Joshua T. Atkinson

I use protein engineering and synthetic biology approaches to study and control bioenergetic processes in bacteria. Specifically, I am fascinated by electron transport and energy conservation in bacterial metabolism. My postdoctoral work is focusing on building synthetic mimics of cable bacteria to study how multicellular communities can evolve to couple distinct metabolic reactions using long-distance electron transfer.

I did my Ph.D. in Systems, Synthetic, and Physical Biology at Rice University in Houston, TX. There I worked in Jonathan Silberg’s lab building ligand-gated protein switches to control electron transfer to control sulfur assimilation in Escherichia coli. I did part of my Ph.D. at Lawrence Berkeley National Lab in Berkeley, CA where I collaborated with Caroline Ajo-Franklin at the Molecular Foundry. We designed strains of E. coli that could perform extracellular electron transfer to reduced electrodes and used the ligand-gated protein switches to control current production. We used these living electronic sensors for real-time reporting on the presence of chemicals in marine and riverine water samples.

news

Sep 5, 2022	Visiting Fellow at Aarhus University
Aug 11, 2022	Josh presented at the Synthetic Biology Young Speaker Series (SynByss)
Aug 31, 2020	Josh presented at the 2020 PEDS Protein Engineering and Design Webinar
Aug 1, 2020	Josh started as an NSF Postdoctoral Fellow in the El-Naggar lab @ USC

selected publications

Real-time bioelectronic sensing of environmental contaminants.

Joshua T Atkinson*, Lin Su*, Xu Zhang, George N Bennett, Jonathan J Silberg, and Caroline M Ajo-Franklin

Nature Nov 2022

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Real-time chemical sensing is crucial for applications in environmental and health monitoring. Biosensors can detect a variety of molecules through genetic circuits that use these chemicals to trigger the synthesis of a coloured protein, thereby producing an optical signal. However, the process of protein expression limits the speed of this sensing to approximately half an hour, and optical signals are often difficult to detect in situ. Here we combine synthetic biology and materials engineering to develop biosensors that produce electrical readouts and have detection times of minutes. We programmed Escherichia coli to produce an electrical current in response to specific chemicals using a modular, eight-component, synthetic electron transport chain. As designed, this strain produced current following exposure to thiosulfate, an anion that causes microbial blooms, within 2 min. This amperometric sensor was then modified to detect an endocrine disruptor. The incorporation of a protein switch into the synthetic pathway and encapsulation of the bacteria with conductive nanomaterials enabled the detection of the endocrine disruptor in urban waterway samples within 3 min. Our results provide design rules to sense various chemicals with mass-transport-limited detection times and a new platform for miniature, low-power bioelectronic sensors that safeguard ecological and human health.
Living Electronics: A catalog of engineered living electronic components

Joshua T Atkinson, Marko S Chavez, Christina Niman, and Mohamed Y El-Naggar

Microb. Biotechnol. Nov 2022

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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 tunable 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.
Light-induced patterning of electroactive bacterial biofilms

Fengjie Zhao, Marko S Chavez, Kyle L Naughton, Christina M Niman, Joshua T Atkinson, Jeffrey A Gralnick, Mohamed Y El-Naggar, and James Q Boedicker

ACS Synth. Biol. Jun 2022

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Electroactive bacterial biofilms can function as living biomaterials that merge the functionality of living cells with electronic components. However, the development of such advanced living electronics has been challenged by the inability to control the geometry of electroactive biofilms relative to solid-state electrodes. Here, we developed a lithographic strategy to pattern conductive biofilms of Shewanella oneidensis by controlling aggregation protein CdrAB expression with a blue light-induced genetic circuit. This controlled deposition enabled S. oneidensis biofilm patterning on transparent electrode surfaces, and electrochemical measurements allowed us to both demonstrate tunable conduction dependent on pattern size and quantify the intrinsic conductivity of the living biofilms. The intrinsic biofilm conductivity measurements enabled us to experimentally confirm predictions based on simulations of a recently proposed collision-exchange electron transport mechanism. Overall, we developed a facile technique for controlling electroactive biofilm formation on electrodes, with implications for both studying and harnessing bioelectronics.
Metalloprotein switches that display chemical-dependent electron transfer in cells

Joshua T Atkinson, Ian J Campbell, Emily E Thomas, Sheila C Bonitatibus, Sean J Elliott, George N Bennett, and Jonathan J Silberg

Nat. Chem. Biol. Feb 2019

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Biological electron transfer is challenging to directly regulate using environmental conditions. To enable dynamic, protein-level control over energy flow in metabolic systems for synthetic biology and bioelectronics, we created ferredoxin logic gates that utilize transcriptional and post-translational inputs to control energy flow through a synthetic electron transfer pathway that is required for bacterial growth. These logic gates were created by subjecting a thermostable, plant-type ferredoxin to backbone fission and fusing the resulting fragments to a pair of proteins that self-associate, a pair of proteins whose association is stabilized by a small molecule, and to the termini of a ligand-binding domain. We show that the latter domain insertion design strategy yields an allosteric ferredoxin switch that acquires an oxygen-tolerant [2Fe-2S] cluster and can use different chemicals, including a therapeutic drug and an environmental pollutant, to control the production of a reduced metabolite in Escherichia coli and cell lysates.