Research

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EXTRACELLULAR ELECTRON TRANSFER (EET)

An orthogonal microbial anaerobic respiratory pathway that uses metals and metal oxides as terminal electron acceptors. EET is important in a number of fields ranging from biogeochemistry to human health.

Biogeochemistry

The reduction and oxidation of iron oxides partially controls the transport of iron in the biosphere. Subsequent iron uptake and use in nitrogen fixation and carbon oxidation influences the nitrogen and carbon cycles.

Bioelectronics

Anaerobic respiration and EET can be used for generating power in microbial fuel cells. Alternatively, reducing equivalents can be supplied via an electrode to enhance the synthesis of reduced metabolites.

Human Health

In anaerobic environments, such as the gut lumen, there is intense competition for respiratory electron acceptors, including metal species. Pathogens can gain a selective advantage using these acceptors.

SYNTHETIC BIOLOGY

Electroactivity allows microbes to interface with a variety of biotic and abiotic systems, including biofilms, fuel cells, and (in)organic materials. Although many EET proteins and metabolites are well-studied, relatively few tools are available to manipulate their function. Thus, chemists and engineers have limited control over biological electron transfer in many applications. To address this, we aim to adapt synthetic biology strategies in the model electroactive bacterium, Shewanella oneidensis. By regulating the expression of key S. oneidensis EET genes with stimuli-responsive genetic circuits, we hypothesize that the magnitude and timing of EET outputs (e.g., Fe(III) reduction, electrical current, redox catalysis) can be drastically modulated. The performance of engineered circuits can be assayed by high-throughput screening and selection methodologies, enabling isolation of bacterial strains with optimal bioelectrical properties. Our designed EET constructs can be integrated with more sophisticated technologies, such as optogenetic circuits and genetic logic gates, and may lead to increased programmability of cellular electron flux.

GENETIC CONTROL OF RADICAL CROSS-LINKING IN A SEMISYNTHETIC HYDROGEL
A.J. Graham, C.M. Dundas, A. Hillsley, D.S. Kasprak, A.M. Rosales, B.K. Keitz.
ACS Biomater. Sci. Eng. 2020, 6(3), 1375-1386 [PDF] [SI] [DATA]

TRANSCRIPTIONAL REGULATION OF SYNTHETIC POLYMER NETWORKS
A.J. Graham, C.M. Dundas*, G. Partipilo*, I.E. Miniel Mahfoud, T. FitzSimons, R. Rinehart, D. Chiu, A.E. Tyndall, A.M. Rosales, B.K. Keitz
bioRxiv 2021 [LINK ]

MICROBIAL REDOX CATALYSIS

Metabolic engineering benefits from the tunable and tightly controlled reactions afforded by biological systems. The reaction space available to specific organisms can be expanded through directed evolution or the insertion of heterologous pathways, but is still relatively limited compared to synthetic chemistry. In an effort to expand the scope of biological catalysis, we are exploring EET as a general means to achieve metabolic control over exogenous transition-metal catalyzed reactions. As an example, we used the bacterium S. oneidensis to control a metal-catalyzed radical polymerization. Metabolic control over polymerization opens avenues for applying synthetic biology and cellular engineering techniques to produce molecules and materials with emergent properties. We are currently applying our expertise in synthetic biology and inorganic chemistry to expand metabolically-controlled redox catalysis to alternative electroactive bacteria and synthetic reactions.

AEROBIC RADICAL POLYMERIZATION MEDIATED BY MICROBIAL METABOLISM
G. Fan, A.J. Graham, J. Kolli, N.A. Lynd, B.K. Keitz
Nat. Chem. 2020, 12, 638–646 [PDF] [SI] [DATA]

SHEWANELLA ONEIDENSIS AS A LIVING ELECTRODE FOR CONTROLLED RADICAL POLYMERIZATION
G. Fan,* C.M. Dundas,* A.J. Graham, N.A. Lynd, B.K. Keitz
Proc. Natl. Acad. Sci. U.S.A. 2018, 115(18), 4559-4564 [PDF] [SI] [DATA]

EXTRACELLULAR ELECTRON TRANSFER ENABLES CELLULAR CONTROL OF CU(I)-CATALYZED ALKYNE-AZIDE CYCLOADDITION
G. Partipilo, A.J. Graham, B. Belardi, B.K. Keitz
ACS Central Science, 2023 [LIN K]

LIVING INORGANIC MATERIALS

EET allows microbes to reduce soluble metals and insoluble metal oxides. Through this mechanism, simple metal salts can be converted to metal nanoparticles. These particles show promise as catalysts for processes relevant to water treatment, environmental remediation, and medicine. In some cases, they exhibit superior activity to nanoparticles synthesized using more traditional methods. However, control over nanoparticle size and crystal morphology is still a challenge and varies significantly between organisms. Well-defined genotype-phenotype linkages must be established to realize microbial production of designer materials. Towards this goal, we engineer the electroactive metabolism of S. oneidensis to better understand the mechanisms of bio-nanoparticle formation.

We are also examining the interaction between electroactive bacteria and synthetic materials. Metal organic frameworks (MOFs) are a class of materials applicable in catalysis, gas storage, and environmental remediation due to their highly porous and tunable nature. In contrast to the metal oxides typically studied using electroactive bacteria, the structure and function of MOFs can be readily varied by changing the identity of the metal node and organic linker. We’ve demonstrated that EET enables S. oneidensis to metabolize MOFs made of particular building-blocks. We exploited this relationship to develop a chemical degradation platform that capitalizes on the synergy between bacterium and material effects, where adsorption and catalytic properties are enhanced relative to either component in isolation. We are applying this system towards the remediation of various environmental pollutants and toxins, including organic and heavy metal species. More broadly, we are exploring the use of MOFs as tunable growth materials for the study and application of electroactive organisms.

EXTRACELLULAR ELECTRON TRANSFER BY SHEWANELLA ONEIDENSIS CONTROLS PALLADIUM NANOPARTICLE PHENOTYPE
C.M. Dundas, A.J. Graham, D.K. Romanovicz, B.K. Keitz
ACS Synth. Biol. 2018, 7(12), 2726-2736 [PDF] [SI] [DATA]

MICROBIAL REDUCTION OF METAL-ORGANIC FRAMEWORKS ENABLES SYNERGISTIC CHROMIUM REMOVAL
S.K. Springthorpe, C.M. Dundas, B.K. Keitz
Nat. Commun. 2019, 10, 5212 [PDF] [SI] [DATA]

SEQUENCE-DEPENDENT PEPTIDE SURFACE FUNCTIONALIZATION OF METAL-ORGANIC FRAMEWORKS
G. Fan, C.M. Dundas, C. Zhang, N.A. Lynd, B.K. Keitz
ACS Appl. Mater. Inter. 2018, 10(22), 18601-18609 [PDF] [SI]

BIOELECTRONICS

The integration of biological processes with electronic systems is not just a mere juxtaposition of the two fields, but a synergistic combination that leverages the sensitivity and precision of electronic technologies with the adaptability and modulability of biological systems. By harnessing the capabilities of cells and biomolecules to communicate and interact with electronic components, we are developing devices that can read, interpret, and even manipulate biological processes. We are exploring EET as a universal method to control microelectronic elements through redox reactions. For instance, we used S. oneidensis to control the doping state of organic electrochemical transistors (OECTs). Aided by transcriptional regulation of the EET genes, the hybrid transistors could not only translate biological activities into electronic signals but also allow direct control over the electrical output with programmed genetic logic. Given the range of biological interactions, we expect that the hybrid transistors may be regulated by a variety of agents including specific chemicals, light, and temperature. Potential applications of this technology are vast, ranging from biocomputing, where the hybrid transistor could be the building blocks of hybrid circuits or neural networks, to healthcare, where bioelectronic devices could provide personalized diagnostics and treatment, to environmental monitoring, where they could be used for detecting and responding to biological changes in ecosystems.

A HYBRID TRANSISTOR WITH TRANSCRIPTIONALLY CONTROLLED COMPUTATION AND PLASTICITY
Y. Gao, Y. Zhou, X. Ji, A.J. Graham, C.M. Dundas, I.E. Miniel Mahfoud, B.M. Tibbett, B. Tan, G. Partipilo, A. Dodabalapur, J. Rivnay, B.K. Keitz
bioRxiv 2023 [LINK]