Reprogramming bacteria to seek and destroy an herbicide

Abstract

A major goal of synthetic biology is to reprogram cells to perform complex tasks. Here we show how a combination of in vitro and in vivo selection rapidly identifies a synthetic riboswitch that activates protein translation in response to the herbicide atrazine. We further demonstrate that this riboswitch can reprogram bacteria to migrate in the presence of atrazine. Finally, we show that incorporating a gene from an atrazine catabolic pathway allows these cells to seek and destroy atrazine.

Synthetic RNA devices to expedite the evolution of metabolite-producing microbes

“…1d,f). As the binding sensitivity of aptamers towards chemicals, as well as the activation ratio of a riboswitch module, can be customized during the riboselector construction process 15,[26][27][28] , the selection cutoff levels could be further modulated according to the physiological conditions of the target strain.…”

“…Recently, various genetic devices combining the riboswitches with reporter genes have been described to modulate genetic switches, discover the genetic pathway and reprogram cellular behaviours 15,16,18,34,36 . However, none of them was directly used for evolving metabolite-producing microbes to increase the yield and the productivity of the target molecules.…”

“…This indicates that there is a strong possibility of generating synthetic aptamers that selectively bind to numerous chemicals by systematic evolution of ligands by exponential enrichment in which we are interested 13 . Then, synthetic riboselectors based on these in vitro-selected aptamers can be easily constructed by applying any of several highthroughput screening methods as shown in this study [14][15][16] . Considering a recent advance in engineering RNA devices that enables such devices to quantitatively programme gene expression based on mathematical models 27 , it should be practicable to expand the use of the synthetic RNA devices developed here to various other metabolites.…”

“…RNA aptamers that bind to target molecules with high selectivity and sensitivity can be readily selected in vitro through systematic evolution of ligands by exponential enrichment 13 . Synthetic riboswitches that actually work in vivo can be generated from these in vitro-selected aptamers and can also be functionally manipulated using various high-throughput screening methods [14][15][16] .…”

Superior cellular activities of azido- over amino-functionalized ligands for engineered preQ1riboswitches inE.coli

“…Nevertheless, the identification of novel potent ligands is a topic of intense research because ever since their discovery, riboswitches have been viewed as promising targets for the development of novel antibiotic strategies [16]. Likewise, efforts to engineer riboswitches for imaging purposes [17–19] or as biotechnological tools for the detection of endogenous and non-endogenous small molecules are in the focus of synthetic biologists interested in understanding and reprogramming cellular behavior [20]. …”