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Josh Atkinson

Principal investigator
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joshatkinsonobfuscate@princeton.edu

I’m an Assistant Professor at Princeton University in the Department of Civil and Environmental Engineering and the Omenn-Darling Bioengineering Institute.

My research program focuses on using protein engineering and synthetic biology approaches to study and control bioenergetic processes in bacteria. I am fascinated by bacterial metabolism and the proteins that have evolved to transport electrons and conserve energy and redox metabolism influences the structure of microbial communities and drive Earth’s geochemical cycles.

Prior to joining Princeton, I was an NSF Postodoctoral Fellow jointly in the lab of Moh El-Naggar at the University of Southern California in Los Angeles, CA, USA and the Center for Electromicrobiology at Aarhus University in Aarhus, DK. I obtained my Ph.D. in Systems, Synthetic, and Physical Biology at Rice University in Houston, TX, USA. 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, USA where I collaborated with Caroline Ajo-Franklin at the Molecular Foundry.

More broadly, I’ve sought to promote eduction in engineering biology and microbial electrochemsistry through hands-on outreach and open access curricula development.

Papers
The biochemical impact of extracting an embedded adenylate kinase domain using circular permutation
A red light-induced genetic system for control of extracellular electron transfer
Introduction to Engineering Biology: A Conceptual Framework for Teaching Synthetic Biology
The energetics and evolution of oxidoreductases in deep time
Living electronics: a catalog of engineered living electronic components
A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase
Real-time bioelectronic sensing of environmental contaminants.
Determinants of multiheme cytochrome extracellular electron transfer uncovered by systematic peptide insertion
Light-induced patterning of electroactive bacterial biofilms.
Solution-deposited and patternable conductive polymer thin-film electrodes for microbial bioelectronics
A split methyl halide transferase AND gate that reports by synthesizing an indicator gas
Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases
Combinatorial design of chemical‐dependent protein switches for controlling intracellular electron transfer
Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts
Overcoming component limitations in synthetic biology through transposon-mediated protein engineering
Metalloprotein switches that display chemical-dependent electron transfer in cells
Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis
PERMutation Using Transposase Engineering (PERMUTE): A simple approach for constructing circularly permuted protein libraries
Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways
The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation
Identification of multiple dityrosine bonds in materials composed of the Drosophila protein Ultrabithorax
Genome sequence of Photobacterium mandapamensis strain svers.1.1, the bioluminescent symbiont of the cardinal fish Siphamia versicolor
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