1
|
Wang C, Long R, Lin X, Liu W, Zhu L, Jiang L. Development and characterization of a bacterial enzyme cascade reaction system for efficient and stable PET degradation. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134480. [PMID: 38703683 DOI: 10.1016/j.jhazmat.2024.134480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/15/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
The widespread use of polyethylene terephthalate (PET) in various industries has led to a surge in microplastics (MPs) pollution, posing a significant threat to ecosystems and human health. To address this, we have developed a bacterial enzyme cascade reaction system (BECRS) that focuses on the efficient degradation of PET. This system harnesses the Escherichia coli (E. coli) surface to display CsgA protein, which forms curli fibers, along with the carbohydrate-binding module 3 (CBM3) and PETases, to enhance the adsorption and degradation of PET. The study demonstrated that the BECRS achieved a notable PET film degradation rate of 3437 ± 148 μg/(d*cm²), with a degradation efficiency of 21.40% for crystalline PET MPs, and the degradation products were all converted to TPA. The stability of the system was evidenced by retaining over 80% of its original activity after multiple uses and during one month of storage. Molecular dynamics simulations confirmed that the presence of CsgA did not interfere with the enzymatic activity of PETases. This BECRS represents a significant step forward in the biodegradation of PET, particularly microplastics, offering a practical and sustainable solution for environmental pollution control.
Collapse
Affiliation(s)
- Chengyong Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Rui Long
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Xiran Lin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Wei Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
| |
Collapse
|
2
|
Liu S, Yang M, Smarr C, Zhang G, Barton H, Xu W. Engineered Living Structures with Shape-Morphing Capability Enabled by 4D Printing with Functional Bacteria. ACS APPLIED BIO MATERIALS 2024; 7:3247-3257. [PMID: 38648508 DOI: 10.1021/acsabm.4c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Engineered living structures with the incorporation of functional bacteria have been explored extensively in recent years and have shown promising potential applications in biosensing, environmental remediation, and biomedicine. However, it is still rare and challenging to achieve multifunctional capabilities such as material production, shape transformation, and sensing in a single-engineered living structure. In this study, we demonstrate bifunctional living structures by synergistically integrating cellulose-generating bacteria with pH-responsive hydrogels, and the entire structures can be precisely fabricated by three-dimensional (3D) printing. Such 3D-printed bifunctional living structures produce cellulose nanofibers in ambient conditions and have reversible and controlled shape-morphing properties (usually referred to as four-dimensional printing). Those functionalities make them biomimetic versions of silkworms in the sense that both can generate nanofibers and have body motion. We systematically investigate the processing-structure-property relationship of the bifunctional living structures. The on-demand separation of 3D cellulose structures from the hydrogel template and the living nature of the bacteria after processing and shape transformation are also demonstrated.
Collapse
Affiliation(s)
- Shan Liu
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Muxuan Yang
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Cade Smarr
- Department of Biomedical Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Ge Zhang
- Department of Biomedical Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Hazel Barton
- Department of Biology, The University of Akron, Akron, Ohio 44325, United States
| | - Weinan Xu
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| |
Collapse
|
3
|
Szulc N, Gąsior-Głogowska M, Żyłka P, Szefczyk M, Wojciechowski JW, Żak AM, Dyrka W, Kaczorowska A, Burdukiewicz M, Tarek M, Kotulska M. Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124094. [PMID: 38503257 DOI: 10.1016/j.saa.2024.124094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
The most studied functional amyloid is the CsgA, major curli subunit protein, which is produced by numerous strains of Enterobacteriaceae. Although CsgA sequences are highly conserved, they exhibit species diversity, which reflects the specific evolutionary and functional adaptability of the major curli subunit. Herein, we performed bioinformatics analyses to uncover the differences in the amyloidogenic properties of the R4 fragments in Escherichia coli and Salmonella enterica and proposed four mutants for more detailed studies: M1, M2, M3, and M4. The mutated sequences were characterized by various experimental techniques, such as circular dichroism, ATR-FTIR, FT-Raman, thioflavin T, transmission electron microscopy and confocal microscopy. Additionally, molecular dynamics simulations were performed to determine the role of buffer ions in the aggregation process. Our results demonstrated that the aggregation kinetics, fibril morphology, and overall structure of the peptide were significantly affected by the positions of charged amino acids within the repeat sequences of CsgA. Notably, substituting glycine with lysine resulted in the formation of distinctive spherically packed globular aggregates. The differences in morphology observed are attributed to the influence of phosphate ions, which disrupt the local electrostatic interaction network of the polypeptide chains. This study provides knowledge on the preferential formation of amyloid fibrils based on charge states within the polypeptide chain.
Collapse
Affiliation(s)
- Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; CNRS, University of Lorraine, F-5400 Nancy, France; Department of Physics and Biophysics, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paweł Żyłka
- Department of Electrical Engineering Fundamentals, Faculty of Electrical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jakub W Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej M Żak
- Institute of Advanced Materials, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Witold Dyrka
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Aleksandra Kaczorowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Michał Burdukiewicz
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Campus Universitat Autònoma de Barcelona Plaça Cívica Bellaterra, s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain; Clinical Research Centre, Medical University of Bialystok, Jana Kilinskiego 1, 15-089 Bialystok, Poland
| | - Mounir Tarek
- CNRS, University of Lorraine, F-5400 Nancy, France.
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
| |
Collapse
|
4
|
Peña-Díaz S, Olsen WP, Wang H, Otzen DE. Functional Amyloids: The Biomaterials of Tomorrow? ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312823. [PMID: 38308110 DOI: 10.1002/adma.202312823] [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: 11/28/2023] [Revised: 01/22/2024] [Indexed: 02/04/2024]
Abstract
Functional amyloid (FAs), particularly the bacterial proteins CsgA and FapC, have many useful properties as biomaterials: high stability, efficient, and controllable formation of a single type of amyloid, easy availability as extracellular material in bacterial biofilm and flexible engineering to introduce new properties. CsgA in particular has already demonstrated its worth in hydrogels for stable gastrointestinal colonization and regenerative tissue engineering, cell-specific drug release, water-purification filters, and different biosensors. It also holds promise as catalytic amyloid; existing weak and unspecific activity can undoubtedly be improved by targeted engineering and benefit from the repetitive display of active sites on a surface. Unfortunately, FapC remains largely unexplored and no application is described so far. Since FapC shares many common features with CsgA, this opens the window to its development as a functional scaffold. The multiple imperfect repeats in CsgA and FapC form a platform to introduce novel properties, e.g., in connecting linkers of variable lengths. While exploitation of this potential is still at an early stage, particularly for FapC, a thorough understanding of their molecular properties will pave the way for multifunctional fibrils which can contribute toward solving many different societal challenges, ranging from CO2 fixation to hydrolysis of plastic nanoparticles.
Collapse
Affiliation(s)
- Samuel Peña-Díaz
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, DK - 8000, Denmark
| | - William Pallisgaard Olsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, DK - 8000, Denmark
| | - Huabing Wang
- Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, Clinical Laboratory Center, Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Shuangyong Road 6, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, DK - 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, Aarhus C, 8000, Denmark
| |
Collapse
|
5
|
Philipp LA, Bühler K, Ulber R, Gescher J. Beneficial applications of biofilms. Nat Rev Microbiol 2024; 22:276-290. [PMID: 37957398 DOI: 10.1038/s41579-023-00985-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 11/15/2023]
Abstract
Many microorganisms live in the form of a biofilm. Although they are feared in the medical sector, biofilms that are composed of non-pathogenic organisms can be highly beneficial in many applications, including the production of bulk and fine chemicals. Biofilm systems are natural retentostats in which the biocatalysts can adapt and optimize their metabolism to different conditions over time. The adherent nature of biofilms allows them to be used in continuous systems in which the hydraulic retention time is much shorter than the doubling time of the biocatalysts. Moreover, the resilience of organisms growing in biofilms, together with the potential of uncoupling growth from catalytic activity, offers a wide range of opportunities. The ability to work with continuous systems using a potentially self-advancing whole-cell biocatalyst is attracting interest from a range of disciplines, from applied microbiology to materials science and from bioengineering to process engineering. The field of beneficial biofilms is rapidly evolving, with an increasing number of applications being explored, and the surge in demand for sustainable and biobased solutions and processes is accelerating advances in the field. This Review provides an overview of the research topics, challenges, applications and future directions in beneficial and applied biofilm research.
Collapse
Affiliation(s)
- Laura-Alina Philipp
- Hamburg University of Technology, Institute of Technical Microbiology, Hamburg, Germany
| | - Katja Bühler
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Roland Ulber
- RPTU Kaiserslautern-Landau, Institute of Bioprocess Engineering, Kaiserslautern, Germany
| | - Johannes Gescher
- Hamburg University of Technology, Institute of Technical Microbiology, Hamburg, Germany.
| |
Collapse
|
6
|
Ye Q, Wang D, Wei N. Engineering biomaterials for the recovery of rare earth elements. Trends Biotechnol 2024; 42:575-590. [PMID: 37985335 DOI: 10.1016/j.tibtech.2023.10.011] [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: 08/31/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023]
Abstract
The escalating global demand for rare earth elements (REEs) and the overabundance of REE-containing waste require innovative technologies for REE recovery from waste to achieve a sustainable supply of REEs while reducing the environmental burden. Biosorption mediated by peptides or proteins has emerged as a promising approach for selective REE recovery. To date, multiple peptides and proteins with high REE-binding affinity and selectivity have been discovered, and various strategies are being exploited to engineer robust and reusable biosorptive materials for selective REE recovery. This review highlights recent advances in discovering and engineering peptides and proteins for REE recovery. Future research prospects and challenges are also discussed.
Collapse
Affiliation(s)
- Quanhui Ye
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dong Wang
- School of Information Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Na Wei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| |
Collapse
|
7
|
Peña-Díaz S, Ferreira P, Ramos MJ, Otzen DE. Mining and engineering activity in catalytic amyloids. Methods Enzymol 2024; 697:345-422. [PMID: 38816129 DOI: 10.1016/bs.mie.2024.03.002] [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: 06/01/2024]
Abstract
This chapter describes how to test different amyloid preparations for catalytic properties. We describe how to express, purify, prepare and test two types of pathological amyloid (tau and α-synuclein) and two functional amyloid proteins, namely CsgA from Escherichia coli and FapC from Pseudomonas. We therefore preface the methods section with an introduction to these two examples of functional amyloid and their remarkable structural and kinetic properties and high physical stability, which renders them very attractive for a range of nanotechnological designs, both for structural, medical and catalytic purposes. The simplicity and high surface exposure of the CsgA amyloid is particularly useful for the introduction of new functional properties and we therefore provide a computational protocol to graft active sites from an enzyme of interest into the amyloid structure. We hope that the methods described will inspire other researchers to explore the remarkable opportunities provided by bacterial functional amyloid in biotechnology.
Collapse
Affiliation(s)
- Samuel Peña-Díaz
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Pedro Ferreira
- Faculdade de Ciencias, Universidad do Porto, Porto, Portugal
| | | | - Daniel E Otzen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
8
|
Huang Y, Wu Y, Hu H, Tong B, Wang J, Zhang S, Wang Y, Zhang J, Yin Y, Dai S, Zhao W, An B, Pu J, Wang Y, Peng C, Li N, Zhou J, Tan Y, Zhong C. Accelerating the design of pili-enabled living materials using an integrative technological workflow. Nat Chem Biol 2024; 20:201-210. [PMID: 38012344 DOI: 10.1038/s41589-023-01489-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/17/2023] [Indexed: 11/29/2023]
Abstract
Bacteria can be programmed to create engineered living materials (ELMs) with self-healing and evolvable functionalities. However, further development of ELMs is greatly hampered by the lack of engineerable nonpathogenic chassis and corresponding programmable endogenous biopolymers. Here, we describe a technological workflow for facilitating ELMs design by rationally integrating bioinformatics, structural biology and synthetic biology technologies. We first develop bioinformatics software, termed Bacteria Biopolymer Sniffer (BBSniffer), that allows fast mining of biopolymers and biopolymer-producing bacteria of interest. As a proof-of-principle study, using existing pathogenic pilus as input, we identify the covalently linked pili (CLP) biosynthetic gene cluster in the industrial workhorse Corynebacterium glutamicum. Genetic manipulation and structural characterization reveal the molecular mechanism of the CLP assembly, ultimately enabling a type of programmable pili for ELM design. Finally, engineering of the CLP-enabled living materials transforms cellulosic biomass into lycopene by coupling the extracellular and intracellular bioconversion ability.
Collapse
Affiliation(s)
- Yuanyuan Huang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
| | - Yanfei Wu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Han Hu
- Shenzhen Xbiome Biotech Co. Ltd, Shenzhen, China
| | | | - Jie Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Siyu Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yanyi Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jicong Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Shengkun Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wenjuan Zhao
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bolin An
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiahua Pu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yaomin Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Nan Li
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiahai Zhou
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
| | - Yan Tan
- Shenzhen Xbiome Biotech Co. Ltd, Shenzhen, China.
| | - Chao Zhong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
| |
Collapse
|
9
|
Siri M, Mangiarotti A, Vázquez-Dávila M, Bidan CM. Curli Amyloid Fibers in Escherichia coli Biofilms: The Influence of Water Availability on their Structure and Functional Properties. Macromol Biosci 2024; 24:e2300234. [PMID: 37776075 DOI: 10.1002/mabi.202300234] [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: 05/24/2023] [Revised: 09/22/2023] [Indexed: 10/01/2023]
Abstract
Escherichia coli biofilms consist of bacteria embedded in a self-produced matrix mainly made of protein fibers and polysaccharides. The curli amyloid fibers found in the biofilm matrix are promising versatile building blocks to design sustainable bio-sourced materials. To exploit this potential, it is crucial to understand i) how environmental cues during biofilm growth influence the molecular structure of these amyloid fibers, and ii) how this translates at higher length scales. To explore these questions, the effect of water availability during biofilm growth on the conformation and functions of curli is studied. Microscopy and spectroscopy are used to characterize the amyloid fibers purified from biofilms grown on nutritive substrates with different water contents, and micro-indentation to measure the rigidity of the respective biofilms. The purified curli amyloid fibers present differences in the yield, structure, and functional properties upon biofilm growth conditions. Fiber packing and β-sheets content correlate with their hydrophobicity and chemical stability, and with the rigidity of the biofilms. This study highlights how E. coli biofilm growth conditions impact curli structure and functions contributing to macroscopic materials properties. These fundamental findings infer an alternative strategy to tune curli structure, which will ultimately benefit engineering hierarchical and functional curli-based materials.
Collapse
Affiliation(s)
- Macarena Siri
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| | - Agustín Mangiarotti
- Max Planck Institute of Colloids and Interfaces, Department of Sustainable and Bio-inspired Materials, 14476, Potsdam, Germany
| | - Mónica Vázquez-Dávila
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| | - Cécile M Bidan
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| |
Collapse
|
10
|
Li C, Wang ZX, Xiao H, Wu FG. Intestinal Delivery of Probiotics: Materials, Strategies, and Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2310174. [PMID: 38245861 DOI: 10.1002/adma.202310174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/04/2024] [Indexed: 01/22/2024]
Abstract
Probiotics with diverse and crucial properties and functions have attracted broad interest from many researchers, who adopt intestinal delivery of probiotics to modulate the gut microbiota. However, the major problems faced for the therapeutic applications of probiotics are the viability and colonization of probiotics during their processing, oral intake, and subsequent delivery to the gut. The challenges of simple oral delivery (stability, controllability, targeting, etc.) have greatly limited the use of probiotics in clinical therapies. Nanotechnology can endow the probiotics to be delivered to the intestine with improved survival rate and increased resistance to the adverse environment. Additionally, the progress in synthetic biology has created new opportunities for efficiently and purposefully designing and manipulating the probiotics. In this article, a brief overview of the types of probiotics for intestinal delivery, the current progress of different probiotic encapsulation strategies, including the chemical, physical, and genetic strategies and their combinations, and the emerging single-cell encapsulation strategies using nanocoating methods, is presented. The action mechanisms of probiotics that are responsible for eliciting beneficial effects are also briefly discussed. Finally, the therapeutic applications of engineered probiotics are discussed, and the future trends toward developing engineered probiotics with advanced features and improved health benefits are proposed.
Collapse
Affiliation(s)
- Chengcheng Li
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Zi-Xi Wang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, New Brunswick, E3B 5A3, Canada
| | - Fu-Gen Wu
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| |
Collapse
|
11
|
Fan R, Aranko AS. Catcher/Tag Toolbox: Biomolecular Click-Reactions For Protein Engineering Beyond Genetics. Chembiochem 2024; 25:e202300600. [PMID: 37851860 DOI: 10.1002/cbic.202300600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/20/2023]
Abstract
Manipulating protein architectures beyond genetic control has attracted widespread attention. Catcher/Tag systems enable highly specific conjugation of proteins in vivo and in vitro via an isopeptide-bond. They provide efficient, robust, and irreversible strategies for protein conjugation and are simple yet powerful tools for a variety of applications in enzyme industry, vaccines, biomaterials, and cellular applications. Here we summarize recent development of the Catcher/Tag toolbox with a particular emphasis on the design of Catcher/Tag pairs targeted for specific applications. We cover the current limitations of the Catcher/Tag systems and discuss the pH sensitivity of the reactions. Finally, we conclude some of the future directions in the development of this versatile protein conjugation method and envision that improved control over inducing the ligation reaction will further broaden the range of applications.
Collapse
Affiliation(s)
- Ruxia Fan
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| |
Collapse
|
12
|
Zhang X, Razanajatovo MR, Du X, Wang S, Feng L, Wan S, Chen N, Zhang Q. Well-designed protein amyloid nanofibrils composites as versatile and sustainable materials for aquatic environment remediation: A review. ECO-ENVIRONMENT & HEALTH (ONLINE) 2023; 2:264-277. [PMID: 38435357 PMCID: PMC10902511 DOI: 10.1016/j.eehl.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 03/05/2024]
Abstract
Amyloid nanofibrils (ANFs) are supramolecular polymers originally classified as pathological markers in various human degenerative diseases. However, in recent years, ANFs have garnered greater interest and are regarded as nature-based sustainable biomaterials in environmental science, material engineering, and nanotechnology. On a laboratory scale, ANFs can be produced from food proteins via protein unfolding, misfolding, and hydrolysis. Furthermore, ANFs have specific structural characteristics such as a high aspect ratio, good rigidity, chemical stability, and a controllable sequence. These properties make them a promising functional material in water decontamination research. As a result, the fabrication and application of ANFs and their composites in water purification have recently gained considerable attention. Despite the large amount of literature in this field, there is a lack of systematic review to assess the gap in using ANFs and their composites to remove contaminants from water. This review discusses significant advancements in design techniques as well as the physicochemical properties of ANFs-based composites. We also emphasize the current progress in using ANFs-based composites to remove inorganic, organic, and biological contaminants. The interaction mechanisms between ANFs-based composites and contaminants are also highlighted. Finally, we illustrate the challenges and opportunities associated with the future preparation and application of ANFs-based composites. We anticipate that this review will shed new light on the future design and use of ANFs-based composites.
Collapse
Affiliation(s)
- Xiaolin Zhang
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse and Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Mamitiana Roger Razanajatovo
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse and Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Xuedong Du
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse and Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Shuo Wang
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse and Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Li Feng
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse and Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Shunli Wan
- College of Life & Environment Sciences, Huangshan University, Huangshan 245041, China
| | - Ningyi Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Qingrui Zhang
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse and Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
- State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China
| |
Collapse
|
13
|
Zhang W, Dong H, Wang X, Zhang L, Chen C, Wang P. Engineered Escherichia coli Consortia Function in a Programmable Pattern for Multiple Enzymatic Biosynthesis. ACS APPLIED MATERIALS & INTERFACES 2023; 15:45886-45894. [PMID: 37738613 DOI: 10.1021/acsami.3c09123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Coordinating microbial consortia to realize complex synthetic pathways is an area of great interest in the rapidly growing field of biomanufacturing. This work presents a programmable method for assembling living cells based on the surface display of affinity groups, enabling whole-cell catalysis with optimized catalytic efficiency through the rational arrangement of cell assemblies and enzymes. In the context of d-phenyllactic acid (d-PLA) synthesis, four enzymes were rationally arranged considering substrate channeling and protein expression levels. The production efficiencies of d-PLA catalyzed by engineered microbial consortia were 1.31- and 2.55-fold higher than those of biofilm and whole-cell catalysts, respectively. Notably, substrate channeling was identified between the coimmobilized rate-limiting enzymes, resulting in a 3.67-fold improvement in catalytic efficiency compared with hybrid catalysts (free enzymes coupled with whole-cell catalysts). The highest yield of d-PLA catalyzed by microbial consortia was 102.85 ± 3.39 mM with 140 mM benzaldehyde as the substrate. This study proposes a novel approach to cell enzyme assembly for coordinating microbial consortia in multiple enzymatic biosynthesis processes.
Collapse
Affiliation(s)
- Wenxue Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Hao Dong
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiaoli Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Liting Zhang
- Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Chao Chen
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
- Institute for Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, Minnesota 55108, United States
| |
Collapse
|
14
|
Peng R, Ba F, Li J, Cao J, Zhang R, Liu WQ, Ren J, Liu Y, Li J, Ling S. Embedding Living Cells with a Mechanically Reinforced and Functionally Programmable Hydrogel Fiber Platform. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2305583. [PMID: 37498452 DOI: 10.1002/adma.202305583] [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: 06/11/2023] [Indexed: 07/28/2023]
Abstract
Living materials represent a new frontier in functional material design, integrating synthetic biology tools to endow materials with programmable, dynamic, and life-like characteristics. However, a major challenge in creating living materials is balancing the tradeoff between structural stability, mechanical performance, and functional programmability. To address this challenge, a sheath-core living hydrogel fiber platform that synergistically integrates living bacteria with hydrogel fibers to achieve both functional diversity and structural and mechanical robustness is proposed. In the design, microfluidic spinning is used to produce hydrogel fiber, which offers advantages in both structural and functional designability due to their hierarchical porous architectures that can be tailored and their mechanical performance that can be enhanced through a variety of post-processing approaches. By introducing living bacteria, the platform is endowed with programmable functionality and life-like capabilities. This work reconstructs the genetic circuits of living bacteria to express chromoproteins and fluorescent proteins as two prototypes that enable the coloration of living fibers and sensing water pollutants by monitoring the amount of fluorescent protein expressed. Altogether, this study establishes a structure-property-function optimized living hydrogel fiber platform, providing a new tool for accelerating the practical applications of the emerging living material systems.
Collapse
Affiliation(s)
- Ruoxuan Peng
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Jie Li
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Jiayi Cao
- College of Fashion and Design, Donghua University, 1882 West Yan'an Road, Shanghai, 200051, China
| | - Rong Zhang
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Jing Ren
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Yifan Liu
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Shengjie Ling
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| |
Collapse
|
15
|
Yin Z, Liu Y, Anniwaer A, You Y, Guo J, Tang Y, Fu L, Yi L, Huang C. Rational Designs of Biomaterials for Combating Oral Biofilm Infections. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2305633. [PMID: 37566788 DOI: 10.1002/adma.202305633] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/24/2023] [Indexed: 08/13/2023]
Abstract
Oral biofilms, which are also known as dental plaque, are the culprit of a wide range of oral diseases and systemic diseases, thus contributing to serious health risks. The manner of how to achieve good control of oral biofilms has been an increasing public concern. Novel antimicrobial biomaterials with highly controllable fabrication and functionalization have been proven to be promising candidates. However, previous reviews have generally emphasized the physicochemical properties, action mode, and application effectiveness of those biomaterials, whereas insufficient attention has been given to the design rationales tailored to different infection types and application scenarios. To offer guidance for better diversification and functionalization of anti-oral-biofilm biomaterials, this review details the up-to-date design rationales in three aspects: the core strategies in combating oral biofilm, as well as the biomaterials with advanced antibiofilm capacity and multiple functions based on the improvement or combination of the abovementioned antimicrobial strategies. Thereafter, insights on the existing challenges and future improvement of biomaterial-assisted oral biofilm treatments are proposed, hoping to provide a theoretical basis and reference for the subsequent design and application of antibiofilm biomaterials.
Collapse
Affiliation(s)
- Zhengrong Yin
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Yaxi Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Annikaer Anniwaer
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Yuan You
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Jingmei Guo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Ying Tang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Lei Fu
- College of Chemistry and Molecular Sciences, Renmin Hospital of Wuhan University, Wuhan University Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430072, China
| | - Luyao Yi
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Cui Huang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| |
Collapse
|
16
|
Kawada M, Jo H, Medina AM, Sim S. Catalytic Materials Enabled by a Programmable Assembly of Synthetic Polymers and Engineered Bacterial Spores. J Am Chem Soc 2023; 145:16210-16217. [PMID: 37458997 DOI: 10.1021/jacs.3c05153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Natural biological materials are formed by self-assembly processes and catalyze a myriad of reactions. Here, we report a programmable molecular assembly of designed synthetic polymers with engineered bacterial spores. This self-assembly process is driven by dynamic covalent bond formation on spore surface glycan and yields macroscopic materials that are structurally stable, self-healing, and recyclable. Molecular programming of polymer species shapes the physical properties of these materials while metabolically dormant spores allow for prolonged ambient storage. Incorporation of spores with genetically encoded functionalities enables operationally simple and repeated enzymatic catalysis. Our work combines molecular and genetic engineering to offer scalable and programmable synthesis of robust materials for sustainable biocatalysis.
Collapse
Affiliation(s)
- Masamu Kawada
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Hyuna Jo
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Alexis M Medina
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Seunghyun Sim
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, California 92697, United States
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States
- Center for Complex and Active Materials, University of California Irvine, Irvine, California 92697, United States
| |
Collapse
|
17
|
Cai A, Abdali Z, Saldanha DJ, Aminzare M, Dorval Courchesne NM. Endowing textiles with self-repairing ability through the fabrication of composites with a bacterial biofilm. Sci Rep 2023; 13:11389. [PMID: 37452128 PMCID: PMC10349112 DOI: 10.1038/s41598-023-38501-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023] Open
Abstract
To address the increasing environmental footprint of the fast-growing textile industry, self-repairing textile composites have been developed to allow torn or damaged textiles to restore their morphological, mechanical, and functional features. A sustainable way to create these textile composites is to introduce a coating material that is biologically derived, biodegradable, and can be produced through scalable processes. Here, we fabricated self-repairing textile composites by integrating the biofilms of Escherichia coli (E. coli) bacteria into conventional knitted textiles. The major structural protein component in E. coli biofilm is a matrix of curli fibers, which has demonstrated extraordinary abilities to self-assemble into mechanically strong macroscopic structures and self-heal upon contact with water. We demonstrated the integration of biofilm through three simple, fast, and scalable methods: adsorption, doctor blading, and vacuum filtration. We confirmed that the composites were breathable and mechanically strong after the integration, with improved Young's moduli or elongation at break depending on the fabrication method used. Through patching and welding, we showed that after rehydration, the composites made with all three methods effectively healed centimeter-scale defects. Upon observing that the biofilm strongly attached to the textiles by covering the extruding textile fibers from the self-repair failures, we proposed that the strength of the self-repairs relied on both the biofilm's cohesion and the biofilm-textile adhesion. Considering that curli fibers are genetically-tunable, the fabrication of self-repairing curli-expressing biofilm-textile composites opens new venues for industrially manufacturing affordable, durable, and sustainable functional textiles.
Collapse
Affiliation(s)
- Anqi Cai
- Department of Chemical Engineering, McGill University, 3610 University Street, Montreal, QC, H3A 0C5, Canada
| | - Zahra Abdali
- Department of Chemical Engineering, McGill University, 3610 University Street, Montreal, QC, H3A 0C5, Canada
| | - Dalia Jane Saldanha
- Department of Chemical Engineering, McGill University, 3610 University Street, Montreal, QC, H3A 0C5, Canada
| | - Masoud Aminzare
- Department of Chemical Engineering, McGill University, 3610 University Street, Montreal, QC, H3A 0C5, Canada
| | | |
Collapse
|
18
|
Nguyen PQ, Huang X, Collins DS, Collins JJ, Lu T. Harnessing synthetic biology to enhance ocean health. Trends Biotechnol 2023; 41:860-874. [PMID: 36669947 DOI: 10.1016/j.tibtech.2022.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023]
Abstract
Ocean health is faltering, its capability for regeneration and renewal being eroded by a steady pulse of anthropomorphic impacts. Plastic waste has infiltrated all ocean biomes, climate change threatens coral reefs with extinction, and eutrophication has unleashed vast algal blooms. In the face of these challenges, synthetic biology approaches may hold untapped solutions to mitigate adverse effects, repair ecosystems, and put us on a path towards sustainable stewardship of our planet. Leveraging synthetic biology tools would enable innovative engineering approaches to augment the natural adaptive capacity of ocean biological systems to cope with the swiftness of human-induced change. Here, we present a framework for developing synthetic biology solutions for the challenges of plastic pollution, coral bleaching, and harmful algal blooms.
Collapse
Affiliation(s)
- Peter Q Nguyen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Xiaoning Huang
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Daniel S Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Department of Biology and Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Ting Lu
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
19
|
Bressler EM, Adams S, Liu R, Colson YL, Wong WW, Grinstaff MW. Boolean logic in synthetic biology and biomaterials: Towards living materials in mammalian cell therapeutics. Clin Transl Med 2023; 13:e1244. [PMID: 37386762 PMCID: PMC10310979 DOI: 10.1002/ctm2.1244] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND The intersection of synthetic biology and biomaterials promises to enhance safety and efficacy in novel therapeutics. Both fields increasingly employ Boolean logic, which allows for specific therapeutic outputs (e.g., drug release, peptide synthesis) in response to inputs such as disease markers or bio-orthogonal stimuli. Examples include stimuli-responsive drug delivery devices and logic-gated chimeric antigen receptor (CAR) T cells. In this review, we explore recent manuscripts highlighting the potential of synthetic biology and biomaterials with Boolean logic to create novel and efficacious living therapeutics. MAIN BODY Collaborations in synthetic biology and biomaterials have led to significant advancements in drug delivery and cell therapy. Borrowing from synthetic biology, researchers have created Boolean-responsive biomaterials sensitive to multiple inputs including pH, light, enzymes and more to produce functional outputs such as degradation, gel-sol transition and conformational change. Biomaterials also enhance synthetic biology, particularly CAR T and adoptive T cell therapy, by modulating therapeutic immune cells in vivo. Nanoparticles and hydrogels also enable in situ generation of CAR T cells, which promises to drive down production costs and expand access to these therapies to a larger population. Biomaterials are also used to interface with logic-gated CAR T cell therapies, creating controllable cellular therapies that enhance safety and efficacy. Finally, designer cells acting as living therapeutic factories benefit from biomaterials that improve biocompatibility and stability in vivo. CONCLUSION By using Boolean logic in both cellular therapy and drug delivery devices, researchers have achieved better safety and efficacy outcomes. While early projects show incredible promise, coordination between these fields is ongoing and growing. We expect that these collaborations will continue to grow and realize the next generation of living biomaterial therapeutics.
Collapse
Affiliation(s)
- Eric M. Bressler
- Department of Biomedical Engineering and Biological Design CenterBoston UniversityBostonMassachusettsUSA
| | - Sarah Adams
- Department of Biomedical Engineering and Biological Design CenterBoston UniversityBostonMassachusettsUSA
| | - Rong Liu
- Division of Thoracic SurgeryDepartment of SurgeryMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Yolonda L. Colson
- Division of Thoracic SurgeryDepartment of SurgeryMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Wilson W. Wong
- Department of Biomedical Engineering and Biological Design CenterBoston UniversityBostonMassachusettsUSA
| | - Mark W. Grinstaff
- Department of Biomedical Engineering and Biological Design CenterBoston UniversityBostonMassachusettsUSA
- Department of Chemistry and Department of Biomedical EngineeringBoston UniversityBostonMassachusettsUSA
| |
Collapse
|
20
|
Sleutel M, Pradhan B, Volkov AN, Remaut H. Structural analysis and architectural principles of the bacterial amyloid curli. Nat Commun 2023; 14:2822. [PMID: 37198180 DOI: 10.1038/s41467-023-38204-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 04/20/2023] [Indexed: 05/19/2023] Open
Abstract
Two decades have passed since the initial proposition that amyloids are not only (toxic) byproducts of an unintended aggregation cascade, but that they can also be produced by an organism to serve a defined biological function. That revolutionary idea was borne out of the realization that a large fraction of the extracellular matrix that holds Gram-negative cells into a persistent biofilm is composed of protein fibers (curli; tafi) with cross-β architecture, nucleation-dependent polymerization kinetics and classic amyloid tinctorial properties. The list of proteins shown to form so-called functional amyloid fibers in vivo has greatly expanded over the years, but detailed structural insights have not followed at a similar pace in part due to the associated experimental barriers. Here we combine extensive AlphaFold2 modelling and cryo-electron transmission microscopy to propose an atomic model of curli protofibrils, and their higher modes of organization. We uncover an unexpected structural diversity of curli building blocks and fibril architectures. Our results allow for a rationalization of the extreme physico-chemical robustness of curli, as well as earlier observations of inter-species curli promiscuity, and should facilitate further engineering efforts to expand the repertoire of curli-based functional materials.
Collapse
Affiliation(s)
- Mike Sleutel
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, Belgium.
| | - Brajabandhu Pradhan
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Alexander N Volkov
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Jean Jeener NMR Center, Brussel, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, Brussels, Belgium.
| |
Collapse
|
21
|
Saldanha DJ, Cai A, Dorval Courchesne NM. The Evolving Role of Proteins in Wearable Sweat Biosensors. ACS Biomater Sci Eng 2023; 9:2020-2047. [PMID: 34491052 DOI: 10.1021/acsbiomaterials.1c00699] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Sweat is an increasingly popular biological medium for fitness monitoring and clinical diagnostics. It contains an abundance of biological information and is available continuously and noninvasively. Sweat-sensing devices often employ proteins in various capacities to create skin-friendly matrices that accurately extract valuable and time-sensitive information from sweat. Proteins were first used in sensors as biorecognition elements in the form of enzymes and antibodies, which are now being tuned to operate at ranges relevant for sweat. In addition, a range of structural proteins, sometimes assembled in conjunction with polymers, can provide flexible and compatible matrices for skin sensors. Other proteins also naturally possess a range of functionalities─as adhesives, charge conductors, fluorescence emitters, and power generators─that can make them useful components in wearable devices. Here, we examine the four main components of wearable sweat sensors─the biorecognition element, the transducer, the scaffold, and the adhesive─and the roles that proteins have played so far, or promise to play in the future, in each component. On a case-by-case basis, we analyze the performance characteristics of existing protein-based devices, their applicable ranges of detection, their transduction mechanism and their mechanical properties. Thereby, we review and compare proteins that can readily be used in sweat sensors and others that will require further efforts to overcome design, stability or scalability challenges. Incorporating proteins in one or multiple components of sweat sensors could lead to the development and deployment of tunable, greener, and safer biosourced devices.
Collapse
Affiliation(s)
- Dalia Jane Saldanha
- Department of Chemical Engineering, McGill University, Montréal, Québec, Canada H3A 0C5
| | - Anqi Cai
- Department of Chemical Engineering, McGill University, Montréal, Québec, Canada H3A 0C5
| | | |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Li Y, Xing Z, Wang S, Wang Y, Wang Z, Dong L. Disruption of biofilms in periodontal disease through the induction of phase transition by cationic dextrans. Acta Biomater 2023; 158:759-768. [PMID: 36638945 DOI: 10.1016/j.actbio.2023.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Biofilm of oral pathogenic microorganisms induced by their multiplication and coaggregation would lead to periodontitis. In biofilms, the extracellular polymeric substances (EPS) as a protective shield encapsulates the individual bacteria, protecting them against attack. To alleviate periodontal disease, disrupting the EPS of pathogenic bacteria is crucial and challenging. Based on the sufficient capacity of disorganizing EPS of our designed cationic dextrans, we hypothesized that these polymers could be competent in relieving periodontitis. We validated that cationic dextrans could induce the phase transition of EPS in biofilms, especially the Porphyromonas gingivalis (P. gingivalis), a keystone periodontal pathogen, thus effectively destroying biofilm in vitro. More importantly, satisfactory in vivo treatment was achieved in a rat periodontal disease model. In summary, the study exploited a practical and effective strategy to treat periodontitis with cationic dextrans' powerful biofilm-controlling potential. STATEMENT OF SIGNIFICANCE: Periodontal disease is closely related to dental plaque biofilms on the tooth surface. The biofilm forms gel structures and shields the bacteria underneath, thus protecting oral pathogens from traditional anti-bacterial reagents. Due to limited penetration into gel, the efficacy of these reagents in biofilm elimination is restricted. Our designed cationic dextran could wipe out the coverage of gel-like EPS to disperse encapsulated bacteria. Such superior capacity endowed them with satisfactory effect in disrupting biofilm. Notably, in a rat periodontitis model, cationic dextrans dramatically suppressed alveolar bone loss and alleviated periodontal inflammation by controlling dental plaque. Given the increasing global concerns about periodontal disease, it's worth expanding the application of cationic dextrans both scientifically and clinically.
Collapse
Affiliation(s)
- Yurong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China
| | - Zhen Xing
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China
| | - Shaocong Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China
| | - Yulian Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China
| | - Zhenzhen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China.
| | - Lei Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China; Wuxi Xishan NJU Institute of Applied Biotechnology, Anzhen Street, Xishan District, Wuxi 214101, China.
| |
Collapse
|
24
|
Luo J, Chen J, Huang Y, You L, Dai Z. Engineering living materials by synthetic biology. BIOPHYSICS REVIEWS 2023; 4:011305. [PMID: 38505813 PMCID: PMC10903423 DOI: 10.1063/5.0115645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/18/2022] [Indexed: 03/21/2024]
Abstract
Natural biological materials are programmed by genetic information and able to self-organize, respond to environmental stimulus, and couple with inorganic matter. Inspired by the natural system and to mimic their complex and delicate fabrication process and functions, the field of engineered living materials emerges at the interface of synthetic biology and materials science. Here, we review the recent efforts and discuss the challenges and future opportunities.
Collapse
Affiliation(s)
- Jiren Luo
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiangfeng Chen
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yaoge Huang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Zhuojun Dai
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
25
|
Atkinson JT, Chavez MS, Niman CM, El-Naggar MY. Living electronics: A catalogue of engineered living electronic components. Microb Biotechnol 2023; 16:507-533. [PMID: 36519191 PMCID: PMC9948233 DOI: 10.1111/1751-7915.14171] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/26/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.
Collapse
Affiliation(s)
- Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.,Department of Chemistry, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
26
|
Xu C, Frigo-Vaz B, Goering J, Wang P. Gas-phase degradation of VOCs using supported bacteria biofilms. Biotechnol Bioeng 2023; 120:1323-1333. [PMID: 36775904 DOI: 10.1002/bit.28348] [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: 09/22/2022] [Revised: 01/13/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
Herein we report the use of Pseudomonas putida F1 biofilms grown on carbonized cellulosic fibers to achieve biodegradation of airborne volatile organic compounds (VOCs) in the absence of any bulk aqueous-phase media. It is believed that direct exposure of gaseous VOC substrates to biomass may eliminate aqueous-phase mass transfer resistance and facilitate VOC capture and degradation. When tested with toluene vapor as a model VOC, the supported biofilm could grow optimally at 300 p.p.m. toluene and 80% relative humidity, with a specific growth rate of 0.425 day-1 . During long-term VOC biodegradation tests in a tubular packed bed reactor, biofilms achieved a toluene degradation rate of 2.5 mg gDCW -1 h-1 during the initial growth phase. Interestingly, the P. putida F1 film kept biodegrading activity even at the stationary nongrowth phase. The supported biofilms with a biomass loading of 20% (wt) could degrade toluene at a rate of 1.9 mg gDCW -1 h-1 during the stationary phase, releasing CO2 at a rate of 6.4 mg gDCW -1 h-1 at the same time (indicating 100% conversion of substrate carbon to CO2 ). All of these observations promised a new type of "dry" biofilm reactors for efficient degradation of toxic VOCs without involving a large amount of water.
Collapse
Affiliation(s)
- Chao Xu
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA.,Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Benjamin Frigo-Vaz
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA.,Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Joshua Goering
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA.,Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| |
Collapse
|
27
|
Zhao D, Peng Z, Fang J, Fang Z, Zhang J. Programmable and low-cost biohybrid membrane for efficient heavy metal removal from water. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2022.122751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
28
|
Engineering Microorganisms to Produce Bio-Based Monomers: Progress and Challenges. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bioplastics are polymers made from sustainable bio-based feedstocks. While the potential of producing bio-based monomers in microbes has been investigated for decades, their economic feasibility is still unsatisfactory compared with petroleum-derived methods. To improve the overall synthetic efficiency of microbial cell factories, three main strategies were summarized in this review: firstly, implementing approaches to improve the microbial utilization ability of cheap and abundant substrates; secondly, developing methods at enzymes, pathway, and cellular levels to enhance microbial production performance; thirdly, building technologies to enhance microbial pH, osmotic, and metabolites stress tolerance. Moreover, the challenges of, and some perspectives on, exploiting microorganisms as efficient cell factories for producing bio-based monomers are also discussed.
Collapse
|
29
|
de Assis SC, Morgado DL, Scheidt DT, de Souza SS, Cavallari MR, Ando Junior OH, Carrilho E. Review of Bacterial Nanocellulose-Based Electrochemical Biosensors: Functionalization, Challenges, and Future Perspectives. BIOSENSORS 2023; 13:142. [PMID: 36671977 PMCID: PMC9856105 DOI: 10.3390/bios13010142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Electrochemical biosensing devices are known for their simple operational procedures, low fabrication cost, and suitable real-time detection. Despite these advantages, they have shown some limitations in the immobilization of biochemicals. The development of alternative materials to overcome these drawbacks has attracted significant attention. Nanocellulose-based materials have revealed valuable features due to their capacity for the immobilization of biomolecules, structural flexibility, and biocompatibility. Bacterial nanocellulose (BNC) has gained a promising role as an alternative to antifouling surfaces. To widen its applicability as a biosensing device, BNC may form part of the supports for the immobilization of specific materials. The possibilities of modification methods and in situ and ex situ functionalization enable new BNC properties. With the new insights into nanoscale studies, we expect that many biosensors currently based on plastic, glass, or paper platforms will rely on renewable platforms, especially BNC ones. Moreover, substrates based on BNC seem to have paved the way for the development of sensing platforms with minimally invasive approaches, such as wearable devices, due to their mechanical flexibility and biocompatibility.
Collapse
Affiliation(s)
- Samuel Chagas de Assis
- Grupo de Pesquisa em Energia e Sustentabilidade Energética-GPEnSE, Universidade Federal da Integração Latino-Americana—UNILA, Av. Sílvio Américo Sasdelli, 1842, Foz do Iguaçu 85866-000, PR, Brazil
| | - Daniella Lury Morgado
- Grupo de Pesquisa em Energia e Sustentabilidade Energética-GPEnSE, Universidade Federal da Integração Latino-Americana—UNILA, Av. Sílvio Américo Sasdelli, 1842, Foz do Iguaçu 85866-000, PR, Brazil
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos 13566-590, SP, Brazil
| | - Desiree Tamara Scheidt
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos 13566-590, SP, Brazil
- Instituto Nacional de Ciência e Tecnologia de Bioanalítica-INCTBio, Campinas 13083-970, SP, Brazil
| | - Samara Silva de Souza
- Grupo de Pesquisa em Energia e Sustentabilidade Energética-GPEnSE, Universidade Federal da Integração Latino-Americana—UNILA, Av. Sílvio Américo Sasdelli, 1842, Foz do Iguaçu 85866-000, PR, Brazil
- Departamento de Engenharia de Bioprocessos e Biotecnologia, Universidade Tecnológica Federal do Paraná—UTFPR, Campus Dois Vizinhos, Dois Vizinhos 85660-000, PR, Brazil
| | - Marco Roberto Cavallari
- School of Electrical and Computer Engineering, University of Campinas (Unicamp), Av. Albert Einstein 400, Campinas 13083-852, SP, Brazil
| | - Oswaldo Hideo Ando Junior
- Grupo de Pesquisa em Energia e Sustentabilidade Energética-GPEnSE, Universidade Federal da Integração Latino-Americana—UNILA, Av. Sílvio Américo Sasdelli, 1842, Foz do Iguaçu 85866-000, PR, Brazil
- Academic Unit of Cabo de Santo Agostinho (UACSA), Universidade Federal Rural de Pernambuco (UFRPE), Rua Cento e Sessenta e Três, 300-Cohab, Cabo de Santo Agostinho 54518-430, PE, Brazil
| | - Emanuel Carrilho
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos 13566-590, SP, Brazil
- Instituto Nacional de Ciência e Tecnologia de Bioanalítica-INCTBio, Campinas 13083-970, SP, Brazil
| |
Collapse
|
30
|
Puri D, Fang X, Allison KR. Evidence of a possible multicellular life cycle in Escherichia coli. iScience 2022; 26:105795. [PMID: 36594031 PMCID: PMC9804144 DOI: 10.1016/j.isci.2022.105795] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Biofilms are surface-attached multicellular microbial communities. Their genetics have been extensively studied, but the cell-scale morphogenetic events of their formation are largely unknown. Here, we recorded the entirety of morphogenesis in Escherichia coli, and discovered a previously unknown multicellular self-assembly process. Unattached, single-cells formed 4-cell rosettes which grew into constant-width chains. After ∼10 cell generations, these multicellular chains attached to surfaces and stopped growing. Chains remained clonal throughout morphogenesis. We showed that this process generates biofilms, which we found are composed of attached clonal chains, aligned in parallel. We investigated genetics of chain morphogenesis: Ag43 facilitates rosette formation and clonality; type-1 fimbriae and curli promote stability and configuration; and extracellular polysaccharide production facilitates attachment. Our study establishes that E. coli, a unicellular organism, can follow a multistage, clonal, genetically-regulated, rosette-initiated multicellular life cycle. These findings have implications for synthetic biology, multicellular development, and the treatment and prevention of bacterial diseases.
Collapse
Affiliation(s)
- Devina Puri
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Xin Fang
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Kyle R. Allison
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA,Corresponding author
| |
Collapse
|
31
|
Park H, Schwartzman AF, Tang TC, Wang L, Lu TK. Ultra-lightweight living structural material for enhanced stiffness and environmental sensing. Mater Today Bio 2022; 18:100504. [PMID: 36504543 PMCID: PMC9729073 DOI: 10.1016/j.mtbio.2022.100504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Natural materials such as bone, wood, and bamboo can inspire the fabrication of stiff, lightweight structural materials. Biofilms are one of the most dominant forms of life in nature. However, little is known about their physical properties as a structural material. Here we report an Escherichia coli biofilm having a Young's modulus close to 10 GPa with ultra-low density, indicating a high-performance structural material. The mechanical and structural characterization of the biofilm and its components illuminates its adaptable bottom-up design, consisting of lightweight microscale cells covered by a dense network of amyloid nanofibrils on the surface. We engineered E. coli such that 1) carbon nanotubes assembled on the biofilm, enhancing its stiffness to over 30 GPa, or that 2) the biofilm sensitively detected heavy metal as an example of an environmental toxin. These demonstrations offer new opportunities for developing responsive living structural materials to serve many real-world applications.
Collapse
Affiliation(s)
- Heechul Park
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alan F. Schwartzman
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tzu-Chieh Tang
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lei Wang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Timothy K. Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Corresponding author. Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
32
|
Lima GM, Atrazhev A, Sarkar S, Sojitra M, Reddy R, Torres-Obreque K, de Oliveira Rangel-Yagui C, Macauley MS, Monteiro G, Derda R. DNA-Encoded Multivalent Display of Chemically Modified Protein Tetramers on Phage: Synthesis and in Vivo Applications. ACS Chem Biol 2022; 17:3024-3035. [PMID: 34928124 DOI: 10.1021/acschembio.1c00835] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Phage display links the phenotype of displayed polypeptides with the DNA sequence in the phage genome and offers a universal method for the discovery of proteins with novel properties. However, the display of large multisubunit proteins on phages remains a challenge. A majority of protein display systems are based on monovalent phagemid constructs, but methods for the robust display of multiple copies of large proteins are scarce. Here, we describe a DNA-encoded display of a ∼ 200 kDa tetrameric l-asparaginase protein on M13 and fd phages produced by ligation of SpyCatcher-Asparaginase fusion (ScA) and PEGylated-ScA (PEG-ScA) to barcoded phage clones displaying SpyTag peptide. Starting from the SpyTag display on p3 or p8 coat proteins yielded constructs with five copies of ScA displayed on p3 (ScA-p3), ∼100 copies of ScA on p8 protein (ScA-p8) and ∼300 copies of PEG-ScA on p8 protein (PEG-ScA-p8). Display constructs of different valencies and chemical modifications on protein (e.g., PEGylation) can be injected into mice and analyzed by deep sequencing of the DNA barcodes associated with phage clones. In these multiplexed studies, we observed a density and protein-dependent clearance rate in vivo. Our observations link the absence of PEGylation and increase in density of the displayed protein with the increased rate of the endocytosis by cells in vivo. In conclusion, we demonstrate that a multivalent display of l-asparaginase on phages could be used to study the circulation life of this protein in vivo, and such an approach opens the possibility to use DNA sequencing to investigate multiplexed libraries of other multisubunit proteins in vivo.
Collapse
Affiliation(s)
- Guilherme M Lima
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, 05508 000, Brazil.,Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Alexey Atrazhev
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Susmita Sarkar
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Mirat Sojitra
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Revathi Reddy
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Karin Torres-Obreque
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, 05508 000, Brazil
| | - Carlota de Oliveira Rangel-Yagui
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, 05508 000, Brazil
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gisele Monteiro
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, 05508 000, Brazil
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| |
Collapse
|
33
|
Birnbaum DP, Vilardi KJ, Anderson CL, Pinto AJ, Joshi NS. Simple Affinity-Based Method for Concentrating Viruses from Wastewater Using Engineered Curli Fibers. ACS ES&T WATER 2022; 2:1836-1843. [PMID: 36778666 PMCID: PMC9916486 DOI: 10.1021/acsestwater.1c00208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Wastewater surveillance is a proven method for tracking community spread and prevalence of some infectious viral diseases. A primary concentration step is often used to enrich viral particles from wastewater prior to subsequent viral quantification and/or sequencing. Here, we present a simple procedure for concentrating viruses from wastewater using bacterial biofilm protein nanofibers known as curli fibers. Through simple genetic engineering, we produced curli fibers functionalized with single-domain antibodies (also known as nanobodies) specific for the coat protein of the model virus bacteriophage MS2. Using these modified fibers in a simple spin-down protocol, we demonstrated efficient concentration of MS2 in both phosphate-buffered saline (PBS) and in the wastewater matrix. Additionally, we produced nanobody-functionalized curli fibers capable of binding the spike protein of SARS-CoV-2, showing the versatility of the system. Our concentration protocol is simple to implement, can be performed quickly under ambient conditions, and requires only components produced through bacterial culture. We believe this technology represents an attractive alternative to existing concentration methods and warrants further research and optimization for field-relevant applications.
Collapse
Affiliation(s)
- Daniel P Birnbaum
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States; Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Katherine J Vilardi
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Christopher L Anderson
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ameet J Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Neel S Joshi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| |
Collapse
|
34
|
Yi Q, Dai X, Park BM, Gu J, Luo J, Wang R, Yu C, Kou S, Huang J, Lakerveld R, Sun F. Directed assembly of genetically engineered eukaryotic cells into living functional materials via ultrahigh-affinity protein interactions. SCIENCE ADVANCES 2022; 8:eade0073. [PMID: 36332017 PMCID: PMC9635822 DOI: 10.1126/sciadv.ade0073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Engineered living materials (ELMs) are gaining traction among synthetic biologists, as their emergent properties and nonequilibrium thermodynamics make them markedly different from traditional materials. However, the aspiration to directly use living cells as building blocks to create higher-order structures or materials, with no need for chemical modification, remains elusive to synthetic biologists. Here, we report a strategy that enables the assembly of engineered Saccharomyces cerevisiae into self-propagating ELMs via ultrahigh-affinity protein/protein interactions. These yeast cells have been genetically engineered to display the protein pairs SpyTag/SpyCatcher or CL7/Im7 on their surfaces, which enable their assembly into multicellular structures capable of further growth and proliferation. The assembly process can be controlled precisely via optical tweezers or microfluidics. Moreover, incorporation of functional motifs such as super uranyl-binding protein and mussel foot proteins via genetic programming rendered these materials suitable for uranium extraction from seawater and bioadhesion, respectively, pointing to their potential in chemical separation and biomedical applications.
Collapse
Affiliation(s)
- Qikun Yi
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518036, China
- Biomedical Research Institute, Shenzhen Peking University–The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Xin Dai
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology, Health@InnoHK, Hong Kong Science Park, Hong Kong SAR, China
| | - Byung Min Park
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Junhao Gu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiren Luo
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Ri Wang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Cong Yu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology of China, Shenzhen 518036, China
| | - Songzi Kou
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518036, China
- Biomedical Research Institute, Shenzhen Peking University–The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology of China, Shenzhen 518036, China
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Richard Lakerveld
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518036, China
- Biomedical Research Institute, Shenzhen Peking University–The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| |
Collapse
|
35
|
Huang Y, Lin X, Yu S, Chen R, Chen W. Intestinal Engineered Probiotics as Living Therapeutics: Chassis Selection, Colonization Enhancement, Gene Circuit Design, and Biocontainment. ACS Synth Biol 2022; 11:3134-3153. [PMID: 36094344 DOI: 10.1021/acssynbio.2c00314] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Intestinal probiotics are often used for the in situ treatment of diseases, such as metabolic disorders, tumors, and chronic inflammatory infections. Recently, there has been an increased emphasis on intelligent, customized treatments with a focus on long-term efficacy; however, traditional probiotic therapy has not kept up with this trend. The use of synthetic biology to construct gut-engineered probiotics as live therapeutics is a promising avenue in the treatment of specific diseases, such as phenylketonuria and inflammatory bowel disease. These studies generally involve a series of fundamental design issues: choosing an engineered chassis, improving the colonization ability of engineered probiotics, designing functional gene circuits, and ensuring the safety of engineered probiotics. In this review, we summarize the relevant past research, the progress of current research, and discuss the key issues that restrict the widespread application of intestinal engineered probiotic living therapeutics.
Collapse
Affiliation(s)
- Yan Huang
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiaojun Lin
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Siyang Yu
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Ruiyue Chen
- Team SZU-China at iGEM 2021, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Weizhao Chen
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.,Shenzhen Key Laboratory for Microbial Gene Engineering, Shenzhen University, Shenzhen 518060, China
| |
Collapse
|
36
|
Özkul G, Kehribar EŞ, Ahan RE, Köksaldı İÇ, Özkul A, Dinç B, Aydoğan S, Şeker UÖŞ. A Genetically Engineered Biofilm Material for SARS-CoV-2 Capturing and Isolation. ADVANCED MATERIALS INTERFACES 2022; 9:2201126. [PMID: 36248312 PMCID: PMC9538133 DOI: 10.1002/admi.202201126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/10/2022] [Indexed: 06/16/2023]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously infecting people all around the world since its outbreak in 2019. Studies for numerous infection detection strategies are continuing. The sensitivity of detection methods is crucial to separate people with mild infections from people who are asymptomatic. In this sense, a strategy that would help to capture and isolate the SARS-CoV-2 virus prior to tests can be effective and beneficial. To this extent, genetically engineered biomaterials grounding from the biofilm protein of Escherichia coli are beneficial due to their robustness and adaptability to various application areas. Through functionalizing the E. coli biofilm protein, diverse properties can be attained such as enzyme display, nanoparticle production, and medical implant structures. Here, E. coli species are employed to express major curli protein CsgA and Griffithsin (GRFT) as fusion proteins, through a complex formation using SpyTag and SpyCatcher domains. In this study, a complex system with a CsgA scaffold harboring the affinity of GRFT against Spike protein to capture and isolate SARS-CoV-2 virus is successfully developed. It is shown that the hybrid recombinant protein can dramatically increase the sensitivity of currently available lateral flow assays for Sars-CoV-2 diagnostics.
Collapse
Affiliation(s)
- Gökçe Özkul
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - Ebru Şahin Kehribar
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - Recep Erdem Ahan
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - İlkay Çisil Köksaldı
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - Aykut Özkul
- Department of VirologyFaculty of Veterinary MedicineAnkara UniversityDışkapıAnkara06110Turkey
| | - Bedia Dinç
- Medical Microbiology Laboratory and Department of Clinical Microbiology and Infectious DiseasesAnkara Bilkent City HospitalHealth Sciences UniversityAnkara06800Turkey
| | - Sibel Aydoğan
- Medical Microbiology Laboratory and Department of Clinical Microbiology and Infectious DiseasesAnkara Bilkent City HospitalHealth Sciences UniversityAnkara06800Turkey
| | | |
Collapse
|
37
|
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: 1] [Impact Index Per Article: 0.5] [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.
Collapse
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
| |
Collapse
|
38
|
Ze Y, Wang R, Deng H, Zhou Z, Chen X, Huang L, Yao Y. Three-dimensional bioprinting: A cutting-edge tool for designing and fabricating engineered living materials. BIOMATERIALS ADVANCES 2022; 140:213053. [PMID: 35964390 DOI: 10.1016/j.bioadv.2022.213053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/12/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The design of engineered living materials (ELMs) is an emerging field developed from synthetic biology and materials science principles. ELMs are multi-scale bulk materials that combine the properties of self-healing and organism adaptability with the designed physicochemical or mechanical properties for functional applications in various fields, including therapy, electronics, and architecture. Among the many ELM design and manufacturing methods, three-dimensional (3D) bioprinting stands out for its precise control over the structure of the fabricated constructs and the spatial distribution of cells. In this review, we summarize the progress in the field, cell type and material selection, and the latest applications of 3D bioprinting to manufacture ELMs, as well as their advantages and limitations, hoping to deepen our understanding and provide new insights into ELM design. We believe that 3D bioprinting will become an important development direction and provide more contributions to this field.
Collapse
Affiliation(s)
- Yiting Ze
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Ruixin Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Hanzhi Deng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zheqing Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoju Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Linyang Huang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yang Yao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.
| |
Collapse
|
39
|
Gelfat I, Aqeel Y, Tremblay JM, Jaskiewicz JJ, Shrestha A, Lee JN, Hu S, Qian X, Magoun L, Sheoran A, Bedenice D, Giem C, Manjula-Basavanna A, Pulsifer AR, Tu HX, Li X, Minus ML, Osburne MS, Tzipori S, Shoemaker CB, Leong JM, Joshi NS. Single domain antibodies against enteric pathogen virulence factors are active as curli fiber fusions on probiotic E. coli Nissle 1917. PLoS Pathog 2022; 18:e1010713. [PMID: 36107831 PMCID: PMC9477280 DOI: 10.1371/journal.ppat.1010713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
Enteric microbial pathogens, including Escherichia coli, Shigella and Cryptosporidium species, take a particularly heavy toll in low-income countries and are highly associated with infant mortality. We describe here a means to display anti-infective agents on the surface of a probiotic bacterium. Because of their stability and versatility, VHHs, the variable domains of camelid heavy-chain-only antibodies, have potential as components of novel agents to treat or prevent enteric infectious disease. We isolated and characterized VHHs targeting several enteropathogenic E. coli (EPEC) virulence factors: flagellin (Fla), which is required for bacterial motility and promotes colonization; both intimin and the translocated intimin receptor (Tir), which together play key roles in attachment to enterocytes; and E. coli secreted protein A (EspA), an essential component of the type III secretion system (T3SS) that is required for virulence. Several VHHs that recognize Fla, intimin, or Tir blocked function in vitro. The probiotic strain E. coli Nissle 1917 (EcN) produces on the bacterial surface curli fibers, which are the major proteinaceous component of E. coli biofilms. A subset of Fla-, intimin-, or Tir-binding VHHs, as well as VHHs that recognize either a T3SS of another important bacterial pathogen (Shigella flexneri), a soluble bacterial toxin (Shiga toxin or Clostridioides difficile toxin TcdA), or a major surface antigen of an important eukaryotic pathogen (Cryptosporidium parvum) were fused to CsgA, the major curli fiber subunit. Scanning electron micrographs indicated CsgA-VHH fusions were assembled into curli fibers on the EcN surface, and Congo Red binding indicated that these recombinant curli fibers were produced at high levels. Ectopic production of these VHHs conferred on EcN the cognate binding activity and, in the case of anti-Shiga toxin, was neutralizing. Taken together, these results demonstrate the potential of the curli-based pathogen sequestration strategy described herein and contribute to the development of novel VHH-based gut therapeutics.
Collapse
Affiliation(s)
- Ilia Gelfat
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Allston, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yousuf Aqeel
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Jacqueline M. Tremblay
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Justyna J. Jaskiewicz
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Anishma Shrestha
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - James N. Lee
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Shenglan Hu
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Xi Qian
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Loranne Magoun
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Abhineet Sheoran
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Daniela Bedenice
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Colter Giem
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Avinash Manjula-Basavanna
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Amanda R. Pulsifer
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Hann X. Tu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Xiaoli Li
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Marilyn L. Minus
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Marcia S. Osburne
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Charles B. Shoemaker
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - John M. Leong
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Medford, Massachusetts, United States of America
| | - Neel S. Joshi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| |
Collapse
|
40
|
Nanocoating of CsgA protein for enhanced cell adhesion and proliferation. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
41
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
42
|
Hu MX, He F, Zhao ZS, Guo YX, Ma XK, Tu CK, Teng H, Chen ZX, Yan H, Shao X. Electrospun Nanofibrous Membranes Accelerate Biofilm Formation and Probiotic Enrichment: Enhanced Tolerances to pH and Antibiotics. ACS APPLIED MATERIALS & INTERFACES 2022; 14:31601-31612. [PMID: 35793165 DOI: 10.1021/acsami.2c04540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biofilms are the oldest, most successful, and most widely distributed form of microorganism life on earth, existing even in extreme environments. Presently, probiotics in biofilm phenotype are thought as the most advanced fourth-generation probiotics. However, high-efficiency and large-scale biofilm enrichment in an artificial way is difficult. Here, fibrous membranes as probiotic biofilm-enriching materials are studied. Electrospun cellulose acetate nanofibrous membranes with nano-sized fibers show outstanding superiority over fibrous membranes with micron-sized fibers in Lactobacillus paracasei biofilm enrichment. The special 3D structure of electrospun nanofibrous membranes makes other facilitating biofilm formation factors insignificant. With a suitable scaffold/culture medium ratio, nearly 100% of L. paracasei cells exist as biofilm phenotype on the membrane from the very beginning, not planktonic state. L. paracasei biofilms possess a potential for long-term survival and high tolerances toward strong acidic and alkali conditions and antibiotics. RNA sequencing results explain why L. paracasei biofilms possess high tolerances toward harsh environments as compared to planktonic L. paracasei. Electrospun nanofibrous membranes can serve as powerful biofilm-enriching scaffolds for probiotics and other valuable microbes.
Collapse
Affiliation(s)
- Meng-Xin Hu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Fei He
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Zi-Shu Zhao
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Ya-Xin Guo
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Xue-Ke Ma
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Cheng-Kai Tu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Hui Teng
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Zhe-Xin Chen
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Hong Yan
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Xin Shao
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| |
Collapse
|
43
|
Chen YY, Yang FQ, Xu N, Wang XQ, Xie PC, Wang YZ, Fang Z, Yong YC. Engineered cytochrome fused extracellular matrix enabled efficient extracellular electron transfer and improved performance of microbial fuel cell. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154806. [PMID: 35341857 DOI: 10.1016/j.scitotenv.2022.154806] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/20/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
Microbial fuel cell (MFC) was a promising technology for energy harvesting from wastewater. However, inefficient bacterial extracellular electron transfer (EET) limited the performance as well as the applications of MFC. Here, a new strategy to reinforce the EET by engineering synthetic extracellular matrix (ECM) with cytochrome fused curli was developed. By genetically fusing a minimal cytochrome domain (MCD) with the curli protein CsgA and heterogeneously expressing in model exoelectrogen of Shewanella oneidensis MR-1, the cytochrome fused electroactive curli network was successfully constructed and assembled. Interestingly, the strain with the MCD fused synthetic ECM delivered about 2.4 times and 2.0 times higher voltage and power density output than these of wild type MR-1 in MFC. More impressively, electrochemical analysis suggested that this synthetic ECM not only introduced cytochrome of MCD, but also attracted more self-secreted electrochemically active substances, which might facilitate the EET and improve the MFC performance. This work demonstrated the possibility to manipulation the EET with ECM engineering, which opened up new path for exoelectrogen design and engineering.
Collapse
Affiliation(s)
- Yuan-Yuan Chen
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Fu-Qiao Yang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Nuo Xu
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xing-Qiang Wang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Peng-Cheng Xie
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yan-Zhai Wang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zhen Fang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yang-Chun Yong
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| |
Collapse
|
44
|
Tyrikos-Ergas T, Gim S, Huang JY, Pinzón Martín S, Varón Silva D, Seeberger PH, Delbianco M. Synthetic phosphoethanolamine-modified oligosaccharides reveal the importance of glycan length and substitution in biofilm-inspired assemblies. Nat Commun 2022; 13:3954. [PMID: 35804023 PMCID: PMC9270332 DOI: 10.1038/s41467-022-31633-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/28/2022] [Indexed: 12/18/2022] Open
Abstract
Bacterial biofilm matrices are nanocomposites of proteins and polysaccharides with remarkable mechanical properties. Efforts understanding and tuning the protein component have been extensive, whereas the polysaccharide part remained mostly overlooked. The discovery of phosphoethanolamine (pEtN) modified cellulose in E. coli biofilms revealed that polysaccharide functionalization alters the biofilm properties. To date, the pattern of pEtN cellulose and its mode of interactions with proteins remains elusive. Herein, we report a model system based on synthetic epitomes to explore the role of pEtN in biofilm-inspired assemblies. Nine pEtN-modified oligosaccharides were synthesized with full control over the length, degree and pattern of pEtN substitution. The oligomers were co-assembled with a representative peptide, triggering the formation of fibers in a length dependent manner. We discovered that the pEtN pattern modulates the adhesion of biofilm-inspired matrices, while the peptide component controls its stiffness. Unnatural oligosaccharides tune or disrupt the assembly morphology, revealing interesting targets for polysaccharide engineering to develop tunable bio-inspired materials.
Collapse
Affiliation(s)
- Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Soeun Gim
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Jhih-Yi Huang
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Sandra Pinzón Martín
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Daniel Varón Silva
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany.,Institute of Chemistry and Bioanalytics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.
| |
Collapse
|
45
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
46
|
Functional Bacterial Amyloids: Understanding Fibrillation, Regulating Biofilm Fibril Formation and Organizing Surface Assemblies. Molecules 2022; 27:molecules27134080. [PMID: 35807329 PMCID: PMC9268375 DOI: 10.3390/molecules27134080] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
Functional amyloid is produced by many organisms but is particularly well understood in bacteria, where proteins such as CsgA (E. coli) and FapC (Pseudomonas) are assembled as functional bacterial amyloid (FuBA) on the cell surface in a carefully optimized process. Besides a host of helper proteins, FuBA formation is aided by multiple imperfect repeats which stabilize amyloid and streamline the aggregation mechanism to a fast-track assembly dominated by primary nucleation. These repeats, which are found in variable numbers in Pseudomonas, are most likely the structural core of the fibrils, though we still lack experimental data to determine whether the repeats give rise to β-helix structures via stacked β-hairpins (highly likely for CsgA) or more complicated arrangements (possibly the case for FapC). The response of FuBA fibrillation to denaturants suggests that nucleation and elongation involve equal amounts of folding, but protein chaperones preferentially target nucleation for effective inhibition. Smart peptides can be designed based on these imperfect repeats and modified with various flanking sequences to divert aggregation to less stable structures, leading to a reduction in biofilm formation. Small molecules such as EGCG can also divert FuBA to less organized structures, such as partially-folded oligomeric species, with the same detrimental effect on biofilm. Finally, the strong tendency of FuBA to self-assemble can lead to the formation of very regular two-dimensional amyloid films on structured surfaces such as graphite, which strongly implies future use in biosensors or other nanobiomaterials. In summary, the properties of functional amyloid are a much-needed corrective to the unfortunate association of amyloid with neurodegenerative disease and a testimony to nature’s ability to get the best out of a protein fold.
Collapse
|
47
|
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: 2.5] [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.
Collapse
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
| | | |
Collapse
|
48
|
Park H, Jeon H, Lee MY, Jeon H, Kwon S, Hong S, Kang K. Designed Amyloid Fibers with Emergent Melanosomal Functions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7077-7084. [PMID: 35608255 DOI: 10.1021/acs.langmuir.2c00904] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Short peptides designed to self-associate into amyloid fibers with metal ion-binding ability have been used to catalyze various types of chemical reactions. This manuscript demonstrates that one of these short-peptide fibers coordinated with CuII can exhibit melanosomal functions. The coordinated CuII and the amyloid structure itself are differentially functional in accelerating oxidative self-association of dopamine into melanin-like species and in regulating their material properties (e.g., water dispersion, morphology, and the density of unpaired electrons). The results have implications for the role of functional amyloids in melanin biosynthesis and for designing peptide-based supramolecular structures with various emergent functions.
Collapse
Affiliation(s)
- Hyeyeon Park
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
| | - Hyeri Jeon
- Department of Chemistry, Sookmyung Women's University, Seoul 04310, South Korea
| | - Min Young Lee
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
| | - Hyojae Jeon
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
| | - Sunbum Kwon
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | - Seungwoo Hong
- Department of Chemistry, Sookmyung Women's University, Seoul 04310, South Korea
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
| |
Collapse
|
49
|
Taylor AIP, Staniforth RA. General Principles Underpinning Amyloid Structure. Front Neurosci 2022; 16:878869. [PMID: 35720732 PMCID: PMC9201691 DOI: 10.3389/fnins.2022.878869] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Amyloid fibrils are a pathologically and functionally relevant state of protein folding, which is generally accessible to polypeptide chains and differs fundamentally from the globular state in terms of molecular symmetry, long-range conformational order, and supramolecular scale. Although amyloid structures are challenging to study, recent developments in techniques such as cryo-EM, solid-state NMR, and AFM have led to an explosion of information about the molecular and supramolecular organization of these assemblies. With these rapid advances, it is now possible to assess the prevalence and significance of proposed general structural features in the context of a diverse body of high-resolution models, and develop a unified view of the principles that control amyloid formation and give rise to their unique properties. Here, we show that, despite system-specific differences, there is a remarkable degree of commonality in both the structural motifs that amyloids adopt and the underlying principles responsible for them. We argue that the inherent geometric differences between amyloids and globular proteins shift the balance of stabilizing forces, predisposing amyloids to distinct molecular interaction motifs with a particular tendency for massive, lattice-like networks of mutually supporting interactions. This general property unites previously characterized structural features such as steric and polar zippers, and contributes to the long-range molecular order that gives amyloids many of their unique properties. The shared features of amyloid structures support the existence of shared structure-activity principles that explain their self-assembly, function, and pathogenesis, and instill hope in efforts to develop broad-spectrum modifiers of amyloid function and pathology.
Collapse
|
50
|
Caparco AA, Dautel DR, Champion JA. Protein Mediated Enzyme Immobilization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106425. [PMID: 35182030 DOI: 10.1002/smll.202106425] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Enzyme immobilization is an essential technology for commercializing biocatalysis. It imparts stability, recoverability, and other valuable features that improve the effectiveness of biocatalysts. While many avenues to join an enzyme to solid phases exist, protein-mediated immobilization is rapidly developing and has many advantages. Protein-mediated immobilization allows for the binding interaction to be genetically coded, can be used to create artificial multienzyme cascades, and enables modular designs that expand the variety of enzymes immobilized. By designing around binding interactions between protein domains, they can be integrated into functional materials for protein immobilization. These materials are framed within the context of biocatalytic performance, immobilization efficiency, and stability of the materials. In this review, supports composed entirely of protein are discussed first, with systems such as cellulosomes and protein cages being discussed alongside newer technologies like spore-based biocatalysts and forizymes. Protein-composite materials such as polymersomes and protein-inorganic supraparticles are then discussed to demonstrate how protein-mediated strategies are applied to many classes of solid materials. Critical analysis and future directions of protein-based immobilization are then discussed, with a particular focus on both computational and design strategies to advance this area of research and make it more broadly applicable to many classes of enzymes.
Collapse
Affiliation(s)
- Adam A Caparco
- Department of Nanoengineering, University of California, San Diego, MC 0448, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Dylan R Dautel
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, GA, 30332, USA
| | - Julie A Champion
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, GA, 30332, USA
| |
Collapse
|