.
| | - Mahab Aljannat
- Hub for Biotechnology in the Built Environment, School of Architecture, Planning and Landscape, Newcastle University, NE1 7RU, UK.
| | - Christopher Markwell
- Department of Applied Sciences, Northumbria University at Newcastle, NE1 8ST, UK.
| | - Paul James
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University at Newcastle, NE1 8ST, UK.
| | - Jane Scott
- Hub for Biotechnology in the Built Environment, School of Architecture, Planning and Landscape, Newcastle University, NE1 7RU, UK.
| | - Yunhong Jiang
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University at Newcastle, NE1 8ST, UK.
| | - Hamdi Torun
- Department of Mathematics, Physics and Electrical Engineering, Faculty of Environment and Engineering, Northumbria University at Newcastle, NE1 8ST, UK.
| | - Martyn Dade-Robertson
- Hub for Biotechnology in the Built Environment, School of Architecture, Planning and Landscape, Newcastle University, NE1 7RU, UK.
| | - Meng Zhang
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University at Newcastle, NE1 8ST, UK.
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5
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Dong H, Zhang W, Zhou S, Ying H, Wang P. Rational Design of Artificial Biofilms as Sustainable Supports for Whole-Cell Catalysis Through Integrating Extra- and Intracellular Catalysis. CHEMSUSCHEM 2022; 15:e202200850. [PMID: 35726119 PMCID: PMC9543694 DOI: 10.1002/cssc.202200850] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/13/2022] [Indexed: 05/31/2023]
Abstract
Biofilms are promising candidates for sustainable bioprocessing applications. This work presents a rational design of biofilm catalysts by integrating extra- and intracellular catalysis systems with optimized substrate channeling to realize efficient multistep biosynthesis. An assembly of four enzymes in a "three-in-one" structure was achieved by rationally placing the enzymes on curli nanofibers, the cell surface, and inside cells. The catalytic efficiency of the biofilm catalysts was over 2.8 folds higher than that of the control whole-cell catalysis when the substrate benzaldehyde was fed at 100 mm. The highest yield of d-phenyllactic acid catalyzed by biofilm catalysts under optimized conditions was 102.19 mm, also much higher than that of the control catalysis test (52.29 mm). The results demonstrate that engineered biofilms are greatly promising in integrating extra- and intracellular catalysis, illustrating great potentials of rational design in constructing biofilm catalysts as sustainable supports for whole-cell catalysis.
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Affiliation(s)
- Hao Dong
- 1 State Key Laboratory of Bioreactor EngineeringSchool of BiotechnologyEast China University of Science and TechnologyShanghai200237P. R. China
- College of Food Science and EngineeringOcean University of ChinaQingdao266003P. R. China
| | - Wenxue Zhang
- 1 State Key Laboratory of Bioreactor EngineeringSchool of BiotechnologyEast China University of Science and TechnologyShanghai200237P. R. China
| | - Shengmin Zhou
- 1 State Key Laboratory of Bioreactor EngineeringSchool of BiotechnologyEast China University of Science and TechnologyShanghai200237P. R. China
| | - Hanjie Ying
- National Engineering Research Center for BiotechnologyNanjing Tech UniversityNO.30 Puzhu Road(S)NanjingJS 211816P. R. China
| | - Ping Wang
- 1 State Key Laboratory of Bioreactor EngineeringSchool of BiotechnologyEast China University of Science and TechnologyShanghai200237P. R. China
- Department of Bioproducts and Biosystems EngineeringUniversity of MinnesotaSt. PaulMN 55108USA
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6
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Matilla-Cuenca L, Taglialegna A, Gil C, Toledo-Arana A, Lasa I, Valle J. Bacterial biofilm functionalization through Bap amyloid engineering. NPJ Biofilms Microbiomes 2022; 8:62. [PMID: 35909185 PMCID: PMC9339546 DOI: 10.1038/s41522-022-00324-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/01/2022] [Indexed: 11/09/2022] Open
Abstract
Biofilm engineering has emerged as a controllable way to fabricate living structures with programmable functionalities. The amyloidogenic proteins comprising the biofilms can be engineered to create self-assembling extracellular functionalized surfaces. In this regard, facultative amyloids, which play a dual role in biofilm formation by acting as adhesins in their native conformation and as matrix scaffolds when they polymerize into amyloid-like fibrillar structures, are interesting candidates. Here, we report the use of the facultative amyloid-like Bap protein of Staphylococcus aureus as a tool to decorate the extracellular biofilm matrix or the bacterial cell surface with a battery of functional domains or proteins. We demonstrate that the localization of the functional tags can be change by simply modulating the pH of the medium. Using Bap features, we build a tool for trapping and covalent immobilizing molecules at bacterial cell surface or at the biofilm matrix based on the SpyTag/SpyCatcher system. Finally, we show that the cell wall of several Gram-positive bacteria could be functionalized through the external addition of the recombinant engineered Bap-amyloid domain. Overall, this work shows a simple and modulable system for biofilm functionalization based on the facultative protein Bap.
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Affiliation(s)
| | - Agustina Taglialegna
- Instituto de Agrobiotecnología (IDAB). CSIC- Gobierno de Navarra, Mutilva, Spain.,The Campus 4 Crinan Street London N1, London, UK
| | - Carmen Gil
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | | | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Jaione Valle
- Instituto de Agrobiotecnología (IDAB). CSIC- Gobierno de Navarra, Mutilva, Spain.
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7
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Shi Y, Chen T, Shaw P, Wang PY. Manipulating Bacterial Biofilms Using Materiobiology and Synthetic Biology Approaches. Front Microbiol 2022; 13:844997. [PMID: 35875573 PMCID: PMC9301480 DOI: 10.3389/fmicb.2022.844997] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
Bacteria form biofilms on material surfaces within hours. Biofilms are often considered problematic substances in the fields such as biomedical devices and the food industry; however, they are beneficial in other fields such as fermentation, water remediation, and civil engineering. Biofilm properties depend on their genome and the extracellular environment, including pH, shear stress, and matrices topography, stiffness, wettability, and charges during biofilm formation. These surface properties have feedback effects on biofilm formation at different stages. Due to emerging technology such as synthetic biology and genome editing, many studies have focused on functionalizing biofilm for specific applications. Nevertheless, few studies combine these two approaches to produce or modify biofilms. This review summarizes up-to-date materials science and synthetic biology approaches to controlling biofilms. The review proposed a potential research direction in the future that can gain better control of bacteria and biofilms.
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Affiliation(s)
- Yue Shi
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tingli Chen
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Peter Shaw
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
| | - Peng-Yuan Wang
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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8
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Huyer C, Modafferi D, Aminzare M, Ferraro J, Abdali Z, Roy S, Saldanha DJ, Wasim S, Alberti J, Feng S, Cicoira F, Dorval Courchesne NM. Fabrication of Curli Fiber-PEDOT:PSS Biomaterials with Tunable Self-Healing, Mechanical, and Electrical Properties. ACS Biomater Sci Eng 2022; 9:2156-2169. [PMID: 35687654 DOI: 10.1021/acsbiomaterials.1c01180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Poly(3,4-ethylenedioxythiophene) polystyrenesulfonate (PEDOT:PSS) is a highly conductive, easily processable, self-healing polymer. It has been shown to be useful in bioelectronic applications, for instance, as a biointerfacing layer for studying brain activity, in biosensitive transistors, and in wearable biosensors. A green and biofriendly method for improving the mechanical properties, biocompatibility, and stability of PEDOT:PSS involves mixing the polymer with a biopolymer. Via structural changes and interactions with PEDOT:PSS, biopolymers have the potential to improve the self-healing ability, flexibility, and electrical conductivity of the composite. In this work, we fabricated novel protein-polymer multifunctional composites by mixing PEDOT:PSS with genetically programmable amyloid curli fibers produced byEscherichia coli bacteria. Curli fibers are among the stiffest protein polymers and, once isolated from bacterial biofilms, can form plastic-like thin films that heal with the addition of water. Curli-PEDOT:PSS composites containing 60% curli fibers exhibited a conductivity 4.5-fold higher than that of pristine PEDOT:PSS. The curli fibers imbued the biocomposites with an immediate water-induced self-healing ability. Further, the addition of curli fibers lowered the Young's and shear moduli of the composites, improving their compatibility for tissue-interfacing applications. Lastly, we showed that genetically engineered fluorescent curli fibers retained their ability to fluoresce within curli-PEDOT:PSS composites. Curli fibers thus allow to modulate a range of properties in conductive PEDOT:PSS composites, broadening the applications of this polymer in biointerfaces and bioelectronics.
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Affiliation(s)
- Catrina Huyer
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada.,Department of Chemical Engineering, Polytechnique Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Daniel Modafferi
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Masoud Aminzare
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Juliana Ferraro
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Zahra Abdali
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Sophia Roy
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Dalia Jane Saldanha
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Saadia Wasim
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Johan Alberti
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada.,Department of Chemical Engineering, Polytechnique Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Shurui Feng
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada.,Department of Chemical Engineering, Polytechnique Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Fabio Cicoira
- Department of Chemical Engineering, Polytechnique Montreal, Montreal, Quebec H3C 3J7, Canada
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9
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Li Z, Wang X, Wang J, Yuan X, Jiang X, Wang Y, Zhong C, Xu D, Gu T, Wang F. Bacterial biofilms as platforms engineered for diverse applications. Biotechnol Adv 2022; 57:107932. [DOI: 10.1016/j.biotechadv.2022.107932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 12/23/2022]
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10
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Dong H, Zhang W, Zhou S, Wang P. Programmable Biofilm-Cellulose Hybrid Platform for Specifically Clustering of Microbial Catalysts with Optimized Cellular Synergy. Chem Commun (Camb) 2022; 58:8222-8225. [DOI: 10.1039/d2cc02473j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A programmable biofilm-cellulose platform is constructed to facilitate the clustering of two Escherichia coli catalysts, which is promising to achieve an efficient transformation by bringing cells into close proximity. This...
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11
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Hernández‐Arriaga AM, Campano C, Rivero‐Buceta V, Prieto MA. When microbial biotechnology meets material engineering. Microb Biotechnol 2022; 15:149-163. [PMID: 34818460 PMCID: PMC8719833 DOI: 10.1111/1751-7915.13975] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
Bacterial biopolymers such as bacterial cellulose (BC), alginate or polyhydroxyalkanotes (PHAs) have aroused the interest of researchers in many fields, for instance biomedicine and packaging, due to their being biodegradable, biocompatible and renewable. Their properties can easily be tuned by means of microbial biotechnology strategies combined with materials science. This provides them with highly diverse properties, conferring them non-native features. Herein we highlight the enormous structural diversity of these macromolecules, how are they produced, as well as their wide range of potential applications in our daily lives. The emergence of new technologies, such as synthetic biology, enables the creation of next-generation-advanced materials presenting smart functional properties, for example the ability to sense and respond to stimuli as well as the capacity for self-repair. All this has given rise to the recent emergence of biohybrid materials, in which a synthetic component is brought to life with living organisms. Two different subfields have recently garnered particular attention: hybrid living materials (HLMs), such as encapsulation or bioprinting, and engineered living materials (ELMs), in which the material is created bottom-up with the use of microbial biotechnology tools. Early studies showed the strong potential of alginate and PHAs as HLMs, whilst BC constituted the most currently promising material for the creation of ELMs.
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Affiliation(s)
- Ana M. Hernández‐Arriaga
- Polymer Biotechnology Group, Department of Plant and Microbial BiotechnologyBiological Research Centre Margarita SalasSpanish National Research Council (CIB‐CSIC)MadridSpain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐CSIC (SusPlast‐CSIC)MadridSpain
| | - Cristina Campano
- Polymer Biotechnology Group, Department of Plant and Microbial BiotechnologyBiological Research Centre Margarita SalasSpanish National Research Council (CIB‐CSIC)MadridSpain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐CSIC (SusPlast‐CSIC)MadridSpain
| | - Virginia Rivero‐Buceta
- Polymer Biotechnology Group, Department of Plant and Microbial BiotechnologyBiological Research Centre Margarita SalasSpanish National Research Council (CIB‐CSIC)MadridSpain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐CSIC (SusPlast‐CSIC)MadridSpain
| | - M. Auxiliadora Prieto
- Polymer Biotechnology Group, Department of Plant and Microbial BiotechnologyBiological Research Centre Margarita SalasSpanish National Research Council (CIB‐CSIC)MadridSpain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐CSIC (SusPlast‐CSIC)MadridSpain
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12
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Konur S, Mierla L, Fellermann H, Ladroue C, Brown B, Wipat A, Twycross J, Dun BP, Kalvala S, Gheorghe M, Krasnogor N. Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation. ACS Synth Biol 2021; 10:1931-1945. [PMID: 34339602 DOI: 10.1021/acssynbio.1c00143] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present the Infobiotics Workbench (IBW), a user-friendly, scalable, and integrated computational environment for the computer-aided design of synthetic biological systems. It supports an iterative workflow that begins with specification of the desired synthetic system, followed by simulation and verification of the system in high-performance environments and ending with the eventual compilation of the system specification into suitable genetic constructs. IBW integrates modeling, simulation, verification, and biocompilation features into a single software suite. This integration is achieved through a new domain-specific biological programming language, the Infobiotics Language (IBL), which tightly combines these different aspects of in silico synthetic biology into a full-stack integrated development environment. Unlike existing synthetic biology modeling or specification languages, IBL uniquely blends modeling, verification, and biocompilation statements into a single file. This allows biologists to incorporate design constraints within the specification file rather than using decoupled and independent formalisms for different in silico analyses. This novel approach offers seamless interoperability across different tools as well as compatibility with SBOL and SBML frameworks and removes the burden of doing manual translations for standalone applications. We demonstrate the features, usability, and effectiveness of IBW and IBL using well-established synthetic biological circuits.
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Affiliation(s)
- Savas Konur
- Department of Computer Science, University of Bradford, Bradford, BD7 1DP, U.K
| | - Laurentiu Mierla
- Department of Computer Science, University of Bradford, Bradford, BD7 1DP, U.K
| | - Harold Fellermann
- Interdisciplinary Computing and Complex Biosystems Research Group, Newcastle University, Newcastle, NE1 7RU, U.K
| | - Christophe Ladroue
- Department of Computer Science, University of Warwick, Coventry, CV4 7AL, U.K
| | - Bradley Brown
- Interdisciplinary Computing and Complex Biosystems Research Group, Newcastle University, Newcastle, NE1 7RU, U.K
| | - Anil Wipat
- Interdisciplinary Computing and Complex Biosystems Research Group, Newcastle University, Newcastle, NE1 7RU, U.K
| | - Jamie Twycross
- School of Computer Science, University of Nottingham, Nottingham, NG8 1BB, U.K
| | - Boyang Peter Dun
- Department of Computer Science, Stanford University, Stanford, California 94305, United States
| | - Sara Kalvala
- Department of Computer Science, University of Warwick, Coventry, CV4 7AL, U.K
| | - Marian Gheorghe
- Department of Computer Science, University of Bradford, Bradford, BD7 1DP, U.K
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex Biosystems Research Group, Newcastle University, Newcastle, NE1 7RU, U.K
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13
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Gilbert C, Tang TC, Ott W, Dorr BA, Shaw WM, Sun GL, Lu TK, Ellis T. Living materials with programmable functionalities grown from engineered microbial co-cultures. NATURE MATERIALS 2021; 20:691-700. [PMID: 33432140 DOI: 10.1038/s41563-020-00857-5] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/14/2020] [Indexed: 05/14/2023]
Abstract
Biological systems assemble living materials that are autonomously patterned, can self-repair and can sense and respond to their environment. The field of engineered living materials aims to create novel materials with properties similar to those of natural biomaterials using genetically engineered organisms. Here, we describe an approach to fabricating functional bacterial cellulose-based living materials using a stable co-culture of Saccharomyces cerevisiae yeast and bacterial cellulose-producing Komagataeibacter rhaeticus bacteria. Yeast strains can be engineered to secrete enzymes into bacterial cellulose, generating autonomously grown catalytic materials and enabling DNA-encoded modification of bacterial cellulose bulk properties. Alternatively, engineered yeast can be incorporated within the growing cellulose matrix, creating living materials that can sense and respond to chemical and optical stimuli. This symbiotic culture of bacteria and yeast is a flexible platform for the production of bacterial cellulose-based engineered living materials with potential applications in biosensing and biocatalysis.
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Affiliation(s)
- Charlie Gilbert
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Tzu-Chieh Tang
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Mediated Matter Group, Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wolfgang Ott
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Brandon A Dorr
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William M Shaw
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - George L Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Timothy K Lu
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
- Department of Bioengineering, Imperial College London, London, UK.
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14
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Dong H, Zhang W, Xuan Q, Zhou Y, Zhou S, Huang J, Wang P. Binding Peptide-Guided Immobilization of Lipases with Significantly Improved Catalytic Performance Using Escherichia coli BL21(DE3) Biofilms as a Platform. ACS APPLIED MATERIALS & INTERFACES 2021; 13:6168-6179. [PMID: 33499600 DOI: 10.1021/acsami.0c18298] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Developing novel immobilization methods to maximize the catalytic performance of enzymes has been a permanent pursuit of scientific researchers. Engineered Escherichia coli biofilms have attracted great concern as surface display platforms for enzyme immobilization. However, current biological conjugation methods, such as the SpyTag/SpyCatcher tagging pair, that immobilize enzymes onto E. coli biofilms seriously hamper enzymatic performance. Through phage display screening of lipase-binding peptides (LBPs) and co-expression of CsgB (nucleation protein of curli nanofibers) and LBP2-modified CsgA (CsgALBP2, major structural subunit of curli nanofibers) proteins, we developed E. coli BL21::ΔCsgA-CsgB-CsgALBP2 (LBP2-functionalized) biofilms as surface display platforms to maximize the catalytic performance of lipase (Lip181). After immobilization onto LBP2-functionalized biofilm materials, Lip181 showed increased thermostability, pH, and storage stability. Surprisingly, the relative activity of immobilized Lip181 increased from 8.43 to 11.33 U/mg through this immobilization strategy. Furthermore, the highest loading of lipase on LBP2-functionalized biofilm materials reached up to 27.90 mg/g of wet biofilm materials, equivalent to 210.49 mg/g of dry biofilm materials, revealing their potential as a surface with high enzyme loading capacity. Additionally, immobilized Lip181 was used to hydrolyze phthalic acid esters, and the hydrolysis rate against dibutyl phthalate was up to 100%. Thus, LBP2-mediated immobilization of lipases was demonstrated to be far more advantageous than the traditional SpyTag/SpyCatcher strategy in maximizing enzymatic performance, thereby providing a better alternative for enzyme immobilization onto E. coli biofilms.
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Affiliation(s)
- Hao Dong
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Wenxue Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Qize Xuan
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Yao Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaofang Huang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, Minnesota 55108, USA
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15
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Abdali Z, Aminzare M, Zhu X, DeBenedictis E, Xie O, Keten S, Dorval Courchesne NM. Curli-Mediated Self-Assembly of a Fibrous Protein Scaffold for Hydroxyapatite Mineralization. ACS Synth Biol 2020; 9:3334-3343. [PMID: 33237760 DOI: 10.1021/acssynbio.0c00415] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nanostructures formed by self-assembled peptides have been increasingly exploited as functional materials for a wide variety of applications, from biotechnology to energy. However, it is sometimes challenging to assemble free short peptides into functional supramolecular structures, since not all peptides have the ability to self-assemble. Here, we report a self-assembly mechanism for short functional peptides that we derived from a class of fiber-forming amyloid proteins called curli. CsgA, the major subunit of curli fibers, is a self-assembling β-helical subunit composed of five pseudorepeats (R1-R5). We first deleted the internal repeats (R2, R3, R4), known to be less essential for the aggregation of CsgA monomers into fibers, forming a truncated CsgA variant (R1/R5). As a proof-of-concept to introduce functionality in the fibers, we then genetically substituted the internal repeats by a hydroxyapatite (HAP)-binding peptide, resulting in a R1/HAP/R5 construct. Our method thus utilizes the R1/R5-driven self-assembly mechanism to assemble the HAP-binding peptide and form hydrogel-like materials in macroscopic quantities suitable for biomineralization. We confirmed the expression and fibrillar morphology of the truncated and HAP-containing curli-like amyloid fibers. X-ray diffraction and TEM showed the functionality of the HAP-binding peptide for mineralization and formation of nanocrystalline HAP. Overall, we show that fusion to the R1 and R5 repeats of CsgA enables the self-assembly of functional peptides into micron long fibers. Further, the mineral-templating ability that the R1/HAP/R5 fibers possesses opens up broader applications for curli proteins in the tissue engineering and biomaterials fields.
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Affiliation(s)
- Zahra Abdali
- Department of Chemical Engineering, McGill University, Montréal, Québec H3A 0C5, Canada
| | - Masoud Aminzare
- Department of Chemical Engineering, McGill University, Montréal, Québec H3A 0C5, Canada
| | - Xiaodan Zhu
- Department of Chemical Engineering, McGill University, Montréal, Québec H3A 0C5, Canada
| | - Elizabeth DeBenedictis
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States of America
| | - Oliver Xie
- Department of Chemical Engineering, McGill University, Montréal, Québec H3A 0C5, Canada
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States of America
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16
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Grobas I, Bazzoli DG, Asally M. Biofilm and swarming emergent behaviours controlled through the aid of biophysical understanding and tools. Biochem Soc Trans 2020; 48:2903-2913. [PMID: 33300966 PMCID: PMC7752047 DOI: 10.1042/bst20200972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023]
Abstract
Bacteria can organise themselves into communities in the forms of biofilms and swarms. Through chemical and physical interactions between cells, these communities exhibit emergent properties that individual cells alone do not have. While bacterial communities have been mainly studied in the context of biochemistry and molecular biology, recent years have seen rapid advancements in the biophysical understanding of emergent phenomena through physical interactions in biofilms and swarms. Moreover, new technologies to control bacterial emergent behaviours by physical means are emerging in synthetic biology. Such technologies are particularly promising for developing engineered living materials (ELM) and devices and controlling contamination and biofouling. In this minireview, we overview recent studies unveiling physical and mechanical cues that trigger and affect swarming and biofilm development. In particular, we focus on cell shape, motion and density as the key parameters for mechanical cell-cell interactions within a community. We then showcase recent studies that use physical stimuli for patterning bacterial communities, altering collective behaviours and preventing biofilm formation. Finally, we discuss the future potential extension of biophysical and bioengineering research on microbial communities through computational modelling and deeper investigation of mechano-electrophysiological coupling.
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Affiliation(s)
- Iago Grobas
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, U.K
| | - Dario G. Bazzoli
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, U.K
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, U.K
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K
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17
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Kantsler V, Ontañón-McDonald E, Kuey C, Ghanshyam MJ, Roffin MC, Asally M. Pattern Engineering of Living Bacterial Colonies Using Meniscus-Driven Fluidic Channels. ACS Synth Biol 2020; 9:1277-1283. [PMID: 32491836 DOI: 10.1021/acssynbio.0c00146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Creating adaptive, sustainable, and dynamic biomaterials is a forthcoming mission of synthetic biology. Engineering spatially organized bacterial communities has a potential to develop such bio-metamaterials. However, generating living patterns with precision, robustness, and a low technical barrier remains as a challenge. Here we present an easily implementable technique for patterning live bacterial populations using a controlled meniscus-driven fluidics system, named as MeniFluidics. We demonstrate multiscale patterning of biofilm colonies and swarms with submillimeter resolution. Utilizing the faster bacterial spreading in liquid channels, MeniFluidics allows controlled bacterial colonies both in space and time to organize fluorescently labeled Bacillus subtilis strains into a converged pattern and to form dynamic vortex patterns in confined bacterial swarms. The robustness, accuracy, and low technical barrier of MeniFluidics offer a tool for advancing and inventing new living materials that can be combined with genetically engineered systems, and adding to fundamental research into ecological, evolutional, and physical interactions between microbes.
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Affiliation(s)
- Vasily Kantsler
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - Cansu Kuey
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Manjari J. Ghanshyam
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Maria Chiara Roffin
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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18
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Abstract
Bacteria are prime cell factories that can efficiently convert carbon and nitrogen sources into a large diversity of intracellular and extracellular biopolymers, such as polysaccharides, polyamides, polyesters, polyphosphates, extracellular DNA and proteinaceous components. Bacterial polymers have important roles in pathogenicity, and their varied chemical and material properties make them suitable for medical and industrial applications. The same biopolymers when produced by pathogenic bacteria function as major virulence factors, whereas when they are produced by non-pathogenic bacteria, they become food ingredients or biomaterials. Interdisciplinary research has shed light on the molecular mechanisms of bacterial polymer synthesis, identified new targets for antibacterial drugs and informed synthetic biology approaches to design and manufacture innovative materials. This Review summarizes the role of bacterial polymers in pathogenesis, their synthesis and their material properties as well as approaches to design cell factories for production of tailor-made bio-based materials suitable for high-value applications.
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Affiliation(s)
- M Fata Moradali
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia.
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19
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Kassinger SJ, van Hoek ML. Biofilm architecture: An emerging synthetic biology target. Synth Syst Biotechnol 2020; 5:1-10. [PMID: 31956705 PMCID: PMC6961760 DOI: 10.1016/j.synbio.2020.01.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/29/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023] Open
Abstract
Synthetic biologists are exploiting biofilms as an effective mechanism for producing various outputs. Metabolic optimization has become commonplace as a method of maximizing system output. In addition to production pathways, the biofilm itself contributes to the efficacy of production. The purpose of this review is to highlight opportunities that might be leveraged to further enhance production in preexisting biofilm production systems. These opportunities may be used with previously established production systems as a method of improving system efficiency further. This may be accomplished through the reduction in the cost of establishing and maintaining biofilms, and maintenance of the enhancement of product yield per unit of time, per unit of area, or per unit of required input.
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Affiliation(s)
| | - Monique L. van Hoek
- George Mason University, School of Systems Biology, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA
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20
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Charlton SGV, White MA, Jana S, Eland LE, Jayathilake PG, Burgess JG, Chen J, Wipat A, Curtis TP. Regulating, Measuring, and Modeling the Viscoelasticity of Bacterial Biofilms. J Bacteriol 2019; 201:e00101-19. [PMID: 31182499 PMCID: PMC6707926 DOI: 10.1128/jb.00101-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Biofilms occur in a broad range of environments under heterogeneous physicochemical conditions, such as in bioremediation plants, on surfaces of biomedical implants, and in the lungs of cystic fibrosis patients. In these scenarios, biofilms are subjected to shear forces, but the mechanical integrity of these aggregates often prevents their disruption or dispersal. Biofilms' physical robustness is the result of the multiple biopolymers secreted by constituent microbial cells which are also responsible for numerous biological functions. A better understanding of the role of these biopolymers and their response to dynamic forces is therefore crucial for understanding the interplay between biofilm structure and function. In this paper, we review experimental techniques in rheology, which help quantify the viscoelasticity of biofilms, and modeling approaches from soft matter physics that can assist our understanding of the rheological properties. We describe how these methods could be combined with synthetic biology approaches to control and investigate the effects of secreted polymers on the physical properties of biofilms. We argue that without an integrated approach of the three disciplines, the links between genetics, composition, and interaction of matrix biopolymers and the viscoelastic properties of biofilms will be much harder to uncover.
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Affiliation(s)
- Samuel G V Charlton
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael A White
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Saikat Jana
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lucy E Eland
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - J Grant Burgess
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Anil Wipat
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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21
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Balasubramanian S, Aubin-Tam ME, Meyer AS. 3D Printing for the Fabrication of Biofilm-Based Functional Living Materials. ACS Synth Biol 2019; 8:1564-1567. [PMID: 31319670 DOI: 10.1021/acssynbio.9b00192] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial biofilms are three-dimensional networks of cells entangled in a self-generated extracellular polymeric matrix composed of proteins, lipids, polysaccharides, and nucleic acids. Biofilms can establish themselves on virtually any accessible surface and lead to varying impacts ranging from infectious diseases to degradation of toxic chemicals. Biofilms exhibit high mechanical stiffness and are inherently tolerant to adverse conditions including the presence of antibiotics, pollutants, detergents, high temperature, changes in pH, etc. These features make biofilms resilient, which is beneficial for applications in dynamic environments such as bioleaching, bioremediation, materials production, and wastewater purification. We have recently described an easy and cost-effective method for 3D printing of bacteria and have extended this technology for 3D printing of genetically engineered Escherichia coli biofilms. Our 3D printing platform exploits simple alginate chemistry for printing of a bacteria-alginate bioink mixture onto calcium-containing agar surfaces, resulting in the formation of bacteria-encapsulating hydrogels with varying geometries. Bacteria in these hydrogels remain intact, spatially patterned, and viable for several days. Printing of engineered bacteria to produce inducible biofilms leads to formation of multilayered three-dimensional structures that can tolerate harsh chemical treatments. Synthetic biology and material science approaches provide the opportunity to append a wide range of useful functionalities to these 3D-printed biofilms. In this article, we describe the wide range of future applications possible for applying functional 3D-printed biofilms to the construction of living biofilm-derived materials in a large-scale and environmentally stable manner.
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Affiliation(s)
- Srikkanth Balasubramanian
- Department of Bionanoscience & Kavli Institute of Nanoscience, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Marie-Eve Aubin-Tam
- Department of Bionanoscience & Kavli Institute of Nanoscience, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Anne S. Meyer
- Department of Biology, University of Rochester, Rochester, New York 14627, United States
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22
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Kan A, Birnbaum DP, Praveschotinunt P, Joshi NS. Congo Red Fluorescence for Rapid In Situ Characterization of Synthetic Curli Systems. Appl Environ Microbiol 2019; 85:e00434-19. [PMID: 31003987 PMCID: PMC6581178 DOI: 10.1128/aem.00434-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/17/2019] [Indexed: 11/20/2022] Open
Abstract
Curli are amyloid proteins that are assembled into extracellular polymeric fibers by bacteria during biofilm formation. The beta-sheet-rich protein CsgA, the primary structural component of the fibers, is secreted through dedicated machinery and self-assembles into cell-anchored fibers many times longer than the cell. Here, we have developed an in situ fluorescence assay for curli production that exploits the fluorescent properties of Congo red (CR) dye when bound to amyloid, allowing for rapid and robust curli quantification. We initially evaluated three amyloid-binding dyes for the fluorescent detection of curli in bacterial culture and found only Congo red compatible with in situ quantification. We further characterized the fluorescent properties of the dye directly in bacterial culture and calibrated the fluorescence using purified CsgA protein. We then used the Congo red assay to rapidly develop and characterize inducible curli-producing constructs in both an MC4100-derived lab strain of Escherichia coli and a derivative of the probiotic strain E. coli Nissle. This technique can be used to evaluate curli production in a minimally invasive manner using a range of equipment, simplifying curli quantification and the development of novel engineered curli systems.IMPORTANCE Curli are proteins produced by many bacteria as a structural component of biofilms, and they have recently emerged as a platform for fabrication of biological materials. Curli fibers are very robust and resistant to degradation, and the curli subunits can tolerate many protein fusions, facilitating the biosynthesis of novel functional materials. A serious bottleneck in the development of more sophisticated engineered curli systems is the rapid quantification of curli production by the bacteria. In this work we address this issue by developing a technique to monitor curli production directly in bacterial cultures, allowing for rapid curli quantification in a manner compatible with many powerful high-throughput techniques that can be used to engineer complex biological material systems.
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Affiliation(s)
- Anton Kan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Daniel P Birnbaum
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Pichet Praveschotinunt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Neel S Joshi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
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23
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Kan A, Joshi NS. Towards the directed evolution of protein materials. MRS COMMUNICATIONS 2019; 9:441-455. [PMID: 31750012 PMCID: PMC6867688 DOI: 10.1557/mrc.2019.28] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 02/22/2019] [Indexed: 05/06/2023]
Abstract
Protein-based materials have emerged as a powerful instrument for a new generation of biological materials, with many chemical and mechanical capabilities. Through the manipulation of DNA, researchers can design proteins at the molecular level, engineering a vast array of structural building blocks. However, our capability to rationally design and predict the properties of such materials is limited by the vastness of possible sequence space. Directed evolution has emerged as a powerful tool to improve biological systems through mutation and selection, presenting another avenue to produce novel protein materials. In this prospective review, we discuss the application of directed evolution for protein materials, reviewing current examples and developments that could facilitate the evolution of protein for material applications.
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Affiliation(s)
- Anton Kan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Neel S. Joshi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
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24
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Gilbert C, Ellis T. Biological Engineered Living Materials: Growing Functional Materials with Genetically Programmable Properties. ACS Synth Biol 2019; 8:1-15. [PMID: 30576101 DOI: 10.1021/acssynbio.8b00423] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Natural biological materials exhibit remarkable properties: self-assembly from simple raw materials, precise control of morphology, diverse physical and chemical properties, self-repair, and the ability to sense-and-respond to environmental stimuli. Despite having found numerous uses in human industry and society, the utility of natural biological materials is limited. But, could it be possible to genetically program microbes to create entirely new and useful biological materials? At the intersection between microbiology, material science, and synthetic biology, the emerging field of biological engineered living materials (ELMs) aims to answer this question. Here we review recent efforts to program cells to produce living materials with novel functional properties, focusing on microbial systems that can be engineered to grow materials and on new genetic circuits for pattern formation that could be used to produce the more complex systems of the future.
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Affiliation(s)
- Charlie Gilbert
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Tom Ellis
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
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25
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Emerging Paradigms for Synthetic Design of Functional Amyloids. J Mol Biol 2018; 430:3720-3734. [DOI: 10.1016/j.jmb.2018.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/08/2018] [Accepted: 04/11/2018] [Indexed: 01/01/2023]
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Volke DC, Nikel PI. Getting Bacteria in Shape: Synthetic Morphology Approaches for the Design of Efficient Microbial Cell Factories. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800111] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel C. Volke
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
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27
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Schmieden DT, Basalo Vázquez SJ, Sangüesa H, van der Does M, Idema T, Meyer AS. Printing of Patterned, Engineered E. coli Biofilms with a Low-Cost 3D Printer. ACS Synth Biol 2018; 7:1328-1337. [PMID: 29690761 DOI: 10.1021/acssynbio.7b00424] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biofilms can grow on virtually any surface available, with impacts ranging from endangering the lives of patients to degrading unwanted water contaminants. Biofilm research is challenging due to the high degree of biofilm heterogeneity. A method for the production of standardized, reproducible, and patterned biofilm-inspired materials could be a boon for biofilm research and allow for completely new engineering applications. Here, we present such a method, combining 3D printing with genetic engineering. We prototyped a low-cost 3D printer that prints bioink, a suspension of bacteria in a solution of alginate that solidifies on a calcium-containing substrate. We 3D-printed Escherichia coli in different shapes and in discrete layers, after which the cells survived in the printing matrix for at least 1 week. When printed bacteria were induced to form curli fibers, the major proteinaceous extracellular component of E. coli biofilms, they remained adherent to the printing substrate and stably spatially patterned even after treatment with a matrix-dissolving agent, indicating that a biofilm-mimicking structure had formed. This work is the first demonstration of patterned, biofilm-inspired living materials that are produced by genetic control over curli formation in combination with spatial control by 3D printing. These materials could be used as living, functional materials in applications such as water filtration, metal ion sequestration, or civil engineering, and potentially as standardizable models for certain curli-containing biofilms.
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Affiliation(s)
- Dominik T. Schmieden
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Samantha J. Basalo Vázquez
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Héctor Sangüesa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Marit van der Does
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Timon Idema
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Anne S. Meyer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
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28
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Romero CM, Martorell PV, López AG, Peñalver CGN, Chaves S, Mechetti M. Architecture and physicochemical characterization of Bacillus biofilm as a potential enzyme immobilization factory. Colloids Surf B Biointerfaces 2017; 162:246-255. [PMID: 29216511 DOI: 10.1016/j.colsurfb.2017.11.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/09/2017] [Accepted: 11/22/2017] [Indexed: 11/18/2022]
Abstract
Biocatalysis for industrial application is based on the use of enzymes to perform complex transformations. However, these systems have some disadvantage related to the costs of the biocatalyst. In this work, an alternative strategy for producing green immobilized biocatalysts based on biofilm was developed.A study of the rheological behavior of the biofilm from Bacillus sp. Mcn4, as well as the determination of its composition, was carried out. The dynamic rheological measurements, viscosity (G") and elasticity (G') module, showed that the biofilm presents appreciable elastic components, which is a recognized property for enzymes immobilization. After the partial purification, the exopolysaccharidewas identified as a levan with a non-Newtonian behavior. Extracellular DNA with fragments between 10,000 and 1000bp was detected also in the biofilm, and amyloid protein in the extracellular matrix using a fluorescence technique was identified. Bacillus sp. Mcn4 biofilms were developed on different surfaces, being the most stable those developed on hydrophilic supports. The biofilm showed lipase activity suggesting the presence of constitutive lipases entrapped into the biofilm. Indeed, two enzymes with lipase activity were identified in native PAGE. These were used as biocatalysts, whose reuse showed a residual lipase activity after more than one cycle of catalysis. The components identified in the biofilm could be the main contributors of the rheological characteristic of this material, giving an exceptional environment to the lipase enzyme. Based on these findings, the current study proposes green and natural biopolymers matrix as support for the enzyme immobilization for industrial applications.
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Affiliation(s)
- C M Romero
- PROIMI, PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB, Tucumán Fac. Bioq., Qca. y Farmacia (UNT), Ayacucho 471, 4000, Tucumán, Argentina.
| | - P V Martorell
- PROIMI, PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB, Tucumán Fac. Bioq., Qca. y Farmacia (UNT), Ayacucho 471, 4000, Tucumán, Argentina
| | - A Gómez López
- Laboratorio de Física de Fluidos y Electrorreología, Instituto de Física del Noroeste Argentino-INFINOA (CONICET-UNT), Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán, Av. Independencia 1800, San Miguel de Tucumán, 4000, Argentina
| | - C G Nieto Peñalver
- PROIMI, PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB, Tucumán Fac. Bioq., Qca. y Farmacia (UNT), Ayacucho 471, 4000, Tucumán, Argentina
| | - S Chaves
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, T4000ILI, San Miguel de Tucumán, Argentina
| | - M Mechetti
- Laboratorio de Física de Fluidos y Electrorreología, Instituto de Física del Noroeste Argentino-INFINOA (CONICET-UNT), Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán, Av. Independencia 1800, San Miguel de Tucumán, 4000, Argentina
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Tay PKR, Nguyen PQ, Joshi NS. A Synthetic Circuit for Mercury Bioremediation Using Self-Assembling Functional Amyloids. ACS Synth Biol 2017; 6:1841-1850. [PMID: 28737385 DOI: 10.1021/acssynbio.7b00137] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Synthetic biology approaches to bioremediation are a key sustainable strategy to leverage the self-replicating and programmable aspects of biology for environmental stewardship. The increasing spread of anthropogenic mercury pollution into our habitats and food chains is a pressing concern. Here, we explore the use of programmed bacterial biofilms to aid in the sequestration of mercury. We demonstrate that by integrating a mercury-responsive promoter and an operon encoding a mercury-absorbing self-assembling extracellular protein nanofiber, we can engineer bacteria that can detect and sequester toxic Hg2+ ions from the environment. This work paves the way for the development of on-demand biofilm living materials that can operate autonomously as heavy-metal absorbents.
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Affiliation(s)
- Pei Kun R. Tay
- School
of Engineering and Applied Sciences, ‡Wyss Institute for Biologically
Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Peter Q. Nguyen
- School
of Engineering and Applied Sciences, ‡Wyss Institute for Biologically
Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Neel S. Joshi
- School
of Engineering and Applied Sciences, ‡Wyss Institute for Biologically
Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, United States
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30
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Zhao Y, Cong L, Jaber V, Lukiw WJ. Microbiome-Derived Lipopolysaccharide Enriched in the Perinuclear Region of Alzheimer's Disease Brain. Front Immunol 2017; 8:1064. [PMID: 28928740 PMCID: PMC5591429 DOI: 10.3389/fimmu.2017.01064] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/16/2017] [Indexed: 12/16/2022] Open
Abstract
Abundant clinical, epidemiological, imaging, genetic, molecular, and pathophysiological data together indicate that there occur an unusual inflammatory reaction and a disruption of the innate-immune signaling system in Alzheimer’s disease (AD) brain. Despite many years of intense study, the origin and molecular mechanics of these AD-relevant pathogenic signals are still not well understood. Here, we provide evidence that an intensely pro-inflammatory bacterial lipopolysaccharide (LPS), part of a complex mixture of pro-inflammatory neurotoxins arising from abundant Gram-negative bacilli of the human gastrointestinal (GI) tract, are abundant in AD-affected brain neocortex and hippocampus. For the first time, we provide evidence that LPS immunohistochemical signals appear to aggregate in clumps in the parenchyma in control brains, and in AD, about 75% of anti-LPS signals were clustered around the periphery of DAPI-stained nuclei. As LPS is an abundant secretory product of Gram-negative bacilli resident in the human GI-tract, these observations suggest (i) that a major source of pro-inflammatory signals in AD brain may originate from internally derived noxious exudates of the GI-tract microbiome; (ii) that due to aging, vascular deficits or degenerative disease these neurotoxic molecules may “leak” into the systemic circulation, cerebral vasculature, and on into the brain; and (iii) that this internal source of microbiome-derived neurotoxins may play a particularly strong role in shaping the human immune system and contributing to neural degeneration, particularly in the aging CNS. This “Perspectives” paper will further highlight some very recent developments that implicate GI-tract microbiome-derived LPS as an important contributor to inflammatory-neurodegeneration in the AD brain.
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Affiliation(s)
- Yuhai Zhao
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Anatomy and Cell Biology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Lin Cong
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Neurology, Shengjing Hospital, China Medical University, Heping District, Shenyang, China
| | - Vivian Jaber
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Walter J Lukiw
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Neurology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Ophthalmology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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