Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface

ABSTRACT Engineering synthetic circuits into intestinal bacteria to sense, record, and respond to in vivo signals is a promising new approach for the diagnosis, treatment, and prevention of disease. However, because the design of disease-responsive circuits is limited by a relatively small pool of k...

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Autores principales:	Alexander D. Naydich, Shannon N. Nangle, Johannes J. Bues, Disha Trivedi, Nabeel Nissar, Mara C. Inniss, Matthew J. Niederhuber, Jeffrey C. Way, Pamela A. Silver, David T. Riglar
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	synthetic biology biosensors Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/a670a59b6f6541ef8395330c64f5fd82
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spelling	oai:doaj.org-article:a670a59b6f6541ef8395330c64f5fd822021-12-02T18:25:16ZSynthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface10.1128/mSystems.00125-192379-5077https://doaj.org/article/a670a59b6f6541ef8395330c64f5fd822019-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00125-19https://doaj.org/toc/2379-5077ABSTRACT Engineering synthetic circuits into intestinal bacteria to sense, record, and respond to in vivo signals is a promising new approach for the diagnosis, treatment, and prevention of disease. However, because the design of disease-responsive circuits is limited by a relatively small pool of known biosensors, there is a need for expanding the capacity of engineered bacteria to sense and respond to the host environment. Here, we apply a robust genetic memory circuit in Escherichia coli to identify new bacterial biosensor triggers responding in the healthy and diseased mammalian gut, which may be used to construct diagnostic or therapeutic circuits. We developed a pipeline for rapid systems-level library construction and screening, using next-generation sequencing and computational analysis, which demonstrates remarkably reliable identification of responsive biosensor triggers from pooled libraries. By testing libraries of potential triggers—each consisting of a promoter and ribosome binding site (RBS)—and using RBS variation to augment the range of trigger sensitivity, we identify and validate triggers that selectively activate our synthetic memory circuit during transit through the gut. We further identify biosensor triggers with increased response in the inflamed gut through comparative screening of one of our libraries in healthy mice and those with intestinal inflammation. Our results demonstrate the power of systems-level screening for the identification of novel biosensor triggers in the gut and provide a platform for disease-specific screening that is capable of contributing to both the understanding and clinical management of intestinal illness. IMPORTANCE The gut is a largely obscure and inaccessible environment. The use of live, engineered probiotics to detect and respond to disease signals in vivo represents a new frontier in the management of gut diseases. Engineered probiotics have also shown promise as a novel mechanism for drug delivery. However, the design and construction of effective strains that respond to the in vivo environment is hindered by our limited understanding of bacterial behavior in the gut. Our work expands the pool of environmentally responsive synthetic circuits for the healthy and diseased gut, providing insight into host-microbe interactions and enabling future development of increasingly complex biosensors. This method also provides a framework for rapid prototyping of engineered systems and for application across bacterial strains and disease models, representing a practical step toward the construction of clinically useful synthetic tools.Alexander D. NaydichShannon N. NangleJohannes J. BuesDisha TrivediNabeel NissarMara C. InnissMatthew J. NiederhuberJeffrey C. WayPamela A. SilverDavid T. RiglarAmerican Society for Microbiologyarticlesynthetic biologybiosensorsMicrobiologyQR1-502ENmSystems, Vol 4, Iss 4 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	synthetic biology biosensors Microbiology QR1-502
spellingShingle	synthetic biology biosensors Microbiology QR1-502 Alexander D. Naydich Shannon N. Nangle Johannes J. Bues Disha Trivedi Nabeel Nissar Mara C. Inniss Matthew J. Niederhuber Jeffrey C. Way Pamela A. Silver David T. Riglar Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface
description	ABSTRACT Engineering synthetic circuits into intestinal bacteria to sense, record, and respond to in vivo signals is a promising new approach for the diagnosis, treatment, and prevention of disease. However, because the design of disease-responsive circuits is limited by a relatively small pool of known biosensors, there is a need for expanding the capacity of engineered bacteria to sense and respond to the host environment. Here, we apply a robust genetic memory circuit in Escherichia coli to identify new bacterial biosensor triggers responding in the healthy and diseased mammalian gut, which may be used to construct diagnostic or therapeutic circuits. We developed a pipeline for rapid systems-level library construction and screening, using next-generation sequencing and computational analysis, which demonstrates remarkably reliable identification of responsive biosensor triggers from pooled libraries. By testing libraries of potential triggers—each consisting of a promoter and ribosome binding site (RBS)—and using RBS variation to augment the range of trigger sensitivity, we identify and validate triggers that selectively activate our synthetic memory circuit during transit through the gut. We further identify biosensor triggers with increased response in the inflamed gut through comparative screening of one of our libraries in healthy mice and those with intestinal inflammation. Our results demonstrate the power of systems-level screening for the identification of novel biosensor triggers in the gut and provide a platform for disease-specific screening that is capable of contributing to both the understanding and clinical management of intestinal illness. IMPORTANCE The gut is a largely obscure and inaccessible environment. The use of live, engineered probiotics to detect and respond to disease signals in vivo represents a new frontier in the management of gut diseases. Engineered probiotics have also shown promise as a novel mechanism for drug delivery. However, the design and construction of effective strains that respond to the in vivo environment is hindered by our limited understanding of bacterial behavior in the gut. Our work expands the pool of environmentally responsive synthetic circuits for the healthy and diseased gut, providing insight into host-microbe interactions and enabling future development of increasingly complex biosensors. This method also provides a framework for rapid prototyping of engineered systems and for application across bacterial strains and disease models, representing a practical step toward the construction of clinically useful synthetic tools.
format	article
author	Alexander D. Naydich Shannon N. Nangle Johannes J. Bues Disha Trivedi Nabeel Nissar Mara C. Inniss Matthew J. Niederhuber Jeffrey C. Way Pamela A. Silver David T. Riglar
author_facet	Alexander D. Naydich Shannon N. Nangle Johannes J. Bues Disha Trivedi Nabeel Nissar Mara C. Inniss Matthew J. Niederhuber Jeffrey C. Way Pamela A. Silver David T. Riglar
author_sort	Alexander D. Naydich
title	Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface
title_short	Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface
title_full	Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface
title_fullStr	Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface
title_full_unstemmed	Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface
title_sort	synthetic gene circuits enable systems-level biosensor trigger discovery at the host-microbe interface
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/a670a59b6f6541ef8395330c64f5fd82
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Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface

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