From 2006.igem.org

Revision as of 15:12, 18 August 2005

Organisational

Group Members

• Christophe, Dominic (coordinator), Giorgia, Herve, Kristian, Zlatko

Group Meeting History

log 2005-08-17: Wednesday, ~13:00 @ polyterasse: Discussion of module, next steps, task distrib.

Input-module Development

Module Description

In a nutshell, this module has 2 system boundaries, both of which are characterized by PoPS. Its purpose is to take a single input PoPS and output 2 different PoPS. One of the outputs should be high and the other low when S is high and vice versa when S is low.

     PoPS_outn
         ^
         ¦
 high    ¦ PoPS_out1 _______           _________ PoPS_out2
         ¦                  \         /
         ¦                   \       /
         ¦                    \     /
         ¦                     \   /
         ¦                      \ /
         ¦                       X
         ¦                      / \
         ¦                     /   \
         ¦                    /     \
         ¦                   /       \
 low     ¦ PoPS_out2 _______/         \_________ PoPS_out1
         ¦--------------------------------------------------> PoPS_in, t
         0                                               1           

Input-module Schematic

Below a preliminary parts-view of the module, i.e. encapsulation of biological specific implementations into a functional box with general PoPS interfaces.

                           -----------------------
                           ¦                     ¦
                           ¦        ,--- a ---.  ¦
                           ¦       /          ¦  ¦
     --------              ¦-------      act  V  ¦
     ¦      ¦              ¦¦     ¦       -- P_a -- PoPS_out1 --> to R_1,R_3
I -> ¦ P_in ¦-- PoPS_in -->¦¦ Reg ¦              ¦ 
     ¦      ¦              ¦¦     ¦       -- P_r -- PoPS_out2 --> to R_2,R_4
     --------              ¦-------      rep --- ¦
                           ¦       \          ¦  ¦
                           ¦        `--- r ---'  ¦
                           ¦                     ¦
                           ----------------------¦

legend: 
I:         input signal that will bind to the promotor P_in, e.g. heat shock dependent etc.
P_in:      promotor that allows the signal of choice I to bind.
PoPS_in:   polymerase per second dependent on promotor and concentration of I
Reg:       regulation genes. there are different solutions possible, see below.
r:         repressing signal. highly dependent on Reg, P_r and of course speed and binding considerations
a:         activating signal. highly dependent on Reg, P_a and of course speed and binding considerations
rep:       repression, indicated by horizontal bar
act:       activation, indicated by arrow
P_r:       promotor region to be repressed and/or "roadblock" region. constitutively active
P_a:       promotor region to be activated and/or "roadblock" region. not constitutively active
PoPS_out1: polymerase per second dependent on P_r and r.
PoPS_out2: polymerase per second dependent on P_a and a.
R_n:       toggle switch gene(s)

Possible Implementations

Check the following page for lists of transcriptional regulators in E.Coli: [http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html] [http://biocyc.org/ECOLI/new-image?object=BC-3.1.2.3]

Two Regulators (a,r)

In the strategies below, the input PoPS regulates two proteins, an activator and a repressor. That has the advantage of being very simple, but requires that both proteins have roughly similar production and degradation speed.

"Basic" (Giorgia)

Antisense (Giorgia)

One Regulator (ar)

In the implementations below, the input PoPs regulate the production of a sole protein that somehow acts as activator and repressor. With only one regulator, production and degradation are perfectly uniform, which is good, but in some cases, it might be harder to obtain a symmetrical activity, which is bad.

AraC (Giorgia)

"Lunatic Activator" (Christophe)

The "Lunatic Activator" is an activator because it is required for the transcription of gene 1 and 3, but is lunatic because it can also acts as a roadblock on genes 2 and 4.

Zinc Finger YY1 (Hervé)

Secondary Metabolism (Christophe)

The idea here would be to use an existing regulator that both activates and represses genes required in the secondary metabolism (e.g. Amino-acid production). To minimize interference with E.Coli, it would be wise to try a system from a very different bacteria (e.g. B. Subtilis).

Fusion Protein (Hervé)

Bidirectional Promoter (Hervé)