1
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Jones AA, Snow CD. Porous protein crystals: synthesis and applications. Chem Commun (Camb) 2024; 60:5790-5803. [PMID: 38756076 DOI: 10.1039/d4cc00183d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Large-pore protein crystals (LPCs) are an emerging class of biomaterials. The inherent diversity of proteins translates to a diversity of crystal lattice structures, many of which display large pores and solvent channels. These pores can, in turn, be functionalized via directed evolution and rational redesign based on the known crystal structures. LPCs possess extremely high solvent content, as well as extremely high surface area to volume ratios. Because of these characteristics, LPCs continue to be explored in diverse applications including catalysis, targeted therapeutic delivery, templating of nanostructures, structural biology. This Feature review article will describe several of the existing platforms in detail, with particular focus on LPC synthesis approaches and reported applications.
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Affiliation(s)
- Alec Arthur Jones
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA.
| | - Christopher D Snow
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA.
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA
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2
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Herdman M, Isbilir B, von Kügelgen A, Schulze U, Wainman A, Bharat TAM. Cell cycle dependent coordination of surface layer biogenesis in Caulobacter crescentus. Nat Commun 2024; 15:3355. [PMID: 38637514 PMCID: PMC11026435 DOI: 10.1038/s41467-024-47529-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Surface layers (S-layers) are proteinaceous, two-dimensional paracrystalline arrays that constitute a major component of the cell envelope in many prokaryotic species. In this study, we investigated S-layer biogenesis in the bacterial model organism Caulobacter crescentus. Fluorescence microscopy revealed localised incorporation of new S-layer at the poles and mid-cell, consistent with regions of cell growth in the cell cycle. Light microscopy and electron cryotomography investigations of drug-treated bacteria revealed that localised S-layer insertion is retained when cell division is inhibited, but is disrupted upon dysregulation of MreB or lipopolysaccharide. We further uncovered that S-layer biogenesis follows new peptidoglycan synthesis and localises to regions of high cell wall turnover. Finally, correlated cryo-light microscopy and electron cryotomographic analysis of regions of S-layer insertion showed the presence of discontinuities in the hexagonal S-layer lattice, contrasting with other S-layers completed by defined symmetric defects. Our findings present insights into how C. crescentus cells form an ordered S-layer on their surface in coordination with the biogenesis of other cell envelope components.
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Affiliation(s)
- Matthew Herdman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Buse Isbilir
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Ulrike Schulze
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Alan Wainman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
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3
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Yun L, Sakkos JK, Ducat DC. Population-level heterogeneity complicates utilization of Synechococcus elongatus PCC 7942 surface display platforms. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001097. [PMID: 38633869 PMCID: PMC11022076 DOI: 10.17912/micropub.biology.001097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Surface display technologies have been primarily developed for heterotrophic microbes, leaving photosynthetic counterparts like cyanobacteria with limited molecular tools. Here, we expanded upon surface display systems in Synechococcus elongatus PCC 7942 by modifying two outer-membrane proteins, SomA and Intimin, to display tags ( e.g. , SpyTag) to mediate physical interactions of living cyanobacteria with other biotic and abiotic targets. While re-engineered SomA constructs successfully translocated to the cell surface and could bind to compatible ligands, the efficacy of the best-performing designs was limited by a poorly-understood heterogeneity in the accessibility of the tags in living cells, resulting in low attachment penetrance.
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Affiliation(s)
- Lisa Yun
- DOE-MSU Plant Research Laboratories, Michigan State University, East Lansing, Michigan, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States
| | - Jonathan K Sakkos
- DOE-MSU Plant Research Laboratories, Michigan State University, East Lansing, Michigan, United States
| | - Daniel C Ducat
- DOE-MSU Plant Research Laboratories, Michigan State University, East Lansing, Michigan, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States
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4
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Yu X, Li H, Tian W, Ge Y, Wang T, Qi Z, Liu J. Single-layer semiconductor-decorated flexible 2D protein nanosheets by engineered anchoring for efficient photocatalytic hydrogen production. Int J Biol Macromol 2024; 261:129819. [PMID: 38290631 DOI: 10.1016/j.ijbiomac.2024.129819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/01/2024]
Abstract
Protein self-assembly can be accurately manipulated to form ordered nanostructures through various supramolecular forces. This strategy is expected to make significant breakthroughs in the field of new biomimetic functional materials. Specifically, the construction of photocatalytic systems on two-dimensional (2D) flexible protein nanosheets meets a great challenge. We introduce a synthetic methodology for creating single-layer semiconductor-decorated protein 2D materials under mild conditions with enhanced light-driven hydrogen production. This approach employs a bioengineered green fluorescent protein (E4P) with the addition of a Cd-binding peptide, enabling precise control of the assembly of CdS quantum dots (QDs) on the protein's surface. Consequently, we obtained 4.3 nm-thin single-layer 2D protein nanosheets with substantial surface areas ideal for accommodating CdS QDs. By orthogonal incorporation of metal-binding peptides and supramolecular coordination, significantly enhancing the overall photocatalytic efficiency. Our findings demonstrate the potential for stable and efficient hydrogen production, highlighting the adaptability and biocompatibility of protein scaffolds for photocatalysis.
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Affiliation(s)
- Xiaoxuan Yu
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China; Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Hui Li
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China; Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Wei Tian
- Shaanxi Key Laboratory of Macromolecular Science and Technology, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yan Ge
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tingting Wang
- Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Zhenhui Qi
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Junqiu Liu
- Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China.
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5
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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.
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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.
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6
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Gambelli L, McLaren M, Conners R, Sanders K, Gaines MC, Clark L, Gold VAM, Kattnig D, Sikora M, Hanus C, Isupov MN, Daum B. Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius. eLife 2024; 13:e84617. [PMID: 38251732 PMCID: PMC10903991 DOI: 10.7554/elife.84617] [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: 11/01/2022] [Accepted: 01/19/2024] [Indexed: 01/23/2024] Open
Abstract
Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single-particle cryo electron microscopy, cryo electron tomography, and Alphafold2 predictions to generate an atomic model of the two-component S-layer of Sulfolobus acidocaldarius. The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesise that jackknife-like conformational changes in SlaA play important roles in S-layer assembly.
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Affiliation(s)
- Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Matthew C Gaines
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Lewis Clark
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Daniel Kattnig
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, Frankfurt, Germany
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Cyril Hanus
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266 - Université Paris Cité, Paris, France
- GHU Psychiatrie et Neurosciences de Paris, Paris, France
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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7
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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.
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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
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8
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von Kügelgen A, van Dorst S, Yamashita K, Sexton DL, Tocheva EI, Murshudov G, Alva V, Bharat TAM. Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium Deinococcus radiodurans. Proc Natl Acad Sci U S A 2023; 120:e2215808120. [PMID: 37043530 PMCID: PMC10120038 DOI: 10.1073/pnas.2215808120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/14/2023] [Indexed: 04/13/2023] Open
Abstract
Deinococcus radiodurans is an atypical diderm bacterium with a remarkable ability to tolerate various environmental stresses, due in part to its complex cell envelope encapsulated within a hyperstable surface layer (S-layer). Despite decades of research on this cell envelope, atomic structural details of the S-layer have remained obscure. In this study, we report the electron cryomicroscopy structure of the D. radiodurans S-layer, showing how it is formed by the Hexagonally Packed Intermediate-layer (HPI) protein arranged in a planar hexagonal lattice. The HPI protein forms an array of immunoglobulin-like folds within the S-layer, with each monomer extending into the adjacent hexamer, resulting in a highly interconnected, stable, sheet-like arrangement. Using electron cryotomography and subtomogram averaging from focused ion beam-milled D. radiodurans cells, we have obtained a structure of the cellular S-layer, showing how this HPI S-layer coats native membranes on the surface of cells. Our S-layer structure from the diderm bacterium D. radiodurans shows similarities to immunoglobulin-like domain-containing S-layers from monoderm bacteria and archaea, highlighting common features in cell surface organization across different domains of life, with connotations on the evolution of immunoglobulin-based molecular recognition systems in eukaryotes.
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Affiliation(s)
- Andriko von Kügelgen
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Sofie van Dorst
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Keitaro Yamashita
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Danielle L. Sexton
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Elitza I. Tocheva
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Garib Murshudov
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen72076, Germany
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
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9
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An B, Wang Y, Huang Y, Wang X, Liu Y, Xun D, Church GM, Dai Z, Yi X, Tang TC, Zhong C. Engineered Living Materials For Sustainability. Chem Rev 2023; 123:2349-2419. [PMID: 36512650 DOI: 10.1021/acs.chemrev.2c00512] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.
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Affiliation(s)
- Bolin An
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yanyi Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuanyuan Huang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xinyu Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuzhu Liu
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dongmin Xun
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - George M Church
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Zhuojun Dai
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiao Yi
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tzu-Chieh Tang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Chao Zhong
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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10
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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.
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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
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11
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Huang S, Ba F, Liu WQ, Li J. Stapled NRPS enhances the production of valinomycin in Escherichia coli. Biotechnol Bioeng 2023; 120:793-802. [PMID: 36510694 DOI: 10.1002/bit.28303] [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: 10/14/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Abstract
Nonribosomal peptides (NRPs) are a large family of secondary metabolites with notable bioactivities, which distribute widely in natural resources across microbes and plants. To obtain these molecules, heterologous production of NRPs in robust surrogate hosts like Escherichia coli represent a feasible approach. However, reconstitution of the full biosynthetic pathway in a host often leads to low productivity, which is at least in part due to the low efficiency of enzyme interaction in vivo except for the well-known reasons of metabolic burden (e.g., expression of large NRP synthetases-NRPSs with molecular weights of >100 kDa) and cellular toxicity on host cells. To enhance the catalytic efficiency of large NRPSs in vivo, here we propose to staple NRPS enzymes by using short peptide/protein pairs (e.g., SpyTag/SpyCatcher) for enhanced NRP production. We achieve this goal by introducing a stapled NRPS system for the biosynthesis of the antibiotic NRP valinomycin in E. coli. The results indicate that stapled valinomycin synthetase (Vlm1 and Vlm2) enables higher product accumulation than those two free enzymes (e.g., the maximum improvement is nearly fourfold). After further optimization by strain and bioprocess engineering, the final valinomycin titer maximally reaches about 2800 µg/L, which is 73 times higher than the initial titer of 38 µg/L. We expect that stapling NRPS enzymes will be a promising catalytic strategy for high-level biosynthesis of NRP natural products.
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Affiliation(s)
- Shuhui Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
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12
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Synchronized Swarmers and Sticky Stalks: Caulobacter crescentus as a Model for Bacterial Cell Biology. J Bacteriol 2023; 205:e0038422. [PMID: 36715542 PMCID: PMC9945503 DOI: 10.1128/jb.00384-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
First isolated and classified in the 1960s, Caulobacter crescentus has been instrumental in the study of bacterial cell biology and differentiation. C. crescentus is a Gram-negative alphaproteobacterium that exhibits a dimorphic life cycle composed of two distinct cell types: a motile swarmer cell and a nonmotile, division-competent stalked cell. Progression through the cell cycle is accentuated by tightly controlled biogenesis of appendages, morphological transitions, and distinct localization of developmental regulators. These features as well as the ability to synchronize populations of cells and follow their progression make C. crescentus an ideal model for answering questions relevant to how development and differentiation are achieved at the single-cell level. This review will explore the discovery and development of C. crescentus as a model organism before diving into several key features and discoveries that have made it such a powerful organism to study. Finally, we will summarize a few of the ongoing areas of research that are leveraging knowledge gained over the last century with C. crescentus to highlight its continuing role at the forefront of cell and developmental biology.
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13
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Davenport B, Hallam SJ. Emerging enzyme surface display systems for waste resource recovery. Environ Microbiol 2023; 25:241-249. [PMID: 36369958 PMCID: PMC10100002 DOI: 10.1111/1462-2920.16284] [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: 08/22/2022] [Accepted: 11/09/2022] [Indexed: 11/15/2022]
Abstract
The current century marks an inflection point for human progress, as the developed world increasingly comes to recognize that the ecological and socioeconomic impacts of resource extraction must be balanced with more sustainable modes of growth that are less reliant on non-renewable sources of energy and materials. This has opened a window of opportunity for cross-sector development of biotechnologies that harness the metabolic problem-solving power of microbial communities. In this context, recovery has emerged as an organizing principal to create value from industrial and municipal waste streams, and the search is on for new enzymes and platforms that can be used for waste resource recovery at scale. Enzyme surface display on cells or functionalized materials has emerged as a promising platform for waste valorization. Typically, surface display involves the use of substrate binding or catalytic domains of interest translationally fused with extracellular membrane proteins in a microbial chassis. Novel display systems with improved performance features include S-layer display with increased protein density, spore display with increased resistance to harsh conditions, and intracellular inclusions including DNA-free cells or nanoparticles with improved social licence for in situ applications. Combining these display systems with advances in bioprinting, electrospinning and high-throughput functional screening have potential to transform outmoded extractive paradigms into 'trans-metabolic" processes for remediation and waste resource recovery within an emerging circular bioeconomy.
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Affiliation(s)
- Beth Davenport
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J Hallam
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Bradshaw Research Institute for Minerals and Mining, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
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14
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A de novo matrix for macroscopic living materials from bacteria. Nat Commun 2022; 13:5544. [PMID: 36130968 PMCID: PMC9492681 DOI: 10.1038/s41467-022-33191-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/08/2022] [Indexed: 11/08/2022] Open
Abstract
Engineered living materials (ELMs) embed living cells in a biopolymer matrix to create materials with tailored functions. While bottom-up assembly of macroscopic ELMs with a de novo matrix would offer the greatest control over material properties, we lack the ability to genetically encode a protein matrix that leads to collective self-organization. Here we report growth of ELMs from Caulobacter crescentus cells that display and secrete a self-interacting protein. This protein formed a de novo matrix and assembled cells into centimeter-scale ELMs. Discovery of design and assembly principles allowed us to tune the composition, mechanical properties, and catalytic function of these ELMs. This work provides genetic tools, design and assembly rules, and a platform for growing ELMs with control over both matrix and cellular structure and function. Engineered living materials (ELMs) embed living cells in a biopolymer matrix to create novel materials with tailored functions. In this work, the authors engineered bacteria to grow novel macroscopic materials that can be reshaped, functionalized, and used to filter contaminated water while also showing that the stiffness of these materials can be tuned through genetic changes.
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15
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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.
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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.
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16
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Wang Y, Liu Y, Li J, Chen Y, Liu S, Zhong C. Engineered living materials (ELMs) design: From function allocation to dynamic behavior modulation. Curr Opin Chem Biol 2022; 70:102188. [PMID: 35970133 DOI: 10.1016/j.cbpa.2022.102188] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/14/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022]
Abstract
Natural materials possess many distinctive "living" attributes, such as self-growth, self-healing, environmental responsiveness, and evolvability, that are beyond the reach of many existing synthetic materials. The emerging field of engineered living materials (ELMs) takes inspiration from nature and harnesses engineered living systems to produce dynamic and responsive materials with genetically programmable functionalities. Here, we identify and review two main directions for the rational design of ELMs: first, engineering of living materials with enhanced performances by incorporating functional material modules, including engineered biological building blocks (proteins, polysaccharides, and nucleic acids) or well-defined artificial materials; second, engineering of smart ELMs that can sense and respond to their surroundings by programming dynamic cellular behaviors regulated via cell-cell or cell-environment interactions. We next discuss the strengths and challenges of current ELMs and conclude by providing a perspective of future directions in this promising area.
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Affiliation(s)
- 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
| | - Yi 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; School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jing Li
- 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
| | - Yue Chen
- 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
| | - Sizhe 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; School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China
| | - Chao Zhong
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Cas Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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17
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In vitro investigation of protein assembly by combined microscopy and infrared spectroscopy at the nanometer scale. Proc Natl Acad Sci U S A 2022; 119:e2200019119. [PMID: 35914130 PMCID: PMC9371722 DOI: 10.1073/pnas.2200019119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The nanoscale structure and dynamics of proteins on surfaces has been extensively studied using various imaging techniques, such as transmission electron microscopy and atomic force microscopy (AFM) in liquid environments. These powerful imaging techniques, however, can potentially damage or perturb delicate biological material and do not provide chemical information, which prevents a fundamental understanding of the dynamic processes underlying their evolution under physiological conditions. Here, we use a platform developed in our laboratory that enables acquisition of infrared (IR) spectroscopy and AFM images of biological material in physiological liquids with nanometer resolution in a cell closed by atomically thin graphene membranes transparent to IR photons. In this work, we studied the self-assembly process of S-layer proteins at the graphene-aqueous solution interface. The graphene acts also as the membrane separating the solution containing the proteins and Ca2+ ions from the AFM tip, thus eliminating sample damage and contamination effects. The formation of S-layer protein lattices and their structural evolution was monitored by AFM and by recording the amide I and II IR absorption bands, which reveal the noncovalent interaction between proteins and their response to the environment, including ionic strength and solvation. Our measurement platform opens unique opportunities to study biological material and soft materials in general.
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18
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SpySwitch enables pH- or heat-responsive capture and release for plug-and-display nanoassembly. Nat Commun 2022; 13:3714. [PMID: 35764623 PMCID: PMC9240080 DOI: 10.1038/s41467-022-31193-8] [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: 01/06/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
Proteins can be empowered via SpyTag for anchoring and nanoassembly, through covalent bonding to SpyCatcher partners. Here we generate a switchable version of SpyCatcher, allowing gentle purification of SpyTagged proteins. We introduce numerous histidines adjacent to SpyTag’s binding site, giving moderate pH-dependent release. After phage-based selection, our final SpySwitch allows purification of SpyTag- and SpyTag003-fusions from bacterial or mammalian culture by capture at neutral pH and release at pH 5, with purity far beyond His-tag methods. SpySwitch is also thermosensitive, capturing at 4 °C and releasing at 37 °C. With flexible choice of eluent, SpySwitch-purified proteins can directly assemble onto multimeric scaffolds. 60-mer multimerization enhances immunogenicity and we use SpySwitch to purify receptor-binding domains from SARS-CoV-2 and 11 other sarbecoviruses. For these receptor-binding domains we determine thermal resilience (for mosaic vaccine development) and cross-recognition by antibodies. Antibody EY6A reacts across all tested sarbecoviruses, towards potential application against new coronavirus pandemic threats. The SpyCatcher-SpyTag system allows protein anchoring and nanoassembly. Here, the authors engineer SpySwitch, a dually switchable Catcher which allows gentle purification of SpyTagged proteins prior to downstream applications such as the assembly of virus-like particles.
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19
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Liu AP, Appel EA, Ashby PD, Baker BM, Franco E, Gu L, Haynes K, Joshi NS, Kloxin AM, Kouwer PHJ, Mittal J, Morsut L, Noireaux V, Parekh S, Schulman R, Tang SKY, Valentine MT, Vega SL, Weber W, Stephanopoulos N, Chaudhuri O. The living interface between synthetic biology and biomaterial design. NATURE MATERIALS 2022; 21:390-397. [PMID: 35361951 PMCID: PMC10265650 DOI: 10.1038/s41563-022-01231-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Recent far-reaching advances in synthetic biology have yielded exciting tools for the creation of new materials. Conversely, advances in the fundamental understanding of soft-condensed matter, polymers and biomaterials offer new avenues to extend the reach of synthetic biology. The broad and exciting range of possible applications have substantial implications to address grand challenges in health, biotechnology and sustainability. Despite the potentially transformative impact that lies at the interface of synthetic biology and biomaterials, the two fields have, so far, progressed mostly separately. This Perspective provides a review of recent key advances in these two fields, and a roadmap for collaboration at the interface between the two communities. We highlight the near-term applications of this interface to the development of hierarchically structured biomaterials, from bioinspired building blocks to 'living' materials that sense and respond based on the reciprocal interactions between materials and embedded cells.
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Affiliation(s)
- Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.
| | - Eric A Appel
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, USA
| | - Paul D Ashby
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brendon M Baker
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Luo Gu
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Karmella Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA, USA
| | - Neel S Joshi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - April M Kloxin
- Department of Chemical and Biomolecular Engineering and Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Paul H J Kouwer
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Leonardo Morsut
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Sapun Parekh
- Department of Biomedical Engineering, University of Texas, Austin, Austin, TX, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sindy K Y Tang
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Megan T Valentine
- Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Sebastián L Vega
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ, USA
| | - Wilfried Weber
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | | | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA.
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20
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McBee RM, Lucht M, Mukhitov N, Richardson M, Srinivasan T, Meng D, Chen H, Kaufman A, Reitman M, Munck C, Schaak D, Voigt C, Wang HH. Engineering living and regenerative fungal-bacterial biocomposite structures. NATURE MATERIALS 2022; 21:471-478. [PMID: 34857911 DOI: 10.1038/s41563-021-01123-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Engineered living materials could have the capacity to self-repair and self-replicate, sense local and distant disturbances in their environment, and respond with functionalities for reporting, actuation or remediation. However, few engineered living materials are capable of both responsivity and use in macroscopic structures. Here we describe the development, characterization and engineering of a fungal-bacterial biocomposite grown on lignocellulosic feedstocks that can form mouldable, foldable and regenerative living structures. We have developed strategies to make human-scale biocomposite structures using mould-based and origami-inspired growth and assembly paradigms. Microbiome profiling of the biocomposite over multiple generations enabled the identification of a dominant bacterial component, Pantoea agglomerans, which was further isolated and developed into a new chassis. We introduced engineered P. agglomerans into native feedstocks to yield living blocks with new biosynthetic and sensing-reporting capabilities. Bioprospecting the native microbiota to develop engineerable chassis constitutes an important strategy to facilitate the development of living biomaterials with new properties and functionalities.
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Affiliation(s)
- Ross M McBee
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Nikita Mukhitov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Miles Richardson
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Tarun Srinivasan
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Dechuan Meng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haorong Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Kaufman
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Christian Munck
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Christopher Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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21
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Liu Y, Ba F, Liu WQ, Wu C, Li J. Plug-and-Play Functionalization of Protein–Polymer Conjugates for Tunable Catalysis Enabled by Genetically Encoded “Click” Chemistry. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yushi Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Changzhu Wu
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
- Danish Institute for Advanced Study (DIAS), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
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22
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Pallares RM, Charrier M, Tejedor-Sanz S, Li D, Ashby PD, Ajo-Franklin CM, Ralston CY, Abergel RJ. Precision Engineering of 2D Protein Layers as Chelating Biogenic Scaffolds for Selective Recovery of Rare-Earth Elements. J Am Chem Soc 2022; 144:854-861. [PMID: 34985894 DOI: 10.1021/jacs.1c10802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rare-earth elements, which include the lanthanide series, are key components of many clean energy technologies, including wind turbines and photovoltaics. Because most of these 4f metals are at high risk of supply chain disruption, the development of new recovery technologies is necessary to avoid future shortages, which may impact renewable energy production. This paper reports the synthesis of a non-natural biogenic material as a potential platform for bioinspired lanthanide extraction. The biogenic material takes advantage of the atomically precise structure of a 2D crystalline protein lattice with the high lanthanide binding affinity of hydroxypyridinonate chelators. Luminescence titration data demonstrated that the engineered protein layers have affinities for all tested lanthanides in the micromolar-range (dissociation constants) and a higher binding affinity for the lanthanide ions with a smaller ionic radius. Furthermore, competitive titrations confirmed the higher selectivity (up to several orders of magnitude) of the biogenic material for lanthanides compared to other cations commonly found in f-element sources. Lastly, the functionalized protein layers could be reused in several cycles by desorbing the bound metal with citrate solutions. Taken together, these results highlight biogenic materials as promising bioadsorption platforms for the selective binding of lanthanides, with potential applications in the recovery of these critical elements from waste.
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Affiliation(s)
- Roger M Pallares
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Marimikel Charrier
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Sara Tejedor-Sanz
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Dong Li
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul D Ashby
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Caroline M Ajo-Franklin
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Corie Y Ralston
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Rebecca J Abergel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Department of Nuclear Engineering, University of California, Berkeley, California 94720, United States
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23
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Pedroso CC, Mann VR, Zuberbühler K, Bohn MF, Yu J, Altoe V, Craik CS, Cohen BE. Immunotargeting of Nanocrystals by SpyCatcher Conjugation of Engineered Antibodies. ACS NANO 2021; 15:18374-18384. [PMID: 34694776 PMCID: PMC9035480 DOI: 10.1021/acsnano.1c07856] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Inorganic nanocrystals such as quantum dots (QDs) and upconverting nanoparticles (UCNPs) are uniquely suited for quantitative live-cell imaging and are typically functionalized with ligands to study specific receptors or cellular targets. Antibodies (Ab) are among the most useful targeting reagents owing to their high affinities and specificities, but common nanocrystal labeling methods may orient Ab incorrectly, be reversible or denaturing, or lead to Ab-NP complexes too large for some applications. Here, we show that SpyCatcher proteins, which bind and spontaneously form covalent isopeptide bonds with cognate SpyTag peptides, can conjugate engineered Ab to nanoparticle surfaces with control over stability, orientation, and stoichiometry. Compact SpyCatcher-functionalized QDs and UCNPs may be labeled with short-chain variable fragment Ab (scFv) engineered to bind urokinase-type plasminogen activator receptors (uPAR) that are overexpressed in many human cancers. Confocal imaging of anti-uPAR scFv-QD conjugates shows the antibody mediates specific binding and internalization by breast cancer cells expressing uPAR. Time-lapse imaging of photostable scFv-UCNP conjugates shows that Ab binding causes uPAR internalization with a ∼20 min half-life on the cell surface, and uPAR is internalized to endolysosomal compartments distinct from general membrane stains and without significant recycling to the cell surface. The controlled and stable conjugation of engineered Ab to NPs enables targeting of diverse receptors for live-cell study of their distribution, trafficking, and physiology.
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Affiliation(s)
- Cassio C.S. Pedroso
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Victor R. Mann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Kathrin Zuberbühler
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, United States
| | - Markus-Frederik Bohn
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, United States
| | - Jessica Yu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Virginia Altoe
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, United States
| | - Bruce E. Cohen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Division of Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Corresponding Author:
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24
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von Kügelgen A, Alva V, Bharat TAM. Complete atomic structure of a native archaeal cell surface. Cell Rep 2021; 37:110052. [PMID: 34818541 PMCID: PMC8640222 DOI: 10.1016/j.celrep.2021.110052] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/28/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
Many prokaryotic cells are covered by an ordered, proteinaceous, sheet-like structure called a surface layer (S-layer). S-layer proteins (SLPs) are usually the highest copy number macromolecules in prokaryotes, playing critical roles in cellular physiology such as blocking predators, scaffolding membranes, and facilitating environmental interactions. Using electron cryomicroscopy of two-dimensional sheets, we report the atomic structure of the S-layer from the archaeal model organism Haloferax volcanii. This S-layer consists of a hexagonal array of tightly interacting immunoglobulin-like domains, which are also found in SLPs across several classes of archaea. Cellular tomography reveal that the S-layer is nearly continuous on the cell surface, completed by pentameric defects in the hexagonal lattice. We further report the atomic structure of the SLP pentamer, which shows markedly different relative arrangements of SLP domains needed to complete the S-layer. Our structural data provide a framework for understanding cell surfaces of archaea at the atomic level.
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Affiliation(s)
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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25
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Herdman M, von Kügelgen A, Kureisaite-Ciziene D, Duman R, El Omari K, Garman EF, Kjaer A, Kolokouris D, Löwe J, Wagner A, Stansfeld PJ, Bharat TAM. High-resolution mapping of metal ions reveals principles of surface layer assembly in Caulobacter crescentus cells. Structure 2021; 30:215-228.e5. [PMID: 34800371 PMCID: PMC8828063 DOI: 10.1016/j.str.2021.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/17/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022]
Abstract
Surface layers (S-layers) are proteinaceous crystalline coats that constitute the outermost component of most prokaryotic cell envelopes. In this study, we have investigated the role of metal ions in the formation of the Caulobacter crescentus S-layer using high-resolution structural and cell biology techniques, as well as molecular simulations. Utilizing optical microscopy of fluorescently tagged S-layers, we show that calcium ions facilitate S-layer lattice formation and cell-surface binding. We report all-atom molecular dynamics simulations of the S-layer lattice, revealing the importance of bound metal ions. Finally, using electron cryomicroscopy and long-wavelength X-ray diffraction experiments, we mapped the positions of metal ions in the S-layer at near-atomic resolution, supporting our insights from the cellular and simulations data. Our findings contribute to the understanding of how C. crescentus cells form a regularly arranged S-layer on their surface, with implications on fundamental S-layer biology and the synthetic biology of self-assembling biomaterials. Live imaging shows Ca2+-dependent expansion of the C. crescentus S-layer Molecular simulations reveal Ca2+-binding properties of the S-layer Ca2+ ion mapping in three-dimensional crystals using in-vacuum X-ray anomalous diffraction Ca2+ replacement by Ho3+ allows cryo-EM mapping of heavy metals
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Affiliation(s)
- Matthew Herdman
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | | | - Ramona Duman
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Andreas Kjaer
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK.
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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26
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Tlusty T. Exceptional topology in ordinary soft matter. Phys Rev E 2021; 104:025002. [PMID: 34525622 DOI: 10.1103/physreve.104.025002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/14/2021] [Indexed: 01/22/2023]
Abstract
Hydrodynamics is shown to induce non-Hermitian topological phenomena in ordinary, passive soft matter. This is demonstrated by subjecting a two-dimensional elastic lattice to a low-Reynolds viscous flow. The interplay of hydrodynamics and elasticity splits Dirac cones into bulk Fermi arcs, pairing exceptional points with opposite half-integer topological charges. The bulk Fermi arc is a generic hallmark of the system exhibited in all lattice and flow symmetries. An analytic model and simulations explain how the emergent singularities shape the spectral bands and give rise to a web of van Hove singularity lines in the density of states. The present findings suggest that non-Hermitian physics can be explored in a broad class of ordinary soft matter, living and artificial alike, opening avenues for topology-based technology in this regime.
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Affiliation(s)
- Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science, and Physics and Chemistry Departments, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
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27
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Abstract
Bacterial surface layers (S-layers) have been observed as the outermost cell envelope component in a wide range of bacteria and most archaea. S-layers are monomolecular lattices composed of a single protein or glycoprotein species and have either oblique, square or hexagonal lattice symmetry with unit cell dimensions ranging from 3 to 30 nm. They are generally 5 to 10 nm thick (up to 70 nm in archaea) and represent highly porous protein lattices (30–70% porosity) with pores of uniform size and morphology in the range of 2 to 8 nm. Since S-layers can be considered as one of the simplest protein lattices found in nature and the constituent units are probably the most abundantly expressed proteins on earth, it seems justified to briefly review the different S-layer lattice types, the need for lattice imperfections and the discussion of S-layers from the perspective of an isoporous protein network in the ultrafiltration region. Finally, basic research on S-layers laid the foundation for applications in biotechnology, synthetic biology, and biomimetics.
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28
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Burgos-Morales O, Gueye M, Lacombe L, Nowak C, Schmachtenberg R, Hörner M, Jerez-Longres C, Mohsenin H, Wagner H, Weber W. Synthetic biology as driver for the biologization of materials sciences. Mater Today Bio 2021; 11:100115. [PMID: 34195591 PMCID: PMC8237365 DOI: 10.1016/j.mtbio.2021.100115] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 01/16/2023] Open
Abstract
Materials in nature have fascinating properties that serve as a continuous source of inspiration for materials scientists. Accordingly, bio-mimetic and bio-inspired approaches have yielded remarkable structural and functional materials for a plethora of applications. Despite these advances, many properties of natural materials remain challenging or yet impossible to incorporate into synthetic materials. Natural materials are produced by living cells, which sense and process environmental cues and conditions by means of signaling and genetic programs, thereby controlling the biosynthesis, remodeling, functionalization, or degradation of the natural material. In this context, synthetic biology offers unique opportunities in materials sciences by providing direct access to the rational engineering of how a cell senses and processes environmental information and translates them into the properties and functions of materials. Here, we identify and review two main directions by which synthetic biology can be harnessed to provide new impulses for the biologization of the materials sciences: first, the engineering of cells to produce precursors for the subsequent synthesis of materials. This includes materials that are otherwise produced from petrochemical resources, but also materials where the bio-produced substances contribute unique properties and functions not existing in traditional materials. Second, engineered living materials that are formed or assembled by cells or in which cells contribute specific functions while remaining an integral part of the living composite material. We finally provide a perspective of future scientific directions of this promising area of research and discuss science policy that would be required to support research and development in this field.
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Affiliation(s)
- O. Burgos-Morales
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - M. Gueye
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
| | - L. Lacombe
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
| | - C. Nowak
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - R. Schmachtenberg
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - M. Hörner
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - C. Jerez-Longres
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine - SGBM, University of Freiburg, Freiburg, 79104, Germany
| | - H. Mohsenin
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - H.J. Wagner
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Department of Biosystems Science and Engineering - D-BSSE, ETH Zurich, Basel, 4058, Switzerland
| | - W. Weber
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine - SGBM, University of Freiburg, Freiburg, 79104, Germany
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29
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Manjula-Basavanna A, Duraj-Thatte AM, Joshi NS. Robust Self-Regeneratable Stiff Living Materials Fabricated from Microbial Cells. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2010784. [PMID: 33994904 PMCID: PMC8115200 DOI: 10.1002/adfm.202010784] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 05/12/2023]
Abstract
Living systems have not only the exemplary capability to fabricate materials (e.g. wood, bone) under ambient conditions but they also consist of living cells that imbue them with properties like growth and self-regeneration. Like a seed that can grow into a sturdy living wood, we wondered: can living cells alone serve as the primary building block to fabricate stiff materials? Here we report the fabrication of stiff living materials (SLMs) produced entirely from microbial cells, without the incorporation of any structural biopolymers (e.g. cellulose, chitin, collagen) or biominerals (e.g. hydroxyapatite, calcium carbonate) that are known to impart stiffness to biological materials. Remarkably, SLMs are also lightweight, strong, resistant to organic solvents and can self-regenerate. This living materials technology can serve as a powerful biomanufacturing platform to design and develop advanced structural and cellular materials in a sustainable manner.
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Affiliation(s)
| | - Anna M Duraj-Thatte
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Neel S Joshi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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30
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Subramanian RH, Suzuki Y, Tallorin L, Sahu S, Thompson M, Gianneschi NC, Burkart MD, Tezcan FA. Enzyme-Directed Functionalization of Designed, Two-Dimensional Protein Lattices. Biochemistry 2021; 60:1050-1062. [PMID: 32706243 PMCID: PMC7855359 DOI: 10.1021/acs.biochem.0c00363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The design and construction of crystalline protein arrays to selectively assemble ordered nanoscale materials have potential applications in sensing, catalysis, and medicine. Whereas numerous designs have been implemented for the bottom-up construction of protein assemblies, the generation of artificial functional materials has been relatively unexplored. Enzyme-directed post-translational modifications are responsible for the functional diversity of the proteome and, thus, could be harnessed to selectively modify artificial protein assemblies. In this study, we describe the use of phosphopantetheinyl transferases (PPTases), a class of enzymes that covalently modify proteins using coenzyme A (CoA), to site-selectively tailor the surface of designed, two-dimensional (2D) protein crystals. We demonstrate that a short peptide (ybbR) or a molecular tag (CoA) can be covalently tethered to 2D arrays to enable enzymatic functionalization using Sfp PPTase. The site-specific modification of two different protein array platforms is facilitated by PPTases to afford both small molecule- and protein-functionalized surfaces with no loss of crystalline order. This work highlights the potential for chemoenzymatic modification of large protein surfaces toward the generation of sophisticated protein platforms reminiscent of the complex landscape of cell surfaces.
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Affiliation(s)
- Rohit H. Subramanian
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Yuta Suzuki
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Current address: Hakubi Center for Advanced Research, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto, Japan, 606-8501
| | - Lorillee Tallorin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Swagat Sahu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Matthew Thompson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Departments of Chemistry, Materials Science & Engineering, Biomedical Engineering, Chemistry of Life Processes Institute, International Institute for Nanotechnology, Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, USA
| | - Nathan C. Gianneschi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Departments of Chemistry, Materials Science & Engineering, Biomedical Engineering, Chemistry of Life Processes Institute, International Institute for Nanotechnology, Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA, USA
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31
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Mann VR, Manea F, Borys NJ, Ajo-Franklin CM, Cohen BE. Controlled and Stable Patterning of Diverse Inorganic Nanocrystals on Crystalline Two-Dimensional Protein Arrays. Biochemistry 2021; 60:1063-1074. [PMID: 33691067 PMCID: PMC8162747 DOI: 10.1021/acs.biochem.1c00032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Controlled patterning of nanoparticles on bioassemblies enables synthesis of complex materials for applications in optics, nanoelectronics, and sensing. Biomolecular self-assembly offers molecular control for engineering patterned nanomaterials, but current approaches have been limited in their ability to combine high nanoparticle coverage with generality that enables incorporation of multiple nanoparticle types. Here, we synthesize photonic materials on crystalline two-dimensional (2D) protein sheets using orthogonal bioconjugation reactions, organizing quantum dots (QDs), gold nanoparticles (AuNPs), and upconverting nanoparticles along the surface-layer (S-layer) protein SbsB from the extremophile Geobacillus stearothermophilus. We use electron and optical microscopy to show that isopeptide bond-forming SpyCatcher and SnoopCatcher systems enable the simultaneous and controlled conjugation of multiple types of nanoparticles (NPs) at high densities along the SbsB sheets. These NP conjugation reactions are orthogonal to each other and to Au-thiol bond formation, allowing tailorable nanoparticle combinations at sufficient labeling efficiencies to permit optical interactions between nanoparticles. Fluorescence lifetime imaging of SbsB sheets conjugated to QDs and AuNPs at distinct attachment sites shows spatially heterogeneous QD emission, with shorter radiative decays and brighter fluorescence arising from plasmonic enhancement at short interparticle distances. This specific, stable, and efficient conjugation of NPs to 2D protein sheets enables the exploration of interactions between pairs of nanoparticles at defined distances for the engineering of protein-based photonic nanomaterials.
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Affiliation(s)
- Victor R. Mann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Francesca Manea
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Current address: Perfect Day Foods, Berkeley, CA 94608
| | - Nicholas J. Borys
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Current address: Department of Physics, Montana State University, Bozeman, MT 59717
| | - Caroline M. Ajo-Franklin
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Division of Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of BioSciences, Rice University, Houston, TX 77005
| | - Bruce E. Cohen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Division of Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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32
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Engineering High-Yield Biopolymer Secretion Creates an Extracellular Protein Matrix for Living Materials. mSystems 2021; 6:6/2/e00903-20. [PMID: 33758029 PMCID: PMC8546985 DOI: 10.1128/msystems.00903-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The bacterial extracellular matrix forms autonomously, giving rise to complex material properties and multicellular behaviors. Synthetic matrix analogues can replicate these functions but require exogenously added material or have limited programmability. Here, we design a two-strain bacterial system that self-synthesizes and structures a synthetic extracellular matrix of proteins. We engineered Caulobacter crescentus to secrete an extracellular matrix protein composed of an elastin-like polypeptide (ELP) hydrogel fused to supercharged SpyCatcher [SC(-)]. This biopolymer was secreted at levels of 60 mg/liter, an unprecedented level of biomaterial secretion by a native type I secretion apparatus. The ELP domain was swapped with either a cross-linkable variant of ELP or a resilin-like polypeptide, demonstrating this system is flexible. The SC(-)-ELP matrix protein bound specifically and covalently to the cell surface of a C. crescentus strain that displays a high-density array of SpyTag (ST) peptides via its engineered surface layer. Our work develops protein design guidelines for type I secretion in C. crescentus and demonstrates the autonomous secretion and assembly of programmable extracellular protein matrices, offering a path forward toward the formation of cohesive engineered living materials.IMPORTANCE Engineered living materials (ELM) aim to mimic characteristics of natural occurring systems, bringing the benefits of self-healing, synthesis, autonomous assembly, and responsiveness to traditional materials. Previous research has shown the potential of replicating the bacterial extracellular matrix (ECM) to mimic biofilms. However, these efforts require energy-intensive processing or have limited tunability. We propose a bacterially synthesized system that manipulates the protein content of the ECM, allowing for programmable interactions and autonomous material formation. To achieve this, we engineered a two-strain system to secrete a synthetic extracellular protein matrix (sEPM). This work is a step toward understanding the necessary parameters to engineering living cells to autonomously construct ELMs.
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33
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Ben-Sasson AJ, Watson JL, Sheffler W, Johnson MC, Bittleston A, Somasundaram L, Decarreau J, Jiao F, Chen J, Mela I, Drabek AA, Jarrett SM, Blacklow SC, Kaminski CF, Hura GL, De Yoreo JJ, Ruohola-Baker H, Kollman JM, Derivery E, Baker D. Design of biologically active binary protein 2D materials. Nature 2021; 589:468-473. [PMID: 33408408 PMCID: PMC7855610 DOI: 10.1038/s41586-020-03120-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/06/2020] [Indexed: 02/07/2023]
Abstract
Ordered two-dimensional arrays such as S-layers1,2 and designed analogues3-5 have intrigued bioengineers6,7, but with the exception of a single lattice formed with flexible linkers8, they are constituted from just one protein component. Materials composed of two components have considerable potential advantages for modulating assembly dynamics and incorporating more complex functionality9-12. Here we describe a computational method to generate co-assembling binary layers by designing rigid interfaces between pairs of dihedral protein building blocks, and use it to design a p6m lattice. The designed array components are soluble at millimolar concentrations, but when combined at nanomolar concentrations, they rapidly assemble into nearly crystalline micrometre-scale arrays nearly identical to the computational design model in vitro and in cells without the need for a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces, which we demonstrate can drive extensive receptor clustering, downstream protein recruitment and signalling. Using atomic force microscopy on supported bilayers and quantitative microscopy on living cells, we show that arrays assembled on membranes have component stoichiometry and structure similar to arrays formed in vitro, and that our material can therefore impose order onto fundamentally disordered substrates such as cell membranes. In contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, we find that large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work provides a foundation for a synthetic cell biology in which multi-protein macroscale materials are designed to modulate cell responses and reshape synthetic and living systems.
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Affiliation(s)
- Ariel J. Ben-Sasson
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA,Institute for Protein Design, University of Washington,
Seattle, WA 98195, USA
| | - Joseph L. Watson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge, UK
| | - William Sheffler
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA,Institute for Protein Design, University of Washington,
Seattle, WA 98195, USA
| | | | - Alice Bittleston
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge, UK
| | - Logeshwaran Somasundaram
- Institute for Stem Cell and Regenerative Medicine,
University of Washington, School of Medicine, Seattle, WA 98109, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA,Institute for Protein Design, University of Washington,
Seattle, WA 98195, USA
| | - Fang Jiao
- Department of Materials Science and Engineering, University
of Washington, Seattle, WA 98195, USA
| | - Jiajun Chen
- Department of Materials Science and Engineering, University
of Washington, Seattle, WA 98195, USA,Physical Sciences Division, Pacific Northwest National
Laboratory, Richland, WA 99352, USA
| | - Ioanna Mela
- Department of Chemical Engineering and Biotechnology,
University of Cambridge, Cambridge, UK
| | - Andrew A. Drabek
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sanchez M. Jarrett
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen C. Blacklow
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA,Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology,
University of Cambridge, Cambridge, UK
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence
Berkeley National Lab, Berkeley, CA 94720, USA
| | - James J De Yoreo
- Department of Materials Science and Engineering, University
of Washington, Seattle, WA 98195, USA,Physical Sciences Division, Pacific Northwest National
Laboratory, Richland, WA 99352, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA,Institute for Stem Cell and Regenerative Medicine,
University of Washington, School of Medicine, Seattle, WA 98109, USA
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA
| | - Emmanuel Derivery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge, UK
| | - David Baker
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA,Institute for Protein Design, University of Washington,
Seattle, WA 98195, USA,Howard Hughes Medical Institute, University of
Washington, Seattle, WA 98195, USA
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34
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Srubar WV. Engineered Living Materials: Taxonomies and Emerging Trends. Trends Biotechnol 2020; 39:574-583. [PMID: 33234328 DOI: 10.1016/j.tibtech.2020.10.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 12/25/2022]
Abstract
At the intersection of synthetic biology and materials science, the field of engineered living materials (ELMs) has evolved into a new, standalone discipline. The fusion of bioengineering's design-build-test-learn approaches with classical materials science has yielded breakthrough innovations in the synthesis of complex, biologically active materials for functional applications in therapeutics, electronics, construction, and beyond. However, the transdisciplinary nature of the ELM field - and its rapid growth - has made holistic comprehension of achievements related to the tools, techniques, and applications of ELMs difficult across disciplines. To this end, this review proposes an emergent taxonomy of ELM research and uses the categorization to discuss current trends and state-of-the-art advancements, significant opportunities, and imminent challenges for scientists and engineers in the field.
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Affiliation(s)
- Wil V Srubar
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, USA; Materials Science and Engineering Program, University of Colorado Boulder, Boulder, CO, USA.
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35
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Bharat TAM, von Kügelgen A, Alva V. Molecular Logic of Prokaryotic Surface Layer Structures. Trends Microbiol 2020; 29:405-415. [PMID: 33121898 PMCID: PMC8559796 DOI: 10.1016/j.tim.2020.09.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022]
Abstract
Most prokaryotic cells are encased in a surface layer (S-layer) consisting of a paracrystalline array of repeating lattice-forming proteins. S-layer proteins populate a vast and diverse sequence space, performing disparate functions in prokaryotic cells, including cellular defense, cell-shape maintenance, and regulation of import and export of materials. This article highlights recent advances in the understanding of S-layer structure and assembly, made possible by rapidly evolving structural and cell biology methods. We underscore shared assembly principles revealed by recent work and discuss a common molecular framework that may be used to understand the structural organization of S-layer proteins across bacteria and archaea. Despite enormous sequence diversity in surface (S)-layer proteins, structural diversity is much lower than previously thought. S-layer proteins have a bipartite arrangement with a lattice-forming and an anchoring segment. Novel structural biology methods are revealing the architectures of S-layers in situ. S-layer assembly across prokaryotes is tightly coupled to the cell cycle, including the cell division machinery.
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Affiliation(s)
- Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford OX1 3RE, UK.
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford OX1 3RE, UK
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen 72076, Germany.
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36
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Zhang F, Zhang W. Encrypting Chemical Reactivity in Protein Sequences toward
Information‐Coded
Reactions
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000083] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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37
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von Kügelgen A, Tang H, Hardy GG, Kureisaite-Ciziene D, Brun YV, Stansfeld PJ, Robinson CV, Bharat TAM. In Situ Structure of an Intact Lipopolysaccharide-Bound Bacterial Surface Layer. Cell 2020; 180:348-358.e15. [PMID: 31883796 PMCID: PMC6978808 DOI: 10.1016/j.cell.2019.12.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/22/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022]
Abstract
Most bacterial and all archaeal cells are encapsulated by a paracrystalline, protective, and cell-shape-determining proteinaceous surface layer (S-layer). On Gram-negative bacteria, S-layers are anchored to cells via lipopolysaccharide. Here, we report an electron cryomicroscopy structure of the Caulobacter crescentus S-layer bound to the O-antigen of lipopolysaccharide. Using native mass spectrometry and molecular dynamics simulations, we deduce the length of the O-antigen on cells and show how lipopolysaccharide binding and S-layer assembly is regulated by calcium. Finally, we present a near-atomic resolution in situ structure of the complete S-layer using cellular electron cryotomography, showing S-layer arrangement at the tip of the O-antigen. A complete atomic structure of the S-layer shows the power of cellular tomography for in situ structural biology and sheds light on a very abundant class of self-assembling molecules with important roles in prokaryotic physiology with marked potential for synthetic biology and surface-display applications.
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Affiliation(s)
- Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Haiping Tang
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
| | - Gail G Hardy
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom.
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38
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Wang C, Cao G, Zhao T, Wang X, Niu X, Fan Y, Li X. Terminal Group Modification of Carbon Nanotubes Determines Covalently Bound Osteogenic Peptide Performance. ACS Biomater Sci Eng 2020; 6:865-878. [PMID: 33464866 DOI: 10.1021/acsbiomaterials.9b01501] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Osteogenic peptides are often introduced to improve biological activities and the osteogenic ability of artificial bone materials as an effective approach. Covalent bindings between the peptide and the host material can increase the molecular interactions and make the functionalized surface more stable. However, covalent bindings through different functional groups can bring different effects on the overall bioactivities. In this study, carboxyl and amino groups were respectively introduced onto carbon nanotubes, a nanoreinforcement for synthetic scaffold materials, which were subsequently covalently attached to the RGD/BMP-2 osteogenic peptide. MC3T3-E1 cells were cultured on scaffolds containing peptide-modified carbon nanotubes. The results showed that the peptide through the amino group binding could promote cell functions more effectively than those through carboxyl groups. The mechanism may be that the amino group could bring more positive charges to carbon nanotube surfaces, which further led to differences in the peptide conformation, protein adsorption, and targeting osteogenic effects. Our results provided an effective way of improving the bioactivities of artificial bone materials by chemically binding osteogenic peptides.
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Affiliation(s)
- Cunyang Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.,Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100083, China
| | - Guangxiu Cao
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.,Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100083, China
| | - Tianxiao Zhao
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Xiumei Wang
- State Key Laboratory of New Ceramic and Fine Processing, Tsinghua University, Beijing 100084, China
| | - Xufeng Niu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.,Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100083, China
| | - Yubo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.,Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100083, China
| | - Xiaoming Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.,Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100083, China
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39
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Resilient living materials built by printing bacterial spores. Nat Chem Biol 2019; 16:126-133. [PMID: 31792444 DOI: 10.1038/s41589-019-0412-5] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/22/2019] [Indexed: 02/01/2023]
Abstract
Materials can be made multifunctional by embedding them with living cells that perform sensing, synthesis, energy production, and physical movement. A challenge is that the conditions needed for living cells are not conducive to materials processing and require continuous water and nutrients. Here, we present a three dimensional (3D) printer that can mix material and cell streams to build 3D objects. Bacillus subtilis spores were printed within the material and germinated on its exterior surface, including spontaneously in new cracks. The material was resilient to extreme stresses, including desiccation, solvents, osmolarity, pH, ultraviolet light, and γ-radiation. Genetic engineering enabled the bacteria to respond to stimuli or produce chemicals on demand. As a demonstration, we printed custom-shaped hydrogels containing bacteria that can sense or kill Staphylococcus aureus, a causative agent of infections. This work demonstrates materials endued with living functions that can be used in applications that require storage or exposure to environmental stresses.
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40
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Zhang G, Johnston T, Quin MB, Schmidt-Dannert C. Developing a Protein Scaffolding System for Rapid Enzyme Immobilization and Optimization of Enzyme Functions for Biocatalysis. ACS Synth Biol 2019; 8:1867-1876. [PMID: 31305981 DOI: 10.1021/acssynbio.9b00187] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Immobilization of enzymes is required for most biocatalytic processes, but chemistries used in enzyme immobilization are limited and can be challenging. Genetically encoded protein-based biomaterials could provide easy-to-use immobilization platforms for biocatalysts. We recently developed a self-assembling protein scaffold that covalently immobilized SpyTagged enzymes by engineering the bacterial microcompartment protein EutM from Salmonella enterica with a SpyCatcher domain. We also identified a range of EutM homologues as robust protein nanostructures with diverse architectures and electrostatic surface properties. In this work, we created a modular immobilization platform with tunable surface properties by developing a toolbox of self-assembling, robust EutM-SpyCatcher scaffolds. Using an alcohol dehydrogenase as model biocatalyst, we show that the scaffolds improve enzyme activity and stability. This work provides a modular, easy-to-use immobilization system that can be tailored for the optimal function of biocatalysts of interest.
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Affiliation(s)
- Guoqiang Zhang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Timothy Johnston
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Maureen B. Quin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
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41
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Wang X, Pu J, Liu Y, Ba F, Cui M, Li K, Xie Y, Nie Y, Mi Q, Li T, Liu L, Zhu M, Zhong C. Immobilization of functional nano-objects in living engineered bacterial biofilms for catalytic applications. Natl Sci Rev 2019; 6:929-943. [PMID: 34691954 PMCID: PMC8291418 DOI: 10.1093/nsr/nwz104] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/12/2022] Open
Abstract
Nanoscale objects feature very large surface-area-to-volume ratios and are now understood as powerful tools for catalysis, but their nature as nanomaterials brings challenges including toxicity and nanomaterial pollution. Immobilization is considered a feasible strategy for addressing these limitations. Here, as a proof-of-concept for the immobilization of nanoscale catalysts in the extracellular matrix of bacterial biofilms, we genetically engineered amyloid monomers of the Escherichia coli curli nanofiber system that are secreted and can self-assemble and anchor nano-objects in a spatially precise manner. We demonstrated three scalable, tunable and reusable catalysis systems: biofilm-anchored gold nanoparticles to reduce nitro aromatic compounds such as the pollutant p-nitrophenol, biofilm-anchored hybrid Cd0.9Zn0.1S quantum dots and gold nanoparticles to degrade organic dyes and biofilm-anchored CdSeS@ZnS quantum dots in a semi-artificial photosynthesis system for hydrogen production. Our work demonstrates how the ability of biofilms to grow in scalable and complex spatial arrangements can be exploited for catalytic applications and clearly illustrates the design utility of segregating high-energy nano-objects from injury-prone cellular components by engineering anchoring points in an extracellular matrix.
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Affiliation(s)
- Xinyu Wang
- Division of Materials and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahua Pu
- Division of Materials and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yi Liu
- Division of Materials and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fang Ba
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengkui Cui
- Division of Materials and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ke Li
- Division of Materials and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yu Xie
- Division of Materials and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Nie
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, China
| | - Qixi Mi
- Division of Materials and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tao Li
- Division of Materials and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lingli Liu
- College of Chemistry & Chemical Engineering, Anhui University, Hefei 230039, China
| | - Manzhou Zhu
- College of Chemistry & Chemical Engineering, Anhui University, Hefei 230039, China
| | - Chao Zhong
- Division of Materials and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
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42
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Topologically-guided continuous protein crystallization controls bacterial surface layer self-assembly. Nat Commun 2019; 10:2731. [PMID: 31227690 PMCID: PMC6588578 DOI: 10.1038/s41467-019-10650-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/16/2019] [Indexed: 12/22/2022] Open
Abstract
Many bacteria and most archaea possess a crystalline protein surface layer (S-layer), which surrounds their growing and topologically complicated outer surface. Constructing a macromolecular structure of this scale generally requires localized enzymatic machinery, but a regulatory framework for S-layer assembly has not been identified. By labeling, superresolution imaging, and tracking the S-layer protein (SLP) from C. crescentus, we show that 2D protein self-assembly is sufficient to build and maintain the S-layer in living cells by efficient protein crystal nucleation and growth. We propose a model supported by single-molecule tracking whereby randomly secreted SLP monomers diffuse on the lipopolysaccharide (LPS) outer membrane until incorporated at the edges of growing 2D S-layer crystals. Surface topology creates crystal defects and boundaries, thereby guiding S-layer assembly. Unsupervised assembly poses challenges for therapeutics targeting S-layers. However, protein crystallization as an evolutionary driver rationalizes S-layer diversity and raises the potential for biologically inspired self-assembling macromolecular nanomaterials. Bacteria assemble the surface layer (S-layer), a crystalline protein coat surrounding the curved surface, using protein self-assembly. Here authors image native and purified RsaA, the S-layer protein from C. crescentus, and show that protein crystallization alone is sufficient to assemble and maintain the S-layer in vivo.
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