Team:Groningen/Brainstorm/Growth Control

From 2009.igem.org

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!align="center"|[[Team:Groningen|Home]]
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::::::::::::::::{{todo|<i><b>Under construction</b></i>}}
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!align="center"|[[Team:Groningen/Team|The Team]]
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!align="center"|[[Team:Groningen/Brainstorm|Brainstorm]]
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!align="center"|[[Team:Groningen/Vision|Our Vision]]
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!align="center"|[[Team:Groningen/Parts|Parts]]
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!align="center"|[[Team:Groningen/Modelling|Modelling]]
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!align="center"|[[Team:Groningen/Notebook|Notebook]]
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::::::::::::::::<span style="color:#FF0000"><i><b>Under construction</b></i></span style>
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==Introduction==
==Introduction==
Bacteria have a choice between using nutrients for growth or for the production of (commercially) valuable proteins. Being able to control the [http://en.wikipedia.org/wiki/Bacterial_growth bacterial growth cycle] and inducing a premature stationary phase will create the possibility to spend more time producing, using less nutrients for biomass and more for desired production. Stationary phase is nothing more than a stop in an increase of cell numbers by cell death being equal to cell growth. Normally this is induced by the limitation of available nutrients or by means of [http://en.wikipedia.org/wiki/Quorum_sensing quorum sensing] in response to high cell density. With this knowledge, a culture can be created that can respond by limited cell death in response to an added molecule that mimics the response to high cell density.
Bacteria have a choice between using nutrients for growth or for the production of (commercially) valuable proteins. Being able to control the [http://en.wikipedia.org/wiki/Bacterial_growth bacterial growth cycle] and inducing a premature stationary phase will create the possibility to spend more time producing, using less nutrients for biomass and more for desired production. Stationary phase is nothing more than a stop in an increase of cell numbers by cell death being equal to cell growth. Normally this is induced by the limitation of available nutrients or by means of [http://en.wikipedia.org/wiki/Quorum_sensing quorum sensing] in response to high cell density. With this knowledge, a culture can be created that can respond by limited cell death in response to an added molecule that mimics the response to high cell density.
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See also [http://en.wikipedia.org/wiki/Chemostat Chemostat]<br>
See also [http://en.wikipedia.org/wiki/Chemostat Chemostat]<br>
One of the most important features of chemostats is that micro-organisms can be grown in a physiological steady state. In steady state, all culture parameters remain constant (culture volume, dissolved oxygen concentration, nutrient and product concentrations, pH, cell density, etc.). Because obtaining a steady state requires at least 5 volume changes, chemostats require large nutrient and waste reservoirs. Creating biological "<i>chemostat</i>" would circumvent these drawbacks.
One of the most important features of chemostats is that micro-organisms can be grown in a physiological steady state. In steady state, all culture parameters remain constant (culture volume, dissolved oxygen concentration, nutrient and product concentrations, pH, cell density, etc.). Because obtaining a steady state requires at least 5 volume changes, chemostats require large nutrient and waste reservoirs. Creating biological "<i>chemostat</i>" would circumvent these drawbacks.
 +
==Approach==
 +
What we want to reach is an early stationary phase that is inducible and can be relieved to continu onto its natural stationary phase upon depleting its nutrients. To be able to leave to early stationary phase the inductor needs to be degradable or blockable. However, to speak of an actual phase the degradation or inhibition should proceed slowly so not to end the phase too soon.
 +
In undertaking such an endeavour there are several approaches possible, one is to create a switch that could simply stop cells from reproducing and focus them on to production. The other is to create a culture that upon induction begins to oscilate between cell death and cell growth. Because creating either possibilities should yield some difficulties, the project could be divided into three parts.
 +
#Inducing an early stationary phase (that focusses its metabolism on protein production, visualized by GFP)
 +
#Leaving the early stationary phase (leaving the early stationary phase should be optional in practice)
 +
#Creating an oscilating culture that remains between predefined limits.
 +
 +
Possibilities to think of might be a time switch so to continu growing after a set period of time, or continu growing as soon as certain demands are fullfilled (certain amount of production). However, both ways of leaving the early stationary phase are then induced intrinsically and not determined by us. The same problem for the idea of adding a substance that induces the production of an autoinducer simultaneous with an slow promotor of an autoinhibitor, as the concentration of the autoinhibitor rises to a certain point the effect of the autoinducer will be block sufficiently to continu growing.
 +
 +
It would be nice to work with NICE
==Previous contests==
==Previous contests==
<b>Quorum Sensing</b>
<b>Quorum Sensing</b>
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:*[http://2007.igem.org/McGill McGill 2007]
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:*[http://2007.igem.org/Chase_Simulator Turkey 2007]
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:*[http://2007.igem.org/Harvard#Quorum_Sensing Harvard 2007]
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:*[http://2007.igem.org/Michigan Michigan 2007]
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:*[http://www.openwetware.org/wiki/IGEM:Peking/2007 Peking 2007]
:*[http://2008.igem.org/Team:Calgary_Wetware/Project#SlideFrame_1 Calgary 2008]
:*[http://2008.igem.org/Team:Calgary_Wetware/Project#SlideFrame_1 Calgary 2008]
:*[http://2008.igem.org/Team:Cambridge/Modelling Cambridge 2008]
:*[http://2008.igem.org/Team:Cambridge/Modelling Cambridge 2008]
:*[http://2008.igem.org/Team:Chiba/Project Chiba 2008]
:*[http://2008.igem.org/Team:Chiba/Project Chiba 2008]
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:*[http://2008.igem.org/Team:Groningen Groningen 2008]
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:*[http://2008.igem.org/Team:Montreal Montreal 2008]
<b>Cell cycle</b>
<b>Cell cycle</b>
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:*[http://parts.mit.edu/wiki/index.php/Synchronization_of_Cell_Cycles Bangalore 2006]
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:*[http://2006.igem.org/Synchronization_of_Cell_Cycles Bangalore 2006]
:*[http://2008.igem.org/Team:ESBS-Strasbourg Strasbourg 2008]
:*[http://2008.igem.org/Team:ESBS-Strasbourg Strasbourg 2008]
:*[http://2008.igem.org/Team:ETH_Zurich/Wetlab/Switch_Circuit#Genetic_Experiments_using_Ribosome_Modulation_Factor_.28RMF.29| Zurich 2008]
:*[http://2008.igem.org/Team:ETH_Zurich/Wetlab/Switch_Circuit#Genetic_Experiments_using_Ribosome_Modulation_Factor_.28RMF.29| Zurich 2008]
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:*[http://2008.igem.org/Team:University_of_Ottawa/Project Ottowa 2008]
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:*[http://2008.igem.org/Team:Paris/Analysis/Design3 Paris 2008]
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<b>Cell death</b>
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:*[http://2008.igem.org/Team:KULeuven/Project/CellDeath Leuven 2008]
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:*[http://2008.igem.org/Team:Minnesota/HomeTimeBomb Minnesota 2008]
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:*[http://2008.igem.org/Team:NTU-Singapore Singapore 2008]
==Parts in the [http://partsregistry.org/Main_Page Registry of Standard Parts]:==
==Parts in the [http://partsregistry.org/Main_Page Registry of Standard Parts]:==
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:*[http://partsregistry.org/Part:BBa_K104001 BBa_K104001]: <i>Sensor for small peptide Subtilin</i>
:*[http://partsregistry.org/Part:BBa_K104001 BBa_K104001]: <i>Sensor for small peptide Subtilin</i>
:*[http://partsregistry.org/Part:BBa_I13211 BBa_I13211]: <i>Biobricked version of the natural Lux quorum sensing system</i>
:*[http://partsregistry.org/Part:BBa_I13211 BBa_I13211]: <i>Biobricked version of the natural Lux quorum sensing system</i>
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:*[http://partsregistry.org/Part:BBa_T9002 BBa_T9002]: <i>AHL to GFP Converter </i>
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:*[http://partsregistry.org/Part:BBa_K09100 BBa_K09100] <i>Receiver for AHL and Outputs GFP when AHL is present</i>
<b>Cell cycle</b>
<b>Cell cycle</b>
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:*[http://partsregistry.org/Part:BBa_K142040 BBa_K142040]: <i>Ribosome modulation factor (RMF)</i>
:*[http://partsregistry.org/Part:BBa_K142040 BBa_K142040]: <i>Ribosome modulation factor (RMF)</i>
:*[http://partsregistry.org/Part:BBa_K142041 BBa_K142041]: <i>Arabinose controlled RMF generator</i>
:*[http://partsregistry.org/Part:BBa_K142041 BBa_K142041]: <i>Arabinose controlled RMF generator</i>
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<b>Cell death</b>
<b>Cell death</b>
:*[http://partsregistry.org/Part:BBa_I745006 BBa_I745006]
:*[http://partsregistry.org/Part:BBa_I745006 BBa_I745006]
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:*[http://www.ncbi.nlm.nih.gov/pubmed/15374644 Quorum sensing control of lantibiotic production; nisin and subtilin autoregulate their own biosynthesis], Kleerebezem
:*[http://www.ncbi.nlm.nih.gov/pubmed/15374644 Quorum sensing control of lantibiotic production; nisin and subtilin autoregulate their own biosynthesis], Kleerebezem
::<i>In this paper, the molecular mechanism underlying regulation of nisin and subtilin production is reviewed.</i>
::<i>In this paper, the molecular mechanism underlying regulation of nisin and subtilin production is reviewed.</i>
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:*[http://www.ncbi.nlm.nih.gov/pubmed/9675856 Induction of entry into the stationary growth phase in Pseudomonas aeruginosa by N-acylhomoserine lactone], You <i>et al.</i>
+
:*[http://www.ncbi.nlm.nih.gov/pubmed/9675856 Induction of entry into the stationary growth phase in <i>Pseudomonas aeruginosa</i> by N-acylhomoserine lactone], You <i>et al.</i>
::<i>Addition of N-acylhomoserine lactone in the exponential growth phase, regardless of cell density, induces a repression of cell growth of P. aeruginosa</i>
::<i>Addition of N-acylhomoserine lactone in the exponential growth phase, regardless of cell density, induces a repression of cell growth of P. aeruginosa</i>
:*[http://www.ncbi.nlm.nih.gov/pubmed/12032343 Induction of natural competence in <i>Streptococcus pneumoniae</i> triggers lysis and DNA release from a subfraction of the cell population], Steinmoen <i>et al.</i>
:*[http://www.ncbi.nlm.nih.gov/pubmed/12032343 Induction of natural competence in <i>Streptococcus pneumoniae</i> triggers lysis and DNA release from a subfraction of the cell population], Steinmoen <i>et al.</i>
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:*<b>[http://www.nature.com/msb/journal/v4/n1/full/msb200824.html A synthetic <i>Escherichia coli</i> predator–prey ecosystem], Balagaddé <i>et al.</i>
:*<b>[http://www.nature.com/msb/journal/v4/n1/full/msb200824.html A synthetic <i>Escherichia coli</i> predator–prey ecosystem], Balagaddé <i>et al.</i>
::<i>In this study they created a synthetic ecosystem with bi-directional communication through quorum sensing which regulate each other's gene expression and survival via engineered gene circuits.</i></b>
::<i>In this study they created a synthetic ecosystem with bi-directional communication through quorum sensing which regulate each other's gene expression and survival via engineered gene circuits.</i></b>
 +
:*<b>[http://www.nature.com/nature/journal/v428/n6985/abs/nature02491.html Programmed population control by cell–cell communication and regulated killing] You <i>et al.</i>
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::<i>In this study they have built and characterized a 'population control' circuit that autonomously regulates the density of an Escherichia coli population, that is lower than the limits imposed by the environment. The cell density is broadcasted and detected by elements from a bacterial quorum-sensing system, which in turn regulate the death rate</i></b>
 +
:*[http://www.ncbi.nlm.nih.gov/pubmed/17959781 Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium], Brenner <i>et al.</i>
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::<i>In this study they created two colocalized populations of Escherichia coli that communicate with each other and exhibit a “consensus” gene expression response. Because neither population can respond without the other's signal, this consensus function can be considered a logical AND gate in which the inputs are cell populations.</i>
<b>Cell cycle</b>
<b>Cell cycle</b>
 +
:*[http://www.ncbi.nlm.nih.gov/pubmed/15107854 Just-in-time transcription program in metabolic pathways] Zaslaver <i>et al.</i>
 +
::<i>A study that showed certain promotors involved in amino acid biosynthesis being downregulated when compounds of the involved pathways were added.</i>
 +
<b>Cell death</b>
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:*[http://2008.igem.org/Team:Edinburgh/Plan#Bacterial_cell_lysis Edinburgh 2008]
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<b>Modelling</b>
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:*[http://bioinformatics.oxfordjournals.org/cgi/content/full/23/18/2415 Robustness analysis and tuning of synthetic gene networks], Batt <i>et al.</i>
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::<i>In this work, they demonstrate the biological relevance of a method specifically developed to support the design of synthetic gene networks.</i>
:*[http://bib.oxfordjournals.org/cgi/content/abstract/bbp005 Computational systems biology of the cell cycle], Csikász-Nagy
:*[http://bib.oxfordjournals.org/cgi/content/abstract/bbp005 Computational systems biology of the cell cycle], Csikász-Nagy
::<i>A review of past and present of computational modeling of cell-cycle regulation</i>
::<i>A review of past and present of computational modeling of cell-cycle regulation</i>
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{{Team:Groningen/Footer}}

Latest revision as of 13:39, 28 November 2009

Igemhomelogo.png
Under construction

Introduction

Bacteria have a choice between using nutrients for growth or for the production of (commercially) valuable proteins. Being able to control the bacterial growth cycle and inducing a premature stationary phase will create the possibility to spend more time producing, using less nutrients for biomass and more for desired production. Stationary phase is nothing more than a stop in an increase of cell numbers by cell death being equal to cell growth. Normally this is induced by the limitation of available nutrients or by means of quorum sensing in response to high cell density. With this knowledge, a culture can be created that can respond by limited cell death in response to an added molecule that mimics the response to high cell density.

See also Chemostat
One of the most important features of chemostats is that micro-organisms can be grown in a physiological steady state. In steady state, all culture parameters remain constant (culture volume, dissolved oxygen concentration, nutrient and product concentrations, pH, cell density, etc.). Because obtaining a steady state requires at least 5 volume changes, chemostats require large nutrient and waste reservoirs. Creating biological "chemostat" would circumvent these drawbacks.

Approach

What we want to reach is an early stationary phase that is inducible and can be relieved to continu onto its natural stationary phase upon depleting its nutrients. To be able to leave to early stationary phase the inductor needs to be degradable or blockable. However, to speak of an actual phase the degradation or inhibition should proceed slowly so not to end the phase too soon.

In undertaking such an endeavour there are several approaches possible, one is to create a switch that could simply stop cells from reproducing and focus them on to production. The other is to create a culture that upon induction begins to oscilate between cell death and cell growth. Because creating either possibilities should yield some difficulties, the project could be divided into three parts.

  1. Inducing an early stationary phase (that focusses its metabolism on protein production, visualized by GFP)
  2. Leaving the early stationary phase (leaving the early stationary phase should be optional in practice)
  3. Creating an oscilating culture that remains between predefined limits.

Possibilities to think of might be a time switch so to continu growing after a set period of time, or continu growing as soon as certain demands are fullfilled (certain amount of production). However, both ways of leaving the early stationary phase are then induced intrinsically and not determined by us. The same problem for the idea of adding a substance that induces the production of an autoinducer simultaneous with an slow promotor of an autoinhibitor, as the concentration of the autoinhibitor rises to a certain point the effect of the autoinducer will be block sufficiently to continu growing.

It would be nice to work with NICE

Previous contests

Quorum Sensing

Cell cycle

Cell death

Parts in the Registry of Standard Parts:

Quorum sensing

  • BBa_K104001: Sensor for small peptide Subtilin
  • BBa_I13211: Biobricked version of the natural Lux quorum sensing system
  • BBa_T9002: AHL to GFP Converter
  • BBa_K09100 Receiver for AHL and Outputs GFP when AHL is present

Cell cycle

Cell death

Related Literature

Quorum sensing

In this paper, the molecular mechanism underlying regulation of nisin and subtilin production is reviewed.
Addition of N-acylhomoserine lactone in the exponential growth phase, regardless of cell density, induces a repression of cell growth of P. aeruginosa
In this study Competence stimulating peptide is shown to initiates release of DNA from a subfraction of the bacterial population, probably by cell lysis.
In this study they created a synthetic ecosystem with bi-directional communication through quorum sensing which regulate each other's gene expression and survival via engineered gene circuits.
In this study they have built and characterized a 'population control' circuit that autonomously regulates the density of an Escherichia coli population, that is lower than the limits imposed by the environment. The cell density is broadcasted and detected by elements from a bacterial quorum-sensing system, which in turn regulate the death rate
In this study they created two colocalized populations of Escherichia coli that communicate with each other and exhibit a “consensus” gene expression response. Because neither population can respond without the other's signal, this consensus function can be considered a logical AND gate in which the inputs are cell populations.

Cell cycle

A study that showed certain promotors involved in amino acid biosynthesis being downregulated when compounds of the involved pathways were added.

Cell death

Modelling

In this work, they demonstrate the biological relevance of a method specifically developed to support the design of synthetic gene networks.
A review of past and present of computational modeling of cell-cycle regulation