A synthetic gene- metabolic oscillator Fung et al. 2005.

Slides:

Advertisements

Similar presentations

Gene regulation Biology, 5 October 2010 Donald Winslow Operons in prokaryotes.

Advertisements

The need for gene regulation Bacterial genome4,000 genes Human genome100,000 genes Not all expressed at any one time May need very high levels e.g. translation.

Metabolic Regulation . : - Enzyme activity - Cell surface receptors.

Lecture #9 Regulation.

MULTIPLICITY OF STEADY STATES IN CONTINUOUS CULTURE OF MAMMALIAN CELLS Andrew Yongky, Tung Le, Simon Grimm, Wei-Shou Hu Department of Chemical Engineering.

PowerPoint Presentation Materials to accompany

Theory. Modeling of Biochemical Reaction Systems 2 Assumptions: The reaction systems are spatially homogeneous at every moment of time evolution. The.

Computer modeling of cellular processes

A SYNTHETIC GENE- METABOLIC OSCILLATOR Reviewed by Fei Chen.

Chapter 18 Regulation of Gene Expression in Prokaryotes

Goal Show the modeling process used by both Collins (toggle switch) and Elowitz (repressilator) to inform design of biological network necessary to encode.

Lecture 3: Models of gene regulation. DNA Replication RNA Protein TranscriptionTranslation.

PowerPoint Presentation Materials to accompany

Repressilator Presentation contents: The idea Experimental overview. The first attemp. The mathematical model. Determination of the appropiate parameters.

Regulation and Control of Metabolism in Bacteria

Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses Chao Wang Jan 23, 2006.

Regulation of Transcription in Prokaryotes

AP Biology Chapter 13: Gene Regulation

The lac Operon of E. Coli AMATH 882 Lecture 8, Feb. 7, 2011.

The Lac Operon Regulation of Prokaryotic Genes. n Scientists investigated a transcriptionally regulation system using the lactose metabolism system in.

Genetic Regulatory Mechanisms

Chapter 11 Molecular Mechanisms of Gene regulation Jones and Bartlett Publishers © 2005.

Announcements 1. Reading Ch. 15: skim btm Look over problems Ch. 15: 5, 6, 7.

CHAPTER 8 Metabolic Respiration Overview of Regulation Most genes encode proteins, and most proteins are enzymes. The expression of such a gene can be.

AP Biology Chapter 18: Gene Regulation. Regulation of Gene Expression Important for cellular control and differentiation. Understanding “expression” is.

Regulation of gene expression References: 1.Stryer: “Biochemistry”, 5 th Ed. 2.Hames & Hooper: “Instant Notes in Biochemistry”, 2 nd Ed.

Signal Processing in Single Cells Tony 03/30/2005.

Deterministic and Stochastic Analysis of Simple Genetic Networks Adiel Loinger MS.c Thesis of under the supervision of Ofer Biham.

Bacterial Keys to Success Respond quickly to environmental changes –Simultaneous transcription and translation Avoid wasteful activities by using biochemical.

Experimental and computational assessment of conditionally essential genes in E. coli Chao WANG, Oct

Deterministic and Stochastic Analysis of Simple Genetic Networks Adiel Loinger Ofer Biham Azi Lipshtat Nathalie Q. Balaban.

Bacterial Physiology (Micr430) Lecture 13 Regulation of Gene Expression (Text Chapter: 6) (Moat book)

Adiel Loinger Ofer Biham Nathalie Q. Balaban Azi Lipshtat

Transcriptional Regulation and RNA Processing

Regulation of gene and cellular activity

Synthetic Gene Circuits Small, Middle-Sized and Huge Molecules Playing Together Within a Cell.

Glycolysis - Enzyme mechanisms 4. Regulating a metabolic pathway Control of flux Metabolic flux = amount of metabolites going through a pathway per unit.

Differential Expression of Genes  Prokaryotes and eukaryotes precisely regulate gene expression in response to environmental conditions  In multicellular.

1. Regulation of Gene Expression Dr. Ishtiaq Ahmad Khan Dr. Panjwani Center for Molecular Medicine and Drug Research.

Metabolic pathway alteration, regulation and control (5) -- Simulation of metabolic network Xi Wang 02/07/2013 Spring 2013 BsysE 595 Biosystems Engineering.

Lecture 4: Metabolism Reaction system as ordinary differential equations Reaction system as stochastic process.

Solution Space? In most cases lack of constraints provide a space of solutions What can we do with this space? 1.Optimization methods (previous lesson)

Bacterial Gene Expression and Regulation

Gene repression and activation

Gene Regulation, Part 1 Lecture 15 Fall Metabolic Control in Bacteria Regulate enzymes already present –Feedback Inhibition –Fast response Control.

Euglycemia Importance of keeping blood [glucose] at 5 mM Hypoglycemia

GENE EXPRESSION.

Anita Nguyen & Harriet Gliddon.  A good characterisation for a part is: “The minimum amount of information someone needs to reuse the part without any.

Glycolysis Regualtion

© 2009 W. H. Freeman and Company

Computer-Aided Design of LIVing systEms CADLIVE automatically converts a biochemical network map to a dynamic model. JAVA application Client-Server System.

CAMPBELL BIOLOGY Reece Urry Cain Wasserman Minorsky Jackson © 2014 Pearson Education, Inc. TENTH EDITION CAMPBELL BIOLOGY Reece Urry Cain Wasserman Minorsky.

Gene Expression Chapter 16. DNA regulatory sequence All on DNA Promoters – Start transcription Promoters – Start transcription Terminators – End Transcription.

Combinatorial Synthesis of Genetic Networks Calin C. Guet, Michael B. Elowitz, Weihong Hsing, Stanislas Leibler Amit Meshulam Bioinformatics Seminar Technion,

Overproduction of Metabolites of Industrial Microorganisms.

Sadia Sayed. The expression of the cloned gene in a selected host organism. It does not necessarily ensure that it will be successfully expressed. A high.

Higher Human Biology Subtopic 6 (b)

The lac Operon of E. Coli AMATH 882 Lecture 11, Feb. 12, 2013

Regulation of gene and cellular activity

Regulation of Gene Expression

Review Warm-Up What is the Central Dogma?

Volume 113, Issue 5, Pages (May 2003)

Emergent genetic oscillations in a synthetic microbial consortium

Noise Induces Hopping between NF-κB Entrainment Modes

Arijit Maitra, Ken A. Dill Biophysical Journal

Maintenance of lysogeny in bacteriophage lambda.

Theodore R. Rieger, Richard I. Morimoto, Vassily Hatzimanikatis

Central Dogma Theory and Kinetic Models

Cellular localization of r-proteins during repression of a 40S or a 60S r-protein gene. Cellular localization of r-proteins during repression of a 40S.

Fluctuation of metabolic gene expression in the ylxR disruptant with glucose. Fluctuation of metabolic gene expression in the ylxR disruptant with glucose.

Presentation transcript:

A synthetic gene- metabolic oscillator Fung et al. 2005

Conceptual design of oscillatory circuit

Realization of the oscillatory circuit using the acetate pathway in E. coli AcP: acetyl phosphate OAc - : acetate HOAc protonated form of acetate Pta: phosphate acetyltransferase Ack: acetate kinase Acs: acetyl-CoA synthetase The induction of Acs by the presence of acetate is under catabolite repression by glucose in wild-type strain so as to avoid futile cycling.

E. coli strain and plasmid constructs AcP Acs LacI Pta Acetyl phosphate in the M 2 pool activates acs expression, and at the same time, represses pta expression indirectly. A GFP is ligated downstream of a plasmid-borne LacI-repressible tac promoter, to be used as a readout.

Representative single cell dynamics About 60% of the initial colonies oscillate with varying amplitude and a period of 45 ± 10 min (for a total of 85 cells in 10 experiments), for a total duration of at least 4 h.

Representative oscillation dynamics of two sibling cells Comparison of sibling cells shows skipped or delayed peaks (compare filled and open circles), which might be partially explained by uneven distribution of cellular materials.

ODE model Metabolites (AcCoA, AcP, OAc−, and HOAc) Proteins LacI, Pta, and Acs

Enzyme kinetics Michaelis-Menten kinetics is the Michaelis-Menten constant.

Gene expression kinetics Hill function TF binding reaction: At equilibrium, where K describes the binding affinity between the TF and promoter. The fraction of promoter binding sites is The expression rate is

Rate expressions and parameters Michaelis-Menten kinetics Gene expression kinetics

Simulations

Simulations

Simulations

Experimental verification Fructose mannose glycerol Glycolytic flux decreases in the following order: glucose, fructose, mannose, and glycerol.

Stability analysis is related to the gene copy number for the synthesis of protein i (where i is LacI, Pta or Acs).

Experimental result Effect of acetate on metabolator dynamics. 10mM external acetate suppressed oscillation but 0.1mM did not.

Discussions ► The unique design of the metabolator represents a fusion of metabolic and transcriptional oscillation. ► The metabolator illustrates the use of metabolic fluxes to control biological oscillation. ► Negative feedback is typically used to stabilize a system, however, it tends to be unstable if the time lag in feedback increases.