1
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Atkinson JT. Inter-kingdom electromechanical communication. Nat Chem Biol 2024:10.1038/s41589-024-01687-1. [PMID: 39030364 DOI: 10.1038/s41589-024-01687-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Affiliation(s)
- Joshua T Atkinson
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ, USA.
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, USA.
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2
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Partipilo G, Bowman EK, Palmer EJ, Gao Y, Ridley RS, Alper HS, Keitz BK. Single-Cell Phenotyping of Extracellular Electron Transfer via Microdroplet Encapsulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598847. [PMID: 38915652 PMCID: PMC11195189 DOI: 10.1101/2024.06.13.598847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes. Studying this phenomenon in high-throughput is challenging since extracellular reduction cannot easily be traced back to its cell of origin within a mixed population. Here, we describe the development of a microdroplet emulsion system to enrich EET-capable organisms. We validated our system using the model electroactive organism S. oneidensis and describe the tooling of a benchtop microfluidic system for oxygen-limited processes. We demonstrated enrichment of EET-capable phenotypes from a mixed wild-type and EET-knockout population. As a proof-of-concept application, bacteria were collected from iron sedimentation from Town Lake (Austin, TX) and subjected to microdroplet enrichment. We observed an increase in EET-capable organisms in the sorted population that was distinct when compared to a population enriched in a bulk culture more closely akin to traditional techniques for discovering EET-capable bacteria. Finally, two bacterial species, C. sakazakii and V. fessus not previously shown to be electroactive, were further cultured and characterized for their ability to reduce channel conductance in an organic electrochemical transistor (OECT) and to reduce soluble Fe(III). We characterized two bacterial species not previously shown to exhibit electrogenic behavior. Our results demonstrate the utility of a microdroplet emulsions for identifying putative EET-capable bacteria and how this technology can be leveraged in tandem with existing methods.
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Affiliation(s)
- Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Emily K. Bowman
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, 78712
| | - Emma J. Palmer
- Civil, Architectural, and Environmental Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Yang Gao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Rodney S. Ridley
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Benjamin K. Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
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3
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Graham AJ, Partipilo G, Dundas CM, Miniel Mahfoud IE, Halwachs KN, Holwerda AJ, Simmons TR, FitzSimons TM, Coleman SM, Rinehart R, Chiu D, Tyndall AE, Sajbel KC, Rosales AM, Keitz BK. Transcriptional regulation of living materials via extracellular electron transfer. Nat Chem Biol 2024:10.1038/s41589-024-01628-y. [PMID: 38783133 DOI: 10.1038/s41589-024-01628-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Engineered living materials combine the advantages of biological and synthetic systems by leveraging genetic and metabolic programming to control material-wide properties. Here, we demonstrate that extracellular electron transfer (EET), a microbial respiration process, can serve as a tunable bridge between live cell metabolism and synthetic material properties. In this system, EET flux from Shewanella oneidensis to a copper catalyst controls hydrogel cross-linking via two distinct chemistries to form living synthetic polymer networks. We first demonstrate that synthetic biology-inspired design rules derived from fluorescence parameterization can be applied toward EET-based regulation of polymer network mechanics. We then program transcriptional Boolean logic gates to govern EET gene expression, which enables design of computational polymer networks that mechanically respond to combinations of molecular inputs. Finally, we control fibroblast morphology using EET as a bridge for programmed material properties. Our results demonstrate how rational genetic circuit design can emulate physiological behavior in engineered living materials.
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Affiliation(s)
- Austin J Graham
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Christopher M Dundas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Ismar E Miniel Mahfoud
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA
| | - Kathleen N Halwachs
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Alexis J Holwerda
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA
| | - Trevor R Simmons
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Thomas M FitzSimons
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Sarah M Coleman
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Rebecca Rinehart
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Darian Chiu
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Avery E Tyndall
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, USA
| | - Kenneth C Sajbel
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA.
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4
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Zhao F, Niman CM, Ostovar G, Chavez MS, Atkinson JT, Bonis BM, Gralnick JA, El-Naggar MY, Boedicker JQ. Red-Light-Induced Genetic System for Control of Extracellular Electron Transfer. ACS Synth Biol 2024; 13:1467-1476. [PMID: 38696739 DOI: 10.1021/acssynbio.3c00684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Optogenetics is a powerful tool for spatiotemporal control of gene expression. Several light-inducible gene regulators have been developed to function in bacteria, and these regulatory circuits have been ported to new host strains. Here, we developed and adapted a red-light-inducible transcription factor for Shewanella oneidensis. This regulatory circuit is based on the iLight optogenetic system, which controls gene expression using red light. A thermodynamic model and promoter engineering were used to adapt this system to achieve differential gene expression in light and dark conditions within a S. oneidensis host strain. We further improved the iLight optogenetic system by adding a repressor to invert the genetic circuit and activate gene expression under red light illumination. The inverted iLight genetic circuit was used to control extracellular electron transfer within S. oneidensis. The ability to use both red- and blue-light-induced optogenetic circuits simultaneously was also demonstrated. Our work expands the synthetic biology capabilities in S. oneidensis, which could facilitate future advances in applications with electrogenic bacteria.
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Affiliation(s)
- Fengjie Zhao
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Ghazaleh Ostovar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08540, United States
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey 08540, United States
| | - Benjamin M Bonis
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota─Twin Cities, St. Paul, Minnesota 55108, United States
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota─Twin Cities, St. Paul, Minnesota 55108, United States
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - James Q Boedicker
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
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5
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Sweet P, Blacutt J, Gordon V, Contreras L. Exposure of Shewanella oneidensis MR-1 to Sublethal Doses of Ionizing Radiation Triggers Short-Term SOS Activation and Longer-Term Prophage Activation. Appl Environ Microbiol 2023; 89:e0171622. [PMID: 36847540 PMCID: PMC10057963 DOI: 10.1128/aem.01716-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/23/2023] [Indexed: 03/01/2023] Open
Abstract
Currently, there is a lack of bacterial biomarkers indicative of exposure to ionizing radiation (IR). IR biomarkers have applications for medical treatment planning, population exposure surveillance, and IR sensitivity studies. In this study, we compared the utility of signals originating from prophages and the SOS regulon as biomarkers of IR exposure in the radiosensitive bacterium Shewanella oneidensis. Using RNA sequencing, we demonstrated that 60 min after exposure to acute doses of IR (40, 1, 0.5, and 0.25 Gy), the transcriptional activation of the SOS regulon and the lytic cycle of the T-even lysogenic prophage So Lambda are comparable. Using quantitative PCR (qPCR), we showed that 300 min after exposure to doses as low as 0.25 Gy, the fold change of transcriptional activation of the So Lambda lytic cycle surpassed that of the SOS regulon. We observed an increase in cell size (a phenotype of SOS activation) and plaque production (a phenotype of prophage maturation) 300 min after doses as low as 1 Gy. While the transcriptional responses of the SOS and So Lambda regulons have been examined in S. oneidensis after lethal IR exposures, the potential of these (and other transcriptome-wide) responses as biomarkers of sublethal levels of IR (<10 Gy) and the longer-term activity of these two regulons have not been investigated. A major finding is that after exposure to sublethal doses of IR, the most upregulated transcripts are associated with a prophage regulon and not with a DNA damage response. Our findings suggest that prophage lytic cycle genes are a promising source of biomarkers of sublethal DNA damage. IMPORTANCE The bacterial minimum threshold of sensitivity to ionizing radiation (IR) is poorly understood, which hinders our understanding of how living systems recover from the doses of IR experienced in medical, industrial, and off-world environments. Using a transcriptome-wide approach, we studied how in the highly radiosensitive bacterium S. oneidensis, genes (including the SOS regulon and the So Lambda prophage) are activated after exposure to low doses of IR. We found that 300 min after exposure to doses as low as 0.25 Gy, genes within the So Lambda regulon remained upregulated. As this is the first transcriptome-wide study of how bacteria respond to acute sublethal doses of IR, these findings serve as a benchmark for future bacterial IR sensitivity studies. This is the first work to highlight the utility of prophages as biomarkers of exposure to very low (i.e., sublethal) doses of IR and to examine the longer-term impacts of sublethal IR exposure on bacteria.
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Affiliation(s)
- Philip Sweet
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Jacob Blacutt
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Vernita Gordon
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, Texas, USA
| | - Lydia Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
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6
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Bird LJ, Mickol RL, Eddie BJ, Thakur M, Yates MD, Glaven SM. Marinobacter: A case study in bioelectrochemical chassis evaluation. Microb Biotechnol 2023; 16:494-506. [PMID: 36464922 PMCID: PMC9948230 DOI: 10.1111/1751-7915.14170] [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: 06/20/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 12/08/2022] Open
Abstract
The junction of bioelectrochemical systems and synthetic biology opens the door to many potentially groundbreaking technologies. When developing these possibilities, choosing the correct chassis organism can save a great deal of engineering effort and, indeed, can mean the difference between success and failure. Choosing the correct chassis for a specific application requires a knowledge of the metabolic potential of the candidate organisms, as well as a clear delineation of the traits, required in the application. In this review, we will explore the metabolic and electrochemical potential of a single genus, Marinobacter. We will cover its strengths, (salt tolerance, biofilm formation and electrochemical potential) and weaknesses (insufficient characterization of many strains and a less developed toolbox for genetic manipulation) in potential synthetic electromicrobiology applications. In doing so, we will provide a roadmap for choosing a chassis organism for bioelectrochemical systems.
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Affiliation(s)
- Lina J Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA
| | - Rebecca L Mickol
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA
| | - Brian J Eddie
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA.,College of Science, George Mason University, Fairfax, Virginia, USA
| | - Matthew D Yates
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA
| | - Sarah M Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA
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7
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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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8
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Gruenberg MC, TerAvest MA. A common inducer molecule enhances sugar utilization by Shewanella oneidensis MR-1. J Ind Microbiol Biotechnol 2023; 50:kuad018. [PMID: 37537149 PMCID: PMC10549210 DOI: 10.1093/jimb/kuad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/02/2023] [Indexed: 08/05/2023]
Abstract
Shewanella oneidensis MR-1 is an electroactive bacterium that is a promising host for bioelectrochemical technologies, which makes it a common target for genetic engineering, including gene deletions and expression of heterologous pathways. Expression of heterologous genes and gene knockdown via CRISPRi in S. oneidensis are both frequently induced by β-D-1-thiogalactopyranoside (IPTG), a commonly used inducer molecule across many model organisms. Here, we report and characterize an unexpected phenotype; IPTG enhances the growth of wild-type S. oneidensis MR-1 on the sugar substrate N-acetylglucosamine (NAG). IPTG improves the carrying capacity of S. oneidensis growing on NAG while the growth rate remains similar to cultures without the inducer. Extracellular acetate accumulates faster and to a higher concentration in cultures without IPTG than those with it. IPTG appears to improve acetate metabolism, which combats the negative effect that acetate accumulation has on the growth of S. oneidensis with NAG. We recommend using extensive experimental controls and careful data interpretation when using both NAG and IPTG in S. oneidensis cultures.
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Affiliation(s)
- Megan C Gruenberg
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Michaela A TerAvest
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
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9
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Szmuc E, Walker DJF, Kireev D, Akinwande D, Lovley DR, Keitz B, Ellington A. Engineering Geobacter pili to produce metal:organic filaments. Biosens Bioelectron 2023; 222:114993. [PMID: 36525710 DOI: 10.1016/j.bios.2022.114993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/15/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
The organized self-assembly of conductive biological structures holds promise for creating new bioelectronic devices. In particular, Geobacter sulfurreducens type IVa pili have proven to be a versatile material for fabricating protein nanowire-based devices. To scale the production of conductive pili, we designed a strain of Shewanella oneidensis that heterologously expressed abundant, conductive Geobacter pili when grown aerobically in liquid culture. S. oneidensis expressing a cysteine-modified pilin, designed to enhance the capability to bind to gold, generated conductive pili that self-assembled into biohybrid filaments in the presence of gold nanoparticles. Elemental composition analysis confirmed the filament-metal interactions within the structures, which were several orders of magnitude larger than previously described metal:organic filaments. The results demonstrate that the S. oneidensis chassis significantly advances the possibilities for facile conductive protein nanowire design and fabrication.
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Affiliation(s)
- Eric Szmuc
- College of Natural Sciences, University of Texas at Austin, Austin, TX, 78712, United States
| | - David J F Walker
- College of Natural Sciences, University of Texas at Austin, Austin, TX, 78712, United States; U.S. Army Engineer Research and Development Center, Environmental Laboratory, University of Texas at Austin, Austin, TX, 78712, United States; Bioconscientia LLC, Austin, TX 78712, United States
| | - Dmitry Kireev
- Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, United States
| | - Deji Akinwande
- Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, United States
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, MA, 01003, United States
| | - Benjamin Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, United States
| | - Andrew Ellington
- College of Natural Sciences, University of Texas at Austin, Austin, TX, 78712, United States.
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10
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Sun H, Tang Q, Li Y, Liang ZH, Li FH, Li WW, Yu HQ. Radionuclide Reduction by Combinatorial Optimization of Microbial Extracellular Electron Transfer with a Physiologically Adapted Regulatory Platform. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:674-684. [PMID: 36576943 DOI: 10.1021/acs.est.2c07697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Microbial extracellular electron transfer (EET) is the basis for many microbial processes involved in element geochemical recycling, bioenergy harvesting, and bioremediation, including the technique for remediating U(VI)-contaminated environments. However, the low EET rate hinders its full potential from being fulfilled. The main challenge for engineering microbial EET is the difficulty in optimizing cell resource allocation for EET investment and basic metabolism and the optimal coordination of the different EET pathways. Here, we report a novel combinatorial optimization strategy with a physiologically adapted regulatory platform. Through exploring the physiologically adapted regulatory elements, a 271.97-fold strength range, autonomous, and dynamic regulatory platform was established for Shewanella oneidensis, a prominent electrochemically active bacterium. Both direct and mediated EET pathways are modularly reconfigured and tuned at various intensities with the regulatory platform, which were further assembled combinatorically. The optimal combinations exhibit up to 16.12-, 4.51-, and 8.40-fold improvements over the control in the maximum current density (1009.2 mA/m2) of microbial electrolysis cells and the voltage output (413.8 mV) and power density (229.1 mW/m2) of microbial fuel cells. In addition, the optimal strains exhibited up to 6.53-fold improvement in the radionuclide U(VI) removal efficiency. This work provides an effective and feasible approach to boost microbial EET performance for environmental applications.
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11
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Kohn EM, Shirley DJ, Hinds NM, Fry HC, Caputo GA. Peptide‐assisted
supramolecular polymerization of the anionic porphyrin
meso‐tetra
(
4‐sulfonatophenyl
)porphine. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Eric M. Kohn
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
- Bantivoglio Honors College Rowan University Glassboro New Jersey USA
- Department of Chemistry University of Wisconsin Madison Wisconsin USA
| | - David J. Shirley
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
- Division of Chemical Biology and Medicinal Chemistry Eshelman School of Pharmacy, University of North Carolina Chapel Hill North Carolina USA
| | - Nicole M. Hinds
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
| | - H. Christopher Fry
- Argonne National Laboratory Center for Nanoscale Materials Lemont Illinois USA
| | - Gregory A. Caputo
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
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12
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Partipilo G, Graham AJ, Belardi B, Keitz BK. Extracellular Electron Transfer Enables Cellular Control of Cu(I)-Catalyzed Alkyne-Azide Cycloaddition. ACS CENTRAL SCIENCE 2022; 8:246-257. [PMID: 35233456 PMCID: PMC8875427 DOI: 10.1021/acscentsci.1c01208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Indexed: 05/03/2023]
Abstract
Extracellular electron transfer (EET) is an anaerobic respiration process that couples carbon oxidation to the reduction of metal species. In the presence of a suitable metal catalyst, EET allows for cellular metabolism to control a variety of synthetic transformations. Here, we report the use of EET from the electroactive bacterium Shewanella oneidensis for metabolic and genetic control over Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC). CuAAC conversion under anaerobic and aerobic conditions was dependent on live, actively respiring S. oneidensis cells. The reaction progress and kinetics were manipulated by tailoring the central carbon metabolism. Similarly, EET-CuAAC activity was dependent on specific EET pathways that could be regulated via inducible expression of EET-relevant proteins: MtrC, MtrA, and CymA. EET-driven CuAAC exhibited modularity and robustness in the ligand and substrate scope. Furthermore, the living nature of this system could be exploited to perform multiple reaction cycles without regeneration, something inaccessible to traditional chemical reductants. Finally, S. oneidensis enabled bioorthogonal CuAAC membrane labeling on live mammalian cells without affecting cell viability, suggesting that S. oneidensis can act as a dynamically tunable biocatalyst in complex environments. In summary, our results demonstrate how EET can expand the reaction scope available to living systems by enabling cellular control of CuAAC.
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Affiliation(s)
- Gina Partipilo
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Dynamics and Control of Materials, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Austin J. Graham
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Dynamics and Control of Materials, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Brian Belardi
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Benjamin K. Keitz
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Dynamics and Control of Materials, University
of Texas at Austin, Austin, Texas 78712, United States
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13
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Graham AJ, Gibbs SL, Saez Cabezas CA, Wang Y, Green AM, Milliron DJ, Keitz BK. In Situ
Optical Quantification of Extracellular Electron Transfer Using Plasmonic Metal Oxide Nanocrystals**. ChemElectroChem 2022. [DOI: 10.1002/celc.202101423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Austin J. Graham
- McKetta Department of Chemical Engineering University of Texas at Austin TX, 78712 Austin United States
- Center for the Dynamics and Control of Materials University of Texas at Austin TX, 78712 Austin United States
| | - Stephen L. Gibbs
- McKetta Department of Chemical Engineering University of Texas at Austin TX, 78712 Austin United States
| | - Camila A. Saez Cabezas
- McKetta Department of Chemical Engineering University of Texas at Austin TX, 78712 Austin United States
- Center for the Dynamics and Control of Materials University of Texas at Austin TX, 78712 Austin United States
| | - Yongdan Wang
- McKetta Department of Chemical Engineering University of Texas at Austin TX, 78712 Austin United States
| | - Allison M. Green
- McKetta Department of Chemical Engineering University of Texas at Austin TX, 78712 Austin United States
- Center for the Dynamics and Control of Materials University of Texas at Austin TX, 78712 Austin United States
| | - Delia J. Milliron
- McKetta Department of Chemical Engineering University of Texas at Austin TX, 78712 Austin United States
- Center for the Dynamics and Control of Materials University of Texas at Austin TX, 78712 Austin United States
| | - Benjamin K. Keitz
- McKetta Department of Chemical Engineering University of Texas at Austin TX, 78712 Austin United States
- Center for the Dynamics and Control of Materials University of Texas at Austin TX, 78712 Austin United States
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Zhuang X, Zhang Y, Xiao AF, Zhang A, Fang B. Applications of Synthetic Biotechnology on Carbon Neutrality Research: A Review on Electrically Driven Microbial and Enzyme Engineering. Front Bioeng Biotechnol 2022; 10:826008. [PMID: 35145960 PMCID: PMC8822124 DOI: 10.3389/fbioe.2022.826008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022] Open
Abstract
With the advancement of science, technology, and productivity, the rapid development of industrial production, transportation, and the exploitation of fossil fuels has gradually led to the accumulation of greenhouse gases and deterioration of global warming. Carbon neutrality is a balance between absorption and emissions achieved by minimizing carbon dioxide (CO2) emissions from human social productive activity through a series of initiatives, including energy substitution and energy efficiency improvement. Then CO2 was offset through forest carbon sequestration and captured at last. Therefore, efficiently reducing CO2 emissions and enhancing CO2 capture are a matter of great urgency. Because many species have the natural CO2 capture properties, more and more scientists focus their attention on developing the biological carbon sequestration technique and further combine with synthetic biotechnology and electricity. In this article, the advances of the synthetic biotechnology method for the most promising organisms were reviewed, such as cyanobacteria, Escherichia coli, and yeast, in which the metabolic pathways were reconstructed to enhance the efficiency of CO2 capture and product synthesis. Furthermore, the electrically driven microbial and enzyme engineering processes are also summarized, in which the critical role and principle of electricity in the process of CO2 capture are canvassed. This review provides detailed summary and analysis of CO2 capture through synthetic biotechnology, which also pave the way for implementing electrically driven combined strategies.
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Affiliation(s)
- Xiaoyan Zhuang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - Yonghui Zhang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - An-Feng Xiao
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - Aihui Zhang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- *Correspondence: Aihui Zhang, ; Baishan Fang,
| | - Baishan Fang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- *Correspondence: Aihui Zhang, ; Baishan Fang,
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Bird LJ, Kundu BB, Tschirhart T, Corts AD, Su L, Gralnick JA, Ajo-Franklin CM, Glaven SM. Engineering Wired Life: Synthetic Biology for Electroactive Bacteria. ACS Synth Biol 2021; 10:2808-2823. [PMID: 34637280 DOI: 10.1021/acssynbio.1c00335] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Electroactive bacteria produce or consume electrical current by moving electrons to and from extracellular acceptors and donors. This specialized process, known as extracellular electron transfer, relies on pathways composed of redox active proteins and biomolecules and has enabled technologies ranging from harvesting energy on the sea floor, to chemical sensing, to carbon capture. Harnessing and controlling extracellular electron transfer pathways using bioengineering and synthetic biology promises to heighten the limits of established technologies and open doors to new possibilities. In this review, we provide an overview of recent advancements in genetic tools for manipulating native electroactive bacteria to control extracellular electron transfer. After reviewing electron transfer pathways in natively electroactive organisms, we examine lessons learned from the introduction of extracellular electron transfer pathways into Escherichia coli. We conclude by presenting challenges to future efforts and give examples of opportunities to bioengineer microbes for electrochemical applications.
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Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Biki B. Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Tanya Tschirhart
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Anna D. Corts
- Joyn Bio, Boston, Massachusetts 02210, United States
| | - Lin Su
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210018, People’s Republic of China
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | | | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
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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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