Team:Groningen/Brainstorm/Growth Control

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
 * McGill 2007
 * Turkey 2007
 * Harvard 2007
 * Michigan 2007
 * Peking 2007
 * Calgary 2008
 * Cambridge 2008
 * Chiba 2008
 * Groningen 2008
 * Montreal 2008

Cell cycle
 * Bangalore 2006
 * Strasbourg 2008
 * | Zurich 2008
 * Ottowa 2008
 * Paris 2008

Cell death
 * Leuven 2008
 * Minnesota 2008
 * Singapore 2008

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
 * BBa_M31201
 * BBa_K105013
 * BBa_K105015
 * BBa_K101017: a cell-cycle dependent promoter that is repressed before initiation of replication and depressed shortly after
 * BBa_J22051: an adenylate cyclase promoter, expression is repressed during cell division
 * BBa_J22052: an adenylate cyclase promoter, expression is repressed during cell division
 * BBa_J22095
 * BBa_J22092
 * BBa_K142040: Ribosome modulation factor (RMF)
 * BBa_K142041: Arabinose controlled RMF generator

Cell death
 * BBa_I745006
 * BBa_I745007
 * BBa_K145008: LuxR Generator
 * BBa_K145009: ccdB cell death gene under control of an activating Lux PR
 * BBa_K145109: ccdB cell death gene under the control of a hybrid LuxPR P22 C2 promotor
 * BBa_K145110: Complete cell death mechanism. Combination of BBa_K145108 and Part:BBa_K145109
 * BBa_K145151: Coding region for the ccdB (control of cell death) gene
 * BBa_K145230: A hybrid promoter controls the production of LuxR and ccdB
 * BBa_K145256: Cell death Part 1
 * BBa_K145257: Cell death Part 2
 * BBa_K124003: Induces lysis in E. Coli bacteria
 * BBa_K124014: Induces lysis faster in E. Coli bacteria
 * BBa_K124017: Complete casette containing BBa_K124014

Related Literature
Quorum sensing
 * Quorum sensing control of lantibiotic production; nisin and subtilin autoregulate their own biosynthesis, Kleerebezem
 * In this paper, the molecular mechanism underlying regulation of nisin and subtilin production is reviewed.
 * Induction of entry into the stationary growth phase in Pseudomonas aeruginosa by N-acylhomoserine lactone, You et al.
 * Addition of N-acylhomoserine lactone in the exponential growth phase, regardless of cell density, induces a repression of cell growth of P. aeruginosa
 * Induction of natural competence in Streptococcus pneumoniae triggers lysis and DNA release from a subfraction of the cell population, Steinmoen et al.
 * In this study Competence stimulating peptide is shown to initiates release of DNA from a subfraction of the bacterial population, probably by cell lysis.
 * A synthetic Escherichia coli predator–prey ecosystem, Balagaddé et al.
 * 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.
 * Programmed population control by cell–cell communication and regulated killing You et al.
 * 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
 * Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium, Brenner et al.
 * 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
 * Just-in-time transcription program in metabolic pathways Zaslaver et al.
 * A study that showed certain promotors involved in amino acid biosynthesis being downregulated when compounds of the involved pathways were added.

Cell death
 * Edinburgh 2008

Modelling
 * Robustness analysis and tuning of synthetic gene networks, Batt et al.
 * In this work, they demonstrate the biological relevance of a method specifically developed to support the design of synthetic gene networks.
 * Computational systems biology of the cell cycle, Csikász-Nagy
 * A review of past and present of computational modeling of cell-cycle regulation