Document Detail


Genetic programs constructed from layered logic gates in single cells.
MedLine Citation:
PMID:  23041931     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits, and they have been used in various cellular engineering applications, including the implementation of process control in metabolic networks and the coordination of spatial differentiation in artificial tissues. A key limitation is that the circuits are based on biochemical interactions occurring in the confined volume of the cell, so the size of programs has been limited to a few circuits. Here we apply part mining and directed evolution to build a set of transcriptional AND gates in Escherichia coli. Each AND gate integrates two promoter inputs and controls one promoter output. This allows the gates to be layered by having the output promoter of an upstream circuit serve as the input promoter for a downstream circuit. Each gate consists of a transcription factor that requires a second chaperone protein to activate the output promoter. Multiple activator-chaperone pairs are identified from type III secretion pathways in different strains of bacteria. Directed evolution is applied to increase the dynamic range and orthogonality of the circuits. These gates are connected in different permutations to form programs, the largest of which is a 4-input AND gate that consists of 3 circuits that integrate 4 inducible systems, thus requiring 11 regulatory proteins. Measuring the performance of individual gates is sufficient to capture the behaviour of the complete program. Errors in the output due to delays (faults), a common problem for layered circuits, are not observed. This work demonstrates the successful layering of orthogonal logic gates, a design strategy that could enable the construction of large, integrated circuits in single cells.
Authors:
Tae Seok Moon; Chunbo Lou; Alvin Tamsir; Brynne C Stanton; Christopher A Voigt
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2012-10-07
Journal Detail:
Title:  Nature     Volume:  491     ISSN:  1476-4687     ISO Abbreviation:  Nature     Publication Date:  2012 Nov 
Date Detail:
Created Date:  2012-11-08     Completed Date:  2013-01-10     Revised Date:  2014-01-30    
Medline Journal Info:
Nlm Unique ID:  0410462     Medline TA:  Nature     Country:  England    
Other Details:
Languages:  eng     Pagination:  249-53     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
DNA-Binding Proteins / metabolism
Directed Molecular Evolution
Escherichia coli / cytology*,  genetics*
Gene Expression Regulation, Bacterial*
Genomic Islands / genetics
Logic*
Models, Genetic*
Molecular Chaperones / metabolism
Molecular Sequence Data
Promoter Regions, Genetic / genetics
Pseudomonas / genetics
Salmonella / genetics
Shigella / genetics
Single-Cell Analysis
Synthetic Biology
Transcription Factors / metabolism
Transcription, Genetic
Grant Support
ID/Acronym/Agency:
AI067699/AI/NIAID NIH HHS; R01 GM095765/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/DNA-Binding Proteins; 0/Molecular Chaperones; 0/Transcription Factors
Comments/Corrections

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