NDLI: A synthetic gene circuit for measuring autoregulatory feedback control

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Integrative Biology Vol -9

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Front cover

Contents list

Biological Insights from Synthetic Biology

From noise to synthetic nucleoli: can synthetic biology achieve new insights?

Build to understand: synthetic approaches to biology

Synthetic biology: applying biological circuits beyond novel therapies

Using synthetic biology to make cells tomorrow's test tubes

Nature versus design: synthetic biology or how to build a biological non-machine

Addressing biological uncertainties in engineering gene circuits

Genetically modified bacteriophages

The appeasement of Doug: a synthetic approach to enhancer biology

A morphospace for synthetic organs and organoids: the possible and the actual

Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing

Synthetic biology: insights into biological computation

Mutual regulation causes co-entrainment between a synthetic oscillator and the bacterial cell cycle

A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection

A synthetic gene circuit for measuring autoregulatory feedback control

Performing selections under dynamic conditions for synthetic biology applications

Chemical communication between bacteria and cell-free gene expression systems within linear chains of emulsion droplets

Rationally rewiring the connectivity of the XylR/Pu regulatory node of the m-xylene degradation pathway in Pseudomonas putida

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A synthetic gene circuit for measuring autoregulatory feedback control

Content Provider	Royal Society of Chemistry (RSC)
Author	Carey, Lucas B. Espinar, Lorena Toscano-Ochoa, Carlos Espinós, Júlia Domingo Schikora-Tamarit, Miquel Àngel
Copyright Year	2016
Abstract	Autoregulatory feedback loops occur in the regulation of molecules ranging from ATP to MAP kinases to zinc. Negative feedback loops can increase a system's robustness, while positive feedback loops can mediate transitions between cell states. Recent genome-wide experimental and computational studies predict hundreds of novel feedback loops. However, not all physical interactions are regulatory, and many experimental methods cannot detect self-interactions. Our understanding of regulatory feedback loops is therefore hampered by the lack of high-throughput methods to experimentally quantify the presence, strength and temporal dynamics of autoregulatory feedback loops. Here we present a mathematical and experimental framework for high-throughput quantification of feedback regulation and apply it to RNA binding proteins (RBPs) in yeast. Our method is able to determine the existence of both direct and indirect positive and negative feedback loops, and to quantify the strength of these loops. We experimentally validate our model using two RBPs which lack native feedback loops and by the introduction of synthetic feedback loops. We find that RBP Puf3 does not natively participate in any direct or indirect feedback regulation, but that replacing the native 3′UTR with that of COX17 generates an auto-regulatory negative feedback loop which reduces gene expression noise. Likewise, RBP Pub1 does not natively participate in any feedback loops, but a synthetic positive feedback loop involving Pub1 results in increased expression noise. Our results demonstrate a synthetic experimental system for quantifying the existence and strength of feedback loops using a combination of high-throughput experiments and mathematical modeling. This system will be of great use in measuring auto-regulatory feedback by RNA binding proteins, a regulatory motif that is difficult to quantify using existing high-throughput methods.
Starting Page	546
Ending Page	555
Page Count	10
File Format	HTM / HTML PDF
ISSN	17579694
Volume Number	8
Issue Number	4
Journal	Integrative Biology
DOI	10.1039/c5ib00230c
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	ATP Adenosine triphosphate Zinc Negative feedback RNA Saccharomyces cerevisiae Gene
Content Type	Text
Resource Type	Article
Subject	Medicine Biochemistry Biophysics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

A synthetic gene circuit for measuring autoregulatory feedback control

RNA Degradation in Yeast and Human Mitochondria $^{☆}$

Cytidines in tRNAs that are required intact by ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and Saccharomyces cerevisiae.

ATP-dependent chromatin remodeling by the Saccharomyces cerevisiae homologous recombination factor Rdh54.

Parameterising Translational Feedback Models of Autoregulatory RNA-Binding Proteins in Saccharomyces cerevisiae

Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae.

Prior interaction of ATP with yeast mRNAs enhances protein synthesis at the initiation step

DNA.RNA helicase activity of RAD3 protein of Saccharomyces cerevisiae.

Pre-mRNA splicing within an assembled yeast spliceosome requires an RNA-dependent ATPase and ATP hydrolysis.

A synthetic gene circuit for measuring autoregulatory feedback control

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A synthetic gene circuit for measuring autoregulatory feedback control

RNA Degradation in Yeast and Human Mitochondria $^{☆}$

Cytidines in tRNAs that are required intact by ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and Saccharomyces cerevisiae.

ATP-dependent chromatin remodeling by the Saccharomyces cerevisiae homologous recombination factor Rdh54.

Parameterising Translational Feedback Models of Autoregulatory RNA-Binding Proteins in Saccharomyces cerevisiae

Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae.

Prior interaction of ATP with yeast mRNAs enhances protein synthesis at the initiation step

DNA.RNA helicase activity of RAD3 protein of Saccharomyces cerevisiae.

Pre-mRNA splicing within an assembled yeast spliceosome requires an RNA-dependent ATPase and ATP hydrolysis.

A synthetic gene circuit for measuring autoregulatory feedback control