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Lei Q, Guo J, Kong F, Cao J, Wang L, Zhu W, Brinker CJ. Bioinspired Cell Silicification: From Extracellular to Intracellular. J Am Chem Soc 2021; 143:6305-6322. [PMID: 33826324 DOI: 10.1021/jacs.1c00814] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In nature, biosilicification directs the formation of elaborate amorphous silica exoskeletons that provide diatoms mechanically strong, chemically inert, non-decomposable silica armor conferring chemical and thermal stability as well as resistance to microbial attack, without changing the optical transparency or adversely effecting nutrient and waste exchange required for growth. These extraordinary silica/cell biocomposites have inspired decades of biomimetic research aimed at replication of diatoms' hierarchically organized exoskeletons, immobilization of cells or living organisms within silica matrices and coatings to protect them against harmful external stresses, genetic re-programming of cellular functions by virtue of physico-chemical confinement within silica, cellular integration into devices, and endowment of cells with non-native, abiotic properties through facile silica functionalization. In this Perspective, we focus our discussions on the development and concomitant challenges of bioinspired cell silicification ranging from "cells encapsulated within 3D silica matrices" and "cells encapsulated within 2D silica shells" to extra- and intracellular silica replication, wherein all biomolecular interfaces are encased within nanoscopic layers of amorphous silica. We highlight notable examples of advances in the science and technology of biosilicification and consider challenges to advancing the field, where we propose cellular "mineralization" with arbitrary nanoparticle exoskeletons as a generalizable means to impart limitless abiotic properties and functions to cells, and, based on the interchangeability of water and silicic acid and analogies between amorphous ice and amorphous silica, we consider "freezing" cells within amorphous silica as an alternative to cryo-preservation.
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Affiliation(s)
- Qi Lei
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jimin Guo
- Center for Micro-Engineered Materials, Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, United States.,Department of Internal Medicine, Molecular Medicine, The University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Fanhui Kong
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jiangfan Cao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Lu Wang
- Department of Biochemistry and Molecular Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - C Jeffrey Brinker
- Center for Micro-Engineered Materials, Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, United States
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Wrist A, Sun W, Summers RM. The Theophylline Aptamer: 25 Years as an Important Tool in Cellular Engineering Research. ACS Synth Biol 2020; 9:682-697. [PMID: 32142605 DOI: 10.1021/acssynbio.9b00475] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The theophylline aptamer was isolated from an oligonucleotide library in 1994. Since that time, the aptamer has found wide utility, particularly in synthetic biology, cellular engineering, and diagnostic applications. The primary application of the theophylline aptamer is in the construction and characterization of synthetic riboswitches for regulation of gene expression. These riboswitches have been used to control cellular motility, regulate carbon metabolism, construct logic gates, screen for mutant enzymes, and control apoptosis. Other applications of the theophylline aptamer in cellular engineering include regulation of RNA interference and genome editing through CRISPR systems. Here we describe the uses of the theophylline aptamer for cellular engineering over the past 25 years. In so doing, we also highlight important synthetic biology applications to control gene expression in a ligand-dependent manner.
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Affiliation(s)
- Alexandra Wrist
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Wanqi Sun
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Ryan M. Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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Mayer M, Baeumner AJ. A Megatrend Challenging Analytical Chemistry: Biosensor and Chemosensor Concepts Ready for the Internet of Things. Chem Rev 2019; 119:7996-8027. [DOI: 10.1021/acs.chemrev.8b00719] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Mayer
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Antje J. Baeumner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
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Johnston RK, Harper JC, Tartis MS. Control over Silica Particle Growth and Particle-Biomolecule Interactions Facilitates Silica Encapsulation of Mammalian Cells with Thickness Control. ACS Biomater Sci Eng 2017; 3:2098-2109. [PMID: 29202010 DOI: 10.1021/acsbiomaterials.7b00185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the last twenty years, many strategies utilizing sol-gel chemistry to integrate biological cells into silica-based materials have been reported. One such strategy, Sol-Generating Chemical Vapor into Liquid (SG-CViL) deposition, shows promise as an efficient encapsulation technique due to the ability to vary the silica encapsulation morphology obtained by this process through variation of SG-CViL reaction conditions. In this report, we develop SG-CViL as a tunable, multi-purpose silica encapsulation strategy by investigating the mechanisms governing both silica particle generation and subsequent interaction with phospholipid assemblies (liposomes and living cells). Using Dynamic Light Scattering (DLS) measurements, linear and exponential silica particle growth dynamics were observed which were dependent on deposition buffer ion constituents and ion concentration. Silica particle growth followed a cluster-cluster growth mechanism at acidic pH, and a monomer-cluster growth mechanism at neutral to basic pH. Increasing silica sol aging temperature resulted in higher rates of particle growth and larger particles. DLS measurements employing PEG coated liposomes and cationic liposomes, serving as model phospholipid assemblies, revealed electrostatic interactions promote more stable liposome-silica interactions than hydrogen bonding and facilitate silica coating on suspension cells. However, continued silica reactivity leads to aggregation of silica coated suspensions cells, revealing the need for cell isolation to tune deposited silica thickness. Utilizing these mechanistic study insights, silica was deposited onto adherent HeLa cells under biocompatible conditions with micron scale control over silica thickness, minimal cell manipulation steps, and retained cell viability over several days.
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Affiliation(s)
- Robert K Johnston
- Department of Materials Engineering, New Mexico Institute of Mining and Technology, 801 Leroy Pl, Socorro, New Mexico 87801, United States
| | - Jason C Harper
- Sandia National Laboratories, Bioenergy and Biodefense Technologies, Albuquerque New Mexico 87185, United States
| | - Michaelann S Tartis
- Department of Materials Engineering, New Mexico Institute of Mining and Technology, 801 Leroy Pl, Socorro, New Mexico 87801, United States.,Department of Chemical Engineering, New Mexico Institute of Mining and Technology, 801 Leroy Pl, Socorro, New Mexico 87801, United States.,Department of Biology, New Mexico Institute of Mining and Technology, 801 Leroy Pl, Socorro, New Mexico 87801, United States
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Harbaugh SV, Goodson MS, Dillon K, Zabarnick S, Kelley-Loughnane N. Riboswitch-Based Reversible Dual Color Sensor. ACS Synth Biol 2017; 6:766-781. [PMID: 28121427 DOI: 10.1021/acssynbio.6b00199] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Riboswitches are RNA-based "sensors" that utilize chemically induced structural changes in the 5'-untranslated region of mRNA to regulate expression of downstream genes. Coupling a specific riboswitch with a reporter gene system translates chemical detection by the cell into a quantifiable reporter protein signal. For the majority of reporter gene systems, the readout signal is only expressed in the presence of the target analyte. This makes it difficult to determine the viability and localization of the uninduced biosensor when it is used for "real-word" applications. To address this problem, we developed a dual-color reporter comprising elements of the E. coli fimbriae phase variation system: recombinase FimE controlled by a synthetic riboswitch and an invertible DNA segment (fimS) containing a constitutively active promoter placed between two fluorescent protein genes. Without an analyte, the fluorescent reporter constitutively expressed green fluorescent protein (GFPa1). Addition of the analyte initiated translation of fimE causing unidirectional inversion of the fimS segment and constitutive expression of red fluorescent protein (mKate2). Thus, the sensor is always fluorescent, but its color is determined by detection of a specific analyte. We demonstrate that the recombinase-based dual-color reporter can be successfully applied to monitor the activation of a theophylline synthetic riboswitch that was used as our model system. To show the feasibility of the FimE recombinase-based system to serve as a reporter for monitoring activation of multiple synthetic riboswitches and, therefore, expand the applicability of the system, we tested a number of previously developed synthetic riboswitches responsive to different analytes. We show that the dual-color reporter system can be successfully used to monitor activation of M6 and M6″ riboswitches responsive to ammeline and pyrimido[4,5-d]pyrimidine-2,4-diamine, respectively, and a 2,4,6-trinitrotoluene-responsive riboswitch developed in this study. We also demonstrate that the system can be reversed by HbiF recombinase-mediated fimS inversion to the initial state of the fluorescent reporter, creating a resettable and reusable cell-based sensor.
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Affiliation(s)
- Svetlana V. Harbaugh
- 711th
Human Performance Wing, Airman Systems Directorate, Air Force Research
Laboratory, Wright-Patterson Air Force Base, Wright-Patterson AFB, Ohio 45433, United States
- The Henry M. Jackson Foundation, 6720A Rockledge Drive, Bethesda, Maryland 20817, United States
| | - Michael S. Goodson
- 711th
Human Performance Wing, Airman Systems Directorate, Air Force Research
Laboratory, Wright-Patterson Air Force Base, Wright-Patterson AFB, Ohio 45433, United States
- UES, Inc., 4401 Dayton-Xenia
Road, Dayton, Ohio 45432, United States
| | - Kateri Dillon
- 711th
Human Performance Wing, Airman Systems Directorate, Air Force Research
Laboratory, Wright-Patterson Air Force Base, Wright-Patterson AFB, Ohio 45433, United States
| | - Sarah Zabarnick
- 711th
Human Performance Wing, Airman Systems Directorate, Air Force Research
Laboratory, Wright-Patterson Air Force Base, Wright-Patterson AFB, Ohio 45433, United States
| | - Nancy Kelley-Loughnane
- 711th
Human Performance Wing, Airman Systems Directorate, Air Force Research
Laboratory, Wright-Patterson Air Force Base, Wright-Patterson AFB, Ohio 45433, United States
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Fazal Z, Pelowitz J, Johnson PE, Harper JC, Brinker CJ, Jakobsson E. Three-Dimensional Encapsulation of Saccharomyces cerevisiae in Silicate Matrices Creates Distinct Metabolic States as Revealed by Gene Chip Analysis. ACS NANO 2017; 11:3560-3575. [PMID: 28287261 DOI: 10.1021/acsnano.6b06385] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In order to design hybrid cellular/synthetic devices such as sensors and vaccines, it is important to understand how the metabolic state of living cells changes upon physical confinement within three-dimensional (3D) matrices. We analyze the gene expression patterns of stationary phase Saccharomyces cerevisiae (S. cerevisiae) cells encapsulated within three distinct nanostructured silica matrices and relate those patterns to known naturally occurring metabolic states. Silica encapsulation methods employed were lipid-templated mesophase silica thin films formed by cell-directed assembly (CDA), lipid-templated mesophase silica particles formed by spray drying (SD), and glycerol-doped silica gel monoliths prepared from an aqueous silicate (AqS+g) precursor solution. It was found that the cells for all three-encapsulated methods enter quiescent states characteristic of response to stress, albeit to different degrees and with differences in detail. By the measure of enrichment of stress-related gene ontology categories, we find that the AqS+g encapsulation is more amenable to the cells than CDA and SD encapsulation. We hypothesize that this differential response in the AqS+g encapsulation is related to four properties of the encapsulating gel: (1) oxygen permeability, (2) relative softness of the material, (3) development of a protective sheath around individual cells (visible in TEM micrographs vide infra), and (4) the presence of glycerol in the gel, which has been previously noted to serve as a protectant for encapsulated cells and can serve as the sole carbon source for S. cerevisiae under aerobic conditions. This work represents a combination of experiment and analysis aimed at the design and development of 3D encapsulation procedures to induce, and perhaps control, well-defined physiological behaviors.
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Affiliation(s)
- Zeeshan Fazal
- Department of Biosciences, COMSATS Institute of Information Technology , Park Road, Tarlai Kalan, Islamabad 45550, Pakistan
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Savage TJ, Dunphy DR, Harbaugh S, Kelley-Loughnane N, Harper JC, Brinker CJ. Influence of Silica Matrix Composition and Functional Component Additives on the Bioactivity and Viability of Encapsulated Living Cells. ACS Biomater Sci Eng 2015; 1:1231-1238. [DOI: 10.1021/acsbiomaterials.5b00261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Travis J. Savage
- Chemical & Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87106, United States
| | - Darren R. Dunphy
- Chemical & Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87106, United States
| | - Svetlana Harbaugh
- Air
Force Research Laboratory, Human Effectiveness Directorate, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Nancy Kelley-Loughnane
- Air
Force Research Laboratory, Human Effectiveness Directorate, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | | | - C. Jeffrey Brinker
- Chemical & Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87106, United States
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Harper JC, Carson BD, Bachand GD, Arndt WD, Finley MR, Brinker CJ, Edwards TL. Laser Machined Plastic Laminates: Towards Portable Diagnostic Devices for Use in Low Resource Environments. ELECTROANAL 2015. [DOI: 10.1002/elan.201500359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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3D hydrodynamic focusing microfluidics for emerging sensing technologies. Biosens Bioelectron 2015; 67:25-34. [DOI: 10.1016/j.bios.2014.07.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/01/2014] [Accepted: 07/01/2014] [Indexed: 12/28/2022]
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Lin XY, Wu LL, Pan ZQ, Shi CG, Bao N, Gu HY. Paper-based analytical devices for electrochemical study of the breathing process of red blood cells. Talanta 2015; 135:23-6. [DOI: 10.1016/j.talanta.2014.12.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/21/2014] [Accepted: 12/25/2014] [Indexed: 10/24/2022]
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Johnston R, Rogelj S, Harper JC, Tartis M. Sol-Generating Chemical Vapor into Liquid (SG-CViL) Deposition- A Facile Method for Encapsulation of Diverse Cell Types in Silica Matrices. J Mater Chem B 2015; 3:1032-1041. [PMID: 25688296 DOI: 10.1039/c4tb01349b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In nature, cells perform a variety of complex functions such as sensing, catalysis, and energy conversion which hold great potential for biotechnological device construction. However, cellular sensitivity to ex-vivo environments necessitates development of bio-nano interfaces which allow integration of cells into devices and maintain their desired functionality. In order to develop such an interface, the use of a novel Sol Generating Chemical Vapor into Liquid (SG-CViL) deposition process for whole cell encapsulation in silica was explored. In SG-CViL, the high vapor pressure of tetramethyl orthosilicate (TMOS) is utilized to deliver silica into an aqueous medium, creating a silica sol. Cells are then mixed with the resulting silica sol, facilitating encapsulation of cells in silica while minimizing cell contact with the cytotoxic products of silica generating reactions (i.e. methanol), and reduce exposure of cells to compressive stresses induced from silica condensation reactions. Using SG-CVIL, Saccharomyces cerevisiae (S. cerevisiae) engineered with an inducible beta galactosidase system were encapsulated in silica solids and remained both viable and responsive 29 days post encapsulation. By tuning SG-CViL parameters thin layer silica deposition on mammalian HeLa and U87 human cancer cells was also achieved. The ability to encapsulate various cell types in either a multi cell (S. cerevisiae) or a thin layer (HeLa and U87 cells) fashion shows the promise of SG-CViL as an encapsulation strategy for generating cell-silica constructs with diverse functions for incorporation into devices for sensing, bioelectronics, biocatalysis, and biofuel applications.
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Affiliation(s)
- Robert Johnston
- Materials Engineering Department, New Mexico Institute of Mining and Technology Socorro NM, 87801
| | - Snezna Rogelj
- Biology Department, New Mexico Institute of Mining and Technology Socorro NM, 87801
| | - Jason C Harper
- Bioenergy & Biodefense Technologies Department, Sandia National Laboratories, Albuquerque New Mexico, 87185
| | - Michaelann Tartis
- Materials Engineering Department, New Mexico Institute of Mining and Technology Socorro NM, 87801 ; Chemical Engineering Department, New Mexico Institute of Mining and Technology Socorro NM, 87801
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Spectral and structural comparison between bright and dim green fluorescent proteins in Amphioxus. Sci Rep 2014; 4:5469. [PMID: 24968921 PMCID: PMC4073121 DOI: 10.1038/srep05469] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 05/23/2014] [Indexed: 11/09/2022] Open
Abstract
The cephalochordate Amphioxus naturally co-expresses fluorescent proteins (FPs) with different brightness, which thus offers the rare opportunity to identify FP molecular feature/s that are associated with greater/lower intensity of fluorescence. Here, we describe the spectral and structural characteristics of green FP (bfloGFPa1) with perfect (100%) quantum efficiency yielding to unprecedentedly-high brightness, and compare them to those of co-expressed bfloGFPc1 showing extremely-dim brightness due to low (0.1%) quantum efficiency. This direct comparison of structure-function relationship indicated that in the bright bfloGFPa1, a Tyrosine (Tyr159) promotes a ring flipping of a Tryptophan (Trp157) that in turn allows a cis-trans transformation of a Proline (Pro55). Consequently, the FP chromophore is pushed up, which comes with a slight tilt and increased stability. FPs are continuously engineered for improved biochemical and/or photonic properties, and this study provides new insight to the challenge of establishing a clear mechanistic understanding between chromophore structural environment and brightness level.
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Drachuk I, Shchepelina O, Harbaugh S, Kelley-Loughnane N, Stone M, Tsukruk VV. Cell surface engineering with edible protein nanoshells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3128-3137. [PMID: 23606641 DOI: 10.1002/smll.201202992] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/07/2013] [Indexed: 06/02/2023]
Abstract
Natural protein (silk fibroin) nanoshells are assembled on the surface of Saccharomyces cerevisiae yeast cells without compromising their viability. The nanoshells facilitate initial protection of the cells and allow them to function in encapsulated state for some time period, afterwards being completely biodegraded and consumed by the cells. In contrast to a traditional methanol treatment, the gentle ionic treatment suggested here stabilizes the shell silk fibroin structure but does not compromise the viability of the cells, as indicated by the fast response of the encapsulated cells, with an immediate activation by the inducer molecules. Extremely high viability rates (up to 97%) and preserved activity of encapsulated cells are facilitated by cytocompatibility of the natural proteins and the formation of highly porous shells in contrast to traditional polyelectrolyte-based materials. Moreover, in a high contrast to traditional synthetic shells, the silk proteins are biodegradable and can be consumed by cells at a later stage of growth, thus releasing the cells from their temporary protective capsules. These on-demand encapsulated cells can be considered a valuable platform for biocompatible and biodegradable cell encapsulation, controlled cell protection in a synthetic environment, transfer to a device environment, and cell implantation followed by biodegradation and consumption of protective protein shells.
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Affiliation(s)
- Irina Drachuk
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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