Cell-Free Characterization of Coherent Feed-Forward Loop-Based Synthetic Genetic Circuits
| Autor: | Tom F. A. de Greef, Pascal A. Pieters, Ardjan J. van der Linden, Jongmin Kim, Bryan L. Nathalia, Wilhelm T. S. Huck, Peng Yin |
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| Přispěvatelé: | Synthetic Biology, Chemical Biology, Computational Biology, Biomedical Engineering, ICMS Core |
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
Transcription Genetic Property (programming) Computer science Noise reduction Biomedical Engineering coherent feed-forward loop temporal decoding 01 natural sciences Biochemistry Genetics and Molecular Biology (miscellaneous) 03 medical and health sciences Synthetic biology Reference circuit cell-free systems 010608 biotechnology Escherichia coli Computer Simulation Gene Regulatory Networks Leakage (electronics) 030304 developmental biology Electronic circuit Feedback Physiological 0303 health sciences Signal processing Cell-Free System Models Genetic Escherichia coli Proteins 030302 biochemistry & molecular biology Feed forward General Medicine Function (mathematics) Microfluidic Analytical Techniques Genes Bacterial Protein Biosynthesis synthetic biology Biophysical Chemistry Biological system Physical Organic Chemistry Decoding methods Transcription Factors Research Article post-transcriptional regulation |
| Zdroj: | ACS Synthetic Biology, 10(6), 1406-1416. American Chemical Society bioRxiv ACS Synthetic Biology Acs Synthetic Biology, 10, 1406-1416 Acs Synthetic Biology, 10, 6, pp. 1406-1416 |
| ISSN: | 2161-5063 |
| DOI: | 10.1021/acssynbio.1c00024 |
| Popis: | Regulatory pathways inside living cells employ feed-forward architectures to fulfill essential signal processing functions that aide in the interpretation of various types of inputs through noise-filtering, fold-change detection and adaptation. Although it has been demonstrated computationally that a coherent feed-forward loop (CFFL) can function as noise filter, a property essential to decoding complex temporal signals, this motif has not been extensively characterized experimentally or integrated into larger networks. Here we use post-transcriptional regulation to implement and characterize a synthetic CFFL in an Escherichia coli cell-free transcription-translation system and build larger composite feed-forward architectures. We employ microfluidic flow reactors to probe the response of the CFFL circuit using both persistent and short, noise-like inputs and analyze the influence of different circuit components on the steady-state and dynamics of the output. We demonstrate that our synthetic CFFL implementation can reliably repress background activity compared to a reference circuit, but displays low potential as a temporal filter, and validate these findings using a computational model. Our results offer practical insight into the putative noise-filtering behavior of CFFLs and show that this motif can be used to mitigate leakage and increase the fold-change of the output of synthetic genetic circuits. |
| Databáze: | OpenAIRE |
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