IGEM:Melbourne/2008/BioClock/SPModel

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Full Diagram
Components

Red light sensor
 * In the dark - EnvZ and OmpR are phosphorylated
 * With red light - EnvZ and OmpR are dephosphorylated
 * See Levskaya et al. Synthetic biology: engineering Escherichia coli to see ligh'. Nature (2005) vol. 438 (7067) pp. 441-2 for more detail

OmpF Promoter
 * Phosphorylated OmpR results in this promoter being repressed
 * Dephosphorylated OmpR results in this promoter being activated
 * See Rampersaud et al. The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation. J Biol Chem (1994) vol. 269 (17) pp. 12559-66 for more detail

Gene X/Y and Px/y)
 * Generic transcription factors that activate the corresponding promoter sequence
 * Candidate proteins/sequences being collected here

RiboLock and RiboKey
 * Riboswitch controls that prevent translation of a sequence with a ribolock unless the corresponding ribokey is also present
 * See Isaacs et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol (2004) vol. 22 (7) pp. 841-7 for more detail

Off X
 * As yet undetermined mechanism for switching off part 1
 * Could be riboswitch, transcription factor, or protein kinase/protease based
 * Must be self maintaining to keep part 1 off for entire cycle but further mechanisms (Off Y etc.) can be transient

GFP/RFP 
 * Used as a reporter gene to determine what state the system is in (GFP = State 1, RFP = State 2)

Initial State

 * Initially in the dark, therefore OmpR phosphorylated and OmpF repressed

First Pulse

 * Red light results in OmpR being dephosphorylated
 * Therefore transcription initiated at OmpF promoters
 * Gene Y transcript is locked off by RiboLock1 therefore no Gene Y is translated
 * Gene X is translated, which activates Px

Eventually...

 * Red light is switched off, therefore OmpF is repressed again
 * The activated Px produces more Gene X, the RiboKey1 and GFP
 * Therefore the system is in state 1 with state 2 prepared for activation on the next pulse of red light

Second Pulse

 * Red light results in OmpR being dephosphorylated
 * Therefore transcription initiated at OmpF promoters
 * RiboKey1 is being produced, therefore RiboLock1 is opened and Gene Y can be translated
 * Gene Y activates Py which kickstarts the activation of part 2 and repression of part 1

Eventually...

 * Red light is switched off, therefore OmpF is repressed again
 * The activated Py produces more Gene Y, RiboKey2, RFP and Off X
 * Off X repressed Px, switching off part 1
 * RiboKey 2 will open RiboLock 2 in part 3 (not shown)
 * RFP indicates that the system is in state 2 with state 3 (not shown) prepared for activation on the next pulse of red light

Extension
Each new part will require the following unique components
 * A Gene X/Px pairing
 * A RiboLock/RiboKey pairing
 * An Off component that will switch off the promoter for the previous part

Conversion to Binary
Leave thoughts of converting this model to a binary counter here...